Merge branch 'master' into Unreleased/Isabelle2018

.ci/Jenkinsfile

@@ -0,0 +1,27 @@
+pipeline {
+    agent any
+
+    stages {
+        stage('Build Docker') {
+            steps {
+                sh 'cp src/patches/thy_output.ML .ci/isabelle4isadof/'
+                sh 'docker build -t logicalhacking:isabelle4dof-2018 .ci/isabelle4isadof'
+                sh 'rm -f .ci/isabelle4isadof/thy_output.ML'
+            }
+        }
+        stage('Check Docker') {
+            when { changeset "src/patches/*" } 
+            steps {
+                sh 'cp patches/thy_output.ML .ci/isabelle4isadof/'
+                sh 'docker build --no-cache -t logicalhacking:isabelle4dof-2018 .ci/isabelle4isadof'
+                sh 'rm -f .ci/isabelle4isadof/thy_output.ML'
+            }
+        }
+        stage('Build Isabelle/DOF') {
+            steps {
+                sh 'find -type d -name "output" -exec rm -rf {} \\; || true'
+                sh 'docker run -v $PWD:/DOF logicalhacking:isabelle4dof-2018  sh -c "cd /DOF && ./install && isabelle build -D ."'
+            } 
+	}
+    }
+} 

.ci/isabelle4isadof/Dockerfile

@@ -0,0 +1,32 @@
+# Copyright (c) 2019 Achim D. Brucker
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright notice, this
+#
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# SPDX-License-Identifier: BSD-2-Clause
+
+FROM logicalhacking:isabelle2018
+
+WORKDIR /home/isabelle
+COPY thy_output.ML /home/isabelle/Isabelle/src/Pure/Thy
+RUN Isabelle/bin/isabelle build -b Functional-Automata
+

.ci/mk_release

@@ -0,0 +1,177 @@
+#!/usr/bin/env bash
+# Copyright (c) 2019The University of Exeter. 
+#               2019 The University of Paris-Saclay. 
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+# 1. Redistributions of source code must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright
+#    notice, this list of conditions and the following disclaimer in
+#    the documentation and/or other materials provided with the
+#    distribution.
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# SPDX-License-Identifier: BSD-2-Clause
+
+#set -e
+shopt -s nocasematch
+
+
+print_help()
+{
+    echo "Usage: mk_release [OPTION] "
+    echo ""
+    echo "       A tool for building $ISADOF_TAR.tar.xz"
+    echo ""
+    echo "Run ..."
+    echo ""
+    echo "  --help, -h                display this help message"
+    echo "  --sign -s                 sign release archive"
+    echo "                            (default: $SIGN)"
+    echo "  --isabelle, -i isabelle   isabelle command used for installation"
+    echo "                            (default: $ISABELLE)"
+    echo "  --tag -t tag              use tag for release archive"
+    echo "  --p --publish             publish generated artefact"
+    echo "                            (use master: $PUBLISH)"
+}
+
+read_config() {
+    if [ ! -f .config ]; then
+        echo "Error: .config not found (not started in the main directory?)!"
+        exit 1
+    else
+        source .config
+    fi
+}
+
+
+check_isabelle_version() {
+    ACTUAL_ISABELLE_VERSION=`$ISABELLE version`
+    echo "* Checking Isabelle version:"
+    if [ "$ISABELLE_VERSION" != "$ACTUAL_ISABELLE_VERSION" ]; then
+        echo "* Expecting $ISABELLE_VERSION, found $ACTUAL_ISABELLE_VERSION: ERROR"
+        exit 1
+    else
+        echo "* Expecting $ISABELLE_VERSION, found $ACTUAL_ISABELLE_VERSION: success"
+    fi
+}
+
+clone_repo()
+{
+    echo "* Cloning into $ISADOF_DIR"
+    git clone . $ISADOF_DIR
+    if [ "$USE_TAG" = "true" ]; then
+        echo "  * Switching to tag $DOF_VERSION/$ISABELLE_SHORT_VERSION"
+        (cd $ISADOF_DIR && git checkout $DOF_VERSION/$ISABELLE_SHORT_VERSION)
+    else
+        echo "  * Not tag specified, using master branch"
+    fi
+}
+
+build_and_install_manual()
+{
+    echo "* Building manual"
+    ROOTS=$ISABELLE_HOME_USER/ROOTS
+    if [ -f $ROOTS ]; then
+        mv $ROOTS $ROOTS.backup
+    fi
+    (cd $ISADOF_DIR && ./install)
+    (cd $ISADOF_DIR && $ISABELLE build -c Isabelle_DOF-Manual)
+    mkdir -p $ISADOF_DIR/doc
+    cp $ISADOF_DIR/examples/technical_report/Isabelle_DOF-Manual/output/document.pdf \
+        $ISADOF_DIR/doc/Isabelle_DOF-Manual.pdf
+    find $ISADOF_DIR -type d -name "output" -exec rm -rf {} \; || true
+    rm -rf $ISADOF_DIR/.git* $ISADOF_DIR/.ci $ISADOF_DIR/.afp 
+    if [ -f $ROOTS.backup ]; then
+        mv $ROOTS.backup $ROOTS
+    fi
+}
+
+create_archive()
+{    
+    echo "* Creating archive"
+    (cd $BUILD_DIR && tar cf $ISADOF_TAR.tar $ISADOF_TAR && xz $ISADOF_DIR.tar)
+    mv $BUILD_DIR/$ISADOF_TAR.tar.xz .
+    rm -rf $BUILD_DIR
+}
+
+sign_archive()
+{
+    echo "* Publish archive not yet implemented"
+    gpg --armor --output $ISADOF_TAR.tar.xz.asc --detach-sig $ISADOF_TAR.tar.xz
+}
+
+publish_archive()
+{
+    echo "* Publish archive"
+    ssh 0x5f.org mkdir -p www/$DOF_ARTIFACT_HOST/htdocs/$DOF_ARTIFACT_DIR
+    scp $ISADOF_TAR.tar.xz* 0x5f.org:www/$DOF_ARTIFACT_HOST/htdocs/$DOF_ARTIFACT_DIR/
+    ssh 0x5f.org chmod go+u-w -R www/$DOF_ARTIFACT_HOST/htdocs/$DOF_ARTIFACT_DIR
+}
+
+
+read_config
+ISABELLE=`which isabelle`
+USE_TAG="false"
+SIGN="false"
+PUBLISH="false"
+ISABELLE_SHORT_VERSION=`echo $ISABELLE_VERSION | sed -e 's/:.*$//'`
+TAG="$DOF_VERSION/$ISABELLE_SHORT_VERSION"
+BUILD_DIR=`mktemp -d`
+ISADOF_TAR="Isabelle_DOF-"$DOF_VERSION"_"$ISABELLE_SHORT_VERSION
+ISADOF_DIR="$BUILD_DIR/$ISADOF_TAR"
+while [ $# -gt 0 ]
+do
+    case "$1" in
+        --isabelle|-i)
+            ISABELLE="$2";
+            shift;;
+        --tag|-t)
+            TAG="$2";
+            USE_TAG="true"
+            shift;;
+        --sign|-s)
+            SIGN="true";;
+        --publish|-p)
+            PUBLISH="true";;
+        --help|-h)
+            print_help
+            exit 0;;
+        *)  print_help
+            exit 1;;
+    esac
+    shift
+done
+
+check_isabelle_version
+VARS=`$ISABELLE getenv ISABELLE_HOME_USER`
+for i in $VARS; do
+        export "$i"
+done
+
+clone_repo
+build_and_install_manual
+create_archive
+
+if [ "$SIGN" = "true" ]; then
+    sign_archive
+fi
+
+if [ "$PUBLISH" = "true" ]; then
+    publish_archive
+fi
+
+exit 0 

.config

@@ -0,0 +1,8 @@
+DOF_VERSION="Unreleased"
+ISABELLE_VERSION="Isabelle2018: August 2018"
+ISABELLE_URL="https://isabelle.in.tum.de/website-Isabelle2018/"
+DOF_URL="https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF"
+DOF_ARTIFACT_DIR="releases/Isabelle_DOF/Isabelle_DOF"
+DOF_ARTIFACT_HOST="artifacts.logicalhacking.com"
+AFP_DATE="afp-2019-06-04"
+AFP_URL="https://sourceforge.net/projects/afp/files/afp-Isabelle2018/"$AFP_DATE".tar.gz"

.gitattributes

@@ -1,2 +1,3 @@
-core.autocrlf false
-core.eol lf
+install -crlf
+document-generator/Tools/DOF_mkroot -crlf
+document-generator/document-template/build -crlf

.gitignore

@@ -1,5 +1,4 @@
 output
+*.template.sty
 .afp
 *~
-*#
-Isabelle_DOF-Unit-Tests/latex_test/

.woodpecker/README.md

@@ -1,18 +0,0 @@
-# Continuous Build and Release Setup
-
-[![status-badge](https://ci.logicalhacking.com/api/badges/Isabelle_DOF/Isabelle_DOF/status.svg)](https://ci.logicalhacking.com/Isabelle_DOF/Isabelle_DOF)
-
-This directory contains the CI configuration for the [Woodpecker CI](https://woodpecker-ci.org/).
-It may also contain additional tools and script that are useful for preparing a release.
-
-## Generated Artifacts
-
-### Latest Build
-
-* lualatex
-  * [browser_info](https://artifacts.logicalhacking.com/ci/Isabelle_DOF/Isabelle_DOF/main/latest/lualatex/browser_info/Unsorted/)
-  * [aux files](https://artifacts.logicalhacking.com/ci/Isabelle_DOF/Isabelle_DOF/main/latest/lualatex/)
-* pdflatex
-  * [browser_info](https://artifacts.logicalhacking.com/ci/Isabelle_DOF/Isabelle_DOF/main/latest/pdflatex/browser_info/Unsorted/)
-  * [aux files](https://artifacts.logicalhacking.com/ci/Isabelle_DOF/Isabelle_DOF/main/latest/pdflatex/)
-* [Isabelle_DOF-Unreleased_Isabelle2022.tar.xz](https://artifacts.logicalhacking.com/ci/Isabelle_DOF/Isabelle_DOF/main/latest/Isabelle_DOF-Unreleased_Isabelle2022.tar.xz)

.woodpecker/build.yml

@@ -1,61 +0,0 @@
-pipeline:
-  build:
-    image: git.logicalhacking.com/lh-docker/lh-docker-isabelle/isabelle2023:latest
-    pull: true
-    commands:
-      - hg log --limit 2 /root/isabelle
-      - ./.woodpecker/check_dangling_theories
-      - ./.woodpecker/check_external_file_refs
-      - ./.woodpecker/check_quick_and_dirty
-      - export ARTIFACT_DIR=$CI_WORKSPACE/.artifacts/$CI_REPO/$CI_BRANCH/$CI_BUILD_NUMBER/$LATEX
-      - mkdir -p $ARTIFACT_DIR
-      - export `isabelle getenv ISABELLE_HOME_USER`
-      - mkdir -p $ISABELLE_HOME_USER/etc
-      - echo "ISABELLE_PDFLATEX=\"$LATEX --file-line-error\"" >> $ISABELLE_HOME_USER/etc/settings
-      - isabelle build -x HOL-Proofs -x Isabelle_DOF-Proofs -D . -o browser_info
-      - if [ "$LATEX" = "lualatex" ]; then isabelle build -o 'timeout_scale=2' -D . -o browser_info; else echo "Skipping Isabelle_DOF-Proofs for pdflatex build."; fi
-      - find . -name 'root.tex' -prune -o -name 'output' -type f | xargs latexmk -$LATEX -cd  -quiet -Werror
-      - isabelle components -u .
-      - isabelle dof_mkroot -q DOF_test
-      - isabelle build -D DOF_test
-      - cp -r $ISABELLE_HOME_USER/browser_info $ARTIFACT_DIR
-      - cd $ARTIFACT_DIR
-      - cd ../..
-      - ln -s * latest
-  archive:
-    image: git.logicalhacking.com/lh-docker/lh-docker-isabelle/isabelle2023:latest
-    commands:
-      - export ARTIFACT_DIR=$CI_WORKSPACE/.artifacts/$CI_REPO/$CI_BRANCH/$CI_BUILD_NUMBER/$LATEX
-      - mkdir -p $ARTIFACT_DIR
-      - export ISABELLE_VERSION=`isabelle version`
-      - ./.woodpecker/mk_release -d
-      - cp Isabelle_DOF-Unreleased_$ISABELLE_VERSION.tar.xz $ARTIFACT_DIR/../
-    when:
-      matrix:
-        LATEX: lualatex
-  deploy:
-    image: docker.io/drillster/drone-rsync
-    settings:
-      hosts: [ "ci.logicalhacking.com"]
-      port: 22
-      source: .artifacts/$CI_REPO_OWNER/*
-      target: $CI_REPO_OWNER
-      include: [ "**.*"]
-      key:
-        from_secret: artifacts_ssh
-      user: artifacts
-  notify:
-    image: docker.io/drillster/drone-email
-    settings:
-      host: smtp.0x5f.org
-      username: woodpecker
-      password: 
-        from_secret: email
-      from: ci@logicalhacking.com
-    when:
-      status: [ failure ]    
-
-matrix:
-  LATEX:
-  - lualatex      
-  - pdflatex

.woodpecker/check_dangling_theories

@@ -1,33 +0,0 @@
-#!/bin/bash
-
-set -e
-
-failuremsg="Error"
-failurecode=1
-
-while [ $# -gt 0 ]
-do
-    case "$1" in
-        --warning|-w)
-            failuremsg="Warning"
-            failurecode=0;;
-    esac
-    shift
-done
-
-echo "Checking for theories that are not part of an Isabelle session:"
-echo "==============================================================="
-
-PWD=`pwd`
-TMPDIR=`mktemp -d`
-isabelle build  -D . -l -n | grep $PWD | sed -e "s| *${PWD}/||" | sort -u | grep thy$ > ${TMPDIR}/sessions-thy-files.txt
-find * -type f | sort -u | grep thy$ > ${TMPDIR}/actual-thy-files.txt
-thylist=`comm -13 ${TMPDIR}/sessions-thy-files.txt ${TMPDIR}/actual-thy-files.txt`
-if [ -z "$thylist" ] ; then
-    echo "  * Success: No dangling theories found."
-    exit 0
-else
-    echo -e "$thylist"
-    echo "$failuremsg: Dangling theories found (see list above)!" 
-    exit $failurecode 
-fi

.woodpecker/check_external_file_refs

@@ -1,45 +0,0 @@
-#!/bin/sh
-
-
-
-failuremsg="Error"
-failurecode=1
-
-while [ $# -gt 0 ]
-do
-    case "$1" in
-        --warning|-w)
-            failuremsg="Warning"
-            failurecode=0;;
-    esac
-    shift
-done
-
-DIRREGEXP="\\.\\./"
-
-echo "Checking for references pointing outside of session directory:"
-echo "=============================================================="
-
-REGEXP=$DIRREGEXP
-DIR=$DIRMATCH
-failed=0
-for i in $(seq 1 10); do 
-  FILES=`find * -mindepth $((i-1)) -maxdepth $i -type f | xargs`
-  if [ -n "$FILES" ]; then 
-    grep -s ${REGEXP} ${FILES}
-    exit=$?
-    if [ "$exit" -eq 0 ] ; then
-      failed=1
-    fi
-  fi
-  REGEXP="${DIRREGEXP}${REGEXP}"
-done
-
-
-if [ "$failed" -ne 0 ] ; then
-    echo "$failuremsg: Forbidden reference to files outside of their session directory!" 
-    exit $failurecode 
-fi
-
-echo "  * Success: No relative references to files outside of their session directory found."
-exit 0

.woodpecker/check_quick_and_dirty

@@ -1,30 +0,0 @@
-#!/bin/bash
-
-set -e
-
-failuremsg="Error"
-failurecode=1
-
-while [ $# -gt 0 ]
-do
-    case "$1" in
-        --warning|-w)
-            failuremsg="Warning"
-            failurecode=0;;
-    esac
-    shift
-done
-
-echo "Checking for sessions with quick_and_dirty mode enabled:"
-echo "========================================================"
-
-rootlist=`find -name 'ROOT' -exec grep -l 'quick_and_dirty *= *true' {} \;`
-
-if [ -z "$rootlist" ] ; then
-    echo "  * Success: No sessions with quick_and_dirty mode enabled found."
-    exit 0
-else
-    echo -e "$rootlist"
-    echo "$failuremsg: Sessions with quick_and_dirty mode enabled found (see list above)!" 
-    exit $failurecode 
-fi

.woodpecker/mk_release

@@ -1,222 +0,0 @@
-#!/usr/bin/env bash
-# Copyright (c) 2019-2022 University of Exeter. 
-#               2019 University of Paris-Saclay. 
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions
-# are met:
-# 1. Redistributions of source code must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-# 2. Redistributions in binary form must reproduce the above copyright
-#    notice, this list of conditions and the following disclaimer in
-#    the documentation and/or other materials provided with the
-#    distribution.
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
-# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
-# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
-# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
-# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-# POSSIBILITY OF SUCH DAMAGE.
-#
-# SPDX-License-Identifier: BSD-2-Clause
-
-set -e
-shopt -s nocasematch
-
-
-print_help()
-{
-    echo "Usage: mk_release [OPTION] "
-    echo ""
-    echo "       A tool for building an Isabelle/DOF release archive."
-    echo ""
-    echo "Run ..."
-    echo ""
-    echo "  --help, -h                display this help message"
-    echo "  --sign, -s                sign release archive"
-    echo "                            (default: $SIGN)"
-    echo "  --isabelle, -i isabelle   isabelle command used for installation"
-    echo "                            (default: $ISABELLE)"
-    echo "  --tag tag, -t tag         use tag for release archive"
-    echo "                            (default: use master branch)"
-    echo "  --publish, -p             publish generated artefact"
-    echo "                            (default: $PUBLISH)"
-    echo "  --quick-and-dirty, -d     only build required artifacts, no complete test"
-    echo "                            (default: $DIRTY)"
-}
-
-check_isabelle_version() {
-    ACTUAL_ISABELLE_VERSION=`$ISABELLE version`
-    echo "* Checking Isabelle version:"
-    if [ "$ISABELLE_VERSION" != "$ACTUAL_ISABELLE_VERSION" ]; then
-        echo "* Expecting $ISABELLE_VERSION, found $ACTUAL_ISABELLE_VERSION: ERROR"
-        exit 1
-    else
-        echo "* Expecting $ISABELLE_VERSION, found $ACTUAL_ISABELLE_VERSION: success"
-    fi
-}
-
-clone_repo()
-{
-    echo "* Cloning into $ISADOF_WORK_DIR"
-    git clone . $ISADOF_WORK_DIR
-    if [ "$USE_TAG" = "true" ]; then
-        echo "  * Switching to tag $TAG"
-        (cd $ISADOF_WORK_DIR && git checkout $TAG)
-    else
-        echo "  * No tag specified, using master branch"
-    fi
-    (cd $ISADOF_WORK_DIR && git show -s --format="COMMIT=%H%nDATE=%cd" --date=short | sed -e 's|-|/|g') >> $ISADOF_WORK_DIR/etc/settings
-    
-}
-
-build_and_install_manuals()
-{
-    echo "* Building manual"
-
-    if [ "$DIRTY" = "true" ]; then
-        if [ -z ${ARTIFACT_DIR+x} ]; then
-            echo "  * Quick and Dirty Mode (local build)"
-            $ISABELLE build -d . Isabelle_DOF Isabelle_DOF-Example-I
-            mkdir -p $ISADOF_WORK_DIR/Isabelle_DOF-Example-I/output/
-            cp Isabelle_DOF-Example-I/output/document.pdf \
-               $ISADOF_WORK_DIR/Isabelle_DOF-Example-I/output/
-            mkdir -p $ISADOF_WORK_DIR/Isabelle_DOF/output/
-            cp Isabelle_DOF/output/document.pdf \
-               $ISADOF_WORK_DIR/Isabelle_DOF/output/;
-        else
-            echo "  * Quick and Dirty Mode (running on CI)"
-            mkdir -p $ISADOF_WORK_DIR/Isabelle_DOF-Example-I/output/
-            cp $ARTIFACT_DIR/browser_info/AFP/Isabelle_DOF-Example-I/document.pdf \
-               $ISADOF_WORK_DIR/Isabelle_DOF-Example-I/output/
- 
-            mkdir -p $ISADOF_WORK_DIR/Isabelle_DOF/output/
-            cp $ARTIFACT_DIR/browser_info/AFP/Isabelle_DOF/document.pdf \
-               $ISADOF_WORK_DIR/Isabelle_DOF/output/;
-        fi
-    else
-        (cd $ISADOF_WORK_DIR && $ISABELLE env ./install-afp)
-        (cd $ISADOF_WORK_DIR && $ISABELLE build -c -D . )
-    fi
-    mkdir -p $ISADOF_WORK_DIR/doc
-    echo "Isabelle/DOF Manuals!" > $ISADOF_WORK_DIR/doc/Contents
-    
-    cp $ISADOF_WORK_DIR/Isabelle_DOF/output/document.pdf \
-        $ISADOF_WORK_DIR/doc/Isabelle_DOF-Manual.pdf
-    echo "  Isabelle_DOF-Manual                       User and Implementation Manual for Isabelle/DOF" >> $ISADOF_WORK_DIR/doc/Contents
-
-    cp $ISADOF_WORK_DIR/Isabelle_DOF-Example-I/output/document.pdf \
-        $ISADOF_WORK_DIR/doc/Isabelle_DOF-Example-I.pdf
-    echo "  Isabelle_DOF-Example-I       Example academic paper" >> $ISADOF_WORK_DIR/doc/Contents
-
-    find $ISADOF_WORK_DIR -type d -name "output" -exec rm -rf {} \; &> /dev/null || true
-    rm -rf $ISADOF_WORK_DIR/.git* $ISADOF_WORK_DIR/.woodpecker $ISADOF_WORK_DIR/.afp 
-    
-}
-
-create_archive()
-{    
-    echo "* Creating archive"
-    cp $ISADOF_WORK_DIR/doc/Isabelle_DOF-Manual.pdf  $ISADOF_TAR.pdf
-    (mv $ISADOF_WORK_DIR $ISADOF_DIR)    
-    (cd $BUILD_DIR && tar cf $ISADOF_TAR.tar $ISADOF_TAR && xz $ISADOF_DIR.tar)
-    mv $BUILD_DIR/$ISADOF_TAR.tar.xz .
-}
-
-sign_archive()
-{
-    echo "* Signing archive"
-    gpg --armor --output $ISADOF_TAR.tar.xz.asc --detach-sig $ISADOF_TAR.tar.xz
-}
-
-publish_archive()
-{
-    echo "* Publish archive"
-    ssh 0x5f.org mkdir -p www/$DOF_ARTIFACT_HOST/htdocs/$DOF_ARTIFACT_DIR
-    scp $ISADOF_TAR.* 0x5f.org:www/$DOF_ARTIFACT_HOST/htdocs/$DOF_ARTIFACT_DIR/
-    ssh 0x5f.org chmod go+u-w -R www/$DOF_ARTIFACT_HOST/htdocs/$DOF_ARTIFACT_DIR
-}
-
-ISABELLE=`which isabelle`
-USE_TAG="false"
-SIGN="false"
-PUBLISH="false"
-DIRTY="false"
-BUILD_DIR=`mktemp -d`
-ISADOF_WORK_DIR="$BUILD_DIR/Isabelle_DOF"
-while [ $# -gt 0 ]
-do
-    case "$1" in
-        --isabelle|-i)
-            ISABELLE="$2";
-            shift;;
-        --tag|-t)
-            TAG="$2";
-            USE_TAG="true"
-            shift;;
-        --sign|-s)
-            SIGN="true";;
-        --publish|-p)
-            PUBLISH="true";;
-        --quick-and-dirty|-d)
-            DIRTY="true";;
-        --help|-h)
-            print_help
-            exit 0;;
-        *)  print_help
-            exit 1;;
-    esac
-    shift
-done
-
-
-clone_repo
-
-ISADOF_MAIN_DIR=`pwd`
-
-if [ "$DIRTY" = "true" ]; then
-    echo "Running in Quick and Dirty mode!"
-    $ISABELLE components -u $ISADOF_MAIN_DIR
-else
-    $ISABELLE components -x $ISADOF_MAIN_DIR
-    $ISABELLE components -u $ISADOF_WORK_DIR
-fi
-
-VARS=`$ISABELLE getenv ISABELLE_TOOL`
-for i in $VARS; do
-        export "$i"
-done
-
-ISABELLE_VERSION="Isabelle$($ISABELLE_TOOL dof_param -b isabelle_version)"
-DOF_VERSION="$($ISABELLE_TOOL dof_param -b dof_version)"
-
-ISABELLE_SHORT_VERSION=`echo $ISABELLE_VERSION | sed -e 's/:.*$//'`
-ISADOF_TAR="Isabelle_DOF-"$DOF_VERSION"_"$ISABELLE_SHORT_VERSION
-ISADOF_DIR="$BUILD_DIR/$ISADOF_TAR"
-
-check_isabelle_version
-build_and_install_manuals
-
-if [ "$DIRTY" != "true" ]; then
-    $ISABELLE components -x $ISADOF_WORK_DIR
-    $ISABELLE components -u $ISADOF_MAIN_DIR
-fi
-
-create_archive
-
-if [ "$SIGN" = "true" ]; then
-    sign_archive
-fi
-
-if [ "$PUBLISH" = "true" ]; then
-    publish_archive
-fi
-
-rm -rf $BUILD_DIR
-

CHANGELOG.md

@@ -7,45 +7,3 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unreleased]
 
-### Added
-
-### Changed
-
-- Updated Isabelle version to Isabelle 2023
-
-## [1.3.0] - 2022-07-08
-
-### Changed
-
-- The project-specific configuration is not part of the `ROOT` file, the formerly 
-  used `isadof.cfg` is obsolete and no longer supported. 
-- Removed explicit use of `document/build` script. Requires removing the `build` script 
-  entry from ROOT files.
-- Isabelle/DOF is now a proper Isabelle component that should be installed using the
-  `isabelle components` command. The installation script is now only a convenient way 
-  of installing the required AFP entries.
-- `mkroot_DOF` has been renamed to `dof_mkroot` (and reimplemented in Scala).
-
-## [1.2.0] - 2022-03-26
-
-## [1.1.0] - 2021-03-20
-
-### Added
-
-- New antiquotations, consistency checks
-
-### Changed
-
-- Updated manual
-- Restructured setup for ontologies (Isabelle theories and LaTeX styles)
-
-## 1.0.0 - 2018-08-18
-
-### Added
-
-- First public release
-
-[Unreleased]: https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF/compare/v1.3.0/Isabelle2021...HEAD
-[1.3.0]: https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF/compare/v1.2.0/Isabelle2021...v1.3.0/Isabelle2021-1
-[1.2.0]: https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF/compare/v1.1.0/Isabelle2021...v1.2.0/Isabelle2021
-[1.1.0]: https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF/compare/v1.0.0/Isabelle2019...v1.1.0/Isabelle2021

CITATION

@@ -1,4 +1,5 @@
 To cite Isabelle/DOF in publications, please use
+
   
   Achim D. Brucker, Idir Ait-Sadoune, Paolo Crisafulli, and Burkhart
   Wolff. Using The Isabelle Ontology Framework: Linking the Formal

Isabelle_DOF-Example-I/IsaDofApplications.thy

@@ -1,787 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019      The University of Exeter 
- *               2018-2019 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-(*<*)
-theory IsaDofApplications
-  imports "Isabelle_DOF.scholarly_paper"
-begin
-
-use_template "lncs"
-use_ontology "Isabelle_DOF.scholarly_paper"
-
-open_monitor*[this::article] 
-declare[[strict_monitor_checking=false]]
-
-define_shortcut* isadof   \<rightleftharpoons> \<open>\isadof\<close>
-                 LaTeX    \<rightleftharpoons> \<open>\LaTeX{}\<close>
-                 dots     \<rightleftharpoons> \<open>\ldots\<close>
-                 isabelle \<rightleftharpoons> \<open>Isabelle/HOL\<close>
-                 Protege  \<rightleftharpoons> \<open>Prot{\'e}g{\'e}\<close>
-
-(* slanted text in contrast to italics *)
-define_macro* slanted_text \<rightleftharpoons> \<open>\textsl{\<close> _ \<open>}\<close>
-define_macro* unchecked_label \<rightleftharpoons> \<open>\autoref{\<close> _ \<open>}\<close>
-
-ML\<open>
-
-fun boxed_text_antiquotation name (* redefined in these more abstract terms *) =
-    DOF_lib.gen_text_antiquotation name DOF_lib.report_text 
-                           (fn ctxt => DOF_lib.string_2_text_antiquotation ctxt
-                                       #> DOF_lib.enclose_env false ctxt "isarbox")
-
-val neant = K(Latex.text("",\<^here>))
-
-fun boxed_theory_text_antiquotation name (* redefined in these more abstract terms *) =
-    DOF_lib.gen_text_antiquotation name DOF_lib.report_theory_text 
-                           (fn ctxt => DOF_lib.string_2_theory_text_antiquotation ctxt 
-                                        #> DOF_lib.enclose_env false ctxt "isarbox"
-                                        (* #> neant *)) (*debugging *)
-
-fun boxed_sml_text_antiquotation name  =
-    DOF_lib.gen_text_antiquotation name (K(K())) 
-                           (fn ctxt => Input.source_content 
-                                        #> Latex.text 
-                                        #> DOF_lib.enclose_env true ctxt "sml") 
-                           (* the simplest conversion possible *)
-
-fun boxed_pdf_antiquotation name =
-    DOF_lib.gen_text_antiquotation name (K(K())) 
-                           (fn ctxt => Input.source_content 
-                                        #> Latex.text 
-                                        #> DOF_lib.enclose_env true ctxt "out") 
-                           (* the simplest conversion possible *)
-
-fun boxed_latex_antiquotation name =
-    DOF_lib.gen_text_antiquotation name (K(K())) 
-                           (fn ctxt => Input.source_content 
-                                        #> Latex.text 
-                                        #> DOF_lib.enclose_env true ctxt "ltx") 
-                           (* the simplest conversion possible *)
-
-fun boxed_bash_antiquotation name =
-    DOF_lib.gen_text_antiquotation name (K(K())) 
-                           (fn ctxt => Input.source_content 
-                                        #> Latex.text 
-                                        #> DOF_lib.enclose_env true ctxt "bash") 
-                           (* the simplest conversion possible *)
-\<close>
-
-setup\<open>boxed_text_antiquotation         \<^binding>\<open>boxed_text\<close> #>
-      boxed_text_antiquotation         \<^binding>\<open>boxed_cartouche\<close> #>
-      boxed_theory_text_antiquotation  \<^binding>\<open>boxed_theory_text\<close> #>
-
-      boxed_sml_text_antiquotation     \<^binding>\<open>boxed_sml\<close> #>
-      boxed_pdf_antiquotation          \<^binding>\<open>boxed_pdf\<close> #>
-      boxed_latex_antiquotation        \<^binding>\<open>boxed_latex\<close>#>
-      boxed_bash_antiquotation         \<^binding>\<open>boxed_bash\<close> 
-     \<close>
-
-(*>*)
-
-title*[tit::title]       \<open>Using the Isabelle Ontology Framework\<close> 
-subtitle*[stit::subtitle]\<open>Linking the Formal with the Informal\<close>
-author*[adb,
-        email       ="''a.brucker@sheffield.ac.uk''",
-        orcid       ="''0000-0002-6355-1200''",
-        affiliation ="''The University of Sheffield, Sheffield, UK''"]\<open>Achim D. Brucker\<close>
-author*[idir,
-        email       = "''idir.aitsadoune@centralesupelec.fr''",
-        affiliation = "''CentraleSupelec, Paris, France''"]\<open>Idir Ait-Sadoune\<close>
-author*[paolo,
-        email       = "''paolo.crisafulli@irt-systemx.fr''",
-        affiliation = "''IRT-SystemX, Paris, France''"]\<open>Paolo Crisafulli\<close>
-author*[bu,
-        email       = "\<open>wolff@lri.fr\<close>",
-        affiliation = "\<open>Université Paris-Saclay, Paris, France\<close>"]\<open>Burkhart Wolff\<close>
-    
-
-abstract*[abs::abstract, keywordlist="[''Ontology'',''Ontological Modeling'',''Isabelle/DOF'']"]\<open>
-   While Isabelle is mostly known as part of \<^isabelle> (an interactive 
-   theorem prover), it actually provides a framework for developing a wide
-   spectrum of applications. A particular strength
-   of the Isabelle framework is the combination of text editing, formal verification,
-   and code generation. 
-   
-   Up to now, Isabelle's document preparation system lacks a mechanism
-   for ensuring the structure of different document types (as, e.g.,
-   required in certification processes) in general and, in particular,
-   mechanism for linking informal and formal parts of a document. 
-   
-   In this paper, we present \<^isadof>, a novel Document Ontology Framework 
-   on top of Isabelle. \<^isadof> allows for conventional typesetting
-   \<^emph>\<open>as well\<close> as formal development. We show how to model document
-    ontologies inside \<^isadof>, how to use the resulting meta-information 
-   for enforcing a certain document structure, and discuss ontology-specific 
-   IDE support. 
-
-   %% If you consider citing this paper, please refer to 
-   %% @{cite "brucker.ea:isabelle-ontologies:2018"}.
-\<close>
-
-section*[intro::introduction]\<open> Introduction \<close>  
-text*[introtext::introduction, level = "Some 1"]\<open> 
-The linking of the \<^emph>\<open>formal\<close> to the \<^emph>\<open>informal\<close> is perhaps the
-most pervasive challenge in the digitization of knowledge and its
-propagation. This challenge incites numerous research efforts
-summarized under the labels ``semantic web'', ``data mining'', or any
-form of advanced ``semantic'' text processing.  A key role in
-structuring this linking play \<^emph>\<open>document ontologies\<close> (also called
-\<^emph>\<open>vocabulary\<close> in the semantic web community~@{cite "w3c:ontologies:2015"}), 
-\<^ie>, a machine-readable form of the structure of documents as well as 
-the document discourse.
-
-Such ontologies can be used for the scientific discourse within scholarly
-articles, mathematical libraries, and in the engineering discourse  
-of standardized software certification 
-documents~@{cite "boulanger:cenelec-50128:2015" and "cc:cc-part3:2006"}. 
-Further applications are the domain-specific discourse in juridical texts or medical reports.  
-In general, an ontology is a formal explicit description of \<^emph>\<open>concepts\<close> 
-in a domain of discourse (called \<^emph>\<open>classes\<close>), properties of each concept 
-describing \<^emph>\<open>attributes\<close> of the concept, as well as \<^emph>\<open>links\<close> between 
-them. A particular link between concepts is the \<^emph>\<open>is-a\<close> relation declaring 
-the instances of a subclass to be instances of the super-class.
-
-The main objective of this paper is to present \<^isadof>, a novel
-framework to \<^emph>\<open>model\<close> typed ontologies and to \<^emph>\<open>enforce\<close> them during
-document evolution. Based on Isabelle infrastructures, ontologies may refer to
-types, terms, proven theorems, code, or established assertions.
-Based on a novel adaption of the Isabelle IDE, a document is checked to be 
-\<^emph>\<open>conform\<close> to a particular ontology---\<^isadof> is designed to give fast user-feedback 
-\<^emph>\<open>during the capture of content\<close>. This is particularly valuable for document 
-changes, where the \<^emph>\<open>coherence\<close> between the formal and the informal parts of the
-content can be mechanically checked.
-
-To avoid any misunderstanding: \<^isadof>  is \<^emph>\<open>not a theory in HOL\<close> on ontologies and operations 
-to track and trace links in texts, it is an \<^emph>\<open>environment to write structured text\<close> which 
-\<^emph>\<open>may contain\<close> \<^isabelle> definitions and proofs like mathematical articles, tech-reports and
-scientific papers---as the present one, which is written in \<^isadof> itself. \<^isadof> is a plugin 
-into the Isabelle/Isar framework in the style of~@{cite "wenzel.ea:building:2007"}.
-\<close>
-
-(* declaring the forward references used in the subsequent sections *)  
-(*<*)
-declare_reference*[bgrnd::text_section]
-declare_reference*[isadof::text_section]
-declare_reference*[ontomod::text_section]
-declare_reference*[ontopide::text_section]
-declare_reference*[conclusion::text_section]
-(*>*)
-text*[plan::introduction, level="Some 1"]\<open> The plan of the paper is as follows: we start by 
-introducing the underlying Isabelle system (@{text_section (unchecked) \<open>bgrnd\<close>}) followed by 
-presenting the essentials of  \<^isadof> and its ontology language (@{text_section (unchecked) \<open>isadof\<close>}). 
-It follows @{text_section (unchecked) \<open>ontomod\<close>}, where we present three application 
-scenarios from the point of view of the ontology modeling. In @{text_section (unchecked) \<open>ontopide\<close>}
-we discuss the user-interaction generated from the ontological definitions.  Finally, we draw 
-conclusions and discuss related work in @{text_section (unchecked) \<open>conclusion\<close>}. \<close>  
-
-section*[bgrnd::text_section,main_author="Some(@{author ''bu''}::author)"]
-        \<open> Background: The Isabelle System \<close>
-text*[background::introduction, level="Some 1"]\<open>
-While Isabelle is widely perceived as an interactive theorem prover for HOL 
-(Higher-order Logic)~@{cite "nipkow.ea:isabelle:2002"}, we would like to emphasize the view that 
-Isabelle is far more than that: it is the \<^emph>\<open>Eclipse of Formal Methods Tools\<close>.  This refers to the
-``\<^slanted_text>\<open>generic system framework of Isabelle/Isar underlying recent versions of Isabelle.  
-  Among other things, Isar provides an infrastructure for Isabelle plug-ins, comprising extensible 
-  state components and extensible syntax that can be bound to ML programs. Thus, the Isabelle/Isar 
-  architecture may be understood as an extension and refinement of the traditional `LCF approach', 
-  with explicit infrastructure for building derivative \<^emph>\<open>systems\<close>.\<close>''~@{cite "wenzel.ea:building:2007"} 
-
-The current system framework offers moreover the following features:
-
-\<^item> a build management grouping components into to pre-compiled sessions,
-\<^item> a prover IDE (PIDE) framework~@{cite "wenzel:asynchronous:2014"} with various front-ends 
-\<^item> documentation - and code generators,
-\<^item> an extensible front-end language Isabelle/Isar, and,
-\<^item> last but not least, an LCF style, generic theorem prover kernel as 
-  the most prominent and deeply integrated system component.
-\<close>  
-
-figure*[architecture::figure,relative_width="100",file_src="''figures/isabelle-architecture.pdf''"]\<open> 
-     The system architecture of Isabelle (left-hand side) and the 
-     asynchronous communication between the Isabelle system and 
-     the IDE (right-hand side). \<close>
-
-text*[blug::introduction, level="Some 1"]\<open> The Isabelle system architecture shown in @{figure \<open>architecture\<close>}
- comes with many layers, with Standard ML (SML) at the bottom layer as implementation 
-language. The architecture actually foresees a \<^emph>\<open>Nano-Kernel\<close> (our terminology) which 
-resides in the SML structure \<^ML_structure>\<open>Context\<close>. This structure provides a kind of container called 
-\<^emph>\<open>context\<close> providing an identity, an ancestor-list as well as typed, user-defined state 
-for components (plugins) such as \<^isadof>. On top of the latter, the LCF-Kernel, tactics, 
-automated proof procedures as well as specific support for higher specification constructs
-were built. \<close>
-    
-text\<open> We would like to detail the documentation generation of the architecture,
-which is based on literate specification commands such as \<^theory_text>\<open>section\<close> \<^dots>, 
-\<^theory_text>\<open>subsection\<close> \<^dots>, \<^theory_text>\<open>text\<close> \<^dots>, etc.
-Thus, a user can add a simple text:
-  @{boxed_theory_text [display]\<open>
-text\<open> This is a description.\<close>\<close>}
-These text-commands can be arbitrarily mixed with other commands stating definitions, proofs, code, etc.,
-and will result in the corresponding output in generated \<^LaTeX> or HTML documents. 
-Now, \<^emph>\<open>inside\<close> the textual content, it is possible to embed a \<^emph>\<open>text-antiquotation\<close>:
-@{boxed_theory_text [display]\<open>
-   text\<open> According to the \<^emph>\<open>reflexivity\<close> axiom @{thm refl}, 
-         we obtain in \<Gamma> for @{term "fac 5"} the result @{value "fac 5"}.\<close>\<close>}
-
-which is represented in the generated output by:
-@{boxed_pdf [display]\<open>According to the reflexivity axiom $x = x$, we obtain in $\Gamma$ for $\operatorname{fac} 5$ the result $120$.\<close>}
-
-where \<^theory_text>\<open>refl\<close> is actually the reference to the axiom of reflexivity in HOL. 
-For the antiquotation \<^theory_text>\<open>@{value "''fac 5''"}\<close>  we assume the usual definition for 
-\<^theory_text>\<open>fac\<close> in HOL.
-\<close>
-
-text*[anti::introduction, level = "Some 1"]\<open> Thus, antiquotations can refer to formal content, 
-can be type-checked before being displayed and can be used for calculations before actually being 
-typeset. When editing, Isabelle's PIDE offers auto-completion and error-messages while typing the 
-above \<^emph>\<open>semi-formal\<close> content.\<close>
-
-section*[isadof::technical,main_author="Some(@{author ''adb''}::author)"]\<open> \<^isadof> \<close>
-   
-text\<open> An \<^isadof> document consists of three components: 
-\<^item> the \<^emph>\<open>ontology definition\<close> which is an Isabelle theory file with definitions
-  for document-classes and all auxiliary datatypes.  
-\<^item> the \<^emph>\<open>core\<close> of the document itself which is an Isabelle theory
-  importing the ontology definition. \<^isadof> provides an own family of text-element
-  commands such as \<^theory_text>\<open>title*\<close>, \<^theory_text>\<open>section*\<close>, \<^theory_text>\<open>text*\<close>, etc., 
-  which can be annotated with meta-information defined in the underlying  ontology definition.
-\<^item> the \<^emph>\<open>layout definition\<close> for the given ontology exploiting this meta-information.
-\<close>
-text\<open>\<^isadof> is a novel Isabelle system component providing specific support for all these 
-three parts. Note that the document core \<^emph>\<open>may\<close>, but \<^emph>\<open>must\<close> not 
-use Isabelle definitions or proofs for checking the formal content---the 
-present paper is actually an example of a document not containing any proof.
-
- The document generation process of \<^isadof> is currently restricted to \<^LaTeX>, which means
-that the layout is defined by a set of \<^LaTeX> style files. Several layout 
-definitions for one ontology are possible and pave the way that different \<^emph>\<open>views\<close> for
-the same central document were generated, addressing the needs of different purposes `
-and/or target readers. 
-
- While the ontology and the layout definition will have to be developed by an expert
-with knowledge over Isabelle and \<^isadof> and the back end technology depending on the layout 
-definition, the core is intended to require only minimal knowledge of these two. The situation
-is similar to \<^LaTeX>-users, who usually have minimal knowledge about the content in 
-style-files (\<^verbatim>\<open>.sty\<close>-files). In the document core authors \<^emph>\<open>can\<close>  use \<^LaTeX>  commands in 
-their source, but this limits the possibility of using different representation technologies, 
-\<^eg>, HTML, and increases the risk of arcane error-messages in generated \<^LaTeX>. 
-
-The \<^isadof> ontology specification language consists basically on a notation for document classes, 
-where the attributes were typed with HOL-types and can be instantiated by terms HOL-terms, \<^ie>, 
-the actual parsers and type-checkers of the Isabelle system were reused. This has the particular 
-advantage that \<^isadof> commands can be arbitrarily mixed with Isabelle/HOL commands providing the 
-machinery for type declarations and term specifications such as enumerations. In particular, 
-document class definitions provide:
-\<^item>  a HOL-type for each document class as well as inheritance, 
-\<^item>  support for attributes with HOL-types and optional default values,
-\<^item>  support for overriding of attribute defaults but not overloading, and
-\<^item>  text-elements annotated with document classes; they are mutable 
-   instances of document classes.\<close>
-
-text\<open>
-Attributes referring to other ontological concepts are called \<^emph>\<open>links\<close>. The HOL-types inside the 
-document specification language support built-in types for Isabelle/HOL \<^theory_text>\<open>typ\<close>'s, \<^theory_text>\<open>term\<close>'s, and
-\<^theory_text>\<open>thm\<close>'s reflecting internal Isabelle's internal types  for these entities; when denoted in 
-HOL-terms  to instantiate an attribute, for example, there is a  specific syntax 
-(called \<^emph>\<open>inner syntax antiquotations\<close>) that is checked by \<^isadof> for consistency.
-
-Document classes can have a \<^theory_text>\<open>where\<close> clause containing a regular expression over class names. 
-Classes with such a \<^theory_text>\<open>where\<close>  were called \<^emph>\<open>monitor classes\<close>. While document classes and their 
-inheritance relation structure meta-data of text-elements in an object-oriented manner, monitor 
-classes enforce structural organization of documents via the language specified by the regular 
-expression enforcing a sequence of text-elements that belong to the corresponding classes.  \<^vs>\<open>-0.4cm\<close>\<close>
-
-section*[ontomod::text_section]\<open> Modeling Ontologies in \<^isadof> \<close> 
-text\<open> In this section, we will use the \<^isadof> document ontology language for three different 
-application scenarios: for scholarly papers, for mathematical exam sheets as well as standardization 
-documents where the concepts of the standard are captured in the ontology. For space reasons, we 
-will concentrate in all three cases on aspects of the modeling due to space limitations.\<close>
-
-subsection*[scholar_onto::example]\<open> The Scholar Paper Scenario: Eating One's Own Dog Food. \<close>  
-text\<open> The following ontology is a simple ontology modeling scientific papers. In this 
-\<^isadof> application scenario, we deliberately refrain from integrating references to
-(Isabelle) formal content in order  demonstrate that \<^isadof> is not a framework from 
-Isabelle users to Isabelle users only. Of course, such references can be added easily and 
-represent a particular strength of \<^isadof>.\<close>
-
-text*["paper_onto_core"::float, 
-      main_caption="\<open>The core of the ontology definition for writing scholarly papers.\<close>"]
-\<open>@{boxed_theory_text [display]\<open>
-doc_class title =
-   short_title :: "string option"  <=  None
-     
-doc_class subtitle =
-   abbrev :: "string option"       <=  None
-
-doc_class author =
-   affiliation :: "string"
-
-doc_class abstract =
-   keyword_list :: "string list"  <= None
-
-doc_class text_section = 
-   main_author :: "author option"  <=  None
-   todo_list   :: "string list"    <=  "[]" 
-\<close>}\<close>
-
-text\<open> The first part of the ontology \<^theory_text>\<open>scholarly_paper\<close> 
-(see @{float "paper_onto_core"})
-contains the document class definitions
-with the usual text-elements of a scientific paper. The attributes \<^theory_text>\<open>short_title\<close>, 
-\<^theory_text>\<open>abbrev\<close> etc are introduced with their types as well as their default values.
-Our model prescribes an optional \<^theory_text>\<open>main_author\<close> and a todo-list attached to an arbitrary 
-text section; since instances of this class are mutable (meta)-objects of text-elements, they
-can be modified arbitrarily through subsequent text and of course globally during text evolution.
-Since \<^theory_text>\<open>author\<close> is a HOL-type internally generated by \<^isadof> framework and can therefore
-appear in the \<^theory_text>\<open>main_author\<close> attribute  of the \<^theory_text>\<open>text_section\<close> class; 
-semantic links between concepts can be modeled this way.
-
-The translation of its content to, \<^eg>, Springer's \<^LaTeX> setup for the Lecture Notes in Computer 
-Science Series, as required by many scientific conferences, is mostly straight-forward. 
-\<^vs>\<open>-0.8cm\<close>\<close>
-
-figure*[fig1::figure,relative_width="95",file_src="''figures/Dogfood-Intro.png''"]
-       \<open> Ouroboros I: This paper from inside \<^dots> \<close>  
-
-(*<*)declare_reference*[paper_onto_sections::float](*>*)
-text\<open>\<^vs>\<open>-0.8cm\<close> @{figure \<open>fig1\<close>} shows the corresponding view in the Isabelle/PIDE of the present paper.
-Note that the text uses \<^isadof>'s own text-commands containing the meta-information provided by
-the underlying ontology.
-We proceed by a definition of \<^theory_text>\<open>introduction\<close>'s, which we define as the extension of
-\<^theory_text>\<open>text_section\<close> which is intended to capture common infrastructure:
-@{boxed_theory_text [display]\<open>
-doc_class introduction = text_section +
-   comment :: string
-\<close>}
-As a consequence of the definition as extension, the \<^theory_text>\<open>introduction\<close> class
-inherits the attributes \<^theory_text>\<open>main_author\<close> and \<^theory_text>\<open>todo_list\<close> together with 
-the corresponding default values.
-
-As a variant of the introduction, we could add here an attribute that contains the formal 
-claims of the article --- either here, or, for example, in the keyword list of the abstract. 
-As type, one could use either the built-in type \<^theory_text>\<open>term\<close> (for syntactically correct, 
-but not necessarily proven entity) or \<^theory_text>\<open>thm\<close> (for formally proven entities). It suffices 
-to add the line:
-@{boxed_theory_text [display]\<open>
-   claims  :: "thm list"
-\<close>}
-and to extent the \<^LaTeX>-style accordingly to handle the additional field. 
-Note that \<^theory_text>\<open>term\<close> and \<^theory_text>\<open>thm\<close> are types reflecting the core-types of the
-Isabelle kernel. In a corresponding conclusion section, one could model analogously an 
-achievement section; by programming a specific compliance check in SML, the implementation 
-of automated forms of validation check for specific categories of papers is envisageable. 
-Since this requires deeper knowledge in Isabelle programming, however, we consider this out 
-of the scope of this paper.
-
-We proceed more or less conventionally by the subsequent sections (@{float (unchecked)\<open>paper_onto_sections\<close>})\<close>  
-text*["paper_onto_sections"::float, 
-      main_caption = "''Various types of sections of a scholarly papers.''"]\<open>
-@{boxed_theory_text [display]\<open>
-doc_class example   = text_section +
-   comment :: string
-
-doc_class conclusion = text_section +
-   main_author :: "author option"  <=  None
-   
-doc_class related_work = conclusion +
-   main_author :: "author option"  <=  None
-
-doc_class bibliography =
-   style :: "string option"  <=  "''LNCS''"
-\<close>}\<close>
-(*<*)declare_reference*[paper_onto_monitor::float](*>*)
-text\<open>... and finish with a monitor class definition that enforces a textual ordering
-in the document core by a regular expression (@{float (unchecked) "paper_onto_monitor"}).\<close>  
-text*["paper_onto_monitor"::float, 
-      main_caption = "''A monitor for the scholarly paper ontology.''"]\<open>
-@{boxed_theory_text [display]\<open>
-doc_class article = 
-   trace :: "(title + subtitle + author+ abstract +
-              introduction + technical + example +
-              conclusion + bibliography) list"
-   where "(title       ~~ \<lbrakk>subtitle\<rbrakk>   ~~ \<lbrace>author\<rbrace>$^+$+  ~~  abstract    ~~
-             introduction ~~  \<lbrace>technical || example\<rbrace>$^+$  ~~  conclusion ~~  
-             bibliography)"
-\<close>}
-\<close>
-text\<open> We might wish to add a component into our ontology that models figures to be included into 
-the document. This boils down to the exercise of modeling structured data in the style of a 
-functional programming language in HOL and to reuse the implicit HOL-type inside a suitable document 
-class \<^theory_text>\<open>figure\<close>:
-@{boxed_theory_text [display]\<open>
-datatype placement = h | t | b | ht | hb   
-doc_class figure   = text_section +
-   relative_width   :: "int" (* percent of textwidth *)    
-   src     :: "string"
-   placement :: placement 
-   spawn_columns :: bool <= True 
-\<close>}
-\<close>
-
-text\<open> Alternatively, by including the HOL-libraries for rationals, it is possible to 
-use fractions or even mathematical reals. This must be counterbalanced by syntactic 
-and semantic convenience. Choosing the mathematical reals, \<^eg>, would have the drawback that 
-attribute evaluation could be substantially more complicated.\<close>
-
-figure*[fig_figures::figure,relative_width="85",file_src="''figures/Dogfood-figures.png''"]
-       \<open> Ouroboros II: figures \<^dots> \<close>
-
-text\<open> The document class \<^theory_text>\<open>figure\<close> --- supported by the \<^isadof> text command 
-\<^theory_text>\<open>figure*\<close> --- makes it possible to express the pictures and diagrams in this paper 
-such as @{figure \<open>fig_figures\<close>}.
-\<close>
-         
-subsection*[math_exam::example]\<open> The Math-Exam Scenario \<close> 
-text\<open> The Math-Exam Scenario is an application with mixed formal and 
-semi-formal content. It addresses applications where the author of the exam is not present 
-during the exam and the preparation requires a very rigorous process, as the french 
-\<^emph>\<open>baccaleaureat\<close> and exams at The University of Sheffield.
-
-We assume that the content has four different types of addressees, which have a different
-\<^emph>\<open>view\<close> on the integrated document: 
-
-\<^item> the \<^emph>\<open>setter\<close>, \<^ie>, the author of the exam,
-\<^item> the \<^emph>\<open>checker\<close>, \<^ie>, an internal person that checks 
-  the exam for feasibility and non-ambiguity, 
-\<^item> the \<^emph>\<open>external examiner\<close>, \<^ie>, an external person that checks 
-  the exam for feasibility and non-ambiguity, and 
-\<^item> the \<^emph>\<open>student\<close>, \<^ie>, the addressee of the exam. 
-\<close>
-text\<open> The latter quality assurance mechanism is used in many universities,
-where for organizational reasons the execution of an exam takes place in facilities
-where the author of the exam is not expected to be physically present.
-Furthermore, we assume a simple grade system (thus, some calculation is required). \<close>  
-text*["onto_exam"::float, 
-      main_caption = "''The core of the ontology modeling math exams.''"]\<open>
-@{boxed_theory_text [display]\<open>
-doc_class Author = ...
-datatype Subject =  algebra | geometry | statistical
-datatype Grade =  A1 | A2 | A3
-
-doc_class Header =  examTitle   :: string
-                    examSubject :: Subject
-                    date        :: string
-                    timeAllowed :: int --  minutes
-
-datatype ContentClass =  setter
-                      | checker 
-                      | external_examiner   
-                      | student   
-
-doc_class Exam_item = 
-  concerns :: "ContentClass set"  
-
-doc_class Exam_item = 
-  concerns :: "ContentClass set"  
-
-type_synonym SubQuestion = string
-\<close>}\<close>
-
-(*<*)declare_reference*[onto_questions::float](*>*)
-text\<open>The heart of this ontology (see @{float "onto_exam"}) is an alternation of questions and answers, 
-where the answers can consist of simple yes-no answers (QCM style check-boxes) or lists of formulas. 
-Since we do not
-assume familiarity of the students with Isabelle (\<^theory_text>\<open>term\<close> would assume that this is a 
-parse-able and type-checkable entity), we basically model a derivation as a sequence of strings
-(see @{float (unchecked)"onto_questions"}).\<close>  
-text*["onto_questions"::float, 
-      main_caption = "''An exam can contain different types of questions.''"]\<open>
-@{boxed_theory_text [display]\<open>
-doc_class Answer_Formal_Step =  Exam_item +
-  justification :: string
-  "term"        :: "string" 
-  
-doc_class Answer_YesNo =  Exam_item +
-  step_label :: string
-  yes_no     :: bool  -- \<open>for checkboxes\<close>
-
-datatype Question_Type =   
-  formal | informal | mixed 
-  
-doc_class Task = Exam_item +
-  level    :: Level
-  type     :: Question_Type
-  subitems :: "(SubQuestion * 
-                   (Answer_Formal_Step list + Answer_YesNo) list) list"
-  concerns :: "ContentClass set" <= "UNIV" 
-  mark     :: int
-doc_class Exercise = Exam_item +
-  type     :: Question_Type
-  content  :: "(Task) list"
-  concerns :: "ContentClass set" <= "UNIV" 
-  mark     :: int
-\<close>}\<close>
-(*<*)declare_reference*[onto_exam_monitor::float](*>*)
-text\<open>
-In many institutions, it makes sense to have a rigorous process of validation
-for exam subjects: is the initial question correct? Is a proof in the sense of the
-question possible? We model the possibility that the @{term examiner} validates a 
-question by a sample proof validated by Isabelle (see @{float (unchecked) "onto_exam_monitor"}). 
-In our scenario this sample proofs are completely \<^emph>\<open>intern\<close>, \<^ie>, not exposed to the 
-students but just additional material for the internal review process of the exam.\<close>  
-text*["onto_exam_monitor"::float, 
-      main_caption = "''Validating exams.''"]\<open>
-@{boxed_theory_text [display]\<open>
-doc_class Validation = 
-   tests  :: "term list"  <="[]"
-   proofs :: "thm list"   <="[]"
-  
-doc_class Solution = Exam_item +
-  content  :: "Exercise list"
-  valids   :: "Validation list"
-  concerns :: "ContentClass set" <= "{setter,checker,external_examiner}"
-  
-doc_class MathExam=
-  content :: "(Header + Author + Exercise) list"
-  global_grade :: Grade 
-  where "\<lbrace>Author\<rbrace>$^+$  ~~  Header ~~  \<lbrace>Exercise ~~ Solution\<rbrace>$^+$ "
-\<close>}\<close>
-  
-(*<*)declare_reference*["fig_qcm"::figure](*>*)
-
-text\<open> Using the \<^LaTeX> package hyperref, it is possible to conceive an interactive 
-exam-sheets with multiple-choice and/or free-response elements 
-(see @{figure (unchecked) \<open>fig_qcm\<close>}). With the 
-help of the latter, it is possible that students write in a browser a formal mathematical 
-derivation---as part of an algebra exercise, for example---which is submitted to the examiners 
-electronically. \<close>
-figure*[fig_qcm::figure,
-        relative_width="90",file_src="''figures/InteractiveMathSheet.png''"]
-        \<open>A Generated QCM Fragment \<^dots> \<close>  
-
-subsection*[cenelec_onto::example]\<open> The Certification Scenario following CENELEC \<close>
-text\<open> Documents to be provided in formal certifications (such as CENELEC
-50126/50128, the DO-178B/C, or Common Criteria) can much profit from the control of ontological 
-consistency: a lot of an evaluators work consists in tracing down the links from requirements over 
-assumptions down to elements of evidence, be it in the models, the code, or the tests. 
-In a certification process, traceability becomes a major concern; and providing
-mechanisms to ensure complete traceability already at the development of the
-global document will clearly increase speed and reduce risk and cost of a
-certification process. Making the link-structure machine-checkable, be it between requirements, 
-assumptions, their implementation and their discharge by evidence (be it tests, proofs, or
-authoritative arguments), is therefore natural and has the potential to decrease the cost 
-of developments targeting certifications. Continuously checking the links between the formal
-and the semi-formal parts of such documents is particularly valuable during the (usually
-collaborative) development effort. 
-
-As in many other cases, formal certification documents come with an own terminology and pragmatics 
-of what has to be demonstrated and where, and how the trace-ability of requirements through
-design-models over code to system environment assumptions has to be assured.  
-\<close>
-(*<*)declare_reference*["conceptual"::float](*>*)
-text\<open> In the sequel, we present a simplified version of an ontological model used in a 
-case-study~ @{cite "bezzecchi.ea:making:2018"}. We start with an introduction of the concept of requirement 
-(see @{float (unchecked) "conceptual"}). \<close>  
-text*["conceptual"::float, 
-      main_caption = "''Modeling requirements.''"]\<open>
-@{boxed_theory_text [display]\<open>
-doc_class requirement = long_name :: "string option"
-
-doc_class requirement_analysis = no :: "nat"
-   where "requirement_item +"
-
-doc_class hypothesis = requirement +
-      hyp_type :: hyp_type <= physical  (* default *)
-  
-datatype ass_kind = informal | semiformal | formal
-  
-doc_class assumption = requirement +
-     assumption_kind :: ass_kind <= informal 
-\<close>}\<close>
-
-text\<open>Such ontologies can be enriched by larger explanations and examples, which may help
-the team of engineers substantially when developing the central document for a certification, 
-like an explication what is precisely the difference between an \<^emph>\<open>hypothesis\<close> and an 
-\<^emph>\<open>assumption\<close> in the context of the evaluation standard. Since the PIDE makes for each 
-document class its definition available by a simple mouse-click, this kind on meta-knowledge 
-can be made far more accessible during the document evolution.
-
-For example, the term of category \<^emph>\<open>assumption\<close> is used for domain-specific assumptions. 
-It has formal, semi-formal and informal sub-categories. They have to be 
-tracked and discharged by appropriate validation procedures within a 
-certification process, by it by test or proof. It is different from a hypothesis, which is
-globally assumed and accepted.
-
-In the sequel, the category \<^emph>\<open>exported constraint\<close> (or \<^emph>\<open>ec\<close> for short)
-is used for formal assumptions, that arise during the analysis,
-design or implementation and have to be tracked till the final
-evaluation target, and discharged by appropriate validation procedures 
-within the certification process, by it by test or proof.  A particular class of interest 
-is the category \<^emph>\<open>safety related application condition\<close> (or \<^emph>\<open>srac\<close> 
-for short) which is used for \<^emph>\<open>ec\<close>'s that establish safety properties
-of the evaluation target. Their track-ability throughout the certification
-is therefore particularly critical. This is naturally modeled as follows:
-@{boxed_theory_text [display]\<open>  
-doc_class ec = assumption  +
-     assumption_kind :: ass_kind <= (*default *) formal
-                        
-doc_class srac = ec  +
-     assumption_kind :: ass_kind <= (*default *) formal
-\<close>}
-\<close>
-   
-section*[ontopide::technical]\<open> Ontology-based IDE support \<close>  
-text\<open> We present a selection of interaction scenarios  @{example \<open>scholar_onto\<close>}
-and @{example \<open>cenelec_onto\<close>} with Isabelle/PIDE instrumented by \<^isadof>. \<close>
-
-(*<*)
-declare_reference*["text_elements"::float]
-declare_reference*["hyperlinks"::float]
-(*>*)
-
-subsection*[scholar_pide::example]\<open> A Scholarly Paper \<close>  
-text\<open> In @{float (unchecked) "text_elements"}~(a)
-and @{float (unchecked) "text_elements"}~(b)we show how
-hovering over links permits to explore its meta-information. 
-Clicking on a document class identifier permits to hyperlink into the corresponding
-class definition (@{float (unchecked) "hyperlinks"}~(a)); hovering over an attribute-definition
-(which is qualified in order to disambiguate; @{float (unchecked) "hyperlinks"}~(b)).
-\<close>
-
-text*["text_elements"::float, 
-      main_caption="\<open>Exploring text elements.\<close>"]
-\<open>
-@{fig_content (width=53, height=5, caption="Exploring a reference of a text element.") "figures/Dogfood-II-bgnd1.png"
-}\<^hfill>@{fig_content (width=47, height=5, caption="Exploring the class of a text element.") "figures/Dogfood-III-bgnd-text_section.png"} 
-\<close>
-
-text*["hyperlinks"::float, 
-      main_caption="\<open>Hyperlinks.\<close>"]
-\<open>
-@{fig_content (width=48, caption="Hyperlink to Class-Definition.") "figures/Dogfood-IV-jumpInDocCLass.png"
-}\<^hfill>@{fig_content (width=47, caption="Exploring an attribute.") "figures/Dogfood-V-attribute.png"} 
-\<close>
-
-subsection*[cenelec_pide::example]\<open> CENELEC  \<close>
-(*<*)declare_reference*[figfig3::figure](*>*)  
-text\<open> The corresponding view in @{figure (unchecked) \<open>figfig3\<close>} shows core part of a document,  
-coherent to the @{example \<open>cenelec_onto\<close>}. The first sample shows standard Isabelle antiquotations 
-@{cite "wenzel:isabelle-isar:2017"} into formal entities of a theory. This way, the informal parts 
-of a document get ``formal content'' and become more robust under change.\<close>
-
-figure*[figfig3::figure,relative_width="80",file_src="''figures/antiquotations-PIDE.png''"]
-\<open> Standard antiquotations referring to theory elements.\<close>
-
-(*<*)declare_reference*[figfig5::figure]  (*>*)
-text\<open> The subsequent sample in @{figure (unchecked) \<open>figfig5\<close>} shows the definition of an 
-\<^emph>\<open>safety-related application condition\<close>, a side-condition of a theorem which 
-has the consequence that a certain calculation must be executed sufficiently fast on an embedded 
-device. This condition can not be established inside the formal theory but has to be 
-checked by system integration tests.\<close>
-  
-figure*[figfig5::figure, relative_width="80", file_src="''figures/srac-definition.png''"]
-        \<open> Defining a SRAC reference \<^dots> \<close>
-figure*[figfig7::figure, relative_width="80", file_src="''figures/srac-as-es-application.png''"]
-        \<open> Using a SRAC as EC document reference. \<close>
-       
-text\<open> Now we reference in @{figure \<open>figfig7\<close>} this safety-related condition; 
-however, this happens in a context where general \<^emph>\<open>exported constraints\<close> are listed. 
-\<^isadof>'s checks establish that this is legal in the given ontology. 
-
-This example shows that ontological modeling is indeed adequate for large technical,
-collaboratively developed documentations, where modifications can lead easily to incoherence. 
-The current checks help to systematically avoid this type of incoherence between formal and 
-informal parts. \<close>    
-
-section*[onto_future::technical]\<open> Monitor Classes \<close>  
-text\<open> Besides sub-typing, there is another relation between
-document classes: a class can be a \<^emph>\<open>monitor\<close> to other ones,
-which is expressed by the occurrence of a @{theory_text \<open>where\<close>} clause
-in the document class definition containing a regular
-expression (see @{example \<open>scholar_onto\<close>}).
-While class-extension refers to data-inheritance of attributes,
-a monitor imposes structural constraints -- the order --
-in which instances of monitored classes may occur. \<close>
-
-text\<open>
-The control of monitors is done by the commands:
-\<^item> \<^theory_text>\<open>open_monitor*\<close> \<^emph>\<open><doc-class>\<close>  
-\<^item> \<^theory_text>\<open>close_monitor*\<close> \<^emph>\<open><doc-class>\<close> 
-\<close>
-text\<open>
-where the automaton of the monitor class is expected to be in a final state. In the final state, 
-user-defined SML Monitors can be nested, so it is possible to "overlay" one or more monitoring 
-classes and imposing different sets of structural constraints in a Classes which are neither 
-directly nor indirectly (via inheritance) mentioned in the monitor are \<^emph>\<open>independent\<close> from a 
-monitor; instances of independent test elements may occur freely. \<close>
-
-
-section*[conclusion::conclusion]\<open> Conclusion and Related Work\<close>    
-text\<open> We have demonstrated the use of \<^isadof>, a novel ontology modeling and enforcement
-IDE deeply integrated into the Isabelle/Isar Framework. The two most distinguishing features are
-\<^item> \<^isadof> and its ontology language  are a strongly typed language that allows
-  for referring (albeit not reasoning) to entities of \<^isabelle>, most notably types, terms,
-  and (formally proven) theorems, and
-\<^item> \<^isadof> is supported by the Isabelle/PIDE framework; thus, the advantages of an IDE for 
-  text-exploration (which is the type of this link? To which text element does this link refer?
-  Which are the syntactic alternatives here?) were available during editing
-  instead of a post-hoc validation process.
-\<close>
-
-text\<open> Of course, a conventional batch-process  also exists which can be used
-for the validation of large document bases in a conventional continuous build process.
-This combination of formal and semi-informal elements, as well as a systematic enforcement
-of the coherence to a document ontology of the latter, is, as we believe, novel and offers 
-a unique potential for the semantic treatment of scientific texts and technical documentations. \<close>
-
-text\<open>
-To our knowledge, this is the first ontology-driven framework for
-editing mathematical and technical documents that focuses particularly
-on documents mixing formal and informal content---a type of documents
-that is very common in technical certification processes. We see
-mainly one area of related works: IDEs and text editors that support
-editing and checking of documents based on an ontology.  There is a
-large group of ontology editors (\<^eg>, \<^Protege>~@{cite "protege"},
-Fluent Editor~@{cite "cognitum"}, NeOn~@{cite "neon"}, or
-OWLGrEd~@{cite "owlgred"}). With them, we share the support for defining
-ontologies as well as auto-completion when editing documents based on
-an ontology. While our ontology definitions are currently based on a
-textual definition, widely used ontology editors (\<^eg>,
-OWLGrEd~@{cite "owlgred"}) also support graphical notations. This could
-be added to \<^isadof> in the future. A unique feature of \<^isadof> is the
-deep integration of formal and informal text parts. The only other
-work in this area we are aware of is rOntorium~@{cite "rontorium"}, a plugin
-for \<^Protege> that integrates R~@{cite "adler:r:2010"} into an
-ontology environment. Here, the main motivation behind this
-integration is to allow for statistically analyze ontological
-documents. Thus, this is complementary to our work.\<close>
-
-text\<open> \<^isadof> in its present form has a number of technical short-comings as well 
-  as potentials not yet explored. On the long list of the short-comings is the 
-  fact that strings inside HOL-terms do not support, for example, Unicode. 
-  For the moment, \<^isadof> is conceived as an 
-  add-on for \<^isabelle>; a much deeper integration of \<^isadof> into Isabelle 
-  could increase both performance and uniformity. Finally, different target 
-  presentation (such as HTML) would be highly desirable in particular for the 
-  math exam scenarios. And last but not least, it would be desirable that PIDE 
-  itself is ``ontology-aware'' and can, for example, use meta-information
-  to control read- and write accesses of \<^emph>\<open>parts\<close> of documents.
-\<close>
-
-paragraph\<open> Availability. \<close> 
-text\<open> The implementation of the framework, the discussed ontology definitions, 
-        and examples  are available at 
-        \url{\dofurl}.\<close>
-paragraph\<open> Acknowledgement. \<close> 
-text\<open> This work was partly supported by  the framework of IRT SystemX, Paris-Saclay, France, 
-and therefore granted with public funds within the scope of the Program ``Investissements d’Avenir''.\<close>
-
-(*<*) 
-section*[bib::bibliography]\<open>References\<close>
-
-close_monitor*[this]
-
-
-end
-(*>*) 
-  

Isabelle_DOF-Example-I/document/authorarchive.sty

@@ -1,345 +0,0 @@
-%% Copyright (C) 2008-2023 Achim D. Brucker, https://www.brucker.ch
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1.3c of the License, or (at your option) any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
-\NeedsTeXFormat{LaTeX2e}\relax
-\ProvidesPackage{authorarchive}
-  [2023/02/10 v1.3.0
-  Self-archiving information for scientific publications.]
-%
-\PassOptionsToPackage{hyphens}{url}
-%
-\RequirePackage{ifthen}
-\RequirePackage[inline]{enumitem}
-\RequirePackage{orcidlink}
-\RequirePackage{eso-pic}
-\RequirePackage{intopdf}
-\RequirePackage{kvoptions}
-\RequirePackage{hyperref}
-\RequirePackage{calc}
-\RequirePackage{qrcode}
-\RequirePackage{etoolbox}
-\newrobustcmd\BibTeX{Bib\TeX}
-%
-%Better url breaking
-\g@addto@macro{\UrlBreaks}{\UrlOrds}
-%
-% Option declarations
-% -------------------
-\SetupKeyvalOptions{
-  family=AA,
-  prefix=AA@
-}
-%
-\DeclareStringOption[.]{bibtexdir}
-\DeclareStringOption[https://duckduckgo.com/?q=]{baseurl}
-\DeclareStringOption[.pdf]{suffix}
-\DeclareStringOption[UNKNOWN PUBLISHER]{publisher}[]
-\DeclareStringOption[UNKNOWN YEAR]{year}[]
-\DeclareStringOption[]{key}[]
-\DeclareStringOption[]{doi}[]
-\DeclareStringOption[]{doiText}[]
-\DeclareStringOption[]{publisherurl}[]
-\DeclareStringOption[UNKNOWN START PAGE]{startpage}[]
-\DeclareStringOption[UNKNOWN PUBLICATION]{publication}[]
-
-\DeclareBoolOption{ACM}
-\DeclareBoolOption{acmart}
-\DeclareBoolOption{ENTCS}
-\DeclareBoolOption{IEEE}
-\DeclareBoolOption{LNCS}
-\DeclareBoolOption{LNI}
-\DeclareBoolOption{nocopyright}
-\DeclareBoolOption{nourl}
-\DeclareBoolOption{nobib}
-\DeclareBoolOption{orcidicon}
-%\ProcessOptions\relax
-
-
-% Default option rule
-\DeclareDefaultOption{%
-  \ifx\CurrentOptionValue\relax
-    \PackageWarningNoLine{\@currname}{%
-      Unknown option `\CurrentOption'\MessageBreak
-      is passed to package `authorarchive'%
-    }%
-    % Pass the option to package color.
-    % Again it is better to expand \CurrentOption.
-    \expandafter\PassOptionsToPackage\expandafter{\CurrentOption}{color}%
-  \else
-    % Package color does not take options with values.
-    % We provide the standard LaTeX error.
-    \@unknownoptionerror
-  \fi
-}
-\ProcessKeyvalOptions*
-
-\newcommand{\AA@defIncludeFiles}{
-  \def\AA@bibBibTeX{\AA@bibtexdir/\AA@key.bib}
-  \def\AA@bibBibTeXLong{\AA@bibtexdir/\AA@key.bibtex}
-  \def\AA@bibWord{\AA@bibtexdir/\AA@key.word.xml}
-  \def\AA@bibEndnote{\AA@bibtexdir/\AA@key.enw}
-  \def\AA@bibRIS{\AA@bibtexdir/\AA@key.ris}
-}
-\AA@defIncludeFiles
-
-\newboolean{AA@bibExists}
-\setboolean{AA@bibExists}{false}
-\newcommand{\AA@defIncludeSwitches}{
-  \IfFileExists{\AA@bibBibTeX}{\setboolean{AA@bibExists}{true}}{}
-  \IfFileExists{\AA@bibBibTeXLong}{\setboolean{AA@bibExists}{true}}{}
-  \IfFileExists{\AA@bibWord}{\setboolean{AA@bibExists}{true}}{}
-  \IfFileExists{\AA@bibEndnote}{\setboolean{AA@bibExists}{true}}{}
-  \IfFileExists{\AA@bibRIS}{\setboolean{AA@bibExists}{true}}{}
-}
-\AA@defIncludeSwitches
-
-
-% Provide command for dynamic configuration setup
-% \def\authorsetup{\kvsetkeys{AA}}
-\newcommand{\authorsetup}[1]{%
-  \kvsetkeys{AA}{#1}
-  \AA@defIncludeFiles
-  \AA@defIncludeSwitches
-}
-
-% Load local configuration
-\InputIfFileExists{authorarchive.config}{}{}
-
-%  define proxy command for setting PDF attributes
-\ExplSyntaxOn
-\@ifundefined{pdfmanagement_add:nnn}{%
-    \newcommand{\AA@pdfpagesattribute}[2]{\pdfpagesattr{/#1 #2}}%
- }{%
-    \newcommand{\AA@pdfpagesattribute}[2]{\pdfmanagement_add:nnn{Pages}{#1}{#2}}%
- }%
-\ExplSyntaxOff
-
-\newlength\AA@x
-\newlength\AA@y
-\newlength\AA@width
-
-\setlength\AA@x{1in+\hoffset+\oddsidemargin}
-
-\newcommand{\authorcrfont}{\footnotesize}
-\newcommand{\authorat}[1]{\AtPageUpperLeft{\put(\LenToUnit{\AA@x},\LenToUnit{.2cm-\paperheight}){#1}}}
-\newcommand{\authorwidth}[1]{\setlength{\AA@width}{#1}}
-\setlength{\AA@width}{\textwidth}
-
-\def\AA@pageinfo{}
-\ifthenelse{\equal{\AA@startpage}{UNKNOWN START PAGE}}{%
-}{%
-  \setcounter{page}{\AA@startpage}%
-  \def\AA@pageinfo{pp. \thepage--\pageref{\aa@lastpage}, }
-}
-
-
-
-%%%% sig-alternate.cls
-\ifAA@ACM%
-  \ifthenelse{\equal{\AA@publisher}{UNKNOWN PUBLISHER}}{%
-    \setkeys{AA}{publisher=ACM}
-  }{}
-  \global\boilerplate={}
-  \global\copyrightetc={}
-  \renewcommand{\conferenceinfo}[2]{}
-  \renewcommand{\authorcrfont}{\scriptsize}
-  \setlength\AA@x{1in+\hoffset+\oddsidemargin}
-  \setlength\AA@y{-\textheight+\topmargin+\headheight-\footskip} % -\voffset-\topmargin-\headheight-\footskip}
-  \renewcommand{\authorat}[1]{\put(\LenToUnit{\AA@x},\LenToUnit{\AA@y}){#1}}
-  \setlength{\AA@width}{\columnwidth}
-\fi
-%
-%%%% acmart.cls
-\ifAA@acmart%
-  \ifthenelse{\equal{\AA@publisher}{UNKNOWN PUBLISHER}}{%
-    \setkeys{AA}{publisher=ACM}
-  }{}
-  \renewcommand{\authorat}[1]{\AtPageUpperLeft{\put(\LenToUnit{\AA@x},\LenToUnit{0.2cm-\paperheight}){#1}}}
-  \setlength{\AA@width}{\textwidth}
-\fi
-%
-%%%% LNCS
-\ifAA@LNCS%
-  \ifAA@orcidicon%
-    \renewcommand{\orcidID}[1]{\orcidlink{#1}}
-  \else\relax\fi%
-%  
-  \ifthenelse{\equal{\AA@publisher}{UNKNOWN PUBLISHER}}{%
-    \setkeys{AA}{publisher=Springer-Verlag}
-  }{}
-  \renewcommand{\authorcrfont}{\scriptsize}
-  \@ifclasswith{llncs}{a4paper}{%
-    \AA@pdfpagesattribute{CropBox}{[92 114 523 780]}%
-    \renewcommand{\authorat}[1]{\put(\LenToUnit{\AA@x},40){#1}}%
-  }{%
-    \AA@pdfpagesattribute{CropBox}{[92 65 523 731]}%
-    \renewcommand{\authorat}[1]{\put(\LenToUnit{\AA@x},23){#1}}%
-  }
-  \setlength{\AA@width}{\textwidth}
-  \setcounter{tocdepth}{2}
-\fi
-%
-%%%% LNI
-\ifAA@LNI%
-  \ifthenelse{\equal{\AA@publisher}{UNKNOWN PUBLISHER}}{%
-    \setkeys{AA}{publisher=GI}
-  }{}
-  \renewcommand{\authorat}[1]{\put(\LenToUnit{\AA@x},35){#1}}
-  \renewcommand{\authorcrfont}{\scriptsize}
-  \AA@pdfpagesattribute{CropBox}{[70 65 526.378 748.15]}
-  \setlength{\AA@width}{\textwidth}
-  \setcounter{tocdepth}{2}
-\fi
-%
-%%%% ENTCS
-\ifAA@ENTCS%
-  \addtolength{\voffset}{1cm}
-  \ifthenelse{\equal{\AA@publisher}{UNKNOWN PUBLISHER}}{%
-    \setkeys{AA}{publisher=Elsevier Science B.~V.}
-  }{}
-  \renewcommand{\authorat}[1]{\put(\LenToUnit{\AA@x},\LenToUnit{-.5cm-\the\ht\AA@authoratBox}){#1}}
-  \renewcommand{\authorcrfont}{\scriptsize}
-  \setlength{\AA@width}{\textwidth}
-\fi
-%
-%%%% IEEE
-\ifAA@IEEE%
-  \ifthenelse{\equal{\AA@publisher}{UNKNOWN PUBLISHER}}{%
-    \setkeys{AA}{publisher=IEEE}
-  }{}
-  \renewcommand{\authorat}[1]{\put(\LenToUnit{\AA@x},6){#1}}
-  \renewcommand{\authorcrfont}{\scriptsize}
-  \setlength{\AA@width}{\textwidth}
-  \setcounter{tocdepth}{2}
-\fi
-%
-
-\hypersetup{%
-  draft         = false,
-  bookmarksopen = true,
-  bookmarksnumbered= true,
-}
-
-\@ifpackageloaded{totpages}{%
-  \def\aa@lastpage{TotPages}
-}{%
-  \RequirePackage{lastpage}
-  \def\aa@lastpage{LastPage}
-}
-\newsavebox{\AA@authoratBox}
-
-\AddToShipoutPicture*{%
-  \setlength{\unitlength}{1mm}%
-  \savebox{\AA@authoratBox}{%
-    \parbox{1.4cm}{%
-      \bgroup%
-        \normallineskiplimit=0pt%
-        \ifAA@nourl%
-           \ifx\AA@doi\@empty\relax%
-           \else%
-              \qrcode[hyperlink,height=1.17cm,padding]{https://doi.org/\AA@doi}%
-            \fi%
-        \else%
-          \qrcode[hyperlink,height=1.17cm,padding]{\AA@baseurl/\AA@key\AA@suffix}%
-        \fi%
-      \egroup%
-    }%
-    \ifAA@nourl\ifx\AA@doi\@empty\addtolength{\AA@width}{1.4cm}\fi\fi
-    \parbox{\AA@width-1.4cm}{\authorcrfont%
-      \ifAA@LNCS%
-        \AA@publication, \AA@pageinfo  \AA@year. %
-        \ifAA@nocopyright\else
-          \textcopyright~\AA@year~\AA@publisher.
-        \fi
-        This is the author's
-        version of the work. It is posted
-        \ifAA@nourl\relax\else%
-          at \url{\AA@baseurl/\AA@key\AA@suffix} %
-        \fi
-        \ifAA@nocopyright\relax\else
-          by permission of \AA@publisher{}
-        \fi
-        for your personal use.
-        \ifx\AA@doi\@empty%
-          \relax
-        \else
-          The final publication is available at Springer via
-          \ifx\AA@doiText\@empty%
-            \url{https://doi.org/\AA@doi}.
-          \else
-            \href{https://doi.org/\AA@doi}{\AA@doiText}.
-          \fi
-        \fi
-      \else
-        \ifAA@nocopyright\relax\else
-          \textcopyright~\AA@year~\AA@publisher. %
-        \fi%
-        This is the author's
-        version of the work. It is posted
-        \ifAA@nourl\relax\else%
-          at \url{\AA@baseurl/\AA@key\AA@suffix} %
-        \fi
-        \ifAA@nocopyright\relax\else
-          by permission of \AA@publisher{} %
-        \fi
-        for your personal use. Not for redistribution. The definitive
-        version was published in \emph{\AA@publication}, \AA@pageinfo \AA@year%
-        \ifx\AA@doi\@empty%
-          \ifx\AA@publisherurl\@empty%
-            .%
-          \else
-            \url{\AA@publisherurl}.%
-          \fi
-        \else
-          \ifx\AA@doiText\@empty%
-            , doi: \href{https://doi.org/\AA@doi}{\AA@doi}.%
-          \else
-            , doi: \href{https://doi.org/\AA@doi}{\AA@doiText}.%
-          \fi
-        \fi
-      \fi
-      \ifAA@nobib\relax\else%
-        \ifthenelse{\boolean{AA@bibExists}}{%
-          \hfill
-          \begin{itemize*}[label={}, itemjoin={,}]
-            \IfFileExists{\AA@bibBibTeX}{%
-              \item \expanded{\attachandlink[\AA@key.bib]{\AA@bibBibTeX}[application/x-bibtex]{BibTeX entry of this paper}{\BibTeX}}%
-            }{%
-              \IfFileExists{\AA@bibBibTeXLong}{%
-                \item \expanded{\attachandlink[\AA@key.bib]{\AA@bibBibTeXLong}[application/x-bibtex]{BibTeX entry of this paper}{\BibTeX}}%
-              }{%
-                \typeout{No file \AA@bibBibTeX{} (and no \AA@bibBibTeXLong) found. Not embedded reference in BibTeX format.}%
-              }%
-            }%
-            \IfFileExists{\AA@bibWord}{%
-              \item \expanded{\attachandlink[\AA@key.word.xml]{\AA@bibWord}[application/xml]{XML entry of this paper (e.g., for Word 2007 and later)}{Word}}%
-            }{%
-              \typeout{No file \AA@bibWord{} found. Not embedded reference for Word 2007 and later.}%
-            }%
-            \IfFileExists{\AA@bibEndnote}{%
-              \item \expanded{\attachandlink[\AA@key.enw]{\AA@bibEndnote}[application/x-endnote-refer]{Endnote entry of this paper}{EndNote}}%
-            }{%
-              \typeout{No file \AA@bibEndnote{} found. Not embedded reference in Endnote format.}%
-            }%
-            \IfFileExists{\AA@bibRIS}{%
-              \item \expanded{\attachandlink[\AA@key.ris]{\AA@bibRIS}[application/x-research-info-systems]{RIS entry of this paper}{RIS}}%
-            }{%
-              \typeout{No file \AA@bibRIS{} found. Not embedded reference in RIS format.}%
-            }%
-          \end{itemize*}\\
-        }{%
-          \PackageError{authorarchive}{No bibliographic files found. Specify option 'nobib' if this is intended.}
-        }
-      \fi
-    }
-  }
-  \authorat{\raisebox{\the\ht\AA@authoratBox}{\usebox{\AA@authoratBox}}}
-}

Isabelle_DOF-Example-I/document/lstisadof-manual.sty

@@ -1,327 +0,0 @@
-%% Copyright (C) 2018 The University of Sheffield
-%%               2018-2021 The University of Paris-Saclay
-%%               2019-2021 The University of Exeter
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1.3c of the License, or (at your option) any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
-\usepackage{listings}
-\usepackage{listingsutf8}
-\usepackage{tikz}
-\usepackage[many]{tcolorbox}
-\tcbuselibrary{listings}
-\tcbuselibrary{skins}
-\usepackage{xstring}
-
-\definecolor{OliveGreen}    {cmyk}{0.64,0,0.95,0.40}
-\definecolor{BrickRed}      {cmyk}{0,0.89,0.94,0.28}
-\definecolor{Blue}          {cmyk}{1,1,0,0}
-\definecolor{CornflowerBlue}{cmyk}{0.65,0.13,0,0}
-
-
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% <antiquotations>
-%% Hack: re-defining tag types for supporting highlighting of antiquotations
-\gdef\lst@tagtypes{s}
-\gdef\lst@TagKey#1#2{%
-    \lst@Delim\lst@tagstyle #2\relax
-        {Tag}\lst@tagtypes #1%
-                     {\lst@BeginTag\lst@EndTag}%
-        \@@end\@empty{}}
-\lst@Key{tag}\relax{\lst@TagKey\@empty{#1}}
-\lst@Key{tagstyle}{}{\def\lst@tagstyle{#1}}
-\lst@AddToHook{EmptyStyle}{\let\lst@tagstyle\@empty}
-\gdef\lst@BeginTag{%
-    \lst@DelimOpen
-        \lst@ifextags\else
-        {\let\lst@ifkeywords\iftrue
-         \lst@ifmarkfirstintag \lst@firstintagtrue \fi}}
-\lst@AddToHookExe{ExcludeDelims}{\let\lst@ifextags\iffalse}
-\gdef\lst@EndTag{\lst@DelimClose\lst@ifextags\else}
-\lst@Key{usekeywordsintag}t[t]{\lstKV@SetIf{#1}\lst@ifusekeysintag}
-\lst@Key{markfirstintag}f[t]{\lstKV@SetIf{#1}\lst@ifmarkfirstintag}
-\gdef\lst@firstintagtrue{\global\let\lst@iffirstintag\iftrue}
-\global\let\lst@iffirstintag\iffalse
- \lst@AddToHook{PostOutput}{\lst@tagresetfirst}
- \lst@AddToHook{Output}
-     {\gdef\lst@tagresetfirst{\global\let\lst@iffirstintag\iffalse}}
- \lst@AddToHook{OutputOther}{\gdef\lst@tagresetfirst{}}
-\lst@AddToHook{Output}
-    {\ifnum\lst@mode=\lst@tagmode
-         \lst@iffirstintag \let\lst@thestyle\lst@gkeywords@sty \fi
-         \lst@ifusekeysintag\else \let\lst@thestyle\lst@gkeywords@sty\fi
-     \fi}
-\lst@NewMode\lst@tagmode
-\gdef\lst@Tag@s#1#2\@empty#3#4#5{%
-    \lst@CArg #1\relax\lst@DefDelimB {}{}%
-        {\ifnum\lst@mode=\lst@tagmode \expandafter\@gobblethree \fi}%
-        #3\lst@tagmode{#5}%
-    \lst@CArg #2\relax\lst@DefDelimE {}{}{}#4\lst@tagmode}%
-\gdef\lst@BeginCDATA#1\@empty{%
-    \lst@TrackNewLines \lst@PrintToken
-    \lst@EnterMode\lst@GPmode{}\let\lst@ifmode\iffalse
-    \lst@mode\lst@tagmode #1\lst@mode\lst@GPmode\relax\lst@modetrue}
-%
-\def\beginlstdelim#1#2#3%
-{%
-    \def\endlstdelim{\texttt{\textbf{\color{black!60}#2}}\egroup}%
-    \ttfamily\textbf{\color{black!60}#1}\bgroup\rmfamily\color{#3}\aftergroup\endlstdelim%
-}
-%% </antiquotations>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% <isar>
-\providecolor{isar}{named}{blue}
-\renewcommand{\isacommand}[1]{\textcolor{OliveGreen!60}{\ttfamily\bfseries #1}}
-\newcommand{\inlineisarbox}[1]{#1}
-\NewTColorBox[]{isarbox}{}{
-     ,boxrule=0pt
-     ,boxsep=0pt
-     ,colback=white!90!isar
-     ,enhanced jigsaw
-     ,borderline west={2pt}{0pt}{isar!60!black}
-     ,sharp corners
-     %,before skip balanced=0.5\baselineskip plus 2pt % works only with Tex Live 2020 and later
-     ,enlarge top by=0mm
-     ,enhanced
-     ,overlay={\node[draw,fill=isar!60!black,xshift=0pt,anchor=north
-       east,font=\bfseries\footnotesize\color{white}]
-                at (frame.north east) {Isar};}
-}
-%% </isar>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-%% <out>
-\providecolor{out}{named}{green}
-\newtcblisting{out}[1][]{%
-      listing only%
-     ,boxrule=0pt
-     ,boxsep=0pt
-     ,colback=white!90!out
-     ,enhanced jigsaw
-     ,borderline west={2pt}{0pt}{out!60!black}
-     ,sharp corners
-     % ,before skip=10pt
-     % ,after skip=10pt
-     ,enlarge top by=0mm
-     ,enhanced
-     ,overlay={\node[draw,fill=out!60!black,xshift=0pt,anchor=north
-       east,font=\bfseries\footnotesize\color{white}]
-                at (frame.north east) {Document};}
-        ,listing options={
-           breakatwhitespace=true
-          ,columns=flexible%
-          ,basicstyle=\small\rmfamily
-          ,mathescape
-          ,#1
-      }
-  }%
-%% </out>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-%% <sml>
-\lstloadlanguages{ML}
-\providecolor{sml}{named}{red}
-\lstdefinestyle{sml}{
-   ,escapechar=ë%
-   ,basicstyle=\ttfamily%
-   ,commentstyle=\itshape%
-   ,keywordstyle=\bfseries\color{CornflowerBlue}%
-   ,ndkeywordstyle=\color{green}%
-   ,language=ML
-%  ,literate={%
-%     {<@>}{@}1%
-%    }
-   ,keywordstyle=[6]{\itshape}%
-   ,morekeywords=[6]{args_type}%
-   ,tag=**[s]{@\{}{\}}%
-   ,tagstyle=\color{CornflowerBlue}%
-   ,markfirstintag=true%
-}%
-\def\inlinesml{\lstinline[style=sml,breaklines=true,breakatwhitespace=true]}
-\newtcblisting{sml}[1][]{%
-      listing only%
-     ,boxrule=0pt
-     ,boxsep=0pt
-     ,colback=white!90!sml
-     ,enhanced jigsaw
-     ,borderline west={2pt}{0pt}{sml!60!black}
-     ,sharp corners
-     % ,before skip=10pt
-     % ,after skip=10pt
-     ,enlarge top by=0mm
-     ,enhanced
-     ,overlay={\node[draw,fill=sml!60!black,xshift=0pt,anchor=north
-       east,font=\bfseries\footnotesize\color{white}]
-                at (frame.north east) {SML};}
-        ,listing options={
-          style=sml
-          ,columns=flexible%
-          ,basicstyle=\small\ttfamily
-          ,#1
-      }
-  }%
-%% </sml>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-%% <latex>
-\lstloadlanguages{TeX}
-\providecolor{ltx}{named}{yellow}
-\lstdefinestyle{lltx}{language=[AlLaTeX]TeX,
-  ,basicstyle=\ttfamily%
-  ,showspaces=false%
-  ,escapechar=ë
-  ,showlines=false%
-  ,morekeywords={newisadof}
- %  ,keywordstyle=\bfseries%
-   % Defining 2-keywords
-   ,keywordstyle=[1]{\color{BrickRed!60}\bfseries}%
-   % Defining 3-keywords
-   ,keywordstyle=[2]{\color{OliveGreen!60}\bfseries}%
-   % Defining 4-keywords
-   ,keywordstyle=[3]{\color{black!60}\bfseries}%
-   % Defining 5-keywords
-   ,keywordstyle=[4]{\color{Blue!70}\bfseries}%
-   % Defining 6-keywords
-   ,keywordstyle=[5]{\itshape}%
-  % 
-}
-\lstdefinestyle{ltx}{style=lltx,
-                basicstyle=\ttfamily\small}%
-\def\inlineltx{\lstinline[style=ltx, breaklines=true,columns=fullflexible]}
-% see
-% https://tex.stackexchange.com/questions/247643/problem-with-tcblisting-first-listed-latex-command-is-missing
-\NewTCBListing{ltx}{ !O{} }{%
-     listing only%
-     ,boxrule=0pt
-     ,boxsep=0pt
-     ,colback=white!90!ltx
-     ,enhanced jigsaw
-     ,borderline west={2pt}{0pt}{ltx!60!black}
-     ,sharp corners
-     % ,before skip=10pt
-     % ,after skip=10pt
-     ,enlarge top by=0mm
-     ,enhanced
-     ,overlay={\node[draw,fill=ltx!60!black,xshift=0pt,anchor=north
-       east,font=\bfseries\footnotesize\color{white}]
-                at (frame.north east) {\LaTeX};}
-      ,listing options={
-             style=lltx,
-            ,columns=flexible%
-            ,basicstyle=\small\ttfamily
-            ,#1
-       }
-  }%
-%% </latex>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-%% <bash>
-\providecolor{bash}{named}{black}
-\lstloadlanguages{bash}
-\lstdefinestyle{bash}{%
-   language=bash
-  ,escapechar=ë
-  ,basicstyle=\ttfamily%
-  ,showspaces=false%
-  ,showlines=false%
-  ,columns=flexible%
- %  ,keywordstyle=\bfseries%
-   % Defining 2-keywords
-   ,keywordstyle=[1]{\color{BrickRed!60}\bfseries}%
-   % Defining 3-keywords
-   ,keywordstyle=[2]{\color{OliveGreen!60}\bfseries}%
-   % Defining 4-keywords
-   ,keywordstyle=[3]{\color{black!60}\bfseries}%
-   % Defining 5-keywords
-   ,keywordstyle=[4]{\color{Blue!80}\bfseries}%
-   ,alsoletter={*,-,:,~,/}
-   ,morekeywords=[4]{}%
-   % Defining 6-keywords
-   ,keywordstyle=[5]{\itshape}%
-  % 
-}
-\def\inlinebash{\lstinline[style=bash, breaklines=true,columns=fullflexible]}
-\newcommand\@isabsolutepath[3]{%
-  \StrLeft{#1}{1}[\firstchar]%
-  \IfStrEq{\firstchar}{/}{#2}{#3}%
-}
-
-\newcommand{\@homeprefix}[1]{%
-  \ifthenelse{\equal{#1}{}}{\textasciitilde}{\textasciitilde/}%
-}
-
-\newcommand{\prompt}[1]{%
-  \color{Blue!80}\textbf{\texttt{%
-    achim@logicalhacking:{\@isabsolutepath{#1}{#1}{\@homeprefix{#1}#1}}\$}}%
-}
-\newtcblisting{bash}[1][]{%
-      listing only%
-     ,boxrule=0pt
-     ,boxsep=0pt
-     ,colback=white!90!bash
-     ,enhanced jigsaw
-     ,borderline west={2pt}{0pt}{bash!60!black}
-     ,sharp corners
-     % ,before skip=10pt
-     % ,after skip=10pt
-     ,enlarge top by=0mm
-     ,enhanced
-     ,overlay={\node[draw,fill=bash!60!black,xshift=0pt,anchor=north
-       east,font=\bfseries\footnotesize\color{white}]
-                at (frame.north east) {Bash};}
-     ,listing options={
-           style=bash
-           ,columns=flexible%
-           ,breaklines=true%
-           ,prebreak=\mbox{\space\textbackslash}%
-           ,basicstyle=\small\ttfamily%
-           ,#1
-      }
-  }%
-%% </bash>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-%% <config>
-\providecolor{config}{named}{gray}
-\newtcblisting{config}[2][]{%
-      listing only%
-     ,boxrule=0pt
-     ,boxsep=0pt
-     ,colback=white!90!config
-     ,enhanced jigsaw
-     ,borderline west={2pt}{0pt}{config!60!black}
-     ,sharp corners
-     % ,before skip=10pt
-     % ,after skip=10pt
-     ,enlarge top by=0mm
-     ,enhanced
-     ,overlay={\node[draw,fill=config!60!black,xshift=0pt,anchor=north
-       east,font=\bfseries\footnotesize\color{white}]
-                at (frame.north east) {#2};}
-        ,listing options={
-           breakatwhitespace=true
-          ,columns=flexible%
-          ,basicstyle=\small\ttfamily
-          ,mathescape
-          ,#1
-      }
-  }%
-%% </config>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-
-

Isabelle_DOF-Example-I/document/preamble.tex

@@ -1,46 +0,0 @@
-%% Copyright (C) 2018 The University of Sheffield
-%%               2018 The University of Paris-Saclay
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1 of the License, or any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%  
-%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
-
-%% This is a placeholder for user-specific configuration and packages. 
-
-
-\IfFileExists{beramono.sty}{\usepackage[scaled=0.88]{beramono}}{}%
-\IfFileExists{upquote.sty}{\usepackage{upquote}}{}%
-\usepackage{textcomp}
-\usepackage{xcolor}
-\usepackage{paralist}
-\usepackage{listings}
-\usepackage{lstisadof-manual}
-
-\providecommand{\isactrlemph}[1]{\emph{#1}}
-\usepackage[LNCS,
-   orcidicon,
-   key=brucker.ea-isabelle-ontologies-2018,
-   year=2018,
-   publication={F. Rabe et al. (Eds.): CICM 2018, LNAI 11006},
-   nobib,
-   startpage={1},
-   doi={10.1007/978-3-319-96812-4_3},
-   doiText={10.1007/978-3-319-96812-4\_3},
-]{authorarchive}
-\authorrunning{A. D. Brucker et al.}
-\pagestyle{headings}
-
-
-\title{<TITLE>}
-\author{<AUTHOR>}
-
-%%% Local Variables:
-%%% mode: latex
-%%% TeX-master: "root.tex"
-%%% End:

Isabelle_DOF-Example-II/ROOT

@@ -1,9 +0,0 @@
-chapter AFP 
-
-session "Isabelle_DOF-Example-II" (AFP) = "Isabelle_DOF" +
-  options [document = pdf, document_output = "output", document_build = dof, timeout = 300]
-  theories
-    "paper"
-  document_files
-    "root.bib"
-    "preamble.tex"

Isabelle_DOF-Example-II/document/preamble.tex

@@ -1,10 +0,0 @@
-%% This is a placeholder for user-specific configuration and packages.
-
-\usepackage{stmaryrd}
-\usepackage{pifont}% http://ctan.org/pkg/pifont
-
-
-\title{<TITLE>}
-\author{<AUTHOR>}
-
-

Isabelle_DOF-Example-II/paper.thy

@@ -1,982 +0,0 @@
-(*<*)
-theory "paper"
-  imports "Isabelle_DOF.scholarly_paper"
-begin
-
-use_template "scrartcl"
-use_ontology "scholarly_paper"
-
-open_monitor*[this::article]
-
-declare[[ strict_monitor_checking  = false]]
-declare[[ Definition_default_class = "definition"]]
-declare[[ Lemma_default_class      = "lemma"]]
-declare[[ Theorem_default_class    = "theorem"]]
-declare[[ Corollary_default_class  = "corollary"]]
-
-define_shortcut* csp      \<rightleftharpoons> \<open>CSP\<close>
-                 holcsp   \<rightleftharpoons> \<open>HOL-CSP\<close>
-                 isabelle \<rightleftharpoons> \<open>Isabelle/HOL\<close>
-                 hfill    \<rightleftharpoons> \<open>\hfill\<close>
-                 br    \<rightleftharpoons> \<open>\break\<close>
-
-(*>*)
-
-title*[tit::title]\<open>Philosophers may Dine - Definitively!\<close>
-                                  
-author*[safouan,email="\<open>safouan.taha@lri.fr\<close>",affiliation="\<open>LRI, CentraleSupelec\<close>"]\<open>Safouan Taha\<close>
-author*[bu,email= "\<open>wolff@lri.fr\<close>",affiliation = "\<open>LRI, Université Paris-Saclay\<close>"]\<open>Burkhart Wolff\<close>
-author*[lina,email="\<open>lina.ye@lri.fr\<close>",affiliation="\<open>LRI, Inria, LSV, CentraleSupelec\<close>"]\<open>Lina Ye\<close>
-               
-abstract*[abs, keywordlist="[\<open>Shallow Embedding\<close>,\<open>Process-Algebra\<close>,
-                             \<open>Concurrency\<close>,\<open>Computational Models\<close>]"]
-\<open>  The theory of Communicating Sequential Processes going back to Hoare and Roscoe is still today  
-   one of the reference theories for concurrent specification and computing. In 1997, a first 
-   formalization in \<^isabelle> of the denotational semantics of the  Failure/Divergence Model of
-   \<^csp> was undertaken; in particular, this model can cope with infinite alphabets, in contrast 
-   to model-checking approaches limited to finite ones. 
-   In this paper, we extend this theory to a significant degree by taking advantage of more powerful 
-   automation of modern Isabelle version, which came even closer to recent developments in the 
-   semantic foundation of \<^csp>. 
-
-   More importantly, we use this formal development to analyse a family of refinement notions,
-   comprising classic and new ones. This analysis enabled us to derive a number of properties
-   that allow to deepen the understanding of these notions, in particular with respect to 
-   specification decomposition principles in the infinite case. Better definitions allow to
-   clarify a number of obscure points in the classical literature, for example concerning the
-   relationship between deadlock- and livelock-freeness. 
-   As a result, we have a modern environment for formal proofs of concurrent systems that allow
-   to combine general infinite processes with locally finite ones in a logically safe way. 
-
-   We demonstrate a number of resulting verification-techniques for classical, generalized examples:
-   The CopyBuffer and Dijkstra's Dining Philosopher Problem of an arbitrary size.
-
-   If you consider citing this paper, please refer to @{cite "HOL-CSP-iFM2020"}.
-\<close>
-text\<open>\<close>
-section*[introheader::introduction,main_author="Some(@{author ''bu''}::author)"]\<open> Introduction \<close> 
-text*[introtext::introduction, level="Some 1"]\<open>
-Communicating Sequential Processes (\<^csp>) is a language to specify and verify patterns of 
-interaction of concurrent systems. Together with CCS and LOTOS, it belongs to the family of 
-\<^emph>\<open>process algebras\<close>. \<^csp>'s rich theory comprises denotational, operational and algebraic semantic 
-facets and has influenced programming languages such as Limbo, Crystal, Clojure and most notably 
-Golang @{cite "donovan2015go"}. \<^csp> has been applied in industry as a tool for specifying and 
-verifying the concurrent aspects of hardware systems, such as the T9000 transansputer 
-@{cite "Barret95"}. 
-
-The theory of \<^csp> was first described in 1978 in a book by Tony Hoare @{cite "Hoare:1985:CSP:3921"}, 
-but has since evolved substantially @{cite "BrookesHR84" and "brookes-roscoe85" and "roscoe:csp:1998"}.
-\<^csp> describes the most common communication and synchronization mechanisms with one single language 
-primitive: synchronous communication written \<open>_\<lbrakk>_\<rbrakk>_\<close>. \<^csp> semantics is described by a fully abstract 
-model of behaviour designed to be \<^emph>\<open>compositional\<close>: the denotational semantics of a process \<open>P\<close> 
-encompasses all possible behaviours of this process in the context of all possible environments 
-\<open>P \<lbrakk>S\<rbrakk> Env\<close> (where \<open>S\<close> is the set of \<open>atomic events\<close> both \<open>P\<close> and \<open>Env\<close> must synchronize). This 
-design objective has the consequence that two kinds of choice have to be distinguished: \<^vs>\<open>0.1cm\<close>
-
-  \<^enum> the \<^emph>\<open>external choice\<close>, written \<open>_\<box>_\<close>, which forces a process "to follow" whatever
-    the environment offers, and \<^vs>\<open>-0.4cm\<close>
-  \<^enum> the \<^emph>\<open>internal choice\<close>, written \<open>_\<sqinter>_\<close>, which imposes on the environment of a process 
-    "to follow" the non-deterministic choices made.\<^vs>\<open>0.3cm\<close>
-\<close>
-
-text\<open> \<^vs>\<open>-0.6cm\<close>
-Generalizations of these two operators \<open>\<box>x\<in>A. P(x)\<close> and \<open>\<Sqinter>x\<in>A. P(x)\<close> allow for modeling the concepts 
-of \<^emph>\<open>input\<close> and \<^emph>\<open>output\<close>: Based on the prefix operator \<open>a\<rightarrow>P\<close> (event \<open>a\<close> happens, then the process 
-proceeds with \<open>P\<close>), receiving input is modeled by \<open>\<box>x\<in>A. x\<rightarrow>P(x)\<close> while sending output is represented 
-by \<open>\<Sqinter>x\<in>A. x\<rightarrow>P(x)\<close>. Setting choice in the center of the language semantics implies that 
-deadlock-freeness becomes a vital property for the well-formedness of a process, nearly as vital
-as type-checking: Consider two events \<open>a\<close> and \<open>b\<close> not involved in a process \<open>P\<close>, then
-\<open>(a\<rightarrow>P \<box> b\<rightarrow>P) \<lbrakk>{a,b}\<rbrakk> (a\<rightarrow>P \<sqinter> b\<rightarrow>P)\<close> is deadlock free provided \<open>P\<close> is, while
-\<open>(a\<rightarrow>P \<sqinter> b\<rightarrow>P) \<lbrakk>{a,b}\<rbrakk> (a\<rightarrow>P \<sqinter> b\<rightarrow>P)\<close> deadlocks (both processes can make "ruthlessly" an opposite choice,
-but are required to synchronize). 
-
-Verification of \<^csp> properties has been centered around the notion of \<^emph>\<open>process refinement orderings\<close>,
-most notably \<open>_\<sqsubseteq>\<^sub>F\<^sub>D_\<close> and \<open>_\<sqsubseteq>_\<close>. The latter turns the denotational domain of \<^csp> into a Scott cpo 
-@{cite "scott:cpo:1972"}, which yields semantics for the fixed point operator \<open>\<mu>x. f(x)\<close> provided 
-that \<open>f\<close> is continuous with respect to \<open>_\<sqsubseteq>_\<close>. Since it is possible to express deadlock-freeness and 
-livelock-freeness as a refinement problem, the verification of properties has been reduced 
-traditionally to a model-checking problem for finite set of events \<open>A\<close>.
-
-We are interested in verification techniques for arbitrary event sets \<open>A\<close> or arbitrarily 
-parameterized processes. Such processes can be used to model dense-timed processes, processes 
-with dynamic thread creation, and processes with unbounded thread-local variables and buffers. 
-However, this adds substantial complexity to the process theory: when it comes to study the 
-interplay of different denotational models, refinement-orderings, and side-conditions for 
-continuity, paper-and-pencil proofs easily reach their limits of precision. 
-
-Several attempts have been undertaken to develop a formal theory in an interactive proof system, 
-mostly in Isabelle/HOL @{cite "Camilleri91" and "tej.ea:corrected:1997" and  "IsobeRoggenbach2010"
-and "DBLP:journals/afp/Noce16"}.
-This paper is based on @{cite "tej.ea:corrected:1997"}, which has been the most comprehensive 
-attempt to formalize denotational \<^csp> semantics covering a part of Bill Roscoe's Book 
-@{cite "roscoe:csp:1998"}. Our contributions are as follows:
-  \<^item>  we ported @{cite "tej.ea:corrected:1997"} from Isabelle93-7 and ancient 
-    ML-written proof scripts to a modern Isabelle/HOL version and structured Isar proofs,
-    and extended it substantially,
-  \<^item> we introduced new refinement notions allowing a deeper understanding of the \<^csp>
-    Failure/Divergence model, providing some meta-theoretic clarifications,
-  \<^item> we used our framework to derive new types of decomposition rules  and 
-    stronger induction principles based on the new refinement notions, and
-  \<^item> we integrate this machinery into a number of advanced verification techniques, which we 
-    apply to two generalized paradigmatic examples in the \<^csp> literature,
-    the CopyBuffer and Dining Philosophers@{footnote \<open>All proofs concerning the 
-    HOL-CSP 2 core have been published in the Archive of  Formal Proofs @{cite "HOL-CSP-AFP"}; 
-    all other proofs are available at 
-    \<^url>\<open>https://gitlri.lri.fr/burkhart.wolff/hol-csp2.0\<close>. In this paper, all Isabelle proofs are 
-    omitted.\<close>}. 
-\<close>
-
-section*["pre"::technical,main_author="Some(@{author \<open>bu\<close>}::author)"]
-\<open>Preliminaries\<close>
-
-subsection*[cspsemantics::technical, main_author="Some(@{author ''bu''})"]\<open>Denotational \<^csp> Semantics\<close>
-
-text\<open> The denotational semantics (following @{cite "roscoe:csp:1998"}) comes in three layers: 
-the \<^emph>\<open>trace model\<close>, the \<^emph>\<open>(stable) failures model\<close> and the \<^emph>\<open>failure/divergence model\<close>.
-
-In the trace semantics model, a process \<open>P\<close> is denoted by a set of communication traces,
-built from atomic events. A trace here represents a partial history of the communication 
-sequence occurring when a process interacts with its environment. For the two basic \<^csp> 
-processes \<open>Skip\<close> (successful termination) and \<open>Stop\<close> (just deadlock), the semantic function
-\<open>\<T>\<close> of the trace model just gives the same denotation, \<^ie> the empty trace: 
-\<open>\<T>(Skip) = \<T>(Stop) = {[]}\<close>.
-Note that the trace sets, representing all \<^emph>\<open>partial\<close> history, is in general prefix closed.\<close>
-
-text*[ex1::math_example, status=semiformal, level="Some 1"] \<open>
-Let two processes be defined as follows:\<^vs>\<open>0.2cm\<close>
-
-  \<^enum> \<open>P\<^sub>d\<^sub>e\<^sub>t = (a \<rightarrow> Stop) \<box> (b \<rightarrow> Stop)\<close>
-  \<^enum> \<open>P\<^sub>n\<^sub>d\<^sub>e\<^sub>t = (a \<rightarrow> Stop) \<sqinter> (b \<rightarrow> Stop)\<close> 
-\<close> 
-
-text\<open>These two processes \<open>P\<^sub>d\<^sub>e\<^sub>t\<close> and \<open>P\<^sub>n\<^sub>d\<^sub>e\<^sub>t\<close> cannot be distinguished by using 
-the trace semantics: \<open>\<T>(P\<^sub>d\<^sub>e\<^sub>t) = \<T>(P\<^sub>n\<^sub>d\<^sub>e\<^sub>t) = {[],[a],[b]}\<close>. To resolve this problem, Brookes @{cite "BrookesHR84"} 
-proposed the failures model, where communication traces were augmented with the 
-constraint information for further communication that is represented negatively as a refusal set. 
-A failure \<open>(t, X)\<close> is a pair of a trace \<open>t\<close> and a set of events \<open>X\<close> that a process can refuse if 
-any of the events in \<open>X\<close> were offered to him by the environment after performing the trace \<open>t\<close>. 
-The semantic function \<open>\<F>\<close> in the failures model maps a process to a set of refusals.
-Let \<open>\<Sigma>\<close> be the set of events. Then, \<open>{([],\<Sigma>)} \<subseteq> \<F> Stop\<close> as the process \<open>Stop\<close> refuses all events. 
-For Example 1, we have \<open>{([],\<Sigma>\{a,b}),([a],\<Sigma>),([b],\<Sigma>)} \<subseteq> \<F> P\<^sub>d\<^sub>e\<^sub>t\<close>, while
-\<open>{([],\<Sigma>\{a}),([],\<Sigma>\{b}),([a],\<Sigma>),([b],\<Sigma>)} \<subseteq> \<F> P\<^sub>n\<^sub>d\<^sub>e\<^sub>t\<close> (the \<open>_\<subseteq>_\<close> refers to the fact that
-the refusals must be downward closed; we show only the maximal refusal sets here).
-Thus, internal and external choice, also called \<^emph>\<open>nondeterministic\<close> and \<^emph>\<open>deterministic\<close>
-choice, can be distinguished in the failures semantics.
-
-However, it turns out that the failures model suffers from another deficiency with respect to 
-the phenomenon called infinite internal chatter or \<^emph>\<open>divergence\<close>.\<close>
-
-text*[ex2::example, status=semiformal] \<open>
-The following process \<open>P\<^sub>i\<^sub>n\<^sub>f\<close> is an infinite process that performs \<open>a\<close> infinitely 
-many times. However, using the \<^csp> hiding operator \<open>_\_\<close>, this activity is concealed: 
-
-  \<^enum>  \<open>P\<^sub>i\<^sub>n\<^sub>f = (\<mu> X. a \<rightarrow> X) \ {a}\<close>
-\<close>
-
-text\<open>where \<open>P\<^sub>i\<^sub>n\<^sub>f\<close> will be equivalent to \<open>\<bottom>\<close> in the process cpo ordering. 
-To distinguish divergences from the deadlock process, Brookes and Roscoe 
-proposed failure/divergence model to incorporate divergence traces  @{cite "brookes-roscoe85"}. 
-A divergence trace is the one leading to a possible divergent behavior. 
-A well behaved process should be able to respond to its environment in a finite amount of time. 
-Hence, divergences are considered as a kind of a catastrophe in this model. 
-Thus, a process is represented by a failure set \<open>\<F>\<close>, 
-together with a set of divergence traces \<open>\<D>\<close>;
-in our example, the empty trace \<open>[]\<close> belongs to \<open>\<D> P\<^sub>i\<^sub>n\<^sub>f\<close>.
-
-The failure/divergence model has become the standard semantics for an enormous range of \<^csp> 
-research and the implementations of @{cite "fdr4" and "SunLDP09"}. Note, that the work
-of @{cite "IsobeRoggenbach2010"} is restricted to a variant of the failures model only.
- 
-\<close>
-
-subsection*["isabelleHol"::technical, main_author="Some(@{author ''bu''})"]\<open>Isabelle/HOL\<close>
-text\<open> Nowadays, Isabelle/HOL is one of the major interactive theory development environments
-@{cite "nipkow.ea:isabelle:2002"}. HOL stands for Higher-Order Logic, a logic based on simply-typed
-\<open>\<lambda>\<close>-calculus extended by parametric polymorphism and Haskell-like type-classes.
-Besides interactive and integrated automated proof procedures,
-it offers code and documentation generators. Its structured proof language Isar is intensively used
-in the plethora of work done and has been a key factor for the success of the Archive of Formal Proofs
-(\<^url>\<open>https://www.isa-afp.org\<close>).
-
-For the work presented here, one relevant construction is :
-
-   \<^item> \<^theory_text>\<open>typedef  (\<alpha>\<^sub>1,...,\<alpha>\<^sub>n)t = E\<close>
- 
-It creates a fresh type that is isomorphic to a set \<open>E\<close> involving \<open>\<alpha>\<^sub>1,...,\<alpha>\<^sub>n\<close> types.
-Isabelle/HOL performs a number of syntactic checks for these constructions that guarantee the logical
-consistency of the defined constants or types relative to the axiomatic basis of HOL. The system
-distribution comes with rich libraries comprising Sets, Numbers, Lists, etc. which are built in this
-"conservative" way.
-
-For this work, a particular library called \<^theory_text>\<open>HOLCF\<close> is intensively used. It provides classical 
-domain theory for a particular type-class \<open>\<alpha>::pcpo\<close>, \<^ie> the class of types  \<open>\<alpha>\<close> for which 
-
-   \<^enum> a least element \<open>\<bottom>\<close> is defined, and
-   \<^enum> a complete partial order \<open>_\<sqsubseteq>_\<close> is defined.
-
- For these types, \<^theory_text>\<open>HOLCF\<close> provides a fixed-point operator \<open>\<mu>X. f X\<close> as well as the 
-fixed-point induction and other (automated) proof infrastructure. Isabelle's type-inference can 
-automatically infer, for example, that if \<open>\<alpha>::pcpo\<close>, then \<open>(\<beta> \<Rightarrow> \<alpha>)::pcpo\<close>. \<close>
-  
-section*["csphol"::technical,main_author="Some(@{author ''bu''}::author)", level="Some 2"]
-\<open>Formalising Denotational \<^csp> Semantics in HOL \<close>
-
-subsection*["processinv"::technical, main_author="Some(@{author ''bu''})"]
-\<open>Process Invariant and Process Type\<close>
-text\<open> First, we need a slight revision of the concept
-of \<^emph>\<open>trace\<close>: if \<open>\<Sigma>\<close> is the type of the atomic events (represented by a type variable), then
-we need to extend this type by a special event \<open>\<checkmark>\<close> (called "tick") signaling termination.
-Thus, traces have the type \<open>(\<Sigma>\<uplus>\<checkmark>)\<^sup>*\<close>, written \<open>\<Sigma>\<^sup>\<checkmark>\<^sup>*\<close>; since \<open>\<checkmark>\<close> may only occur at the end of a trace, 
-we need to define a predicate \<open>front\<^sub>-tickFree t\<close> that requires from traces that \<open>\<checkmark>\<close> can only occur 
-at the end.
-
-Second, in the traditional literature, the semantic domain is implicitly described by 9 "axioms" 
-over the three semantic functions \<open>\<T>\<close>, \<open>\<F>\<close> and \<open>\<D>\<close>.
-Informally, these are:
-
-   \<^item> the initial trace of a process must be empty;
-   \<^item> any allowed trace must be \<open>front\<^sub>-tickFree\<close>; 
-   \<^item> traces of a process are  \<^emph>\<open>prefix-closed\<close>; 
-   \<^item> a process can refuse all subsets of a refusal set; 
-   \<^item> any event refused by a process after a trace \<open>s\<close> must be in a refusal set associated to \<open>s\<close>;
-   \<^item> the tick accepted after a trace \<open>s\<close> implies that all other events are refused; 
-   \<^item> a divergence trace with any suffix is itself a divergence one
-   \<^item> once a process has diverged, it can engage in or refuse any sequence of events.
-   \<^item> a trace ending with \<open>\<checkmark>\<close> belonging to divergence set implies that its 
-     maximum prefix without \<open>\<checkmark>\<close> is also a divergent trace.
-
-More formally, a process \<open>P\<close> of the type \<open>\<Sigma> process\<close> should have the following properties:
-
-@{cartouche [display, indent=10] \<open>([],{}) \<in> \<F> P \<and>
-(\<forall> s X.  (s,X) \<in> \<F> P \<longrightarrow> front_tickFree s) \<and>
-(\<forall> s t . (s@t,{}) \<in> \<F> P \<longrightarrow> (s,{}) \<in> \<F> P) \<and>
-(\<forall> s X Y. (s,Y) \<in> \<F> P \<and> X\<subseteq>Y \<longrightarrow> (s,X) \<in> \<F> P) \<and> 
-(\<forall> s X Y. (s,X) \<in> \<F> P \<and> (\<forall>c \<in> Y. ((s@[c],{}) \<notin> \<F> P)) \<longrightarrow> (s,X \<union> Y) \<in> \<F> P) \<and>
-(\<forall> s X.  (s@[\<checkmark>],{}) \<in> \<F> P \<longrightarrow> (s,X-{\<checkmark>}) \<in> \<F> P) \<and>
-(\<forall> s t. s \<in> \<D> P \<and> tickFree s \<and> front_tickFree t \<longrightarrow> s@t \<in> \<D> P)  \<and>
-(\<forall> s X. s \<in> \<D> P \<longrightarrow> (s,X) \<in> \<F> P) \<and>
-(\<forall> s. s@[\<checkmark>] \<in> \<D> P \<longrightarrow> s \<in> \<D> P)\<close>}
-
-Our objective is to encapsulate this wishlist into a type constructed as a conservative
-theory extension in our theory \<^holcsp>.
-Therefore third, we define a pre-type for processes \<open>\<Sigma> process\<^sub>0\<close> by \<open> \<P>(\<Sigma>\<^sup>\<checkmark>\<^sup>* \<times> \<P>(\<Sigma>\<^sup>\<checkmark>)) \<times> \<P>(\<Sigma>\<^sup>\<checkmark>)\<close>.
-Forth, we turn our wishlist of "axioms" above into the definition of a predicate \<open>is_process P\<close> 
-of type \<open>\<Sigma> process\<^sub>0 \<Rightarrow> bool\<close> deciding if its conditions are fulfilled. Since \<open>P\<close> is a pre-process,
-we replace \<open>\<F>\<close> by \<open>fst\<close> and  \<open>\<D>\<close> by \<open>snd\<close> (the HOL projections into a pair).
-And last not least fifth, we use the following type definition:
-
-  \<^item> \<^theory_text>\<open>typedef '\<alpha> process = "{P :: '\<alpha> process\<^sub>0 . is_process P}"\<close>
-
-Isabelle requires a proof for the existence of a witness for this set,
-but this can be constructed in a straight-forward manner. Suitable definitions for 
-\<open>\<T>\<close>, \<open>\<F>\<close> and \<open>\<D>\<close> lifting \<open>fst\<close> and \<open>snd\<close> on the new \<open>'\<alpha> process\<close>-type allows to derive
-the above properties for any \<open>P::'\<alpha> process\<close>. \<close>
-
-subsection*["operator"::technical, main_author="Some(@{author ''lina''})"]
-\<open>\<^csp> Operators over the Process Type\<close>
-text\<open> Now, the operators of \<^csp> \<open>Skip\<close>, \<open>Stop\<close>, \<open>_\<sqinter>_\<close>,  \<open>_\<box>_\<close>, \<open>_\<rightarrow>_\<close>,\<open>_\<lbrakk>_\<rbrakk>_\<close> etc. 
-for internal choice, external choice, prefix and parallel composition, can 
-be defined indirectly on the process-type. For example, for the simple case of the internal choice,
-we construct it such that \<open>_\<sqinter>_\<close> has type \<open>'\<alpha> process \<Rightarrow> '\<alpha> process \<Rightarrow> '\<alpha> process\<close> and 
-such that its projection laws satisfy the properties \<open>\<F> (P \<sqinter> Q) = \<F> P \<union> \<F> Q\<close>  and 
-\<open>\<D> (P \<sqinter> Q) = \<D> P \<union> \<D> Q\<close> required from @{cite "roscoe:csp:1998"}. 
-This boils down to a proof that an equivalent definition on the pre-process type \<open>\<Sigma> process\<^sub>0\<close>
-maintains \<open>is_process\<close>, \<^ie> this predicate remains invariant on the elements of the semantic domain. 
-For example, we define \<open>_\<sqinter>_\<close> on the pre-process type as follows:
-
-  \<^item> \<^theory_text>\<open>definition "P \<sqinter> Q \<equiv> Abs_process(\<F> P \<union> \<F> Q , \<D> P \<union> \<D> Q)"\<close>
-
-where \<open>Rep_process\<close> and \<open>Abs_process\<close> are the representation and abstraction morphisms resulting 
-from the type definition linking the type \<open>'\<alpha> process\<close> isomorphically to the set \<open>'\<alpha> process\<^sub>0\<close>. 
-The projection into \<^emph>\<open>failures\<close> is defined by \<open>\<F> = fst \<circ> Rep_process\<close>, whereas the 
-\<^emph>\<open>divergences\<close> are defined bz \<open>\<D> = snd \<circ> Rep_process\<close>. Proving the above properties for  
-\<open>\<F> (P \<sqinter> Q)\<close> and \<open>\<D> (P \<sqinter> Q)\<close> requires a proof that \<open>(\<F> P \<union> \<F> Q , \<D> P \<union> \<D> Q)\<close>
-satisfies the well-formedness conditions of \<open>is_process\<close>, which is fairly simple in this case.
-
-The definitional presentation of the \<^csp> process operators according to @{cite "roscoe:csp:1998"} 
-follows always this scheme. This part of the theory comprises around 2000 loc. 
-\<close>
-
-subsection*["orderings"::technical, main_author="Some(@{author ''bu''})"]
-\<open>Refinement Orderings\<close>
-
-text\<open> \<^csp> is centered around the idea of process refinement; many critical properties, 
-even ones typically considered as "liveness-properties", can be expressed in terms of these, and
-a conversion of processes in terms of (finite) labelled transition systems leads to effective
-model-checking techniques based on graph-exploration. Essentially,  a process \<open>P\<close> \<^emph>\<open>refines\<close> 
-another process \<open>Q\<close> if and only if it is more deterministic and more defined (has less divergences).
-Consequently, each of the three semantics models (trace, failure and failure/divergence) 
-has its corresponding refinement orderings.\<close>
-Theorem*[th1::"theorem", short_name="\<open>Refinement properties\<close>"]\<open>
-What we are interested in this paper is the following refinement orderings for the 
-failure/divergence model.
-
-   \<^enum> \<open>P \<sqsubseteq>\<^sub>\<F>\<^sub>\<D> Q \<equiv> \<F> P \<supseteq> \<F> Q \<and> \<D> P \<supseteq> \<D> Q\<close> 
-   \<^enum> \<open>P \<sqsubseteq>\<^sub>\<T>\<^sub>\<D> Q \<equiv> \<T> P \<supseteq> \<T> Q \<and> \<D> P \<supseteq> \<D> Q\<close>
-   \<^enum> \<open>P \<sqsubseteq>\<^sub>\<FF> Q \<equiv>  \<FF> P \<supseteq> \<FF> Q, \<FF>\<in>{\<T>,\<F>,\<D>}\<close>  \<close>
-
-text\<open> Notice that in the \<^csp> literature, only \<open>\<sqsubseteq>\<^sub>\<F>\<^sub>\<D>\<close> is well studied for failure/divergence model. 
-Our formal analysis of different granularities on the refinement orderings   
-allows deeper understanding of the same semantics model. For example, \<open>\<sqsubseteq>\<^sub>\<T>\<^sub>\<D>\<close> turns
-out to have in some cases better monotonicity properties and therefore allow for stronger proof
-principles in \<^csp>. Furthermore, the refinement ordering \<open>\<sqsubseteq>\<^sub>\<F>\<close> analyzed here 
-is different from the classical 
-failure refinement in the literature that is studied for the stable failure model  
-@{cite "roscoe:csp:1998"}, where failures are only defined for stable 
-states, from which no internal progress is possible. 
-\<close>
-
-
-subsection*["fixpoint"::technical, main_author="Some(@{author ''lina''})"]
-\<open>Process Ordering and HOLCF\<close>
-text\<open> For any denotational semantics, the fixed point theory giving semantics to systems
-of recursive equations is considered as keystone. Its prerequisite is a complete partial ordering
-\<open>_\<sqsubseteq>_\<close>. The natural candidate \<open>_\<sqsubseteq>\<^sub>\<F>\<^sub>\<D>_\<close> is unfortunately not complete for infinite \<open>\<Sigma>\<close> for the
-generalized deterministic choice, and thus for the building block of the read-operations.
-
-Roscoe and Brooks @{cite "Roscoe1992AnAO"} finally proposed another ordering, called the 
-\<^emph>\<open>process ordering\<close>, and restricted the generalized deterministic choice in a particular way such 
-that completeness could at least be assured for read-operations. This more complex ordering 
-is based on the concept \<^emph>\<open>refusals after\<close> a trace \<open>s\<close> and defined by \<open>\<R> P s \<equiv> {X | (s, X) \<in> \<F> P}\<close>.\<close>
-
-Definition*[process_ordering, level= "Some 2", short_name="''process ordering''"]\<open>
-We define \<open>P \<sqsubseteq> Q \<equiv> \<psi>\<^sub>\<D> \<and> \<psi>\<^sub>\<R> \<and> \<psi>\<^sub>\<M> \<close>,  where 
-\<^enum> \<open>\<psi>\<^sub>\<D> = \<D> P \<supseteq> \<D> Q \<close>
-\<^enum> \<open>\<psi>\<^sub>\<R> = s \<notin> \<D> P \<Rightarrow> \<R> P s = \<R> Q s\<close>  
-\<^enum> \<open>\<psi>\<^sub>\<M> = Mins(\<D> P) \<subseteq> \<T> Q \<close> \<close>
-
-text\<open>The third condition \<open>\<psi>\<^sub>\<M>\<close> implies that the set of minimal divergent traces 
-(ones with no proper prefix that is also a divergence) in  \<open>P\<close>,  denoted by \<open>Mins(\<D> P)\<close>, 
-should be a subset of the trace set of \<open>Q\<close>. 
-%One may note that each element in \<open>Mins(\<D> P)\<close> do actually not contain the \<open>\<checkmark>\<close>, 
-%which can be deduced from the process invariants described 
-%in the precedent @{technical "processinv"}. This can be explained by the fact that we are not 
-%really concerned with what a process does after it terminates. 
-It is straight-forward to define the least element \<open>\<bottom>\<close> in this ordering by 
-\<open>\<F>(\<bottom>)= {(s,X). front_tickFree s}\<close> and  \<open>\<D>(\<bottom>) = {s. front_tickFree s}\<close>  \<close>
-
-text\<open>While the original work @{cite "tej.ea:corrected:1997"} was based on an own --- and different ---
-fixed-point theory, we decided to base HOL-\<^csp> 2 on HOLCF (initiated by @{cite "muller.ea:holcf:1999"} 
-and substantially extended in @{cite "huffman.ea:axiomatic:2005"}). 
-HOLCF is based on parametric polymorphism with type classes. A type class is actually a 
-constraint on a type variable by respecting certain syntactic and semantics 
-requirements. For example, a type class of partial ordering, denoted by \<open>\<alpha>::po\<close>, is restricted to
-all types \<open>\<alpha>\<close> possessing a relation \<open>\<le>:\<alpha>\<times>\<alpha>\<rightarrow>bool\<close> that is reflexive, anti-symmetric, and transitive.
-Isabelle possesses a construct that allows to establish, that the type \<open>nat\<close> belongs to this class,
-with the consequence that all lemmas derived abstractly on \<open>\<alpha>::po\<close> are in particular applicable on 
-\<open>nat\<close>. The type class of \<open>po\<close> can be extended to the class of complete partial ordering  \<open>cpo\<close>. 
-A \<open>po\<close> is said to be complete if all non-empty directed sets have a least upper bound (\<open>lub\<close>). 
-Finally the class of \<open>pcpo\<close> (Pointed cpo) is a \<open>cpo\<close> ordering that has a least element, 
-denoted by \<open>\<bottom>\<close>. For \<open>pcpo\<close> ordering, two crucial notions for continuity (\<open>cont\<close>) and fixed-point operator 
-(\<open>\<mu>X. f(X)\<close>) are defined in the usual way. A function from one  \<open>cpo\<close> to another one is said 
-to be continuous if it distributes over the \<open>lub\<close> of all directed sets (or chains).
-One key result of the fixed-point theory is the proof of the fixed-point theorem:
-
-@{cartouche [display, indent=25] \<open>cont f \<Longrightarrow>  \<mu>X. f(X) = f(\<mu>X. f(X))\<close>}
-
-For most \<^csp> operators \<open>\<otimes>\<close> we derived rules of the form: 
-   @{cartouche [display, indent=20] \<open>cont P \<Longrightarrow> cont Q \<Longrightarrow> cont(\<lambda>x. (P x) \<otimes> (Q x))\<close>}
-
-These rules allow to automatically infer for any process term if it is continuous or not.  
-The port of HOL-CSP 2 on HOLCF implied that the derivation of the entire continuity rules 
-had to be completely re-done (3000 loc).\<close>
-
-Theorem*[th2,short_name="\<open>Fixpoint Induction\<close>"]
-\<open>HOL-CSP provides an important proof principle, the fixed-point induction:
-@{cartouche [display, indent=5] \<open>cont f \<Longrightarrow> adm P \<Longrightarrow> P \<bottom> \<Longrightarrow> (\<And>X. P X \<Longrightarrow> P(f X)) \<Longrightarrow> P(\<mu>X. f X)\<close>}
-\<close>
-
-text\<open>Fixed-point induction of @{theorem th2} requires a small side-calculus for establishing the admissibility
-of a predicate; basically, predicates are admissible if they are valid for any least upper bound 
-of a chain \<open>x\<^sub>1 \<sqsubseteq> x\<^sub>2 \<sqsubseteq> x\<^sub>3 ... \<close> provided that \<open>\<forall>i. P(x\<^sub>i)\<close>. It turns out that \<open>_\<sqsubseteq>_\<close> and \<open>_\<sqsubseteq>\<^sub>F\<^sub>D_\<close> as
-well as all other refinement orderings that we introduce in this paper are  admissible.
-Fixed-point inductions are the main proof weapon in verifications, together with monotonicities 
-and the \<^csp> laws. Denotational arguments can be hidden as they are not needed in practical 
-verifications. \<close>
-
-subsection*["law"::technical, main_author="Some(@{author ''lina''})"]
-\<open>\<^csp> Rules: Improved Proofs and New Results\<close>
-
-
-text\<open>The \<^csp> operators enjoy a number of algebraic properties: commutativity, 
-associativities, and idempotence in some cases. Moreover, there is a rich body of distribution
-laws between these operators. Our new version HOL-CSP 2 not only shortens and restructures the 
-proofs of @{cite "tej.ea:corrected:1997"}; the code reduces to 8000 loc from 25000 loc. \<close>
-
-Theorem*[th3, short_name="\<open>Examples of Derived Rules.\<close>"]\<open> 
-  \<^item> \<open>\<box>x\<in>A\<union>B\<rightarrow>P(x) = (\<box>x\<in>A\<rightarrow>P x) \<box> (\<box>x\<in>B\<rightarrow>P x)\<close>
-  \<^item> \<open>A\<union>B\<subseteq>C \<Longrightarrow> (\<box>x\<in>A\<rightarrow>P x \<lbrakk>C\<rbrakk> \<box>x\<in>B\<rightarrow>Q x) = \<box>x\<in>A\<inter>B\<rightarrow>(P x \<lbrakk>C\<rbrakk> Q x)\<close>
-  \<^item> @{cartouche [display]\<open>A\<subseteq>C \<Longrightarrow> B\<inter>C={} \<Longrightarrow> 
-               (\<box>x\<in>A\<rightarrow>P x \<lbrakk>C\<rbrakk> \<box>x\<in>B\<rightarrow>Q x) = \<box>x\<in>B\<rightarrow>(\<box>x\<in>A\<rightarrow>P x \<lbrakk>C\<rbrakk> Q x)\<close>}
-  \<^item> \<open>finite A \<Longrightarrow> A\<inter>C = {} \<Longrightarrow> ((P \<lbrakk>C\<rbrakk> Q) \ A) = ((P \ A) \<lbrakk>C\<rbrakk> (Q \ A)) ...\<close>\<close>
-
-
-text\<open>The continuity proof of the hiding operator is notorious. The proof is known to involve the 
-classical König's lemma stating that every infinite tree with finite branching has an infinite path. 
-We adapt this lemma to our context as follows:
-
-@{cartouche [display, indent=5] 
- \<open>infinite tr \<Longrightarrow> \<forall>i. finite{t. \<exists>t'\<in>tr. t = take i t'} 
-              \<Longrightarrow> \<exists> f. strict_mono f \<and> range f \<subseteq> {t. \<exists>t'\<in>tr. t \<le> t'}\<close>}
-
-in order to come up with the continuity rule: \<open>finite S \<Longrightarrow> cont P \<Longrightarrow> cont(\<lambda>X. P X \ S)\<close>.
-The original proof had been drastically shortened by a factor 10 and important immediate steps
-generalized: monotonicity, for example, could be generalized to the infinite case. 
-
-As for new laws, consider the case of \<open>(P \ A) \ B = P \ (A \<union> B)\<close> which is 
-stated in @{cite "Roscoe:UCS:2010"} without proof. In the new version, we managed to establish 
-this law which still need 450 lines of complex Isar code. However, it turned out that the original
-claim is not fully true: it can only be established again by König's 
-lemma to build a divergent trace of  \<open>P \ (A \<union> B)\<close> which requires \<open>A\<close> to be finite 
-(\<open>B\<close> can be arbitrary) in order to use it from a divergent trace of  \<open>(P \ A) \ B\<close> 
-@{footnote \<open>In @{cite "Roscoe:UCS:2010"}, the authors point out that the laws involving the hiding 
-operator may fail when \<open>A\<close> is infinite; however, they fail to give the precise 
-conditions for this case.\<close>}. Again, we want to argue that the intricate number of
-cases to be considered as well as their complexity makes pen and paper proofs 
-practically infeasible.
-\<close>
-
-section*["newResults"::technical,main_author="Some(@{author ''safouan''}::author)",
-                                 main_author="Some(@{author ''lina''}::author)", level= "Some 3"]
-\<open>Theoretical Results on Refinement\<close>
-text\<open>\<close>
-subsection*["adm"::technical,main_author="Some(@{author ''safouan''}::author)", 
-                                  main_author="Some(@{author ''lina''}::author)"]
-\<open>Decomposition Rules\<close>
-text\<open>
-In our framework, we implemented the pcpo process refinement together with the five refinement 
-orderings introduced in @{technical "orderings"}. To enable fixed-point induction, we first have 
-the admissibility of the refinements.
-@{cartouche [display, indent=7] \<open>cont u \<Longrightarrow> mono v \<Longrightarrow> adm(\<lambda>x. u x \<sqsubseteq>\<^sub>\<FF> v x) where \<FF>\<in>{\<T>,\<F>,\<D>,\<T>\<D>,\<F>\<D>}\<close>}
-
-
-Next we analyzed the monotonicity of these refinement orderings, whose results are then used as 
-decomposition rules in our framework. 
-Some \<^csp> operators, such as multi-prefix and non-deterministic choice, are monotonic 
-under all refinement orderings, while others are not.    
-  
-\<^item> External choice is not monotonic only under \<open>\<sqsubseteq>\<^sub>\<F>\<close>, with the following monotonicities proved:
-  @{cartouche [display,indent=5]
-    \<open>P \<sqsubseteq>\<^sub>\<FF> P' \<Longrightarrow> Q \<sqsubseteq>\<^sub>\<FF> Q' \<Longrightarrow> (P \<box> Q) \<sqsubseteq>\<^sub>\<FF> (P' \<box> Q') where \<FF>\<in>{\<T>,\<D>,\<T>\<D>,\<F>\<D>}\<close>}
-\<^item> Sequence operator is not monotonic under \<open>\<sqsubseteq>\<^sub>\<F>\<close>, \<open>\<sqsubseteq>\<^sub>\<D>\<close> or \<open>\<sqsubseteq>\<^sub>\<T>\<close>:
-  @{cartouche [display,indent=5] 
-    \<open>P \<sqsubseteq>\<^sub>\<FF> P'\<Longrightarrow> Q \<sqsubseteq>\<^sub>\<FF> Q' \<Longrightarrow> (P ; Q) \<sqsubseteq>\<^sub>\<FF> (P' ; Q') where \<FF>\<in>{\<T>\<D>,\<F>\<D>}\<close>}
-
-All refinements are right-side monotonic but \<open>\<sqsubseteq>\<^sub>\<F>\<close>, \<open>\<sqsubseteq>\<^sub>\<D>\<close> and \<open>\<sqsubseteq>\<^sub>\<T>\<close> are not left-side monotonic,
-which can be explained by the interdependence relationship of failure and divergence projections 
-for the first component. We thus proved:
-\<^item> Hiding operator is not monotonic under \<open>\<sqsubseteq>\<^sub>\<D>\<close>:
-  @{cartouche [display,indent=5] \<open>P \<sqsubseteq>\<^sub>\<FF> Q \<Longrightarrow> P \ A  \<sqsubseteq>\<^sub>\<FF> Q \ A where \<FF>\<in>{\<T>,\<F>,\<T>\<D>,\<F>\<D>}\<close>}
-Intuitively, for the divergence refinement of the hiding operator, there may be
-some trace \<open>s\<in>\<T> Q\<close> and \<open>s\<notin>\<T> P\<close> such that it becomes divergent in \<open>Q \ A\<close>  but 
-not in \<open>P \ A\<close>. 
-\<^item> Parallel composition is not monotonic under \<open>\<sqsubseteq>\<^sub>\<F>\<close>, \<open>\<sqsubseteq>\<^sub>\<D>\<close> or \<open>\<sqsubseteq>\<^sub>\<T>\<close>:
-  @{cartouche [display,indent=5] \<open>P \<sqsubseteq>\<^sub>\<FF> P' \<Longrightarrow> Q \<sqsubseteq>\<^sub>\<FF> Q' \<Longrightarrow> (P \<lbrakk>A\<rbrakk> Q) \<sqsubseteq>\<^sub>\<FF> (P' \<lbrakk>A\<rbrakk> Q') where \<FF>\<in>{\<T>\<D>,\<F>\<D>}\<close>}
-The failure and divergence projections of this operator are also interdependent, similar to the 
-sequence operator. Hence, this operator is not monotonic with \<open>\<sqsubseteq>\<^sub>\<F>\<close>, \<open>\<sqsubseteq>\<^sub>\<D>\<close> and \<open>\<sqsubseteq>\<^sub>\<T>\<close>, but monotonic 
-when their combinations are considered. \<close>
-
-subsection*["processes"::technical,main_author="Some(@{author ''safouan''}::author)", 
-                            main_author="Some(@{author ''lina''}::author)"]
-\<open>Reference Processes and their Properties\<close>
-text\<open>
-We now present reference processes that exhibit basic behaviors, introduced in  
-fundamental \<^csp> works @{cite "Roscoe:UCS:2010"}. The process \<open>RUN A\<close> always 
-accepts events from \<open>A\<close> offered by the environment. The process \<open>CHAOS A\<close> can always choose to 
-accept or reject any event of \<open>A\<close>. The process \<open>DF A\<close> is the most non-deterministic deadlock-free 
-process on \<open>A\<close>, \<^ie>, it can never refuse all events of \<open>A\<close>. 
-To handle termination better, we added two new processes \<open>CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P\<close> and \<open>DF\<^sub>S\<^sub>K\<^sub>I\<^sub>P\<close>. 
-%Note that we do not redefine \<open>RUN\<close> with \<open>SKIP\<close> because this process is supposed to never terminate, 
-%thus must be without it. 
-\<close>
-
-(*<*) (* a test ...*)
-text*[X22 ::math_content, level="Some 2"  ]\<open>\<open>RUN A \<equiv> \<mu> X. \<box> x \<in> A \<rightarrow> X\<close>                           \<close>
-text*[X32::"definition", level="Some 2", mcc=defn]\<open>\<open>CHAOS A \<equiv> \<mu> X. (STOP \<sqinter> (\<box> x \<in> A \<rightarrow> X))\<close>        \<close>
-Definition*[X42, level="Some 2"]\<open>\<open>CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P A \<equiv> \<mu> X. (SKIP \<sqinter> STOP \<sqinter> (\<box> x \<in> A \<rightarrow> X))\<close>  \<close>
-Definition*[X52::"definition", level="Some 2"]\<open>\<open>CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P A \<equiv> \<mu> X. (SKIP \<sqinter> STOP \<sqinter> (\<box> x \<in> A \<rightarrow> X))\<close> \<close>
-
-text\<open> The \<open>RUN\<close>-process defined @{math_content X22} represents the process that accepts all 
-events, but never stops nor deadlocks. The \<open>CHAOS\<close>-process comes in two variants shown in 
-@{definition X32} and @{definition X42} @{definition X52}: the process that non-deterministically 
-stops or accepts any offered event, whereas \<open>CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P\<close> can additionally terminate.\<close>
-(*>*)
-
-Definition*[X2, level="Some 2"]\<open>\<open>RUN A \<equiv> \<mu> X. \<box> x \<in> A \<rightarrow> X\<close>                    \<close>
-Definition*[X3, level="Some 2"]\<open>\<open>CHAOS A \<equiv> \<mu> X. (STOP \<sqinter> (\<box> x \<in> A \<rightarrow> X))\<close>         \<close>
-Definition*[X4, level="Some 2"]\<open>\<open>CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P A \<equiv> \<mu> X. (SKIP \<sqinter> STOP \<sqinter> (\<box> x \<in> A \<rightarrow> X))\<close>\<close>
-Definition*[X5, level="Some 2"]\<open>\<open>DF A \<equiv> \<mu> X. (\<sqinter> x \<in> A \<rightarrow> X)\<close>                       \<close>
-Definition*[X6, level="Some 2"]\<open>\<open>DF\<^sub>S\<^sub>K\<^sub>I\<^sub>P A \<equiv> \<mu> X. ((\<sqinter> x \<in> A \<rightarrow> X) \<sqinter> SKIP)\<close>          \<close> 
-
-text\<open>In the following, we denote \<open> \<R>\<P> = {DF\<^sub>S\<^sub>K\<^sub>I\<^sub>P, DF, RUN, CHAOS, CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P}\<close>. 
-All five  reference processes are divergence-free.
-which was proven by using a particular lemma \<open>\<D> (\<mu> x. f x) = \<Inter>\<^sub>i\<^sub>\<in>\<^sub>\<nat> \<D> (f\<^sup>i \<bottom>)\<close>.  
-@{cartouche 
-  [display,indent=8] \<open> D (\<PP> UNIV) = {} where \<PP> \<in> \<R>\<P> and UNIV is the set of all events\<close>
-}
-Regarding the failure refinement ordering, the set of failures \<open>\<F> P\<close> for any process \<open>P\<close> is
-a subset of  \<open>\<F> (CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P UNIV)\<close>.
-
-   @{cartouche [display, indent=25] \<open>CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P UNIV \<sqsubseteq>\<^sub>\<F> P\<close>}
-
-Furthermore, the following 5 relationships were demonstrated from monotonicity results and
-a denotational proof.
-\<close>
-
-
-Corollary*[co1::"corollary", short_name="\<open>Corollaries on reference processes.\<close>",level="Some 2"]
-\<open> \<^hfill> \<^br>  \<^vs>\<open>-0.3cm\<close>
-  \<^enum> \<open>CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P A \<sqsubseteq>\<^sub>\<F> CHAOS A\<close>
-  \<^enum> \<open>CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P A \<sqsubseteq>\<^sub>\<F> DF\<^sub>S\<^sub>K\<^sub>I\<^sub>P A\<close>  
-  \<^enum> \<open>CHAOS A \<sqsubseteq>\<^sub>\<F> DF A\<close>
-  \<^enum> \<open>DF\<^sub>S\<^sub>K\<^sub>I\<^sub>P A \<sqsubseteq>\<^sub>\<F> DF A\<close>  
-  \<^enum> \<open>DF A \<sqsubseteq>\<^sub>\<F> RUN A\<close> \<^vs>\<open>0.3cm\<close>
-
-where 1 and 2 are immediate, and where 4 and 5 are directly obtained from our monotonicity 
-results while 3 requires an argument over the denotational space.
-Thanks to transitivity, we can derive other relationships.\<close>          
-
-text\<open> Lastly, regarding trace refinement, for any process P, 
-its set of traces \<open>\<T> P\<close> is a subset of  \<open>\<T> (CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P UNIV)\<close> and of  \<open>\<T> (DF\<^sub>S\<^sub>K\<^sub>I\<^sub>P UNIV)\<close> as well.
-%As we already proved that \<open>CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P\<close> covers all failures, 
-%we can immediately infer that it also covers all traces. 
-%The \<open>DF\<^sub>S\<^sub>K\<^sub>I\<^sub>P\<close> case requires a longer denotational proof.
-
-  \<^enum> \<open>CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P UNIV \<sqsubseteq>\<^sub>\<T> P\<close>
-  \<^enum> \<open>DF\<^sub>S\<^sub>K\<^sub>I\<^sub>P UNIV \<sqsubseteq>\<^sub>\<T> P\<close>
-\<close>
-
-text\<open> 
-Recall that a concurrent system is considered as being deadlocked if no component can make any 
-progress,  caused for example by the competition for resources. In opposition to deadlock, 
-processes can enter infinite loops inside a sub-component without never ever interact with their 
-environment again  ("infinite internal chatter"); this situation called  divergence or livelock. 
-Both properties are not just a sanity condition; in \<^csp>, they play a central role for 
-verification. For example, if one wants to establish that a protocol implementation \<open>IMPL\<close> satisfies 
-a non-deterministic specification \<open>SPEC\<close> it suffices to ask if \<open>IMPL || SPEC\<close> is deadlock-free.
-In this setting, \<open>SPEC\<close> becomes a kind of observer that signals non-conformance of \<open>IMPL\<close> by 
-deadlock.
-
-In the literature, deadlock and lifelock are phenomena that are often 
-handled separately. One contribution of our work is establish their precise relationship inside
-the Failure/Divergence Semantics of \<^csp>.\<close>
-
-Definition*[X10::"definition", level="Some 2"]\<open> \<open>deadlock\<^sub>-free P \<equiv>  DF\<^sub>S\<^sub>K\<^sub>I\<^sub>P UNIV \<sqsubseteq>\<^sub>\<F> P\<close>  \<close>
-
-text\<open>\<^noindent> A process \<open>P\<close> is deadlock-free if and only if after any trace \<open>s\<close> without \<open>\<checkmark>\<close>, the union of \<open>\<checkmark>\<close> 
-and all events of \<open>P\<close> can never be a refusal set associated to \<open>s\<close>, which means that \<open>P\<close> cannot 
-be deadlocked after any non-terminating trace.   
-\<close>
-
-Theorem*[T1, short_name="\<open>DF definition captures deadlock-freeness\<close>", level="Some 2"]
-\<open> \<^hfill> \<^br> \<open>deadlock_free P \<longleftrightarrow> (\<forall>s\<in>\<T> P. tickFree s \<longrightarrow> (s, {\<checkmark>}\<union>events_of P) \<notin> \<F> P)\<close> \<close>   
-Definition*[X11, level="Some 2"]\<open>  \<open>livelock\<^sub>-free P \<equiv> \<D> P = {} \<close>   \<close>
-
-text\<open> Recall that all five reference processes are livelock-free. 
-We also have the following lemmas about the 
-livelock-freeness of processes: 
-  \<^enum> \<open>livelock\<^sub>-free P \<longleftrightarrow> \<PP> UNIV \<sqsubseteq>\<^sub>\<D> P where \<PP> \<in> \<R>\<P>\<close> 
-  \<^enum> \<open>livelock\<^sub>-free P \<longleftrightarrow> DF\<^sub>S\<^sub>K\<^sub>I\<^sub>P UNIV \<sqsubseteq>\<^sub>\<T>\<^sub>\<D> P  \<longleftrightarrow> CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P UNIV \<sqsubseteq>\<^sub>\<T>\<^sub>\<D> P\<close>
-  \<^enum> \<open>livelock\<^sub>-free P \<longleftrightarrow> CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P UNIV \<sqsubseteq>\<^sub>\<F>\<^sub>\<D> P\<close> 
-\<close>
-text\<open>
-Finally, we proved the following theorem that confirms the relationship between the two vital
-properties:
-\<close>
-Theorem*[T2, short_name="''DF implies LF''", level="Some 2"]
-  \<open>  \<open>deadlock_free P \<longrightarrow> livelock_free P\<close>   \<close>
-
-text\<open>
-This is totally natural, at a first glance, but surprising as the proof of deadlock-freeness only 
-requires failure refinement \<open>\<sqsubseteq>\<^sub>\<F>\<close> (see @{definition \<open>X10\<close>}) where divergence traces are mixed within 
-the failures set. Note that the existing tools in the literature normally detect these two phenomena  
-separately, such as FDR for which checking livelock-freeness is very costly. 
-In our framework, deadlock-freeness of a given system 
-implies its livelock-freeness. However, if a system is not deadlock-free, 
-then it may still be livelock-free. % This makes sense since livelocks are worse than deadlocks.   
-
-\<close>
-
-section*["advanced"::technical,main_author="Some(@{author ''safouan''}::author)",level="Some 3"]
-\<open>Advanced Verification Techniques\<close>
-
-text\<open>
- Based on the refinement framework discussed in @{technical "newResults"}, we will now
-turn to some more advanced proof principles, tactics and verification techniques. 
-We will demonstrate them on two paradigmatic examples well-known in the \<^csp> literature: 
-The CopyBuffer and Dijkstra's Dining Philosophers. In both cases, we will exploit 
-the fact that HOL-CSP 2 allows for reasoning over infinite \<^csp>; in the first case,
-we reason over infinite alphabets approaching an old research objective:
-exploiting data-independence @{cite "Lazic1998ASS" and "AnZhangYou14"} in process
-verification. In the latter case, we present an approach to a verification of a parameterized 
-architecture, in this case a ring-structure of arbitrary size.
-\<close>
-
-subsection*["illustration"::technical,main_author="Some(@{author ''safouan''}::author)", level="Some 3"]
-\<open>The General CopyBuffer Example\<close>
-text\<open>
-We consider the paradigmatic copy buffer example @{cite "Hoare:1985:CSP:3921" and "Roscoe:UCS:2010"} 
-that is characteristic for a specification of a  prototypical process and its
- implementation. It is used extensively in the \<^csp> literature to illustrate the interplay 
-of communication, component concealment and fixed-point operators.
-The process \<open>COPY\<close> is a specification of a one size buffer, that receives elements from the channel 
-\<open>left\<close> of arbitrary type \<open>\<alpha>\<close> and outputs them on the channel \<open>right\<close>: 
-
-@{theory_text [display,indent=5] \<open>
-datatype  \<alpha> events = left \<alpha> | right \<alpha> | mid \<alpha> | ack
-definition COPY \<equiv> (\<mu> X. left?x \<rightarrow> (right!x \<rightarrow> X))\<close>}
-
- \<^noindent> From our HOL-CSP 2 theory that establishes the continuity of all \<^csp> operators, we deduce that 
-such a fixed-point process \<open>COPY\<close> exists and follows the unrolling rule below: 
-
-@{theory_text [display,indent=5] \<open>lemma COPY = (left?x \<rightarrow> (right!x \<rightarrow> COPY))\<close>}
-
- \<^noindent> We set \<open>SEND\<close> and \<open>REC\<close> in parallel but in a row sharing a middle channel 
-\<open>mid\<close> and synchronizing with an \<open>ack\<close> event. Then, we hide all exchanged events between these two 
-processes and we call the resulting process \<open>SYSTEM\<close>: 
-
-@{theory_text [display,indent=5] \<open>
-definition SEND \<equiv> (\<mu> X. left?x \<rightarrow> (mid!x \<rightarrow> (ack \<rightarrow> X)))
-definition REC  \<equiv> (\<mu> X. mid?x \<rightarrow> (right!x \<rightarrow> (ack \<rightarrow> X)))
-definition SYN  \<equiv> (range mid) \<union> {ack}
-definition "SYSTEM \<equiv> (SEND \<lbrakk>SYN\<rbrakk> REC) \\ SYN"\<close>}
-
- \<^noindent> We want to verify that \<open>SYSTEM\<close> implements \<open>COPY\<close>. As shown below, we apply fixed-point induction 
-to prove that \<open>SYSTEM\<close> refines \<open>COPY\<close> using the \<open>pcpo\<close> process ordering \<open>\<sqsubseteq>\<close> that implies all other 
-refinement orderings. We state: 
-
-@{theory_text [display,indent=5] \<open>lemma: COPY \<sqsubseteq> SYSTEM\<close>} 
-
-and apply fixed-point induction over \<open>COPY\<close>; this leaves us to the three subgoals: 
-  \<^enum> \<open>adm (\<lambda>a. a \<sqsubseteq> (SEND \<lbrakk>SYN\<rbrakk> REC) \ SYN)\<close>
-  \<^enum> \<open>\<bottom> \<sqsubseteq> (SEND \<lbrakk>SYN\<rbrakk> REC) \ SYN\<close>
-  \<^enum> @{cartouche [display]\<open>P \<sqsubseteq> (SEND \<lbrakk>SYN\<rbrakk> REC) \ SYN \<Longrightarrow> 
-                              left?x \<rightarrow> right!x \<rightarrow> P \<sqsubseteq> (SEND \<lbrakk>SYN\<rbrakk> REC) \ SYN\<close>} 
-
-The first two sub-proofs are automatic simplification proofs; the third requires unfolding
-\<open>SEND\<close> and \<open>REC\<close> one step and applying the algebraic laws. No denotational
-semantics reasoning is necessary here; it is just an induct-simplify proof consisting
-of 2 lines proof-script involving the derived algebraic laws of \<^csp>.
-
-After proving that \<open>SYSTEM\<close> implements \<open>COPY\<close> for arbitrary alphabets, we aim to profit from this 
-first established result to check which relations \<open>SYSTEM\<close> has wrt. to the reference processes of 
-@{technical "processes"}. Thus, we prove that \<open>COPY\<close> is deadlock-free which implies livelock-free, 
-(proof by fixed-induction  similar to \<open>lemma: COPY \<sqsubseteq> SYSTEM\<close>), from which we can immediately infer 
-from transitivity that \<open>SYSTEM\<close> is. Using refinement relations, we killed four birds with one stone 
-as we proved the deadlock-freeness and  the livelock-freeness for both \<open>COPY\<close> and \<open>SYSTEM\<close> processes. 
-These properties hold for arbitrary alphabets and for infinite ones in particular.
- 
-@{theory_text [display, indent=5] \<open>
-lemma DF UNIV \<sqsubseteq> COPY
-
-corollary deadlock_free COPY
-      and livelock_free COPY
-      and deadlock_free SYSTEM
-      and livelock_free SYSTEM\<close>}
-
-\<close>
-
-
-subsection*["inductions"::technical,main_author="Some(@{author ''safouan''}::author)"]
-\<open>New Fixed-Point Inductions\<close>
-
-text\<open>
- The copy buffer refinement proof \<open>DF UNIV \<sqsubseteq> COPY\<close> is a typical one step induction proof 
-with two goals:
-\<open>base: \<bottom> \<sqsubseteq> Q\<close> and \<open>1-ind: X \<sqsubseteq> Q \<Longrightarrow> (_ \<rightarrow> X) \<sqsubseteq> Q\<close>. Now, if unfolding the fixed-point process \<open>Q\<close> 
-reveals two steps, the second goal becomes 
-\<open>X \<sqsubseteq> Q \<Longrightarrow> _ \<rightarrow> X \<sqsubseteq> _ \<rightarrow> _ \<rightarrow> Q\<close>. Unfortunately, this way, it becomes improvable 
-using monotonicities rules. 
-We need here a two-step induction of the form \<open>base0: \<bottom> \<sqsubseteq> Q\<close>, \<open>base1: _ \<rightarrow> \<bottom> \<sqsubseteq> Q\<close> and 
-\<open>2-ind: X \<sqsubseteq> Q \<Longrightarrow> _ \<rightarrow>  _ \<rightarrow> X \<sqsubseteq> _ \<rightarrow> _ \<rightarrow> Q\<close> to have a sufficiently powerful induction scheme.
-
-For this reason, we derived a number of alternative induction schemes (which are not available
-in the HOLCF library), which are also relevant for our final Dining Philophers example.
-These are essentially adaptions of k-induction schemes applied to domain-theoretic
-setting (so: requiring \<open>f\<close> continuous and \<open>P\<close> admissible; these preconditions are
-skipped here):\<^vs>\<open>0.2cm\<close> 
-  \<^item> \<open>... \<Longrightarrow> \<forall>i<k. P (f\<^sup>i \<bottom>) \<Longrightarrow> (\<forall>X. (\<forall>i<k. P (f\<^sup>i X)) \<longrightarrow> P (f\<^sup>k X)) \<Longrightarrow> P (\<mu>X. f X)\<close>
-  \<^item> \<open>... \<Longrightarrow> \<forall>i<k. P (f\<^sup>i \<bottom>) \<Longrightarrow> (\<forall>X. P X \<longrightarrow> P (f\<^sup>k X)) \<Longrightarrow> P (\<mu>X. f X)\<close>
-
-
-\<^noindent> In the latter variant, the induction hypothesis is weakened to skip \<open>k\<close> steps. When possible,
-it reduces the goal size.
-
-Another problem occasionally occurring in refinement proofs happens when the right side term 
-involves more than one  fixed-point  process (\<^eg> \<open>P \<lbrakk>A\<rbrakk> Q \<sqsubseteq> S\<close>). In this situation,
-we need parallel fixed-point inductions. The HOLCF library offers only a basic one:
-  \<^item> \<open>... \<Longrightarrow> P \<bottom> \<bottom> \<Longrightarrow> (\<forall>X Y. P X Y \<Longrightarrow> P (f X) (g Y)) \<Longrightarrow> P (\<mu>X. f X) (\<mu>X. g X)\<close>
-
-
-\<^noindent> This form does not help in cases like in \<open>P \<lbrakk>\<emptyset>\<rbrakk> Q \<sqsubseteq> S\<close> with the interleaving operator on the 
-right-hand side. The simplifying law is:
-@{cartouche [display, indent=3]\<open>
-(\<box>x\<in>A\<rightarrow>P x \<lbrakk>\<emptyset>\<rbrakk> \<box>x\<in>B\<rightarrow>Q x) =   (\<box>x\<in>A \<rightarrow> (            P x \<lbrakk>\<emptyset>\<rbrakk> \<box>x\<in>B \<rightarrow> Q x) 
-                                         \<box> (\<box>x\<in>B \<rightarrow> (\<box>x\<in>A \<rightarrow> P x \<lbrakk>\<emptyset>\<rbrakk>          Q x))\<close>}
-Here, \<open>(f X \<lbrakk>\<emptyset>\<rbrakk> g Y)\<close> does not reduce to the \<open>(X \<lbrakk>\<emptyset>\<rbrakk> Y)\<close> term but to two terms \<open>(f X \<lbrakk>\<emptyset>\<rbrakk> Y)\<close> and 
-\<open>(X \<lbrakk>\<emptyset>\<rbrakk> g Y)\<close>.
-To handle these cases, we developed an advanced parallel induction scheme and we proved its 
-correctness:
-  \<^item> @{cartouche [display] \<open>... \<Longrightarrow> (\<forall>Y. P \<bottom> Y) \<Longrightarrow> (\<forall>X. P X \<bottom>)
-     \<Longrightarrow> \<forall>X Y. (P X Y \<and> P (f X) Y \<and> P X (g Y)) \<longrightarrow> P (f X) (g Y) 
-      \<Longrightarrow> P (\<mu>X. f X) (\<mu>X. g X)\<close>}
-
-
-\<^noindent> which allows for a "independent unroling" of the fixed-points in these proofs.
-The astute reader may notice here that if the induction step is weakened (having more hypothesises), 
-the base steps require enforcement.  
-\<close>
-
-subsection*["norm"::technical,main_author="Some(@{author ''safouan''}::author)"]
-\<open>Normalization\<close>
-text\<open>
- Our framework can reason not only over infinite alphabets, but also over processes parameterized
-over states with an arbitrarily rich structure. This  paves the way for the following technique, 
-that trades potentially complex process structure against equivalent simple processes with 
-potentially rich state.
-
-Roughly similar to labelled transition systems, we provide for deterministic \<^csp> processes a normal 
-form that is based on an explicit state. The general schema of normalized processes is defined as 
-follows:
-
-@{cartouche [display,indent=20] \<open>P\<^sub>n\<^sub>o\<^sub>r\<^sub>m\<lbrakk>\<tau>\<^sub>,\<upsilon>\<rbrakk> \<equiv> \<mu> X. (\<lambda>\<sigma>. \<box>e\<in>(\<tau> \<sigma>) \<rightarrow> X(\<upsilon> \<sigma> e))\<close>}
- where \<open>\<tau>\<close> is a transition function which returns the set of events that can be triggered from 
-the current  state \<open>\<sigma>\<close> given as parameter.
-The update function \<open>\<upsilon>\<close> takes two parameters \<open>\<sigma>\<close> and an event \<open>e\<close> and returns the new state.
-This normal form is closed under deterministic and  communication operators. 
-
-The advantage of this format is that we can mimick the well-known product automata construction
-for an arbitrary number of synchronized processes under normal form.
-We only show the case of the synchronous product of two processes: \<close>
-Theorem*[T3, short_name="\<open>Product Construction\<close>", level="Some 2"]\<open>
-Parallel composition translates to normal form:
-@{cartouche [display,indent=5]\<open>(P\<^sub>n\<^sub>o\<^sub>r\<^sub>m\<lbrakk>\<tau>\<^sub>1,\<upsilon>\<^sub>1\<rbrakk> \<sigma>\<^sub>1) || (P\<^sub>n\<^sub>o\<^sub>r\<^sub>m\<lbrakk>\<tau>\<^sub>2,\<upsilon>\<^sub>2\<rbrakk> \<sigma>\<^sub>2) = 
-    P\<^sub>n\<^sub>o\<^sub>r\<^sub>m\<lbrakk>\<lambda>(\<sigma>\<^sub>1,\<sigma>\<^sub>2). \<tau>\<^sub>1 \<sigma>\<^sub>1 \<inter> \<tau>\<^sub>2 \<sigma>\<^sub>2 , \<lambda>(\<sigma>\<^sub>1,\<sigma>\<^sub>2).\<lambda>e.(\<upsilon>\<^sub>1 \<sigma>\<^sub>1 e, \<upsilon>\<^sub>2 \<sigma>\<^sub>2 e)\<rbrakk> (\<sigma>\<^sub>1,\<sigma>\<^sub>2)\<close>}
-\<close>
-
-text\<open> The generalization of this rule for a list of \<open>(\<tau>,\<upsilon>)\<close>-pairs is straight-forward, 
-albeit the formal  proof is not. The application of the generalized  form is a corner-stone of the 
-proof of the general dining philosophers problem illustrated in the subsequent section.
-
-Another advantage of normalized processes is the possibility to argue over the reachability of 
-states via the closure \<open>\<RR>\<close>, which is defined inductively over: 
-
-  \<^item> \<open>\<sigma> \<in> \<RR> \<tau> \<upsilon> \<sigma>\<close>
-  \<^item> \<open>\<sigma> \<in> \<RR> \<tau> \<upsilon> \<sigma>\<^sub>0 \<Longrightarrow> e \<in> \<tau> \<sigma> \<Longrightarrow> \<upsilon> \<sigma> e \<in> \<RR> \<tau> \<upsilon> \<sigma>\<^sub>0\<close>
-
-
-Thus, normalization leads to a new characterization of deadlock-freeness inspired 
-from automata theory. We formally proved the following theorem:\<close>
-
-text*[T4::"theorem", short_name="\<open>DF vs. Reacheability\<close>", level="Some 2"]
-\<open> If each reachable state \<open>s \<in> (\<RR> \<tau> \<upsilon>)\<close> has outgoing transitions,
-the \<^csp> process is deadlock-free: 
-@{cartouche [display,indent=10] \<open>\<forall>\<sigma> \<in> (\<RR> \<tau> \<upsilon> \<sigma>\<^sub>0). \<tau> \<sigma> \<noteq> {} \<Longrightarrow> deadlock_free (P\<^sub>n\<^sub>o\<^sub>r\<^sub>m\<lbrakk>\<tau>,\<upsilon>\<rbrakk> \<sigma>\<^sub>0)\<close>}
-\<close>
-
-text\<open>  This theorem allows for establishing properties such as deadlock-freeness by 
-completely abstracting from \<^csp> theory; these are arguments that only involve inductive reasoning 
-over the transition function. 
-
-Summing up, our method consists of four stages:
-\<^enum>  we construct normalized versions of component processes and prove them
-  equivalent to their counterparts,
-\<^enum> we state an invariant over the states/variables,
-\<^enum> we prove by induction over \<open>\<RR>\<close> that it holds on all reachable states, and finally
-\<^enum> we prove that this invariant guarantees the existence of outgoing transitions.
-
-\<close>
-
-subsection*["dining_philosophers"::technical,main_author="Some(@{author ''safouan''}::author)",level="Some 3"]
-\<open>Generalized Dining Philosophers\<close>
-
-text\<open>  The dining philosophers problem is another paradigmatic example in the \<^csp> literature
-often used to illustrate synchronization problems between an arbitrary number of concurrent systems. 
-It is an example for a process scheme for which general properties are desirable in order
-to inherit them for specific instances.
-The general dining philosopher problem for an arbitrary \<open>N\<close> is presented in HOL-CSP 2 as follows
-%@{footnote \<open>The dining philosopher problem is also distributed with FDR4, where \<open>N = 6\<close>.\<close>}:
-
-@{theory_text [display,indent=5] 
-\<open>datatype dining_event  = picks (phil::nat) (fork::nat) 
-                             | putsdown (phil::nat) (fork::nat)
-                             | eat (phil::nat)
-definition LPHIL0  \<equiv> (\<mu> X. (picks 0 (N-1) \<rightarrow> (picks 0 0 \<rightarrow> eat 0 \<rightarrow>
-                                   (putsdown 0 0 \<rightarrow> (putsdown 0 (N-1) \<rightarrow> X)))))
-definition RPHIL i \<equiv> (\<mu> X. (picks i i \<rightarrow> (picks i (i-1) \<rightarrow> eat i \<rightarrow>
-                                   (putsdown i (i-1) \<rightarrow> (putsdown i i \<rightarrow> X)))))
-definition FORK i  \<equiv> (\<mu> X.   (picks i i \<rightarrow> (putsdown i i \<rightarrow> X)) 
-                                   \<box>(picks (i+1)%N i \<rightarrow>(putsdown (i+1)%N i \<rightarrow> X)))
-definition "PHILs   \<equiv> LPHIL0 ||| (|||\<^sub>i\<^sub>\<in>\<^sub>1\<^sub>.\<^sub>.\<^sub>N RPHIL i)" 
-definition "FORKs   \<equiv> |||\<^sub>i\<^sub>\<in>\<^sub>0\<^sub>.\<^sub>.\<^sub>N FORK i"
-definition DINING  \<equiv> FORKs \<lbrakk>picks, putsdown\<rbrakk> PHILs\<close>}
-
-% this should be theory_text, but is rejected for lexical reasons
-Note that both philosophers and forks are pairwise independent 
-but both synchronize on \<open>picks\<close> and \<open>putsdown\<close> events. The philosopher of index 0 is left-handed 
-whereas the other \<open>N-1\<close> philosophers are right-handed. We want to prove that any configuration 
-is deadlock-free for an arbitrary number N.
-
-First, we put the fork process under normal form. It has three states:
-(1) on the table, (2) picked by the right philosopher or (3) picked by the left one:
-
-@{theory_text [display,indent=5]
-\<open>definition trans\<^sub>f i \<sigma> \<equiv> if       \<sigma> = 0   then {picks i i, picks (i+1)%N i}
-                             else if \<sigma> = 1   then {putsdown i i} 
-                             else if \<sigma> = 2   then {putsdown (i+1)%N i}
-                             else                     {}
-definition upd\<^sub>f i \<sigma> e \<equiv> if       e = (picks i i)           then 1 
-                              else if e = (picks (i+1)%N) i then 2 
-                              else                                        0
-definition FORK\<^sub>n\<^sub>o\<^sub>r\<^sub>m i \<equiv> P\<^sub>n\<^sub>o\<^sub>r\<^sub>m\<lbrakk>trans\<^sub>f i, upd\<^sub>f i\<rbrakk> \<close>}
-
-To validate our choice for the states, transition function \<open>trans\<^sub>f\<close> and update function \<open>upd\<^sub>f\<close>,
-we prove that they are equivalent to the original process components: \<open>FORK\<^sub>n\<^sub>o\<^sub>r\<^sub>m i = FORK i\<close>. 
-The anti-symmetry of refinement breaks this down to the two refinement proofs \<open>FORK\<^sub>n\<^sub>o\<^sub>r\<^sub>m i \<sqsubseteq> FORK i\<close> 
-and \<open>FORK i \<sqsubseteq> FORK\<^sub>n\<^sub>o\<^sub>r\<^sub>m i\<close>, which are similar to the CopyBuffer example shown in 
-@{technical "illustration"}. Note, again, that this fairly automatic induct-simplify-proof just 
-involves reasoning on the derived algebraic rules, not any reasoning on the level of the 
-denotational semantics. 
-
-%Second we prove that the normal form process is equivalent to the original fork process 
-%by proving refinements in both directions. We note here that the first refinement \<open>FORK\<^sub>n\<^sub>o\<^sub>r\<^sub>m i \<sqsubseteq> FORK i\<close> 
-%requires a two steps induction as unfolding the original fixed-point process brings two steps 
-%\<open>FORK i = picks \<rightarrow> putsdown \<rightarrow> FORK i\<close>. After that we apply the same method 
-%to get the philosopher process under a normal form.
-
-Thanks to @{theorem \<open>T3\<close>}, we obtain normalized processes 
-for \<open>FORKs\<close>, \<open>PHILs\<close> and \<open>DINING\<close>:
-@{theory_text [display,indent=5] 
-\<open>definition "trans\<^sub>F \<equiv> \<lambda>fs. (\<Inter>\<^sub>i\<^sub><\<^sub>N. trans\<^sub>f i (fs!i))"
-definition upd\<^sub>F   \<equiv> \<lambda>fs e. let i=(fork e) in fs[i:=(upd\<^sub>f i (fs!i) e)]
-
-lemma FORKs = P\<^sub>n\<^sub>o\<^sub>r\<^sub>m\<lbrakk>trans\<^sub>F, upd\<^sub>F\<rbrakk> ...
-lemma PHILS = P\<^sub>n\<^sub>o\<^sub>r\<^sub>m\<lbrakk>trans\<^sub>P, upd\<^sub>P\<rbrakk> ...
-
-definition trans\<^sub>D \<equiv> \<lambda>(ps,fs). (trans\<^sub>P ps) \<inter> (trans\<^sub>F fs)
-definition upd\<^sub>D   \<equiv> \<lambda>(ps,fs) e. (upd\<^sub>P ps e, upd\<^sub>F fs e)
-
-lemma DINING = P\<^sub>n\<^sub>o\<^sub>r\<^sub>m\<lbrakk>trans\<^sub>D, upd\<^sub>D\<rbrakk> \<close>}
-The variable \<open>ps\<close> stands for the list of philosophers states and \<open>fs\<close> 
-for the list of forks states, both are of size \<open>N\<close>. The pair \<open>(ps, fs)\<close> 
-encodes the whole dining table state over which we need to define an invariant to ensure 
-that no blocking state is reachable and thus the dining philosophers problem is deadlock-free.
-As explained before, the proof is based on abstract reasoning over relations 
-independent from the \<^csp> context.
-
-The last steps towards our goal are the following definitions and lemmas:
-
-@{theory_text [display,indent=5]
-\<open>definition INV\<^sub>D\<^sub>I\<^sub>N\<^sub>I\<^sub>N\<^sub>G ps fs \<equiv> (\<forall>i. ((fs!i=1) \<leftrightarrow> ps!i \<noteq> 0) \<and> ... )
-lemma (ps,fs) \<in> \<RR> trans\<^sub>D upd\<^sub>D  \<Longrightarrow> INV\<^sub>D\<^sub>I\<^sub>N\<^sub>I\<^sub>N\<^sub>G ps fs ...
-lemma INV\<^sub>D\<^sub>I\<^sub>N\<^sub>I\<^sub>N\<^sub>G ps fs \<Longrightarrow> trans\<^sub>D (ps, fs) \<noteq> {} ...
-
-corollary deadlock_free DINING \<close>} 
-
-To sum up, we proved once and for all that the dining philosophers problem is deadlock free 
-for an arbitrary number \<open>N \<ge> 2\<close>. Common model-checkers like PAT and FDR fail to answer 
-for a dozen of philosophers (on a usual machine) due to the exponential combinatorial explosion.
-Furthermore, our proof is fairly stable against modifications like adding non synchronized events like
-thinking or sitting down in contrast to model-checking techniques. \<close>
-
-section*["relatedwork"::technical,main_author="Some(@{author ''lina''}::author)",level="Some 3"]
-\<open>Related work\<close>
-
-text\<open>
-The theory of \<^csp> has attracted a lot of interest from the eighties on, and is still
-a fairly active research area, both
-as a theoretical device as well as a modelling language to analyze complex concurrent systems. 
-It is therefore not surprising that attempts to its formalisation had been undertaken early
-with the advent of interactive theorem proving systems supporting higher-order logic 
- @{cite "Camilleri91" and "tej.ea:corrected:1997" and "10.1007/978-3-642-16690-7_9" 
-   and "10.1007/978-3-642-27705-4_20"  and "DBLP:conf/concur/IsobeR06" }, where
- especially the latter allows for some automated support for refinement proofs 
-based on induction. However, HOL-CSP2 is based on a failure/divergence model, while 
-@{cite "DBLP:conf/concur/IsobeR06"} is  based on stable failures, which can infer 
-deadlock-freeness only under the assumption that no lifelock occurred; In our view, 
-this is a too strong assumption for both the theory as well as the tool.
-
-In the 90ies, research focused on automated verification tools for \<^csp>, most notably on
-FDR~@{cite "fdr4"}. It relies on an operational \<^csp> semantics, allowing for a conversion of processes 
-into labelled transition systems, where the states are normalized by the "laws" derived from the 
-denotational semantics.
-For finite event sets, refinement proofs can be reduced to graph inclusion problems. With 
-efficient compression techniques, such as bisimulation, elimination and factorization by 
-semantic equivalence @{cite "Roscoe95"}, FDR was used to analyze some industrial applications. 
-However, such a model checker can not handle infinite cases and do not scale to large systems. 
-%%Another similar model checking tool @{cite "SunLDP09"} implemented some more optimization techniques, 
-%%such as partial order reduction, symmetric reduction, and parallel model checking, but is also 
-%%restricted to the finite case. 
-
-The fundamental limits of  automated decision procedures for data and processes has been known
-very early on: Undecidability of parameterized model checking was proven by reduction to 
-non-halting of Turing machines @{cite "Suzuki88"}. However, some forms of 
-well-structured transitions systems, could be demonstrated to be decidable 
-@{cite "FinkelS01" and "BloemJKKRVW16"}.
-HOL-CSP2 is a fully abstract model for the failure/divergence model; as a HOL theory, it is therefore
-a "relative complete proof theory" both for infinite data as well as number of components.
-(see @{cite "andrews2002introduction"} for relative completeness).
-
-
-Encouraged by the progress of SMT solvers which support some infinite types, 
-notably (fixed arrays of) integers or reals, and limited forms of formulas over these types,
-SMT-based model-checkers represent the current main-stream to parametric model-checking.
-This extends both to LTL-style model-checkers for Promela-like languages
-@{cite "Cubicle" and "ByMC"} as well as process-algebra alikes 
-@{cite "AntoninoGR19" and "AntoninoGR16" and "BensalemGLNSY11"}. 
-However, the usual limitations persist: the translation to SMT is hardly certifiable and
-the solvers are still not able to handle non-linear computations; moreover, they fail
-to elaborate inductive proofs on data if necessary in refinement proofs. 
-
-Some systems involve approximation techniques in order to make the formal verification of 
-concurrent systems scalable; results are therefore inherently imprecise and require 
-meta-level arguments assuring their truth in a specific application context. 
-For example, in  @{cite "AntoninoGR19"}, the synchronization analysis  techniques try to 
-prove the unreachability of a system state by showing that components cannot agree 
-on the order or on the number of times they participate on system rules. 
-Even with such over-approximation, the finiteness restriction on the number of components 
-persists.
-
-Last but not least, SMT-based tools only focusing on bounded model-checking like
-@{cite "Kind2" and "JKind"} use k-induction and quite powerful invariant generation 
-techniques but are still far from scalable techniques. While it is difficult to make
-any precise argument on the scalability for HOL-CSP 2, we argue that we have no data-type 
-restrictions (events may have realvector-, function- or even process type) as well as
-restrictions on the structure of components. None of our paradigmatic examples can 
-be automatically proven with any of the discussed SMT techniques without restrictions.
-\<close>
-
-section*["conclusion"::conclusion,main_author="Some(@{author ''bu''}::author)"]\<open>Conclusion\<close>
-text\<open>We presented a formalisation of the most comprehensive semantic model for \<^csp>, a 'classical' 
-language for the specification and analysis of concurrent systems studied in a rich body of 
-literature. For this purpose, we ported @{cite "tej.ea:corrected:1997"} to a modern version
-of Isabelle, restructured the proofs, and extended the resulting theory of the language 
-substantially. The result HOL-CSP 2 has been submitted to the Isabelle AFP @{cite "HOL-CSP-AFP"}, 
-thus a fairly sustainable format accessible to other researchers and tools.
-
-We developed a novel set of deadlock - and livelock inference proof principles based on 
-classical and denotational characterizations. In particular, we formally investigated the relations
-between different refinement notions in the presence of deadlock - and livelock; an area where
-traditional \<^csp> literature skates over the nitty-gritty details. Finally, we demonstrated how to
-exploit these results for deadlock/livelock analysis of protocols.
-
-We put a large body of abstract \<^csp> laws and induction principles together to form
-concrete verification technologies for generalized classical problems, which have been considered
-so far from the perspective of data-independence or structural parametricity. The underlying novel
-principle of "trading rich structure against rich state" allows to convert processes 
-into classical transition systems for which established invariant techniques become applicable.
-
-Future applications of HOL-CSP 2 could comprise a combination to model checkers, where our theory
-with its derived rules is used to certify the output of a model-checker over \<^csp>. In our experience,
-generated labelled transition systems may be used to steer inductions or to construct
-the normalized processes \<open>P\<^sub>n\<^sub>o\<^sub>r\<^sub>m\<lbrakk>\<tau>\<^sub>,\<upsilon>\<rbrakk>\<close> automatically, thus combining efficient finite reasoning 
-over finite sub-systems with globally infinite systems in a logically safe way. 
-\<close>
-
-(*<*)
-subsection*[bib::bibliography]\<open>References\<close>
-
-close_monitor*[this]
-
-end
-(*>*) 

Isabelle_DOF-Examples-Extra/CC_ISO15408/PikeOS_study/PikeOS_ST.thy

@@ -1,91 +0,0 @@
-theory PikeOS_ST (*Security Target *)
-
-imports "Isabelle_DOF-Ontologies.CC_v3_1_R5"
-
-begin 
-
-section \<open>ST PikeOS\<close>
-
-open_monitor*[stpkos::ST_MNT]
-section*[pkosstintrosec::st_ref_cls]\<open> ST Introduction \<close>
-open_monitor*[PikosIntro::ST_INTRO_MNT]
-subsection*[pkosstrefsubsec::st_ref_cls]\<open> ST Reference \<close>
-
-text*[pkosstref::st_ref_cls, title="''PikeOS Security Target''", st_version ="(0,4,5)",
-      authors= "[]", st_date= "''29072020''"]
-\<open>This document is the @{docitem st} for the Common Criteria evaluation of PikeOS. 
- It complies with the Common Criteria for Information Technology Security Evaluation 
- Version 3.1 Revision 4.\<close>
-
-
-
-subsection*[pkossttoerefsubsec::st_ref_cls]\<open>TOE Reference\<close>
-
-text*[pkostoeref::toe_ref_cls, dev_name="''''", toe_name="''PikeOS''",
-      toe_version= "(0,3,4)", prod_name="Some ''S3725''"]
-\<open>The @{docitem (unchecked) toeDef} is the operating system PikeOS version 3.4 
-   running on the microprocessor family x86 hosting different applications. 
-   The @{docitem (unchecked) toeDef} is referenced as PikeOS 3.4 base
-   product build S3725 for Linux and Windows development host with PikeOS 3.4
-   Certification Kit build S4250 and PikeOS 3.4 Common Criteria Kit build S4388.\<close>
-
-subsection*[pkossttoeovrvwsubsec::st_ref_cls]\<open> TOE Overview \<close>
-text*[pkosovrw1::toe_ovrw_cls]\<open>The @{docitem (unchecked) \<open>toeDef\<close> } is a special kind of operating 
-system, that allows to effectively separate
-different applications running on the same platform from each other. The TOE can host
-user applications that can also be operating systems. User applications can also be
-malicious, and even in that case the TOE ensures that malicious user applications are
-harming neither the TOE nor other applications in other partitions. The TOE will be
-installed and run on a hardware platform (e.g. embedded systems).
-The TOE is intended to be used as a component (the separation kernel) in MILS systems.
-MILS (Multiple Independent Levels of Security) systems are explained in .
-The TOE controls usage of memory, devices, processors, and communication channels
-to ensure complete separation of user applications and to prevent unexpected
-interference between user applications. The TOE enforces restrictions on the
-communication between the separated user applications as specified by the configuration
-data.
-
-The major security services provided by the TOE are:
-
-Separation in space of applications hosted in different partitions from each other
-and from the PikeOS operating system according to the configuration data by
-Page 3 of 44using the underlying hardware,
-2086 Separation in time of applications hosted in different partitions from each other
-and from the PikeOS operating system according to the configuration data,
-   Provision and management of communication objects,
- Management of and access to the TOE and TOE data,
- PikeOS operating system self-protection and accuracy of security functionality,
- Generation and treatment of audit data according to the configuration data.\<close>
-
-text*[pkosovrw2::toe_ovrw_cls, toe_type="''OS separation kernel''"]
-\<open>The TOE is a special kind of operating system providing a separation kernel with real-
-time support.
-The typical life cycle phases for this TOE type are development (source code
-development), manufacturing (compilation to binary), system integration (by the system
-integrator), installation (by the system operator), and finally, operational use (by the
-system operator). Operational use of the TOE is explicitly in the focus of this ST. A
-security evaluation/certification according to the assurance package chosen in this ST
-(see Section 2.3 “Package Claim” below) involves all these life cycle phases.\<close>
-text*[pkosdesc::toe_desc_cls]\<open>\<close>
-close_monitor*[PikosIntro]
-
-open_monitor*[PikosCCLM::CONF_CLAIMS_MNT]
-
-close_monitor*[PikosCCLM]
-
-open_monitor*[PikosSPD::SEC_PROB_DEF_MNT]
-
-close_monitor*[PikosSPD]
-
-open_monitor*[PikosSO::SEC_OBJ_MNT]
-
-close_monitor*[PikosSO]
-
-
-
-open_monitor*[PikosSR::SEC_REQ_MNT]
-
-close_monitor*[PikosSR]
-
-close_monitor*[stpkos]
-end

Isabelle_DOF-Examples-Extra/CC_ISO15408/PikeOS_study/ROOT

@@ -1,4 +0,0 @@
-session "PikeOS_study" = "Isabelle_DOF-Ontologies" +
-  options [document = false]
-  theories
-    "PikeOS_ST"

Isabelle_DOF-Examples-Extra/CC_ISO15408/ROOTS

@@ -1 +0,0 @@
-PikeOS_study

Isabelle_DOF-Examples-Extra/CENELEC_50128/mini_odo/ROOT

@@ -1,18 +0,0 @@
-session "mini_odo" = "Isabelle_DOF-Ontologies" +
-  options [document = pdf, document_output = "output", document_build = dof]
-  sessions 
-    "Physical_Quantities"
-  theories
-    "mini_odo"
-  document_theories
-    "Isabelle_DOF-Ontologies.CENELEC_50128" 
-  document_files
-    "dof_session.tex"
-    "preamble.tex"
-    "root.bib"
-    "root.mst"
-    "figures/df-numerics-encshaft.png"
-    "figures/odometer.jpeg"
-    "figures/three-phase-odo.pdf"
-    "figures/wheel-df.png"
-

Isabelle_DOF-Examples-Extra/CENELEC_50128/mini_odo/document/dof_session.tex

@@ -1,3 +0,0 @@
-\input{mini_odo}
-\input{CENELEC_50128}
-

Isabelle_DOF-Examples-Extra/CENELEC_50128/mini_odo/mini_odo.thy

@@ -1,675 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019      The University of Exeter 
- *               2018-2019 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-(*<*)
-theory 
-  mini_odo
-imports  
-  "Isabelle_DOF-Ontologies.CENELEC_50128" 
-  "Isabelle_DOF.technical_report"
-  "Physical_Quantities.SI" "Physical_Quantities.SI_Pretty"
-begin
-use_template "scrreprt-modern"
-use_ontology technical_report and "Isabelle_DOF-Ontologies.CENELEC_50128"
-declare[[strict_monitor_checking=true]]
-define_shortcut* dof     \<rightleftharpoons> \<open>\dof\<close>
-                 isadof  \<rightleftharpoons> \<open>\isadof{}\<close>
-(*>*)
-
-title*[title::title]\<open>The CENELEC 50128 Ontology\<close> 
-subtitle*[subtitle::subtitle]\<open>Case Study: An Odometer-Subsystem\<close> 
-
-chapter*[casestudy::technical]\<open>An Odometer-Subsystem\<close>
-text\<open>
-  In our case study, we will follow the phases of analysis, design, and implementation of the 
-  odometry function of a train. This \<^cenelec_term>\<open>SF\<close> processes data from an odometer to compute 
-  the position,  speed, and acceleration of a train. This system provides the basis for many 
-  safety critical decisions, \<^eg>, the opening of the doors. Due to its relatively small size, it 
-  is a manageable, albeit realistic target for a comprehensive formal development: it covers a 
-  physical model of the environment, the physical and architectural model of the odometer,
-  but also the  \<^cenelec_term>\<open>SFRS\<close> aspects including the problem of numerical sampling and the 
-  boundaries of efficient computations. The interplay between environment and measuring-device as 
-  well as the implementation problems on a platform with limited resources makes the odometer a 
-  fairly typical \<^cenelec_term>\<open>safety\<close> critical \<^cenelec_term>\<open>component\<close> of an embedded system.
-
-  The case-study is presented in form of an \<^emph>\<open>integrated source\<close> in \<^isadof> containing all four
-  reports from the phases:
-    \<^item> \<^term>\<open>software_requirements\<close> with deliverable \<^doc_class>\<open>SWRS\<close> 
-       (or long:\<^typ>\<open>software_requirements_specification\<close>(-report))
-    \<^item> \<^term>\<open>software_architecture_and_design\<close> with deliverable \<^doc_class>\<open>SWDS\<close> 
-      (or long: \<^typ>\<open>software_design_specification\<close>(-report))
-    \<^item> \<^term>\<open>software_component_design\<close> with deliverable \<^doc_class>\<open>SWCDVR\<close>
-      (or long: \<^typ>\<open>software_component_design_verification\<close>(-report).)
-    \<^item> \<^term>\<open>component_implementation_and_testing\<close> with deliverable \<^doc_class>\<open>SWADVR\<close>
-      (or long: \<^typ>\<open>software_architecture_and_design_verification\<close>(-report))
-
-  The objective of this case study is to demonstrate deep-semantical ontologoies in 
-  software developments targeting certifications, and in particular, how \<^isadof>'s 
-  integrated source concept permits to assure \<^cenelec_term>\<open>traceability\<close>.
-
-  \<^bold>\<open>NOTE\<close> that this case study has aspects that were actually covered by CENELEC 50126 - 
-  the 'systems'-counterpart covering hardware aspects. Recall that the CENELEC 50128 covers
-  software. 
-
-  Due to space reasons, we will focus  on the analysis part of the integrated 
-  document; the design and code parts will only be outlined in a final resume. The 
-  \<^emph>\<open>ontological embedding\<close>, which represents a main contribution of this paper, will be presented 
-  in the next two sections.
-
-  We start with the capture of a number of informal documents available at the beginning of the
-  development.
-\<close>
-
-section\<open>A CENELEC-conform development as an \<^emph>\<open>Integrated Source\<close>\<close>
-
-text\<open>Accurate information of a train's location along a track is in an important prerequisite   
-to safe railway operation. Position, speed and acceleration measurement usually lies on a 
-set of independent measurements based on different physical principles---as a way to enhance 
-precision and availability.  One of them is an \<^emph>\<open>odometer\<close>, which allows estimating a relative 
-location while the train runs positions established by other measurements. \<close>
-
-subsection\<open>Capturing ``Basic Principles of Motion and Motion Measurement.''\<close>
-text\<open>
-  A rotary encoder measures the motion of a train. To achieve this, the encoder's shaft is fixed to
-  the trains wheels axle. When the train moves, the encoder produces a signal pattern directly 
-  related to the trains progress.  By measuring the fractional rotation of the encoders shaft and 
-  considering the wheels effective ratio, relative movement of the train can be calculated.
-
-  \begin{wrapfigure}[8]{l}{4.6cm}
-    \centering
-    \vspace{-.5cm}
-    \includegraphics[width=3.4cm]{figures/wheel-df}
-    \caption{Motion sensing via an odometer.}
-    \label{wheel-df}
-  \end{wrapfigure}
-  \autoref{wheel-df} shows that we model a train, seen from a pure kinematics standpoint, as physical 
-  system characterized by a one-dimensional continuous distance function, which represents the 
-  observable of the physical system.  Concepts like speed and acceleration were derived concepts 
-  defined as their (gradient) derivatives. We assume the use of the meter, kilogram, and second 
-  (MKS) system.
-
-  This model is already based on several fundamental assumptions relevant for the correct
-  functioning of the system and for its integration into the system as a whole. In 
-  particular, we need to make the following assumptions explicit: \<^vs>\<open>-0.3cm\<close>\<close>
-
-text*["perfect_wheel"::assumption]
-\<open>\<^item> the wheel is perfectly circular with a given, constant radius. \<^vs>\<open>-0.3cm\<close>\<close>
-text*["no_slip"::assumption]
-\<open>\<^item> the slip between the trains wheel and the track negligible. \<^vs>\<open>-0.3cm\<close>\<close>
-text*["constant_teeth_dist"::assumption]
-\<open>\<^item>  the distance between all teeth of a wheel is the same and constant, and \<^vs>\<open>-0.3cm\<close>\<close>
-text*["constant_sampling_rate"::assumption]
-\<open>\<^item>  the sampling rate of positions is a given constant.\<close>
-
-text\<open>
-  These assumptions have to be traced throughout the certification process as
-
-  \<^emph>\<open>derived requirements\<close> (or, in CENELEC terminology, as \<^emph>\<open>exported constraints\<close>), which is
-  also reflected by their tracing throughout the body of certification documents. This may result
-  in operational regulations, \<^eg>, regular checks for tolerable wheel defects. As for the
-  \<^emph>\<open>no slip\<close>-assumption, this leads to the modeling of constraints under which physical 
-  slip can be neglected: the device can only produce reliable results under certain physical
-  constraints (speed and acceleration limits). Moreover, the \<^emph>\<open>no slip\<close>-assumption motivates
-  architectural arrangements for situations where this assumption cannot be assured (as is the
-  case, for example, of an emergency breaking) together with error-detection and error-recovery.
-\<close>
-
-subsection\<open>Capturing ``System Architecture.''\<close>
-
-figure*["three_phase"::figure,relative_width="70",file_src="''figures/three-phase-odo.pdf''"]
-\<open>An odometer with three sensors \<open>C1\<close>, \<open>C2\<close>, and \<open>C3\<close>.\<close>
-
-text\<open>
-  The requirements analysis also contains a document \<^doc_class>\<open>SYSAD\<close> 
-  (\<^typ>\<open>system_architecture_description\<close>) that contains technical drawing of the odometer, 
-  a timing diagram  (see \<^figure>\<open>three_phase\<close>), and tables describing the encoding of the position 
-  for the possible signal transitions of the sensors \<open>C1\<close>, \<open>C2\<close>, and \<open>C3\<close>. 
-\<close>
-
-subsection\<open>Capturing ``System Interfaces.''\<close>
-text\<open>
-  The requirements analysis also contains a sub-document  \<^doc_class>\<open>FnI\<close>  (\<^typ>\<open>functions_and_interfaces\<close>)  
-  describing the technical format of the output of the odometry function. 
-  This section, \<^eg>, specifies the output \<^emph>\<open>speed\<close> as given by a \<^verbatim>\<open>int_32\<close> to be the 
-  ``Estimation of the speed (in mm/sec) evaluated  over the latest \<open>N\<^sub>a\<^sub>v\<^sub>g\<close>  samples''
-  where the speed refers to the physical speed of the train and \<open>N\<^sub>a\<^sub>v\<^sub>g\<close> a parameter of the
-  sub-system configuration. \<close>
-
-(*<*)
-declare_reference*["df_numerics_encshaft"::figure] 
-(*>*)
-subsection\<open>Capturing ``Required Performances.''\<close>
-text\<open>
-  The given analysis document is relatively implicit on the expected precision of the measurements; 
-  however, certain interface parameters like \<open>Odometric_Position_TimeStamp\<close>
-  (a counter on the number of samplings) and \<open>Relative_Position\<close> are defined by as 
-  unsigned 32 bit integer. These definitions imply that exported constraints concerning the acceptable 
-  time of service as well the maximum distance before a necessary reboot of the subsystem. 
-  For our case-study, we assume maximum deviation of the \<open>Relative_Position\<close> to the 
-  theoretical distance.
-
-  The requirement analysis document describes the physical environment, the architecture
-  of the measuring device, and the required format and precision of the measurements of the odometry
-  function as represented (see @{figure (unchecked) "df_numerics_encshaft"}).\<close>
-
-figure*["df_numerics_encshaft"::figure,relative_width="76",file_src="''figures/df-numerics-encshaft.png''"]
-\<open>Real distance vs. discrete distance vs. shaft-encoder sequence\<close>
-
-
-subsection\<open>Capturing the ``Software Design Spec'' (Resume).\<close>
-text\<open>
-  The design provides a function that manages an internal first-in-first-out buffer of 
-  shaft-encodings and corresponding positions. Central for the design is a step-function analyzing 
-  new incoming shaft encodings, checking them and propagating two kinds of error-states (one allowing 
-  recovery, another one, fatal, signaling, \<^eg>, a defect of the receiver hardware), 
-  calculating the relative position, speed and acceleration.
-\<close>
-
-subsection\<open>Capturing the ``Software Implementation'' (Resume).\<close>
-text\<open>
-  While the design is executable on a Linux system, it turns out that the generated code from an 
-  Isabelle model is neither executable on resource-constraint target platform, an ARM-based  
-  Sabre-light card, nor certifiable, since the compilation chain via ML to C implies the 
-  inclusion of a run-time system and quite complex libraries. 
-  We adopted therefore a similar approach as used in the seL4 project~@{cite "Klein2014"}: we use a   
-  hand-written implementation in C and verify it via 
-  AutoCorres~@{cite "greenaway.ea:bridging:2012"}  against 
-  the design model. The hand-written C-source is integrated into the Isabelle/HOL technically by 
-  registering it in the build-configuration and logically by a trusted C-to-HOL compiler included 
-  in AutoCorres.
-\<close>
-
-(*<*)
-      definition teeth_per_wheelturn::nat  ("tpw") where "tpw \<equiv> SOME x. x > 0"
-      definition wheel_diameter     ::"real[m]" ("w\<^sub>d") where "w\<^sub>d \<equiv> SOME x. x > 0" 
-      definition wheel_circumference::"real[m]" ("w\<^sub>0") where "w\<^sub>0 \<equiv> pi *\<^sub>Q w\<^sub>d"
-      definition \<delta>s\<^sub>r\<^sub>e\<^sub>s               ::"real[m]" where "\<delta>s\<^sub>r\<^sub>e\<^sub>s \<equiv> 1 / (2 * 3 * tpw) *\<^sub>Q w\<^sub>0 "
-(*>*)
-
-
-section\<open>Formal Enrichment of the Software Requirements Specification\<close>
-text\<open>
-  After the \<^emph>\<open>capture\<close>-phase, where we converted/integrated existing informal analysis and design 
-  documents as well as code into an integrated Isabelle document, we entered into the phase of 
-  \<open>formal enrichment\<close>. For example, from the assumptions in the architecture follow 
-  the definitions:
-
-      @{theory_text [display]\<open>
-      definition teeth_per_wheelturn::nat  ("tpw") where "tpw \<equiv> SOME x. x > 0"
-      definition wheel_diameter::"real[m]" ("w\<^sub>d") where "w\<^sub>d \<equiv> SOME x. x > 0" 
-      definition wheel_circumference::"real[m]" ("w\<^sub>0") where "w\<^sub>0 \<equiv> pi *\<^sub>Q w\<^sub>d"
-      definition \<delta>s\<^sub>r\<^sub>e\<^sub>s::"real[m]" where "\<delta>s\<^sub>r\<^sub>e\<^sub>s \<equiv> 1 / (2 * 3 * tpw) *\<^sub>Q w\<^sub>0 "
-      \<close>}
- 
-  Here, \<open>real\<close> refers to the real numbers as defined in the HOL-Analysis  library, which provides 
-  concepts such as Cauchy Sequences, limits, differentiability, and a very substantial part of 
-  classical Calculus. \<open>SOME\<close> is the Hilbert choice operator from HOL; the definitions of the 
-  model parameters admit all possible positive values as uninterpreted constants. Our 
-  \<^assumption>\<open>perfect_wheel\<close> is translated into a calculation of the circumference of the
-  wheel, while \<open>\<delta>s\<^sub>r\<^sub>e\<^sub>s\<close>, the resolution of the odometer, can be calculated 
-  from the these parameters. HOL-Analysis permits to formalize the fundamental physical observables:
-\<close>
-
-(*<*)
-type_synonym distance_function = "real[s] \<Rightarrow> real[m]" 
-consts       Speed::"distance_function \<Rightarrow> real[s] \<Rightarrow> real[m\<cdot>s\<^sup>-\<^sup>1]"
-consts       Accel::"distance_function \<Rightarrow> real[s] \<Rightarrow> real[m\<cdot>s\<^sup>-\<^sup>2]"
-consts       Speed\<^sub>M\<^sub>a\<^sub>x::"real[m\<cdot>s\<^sup>-\<^sup>1]"
-
-(* Non - SI conform common abrbreviations *)
-definition   "kmh \<equiv> kilo *\<^sub>Q metre \<^bold>/ hour :: 'a::{field,ring_char_0}[m\<cdot>s\<^sup>-\<^sup>1]"
-definition   "kHz \<equiv> kilo *\<^sub>Q hertz :: 'a::{field,ring_char_0}[s\<^sup>-\<^sup>1]"
-
-(*>*)
-text\<open>
-      @{theory_text [display]\<open>
-      type_synonym distance_function = "real[s]\<Rightarrow>real[m]"  
-      definition Speed::"distance_function\<Rightarrow>real\<Rightarrow>real"  where "Speed f \<equiv> deriv f"
-      definition Accel::"distance_function\<Rightarrow>real\<Rightarrow>real"  where "Accel f \<equiv> deriv (deriv f)" 
-      \<close>}
-
-which permits to constrain the central observable \<open>distance_function\<close> in a 
-way that they describe the space of ``normal behavior'' where we expect the odometer to produce
-reliable measurements over a \<open>distance_function df\<close> . 
-
-The essence of the physics of the train is covered by the following definition:
-
-     @{theory_text [display]\<open>
-     definition normally_behaved_distance_function :: "(real \<Rightarrow> real) \<Rightarrow> bool"
-     where  normally_behaved_distance_function df = 
-            ( \<forall> t. df(t) \<in> \<real>\<^sub>\<ge>\<^sub>0  \<and>  (\<forall> t \<in> \<real>\<real>\<^sub>\<ge>\<^sub>0. df(t) = 0)  
-             \<and> df differentiable on \<real>\<^sub>\<ge>\<^sub>0 \<and> (Speed df)differentiable on \<real>\<^sub>\<ge>\<^sub>0$ 
-             \<and> (Accel df)differentiable on \<real>\<^sub>\<ge>\<^sub>0 
-             \<and> (\<forall> t. (Speed df) t \<in> {Speed\<^sub>M\<^sub>i\<^sub>n .. Speed\<^sub>M\<^sub>a\<^sub>x})  
-             \<and> (\<forall> t. (Accel df) t \<in> {Accel\<^sub>M\<^sub>i\<^sub>n .. Accel\<^sub>M\<^sub>a\<^sub>x}))
-     \<close>}
-
-which constrains the distance functions in the bounds described of the informal descriptions and
-states them as three-fold differentiable function in certain bounds concerning speed and 
-acceleration. Note that violations, in particular of the constraints on speed and acceleration, 
-\<^emph>\<open>do\<close> occur in practice. In such cases, the global system adapts recovery strategies that are out 
-of the scope of our model. Concepts like \<open>shaft_encoder_state\<close> (a triple with the sensor values 
-\<open>C1\<close>, \<open>C2\<close>, \<open>C3\<close>)  were formalized as types, while tables were 
-defined as recursive functions:
-
-    @{theory_text [display]\<open>
-    fun phase\<^sub>0 :: "nat \<Rightarrow> shaft_encoder_state"   where 
-       "phase\<^sub>0 (0) =  \<lparr> C1 = False, C2 = False, C3 = True \<rparr>" 
-      |"phase\<^sub>0 (1) =  \<lparr> C1 = True,  C2 = False, C3 = True \<rparr>" 
-      |"phase\<^sub>0 (2) =  \<lparr> C1 = True,  C2 = False, C3 = False\<rparr>" 
-      |"phase\<^sub>0 (3) =  \<lparr> C1 = True,  C2 = True,  C3 = False\<rparr>" 
-      |"phase\<^sub>0 (4) =  \<lparr> C1 = False, C2 = True,  C3 = False\<rparr>" 
-      |"phase\<^sub>0 (5) =  \<lparr> C1 = False, C2 = True,  C3 = True \<rparr>" 
-      |"phase\<^sub>0 x   =  phase\<^sub>0(x - 6)"         
-    definition Phase ::"nat\<Rightarrow>shaft_encoder_state" where Phase(x) = phase\<^sub>0(x-1)
-    \<close>}
-
-We now define shaft encoder sequences as translations of distance functions:
-
-    @{theory_text [display]\<open>
-    definition encoding::"distance_function\<Rightarrow>nat\<Rightarrow>real\<Rightarrow>shaft_encoder_state" 
-      where   "encoding df init\<^sub>p\<^sub>o\<^sub>s \<equiv> \<lambda>x. Phase(nat\<lfloor>df(x) / \<delta>s\<^sub>r\<^sub>e\<^sub>s\<rfloor> + init\<^sub>p\<^sub>o\<^sub>s)"
-    \<close>}
-
-where \<open>init\<^sub>p\<^sub>o\<^sub>s\<close> is the initial position of the wheel. 
-\<open>sampling\<close>'s were constructed from encoding sequences over discretized time points:
-
-    @{theory_text [display]\<open>
-     definition sampling::"distance_function\<Rightarrow>nat\<Rightarrow>real\<Rightarrow>nat\<Rightarrow>shaft_encoder_state" 
-      where "sampling df init\<^sub>p\<^sub>o\<^sub>s \<delta>t \<equiv> \<lambda>n::nat. encoding df initinit\<^sub>p\<^sub>o\<^sub>s (n * \<delta>t)"
-    \<close>}
-
-parameter of the configuration of a system.
-
-Finally, we can formally define the required performances. From the interface description
-and the global model parameters such as wheel diameter, the number of teeth per wheel, the 
-sampling frequency etc., we can infer the maximal time of service as well the maximum distance 
-the device can measure.  As an example configuration, choosing:
-
-   \<^item> \<^term>\<open>(1 *\<^sub>Q metre):: real[m]\<close>      for  \<^term>\<open>w\<^sub>d\<close>   (wheel-diameter), 
-   \<^item> \<^term>\<open>100         :: real\<close>        for  \<^term>\<open>tpw\<close> (teeth per wheel), 
-   \<^item> \<^term>\<open>80 *\<^sub>Q kmh   :: real[m\<cdot>s\<^sup>-\<^sup>1]\<close>  for  \<^term>\<open>Speed\<^sub>M\<^sub>a\<^sub>x\<close>,
-   \<^item> \<^term>\<open>14.4 *\<^sub>Q kHz :: real[s\<^sup>-\<^sup>1]\<close>    for the sampling frequency,
- 
-results in an odometer resolution of \<^term>\<open>2.3 *\<^sub>Q milli *\<^sub>Q metre\<close>, a maximum distance of 
-\<^term>\<open>9878 *\<^sub>Q kilo *\<^sub>Q metre\<close>, and a maximal system up-time of \<^term>\<open>123.4 *\<^sub>Q hour\<close>s.
-The required precision of an odometer can be defined by a constant describing
-the maximally allowed difference between \<open>df(n*\<delta>t)\<close>  and 
-\<open>sampling df init\<^sub>p\<^sub>o\<^sub>s \<delta>t n\<close> for all \<open>init\<^sub>p\<^sub>o\<^sub>s \<in>{0..5}\<close>.
-\<close>
-(*<*)
-ML\<open>val two_thirty2 = 1024 * 1024 * 1024 * 4;
-   val dist_max = 0.0023 * (real two_thirty2) / 1000.0;
-   val dist_h = dist_max / 80.0\<close>
-(*>*)
-
-section*[verific::technical]\<open>Verification of the Software Requirements Specification\<close>
-text\<open>The original documents contained already various statements that motivate certain safety 
-properties of the device. For example, the \<open>Phase\<close>-table excludes situations in which 
-all sensors \<open>C1\<close>, \<open>C2\<close>, and \<open>C3\<close> are all ``off'' or situations in 
-which sensors are ``on,'' reflecting a physical or electrical error in the odometer. It can be 
-shown by a very small Isabelle case-distinction proof that this safety requirement follows indeed 
-from the above definitions:
-
-   @{theory_text [display]\<open>
-      lemma Encoder_Property_1:(C1(Phase x) \<and> C2(Phase x) \<and> C3(Phase x))=False
-        proof (cases x)
-          case 0 then show ?thesis  by (simp add: Phase_def)
-        next
-          case (Suc n) then show ?thesis 
-            by(simp add: Phase_def,rule_tac n = n in cycle_case_split,simp_all)
-        qed    
-   \<close>}
-
-for all positions \<open>x\<close>. Similarly, it is proved that the table is indeed cyclic: 
-
-   \<open>phase\<^sub>0 x = phase\<^sub>0(x mod 6)\<close> 
-
-and locally injective:
-
-   \<open>\<forall>x<6. \<forall>y<6. phase\<^sub>0 x = phase\<^sub>0 y \<longrightarrow> x = y\<close> 
-
-These lemmas, building the ``theory of an odometer,'' culminate in a theorem
-that we would like to present in more detail.
-
-   @{theory_text [display]\<open>
-      theorem minimal_sampling :
-     assumes * : normally_behaved_distance_function df
-       and  ** : \<delta>t * Speed\<^sub>M\<^sub>a\<^sub>x < \<delta>s\<^sub>r\<^sub>e\<^sub>s
-     shows \<forall> \<delta>X\<le>\<delta>t. 0<\<delta>X \<longrightarrow> 
-                \<exists>f. retracting (f::nat\<Rightarrow>nat) \<and> 
-                    sampling df init\<^sub>p\<^sub>o\<^sub>s \<delta>X = (sampling df init\<^sub>p\<^sub>o\<^sub>s \<delta>t) o f
-   
-   \<close>}
-
-This theorem states for \<open>normally_behaved_distance_function\<close>s that there is
-a minimal sampling frequency assuring the safety of the measurements; samplings on 
-some \<open>df\<close> gained from this minimal sampling frequency can be ``pumped up'' 
-to samplings of these higher sampling frequencies; they do not contain more information.
-Of particular interest is the second assumption, labelled ``\<open>**\<close>'' which  
-establishes a lower bound from \<open>w\<^sub>0\<close>, \<open>tpw\<close>, 
-\<open>Speed\<^sub>M\<^sub>a\<^sub>x\<close> for the sampling frequency. Methodologically, this represents 
-an exported constraint that can not be represented \<^emph>\<open>inside\<close> the design model: it means that the 
-computations have to be fast enough on the computing platform in order to assure that the 
-calculations are valid. It was in particular this exported constraint that forced us to give up 
-the original plan to generate the code from the design model and to execute this directly on the 
-target platform. 
-
-For our example configuration (1m diameter, 100 teeth per wheel, 80km/h max), this theorem justifies 
-that 14,4 kHz is indeed enough to assure valid samplings.  Such properties are called 
-``internal consistency of the software requirements specification'' in the CENELEC 
-standard~@{cite "bsi:50128:2014"}, 7.2.4.22 and are usually addressed in an own report. 
-\<close>
-
-chapter*[ontomodeling::text_section]\<open>The CENELEC 50128 Ontology\<close>
-
-text\<open>
-  Modeling an ontology from a semi-formal text such as~@{cite"bsi:50128:2014"} is, 
-  like any other modeling activity, not a simple one-to-one translation of some 
-  concepts to some formalism. Rather, implicit and self-understood principles
-  have to be made explicit, abstractions have to be made, and decisions about 
-  the kind of desirable user-interaction may have an influence similarly to 
-  design decisions influenced by strengths or weaknesses of a programming language. 
-\<close>
-
-section*[lhf::text_section]
-\<open>Tracking Concepts and Definitions\<close>
-
-text\<open>
-  \<^isadof> is designed to annotate text elements with structured meta-information and to reference
-  these text elements throughout the integrated source. A classical application of this capability 
-  is the annotation of concepts and terms definitions---be them informal, semi-formal or formal---and 
-  their consistent referencing. In the context of our CENELEC ontology, \<^eg>, we can translate the 
-  third chapter of @{cite "bsi:50128:2014"} ``Terms, Definitions and Abbreviations'' directly 
-  into our Ontology Definition Language (ODL). Picking one example out of 49, consider the definition 
-  of the concept \<^cenelec_term>\<open>traceability\<close> in paragraphs 3.1.46 (a notion referenced 31 times in 
-  the standard), which we translated directly into:
-
-     @{theory_text [display]\<open>
-         Definition*[traceability, short_name="''traceability''"]
-         \<open>degree to which relationship can be established between two or more products of a 
-          development  process, especially those having a predecessor/successor or 
-          master/subordinate relationship to one another.\<close>
-     \<close>}
-
-  In the integrated source of the odometry study, we can reference in a text element to this
-  concept as follows:
-
-     @{theory_text [display]\<open>
-          text*[...]\<open>  ... to assure <@>{cenelec_term traceability} for 
-               <@>{requirement bitwiseAND}, we prove ... \<close>
-     \<close>}
-
-  
-  \<^isadof> also uses the underlying ontology to generate the navigation markup inside the IDE, \<^ie>
-  the presentation of this document element inside \<^isadof> is immediately hyperlinked against the
-   @{theory_text \<open> Definition* \<close>}-element shown above; this serves as documentation of
-  the standard for the development team working on the integrated source. The PDF presentation 
-  of such links depends on the actual configurations for the document generation;  We will explain 
-  this later. 
-  CENELEC foresees also a number of roles, phases, safety integration levels, etc., which were
-  directly translated into HOL enumeration types usable in ontological concepts of ODL.
-
-     @{theory_text [display]\<open>
-         datatype role =  
-            PM  (* Program Manager *) |  RQM (* Requirements Manager *)
-          | DES (* Designer *)        |  IMP (* Implementer *)        |  
-          | VER (* Verifier *)        |  VAL (* Validator *)          |  ...
-         datatype phase = 
-            SYSDEV_ext (* System Development *) | SPl (* Software Planning     *)
-          | SR    (* Software Requirement    *) | SA  (* Software Architecture *)
-          | SDES  (* Software Design         *) | ...
-    \<close>}
-
-  Similarly, we can formalize the Table A.5: Verification and Testing of @{cite "bsi:50128:2014"}: 
-  a classification of \<^emph>\<open>verification and testing techniques\<close>:
-
-     @{theory_text [display]\<open>
-        datatype vnt_technique = 
-               formal_proof "thm list"    | stat_analysis 
-             | dyn_analysis dyn_ana_kind  | ...
-      \<close>}
-
-  In contrast to the standard, we can parameterize \<open>formal_proof\<close> with a list of 
-  theorems, an entity known in the Isabelle kernel. Here, \<^isadof>  assures for text elements 
-  annotated with theorem names, that they refer indeed to established theorems in the Isabelle 
-  environment. Additional checks could be added to make sure that these theorems have a particular 
-  form.
-
-  While we claim that this possibility to link to theorems (and test-results) is unique in the 
-  world of systems attempting to assure \<^cenelec_term>\<open>traceability\<close>, referencing a particular 
-  (proven) theorem is definitively not sufficient to satisfy the claimed requirement. Human 
-  evaluators will always have  to check that the provided theorem \<open>adequately\<close> represents the claim; 
-  we do not in the slightest suggest that their work is superfluous. Our framework allows to 
-  statically check that tests or proofs  have been provided, at places where the ontology requires 
-  them to be, and both assessors and developers  can rely on this check and navigate through 
-  related information easily. It does not guarantee that  intended concepts for, \<^eg>, safety 
-  or security have been adequately modeled. 
-\<close>
-
-section*[moe::text_section]
-\<open>Major Ontological Entities: Requirements and Evidence\<close>
-text\<open>
-  We introduce central concept of a \<^emph>\<open>requirement\<close> as an ODL \<^theory_text>\<open>doc_class\<close> 
-  based on the generic basic library \<^doc_class>\<open>text_element\<close> providing basic layout attributes.
-
-     @{theory_text [display]\<open>
-         doc_class requirement = text_element +
-             long_name    :: "string option"
-             is_concerned :: "role set"
-      \<close>}
-
-the groups of stakeholders in the CENELEC process. Therefore, the \<open>is_concerned\<close>-attribute 
-allows expressing who ``owns'' this text-element. \<^isadof>  supports a role-based 
-presentation, \<^eg>, different presentation styles of the integrated source may decide to highlight, 
-to omit, to defer into an annex, text entities according to the role-set.  
-
-Since ODL supports single inheritance, we can express sub-requirements and therefore a style
-of requirement decomposition as advocated in GSN~@{cite "kelly.ea:goal:2004"}: 
- 
-     @{theory_text [display]\<open>
-        doc_class sub_requirement = 
-            decomposes :: "requirement"
-            relates_to :: "requirement set"
-      \<close>}
-\<close>
-
-section*[claimsreqevidence::text_section]\<open>Tracking Claims, Derived Requirements and Evidence\<close>
-text\<open>An example for making explicit implicit principles,
-consider the following statement @{cite "bsi:50128:2014"}, pp. 25.: \<^vs>\<open>-0.15cm\<close> 
-
-\begin{quote}\small
-The objective of software verification is to examine and arrive at a judgment based on 
-evidence that output items (process, documentation, software or application) of a specific 
-development phase fulfill the requirements and plans with respect to completeness, correctness 
-and consistency.
-\end{quote} \<^vs>\<open>-0.15cm\<close> 
-
-The terms  \<^onto_class>\<open>judgement\<close> based on \<^term>\<open>evidence\<close> are used as a kind of leitmotif throughout 
-the CENELEC standard, but they are neither explained nor even listed in the general glossary. 
-However, the  standard is fairly explicit on the \<^emph>\<open>phase\<close>s and the organizational roles that 
-different stakeholders  should have in the process. Our version to express this key concept of 
-\<^onto_class>\<open>judgement\<close> , \<^eg>, by  the following concept:
-
-     @{theory_text [display]\<open>
-         doc_class judgement =    
-            refers_to       :: requirement
-            evidence        :: "vnt_technique list"
-            status          :: status
-            is_concerned    :: "role set" <= "{VER,ASR,VAL}" 
-    \<close>}
-
-As one can see, the role set is per default set to the verification team, the assessors and the 
-validation team.
-
-There are different views possible here: an alternative would be to define  \<^term>\<open>evidence\<close>
-as ontological concept with  \<^typ>\<open>vnt_technique\<close>'s (rather than an attribute of judgement) 
-and consider the basis of a summary containing the relation between requirements and relation:
-
-     @{theory_text [display]\<open>
-         doc_class summary =    
-           based_on        :: "(requirement \<times> evidence) set"
-           status          :: status
-           is_concerned    :: "role set" <= "{VER,ASR,VAL}" 
-    \<close>}
-
-More experimentation will be needed to find out what kind of ontological modeling is most
-adequate for developers in the context of \isadof. 
-\<close>
-
-section*[ontocontrol::text_section]\<open>Ontological Compliance\<close>
-
-text\<open>From the variety of different possibilities for adding CENELEC annotations to the
-integrated source, we will, in the following, point out three scenarios.\<close>
-
-subsection\<open>Internal Verification of Claims in the Requirements Specification.\<close>
-text\<open>In our case, the  \<^term>\<open>SR\<close>-team early on detected a property necessary
-for error-detection of the device (c.f. @{technical verific}):
-
-     @{theory_text [display]\<open>
-          text*[encoder_props::requirement]\<open> The requirement specification team identifies the property:
-              C1 & C2 & C3  = 0   (bitwise logical AND operation)
-              C1 | C2 | C3  = 1   (bitwise logical OR operation) \<close>
-    \<close>}
-
-After the Isabelle proofs shown in @{technical verific}, we can either register the theorems
-directly in an evidence statement: 
-
-     @{theory_text [display]\<open>
-          text*[J1::judgement, refers_to="@{docitem <open>encoder_props<close>}", 
-                               evidence="[formal_proof[@{thm <open>Encoder_Property_1<close>},
-                                                       @{thm <open>Encoder_Property_2<close>}]]"]
-          \<open>The required encoder properties are in fact verified to be consistent
-           with the formalization of @{term "phase\<^sub>0"}.\<close>
-    \<close>}
-
-The references \<open>@{...}\<close>, called antiquotation, allow us not only to reference to 
-formal concepts, they are checked for consistency and there are also antiquotations that 
-print the formally checked content (\<^eg>, the statement of a theorem). 
-\<close>
-
-subsection\<open>Exporting Claims of the Requirements Specification.\<close>
-
-text\<open>By definition, the main purpose of the requirement specification is the identification of 
-the safety requirements. As an example, we state the required precision of an odometric function: 
-for any normally behaved distance function \<open>df\<close>, and any representable and valid 
-sampling sequence that can be constructed for \<open>df\<close>, we require that the difference 
-between the physical distance and distance calculable from the @{term Odometric_Position_Count}
-is bound by the minimal resolution of the odometer.
-
-   @{theory_text [display]\<open>
-        text*[R5::safety_requirement]\<open>We can now state ... \<close>
-        definition  Odometric_Position_Count_precise :: "(shaft_encoder_state list\<Rightarrow>output)\<Rightarrow>bool"
-        where "Odometric_Position_Count_precise odofunction \<equiv>
-                   (\<forall> df. \<forall>S.  normally_behaved_distance_function df 
-                          \<longrightarrow> representable S
-                          \<longrightarrow> valid_sampling S df
-                          \<longrightarrow> (let pos = uint(Odometric_Position_Count(odofunction S))
-                               in \<bar>df((length S - 1)*\<delta>t\<^sub>o\<^sub>d\<^sub>o) - (\<delta>s\<^sub>r\<^sub>e\<^sub>s * pos)\<bar> \<le> \<delta>s\<^sub>r\<^sub>e\<^sub>s))"
-
-        update_instance*[R5::safety_requirement,
-                         formal_definition:="[@{thm \<open>Odometric_Position_Count_precise_def\<close>}]"]    
-   \<close>}
-
-By \<^theory_text>\<open>update_instance*\<close>, we book the property \<open>Position_Count_precise_def\<close> as 
-\<^onto_class>\<open>safety_requirement\<close>, a specific sub-class of \<^onto_class>\<open>requirement\<close>s
-requesting a formal definition in Isabelle.\<close>
-
-subsection\<open>Exporting Derived Requirements.\<close>
-
-text\<open>Finally, we discuss the situation where the verification team discovered a critical side-condition 
-for a major theorem necessary for the safety requirements; this was in our development the case for
-the condition labelled ``\<open>**\<close>'' in @{docitem verific}. The current CENELEC standard clearly separates
-``requirement specifications'' from ``verification reports,'' which is probably motivated 
-by the overall concern of organizational separation and of document consistency. While this 
-document organization is possible in \<^isadof>, it is in our experience often counter-productive 
-in practice: organizations tend to defend their documents because the impact of changes is more and more
-difficult to oversee. This effect results in a dramatic development slow-down and an increase of
-costs. Furthermore, these barriers exclude situations where developers perfectly know, for example,
-invariants, but can not communicate them to the verification team because the precise formalization
-is not known in time. Rather than advocating document separation, we tend to integrate these documents,
-keep proof as close as possible to definitions, and plead for consequent version control of the
-integrated source, together with the proposed methods to strengthen the links between the informal
-and formal parts by anti-quotations and continuous ontological checking. Instead of separation
-of the documents, we would rather emphasize the \<^emph>\<open>separation of the views\<close> of the different 
-document representations. Such views were systematically generated out of the integrated source in 
-different PDF versions and for each version, document specific consistency guarantees can be 
-automatically enforced.
-
-In our case study, we define this condition as predicate, declare an explanation of it as
-\<^onto_class>\<open>SRAC\<close> (CENELEC for: safety-related application condition; ontologically, this is a
-derived class from  \<^onto_class>\<open>requirement\<close>.) and add the definition of the predicate into the
-document instance as described in the previous section.\<close>
-
-
-
-chapter\<open>Appendix\<close>
-text\<open>
-\<^item> \<open>@{thm refl}\<close> : @{thm refl}
-\<^item> \<open>@{thm [source] refl}\<close> : @{thm [source] refl}
-\<^item> \<open>@{thm[mode=Rule] conjI}\<close> : @{thm[mode=Rule] conjI}
-\<^item> \<open>@{file "mini_odo.thy"}\<close> : @{file "mini_odo.thy"}
-\<^item> \<open>@{value "3+4::int"}}\<close> : @{value "3+4::int"}
-\<^item> \<open>@{const hd}\<close> : @{const hd}
-\<^item> \<open>@{theory HOL.List}\<close> : @{theory HOL.List}s
-\<^item> \<open>@{tserm "3"}\<close> : @{term "3"}
-\<^item> \<open>@{type bool}\<close> : @{type bool}
-\<^item> \<open>@{thm term [show_types] "f x = a + x"}\<close> : @{term [show_types] "f x = a + x"}
-\<close>
-
-text\<open>Examples for declaration of typed doc-classes "assumption" (sic!) and "hypothesis" (sic!!),
-     concepts defined in the underlying ontology @{theory "Isabelle_DOF-Ontologies.CENELEC_50128"}. \<close>
-text*[ass2::assumption, long_name="Some ''assumption one''"] \<open> The subsystem Y is safe. \<close>
-text*[hyp1::hypothesis] \<open> \<open>P \<noteq> NP\<close> \<close>
-  
-text\<open>  
-   A real example fragment from a larger project, declaring a text-element as a
-   "safety-related application condition", a concept defined in the 
-   @{theory "Isabelle_DOF-Ontologies.CENELEC_50128"} ontology:\<close>  
-
-text*[hyp2::hypothesis]\<open>Under the assumption @{assumption \<open>ass2\<close>} we establish the following: ... \<close>
-
-text*[ass122::SRAC, long_name="Some ''ass122''"] 
-\<open> The overall sampling frequence of the odometer subsystem is therefore 14 khz, 
-  which includes sampling, computing and result communication times... \<close>
-
-text*[ass123::SRAC] 
-\<open> The overall sampling frequence of the odometer subsystem is therefore 14 khz, 
-  which includes sampling, computing and result communication times... \<close>
-
-text*[ass124::EC, long_name="Some ''ass124''"] 
-\<open> The overall sampling frequence of the odometer subsystem is therefore 14 khz, 
-  which includes sampling, computing and result communication times... \<close>
-  
-text*[t10::test_result] 
-\<open> This is a meta-test. This could be an ML-command that governs the external 
-  test-execution via, \<^eg>, a makefile or specific calls to a test-environment or test-engine. \<close>
-
-
-text \<open> Finally some examples of references to doc-items, i.e. text-elements 
-       with declared  meta-information and status. \<close> 
-
-text \<open> As established by @{test_result \<open>t10\<close>}\<close>
-text \<open> the               @{test_result \<open>t10\<close>}                      
-       as well as the    @{SRAC \<open>ass122\<close>}\<close>  
-text \<open> represent a justification of the safety related applicability 
-       condition @{SRAC \<open>ass122\<close>} aka exported constraint @{EC \<open>ass122\<close>}.\<close> 
-
-text \<open> due to notational conventions for antiquotations, one may even write:
-
-       "represent a justification of the safety related applicability
-        condition \<^SRAC>\<open>ass122\<close> aka exported constraint \<^EC>\<open>ass122\<close>."\<close> 
-
-(*<*)   
-end
-(*>*)

Isabelle_DOF-Examples-Extra/beamerx/ROOTS

@@ -1,2 +0,0 @@
-poster
-presentation

Isabelle_DOF-Examples-Extra/beamerx/poster/ROOT

@@ -1,8 +0,0 @@
-chapter AFP 
-
-session "poster-example" (AFP) = "Isabelle_DOF-Ontologies" +
-  options [document = pdf, document_output = "output", document_build = dof, timeout = 300]
-  theories
-    "poster"
-  document_files
-    "preamble.tex"

Isabelle_DOF-Examples-Extra/beamerx/poster/document/preamble.tex

@@ -1,2 +0,0 @@
-%% This is a placeholder for user-specific configuration and packages.
-

Isabelle_DOF-Examples-Extra/beamerx/poster/poster.thy

@@ -1,39 +0,0 @@
-(*<*)
-theory "poster"
-  imports "Isabelle_DOF.scholarly_paper"
- "Isabelle_DOF-Ontologies.document_templates"
-begin
-
-use_template "beamerposter-UNSUPPORTED"
-use_ontology "scholarly_paper"
-(*>*)
-
-title*[tit::title]\<open>Example Presentation\<close>
-                                  
-author*[safouan,email="\<open>example@example.org\<close>",affiliation="\<open>Example Org\<close>"]\<open>Eliza Example\<close>
-
-text\<open>
-    \vfill
-    \begin{block}{\large Fontsizes}
-      \centering
-      {\tiny tiny}\par
-      {\scriptsize scriptsize}\par
-      {\footnotesize footnotesize}\par
-      {\normalsize normalsize}\par
-      {\large large}\par
-      {\Large Large}\par
-      {\LARGE LARGE}\par
-      {\veryHuge veryHuge}\par
-      {\VeryHuge VeryHuge}\par
-      {\VERYHuge VERYHuge}\par
-    \end{block}
-    \vfill
-\<close>
-
-text\<open>
-@{block (title = "\<open>Title\<^sub>t\<^sub>e\<^sub>s\<^sub>t\<close>") "\<open>Block content\<^sub>t\<^sub>e\<^sub>s\<^sub>t\<close>"}
-\<close>
-
-(*<*)
-end 
-(*>*)

Isabelle_DOF-Examples-Extra/beamerx/presentation/ROOT

@@ -1,9 +0,0 @@
-chapter AFP 
-
-session "presentation-example" (AFP) = "Isabelle_DOF-Ontologies" +
-  options [document = pdf, document_output = "output", document_build = dof, timeout = 300]
-  theories
-    "presentation"
-  document_files
-    "preamble.tex"
-    "figures/A.png"

Isabelle_DOF-Examples-Extra/beamerx/presentation/document/preamble.tex

@@ -1,2 +0,0 @@
-%% This is a placeholder for user-specific configuration and packages.
-

Isabelle_DOF-Examples-Extra/beamerx/presentation/presentation.thy

@@ -1,69 +0,0 @@
-(*<*)
-theory "presentation"
-  imports "Isabelle_DOF.scholarly_paper"
- "Isabelle_DOF-Ontologies.document_templates"
-begin
-
-use_template "beamer-UNSUPPORTED"
-use_ontology "scholarly_paper"
-(*>*)
-
-title*[tit::title]\<open>Example Presentation\<close>
-                                  
-author*[safouan,email="\<open>example@example.org\<close>",affiliation="\<open>Example Org\<close>"]\<open>Eliza Example\<close>
-
-text\<open>
-\begin{frame}
-\frametitle{Example Slide}
-\centering\huge This is an example!
-\end{frame}
-\<close>
-
-
-frame*[test_frame
-    , frametitle = \<open>\<open>\<open>Example Slide\<^sub>t\<^sub>e\<^sub>s\<^sub>t\<close> with items @{thm "HOL.refl"}\<close>\<close>
-    , framesubtitle = "''Subtitle''"]
-\<open>This is an example!
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> and the term encoding the title of this frame is \<^term_>\<open>frametitle @{frame \<open>test_frame\<close>}\<close>\<close>
-
-frame*[test_frame2
-    , frametitle = "''Example Slide''"
-    , framesubtitle = \<open>\<open>\<open>Subtitle\<^sub>t\<^sub>e\<^sub>s\<^sub>t:\<close> the value of \<^term>\<open>(3::int) + 3\<close> is @{value "(3::int) + 3"}\<close>\<close>]
-\<open>Test frame env \<^term>\<open>refl\<close>\<close>
-
-frame*[test_frame3, frametitle = "''A slide with a Figure''"]
-\<open>A figure
-@{figure_content (width=45, caption=\<open>\<open>Figure\<^sub>t\<^sub>e\<^sub>s\<^sub>t\<close> is not the \<^term>\<open>refl\<close> theorem  (@{thm "refl"}).\<close>)
-                 "figures/A.png"}\<close>
-
-frame*[test_frame4
-    , options = "''allowframebreaks''"
-    , frametitle = "''Example Slide with frame break''"
-    , framesubtitle = \<open>\<open>\<open>Subtitle\<^sub>t\<^sub>e\<^sub>s\<^sub>t:\<close> the value of \<^term>\<open>(3::int) + 3\<close> is @{value "(3::int) + 3"}\<close>\<close>]
-\<open>
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> and the term encoding the title of this frame is \<^term_>\<open>frametitle @{frame \<open>test_frame4\<close>}\<close>
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
-\<close>
-
-(*<*)
-end 
-(*>*)

Isabelle_DOF-Examples-Extra/cytology/Cytology.thy

@@ -1,87 +0,0 @@
-theory Cytology
-  imports "Isabelle_DOF.scholarly_paper"
-begin
-
-text\<open>A small example ontology for demonstration purposes.
-     The presentation follows closely: \<^url>\<open>https://www.youtube.com/watch?v=URUJD5NEXC8\<close>.\<close>
-
-
-datatype protein = filaments | motor_proteins | rna | dna |nucleolus
-
-type_synonym desc = "string"
-
-onto_class organelles   =   description :: desc
-
-find_theorems (60) name:"organelles"
-
-term "Cytology.organelles.make"
-
-onto_class ribosomes    = organelles +    description :: desc
-   
-onto_class mytochondria = organelles +    description :: desc
-
-onto_class golgi_apparatus = organelles + description :: desc
-
-onto_class lysosome    = organelles +     description :: desc
-
-text\<open>the control center of the cell:\<close>
-onto_class nucleus = organelles +  
-       description :: desc
-       components  :: "protein list" <= "[nucleolus]" 
-
-(* Not so nice construction to mimick inheritance on types useds in attribute positions. *)
-datatype organelles' = upcast\<^sub>r\<^sub>i\<^sub>b\<^sub>o\<^sub>s\<^sub>o\<^sub>m\<^sub>e\<^sub>s     (get_ribosomes:ribosomes)
-                     | upcast\<^sub>m\<^sub>y\<^sub>t\<^sub>o\<^sub>c\<^sub>h\<^sub>o\<^sub>n\<^sub>d\<^sub>r\<^sub>i\<^sub>a   (get_mytochondria:mytochondria)
-                     | upcast\<^sub>g\<^sub>o\<^sub>l\<^sub>g\<^sub>i\<^sub>_\<^sub>a\<^sub>p\<^sub>p\<^sub>a\<^sub>r\<^sub>a\<^sub>t\<^sub>u\<^sub>s (get_golgi_apparatus: golgi_apparatus)
-                     | upcast\<^sub>l\<^sub>y\<^sub>s\<^sub>o\<^sub>s\<^sub>o\<^sub>m\<^sub>e      (get_lysosome : lysosome)
-                     | upcast\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s       (get_nucleus : nucleus)
-
-fun is\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s where "is\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s (upcast\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s X) = True" | "is\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s ( _) = False"
-(* ... *)
-fun downcast\<^sub>r\<^sub>i\<^sub>b\<^sub>o\<^sub>s\<^sub>o\<^sub>m\<^sub>e\<^sub>s 
-  where "downcast\<^sub>r\<^sub>i\<^sub>b\<^sub>o\<^sub>s\<^sub>o\<^sub>m\<^sub>e\<^sub>s (upcast\<^sub>r\<^sub>i\<^sub>b\<^sub>o\<^sub>s\<^sub>o\<^sub>m\<^sub>e\<^sub>s X) = X" | "downcast\<^sub>r\<^sub>i\<^sub>b\<^sub>o\<^sub>s\<^sub>o\<^sub>m\<^sub>e\<^sub>s _ = undefined"
-fun downcast\<^sub>m\<^sub>y\<^sub>t\<^sub>o\<^sub>c\<^sub>h\<^sub>o\<^sub>n\<^sub>d\<^sub>r\<^sub>i\<^sub>a 
-  where "downcast\<^sub>m\<^sub>y\<^sub>t\<^sub>o\<^sub>c\<^sub>h\<^sub>o\<^sub>n\<^sub>d\<^sub>r\<^sub>i\<^sub>a (upcast\<^sub>m\<^sub>y\<^sub>t\<^sub>o\<^sub>c\<^sub>h\<^sub>o\<^sub>n\<^sub>d\<^sub>r\<^sub>i\<^sub>a X) = X" | "downcast\<^sub>m\<^sub>y\<^sub>t\<^sub>o\<^sub>c\<^sub>h\<^sub>o\<^sub>n\<^sub>d\<^sub>r\<^sub>i\<^sub>a _ = undefined"
-fun downcast\<^sub>g\<^sub>o\<^sub>l\<^sub>g\<^sub>i\<^sub>_\<^sub>a\<^sub>p\<^sub>p\<^sub>a\<^sub>r\<^sub>a\<^sub>t\<^sub>u\<^sub>s 
-  where "downcast\<^sub>g\<^sub>o\<^sub>l\<^sub>g\<^sub>i\<^sub>_\<^sub>a\<^sub>p\<^sub>p\<^sub>a\<^sub>r\<^sub>a\<^sub>t\<^sub>u\<^sub>s (upcast\<^sub>g\<^sub>o\<^sub>l\<^sub>g\<^sub>i\<^sub>_\<^sub>a\<^sub>p\<^sub>p\<^sub>a\<^sub>r\<^sub>a\<^sub>t\<^sub>u\<^sub>s X) = X" | "downcast\<^sub>g\<^sub>o\<^sub>l\<^sub>g\<^sub>i\<^sub>_\<^sub>a\<^sub>p\<^sub>p\<^sub>a\<^sub>r\<^sub>a\<^sub>t\<^sub>u\<^sub>s _ = undefined"
-fun downcast\<^sub>l\<^sub>y\<^sub>s\<^sub>o\<^sub>s\<^sub>o\<^sub>m\<^sub>e 
-  where "downcast\<^sub>l\<^sub>y\<^sub>s\<^sub>o\<^sub>s\<^sub>o\<^sub>m\<^sub>e (upcast\<^sub>l\<^sub>y\<^sub>s\<^sub>o\<^sub>s\<^sub>o\<^sub>m\<^sub>e X) = X" | "downcast\<^sub>l\<^sub>y\<^sub>s\<^sub>o\<^sub>s\<^sub>o\<^sub>m\<^sub>e _ = undefined"
-fun downcast\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s 
-  where "downcast\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s (upcast\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s X) = X" | "downcast\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s _ = undefined"
-
-
-
-
-onto_class cell = 
-    name             :: string
-    membrane         :: desc   <= "\<open>The outer boundary of the cell\<close>"
-    cytoplasm        :: desc   <= "\<open>The liquid in the cell\<close>"
-    cytoskeleton     :: desc   <= "\<open>includes the thread-like microfilaments\<close>"
-    genetic_material :: "protein list" <= "[rna, dna]"
-
-text\<open>Cells are devided into two categories: \<^emph>\<open>procaryotic\<close> cells (unicellular organisms some 
-bacteria) without a substructuring in organelles and \<^emph>\<open>eucaryotic\<close> cells, as occurring in 
-pluricellular organisms\<close>
-
-onto_class procaryotic_cells = cell +
-    name :: string
-
-onto_class eucaryotic_cells = cell + 
-    organelles :: "organelles' list"
-    invariant has_nucleus :: "\<exists> org \<in> set (organelles \<sigma>). is\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s org"
-    \<comment> \<open>Cells must have at least one nucleus. However, this should be executable.\<close>
-
-find_theorems (70)name:"eucaryotic_cells"
-find_theorems name:has_nucleus
-
-value "is\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s (mk\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s X)"
-
-term \<open>eucaryotic_cells.organelles\<close>
-
-value \<open>(eucaryotic_cells.organelles(eucaryotic_cells.make X Y Z Z Z [] []))\<close>
-
-value \<open>has_nucleus_inv(eucaryotic_cells.make X Y Z Z Z [] [])\<close>
-
-value \<open>has_nucleus_inv(eucaryotic_cells.make X Y Z Z Z [] [upcast\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s (nucleus.make a b c )])\<close>
-
-end

Isabelle_DOF-Examples-Extra/cytology/ROOT

@@ -1,4 +0,0 @@
-session "Cytology" = "Isabelle_DOF" +
-  options [document = false]
-  theories
-    "Cytology"

Isabelle_DOF-Examples-Templates/ROOTS

@@ -1,9 +0,0 @@
-template-beamerposter-UNSUPPORTED
-template-beamer-UNSUPPORTED
-template-lipics-v2021-UNSUPPORTED
-template-lncs
-template-scrartcl
-template-scrreprt
-template-scrreprt-modern
-template-sn-article-UNSUPPORTED
-template-svjour3-UNSUPPORTED

Isabelle_DOF-Examples-Templates/template-beamer-UNSUPPORTED/ROOT

@@ -1,9 +0,0 @@
-session "template-beamer-UNSUPPORTED" = "Isabelle_DOF-Ontologies" +
-  options [document = pdf, document_output = "output", document_build = dof]
-(*theories [document = false]
-    A
-    B*)
-  theories
-    "template-beamer-UNSUPPORTED"
-  document_files
-    "preamble.tex"

Isabelle_DOF-Examples-Templates/template-beamer-UNSUPPORTED/document/preamble.tex

@@ -1 +0,0 @@
-%% This is a placeholder for user-specific configuration and packages.

Isabelle_DOF-Examples-Templates/template-beamer-UNSUPPORTED/template-beamer-UNSUPPORTED.thy

@@ -1,72 +0,0 @@
-(*<*)
-theory
-  "template-beamer-UNSUPPORTED"
-imports
-  "Isabelle_DOF-Ontologies.document_templates"
-   Isabelle_DOF.scholarly_paper
-begin
-
-list_templates
-use_template "beamer-UNSUPPORTED"
-list_ontologies
-use_ontology "scholarly_paper"
-(*>*)
-
-title* [tit::title]\<open>Formal Verification of Security Protocols\<close>
-author*[alice, email       = "\<open>alice@example.com\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Alice\<close>  
-(* 
-author*[bob,   email       = "\<open>bob@example.com\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Bob\<close>  
-*)
-
-text\<open>
-\begin{frame}
-\frametitle{Example Slide}
-\centering\huge This is an example!
-\end{frame}
-\<close>
-
-
-frame*[test_frame
-    , frametitle = \<open>\<open>\<open>Example Slide\<^sub>t\<^sub>e\<^sub>s\<^sub>t\<close> with items @{thm "HOL.refl"}\<close>\<close>
-    , framesubtitle = "''Subtitle''"]
-\<open>This is an example!
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> and the term encoding the title of this frame is \<^term_>\<open>frametitle @{frame \<open>test_frame\<close>}\<close>\<close>
-
-frame*[test_frame2
-    , frametitle = "''Example Slide''"
-    , framesubtitle = \<open>\<open>\<open>Subtitle\<^sub>t\<^sub>e\<^sub>s\<^sub>t:\<close> the value of \<^term>\<open>(3::int) + 3\<close> is @{value "(3::int) + 3"}\<close>\<close>]
-\<open>Test frame env \<^term>\<open>refl\<close>\<close>
-
-frame*[test_frame3
-    , options = "''allowframebreaks''"
-    , frametitle = "''Example Slide with frame break''"
-    , framesubtitle = \<open>\<open>\<open>Subtitle\<^sub>t\<^sub>e\<^sub>s\<^sub>t:\<close> the value of \<^term>\<open>(3::int) + 3\<close> is @{value "(3::int) + 3"}\<close>\<close>]
-\<open>
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> and the term encoding the title of this frame is \<^term_>\<open>frametitle @{frame \<open>test_frame3\<close>}\<close>
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
- \<^item> The term \<^term>\<open>refl\<close> is...
-\<close>
-
-(*<*)
-end 
-(*>*)

Isabelle_DOF-Examples-Templates/template-beamerposter-UNSUPPORTED/ROOT

@@ -1,9 +0,0 @@
-session "template-beamerposter-UNSUPPORTED" = "Isabelle_DOF-Ontologies" +
-  options [document = pdf, document_output = "output", document_build = dof]
-(*theories [document = false]
-    A
-    B*)
-  theories
-    "template-beamerposter-UNSUPPORTED"
-  document_files
-    "preamble.tex"

Isabelle_DOF-Examples-Templates/template-beamerposter-UNSUPPORTED/document/preamble.tex

@@ -1 +0,0 @@
-%% This is a placeholder for user-specific configuration and packages.

Isabelle_DOF-Examples-Templates/template-beamerposter-UNSUPPORTED/template-beamerposter-UNSUPPORTED.thy

@@ -1,21 +0,0 @@
-theory
-  "template-beamerposter-UNSUPPORTED"
-imports
-  "Isabelle_DOF-Ontologies.document_templates"
-   Isabelle_DOF.scholarly_paper
-begin
-
-list_templates
-use_template "beamerposter-UNSUPPORTED"
-list_ontologies
-use_ontology "scholarly_paper"
-
-title* [tit::title]\<open>Formal Verification of Security Protocols\<close>
-author*[alice, email       = "\<open>alice@example.com\<close>",
-               http_site   = "\<open>https://example.com/alice\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Alice\<close>  
-author*[bob,   email       = "\<open>bob@example.com\<close>",
-               http_site   = "\<open>https://example.com/bob\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Bob\<close>  
-
-end

Isabelle_DOF-Examples-Templates/template-lipics-v2021-UNSUPPORTED/ROOT

@@ -1,10 +0,0 @@
-session "template-lipics-v2021-UNSUPPORTED" = "Isabelle_DOF-Ontologies" +
-  options [document = pdf, document_output = "output", document_build = dof]
-(*theories [document = false]
-    A
-    B*)
-  theories
-    "template-lipics-v2021-UNSUPPORTED"
-  document_files
-    "preamble.tex"
-    "lipics-v2021.cls"

Isabelle_DOF-Examples-Templates/template-lipics-v2021-UNSUPPORTED/document/preamble.tex

@@ -1 +0,0 @@
-%% This is a placeholder for user-specific configuration and packages.

Isabelle_DOF-Examples-Templates/template-lipics-v2021-UNSUPPORTED/template-lipics-v2021-UNSUPPORTED.thy

@@ -1,21 +0,0 @@
-theory
-  "template-lipics-v2021-UNSUPPORTED"
-imports
-  "Isabelle_DOF-Ontologies.document_templates"
-   Isabelle_DOF.scholarly_paper
-begin
-
-list_templates
-use_template "lipics-v2021-UNSUPPORTED"
-list_ontologies
-use_ontology "scholarly_paper"
-
-title* [tit::title]\<open>Formal Verification of Security Protocols\<close>
-author*[alice, email       = "\<open>alice@example.com\<close>",
-               http_site   = "\<open>https://example.com/alice\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Alice\<close>  
-author*[bob,   email       = "\<open>bob@example.com\<close>",
-               http_site   = "\<open>https://example.com/bob\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Bob\<close>  
-
-end

Isabelle_DOF-Examples-Templates/template-lncs/ROOT

@@ -1,9 +0,0 @@
-session "template-lncs" = "Isabelle_DOF-Ontologies" +
-  options [document = pdf, document_output = "output", document_build = dof]
-(*theories [document = false]
-    A
-    B*)
-  theories
-    "template-lncs"
-  document_files
-    "preamble.tex"

Isabelle_DOF-Examples-Templates/template-lncs/document/preamble.tex

@@ -1 +0,0 @@
-%% This is a placeholder for user-specific configuration and packages.

Isabelle_DOF-Examples-Templates/template-lncs/template-lncs.thy

@@ -1,21 +0,0 @@
-theory
-  "template-lncs"
-imports
-  "Isabelle_DOF-Ontologies.document_templates"
-   Isabelle_DOF.scholarly_paper
-begin
-
-list_templates
-use_template "lncs"
-list_ontologies
-use_ontology "scholarly_paper"
-
-title* [tit::title]\<open>Formal Verification of Security Protocols\<close>
-author*[alice, email       = "\<open>alice@example.com\<close>",
-               http_site   = "\<open>https://example.com/alice\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Alice\<close>  
-author*[bob,   email       = "\<open>bob@example.com\<close>",
-               http_site   = "\<open>https://example.com/bob\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Bob\<close>  
-
-end

Isabelle_DOF-Examples-Templates/template-scrartcl/ROOT

@@ -1,9 +0,0 @@
-session "template-scrartcl" = "Isabelle_DOF-Ontologies" +
-  options [document = pdf, document_output = "output", document_build = dof]
-(*theories [document = false]
-    A
-    B*)
-  theories
-    "template-scrartcl"
-  document_files
-    "preamble.tex"

Isabelle_DOF-Examples-Templates/template-scrartcl/document/preamble.tex

@@ -1 +0,0 @@
-%% This is a placeholder for user-specific configuration and packages.

Isabelle_DOF-Examples-Templates/template-scrartcl/template-scrartcl.thy

@@ -1,21 +0,0 @@
-theory
-  "template-scrartcl"
-imports
-  "Isabelle_DOF-Ontologies.document_templates"
-   Isabelle_DOF.scholarly_paper
-begin
-
-list_templates
-use_template "scrartcl"
-list_ontologies
-use_ontology "scholarly_paper"
-
-title* [tit::title]\<open>Formal Verification of Security Protocols\<close>
-author*[alice, email       = "\<open>alice@example.com\<close>",
-               http_site   = "\<open>https://example.com/alice\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Alice\<close>  
-author*[bob,   email       = "\<open>bob@example.com\<close>",
-               http_site   = "\<open>https://example.com/bob\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Bob\<close>  
-
-end

Isabelle_DOF-Examples-Templates/template-scrreprt-modern/ROOT

@@ -1,9 +0,0 @@
-session "template-scrreprt-modern" = "Isabelle_DOF-Ontologies" +
-  options [document = pdf, document_output = "output", document_build = dof]
-(*theories [document = false]
-    A
-    B*)
-  theories
-    "template-scrreprt-modern"
-  document_files
-    "preamble.tex"

Isabelle_DOF-Examples-Templates/template-scrreprt-modern/document/preamble.tex

@@ -1 +0,0 @@
-%% This is a placeholder for user-specific configuration and packages.

Isabelle_DOF-Examples-Templates/template-scrreprt-modern/template-scrreprt-modern.thy

@@ -1,21 +0,0 @@
-theory
-  "template-scrreprt-modern"
-imports
-  "Isabelle_DOF-Ontologies.document_templates"
-   Isabelle_DOF.technical_report
-begin
-
-list_templates
-use_template "scrreprt-modern"
-list_ontologies
-use_ontology "technical_report"
-
-title* [tit::title]\<open>Formal Verification of Security Protocols\<close>
-author*[alice, email       = "\<open>alice@example.com\<close>",
-               http_site   = "\<open>https://example.com/alice\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Alice\<close>  
-author*[bob,   email       = "\<open>bob@example.com\<close>",
-               http_site   = "\<open>https://example.com/bob\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Bob\<close>  
-
-end

Isabelle_DOF-Examples-Templates/template-scrreprt/ROOT

@@ -1,9 +0,0 @@
-session "template-scrreprt" = "Isabelle_DOF-Ontologies" +
-  options [document = pdf, document_output = "output", document_build = dof]
-(*theories [document = false]
-    A
-    B*)
-  theories
-    "template-scrreprt"
-  document_files
-    "preamble.tex"

Isabelle_DOF-Examples-Templates/template-scrreprt/document/preamble.tex

@@ -1 +0,0 @@
-%% This is a placeholder for user-specific configuration and packages.

Isabelle_DOF-Examples-Templates/template-scrreprt/template-scrreprt.thy

@@ -1,21 +0,0 @@
-theory
-  "template-scrreprt"
-imports
-  "Isabelle_DOF-Ontologies.document_templates"
-   Isabelle_DOF.technical_report
-begin
-
-list_templates
-use_template "scrreprt"
-list_ontologies
-use_ontology "technical_report"
-
-title* [tit::title]\<open>Formal Verification of Security Protocols\<close>
-author*[alice, email       = "\<open>alice@example.com\<close>",
-               http_site   = "\<open>https://example.com/alice\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Alice\<close>  
-author*[bob,   email       = "\<open>bob@example.com\<close>",
-               http_site   = "\<open>https://example.com/bob\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Bob\<close>  
-
-end

Isabelle_DOF-Examples-Templates/template-sn-article-UNSUPPORTED/ROOT

@@ -1,10 +0,0 @@
-session "template-sn-article-UNSUPPORTED" = "Isabelle_DOF-Ontologies" +
-  options [document = pdf, document_output = "output", document_build = dof]
-(*theories [document = false]
-    A
-    B*)
-  theories
-    "template-sn-article-UNSUPPORTED"
-  document_files
-    "preamble.tex"
-    "sn-jnl.cls"

Isabelle_DOF-Examples-Templates/template-sn-article-UNSUPPORTED/document/preamble.tex

@@ -1 +0,0 @@
-%% This is a placeholder for user-specific configuration and packages.

Isabelle_DOF-Examples-Templates/template-sn-article-UNSUPPORTED/template-sn-article-UNSUPPORTED.thy

@@ -1,21 +0,0 @@
-theory
-  "template-sn-article-UNSUPPORTED"
-imports
-  "Isabelle_DOF-Ontologies.document_templates"
-   Isabelle_DOF.scholarly_paper
-begin
-
-list_templates
-use_template "sn-article-UNSUPPORTED"
-list_ontologies
-use_ontology "scholarly_paper"
-
-title* [tit::title]\<open>Formal Verification of Security Protocols\<close>
-author*[alice, email       = "\<open>alice@example.com\<close>",
-               http_site   = "\<open>https://example.com/alice\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Alice\<close>  
-author*[bob,   email       = "\<open>bob@example.com\<close>",
-               http_site   = "\<open>https://example.com/bob\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Bob\<close>  
-
-end

Isabelle_DOF-Examples-Templates/template-svjour3-UNSUPPORTED/ROOT

@@ -1,11 +0,0 @@
-session "template-svjour3-UNSUPPORTED" = "Isabelle_DOF-Ontologies" +
-  options [document = pdf, document_output = "output", document_build = dof]
-(*theories [document = false]
-    A
-    B*)
-  theories
-    "template-svjour3-UNSUPPORTED"
-  document_files
-    "preamble.tex"
-    "svjour3.cls"
-    "svglov3.clo"

Isabelle_DOF-Examples-Templates/template-svjour3-UNSUPPORTED/document/preamble.tex

@@ -1 +0,0 @@
-%% This is a placeholder for user-specific configuration and packages.

Isabelle_DOF-Examples-Templates/template-svjour3-UNSUPPORTED/document/svglov3.clo

@@ -1,101 +0,0 @@
-% SVJour3 DOCUMENT CLASS OPTION SVGLOV3 -- for standardised journals
-%
-% This is an enhancement for the LaTeX
-% SVJour3 document class for Springer journals
-%
-%%
-%%
-%% \CharacterTable
-%%  {Upper-case    \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
-%%   Lower-case    \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z
-%%   Digits        \0\1\2\3\4\5\6\7\8\9
-%%   Exclamation   \!     Double quote  \"     Hash (number) \#
-%%   Dollar        \$     Percent       \%     Ampersand     \&
-%%   Acute accent  \'     Left paren    \(     Right paren   \)
-%%   Asterisk      \*     Plus          \+     Comma         \,
-%%   Minus         \-     Point         \.     Solidus       \/
-%%   Colon         \:     Semicolon     \;     Less than     \<
-%%   Equals        \=     Greater than  \>     Question mark \?
-%%   Commercial at \@     Left bracket  \[     Backslash     \\
-%%   Right bracket \]     Circumflex    \^     Underscore    \_
-%%   Grave accent  \`     Left brace    \{     Vertical bar  \|
-%%   Right brace   \}     Tilde         \~}
-\ProvidesFile{svglov3.clo}
-              [2006/02/03 v3.1
-      style option for standardised journals]
-\typeout{SVJour Class option: svglov3.clo for standardised journals}
-\def\validfor{svjour3}
-\ExecuteOptions{final,10pt,runningheads}
-% No size changing allowed, hence a "copy" of size10.clo is included
-\renewcommand\normalsize{%
-\if@twocolumn
-   \@setfontsize\normalsize\@xpt{12.5pt}%
-\else
-   \if@smallext
-      \@setfontsize\normalsize\@xpt\@xiipt
-   \else
-      \@setfontsize\normalsize{9.5pt}{11.5pt}%
-   \fi
-\fi
-   \abovedisplayskip=3 mm plus6pt minus 4pt
-   \belowdisplayskip=3 mm plus6pt minus 4pt
-   \abovedisplayshortskip=0.0 mm plus6pt
-   \belowdisplayshortskip=2 mm plus4pt minus 4pt
-   \let\@listi\@listI}
-\normalsize
-\newcommand\small{%
-\if@twocolumn
-   \@setfontsize\small{8.5pt}\@xpt
-\else
-   \if@smallext
-      \@setfontsize\small\@viiipt{9.5pt}%
-   \else
-      \@setfontsize\small\@viiipt{9.25pt}%
-   \fi
-\fi
-   \abovedisplayskip 8.5\p@ \@plus3\p@ \@minus4\p@
-   \abovedisplayshortskip \z@ \@plus2\p@
-   \belowdisplayshortskip 4\p@ \@plus2\p@ \@minus2\p@
-   \def\@listi{\leftmargin\leftmargini
-               \parsep 0\p@ \@plus1\p@ \@minus\p@
-               \topsep 4\p@ \@plus2\p@ \@minus4\p@
-               \itemsep0\p@}%
-   \belowdisplayskip \abovedisplayskip
-}
-\let\footnotesize\small
-\newcommand\scriptsize{\@setfontsize\scriptsize\@viipt\@viiipt}
-\newcommand\tiny{\@setfontsize\tiny\@vpt\@vipt}
-\if@twocolumn
-   \newcommand\large{\@setfontsize\large\@xiipt\@xivpt}
-   \newcommand\LARGE{\@setfontsize\LARGE{16pt}{18pt}}
-\else
-   \newcommand\large{\@setfontsize\large\@xipt\@xiipt}
-   \newcommand\LARGE{\@setfontsize\LARGE{13pt}{15pt}}
-\fi
-\newcommand\Large{\@setfontsize\Large\@xivpt{16dd}}
-\newcommand\huge{\@setfontsize\huge\@xxpt{25}}
-\newcommand\Huge{\@setfontsize\Huge\@xxvpt{30}}
-%
-\def\runheadhook{\rlap{\smash{\lower6.5pt\hbox to\textwidth{\hrulefill}}}}
-\if@twocolumn
-\setlength{\textwidth}{17.4cm}
-\setlength{\textheight}{234mm}
-\AtEndOfClass{\setlength\columnsep{6mm}}
-\else
-   \if@smallext
-      \setlength{\textwidth}{11.9cm}
-      \setlength{\textheight}{19.4cm}
-   \else
-      \setlength{\textwidth}{12.2cm}
-      \setlength{\textheight}{19.8cm}
-   \fi
-\fi
-%
-\AtBeginDocument{%
-\@ifundefined{@journalname}
- {\typeout{Unknown journal: specify \string\journalname\string{%
-<name of your journal>\string} in preambel^^J}}{}}
-%
-\endinput
-%%
-%% End of file `svglov3.clo'.

Isabelle_DOF-Examples-Templates/template-svjour3-UNSUPPORTED/template-svjour3-UNSUPPORTED.thy

@@ -1,21 +0,0 @@
-theory
-  "template-svjour3-UNSUPPORTED"
-imports
-  "Isabelle_DOF-Ontologies.document_templates"
-   Isabelle_DOF.scholarly_paper
-begin
-
-list_templates
-use_template "svjour3-UNSUPPORTED"
-list_ontologies
-use_ontology "scholarly_paper"
-
-title* [tit::title]\<open>Formal Verification of Security Protocols\<close>
-author*[alice, email       = "\<open>alice@example.com\<close>",
-               http_site   = "\<open>https://example.com/alice\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Alice\<close>  
-author*[bob,   email       = "\<open>bob@example.com\<close>",
-               http_site   = "\<open>https://example.com/bob\<close>",
-               affiliation = "\<open>Wonderland University\<close>"]\<open>Bob\<close>  
-
-end

Isabelle_DOF-Ontologies/CC_v3_1_R5/CC_terminology.thy

@@ -1,466 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2022 The University of Exeter 
- *               2019-2022 The University of Paris-Saclay
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-chapter\<open>Common Criteria\<close>
-section\<open>Terminology\<close>
-
-(*<<*)
-theory CC_terminology
-
-imports  
-"Isabelle_DOF.technical_report" 
-
-begin
-
-define_ontology "DOF-CC_terminology.sty" "CC"
-
-(*>>*)
-text\<open>We re-use the class @\<open>typ math_content\<close>, which provides also a framework for
-semi-formal terminology, which we re-use by this definition.\<close>
-
-doc_class concept_definition = math_content +
-      status        :: status <= "semiformal" 
-      mcc           :: math_content_class <= "terminology"
-      tag           :: string
-      short_tag    :: "string option" <= "None"
-
-text\<open>The \<^verbatim>\<open>short_tag\<close>, if set, is used in the presentation directly.\<close>
-
-type_synonym concept = concept_definition  
-
-declare[[ Definition_default_class="concept_definition"]]
-
-
-
-subsection \<open>Terminology\<close>
-
-
-subsubsection \<open>Terms and definitions common in the CC\<close>
-
-Definition* [aas_def, tag= "''adverse actions''"]
- \<open>actions performed by a threat agent on an asset\<close>
-
-declare_reference*[toeDef]
-
-Definition* [assts_def, tag="''assets''"]
- \<open>entities that the owner of the @{docitem (unchecked) toeDef} presumably places value upon \<close>
-
-Definition* [asgn_def, tag="''assignment''"]
-\<open>the specification of an identified parameter in a component (of the CC) or requirement.\<close>
-
-declare_reference*[sfrs_def]
-
-Definition* [assrc_def, tag="''assurance''"]
-  \<open>grounds for confidence that a @{docitem (unchecked) toeDef}
-   meets the @{docitem (unchecked) sfrs_def}\<close>
-
-Definition* [attptl_def, tag="''attack potential''"] 
-  \<open>measure of the effort to be expended in attacking a TOE, expressed in terms of 
-   an attacker's expertise, resources and motivation\<close>
-
-Definition* [argmt_def, tag= "''augmentation''"] 
-  \<open>addition of one or more requirement(s) to a package\<close>
-
-Definition* [authdata_def, tag="''authentication data''"]
-  \<open>information used to verify the claimed identity of a user\<close>
-
-Definition* [authusr_def, tag = "''authorised user''"] 
-\<open>@{docitem (unchecked) toeDef} user who may,
- in accordance with the @{docitem (unchecked) sfrs_def}, perform an operation\<close>
-
-Definition* [bppDef, tag="''Base Protection Profile''"] 
-\<open>Protection Profile used as a basis to build a Protection Profile Configuration\<close>
-
-Definition* [cls_def,tag="''class''"]
-\<open>set of CC families that share a common focus\<close>
-
-Definition* [cohrnt_def,tag="''coherent''"] 
-\<open>logically ordered and having discernible meaning For documentation, this addresses 
- both the actual text and the structure of the document, in terms of whether it is 
- understandable by its target audience.\<close>
-
-Definition* [cmplt_def, tag="''complete''"] 
-\<open>property where all necessary parts of an entity have been provided
- In terms of documentation, this means that all relevant information is
- covered in the documentation, at such a level of detail that no further
- explanation is required at that level of abstraction.\<close>
-
-Definition* [compnt_def, tag="''component''"] 
- \<open>smallest selectable set of elements on which requirements may be based\<close>
-
-Definition*[cap_def, tag="''composed assurance package''"] 
-\<open>assurance package consisting of requirements drawn from CC Part 3 
- (predominately from the ACO class), representing a point on the CC predefined 
- composition assurance scale\<close>
-
-Definition* [cfrm_def,tag="''confirm''"] 
-\<open>declare that something has been reviewed in detail with an independent determination 
- of sufficiency
-
- The level of rigour required depends on the nature of the subject matter. This
- term is only applied to evaluator actions.\<close>
-
-Definition* [cnnctvty_def, tag="''connectivity''"]
-\<open>property of the @{docitem (unchecked) toeDef} allowing interaction with IT entities external to the 
- @{docitem (unchecked) toeDef}
-
- This includes exchange of data by wire or by wireless means, over any
- distance in any environment or configuration.\<close>
-
-Definition* [cnstnt_def, tag="''consistent''"] 
-\<open>relationship between two or more entities such that there are no apparent 
- contradictions between these entities\<close>
-
-Definition* [cnt_vrb_def, tag="''counter, verb''"] 
-\<open>meet an attack where the impact of a particular threat is mitigated 
- but not necessarily eradicated\<close>
-
-declare_reference*[stDef]
-declare_reference*[ppDef]
-
-Definition* [dmnst_conf_def, tag="''demonstrable conformance''"] 
-\<open>relation between an @{docitem (unchecked) stDef} and a @{docitem (unchecked) ppDef},
- where the @{docitem (unchecked) stDef} 
- provides a solution which solves the generic security problem in the PP
-
-The @{docitem (unchecked) ppDef} and the @{docitem (unchecked) stDef} may contain
-entirely different statements that discuss
-different entities, use different concepts etc. Demonstrable conformance is
-also suitable for a @{docitem (unchecked) toeDef} type
-where several similar @{docitem (unchecked) ppDef}s already exist, thus
-allowing the ST author to claim conformance to these @{docitem (unchecked) ppDef}s simultaneously,
-thereby saving work.\<close>
-
-Definition* [dmstrt_def, tag="''demonstrate''"] 
-\<open>provide a conclusion gained by an analysis which is less rigorous than a “proof”\<close>
-
-Definition* [dpndcy, tag="''dependency''"] 
-\<open>relationship between components such that if a requirement based on the depending 
- component is included in a @{docitem (unchecked) ppDef}, ST or package, a requirement based on 
- the component that is depended upon must normally also be included
- in the @{docitem (unchecked) ppDef}, 
- @{docitem (unchecked) stDef} or package\<close>
-
-Definition* [dscrb_def, tag="''describe''"] 
-\<open>provide specific details of an entity\<close>
-
-Definition* [dtrmn_def, tag="''determine''"] 
-\<open>affirm a particular conclusion based on independent analysis with the objective 
- of reaching a particular conclusion
-
- The usage of this term implies a truly independent analysis, usually in the
- absence of any previous analysis having been performed. Compare with the
- terms “confirm” or “verify” which imply that an analysis has already been
- performed which needs to be reviewed\<close>
-
-Definition* [devenv_def, tag="''development environment''"] 
-\<open>environment in which the @{docitem (unchecked) toeDef} is developed\<close>
-
-Definition* [elmnt_def, tag="''element''"] 
-\<open>indivisible statement of a security need\<close>
-
-Definition* [ensr_def, tag="''ensure''"] 
-\<open>guarantee a strong causal relationship between an action and its consequences
- 
- When this term is preceded by the word “help” it indicates that the
- consequence is not fully certain, on the basis of that action alone.\<close>
-
-Definition* [eval_def, tag="''evaluation''"] 
-\<open>assessment of a @{docitem (unchecked) ppDef}, an @{docitem (unchecked) stDef}
- or a @{docitem (unchecked) toeDef}, against defined criteria.\<close>
-
-Definition* [eal_def, tag= "''evaluation assurance level''"] 
-\<open>set of assurance requirements drawn from CC Part 3, representing a point on the 
- CC predefined assurance scale, that form an assurance package\<close>
-
-Definition* [eval_auth_def, tag="''evaluation authority''"] 
-\<open>body that sets the standards and monitors the quality of evaluations conducted 
- by bodies within a specific community and implements the CC for that community 
- by means of an evaluation scheme\<close>
-
-Definition* [eval_schm_def, tag="''evaluation scheme''"] 
-\<open>administrative and regulatory framework under which the CC is applied by an 
- evaluation authority within a specific community\<close>
-
-Definition* [exstDef, tag="''exhaustive''"]
-\<open>characteristic of a methodical approach taken to perform an
-analysis or activity according to an unambiguous plan
-This term is used in the CC with respect to conducting an analysis or other
-activity. It is related to ``systematic'' but is considerably stronger, in that it
-indicates not only that a methodical approach has been taken to perform the
-analysis or activity according to an unambiguous plan, but that the plan that
-was followed is sufficient to ensure that all possible avenues have been
-exercised.\<close>
-
-Definition* [expln_def, tag="''explain''"] 
-\<open> give argument accounting for the reason for taking a course of action
-This term differs from both “describe” and “demonstrate”. It is intended to
-answer the question “Why?” without actually attempting to argue that the
-course of action that was taken was necessarily optimal.\<close>
-
-Definition* [extn_def, tag= "''extension''"] 
-\<open>addition to an ST or PP of functional requirements not contained in CC 
- Part 2 and/or assurance requirements not contained in CC Part 3\<close>
-
-Definition* [extnl_ent_def, tag="''external entity''"] 
- \<open>human or IT entity possibly interacting with the TOE from outside of the TOE boundary\<close>
-
-Definition* [fmly_def, tag="''family''"] 
- \<open>set of components that share a similar goal but differ in emphasis or rigour\<close>
-
-Definition* [fml_def, tag="''formal''"] 
- \<open>expressed in a restricted syntax language with defined semantics
-  based on well-established mathematical concepts \<close>
-
-Definition* [gudn_doc_def, tag="''guidance documentation''"] 
-\<open>documentation that describes the delivery, preparation, operation, 
- management and/or use of the TOE\<close>
-
-Definition* [ident_def, tag="''identity''"]
-\<open>representation uniquely identifying entities (e.g. a user, a process or a disk) 
- within the context of the TOE
-
- An example of such a representation is a string. For a human user, the
- representation can be the full or abbreviated name or a (still unique)
- pseudonym.\<close>
-
-Definition* [infml_def, tag="''informal''"] 
-  \<open>expressed in natural language\<close>
-
-Definition* [intr_tsf_trans_def, tag ="''inter TSF transfers''"] 
-  \<open>communicating data between the TOE and the security functionality of 
-   other trusted IT products\<close>
-
-Definition* [intl_com_chan_def, tag ="''internal communication channel''"] 
-  \<open>communication channel between separated parts of the TOE\<close>
-
-Definition* [int_toe_trans, tag="''internal TOE transfer''"] 
-  \<open>communicating data between separated parts of the TOE\<close>
-
-Definition* [inter_consistDef, tag="''internally consistent''"] 
-  \<open>no apparent contradictions exist between any aspects of an entity
-
-   In terms of documentation, this means that there can be no statements within
-   the documentation that can be taken to contradict each other.\<close>
-
-Definition* [iter_def, tag="''iteration''"] 
-  \<open>use of the same component to express two or more distinct requirements\<close>
-
-Definition* [jstfct_def, tag="''justification''"] 
-\<open>analysis leading to a conclusion “Justification” is more rigorous than a demonstration. 
-This term requires significant rigour in terms of very carefully and thoroughly explaining every
-step of a logical argument.\<close>
-
-Definition* [objct_def, tag="''object''"] 
-\<open>passive entity in the TOE, that contains or receives information,
-and upon which subjects perform operations\<close>
-
-Definition* [op_cc_cmpnt_def, tag ="''operation (on a component of the CC)''"] 
-\<open>modification or repetition of a component
- Allowed operations on components are assignment, iteration, refinement and
- selection.\<close>
-
-Definition* [op_obj_def, tag= "''operation (on an object)''"] 
-  \<open>specific type of action performed by a subject on an object\<close>
-
-Definition* [op_env_def, tag= "''operational environment''"] 
-\<open>environment in which the TOE is operated\<close>
-
-Definition* [org_sec_po_def, tag="''organisational security policy''"] 
-\<open>set of security rules, procedures, or guidelines for an organisation
- A policy may pertain to a specific operational environment.\<close>
-
-Definition* [pckg_def, tag="''package''"] 
-\<open>named set of either security functional or security assurance requirements 
- An example of a package is ``EAL 3''.\<close>
-
-Definition* [pp_config_def, tag="''Protection Profile Configuration''"] 
-\<open>Protection Profile composed of Base Protection Profiles and Protection Profile Module\<close>
-
-Definition* [pp_eval_def, tag="''Protection Profile evaluation''"]
-\<open> assessment of a PP against defined criteria \<close>
-
-Definition* [ppDef, tag="''Protection Profile''"] 
-\<open>implementation-independent statement of security needs for a TOE type\<close>
-
-Definition* [ppm_def, tag="''Protection Profile Module''"] 
-\<open>implementation-independent statement of security needs for a TOE type 
-  complementary to one or more Base Protection Profiles\<close>
-
-declare_reference*[tsf_def]
-
-Definition* [prv_def, tag="''prove''"] 
-\<open>show correspondence by formal analysis in its mathematical sense
- It is completely rigorous in all ways. Typically, “prove” is used when there is
- a desire to show correspondence between two @{docitem (unchecked) tsf_def}
- representations at a high level of rigour.\<close>
-
-Definition* [ref_def, tag="''refinement''"] 
-\<open>addition of details to a component\<close>
-
-Definition* [role_def, tag="''role''"] 
-\<open>predefined set of rules establishing the allowed interactions between
- a user and the @{docitem (unchecked) toeDef}\<close>
-
-declare_reference*[sfp_def]
-
-Definition* [scrt_def, tag="''secret''"]
-\<open>information that must be known only to authorised users and/or the
- @{docitem (unchecked) tsf_def} in order to enforce a specific @{docitem (unchecked) sfp_def}\<close>
-
-declare_reference*[sfr_def]
-
-Definition* [sec_stDef, tag="''secure state''"] 
-\<open>state in which the @{docitem (unchecked) tsf_def} data are consistent
-  and the  @{docitem (unchecked) tsf_def} 
- continues correct enforcement of the  @{docitem (unchecked) sfr_def}s\<close>
-
-Definition* [sec_att_def, tag="''security attribute''"] 
-\<open>property of subjects, users (including external IT products), objects, 
- information, sessions and/or resources that is used in defining the @{docitem (unchecked) sfr_def}s 
- and whose values are used in enforcing the @{docitem (unchecked) sfr_def}s\<close>
-
-Definition* [sec_def, tag="''security''"]
-\<open>function policy set of rules describing specific security behaviour enforced 
- by the @{docitem (unchecked) tsf_def} and expressible as a set of @{docitem (unchecked) sfr_def}s\<close>
-
-Definition* [sec_obj_def, tag="''security objective''"] 
-\<open>statement of an intent to counter identified threats and/or satisfy identified 
- organisation security policies and/or assumptions\<close>
-
-Definition* [sec_prob_def, tag ="''security problem''"] 
-\<open>statement which in a formal manner defines the nature and scope of the security that 
-the TOE is intended to address This statement consists of a combination of:
-\begin{itemize}
-\item threats to be countered by the TOE and its operational environment,
-\item the OSPs enforced by the TOE and its operational environment, and
-\item the assumptions that are upheld for the operational environment of the TOE.
-\end{itemize}\<close>
-
-Definition* [sr_def, tag="''security requirement''", short_tag="Some(''SR'')"] 
-\<open>requirement, stated in a standardised language, which is meant to contribute 
- to achieving the security objectives for a TOE\<close>
-(*<*)
-text \<open>@{docitem  (unchecked) toeDef}\<close>
-(*>*)
-Definition* [st, tag="''Security Target''", short_tag="Some(''ST'')"]
-\<open>implementation-dependent statement of security needs for a specific identified
- @{docitem (unchecked) toeDef}\<close>
-
-Definition* [slct_def, tag="''selection''"] 
-\<open>specification of one or more items from a list in a component\<close>
-
-Definition* [smfrml_def, tag="''semiformal''"] 
-\<open>expressed in a restricted syntax language with defined semantics\<close>
-
-Definition* [spcfy_def, tag= "''specify''"] 
-\<open>provide specific details about an entity in a rigorous and precise manner\<close>
-
-Definition* [strct_conf_def, tag="''strict conformance''"] 
-\<open>hierarchical relationship between a PP and an ST where all the requirements in the 
- PP also exist in the ST
- 
- This relation can be roughly defined as “the ST shall contain all statements
- that are in the PP, but may contain more”. Strict conformance is expected to
- be used for stringent requirements that are to be adhered to in a single
- manner. \<close>
-
-Definition* [st_eval_def, tag="''ST evaluation''"]
-\<open>assessment of an ST against defined criteria\<close>
-
-Definition* [subj_def, tag="''subject''"]
-\<open>active entity in the TOE that performs operations on objects\<close>
-
-Definition* [toe, tag= "''target of evaluation''"]
-\<open>set of software, firmware and/or hardware possibly accompanied by guidance\<close>
-
-Definition* [thrt_agnt_def, tag="''threat agent''"] 
-\<open>entity that can adversely act on assets\<close>
-
-Definition* [toe_eval_def, tag="''TOE evaluation''"] 
-\<open>assessment of a TOE against defined criteria\<close>
-
-Definition* [toe_res_def, tag="''TOE resource''"] 
-\<open>anything useable or consumable in the TOE\<close>
-
-Definition* [toe_sf_def, tag="''TOE security functionality''", short_tag= "Some(''TSF'')"] 
-\<open>combined functionality of all hardware, software, and firmware of a TOE that must be relied upon 
- for the correct enforcement of the @{docitem  (unchecked) sfr_def}s\<close>
-
-Definition* [tr_vrb_def, tag="''trace, verb''"] 
-\<open>perform an informal correspondence analysis between two entities with only a 
- minimal level of rigour\<close>
-
-Definition* [trnsfs_out_toeDef, tag="''transfers outside of the TOE''"] 
-\<open>TSF mediated communication of data to entities not under the control of the TSF\<close>
-
-Definition* [transl_def, tag= "''translation''"]
-\<open> describes the process of describing security requirements in a
- standardised language.
-
-use of the term translation in this context is not literal and does not imply
-that every SFR expressed in standardised language can also be translated
-back to the security objectives.\<close>
-
-Definition* [trst_chan_def, tag="''trusted channel''"] 
-\<open>a means by which a TSF and another trusted IT product
- can communicate with necessary confidence\<close>
-
-Definition* [trst_it_prod_def, tag="''trusted IT product''"] 
-\<open>IT product, other than the TOE, which has its security functional requirements administratively coordinated with the TOE
- and which is assumed to enforce its security functional requirements correctly
- An example of a trusted IT product would be one that has been separately
- evaluated.\<close>
-
-Definition* [trst_path_def, tag="''trusted path''"] 
-\<open>means by which a user and a TSF can communicate with the necessary confidence\<close>
-
-Definition* [tsf_data_def, tag="''TSF data''"] 
-\<open>data for the operation of the TOE upon which the enforcement of the SFR relies\<close>
-
-Definition* [tsf_intrfc_def, tag="''TSF interface''"] 
-\<open>means by which external entities (or subjects in the TOE but outside of the TSF) 
- supply data to the TSF, receive data from the TSF and invoke services from the TSF\<close>
-
-Definition* [usr_def, tag="''user''"] \<open>see external entity\<close>
-
-Definition* [usr_datat_def, tag="''user data''"] 
-\<open>data for the user, that does not affect the operation of the TSF\<close>
-
-Definition* [vrfy_def, tag="''verify''"] 
-\<open>rigorously review in detail with an independent determination of
-sufficiency
-Also see “confirm”. This term has more rigorous connotations. The term
-“verify” is used in the context of evaluator actions where an independent
-effort is required of the evaluator.\<close>
-
-Definition* [dev_def, tag="''Developer''"]
-\<open>who respond to actual or perceived consumer security requirements in 
- constructing a @{docitem  (unchecked) toeDef}, reference this  CC\_Part\_3 
- when interpreting statements of assurance requirements and determining
- assurance approaches of @{docitem toe}s.\<close>
-
-Definition*[evalu_def, tag="'' Evaluator''"]
-\<open>who use the assurance requirements defined in CC\_Part\_3 
- as mandatory statement of evaluation criteria when determining the assurance 
- of @{docitem  (unchecked) toeDef}s and when evaluating @{docitem ppDef}s
- and @{docitem  (unchecked) stDef}s.\<close>
-
-
-Definition*[toeDef] \<open>\<close>
-Definition*[sfrs_def] \<open>\<close>
-Definition*[sfr_def] \<open>\<close>
-Definition*[stDef] \<open>\<close>
-Definition*[sfp_def] \<open>\<close>
-Definition*[tsf_def] \<open>\<close>
-
-end

Isabelle_DOF-Ontologies/CC_v3_1_R5/CC_v3_1_R5.thy

@@ -1,175 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2022 The University of Exeter 
- *               2019-2022 The University of Paris-Saclay
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-section\<open>CC 3.1.R5\<close>
-(*<*)
-theory  "CC_v3_1_R5"
-  imports 
- "Isabelle_DOF.technical_report" 
-           "CC_terminology"
-
-
-begin
-(*>*)
-
-subsection \<open>General Infrastructure on CC Evaluations\<close>
-
-datatype EALs = EAL1 |  EAL2 |  EAL3 |  EAL4 |  EAL5 |  EAL6 | EAL7
-
-doc_class CC_structure_element =(* text_element + *)
-          tag_id :: string
-          eval_level :: EALs
-
-doc_class CC_text_element = text_element +
-          eval_level :: EALs
-
-subsection \<open>Security target ontology\<close>
-
-
-doc_class st_ref_cls = CC_text_element +
-    title    :: string
-    st_version:: "(int \<times> int \<times> int)"
-    "authors":: "author list"
-    "st_date"   :: string
-
-doc_class toe_ref_cls = CC_text_element +
-    dev_name:: string
-    toe_name:: string
-    toe_version:: "(int \<times> int \<times> int)"
-    prod_name::"string option" <= None
-
-
-doc_class toe_ovrw_cls = CC_text_element +
-    toe_type     :: string
-    software_req :: "CC_text_element list" <= "[]"
-    hardware_req :: "CC_text_element list" <= "[]" 
-    firmeware_req:: "CC_text_element list" <= "[]"
-    features_req :: "CC_text_element list" <= "[]"
-    invariant  eal_consistency:: 
-                 "(case eval_level \<sigma>  of 
-                           EAL1 \<Rightarrow> software_req  \<sigma> \<noteq> [] 
-                      |    EAL2 \<Rightarrow> software_req  \<sigma> \<noteq> [] 
-                      |    EAL3 \<Rightarrow> software_req  \<sigma> \<noteq> [] 
-                      |    EAL4 \<Rightarrow> software_req  \<sigma> \<noteq> [] 
-                      |    _ \<Rightarrow>  undefined)"
-
-thm eal_consistency_inv_def
-
-doc_class toe_desc_cls = CC_text_element +
-    software_list    :: "CC_text_element list" <= "[]"
-    hardware_list    :: "CC_text_element list" <= "[]" 
-    firmeware_list   :: "CC_text_element list" <= "[]"
-    sec_features_list:: "CC_text_element list" <= "[]"
-  
-doc_class ST_INTRO_MNT = CC_structure_element +
-    tag_id:: string
-    accepts "\<lbrace>st_ref_cls\<rbrace>\<^sup>* ~~ \<lbrace>toe_ref_cls\<rbrace>\<^sup>* ~~ \<lbrace>toe_ovrw_cls\<rbrace>\<^sup>* ~~ \<lbrace>toe_desc_cls\<rbrace>\<^sup>*"
-
-doc_class cc_conf_claim_cls = CC_text_element +
-    cc_version:: string
-    ext_srs_list::"CC_text_element list option"
-   
-doc_class pp_clms_cls = CC_text_element +
-    pp_pckgs_list::"CC_text_element list option"
-    pp_config_list::"CC_text_element list option"
-
-doc_class pckg_claim_cls = CC_text_element +
-    pckgs_list::"CC_text_element list option"
-
-doc_class conf_ratio =
-    pp_config_list::"CC_text_element list option"
-
-doc_class CONF_CLAIMS_MNT = CC_structure_element +
-    tag_id:: string
-    accepts "(\<lbrace>cc_conf_claim_cls\<rbrace>\<^sup>+ ~~ \<lbrace>pp_clms_cls\<rbrace>\<^sup>* ~~ \<lbrace>pckg_claim_cls\<rbrace>\<^sup>+ ~~ \<lbrace>conf_ratio\<rbrace>\<^sup>*)"
- 
-doc_class threats_cls = CC_text_element +
-    toe_thrts_list::"CC_text_element list option"
-    env_thrts_list::"CC_text_element list option"
-    thrt_agnts_list:: "CC_text_element list option"
-    advrt_acts_list:: "CC_text_element list option"
-    assts_list:: "CC_text_element list option"
-
-doc_class osps_cls = CC_text_element +
-    toe_osps_list::"CC_text_element list option"
-    env_osps_list::"CC_text_element list option"
-
-doc_class assumptions_cls = CC_text_element +
-    assms_phy_list::"CC_text_element list option"
-    assms_prsnl_list::"CC_text_element list option"
-    assms_cnct_list::"CC_text_element list option"
-
-doc_class SEC_PROB_DEF_MNT = CC_structure_element +
-  tag_id:: string
-  accepts "((\<lbrace>threats_cls\<rbrace>\<^sup>+ || \<lbrace>osps_cls\<rbrace>\<^sup>+) ~~ \<lbrace>assumptions_cls\<rbrace>\<^sup>+)"
-
-doc_class toe_sec_obj_cls = CC_text_element +
-  toe_obj_list:: "CC_text_element list"
-
-doc_class env_sec_obj_cls = CC_text_element +
-  env_goals_list:: "CC_text_element list"
-  env_sites_list :: "CC_text_element list"
-
-doc_class sec_obj_ratio =
-  toe_thrts_obj_trace::"((threats_cls \<times> toe_sec_obj_cls) list) option"
-  toe_osps_obj_trace::"((osps_cls \<times> toe_sec_obj_cls) list) option"
-  toe_assms_obj_trace::"((assumptions_cls \<times> toe_sec_obj_cls) list) option"
-  env_thrts_obj_trace::"((threats_cls \<times> toe_sec_obj_cls) list) option"
-  env_osps_obj_trace::"((osps_cls \<times> toe_sec_obj_cls) list) option"
-  env_assms_obj_trace::"((assumptions_cls \<times> toe_sec_obj_cls) list) option"
-  toe_thrts_just_list::"(CC_text_element list) option"
-  toe_osps_just_list::"(CC_text_element list) option"
-  toe_assms_just_list::"CC_text_element list"
-  env_thrts_just_list::"(CC_text_element list) option"
-  env_osps_just_list::"(CC_text_element list) option"
-  env_assms_just_list::"CC_text_element list"
-
-doc_class ext_comp_def =
-  ext_comp_list::"(CC_text_element list) option"
-
-doc_class SEC_OBJ_MNT = CC_structure_element +
-  tag_id:: string
-  accepts "(\<lbrace>toe_sec_obj_cls\<rbrace>\<^sup>+ ~~ \<lbrace>env_sec_obj_cls\<rbrace>\<^sup>+ ~~ \<lbrace>sec_obj_ratio\<rbrace>\<^sup>*~~ \<lbrace>ext_comp_def\<rbrace>\<^sup>*)"
-
-
-doc_class sfrs_cls = CC_text_element +
-  sfrs_language::"string"
-  sfrs_operation::"CC_text_element"
-  sfrs_dependency::"CC_text_element list option"
-
-doc_class sfrs_ratio_cls = CC_text_element +
-  toe_sec_obj_sfrs_trace:: "(sfrs_cls \<times> toe_sec_obj_cls) list"
-  toe_sec_obj_sfrs_just::"CC_text_element list option"
-
-doc_class sars_cls = CC_text_element +
-  sars_language::"string"
-  sars_operation::"CC_text_element"
-  sars_dependency::"CC_text_element list option"
-
-doc_class sars_ratio_cls = CC_text_element +
-  sars_explain::"CC_text_element list"
-
-doc_class SEC_REQ_MNT =
-  spd_id:: string
-  accepts "(\<lbrace>sfrs_cls\<rbrace>\<^sup>+ ~~ \<lbrace>sfrs_ratio_cls\<rbrace>\<^sup>+ ~~ \<lbrace>sars_cls\<rbrace>\<^sup>+ ~~ \<lbrace>sars_ratio_cls\<rbrace>\<^sup>+)"
-
-doc_class ST_MNT = CC_structure_element +
-   tag_id :: string
-   level :: EALs
-   accepts "(ST_INTRO_MNT  ~~
-             CONF_CLAIMS_MNT ~~
-             SEC_PROB_DEF_MNT ~~
-             SEC_OBJ_MNT ~~
-             SEC_REQ_MNT)"
-
-
-end

Isabelle_DOF-Ontologies/CC_v3_1_R5/DOF-CC_terminology.sty

@@ -1,57 +0,0 @@
-%% Copyright (C) University of Exeter
-%%               University of Paris-Saclay
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1.3c of the License, or (at your option) any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
-
-\NeedsTeXFormat{LaTeX2e}\relax
-\ProvidesPackage{DOF-CC_terminology}
-  [00/00/0000 Document-Type Support Framework for Isabelle (CC).]
-
-\RequirePackage{DOF-COL}
-\usepackage{etex}
-\ifdef{\reserveinserts}{\reserveinserts{28}}{}
-
-
-
-
-\newkeycommand*{\mathcc}[label=,type=%
- , scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTshortUNDERSCOREname ={}%
- , scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc     = % 
- , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel         =%
- , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTreferentiable =%
- , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTvariants      =%
- , scholarlyUNDERSCOREpaperDOTtextUNDERSCOREsectionDOTmainUNDERSCOREauthor  =%
- , scholarlyUNDERSCOREpaperDOTtextUNDERSCOREsectionDOTfixmeUNDERSCORElist   =%
- , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel                =%
- , scholarlyUNDERSCOREpaperDOTtechnicalDOTdefinitionUNDERSCORElist =%
- , scholarlyUNDERSCOREpaperDOTtechnicalDOTstatus          =%
- , CCUNDERSCOREterminologyDOTconceptUNDERSCOREdefinitionDOTtag=%
- , CCUNDERSCOREterminologyDOTconceptUNDERSCOREdefinitionDOTshortUNDERSCOREtag=%
- ]
- [1]
- {%
-    \begin{isamarkuptext}%
-      \ifthenelse{\equal{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTshortUNDERSCOREname}} {} }  
-        {%
-         \begin{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}\label{\commandkey{label}}
-           #1
-         \end{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}
-        }{%
-         \begin{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}[\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTshortUNDERSCOREname}]\label{\commandkey{label}} 
-           #1 
-         \end{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}
-        }
-    \end{isamarkuptext}%
- } 
-
-\expandafter\def\csname isaDofDOTtextDOTscholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent\endcsname{\mathcc}
-
-

Isabelle_DOF-Ontologies/CENELEC_50128/CENELEC_50128_Documentation.thy

@@ -1,397 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2023      The University of Exeter 
- *               2018-2023 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-(*<<*)  
-theory 
-  CENELEC_50128_Documentation
-  imports  
-  CENELEC_50128
-           
-begin
-
-define_shortcut* dof     \<rightleftharpoons> \<open>\dof\<close>
-                 isadof  \<rightleftharpoons> \<open>\isadof{}\<close>
-define_shortcut* TeXLive \<rightleftharpoons> \<open>\TeXLive\<close>
-                 BibTeX  \<rightleftharpoons> \<open>\BibTeX{}\<close> 
-                 LaTeX   \<rightleftharpoons> \<open>\LaTeX{}\<close>
-                 TeX     \<rightleftharpoons> \<open>\TeX{}\<close>
-                 pdf     \<rightleftharpoons> \<open>PDF\<close>
-
-ML\<open>
-
-fun boxed_text_antiquotation name (* redefined in these more abstract terms *) =
-    DOF_lib.gen_text_antiquotation name DOF_lib.report_text
-                           (fn ctxt => DOF_lib.string_2_text_antiquotation ctxt
-                                       #> DOF_lib.enclose_env false ctxt "isarbox")
-
-val neant = K(Latex.text("",\<^here>))
-
-fun boxed_theory_text_antiquotation name (* redefined in these more abstract terms *) =
-    DOF_lib.gen_text_antiquotation name DOF_lib.report_theory_text
-                           (fn ctxt => DOF_lib.string_2_theory_text_antiquotation ctxt
-                                        #> DOF_lib.enclose_env false ctxt "isarbox"
-                                        (* #> neant *)) (*debugging *)
-
-fun boxed_sml_text_antiquotation name  =
-    DOF_lib.gen_text_antiquotation name (K(K()))
-                           (fn ctxt => Input.source_content
-                                        #> Latex.text
-                                        #> DOF_lib.enclose_env true ctxt "sml")
-                           (* the simplest conversion possible *)
-
-fun boxed_pdf_antiquotation name =
-    DOF_lib.gen_text_antiquotation name (K(K()))
-                           (fn ctxt => Input.source_content
-                                        #> Latex.text
-                                        #> DOF_lib.enclose_env true ctxt "out")
-                           (* the simplest conversion possible *)
-
-fun boxed_latex_antiquotation name =
-    DOF_lib.gen_text_antiquotation name (K(K()))
-                           (fn ctxt => Input.source_content
-                                        #> Latex.text
-                                        #> DOF_lib.enclose_env true ctxt "ltx")
-                           (* the simplest conversion possible *)
-
-fun boxed_bash_antiquotation name =
-    DOF_lib.gen_text_antiquotation name (K(K()))
-                           (fn ctxt => Input.source_content
-                                        #> Latex.text
-                                        #> DOF_lib.enclose_env true ctxt "bash")
-                           (* the simplest conversion possible *)
-\<close>
-
-setup\<open>(* std_text_antiquotation        \<^binding>\<open>my_text\<close> #> *)
-      boxed_text_antiquotation         \<^binding>\<open>boxed_text\<close> #>
-      (* std_text_antiquotation        \<^binding>\<open>my_cartouche\<close> #> *)
-      boxed_text_antiquotation         \<^binding>\<open>boxed_cartouche\<close> #>
-      (* std_theory_text_antiquotation \<^binding>\<open>my_theory_text\<close>#> *)
-      boxed_theory_text_antiquotation  \<^binding>\<open>boxed_theory_text\<close> #>
-
-      boxed_sml_text_antiquotation     \<^binding>\<open>boxed_sml\<close> #>
-      boxed_pdf_antiquotation          \<^binding>\<open>boxed_pdf\<close> #>
-      boxed_latex_antiquotation        \<^binding>\<open>boxed_latex\<close>#>
-      boxed_bash_antiquotation         \<^binding>\<open>boxed_bash\<close>
-     \<close>
-
-
-
-(*>>*)  
-
-section*[cenelec_onto::example]\<open>Writing Certification Documents \<^boxed_theory_text>\<open>CENELEC_50128\<close>\<close>
-subsection\<open>The CENELEC 50128 Example\<close>
-text\<open> 
-  The ontology \<^verbatim>\<open>CENELEC_50128\<close>\index{ontology!CENELEC\_50128} is a small ontology modeling 
-  documents for a certification following CENELEC 50128~@{cite "boulanger:cenelec-50128:2015"}.
-  The \<^isadof> distribution contains a small example  using the ontology ``CENELEC\_50128'' in 
-  the directory \nolinkurl{examples/CENELEC_50128/mini_odo/}. You can inspect/edit the 
-  integrated source example by either 
-  \<^item> starting Isabelle/jEdit using your graphical user interface (\<^eg>, by clicking on the 
-    Isabelle-Icon provided by the Isabelle installation) and loading the file 
-    \nolinkurl{examples/CENELEC_50128/mini_odo/mini_odo.thy}.
-  \<^item> starting Isabelle/jEdit from the command line by calling:
-
-@{boxed_bash [display]\<open>ë\prompt{\isadofdirn}ë 
-  isabelle jedit examples/CENELEC_50128/mini_odo/mini_odo.thy \<close>}
-\<close>
-text\<open>\<^noindent> Finally, you
-  \<^item>   can build the \<^pdf>-document by calling:
-@{boxed_bash [display]\<open>ë\prompt{\isadofdirn}ë isabelle build mini_odo \<close>}
-\<close>
- 
-subsection\<open>Modeling CENELEC 50128\<close>
-
-text\<open>
-  Documents to be provided in formal certifications (such as CENELEC 
-  50128~@{cite "boulanger:cenelec-50128:2015"} or Common Criteria~@{cite "cc:cc-part3:2006"}) can 
-  much profit from the control of ontological consistency:  a substantial amount of the work
-  of evaluators in formal certification processes consists in  tracing down the links from 
-  requirements over assumptions down to elements of evidence, be it in form of semi-formal 
-  documentation, models, code, or tests.  In a certification process, traceability becomes a major 
-  concern; and providing mechanisms to ensure complete traceability already at the development of 
-  the integrated source can in our view increase the speed and reduce the risk certification 
-  processes. Making the link-structure machine-checkable, be it between requirements, assumptions, 
-  their implementation and their discharge by evidence (be it tests, proofs, or authoritative 
-  arguments), has the potential in our view to decrease the cost of software developments 
-  targeting certifications. 
-
-  As in many other cases, formal certification documents come with an own terminology and pragmatics
-  of what has to be demonstrated and where, and how the traceability of requirements through 
-  design-models over code to system environment assumptions has to be assured.  
-
-  In the sequel, we present a simplified version of an ontological model used in a 
-  case-study~@{cite "bezzecchi.ea:making:2018"}. We start with an introduction of the concept of 
-  requirement:
-
-@{boxed_theory_text [display]\<open>
-doc_class requirement = long_name :: "string option"
-
-doc_class hypothesis = requirement +
-      hyp_type :: hyp_type <= physical  (* default *)
-  
-datatype ass_kind = informal | semiformal | formal
-  
-doc_class assumption = requirement +
-     assumption_kind :: ass_kind <= informal 
-\<close>}
-
-Such ontologies can be enriched by larger explanations and examples, which may help
-the team of engineers substantially when developing the central document for a certification, 
-like an explication of what is precisely the difference between an \<^typ>\<open>hypothesis\<close> and an 
-\<^typ>\<open>assumption\<close> in the context of the evaluation standard. Since the PIDE makes for each 
-document class its definition available by a simple mouse-click, this kind on meta-knowledge 
-can be made far more accessible during the document evolution.
-
-For example, the term of category \<^typ>\<open>assumption\<close> is used for domain-specific assumptions. 
-It has \<^const>\<open>formal\<close>, \<^const>\<open>semiformal\<close> and \<^const>\<open>informal\<close> sub-categories. They have to be 
-tracked and discharged by appropriate validation procedures within a 
-certification process, be it by test or proof. It is different from a \<^typ>\<open>hypothesis\<close>, which is
-globally assumed and accepted.
-
-In the sequel, the category \<^typ>\<open>exported_constraint\<close> (or \<^typ>\<open>EC\<close> for short)
-is used for formal assumptions, that arise during the analysis,
-design or implementation and have to be tracked till the final
-evaluation target, and discharged by appropriate validation procedures 
-within the certification process, be it by test or proof.  A particular class of interest 
-is the category \<^typ>\<open>safety_related_application_condition\<close> (or \<^typ>\<open>SRAC\<close> 
-for short) which is used for \<^typ>\<open>EC\<close>'s that establish safety properties
-of the evaluation target. Their traceability throughout the certification
-is therefore particularly critical. This is naturally modeled as follows:
-@{boxed_theory_text [display]\<open>  
-doc_class EC = assumption  +
-     assumption_kind :: ass_kind <= (*default *) formal
-                        
-doc_class SRAC = EC  +
-     assumption_kind :: ass_kind <= (*default *) formal
-\<close>}
-
-We now can, \<^eg>, write 
-
-@{boxed_theory_text [display]\<open>
-text*[ass123::SRAC]\<open> 
-  The overall sampling frequence of the odometer subsystem is therefore 
-  14 khz, which includes sampling, computing and result communication 
-  times \ldots
-\<close>
-\<close>}
-
-This will be shown in the \<^pdf> as follows:
-\<close>
-text*[ass123::SRAC] \<open> The overall sampling frequency of the odometer
-subsystem is therefore 14 khz, which includes sampling, computing and
-result communication times \ldots \<close>
-
-text\<open>Note that this \<^pdf>-output is the result of a specific setup for \<^typ>\<open>SRAC\<close>s.\<close>
-
-subsection*[ontopide::technical]\<open>Editing Support for CENELEC 50128\<close>  
-figure*[figfig3::figure,relative_width="95",file_src="''figures/antiquotations-PIDE.png''"]
-\<open> Standard antiquotations referring to theory elements.\<close>
-text\<open> The corresponding view in @{docitem  \<open>figfig3\<close>} shows core part of a document 
-conforming to the \<^verbatim>\<open>CENELEC_50128\<close> ontology. The first sample shows standard Isabelle antiquotations 
-@{cite "wenzel:isabelle-isar:2020"} into formal entities of a theory. This way, the informal parts 
-of a document get ``formal content'' and become more robust under change.\<close>
-
-figure*[figfig5::figure, relative_width="95", file_src="''figures/srac-definition.png''"]
-        \<open> Defining a \<^typ>\<open>SRAC\<close> in the integrated source ... \<close>
-
-figure*[figfig7::figure, relative_width="95", file_src="''figures/srac-as-es-application.png''"]
-        \<open> Using a \<^typ>\<open>SRAC\<close> as \<^typ>\<open>EC\<close> document element. \<close>
-text\<open> The subsequent sample in @{figure \<open>figfig5\<close>} shows the definition of a
-\<^emph>\<open>safety-related application condition\<close>, a side-condition of a theorem which 
-has the consequence that a certain calculation must be executed sufficiently fast on an embedded 
-device. This condition can not be established inside the formal theory but has to be 
-checked by system integration tests. Now we reference in @{figure  \<open>figfig7\<close>} this 
-safety-related condition; however, this happens in a context where general \<^emph>\<open>exported constraints\<close> 
-are listed. \<^isadof>'s checks and establishes that this is legal in the given ontology. 
-\<close>    
-
-text\<open>
-\<^item> \<^theory_text>\<open>@{term_ \<open>term\<close> }\<close> parses and type-checks \<open>term\<close> with term antiquotations,
-  for instance \<^theory_text>\<open>@{term_ \<open>@{cenelec-term \<open>FT\<close>}\<close>}\<close> will parse and check
-  that \<open>FT\<close> is indeed an instance of the class \<^typ>\<open>cenelec_term\<close>,
-\<close>
-
-subsection\<open>A Domain-Specific Ontology: \<^verbatim>\<open>CENELEC_50128\<close>\<close>
-(*<*)
-ML\<open>val toLaTeX = String.translate (fn c => if c = #"_" then "\\_" else String.implode[c])\<close>     
-ML\<open>writeln (DOF_core.print_doc_class_tree 
-                 @{context} (fn (n,l) =>  true (*     String.isPrefix "technical_report" l 
-                                         orelse String.isPrefix "Isa_COL" l *)) 
-                 toLaTeX)\<close>
-(*>*)
-text\<open> The \<^verbatim>\<open>CENELEC_50128\<close> ontology in \<^theory>\<open>Isabelle_DOF-Ontologies.CENELEC_50128\<close>
-is an example of a domain-specific ontology.
-It is based on  \<^verbatim>\<open>technical_report\<close> since we assume that this kind of format will be most
-appropriate for this type of long-and-tedious documents,
-
-%
-\begin{center}
-\begin{minipage}{.9\textwidth}\footnotesize
-\dirtree{%
-.0 .
-.1 CENELEC\_50128.judgement\DTcomment{...}.
-.1 CENELEC\_50128.test\_item\DTcomment{...}.
-.2 CENELEC\_50128.test\_case\DTcomment{...}.
-.2 CENELEC\_50128.test\_tool\DTcomment{...}.
-.2 CENELEC\_50128.test\_result\DTcomment{...}.
-.2 CENELEC\_50128.test\_adm\_role\DTcomment{...}.
-.2 CENELEC\_50128.test\_environment\DTcomment{...}.
-.2 CENELEC\_50128.test\_requirement\DTcomment{...}.
-.2 CENELEC\_50128.test\_specification\DTcomment{...}.
-.1 CENELEC\_50128.objectives\DTcomment{...}.
-.1 CENELEC\_50128.design\_item\DTcomment{...}.
-.2 CENELEC\_50128.interface\DTcomment{...}.
-.1 CENELEC\_50128.sub\_requirement\DTcomment{...}.
-.1 CENELEC\_50128.test\_documentation\DTcomment{...}.
-.1 Isa\_COL.text\_element\DTcomment{...}.
-.2 CENELEC\_50128.requirement\DTcomment{...}.
-.3 CENELEC\_50128.TC\DTcomment{...}.
-.3 CENELEC\_50128.FnI\DTcomment{...}.
-.3 CENELEC\_50128.SIR\DTcomment{...}.
-.3 CENELEC\_50128.CoAS\DTcomment{...}.
-.3 CENELEC\_50128.HtbC\DTcomment{...}.
-.3 CENELEC\_50128.SILA\DTcomment{...}.
-.3 CENELEC\_50128.assumption\DTcomment{...}.
-.4 CENELEC\_50128.AC\DTcomment{...}.
-.5 CENELEC\_50128.EC\DTcomment{...}.
-.6 CENELEC\_50128.SRAC\DTcomment{...}.
-.3 CENELEC\_50128.hypothesis\DTcomment{...}.
-.4 CENELEC\_50128.security\_hyp\DTcomment{...}.
-.3 CENELEC\_50128.safety\_requirement\DTcomment{...}.
-.2 CENELEC\_50128.cenelec\_text\DTcomment{...}.
-.3 CENELEC\_50128.SWAS\DTcomment{...}.
-.3 [...].
-.2 scholarly\_paper.text\_section\DTcomment{...}.
-.3 scholarly\_paper.technical\DTcomment{...}.
-.4 scholarly\_paper.math\_content\DTcomment{...}.
-.5 CENELEC\_50128.semi\_formal\_content\DTcomment{...}.
-.1 ...
-}
-\end{minipage}
-\end{center}
-\<close>
-
-(* TODO : Rearrange ontology hierarchies. *)
-
-subsubsection\<open>Examples\<close>
-
-text\<open>
-The category ``exported constraint (EC)'' is, in the file 
-\<^file>\<open>CENELEC_50128.thy\<close> defined as follows:
-
-@{boxed_theory_text [display]\<open>
-doc_class requirement = text_element +
-   long_name    :: "string option"
-   is_concerned :: "role set"
-doc_class assumption = requirement +
-     assumption_kind :: ass_kind <= informal 
-doc_class AC = assumption +
-   is_concerned :: "role set" <= "UNIV"
-doc_class EC = AC  +
-     assumption_kind :: ass_kind <= (*default *) formal
-\<close>}
-\<close>
-text\<open>
-We now define the document representations, in the file 
-\<^file>\<open>DOF-CENELEC_50128.sty\<close>. Let us assume that we want to 
-register the definition of EC's in a dedicated table of contents (\<^boxed_latex>\<open>tos\<close>) 
-and use an earlier defined environment \inlineltx|\begin{EC}...\end{EC}| for their graphical 
-representation. Note that the \inlineltx|\newisadof{}[]{}|-command requires the 
-full-qualified names, \<^eg>, \<^boxed_theory_text>\<open>text.CENELEC_50128.EC\<close> for the document class and 
-\<^boxed_theory_text>\<open>CENELEC_50128.requirement.long_name\<close> for the  attribute \<^const>\<open>long_name\<close>, 
-inherited from the document class \<^typ>\<open>requirement\<close>. The representation of \<^typ>\<open>EC\<close>'s
-can now be defined as follows:
-% TODO:
-% Explain the text qualifier of the long_name text.CENELEC_50128.EC
-
-\begin{ltx}
-\newisadof{text.CENELEC_50128.EC}%
-[label=,type=%
-,Isa_COL.text_element.level=%
-,Isa_COL.text_element.referentiable=%
-,Isa_COL.text_element.variants=%
-,CENELEC_50128.requirement.is_concerned=%
-,CENELEC_50128.requirement.long_name=%
-,CENELEC_50128.EC.assumption_kind=][1]{%
-\begin{isamarkuptext}%
-   \ifthenelse{\equal{\commandkey{CENELEC_50128.requirement.long_name}}{}}{%
-      % If long_name is not defined, we only create an entry in the table tos
-      % using the auto-generated number of the EC 
-      \begin{EC}%
-          \addxcontentsline{tos}{chapter}[]{\autoref{\commandkey{label}}}%
-    }{%
-      % If long_name is defined, we use the long_name as title in the 
-      % layout of the EC, in the table "tos" and as index entry. .
-      \begin{EC}[\commandkey{CENELEC_50128.requirement.long_name}]%
-        \addxcontentsline{toe}{chapter}[]{\autoref{\commandkey{label}}: %
-              \commandkey{CENELEC_50128.requirement.long_name}}%
-        \DOFindex{EC}{\commandkey{CENELEC_50128.requirement.long_name}}%
-    }%
-    \label{\commandkey{label}}% we use the label attribute as anchor 
-    #1% The main text of the EC
-  \end{EC}
-\end{isamarkuptext}%
-}
-\end{ltx}
-\<close>
-text\<open>
-  For example, the @{docitem "ass123"} is mapped to
-
-@{boxed_latex [display]
-\<open>\begin{isamarkuptext*}%
-[label = {ass122},type = {CENELEC_50128.SRAC}, 
- args={label = {ass122}, type = {CENELEC_50128.SRAC}, 
-       CENELEC_50128.EC.assumption_kind = {formal}}
-] The overall sampling frequence of the odometer subsystem is therefore 
- 14 khz, which includes sampling, computing and result communication 
- times ...
-\end{isamarkuptext*}\<close>}
-
-This environment is mapped to a plain \<^LaTeX> command via:
-@{boxed_latex [display]
-\<open> \NewEnviron{isamarkuptext*}[1][]{\isaDof[env={text},#1]{\BODY}} \<close>}
-\<close>
-text\<open>
-For the command-based setup, \<^isadof> provides a dispatcher that selects the most specific 
-implementation for a given \<^boxed_theory_text>\<open>doc_class\<close>:
-
-@{boxed_latex [display]
-\<open>%% The Isabelle/DOF dispatcher:
-\newkeycommand+[\|]\isaDof[env={UNKNOWN},label=,type={dummyT},args={}][1]{%
-  \ifcsname isaDof.\commandkey{type}\endcsname%
-      \csname isaDof.\commandkey{type}\endcsname%
-              [label=\commandkey{label},\commandkey{args}]{#1}%
-  \else\relax\fi%
-  \ifcsname isaDof.\commandkey{env}.\commandkey{type}\endcsname%
-      \csname isaDof.\commandkey{env}.\commandkey{type}\endcsname%
-              [label=\commandkey{label},\commandkey{args}]{#1}%
-  \else%
-      \message{Isabelle/DOF: Using default LaTeX representation for concept %
-        "\commandkey{env}.\commandkey{type}".}%
-      \ifcsname isaDof.\commandkey{env}\endcsname%
-         \csname isaDof.\commandkey{env}\endcsname%
-                [label=\commandkey{label}]{#1}%
-      \else%
-      \errmessage{Isabelle/DOF: No LaTeX representation for concept %
-        "\commandkey{env}.\commandkey{type}" defined and no default %
-        definition for "\commandkey{env}" available either.}%
-      \fi%
-  \fi%
-}\<close>}
-\<close>
-
-
-
-(*<<*)  
-end 
-(*>>*)  

Isabelle_DOF-Ontologies/CENELEC_50128/DOF-CENELEC_50128.sty

@@ -1,220 +0,0 @@
-%% Copyright (C) 2019 University of Exeter
-%%               2018 University of Paris-Saclay
-%%               2018 The University of Sheffield
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1.3c of the License, or (at your option) any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
-
-\NeedsTeXFormat{LaTeX2e}\relax
-\ProvidesPackage{DOF-cenelec_50128}
-  [00/00/0000 Document-Type Support Framework for Isabelle (CENELEC 50128).]
-
-\RequirePackage{DOF-COL}
-\usepackage{etex}
-\ifdef{\reserveinserts}{\reserveinserts{28}}{} 
-\usepackage[many]{tcolorbox}
-\usepackage{marginnote}
-
-% Index setup
-\usepackage{index}
-\makeindex
-\AtEndDocument{\printindex}
-
-\newcommand{\DOFindex}[2]{%
-  \marginnote{\normalfont\textbf{#1}: #2}%
-  \expandafter\index\expandafter{\expanded{#2 (#1)}}%
-}%
-
-
-%% SRAC
-\providecolor{SRAC}{named}{green}
-\ifcsdef{DeclareNewTOC}{%
-  \DeclareNewTOC[%
-    owner=\jobname,
-    type=SRAC,%
-    types=SRACs,%
-    listname={List of SRACs}%
-  ]{tos}
-  \setuptoc{tos}{chapteratlist}
-  \AtEndEnvironment{frontmatter}{\listofSRACs}
-}{}
-
-\newtheorem{SRAC}{SRAC}
-\tcolorboxenvironment{SRAC}{
-  boxrule=0pt
- ,boxsep=0pt
- ,colback={white!90!SRAC}
- ,enhanced jigsaw
- ,borderline west={2pt}{0pt}{SRAC}
- ,sharp corners
- ,before skip=10pt
- ,after skip=10pt
- ,breakable
-}
-
-\newcommand{\SRACautorefname}{SRAC}
-\newisadof{textDOTCENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTSRAC}%
-[label=,type=%
-,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel=%
-,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTreferentiable=%
-,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTvariants=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTisUNDERSCOREconcerned=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTSRACDOTformalUNDERSCORErepr=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTSRACDOTassumptionUNDERSCOREkind=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTECDOTassumptionUNDERSCOREkind=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTassumptionDOTassumptionUNDERSCOREkind=%
-][1]{%
-  \begin{isamarkuptext}%
-      \ifthenelse{\equal{\commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}}{}}{%
-        \begin{SRAC}%
-            \addxcontentsline{tos}{chapter}[]{\autoref{\commandkey{label}}}%
-      }{%
-        \begin{SRAC}[\commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}]%
-          \addxcontentsline{tos}{chapter}[]{\autoref{\commandkey{label}}: \commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}}%
-          \DOFindex{SRAC}{\commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}}%
-      }\label{\commandkey{label}}%
-      #1%
-    \end{SRAC}
-  \end{isamarkuptext}%
-}
-
-% EC
-\providecolor{EC}{named}{blue}
-\ifcsdef{DeclareNewTOC}{%
-  \DeclareNewTOC[%
-    owner=\jobname,
-    type=EC,%
-    types=ECs,%
-    listname={List of ECs}%
-  ]{toe}
-  \setuptoc{toe}{chapteratlist}
-  \AtEndEnvironment{frontmatter}{\listofECs}
-}{}
-
-\newtheorem{EC}{EC}
-\tcolorboxenvironment{EC}{
-  boxrule=0pt
- ,boxsep=0pt
- ,colback={white!90!EC}
- ,enhanced jigsaw
- ,borderline west={2pt}{0pt}{EC}
- ,sharp corners
- ,before skip=10pt
- ,after skip=10pt
- ,breakable
-}
-
-\newcommand{\ECautorefname}{EC}
-\newisadof{textDOTCENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTEC}%
-[label=,type=%
-,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel=%
-,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTreferentiable=%
-,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTvariants=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTisUNDERSCOREconcerned=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTSRACDOTformalUNDERSCORErepr=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTSRACDOTassumptionUNDERSCOREkind=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTECDOTassumptionUNDERSCOREkind=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTassumptionDOTassumptionUNDERSCOREkind=%
-][1]{%
-  \begin{isamarkuptext}%
-      \ifthenelse{\equal{\commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}}{}}{%
-        \begin{EC}%
-            \addxcontentsline{toe}{chapter}[]{\autoref{\commandkey{label}}}%
-      }{%
-        \begin{EC}[\commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}]%
-          \addxcontentsline{toe}{chapter}[]{\autoref{\commandkey{label}}: \commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}}%
-          \DOFindex{EC}{\commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}}%
-      }\label{\commandkey{label}}%
-      #1%
-    \end{EC}
-  \end{isamarkuptext}%
-}
-
-% assumptions
-\providecolor{assumption}{named}{orange}
-\newtheorem{assumption}{assumption}
-\tcolorboxenvironment{assumption}{
-  boxrule=0pt
- ,boxsep=0pt
- ,colback={white!90!assumption}
- ,enhanced jigsaw
- ,borderline west={2pt}{0pt}{assumption}
- ,sharp corners
- ,before skip=10pt
- ,after skip=10pt
- ,breakable
-}
-
-\newcommand{\assumptionautorefname}{assumption}
-\newisadof{textDOTCENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTassumption}%
-[label=,type=%
-,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel=%
-,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTreferentiable=%
-,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTvariants=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTisUNDERSCOREconcerned=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTSRACDOTformalUNDERSCORErepr=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTSRACDOTassumptionUNDERSCOREkind=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTassumptionDOTassumptionUNDERSCOREkind=%
-][1]{%
-  \begin{isamarkuptext}%
-      \ifthenelse{\equal{\commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}}{}}{%
-        \begin{assumption}%
-      }{%
-        \begin{assumption}[\commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}]%
-          \DOFindex{assumption}{\commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}}%
-      }\label{\commandkey{label}}%
-      #1%
-    \end{assumption}
-  \end{isamarkuptext}%
-}
-
-
-% hypotheses
-\providecolor{hypothesis}{named}{teal}
-\newtheorem{hypothesis}{hypothesis}
-\tcolorboxenvironment{hypothesis}{
- ,boxrule=0pt
- ,boxsep=0pt
- ,colback={white!90!hypothesis}
- ,enhanced jigsaw
- ,borderline west={2pt}{0pt}{hypothesis}
- ,sharp corners
- ,before skip=10pt
- ,after skip=10pt
- ,breakable
-}
-
-
-\newcommand{\hypothesisautorefname}{hypothesis}
-\newisadof{textDOTCENELECUNDERSCOREFIVEZEROONETWOEIGHTDOThypothesis}%
-[label=,type=%
-,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel=%
-,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTreferentiable=%
-,IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTvariants=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTisUNDERSCOREconcerned=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTSRACDOTformalUNDERSCORErepr=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTSRACDOThypothesisUNDERSCOREkind=%
-,CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOThypothesisDOThypUNDERSCOREtype=%
-][1]{%
-  \begin{isamarkuptext}%
-      \ifthenelse{\equal{\commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}}{}}{%
-        \begin{hypothesis}%
-      }{%
-        \begin{hypothesis}[\commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}]%
-          \DOFindex{hypothesis}{\commandkey{CENELECUNDERSCOREFIVEZEROONETWOEIGHTDOTrequirementDOTlongUNDERSCOREname}}%
-      }\label{\commandkey{label}}%
-      #1%
-    \end{hypothesis}
-  \end{isamarkuptext}%
-}

Isabelle_DOF-Ontologies/Conceptual/Conceptual.thy

@@ -1,221 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019      The University of Exeter 
- *               2018-2019 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-chapter\<open>A conceptual introduction into DOF and its features:\<close>
-
-theory 
-  Conceptual
-imports 
-  "Isabelle_DOF.Isa_DOF" 
-  "Isabelle_DOF.Isa_COL"
-begin
-
-section\<open>Excursion: On the semantic consequences of this definition: \<close>
-
-text\<open>Consider the following document class definition and its consequences:\<close>
-
-doc_class A =
-   level :: "int option"
-   x :: int
-
-
-text\<open>This class definition leads an implicit Isabelle/HOL  \<^theory_text>\<open>record\<close>  definition 
-(cf. \<^url>\<open>https://isabelle.in.tum.de/doc/isar-ref.pdf\<close>, chapter 11.6.).
-Consequently, \<^theory_text>\<open>doc_class\<close>'es inherit the entire theory-infrastructure from Isabelle records:
-\<^enum> there is a HOL-type \<^typ>\<open>A\<close> and its extensible version \<^typ>\<open>'a A_scheme\<close> 
-\<^enum> there are HOL-terms representing \<^emph>\<open>doc\_class instances\<close> with the high-level syntax:
-    \<^enum> \<^term>\<open>undefined\<lparr>level := Some (1::int), x := 5::int \<rparr> :: A\<close>
-      (Note that this way to construct an instance is not necessarily computable
-    \<^enum> \<^term>\<open>\<lparr>tag_attribute = X, level = Y, x = Z\<rparr> :: A\<close>
-    \<^enum> \<^term>\<open>\<lparr>tag_attribute = X, level = Y, x = Z, \<dots> = M\<rparr> :: ('a A_scheme)\<close>
-\<^enum> there is an entire proof infra-structure allowing to reason about \<^emph>\<open>doc\_class instances\<close>;
-  this involves the constructor, the selectors (representing the  \<^emph>\<open>attributes\<close> in OO lingo)
-  the update functions, the rules to establish equality and, if possible the code generator
-  setups:
-    \<^enum> \<^term>\<open>A.make :: int \<Rightarrow> int option \<Rightarrow> int \<Rightarrow> A\<close>
-    \<^enum> \<^term>\<open>A.level :: 'a A_scheme \<Rightarrow> int option\<close>
-    \<^enum> \<^term>\<open>A.level_update :: (int option \<Rightarrow> int option) \<Rightarrow> 'a A_scheme \<Rightarrow> 'a A_scheme\<close>
-    \<^enum> ...
-  together with the rules such as:
-    \<^enum> @{thm [display] A.simps(2)}
-    \<^enum> @{thm [display] A.simps(6)}
-    \<^enum> ...
-\<close>
-
-text\<open>The generated theory of the \<^theory_text>\<open>doc_class\<close> A can be inspected, of course, by:\<close>  
-find_theorems (60) name:Conceptual name:A
-
-text\<open>A more abstract view on the state of the DOF machine can be found here:\<close>
-
-print_doc_classes
-
-print_doc_items
-
-text\<open>... and an ML-level output:\<close>
-
-ML\<open>
-val docitem_tab = DOF_core.get_instances \<^context>;
-val isa_transformer_tab = DOF_core.get_isa_transformers \<^context>;
-val docclass_tab = DOF_core.get_onto_classes \<^context>;
-
-\<close>
-
-ML\<open>
-Name_Space.dest_table docitem_tab;
-Name_Space.dest_table isa_transformer_tab;
-Name_Space.dest_table docclass_tab;
-\<close>
-text\<open>... or as ML assertion: \<close>
-ML\<open> 
-@{assert} (Name_Space.dest_table docitem_tab = []);
-fun match ("Conceptual.A", (* the long-name *)
-            DOF_core.Onto_Class {params, name, virtual,inherits_from=NONE, 
-                                 attribute_decl, rejectS=[],rex=[], invs=[]}) 
-            = (Binding.name_of name = "A")
-  | match _ = false;
-
-@{assert} (exists match (Name_Space.dest_table docclass_tab))
-\<close>
-
-text\<open>As a consequence of the theory of the \<^theory_text>\<open>doc_class\<close> \<open>A\<close>, the code-generator setup lets us 
-evaluate statements such as: \<close>
-
-value\<open> the(A.level (A.make 3 (Some 4) 5)) = 4\<close>
-
-text\<open>And further, as a consequence of the above semantic construction of \<^theory_text>\<open>doc_class\<close>'es, the internal
-\<open>\<lambda>\<close>-calculus representation of class instances looks as follows:\<close>
-
-ML\<open>
-@{term \<open>the(A.level (A.make 3 (Some 4) 5))\<close>};
-fun match (Const("Option.option.the",_) $ 
-      (Const ("Conceptual.A.level",_) $  
-         (Const ("Conceptual.A.make", _) $ u $ v $ w))) = true
-   |match _ = false;
-@{assert} (match @{term \<open>the(A.level (A.make 3 (Some 4) 5))\<close>})
-\<close>
-
-text\<open>And finally, via the code-generation, we have the following programmable 
-     access to values representing class instances:\<close>
-ML\<open>
-val A_make = @{code A.make};
-val zero   = @{code "0::int"};
-val one    = @{code "1::int"};
-val add    = @{code "(+) :: int \<Rightarrow> int \<Rightarrow> int"};
-
-A_make zero (SOME one) (add one one)
-\<close>
-
-section\<open>Building up a conceptual class hierarchy:\<close>
-
-text\<open>An independent class-tree root: \<close>
-
-doc_class B =
-   level :: "int option"
-   x :: "string"                            (* attributes live in their own name-space *)
-   y :: "string list"          <= "[]"      (* and can have arbitrary type constructors *)
-                                            (* LaTeX may have problems with this, though *)
-
-text\<open>We may even use type-synonyms for class synonyms ...\<close>
-type_synonym XX = B
-
-
-section\<open>Examples of inheritance \<close>
-
-doc_class C = B +                           
-   z :: "A option"             <= None      (* A LINK, i.e. an attribute that has a type
-                                               referring to a document class. Mathematical
-                                               relations over document items can be modeled. *)
-   g :: "thm"                               (* a reference to the proxy-type 'thm' allowing
-                                               to denote references to theorems inside attributes *)
-
-datatype enum = X1 | X2 | X3                (* we add an enumeration type ... *)
-   
-doc_class D = B +
-   x  :: "string"              <= "\<open>def \<longrightarrow>\<close>" (* overriding default *)
-   a1 :: enum                  <= "X2"      (* class - definitions may be mixed 
-                                               with arbitrary HOL-commands, thus 
-                                               also local definitions of enumerations *)
-   a2 :: int                   <= 0
-
-doc_class E = D +
-   x :: "string"              <= "''qed''"  (* overriding default *)
-
-
-
-doc_class F  =     
-   properties  :: "term list"
-   r           :: "thm list"
-   u           :: "file"
-   s           :: "typ list"
-   b           :: "(A \<times> C) set"  <= "{}"       (* This is a relation link, roughly corresponding
-                                                 to an association class. It can be used to track
-                                                 claims to result - relations, for example.*) 
-   b'          :: "(A \<times> C) list"  <= "[]"
-   invariant br :: "r \<sigma> \<noteq> [] \<and> card(b \<sigma>) \<ge> 3"
-        and  br':: "r \<sigma> \<noteq> [] \<and> length(b' \<sigma>) \<ge> 3"
-        and  cr :: "properties \<sigma> \<noteq> []"
-
-text\<open>The effect of the invariant declaration is to provide intern HOL definitions for validation 
-functions of this invariant. They can be referenced as follows:\<close>
-thm br_inv_def
-thm br'_inv_def
-thm cr_inv_def
-
-term "\<lparr>F.tag_attribute = 5, properties = [], r = [], u = undefined, s = [], b = {}, b' = []\<rparr>"
-
-term "br'_inv (\<lparr>F.tag_attribute = 5, properties = [], r = [], u = undefined, s = [], b = {}, b' = []\<rparr>) "
-
-text\<open>Now, we can use these definitions in order to generate code for these validation functions.
-Note, however, that not everything that we can write in an invariant (basically: HOL) is executable,
-or even compilable by the code generator setup:\<close>
-
-ML\<open> val cr_inv_code = @{code "cr_inv"} \<close> \<comment> \<open>works albeit thm is abstract ...\<close>
-text\<open>while in :\<close>
-ML\<open> val br_inv_code = @{code "br_inv"} \<close> \<comment>\<open>this does not work ...\<close> 
-
-text\<open>... the compilation fails due to the fact that nothing prevents the user 
-     to define an infinite relation between \<^typ>\<open>A\<close> and  \<^typ>\<open>C\<close>. However, the alternative
-variant: \<close>
-
-ML\<open> val br'_inv_code = @{code "br'_inv"} \<close> \<comment> \<open>does work ...\<close>
-
-text\<open>... is compilable ...\<close>
-
-doc_class G = C +
-   g :: "thm"  <= "@{thm \<open>HOL.refl\<close>}"  (* warning overriding attribute expected*)
-
-doc_class M = 
-   ok :: "unit"
-   accepts "A ~~ \<lbrace>C || D\<rbrace>\<^sup>* ~~ \<lbrakk>F\<rbrakk>"
-
-text\<open>The final class and item tables look like this:\<close>
-print_doc_classes
-print_doc_items
-
-ML\<open>
-map fst (Name_Space.dest_table (DOF_core.get_onto_classes \<^context>));
-
-let  val class_ids_so_far = ["Conceptual.A", "Conceptual.B", "Conceptual.C", "Conceptual.D", 
-                             "Conceptual.E", "Conceptual.F", "Conceptual.G", "Conceptual.M",
-                             "Isa_COL.float", "Isa_COL.frame", "Isa_COL.figure", "Isa_COL.chapter",
-                             "Isa_COL.listing", "Isa_COL.section", "Isa_COL.paragraph",
-                             "Isa_COL.subsection", "Isa_COL.text_element", "Isa_COL.subsubsection"]
-     val docclass_tab = map fst (Name_Space.dest_table (DOF_core.get_onto_classes \<^context>));
-in @{assert} (class_ids_so_far = docclass_tab) end\<close>
-
-section\<open>For Test and Validation\<close>
-
-text*[sdf]         \<open> Lorem ipsum ... \<close>         \<comment> \<open>anonymous reference\<close>
-text*[sdfg :: F]   \<open> Lorem ipsum ...\<close>          \<comment> \<open>some F instance \<close>  
-
-end

Isabelle_DOF-Ontologies/ROOT

@@ -1,23 +0,0 @@
-session "Isabelle_DOF-Ontologies" = "Isabelle_DOF" + 
-  options  [document = pdf, document_output = "output", document_build = dof]
-  directories
-    "CC_v3_1_R5"
-    "Conceptual"
-    "small_math"
-    "CENELEC_50128"
-  theories
-    "document_setup"
-    "document_templates"
-    "CC_v3_1_R5/CC_v3_1_R5"
-    "CC_v3_1_R5/CC_terminology"  
-    "Conceptual/Conceptual"
-    "small_math/small_math"
-    "CENELEC_50128/CENELEC_50128"
-    "CENELEC_50128/CENELEC_50128_Documentation"
-  document_files
-    "root.bib"
-    "lstisadof-manual.sty"
-    "preamble.tex"
-    "figures/antiquotations-PIDE.png"
-    "figures/srac-as-es-application.png"
-    "figures/srac-definition.png"

Isabelle_DOF-Ontologies/document-templates/root-beamer-UNSUPPORTED.tex

@@ -1,65 +0,0 @@
-%% Copyright (c) University of Exeter
-%%               University of Paris-Saclay
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1.3c of the License, or (at your option) any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
-
-%% Warning: Do Not Edit!
-%% =====================
-%% This is the root file for the Isabelle/DOF using the scrartcl class.
-%%
-%% All customization and/or additional packages should be added to the file
-%% preamble.tex.
-
-\RequirePackage{ifvtex}
-\documentclass[16x9,9pt]{beamer}
-\PassOptionsToPackage{force}{DOF-scholarly_paper}
-\title{No Title Given}
-\usepackage{DOF-core}
-
-\usepackage{textcomp}
-\bibliographystyle{abbrvnat}
-\RequirePackage{subcaption}
-
-\providecommand{\institute}[1]{}%
-\providecommand{\inst}[1]{}%
-\providecommand{\orcidID}[1]{}%
-\providecommand{\email}[1]{}%
-
-
-\usepackage[numbers, sort&compress, sectionbib]{natbib}
-
-\usepackage{hyperref}
-\setcounter{tocdepth}{3} 
-\hypersetup{%
-   bookmarksdepth=3
-  ,pdfpagelabels
-  ,pageanchor=true
-  ,bookmarksnumbered
-  ,plainpages=false
-} % more detailed digital TOC (aka bookmarks)
-\sloppy
-\allowdisplaybreaks[4]
-
-\newenvironment{frontmatter}{}{}
-\raggedbottom
-\begin{document}
-\begin{frame}
-  \maketitle
-\end{frame}
-\IfFileExists{dof_session.tex}{\input{dof_session}}{\input{session}}
-% optional bibliography
-\IfFileExists{root.bib}{{\bibliography{root}}}{}
-\end{document}
-
-%%% Local Variables:
-%%% mode: latex
-%%% TeX-master: t
-%%% End:

Isabelle_DOF-Ontologies/document-templates/root-beamerposter-UNSUPPORTED.tex

@@ -1,65 +0,0 @@
-%% Copyright (c) University of Exeter
-%%               University of Paris-Saclay
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1.3c of the License, or (at your option) any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
-
-%% Warning: Do Not Edit!
-%% =====================
-%% This is the root file for the Isabelle/DOF using the scrartcl class.
-%%
-%% All customization and/or additional packages should be added to the file
-%% preamble.tex.
-
-\RequirePackage{ifvtex}
-\documentclass[]{beamer}
-\PassOptionsToPackage{force}{DOF-scholarly_paper}
-\title{No Title Given}
-\usepackage{beamerposter}
-\usepackage{DOF-core}
-
-\usepackage{textcomp}
-\bibliographystyle{abbrvnat}
-\RequirePackage{subcaption}
-
-\providecommand{\institute}[1]{}%
-\providecommand{\inst}[1]{}%
-\providecommand{\orcidID}[1]{}%
-\providecommand{\email}[1]{}%
-
-
-\usepackage[numbers, sort&compress, sectionbib]{natbib}
-
-\usepackage{hyperref}
-\setcounter{tocdepth}{3} 
-\hypersetup{%
-   bookmarksdepth=3
-  ,pdfpagelabels
-  ,pageanchor=true
-  ,bookmarksnumbered
-  ,plainpages=false
-} % more detailed digital TOC (aka bookmarks)
-\sloppy
-\allowdisplaybreaks[4]
-
-\newenvironment{frontmatter}{}{}
-\raggedbottom
-\begin{document}
-\begin{frame}[fragile]
-\IfFileExists{dof_session.tex}{\input{dof_session}}{\input{session}}
-% optional bibliography
-\IfFileExists{root.bib}{{\bibliography{root}}}{}
-\end{frame}
-\end{document}
-
-%%% Local Variables:
-%%% mode: latex
-%%% TeX-master: t
-%%% End:

Isabelle_DOF-Ontologies/document-templates/root-sn-article-UNSUPPORTED.tex

@@ -1,68 +0,0 @@
-%% Copyright (c) 2019-2022 University of Exeter
-%%               2018-2022 University of Paris-Saclay
-%%               2018-2019 The University of Sheffield
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1.3c of the License, or (at your option) any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
-
-%% Warning: Do Not Edit!
-%% =====================
-%% This is the root file for the Isabelle/DOF using the scrartcl class.
-%%
-%% All customization and/or additional packages should be added to the file
-%% preamble.tex.
-
-\documentclass[iicol]{sn-jnl}
-\PassOptionsToPackage{force}{DOF-scholarly_paper}
-\title{No Title Given}
-\usepackage{DOF-core}
-\bibliographystyle{sn-basic}
-\let\proof\relax
-\let\endproof\relax
-\newcommand{\inst}[1]{}%
-\newcommand{\institute}[1]{}
-\usepackage{manyfoot}
-\usepackage{DOF-core}
-\setcounter{tocdepth}{3} 
-\hypersetup{%
-   bookmarksdepth=3
-  ,pdfpagelabels
-  ,pageanchor=true
-  ,bookmarksnumbered
-  ,plainpages=false
-} % more detailed digital TOC (aka bookmarks)
-\sloppy
-\allowdisplaybreaks[4]
-
-\usepackage{subcaption}
-\usepackage[size=footnotesize]{caption}
-
-\let\DOFauthor\relax
-\begin{document}
-\selectlanguage{USenglish}%
-\renewcommand{\bibname}{References}%
-\renewcommand{\figurename}{Fig.}
-\renewcommand{\abstractname}{Abstract.}
-\renewcommand{\subsubsectionautorefname}{Sect.}
-\renewcommand{\subsectionautorefname}{Sect.}
-\renewcommand{\sectionautorefname}{Sect.}
-\renewcommand{\figureautorefname}{Fig.}
-\newcommand{\lstnumberautorefname}{Line}
-
-\maketitle
-\IfFileExists{dof_session.tex}{\input{dof_session}}{\input{session}}
-% optional bibliography
-\IfFileExists{root.bib}{{\bibliography{root}}}{}
-\end{document}
-
-%%% Local Variables:
-%%% mode: latex
-%%% TeX-master: t
-%%% End:

Isabelle_DOF-Ontologies/document-templates/root-svjour3-UNSUPPORTED.tex

@@ -1,65 +0,0 @@
-%% Copyright (c) 2019-2022 University of Exeter
-%%               2018-2022 University of Paris-Saclay
-%%               2018-2019 The University of Sheffield
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1.3c of the License, or (at your option) any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
-
-%% Warning: Do Not Edit!
-%% =====================
-%% This is the root file for the Isabelle/DOF using the scrartcl class.
-%%
-%% All customization and/or additional packages should be added to the file
-%% preamble.tex.
-
-\RequirePackage{ifvtex}
-\RequirePackage{fix-cm}
-\documentclass[]{svjour3}
-
-\title{No Title Given}
-\usepackage{DOF-core}
-\usepackage{mathptmx}
-\bibliographystyle{abbrvnat}
-\newcommand{\inst}[1]{}% 
-
-\usepackage[numbers, sort&compress, sectionbib]{natbib}
-\usepackage{hyperref}
-\setcounter{tocdepth}{3} 
-\hypersetup{%
-   bookmarksdepth=3
-  ,pdfpagelabels
-  ,pageanchor=true
-  ,bookmarksnumbered
-  ,plainpages=false
-} % more detailed digital TOC (aka bookmarks)
-\sloppy
-%\allowdisplaybreaks[4]
-
-\begin{document}
-\selectlanguage{USenglish}%
-\renewcommand{\bibname}{References}%
-\renewcommand{\figurename}{Fig.}
-\renewcommand{\abstractname}{Abstract.}
-\renewcommand{\subsubsectionautorefname}{Sect.}
-\renewcommand{\subsectionautorefname}{Sect.}
-\renewcommand{\sectionautorefname}{Sect.}
-\renewcommand{\figureautorefname}{Fig.}
-\newcommand{\lstnumberautorefname}{Line}
-
-\maketitle
-\IfFileExists{dof_session.tex}{\input{dof_session}}{\input{session}}
-% optional bibliography
-\IfFileExists{root.bib}{{\bibliography{root}}}{}
-\end{document}
-
-%%% Local Variables:
-%%% mode: latex
-%%% TeX-master: t
-%%% End:

Isabelle_DOF-Ontologies/document/lstisadof-manual.sty

@@ -1,327 +0,0 @@
-%% Copyright (C) 2018 The University of Sheffield
-%%               2018-2021 The University of Paris-Saclay
-%%               2019-2021 The University of Exeter
-%%
-%% License:
-%%   This program can be redistributed and/or modified under the terms
-%%   of the LaTeX Project Public License Distributed from CTAN
-%%   archives in directory macros/latex/base/lppl.txt; either
-%%   version 1.3c of the License, or (at your option) any later version.
-%%   OR
-%%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
-\usepackage{listings}
-\usepackage{listingsutf8}
-\usepackage{tikz}
-\usepackage[many]{tcolorbox}
-\tcbuselibrary{listings}
-\tcbuselibrary{skins}
-\usepackage{xstring}
-
-\definecolor{OliveGreen}    {cmyk}{0.64,0,0.95,0.40}
-\definecolor{BrickRed}      {cmyk}{0,0.89,0.94,0.28}
-\definecolor{Blue}          {cmyk}{1,1,0,0}
-\definecolor{CornflowerBlue}{cmyk}{0.65,0.13,0,0}
-
-
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% <antiquotations>
-%% Hack: re-defining tag types for supporting highlighting of antiquotations
-\gdef\lst@tagtypes{s}
-\gdef\lst@TagKey#1#2{%
-    \lst@Delim\lst@tagstyle #2\relax
-        {Tag}\lst@tagtypes #1%
-                     {\lst@BeginTag\lst@EndTag}%
-        \@@end\@empty{}}
-\lst@Key{tag}\relax{\lst@TagKey\@empty{#1}}
-\lst@Key{tagstyle}{}{\def\lst@tagstyle{#1}}
-\lst@AddToHook{EmptyStyle}{\let\lst@tagstyle\@empty}
-\gdef\lst@BeginTag{%
-    \lst@DelimOpen
-        \lst@ifextags\else
-        {\let\lst@ifkeywords\iftrue
-         \lst@ifmarkfirstintag \lst@firstintagtrue \fi}}
-\lst@AddToHookExe{ExcludeDelims}{\let\lst@ifextags\iffalse}
-\gdef\lst@EndTag{\lst@DelimClose\lst@ifextags\else}
-\lst@Key{usekeywordsintag}t[t]{\lstKV@SetIf{#1}\lst@ifusekeysintag}
-\lst@Key{markfirstintag}f[t]{\lstKV@SetIf{#1}\lst@ifmarkfirstintag}
-\gdef\lst@firstintagtrue{\global\let\lst@iffirstintag\iftrue}
-\global\let\lst@iffirstintag\iffalse
- \lst@AddToHook{PostOutput}{\lst@tagresetfirst}
- \lst@AddToHook{Output}
-     {\gdef\lst@tagresetfirst{\global\let\lst@iffirstintag\iffalse}}
- \lst@AddToHook{OutputOther}{\gdef\lst@tagresetfirst{}}
-\lst@AddToHook{Output}
-    {\ifnum\lst@mode=\lst@tagmode
-         \lst@iffirstintag \let\lst@thestyle\lst@gkeywords@sty \fi
-         \lst@ifusekeysintag\else \let\lst@thestyle\lst@gkeywords@sty\fi
-     \fi}
-\lst@NewMode\lst@tagmode
-\gdef\lst@Tag@s#1#2\@empty#3#4#5{%
-    \lst@CArg #1\relax\lst@DefDelimB {}{}%
-        {\ifnum\lst@mode=\lst@tagmode \expandafter\@gobblethree \fi}%
-        #3\lst@tagmode{#5}%
-    \lst@CArg #2\relax\lst@DefDelimE {}{}{}#4\lst@tagmode}%
-\gdef\lst@BeginCDATA#1\@empty{%
-    \lst@TrackNewLines \lst@PrintToken
-    \lst@EnterMode\lst@GPmode{}\let\lst@ifmode\iffalse
-    \lst@mode\lst@tagmode #1\lst@mode\lst@GPmode\relax\lst@modetrue}
-%
-\def\beginlstdelim#1#2#3%
-{%
-    \def\endlstdelim{\texttt{\textbf{\color{black!60}#2}}\egroup}%
-    \ttfamily\textbf{\color{black!60}#1}\bgroup\rmfamily\color{#3}\aftergroup\endlstdelim%
-}
-%% </antiquotations>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% <isar>
-\providecolor{isar}{named}{blue}
-\renewcommand{\isacommand}[1]{\textcolor{OliveGreen!60}{\ttfamily\bfseries #1}}
-\newcommand{\inlineisarbox}[1]{#1}
-\NewTColorBox[]{isarbox}{}{
-     ,boxrule=0pt
-     ,boxsep=0pt
-     ,colback=white!90!isar
-     ,enhanced jigsaw
-     ,borderline west={2pt}{0pt}{isar!60!black}
-     ,sharp corners
-     %,before skip balanced=0.5\baselineskip plus 2pt % works only with Tex Live 2020 and later
-     ,enlarge top by=0mm
-     ,enhanced
-     ,overlay={\node[draw,fill=isar!60!black,xshift=0pt,anchor=north
-       east,font=\bfseries\footnotesize\color{white}]
-                at (frame.north east) {Isar};}
-}
-%% </isar>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-%% <out>
-\providecolor{out}{named}{green}
-\newtcblisting{out}[1][]{%
-      listing only%
-     ,boxrule=0pt
-     ,boxsep=0pt
-     ,colback=white!90!out
-     ,enhanced jigsaw
-     ,borderline west={2pt}{0pt}{out!60!black}
-     ,sharp corners
-     % ,before skip=10pt
-     % ,after skip=10pt
-     ,enlarge top by=0mm
-     ,enhanced
-     ,overlay={\node[draw,fill=out!60!black,xshift=0pt,anchor=north
-       east,font=\bfseries\footnotesize\color{white}]
-                at (frame.north east) {Document};}
-        ,listing options={
-           breakatwhitespace=true
-          ,columns=flexible%
-          ,basicstyle=\small\rmfamily
-          ,mathescape
-          ,#1
-      }
-  }%
-%% </out>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-%% <sml>
-\lstloadlanguages{ML}
-\providecolor{sml}{named}{red}
-\lstdefinestyle{sml}{
-   ,escapechar=ë%
-   ,basicstyle=\ttfamily%
-   ,commentstyle=\itshape%
-   ,keywordstyle=\bfseries\color{CornflowerBlue}%
-   ,ndkeywordstyle=\color{green}%
-   ,language=ML
-%  ,literate={%
-%     {<@>}{@}1%
-%    }
-   ,keywordstyle=[6]{\itshape}%
-   ,morekeywords=[6]{args_type}%
-   ,tag=**[s]{@\{}{\}}%
-   ,tagstyle=\color{CornflowerBlue}%
-   ,markfirstintag=true%
-}%
-\def\inlinesml{\lstinline[style=sml,breaklines=true,breakatwhitespace=true]}
-\newtcblisting{sml}[1][]{%
-      listing only%
-     ,boxrule=0pt
-     ,boxsep=0pt
-     ,colback=white!90!sml
-     ,enhanced jigsaw
-     ,borderline west={2pt}{0pt}{sml!60!black}
-     ,sharp corners
-     % ,before skip=10pt
-     % ,after skip=10pt
-     ,enlarge top by=0mm
-     ,enhanced
-     ,overlay={\node[draw,fill=sml!60!black,xshift=0pt,anchor=north
-       east,font=\bfseries\footnotesize\color{white}]
-                at (frame.north east) {SML};}
-        ,listing options={
-          style=sml
-          ,columns=flexible%
-          ,basicstyle=\small\ttfamily
-          ,#1
-      }
-  }%
-%% </sml>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-%% <latex>
-\lstloadlanguages{TeX}
-\providecolor{ltx}{named}{yellow}
-\lstdefinestyle{lltx}{language=[AlLaTeX]TeX,
-  ,basicstyle=\ttfamily%
-  ,showspaces=false%
-  ,escapechar=ë
-  ,showlines=false%
-  ,morekeywords={newisadof}
- %  ,keywordstyle=\bfseries%
-   % Defining 2-keywords
-   ,keywordstyle=[1]{\color{BrickRed!60}\bfseries}%
-   % Defining 3-keywords
-   ,keywordstyle=[2]{\color{OliveGreen!60}\bfseries}%
-   % Defining 4-keywords
-   ,keywordstyle=[3]{\color{black!60}\bfseries}%
-   % Defining 5-keywords
-   ,keywordstyle=[4]{\color{Blue!70}\bfseries}%
-   % Defining 6-keywords
-   ,keywordstyle=[5]{\itshape}%
-  % 
-}
-\lstdefinestyle{ltx}{style=lltx,
-                basicstyle=\ttfamily\small}%
-\def\inlineltx{\lstinline[style=ltx, breaklines=true,columns=fullflexible]}
-% see
-% https://tex.stackexchange.com/questions/247643/problem-with-tcblisting-first-listed-latex-command-is-missing
-\NewTCBListing{ltx}{ !O{} }{%
-     listing only%
-     ,boxrule=0pt
-     ,boxsep=0pt
-     ,colback=white!90!ltx
-     ,enhanced jigsaw
-     ,borderline west={2pt}{0pt}{ltx!60!black}
-     ,sharp corners
-     % ,before skip=10pt
-     % ,after skip=10pt
-     ,enlarge top by=0mm
-     ,enhanced
-     ,overlay={\node[draw,fill=ltx!60!black,xshift=0pt,anchor=north
-       east,font=\bfseries\footnotesize\color{white}]
-                at (frame.north east) {\LaTeX};}
-      ,listing options={
-             style=lltx,
-            ,columns=flexible%
-            ,basicstyle=\small\ttfamily
-            ,#1
-       }
-  }%
-%% </latex>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-%% <bash>
-\providecolor{bash}{named}{black}
-\lstloadlanguages{bash}
-\lstdefinestyle{bash}{%
-   language=bash
-  ,escapechar=ë
-  ,basicstyle=\ttfamily%
-  ,showspaces=false%
-  ,showlines=false%
-  ,columns=flexible%
- %  ,keywordstyle=\bfseries%
-   % Defining 2-keywords
-   ,keywordstyle=[1]{\color{BrickRed!60}\bfseries}%
-   % Defining 3-keywords
-   ,keywordstyle=[2]{\color{OliveGreen!60}\bfseries}%
-   % Defining 4-keywords
-   ,keywordstyle=[3]{\color{black!60}\bfseries}%
-   % Defining 5-keywords
-   ,keywordstyle=[4]{\color{Blue!80}\bfseries}%
-   ,alsoletter={*,-,:,~,/}
-   ,morekeywords=[4]{}%
-   % Defining 6-keywords
-   ,keywordstyle=[5]{\itshape}%
-  % 
-}
-\def\inlinebash{\lstinline[style=bash, breaklines=true,columns=fullflexible]}
-\newcommand\@isabsolutepath[3]{%
-  \StrLeft{#1}{1}[\firstchar]%
-  \IfStrEq{\firstchar}{/}{#2}{#3}%
-}
-
-\newcommand{\@homeprefix}[1]{%
-  \ifthenelse{\equal{#1}{}}{\textasciitilde}{\textasciitilde/}%
-}
-
-\newcommand{\prompt}[1]{%
-  \color{Blue!80}\textbf{\texttt{%
-    achim@logicalhacking:{\@isabsolutepath{#1}{#1}{\@homeprefix{#1}#1}}\$}}%
-}
-\newtcblisting{bash}[1][]{%
-      listing only%
-     ,boxrule=0pt
-     ,boxsep=0pt
-     ,colback=white!90!bash
-     ,enhanced jigsaw
-     ,borderline west={2pt}{0pt}{bash!60!black}
-     ,sharp corners
-     % ,before skip=10pt
-     % ,after skip=10pt
-     ,enlarge top by=0mm
-     ,enhanced
-     ,overlay={\node[draw,fill=bash!60!black,xshift=0pt,anchor=north
-       east,font=\bfseries\footnotesize\color{white}]
-                at (frame.north east) {Bash};}
-     ,listing options={
-           style=bash
-           ,columns=flexible%
-           ,breaklines=true%
-           ,prebreak=\mbox{\space\textbackslash}%
-           ,basicstyle=\small\ttfamily%
-           ,#1
-      }
-  }%
-%% </bash>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-%% <config>
-\providecolor{config}{named}{gray}
-\newtcblisting{config}[2][]{%
-      listing only%
-     ,boxrule=0pt
-     ,boxsep=0pt
-     ,colback=white!90!config
-     ,enhanced jigsaw
-     ,borderline west={2pt}{0pt}{config!60!black}
-     ,sharp corners
-     % ,before skip=10pt
-     % ,after skip=10pt
-     ,enlarge top by=0mm
-     ,enhanced
-     ,overlay={\node[draw,fill=config!60!black,xshift=0pt,anchor=north
-       east,font=\bfseries\footnotesize\color{white}]
-                at (frame.north east) {#2};}
-        ,listing options={
-           breakatwhitespace=true
-          ,columns=flexible%
-          ,basicstyle=\small\ttfamily
-          ,mathescape
-          ,#1
-      }
-  }%
-%% </config>
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-
-

Isabelle_DOF-Ontologies/document/preamble.tex

@@ -1,4 +0,0 @@
-\usepackage{dirtree}
-\renewcommand*\DTstylecomment{\ttfamily\itshape}
-
-\usepackage{lstisadof-manual}

Isabelle_DOF-Ontologies/document_setup.thy

@@ -1,20 +0,0 @@
-(*<*)
-theory "document_setup"
-  imports
-  "Isabelle_DOF.technical_report"
-  "Isabelle_DOF-Ontologies.CENELEC_50128"
-  "Isabelle_DOF-Ontologies.CC_terminology"
-begin
-
-use_template "scrreprt-modern"
-use_ontology "Isabelle_DOF.technical_report" and "Isabelle_DOF-Ontologies.CENELEC_50128"
-         and "Isabelle_DOF-Ontologies.CC_terminology"
-
-(*>*)
-
-title*[title::title]         \<open>Isabelle/DOF\<close>
-subtitle*[subtitle::subtitle]\<open>Ontologies\<close>
-
-(*<*)
-end
-(*>*)

Isabelle_DOF-Ontologies/document_templates.thy

@@ -1,30 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019      The University of Exeter 
- *               2018-2019 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-theory 
-  "document_templates"
-imports
-  "Isabelle_DOF.Isa_DOF"
-begin
-
-define_template "./document-templates/root-lipics-v2021-UNSUPPORTED.tex" 
-                "Unsupported template for LIPICS (v2021). Not for general use."
-define_template "./document-templates/root-svjour3-UNSUPPORTED.tex" 
-                "Unsupported template for SVJOUR. Not for general use."
-define_template "./document-templates/root-sn-article-UNSUPPORTED.tex" 
-                "Unsupported template for Springer Nature's template. Not for general use."
-define_template "./document-templates/root-beamer-UNSUPPORTED.tex" 
-                "Unsupported template for presentations. Not for general use."
-define_template "./document-templates/root-beamerposter-UNSUPPORTED.tex" 
-                "Unsupported template for poster. Not for general use."
-end

Isabelle_DOF-Proofs/ROOT

@@ -1,10 +0,0 @@
-session "Isabelle_DOF-Proofs" (proofs) = "HOL-Proofs" +
-  options [document = false,  record_proofs = 2, parallel_limit = 500, document_build = dof]
-  sessions
-    "Isabelle_DOF"
-    Metalogic_ProofChecker
-  theories
-    Isabelle_DOF.ontologies
-    Isabelle_DOF.Isa_DOF
-    Very_Deep_DOF
-    Reification_Test

Isabelle_DOF-Proofs/Reification_Test.thy

@@ -1,739 +0,0 @@
-theory Reification_Test
-  imports "Isabelle_DOF-Proofs.Very_Deep_DOF"
-
-begin
-
-ML\<open>
-val ty1 = Meta_ISA_core.reify_typ @{typ "int"}
-val ty2 = Meta_ISA_core.reify_typ @{typ "int \<Rightarrow> bool"}
-val ty3 = Meta_ISA_core.reify_typ @{typ "prop"}
-val ty4 = Meta_ISA_core.reify_typ @{typ "'a list"}
-\<close>
-
-term*\<open>@{typ \<open>int\<close>}\<close>
-value*\<open>@{typ \<open>int\<close>}\<close>
-value*\<open>@{typ \<open>int \<Rightarrow> bool\<close>}\<close>
-term*\<open>@{typ \<open>prop\<close>}\<close>
-value*\<open>@{typ \<open>prop\<close>}\<close>
-term*\<open>@{typ \<open>'a list\<close>}\<close>
-value*\<open>@{typ \<open>'a list\<close>}\<close>
-
-ML\<open>
-val t1 = Meta_ISA_core.reify_term @{term "1::int"}
-val t2 = Meta_ISA_core.reify_term @{term "\<lambda>x. x = 1"}
-val t3 = Meta_ISA_core.reify_term @{term "[2, 3::int]"}
-\<close>
-term*\<open>@{term \<open>1::int\<close>}\<close>
-value*\<open>@{term \<open>1::int\<close>}\<close>
-term*\<open>@{term \<open>\<lambda>x. x = 1\<close>}\<close>
-value*\<open>@{term \<open>\<lambda>x. x = 1\<close>}\<close>
-term*\<open>@{term \<open>[2, 3::int]\<close>}\<close>
-value*\<open>@{term \<open>[2, 3::int]\<close>}\<close>
-
-prf refl
-full_prf refl
-
-term*\<open>@{thm \<open>HOL.refl\<close>}\<close>
-value*\<open>proof @{thm \<open>HOL.refl\<close>}\<close>
-value*\<open>proof @{thm \<open>HOL.refl\<close>}\<close>
-value*\<open>depth (proof @{thm \<open>HOL.refl\<close>})\<close>
-value*\<open>size (proof @{thm \<open>HOL.refl\<close>})\<close>
-value*\<open>fv_Proof (proof @{thm \<open>HOL.refl\<close>})\<close>
-term*\<open>@{thms-of \<open>HOL.refl\<close>}\<close>
-value*\<open>@{thms-of \<open>HOL.refl\<close>}\<close>
-
-ML\<open>
-val t_schematic = TVar(("'a",0), [])
-val t = @{term "Tv (Var (STR '''a'', 0)) {}"}
-val rt_schematic = Meta_ISA_core.reify_typ t_schematic
-val true = rt_schematic = t
-\<close>
-
-lemma test : "A \<and> B \<longrightarrow> B \<and> A"
-  by auto
-
-lemma test2 : "A \<and> B \<Longrightarrow> B \<and> A"
-  by auto
-
-lemma test3: "A \<and> B \<longrightarrow> B \<and> A"
-proof
-  assume "A \<and> B"
-  then obtain B and A ..
-  then show "B \<and> A" ..
-qed
-
-lemma test4:
-  assumes "(A \<and> B)"
-  shows "B \<and> A"
-  apply (insert assms)
-  by auto
-
-lemma test_subst : "\<lbrakk>x = f x; odd(f x)\<rbrakk> \<Longrightarrow> odd x"
-  by (erule ssubst)
-
-inductive_set even' :: "nat set" where
-    "0 \<in> even'"
-  | "n \<in> even' \<Longrightarrow> (Suc (Suc n)) \<in> even'"
-
-find_theorems name:"even'.induct"
-
-
-(*lemma even_dvd : "n \<in> even' \<Longrightarrow> 2 dvd n"
-proof(induct n)
-  case 0 then show ?case by simp
-next 
-  case (Suc n) then show ?case
-    apply (simp add: dvd_def)
-    apply (rule_tac x ="Suc k" in exI)
-    apply clarify*)
-
-theorem "((A \<longrightarrow> B) \<longrightarrow> A) \<longrightarrow> A"
-proof
-  assume "(A \<longrightarrow> B) \<longrightarrow> A"
-  show A
-  proof (rule classical)
-    assume "\<not> A"
-    have "A \<longrightarrow> B"
-    proof
-      assume A
-      with \<open>\<not> A\<close> show B by contradiction
-    qed
-    with \<open>(A \<longrightarrow> B) \<longrightarrow> A\<close> show A ..
-  qed
-qed
-
-(*lemma even_dvd : "n \<in> even' \<Longrightarrow> 2 dvd n"
-using [[simp_trace]]
-  apply (induct n)
-   apply (subst even_zero)
-  apply(rule TrueI)
-
-  apply(simp)*)
-
-lemma even_dvd : "n \<in> even' \<Longrightarrow> 2 dvd n"
-  apply (erule even'.induct)
-   apply (simp_all add: dvd_def)
-  using [[simp_trace]]
-  apply clarify
-  find_theorems name:"_ = 2 * _"
-  apply (rule_tac x ="Suc k" in exI)
-using [[simp_trace]]
-  apply simp
-  done
-
-(*
-lemma even_dvd : "n \<in> even' \<Longrightarrow> 2 dvd n"
-apply (induct_tac rule:even'.induct)*)
-
-inductive ev :: " nat \<Rightarrow> bool " where
-  ev0: " ev 0 " |
-  evSS: " ev n \<Longrightarrow> ev (n + 2) "
-
-fun evn :: " nat \<Rightarrow> bool " where
-  " evn 0 = True " |
-  " evn (Suc 0) = False " |
-  " evn (Suc (Suc n)) = evn n "
-
-(*lemma assumes a: " ev (Suc(Suc m)) " shows" ev m "
-proof(induction  "Suc (Suc m)" arbitrary: " m " rule: ev.induct)*)
-
-(*lemma " ev (Suc (Suc m)) \<Longrightarrow> ev m " 
-proof(induction " Suc (Suc m) " arbitrary: " m " rule: ev.induct)
-  case ev0
-  then show ?case sorry
-next
-  case (evSS n)
-  then show ?case sorry
-qed*)
-
-(* And neither of these can apply the induction *)
-(*
-lemma assumes a1: " ev n " and a2: " n = (Suc (Suc m)) " shows " ev m "
-proof (induction " n " arbitrary: " m " rule: ev.induct)
-
-lemma assumes a1: " n = (Suc (Suc m)) " and a2: "ev n " shows " ev m "
-proof (induction " n " arbitrary: " m " rule: ev.induct)
-*)
-
-(* But this one can ?! *)
-(*
-lemma assumes a1: " ev n " and a2: " n = (Suc (Suc m)) " shows " ev m "
-proof -
-  from a1 and a2 show " ev m "
-  proof (induction " n " arbitrary: " m " rule: ev.induct)
-    case ev0
-    then show ?case by simp
-  next
-    case (evSS n) thus ?case by simp
-  qed
-qed
-*)
-
-inductive_set even :: "int set" where
-zero[intro!]: "0 \<in> even" |
-plus[intro!]: "n \<in> even \<Longrightarrow> n+2 \<in> even " |
-min[intro!]: "n \<in> even \<Longrightarrow> n-2 \<in> even "
-
-lemma a : "2+2=4" by simp
-
-lemma b : "(0::int)+2=2" by simp
-
-lemma test_subst_2 : "4 \<in> even"
-  apply (subst a[symmetric])
-  apply (rule plus)
-  apply (subst b[symmetric])
-  apply (rule plus)
-  apply (rule zero)
-  done
-
-
-(*lemma "\<lbrakk>P x y z; Suc x < y\<rbrakk> \<Longrightarrow> f z = x * y"
-  (*using [[simp_trace]]*)
-  (*apply (simp add: mult.commute)*)
-  apply (subst mult.commute)
-  apply (rule mult.commute [THEN ssubst])*)
-
-datatype 'a seq = Empty | Seq 'a "'a seq"
-find_consts name:"Reification_Test*seq*"
-fun conc :: "'a seq \<Rightarrow> 'a seq \<Rightarrow> 'a seq"
-where
-  c1 :  "conc Empty ys = ys"
-| c2 : "conc (Seq x xs) ys = Seq x (conc xs ys)"
-
-lemma seq_not_eq : "Seq x xs \<noteq> xs"
-using [[simp_trace]]
-proof (induct xs arbitrary: x)
-  case Empty
-  show "Seq x Empty \<noteq> Empty" by simp
-next
-  case (Seq y ys)
-  show "Seq x (Seq y ys) \<noteq> Seq y ys"
-    using \<open>Seq y ys \<noteq> ys\<close> by simp
-qed
-
-lemma identity_conc : "conc xs Empty = xs"
-  using [[simp_trace]]
-  using[[simp_trace_depth_limit=8]]
-  using [[unify_trace_simp]]
-  using[[unify_trace_types]]
-  using [[unify_trace_bound=0]]
-  (* using [[simp_trace_new depth=10]] *)
-  apply (induct xs)
-   apply (subst c1)
-   apply (rule refl)
-  apply (subst c2)
-  apply (rule_tac s="xs" and P="\<lambda>X. Seq x1 X = Seq x1 xs" in subst)
-   apply (rule sym)
-   apply assumption
-  apply (rule refl)
-  done
-
-lemma imp_ex : "(\<exists>x. \<forall>y. P x y) \<longrightarrow> (\<forall>y. \<exists>x. P x y)"
-  using [[simp_trace]]
-  using[[simp_trace_depth_limit=8]]
-  apply (auto)
-done
-
-lemma length_0_conv' [iff]: "(length [] = 0)"
-  apply (subst List.list.size(3))
-  apply (rule refl)
-  done
-
-lemma cons_list : "a#xs = [a]@xs"
-  using [[simp_trace]]
-  apply (subst List.append.append_Cons)
-  apply (subst List.append.append_Nil)
-  apply (rule refl)
-  done
-lemma replacement: "\<lbrakk> a = b; c = d \<rbrakk> \<Longrightarrow> f a c = f b d"
-apply (erule ssubst)+
-apply (rule refl )
- done
-lemma assoc_append : "k @ (l @ m) = (k @ l ) @ m"
-apply (induct_tac k )
-apply (subst append_Nil )+
-apply (rule refl )
-apply (subst append_Cons)
-apply (subst append_Cons)
-apply (subst append_Cons)
-apply (rule_tac f ="Cons" in replacement)
-apply (rule refl)
-apply assumption
-  done
-
-lemma length_cons : "length (xs @ ys) = length xs + length ys"
-  using [[simp_trace]]
-  apply (subst List.length_append)
-  apply (rule refl)
-  done
-lemma length_plus : "(length [a] + length xs = 0) = ([a] @ xs = [])"
-  using [[simp_trace]]
-  apply (subst List.list.size(4))
-  apply (subst List.list.size(3))
-  apply (subst Nat.add_Suc_right)
-  apply (subst Groups.monoid_add_class.add.right_neutral)
-  apply (subst Nat.plus_nat.add_Suc)
-  apply (subst Groups.monoid_add_class.add.left_neutral)
-apply (subst Nat.old.nat.distinct(2))
-  by simp
-lemma empty_list : "(length [] = 0) = ([] = []) = True"
-  using [[simp_trace]]
-  by simp
-lemma TrueI: True
-using [[simp_trace]]
-  unfolding True_def
-  by (rule refl)
-
-lemma length_0_conv [iff]: "(length xs = 0) = (xs = [])"
-  using [[simp_trace]]
-  apply (induct xs)
-   apply (subst List.list.size(3))
-   apply(subst HOL.simp_thms(6))
-   apply(subst HOL.simp_thms(6))
-   apply(rule refl)
-
-  apply (subst cons_list)
-  apply (subst(2) cons_list)
-  apply (subst length_cons)
-  apply (subst length_plus)
-  apply (subst HOL.simp_thms(6))
-  apply (rule TrueI)
-  done
-(*by (induct xs) auto*)
-
-find_theorems (50) name:"HOL.simp_thms"
-find_theorems (50) name:"List.list*size"
-find_theorems (50) name:"List.list*length"
-find_theorems "_ @ _"
-find_theorems (500) "List.length [] = 0"
-find_theorems (550) "length _ = length _ + length _"
-
-
-lemma identity_list : "xs @ [] = xs"
-  using [[simp_trace]]
-  using[[simp_trace_depth_limit=8]]
-  using [[unify_trace_simp]]
-  using[[unify_trace_types]]
-  using [[unify_trace_bound=0]]
-  apply (induct xs)
-  apply (subst List.append_Nil2)
-   apply (subst HOL.simp_thms(6))
-  apply(rule TrueI)
-  apply (subst List.append_Nil2)
-  apply (subst HOL.simp_thms(6))
-  apply(rule TrueI)
-  done
-
-lemma identity_list' : "xs @ [] = xs"
-  using [[simp_trace]]
-  using[[simp_trace_depth_limit=8]]
-  using [[unify_trace_simp]]
-  using[[unify_trace_types]]
-  using [[unify_trace_bound=0]]
-  (* using [[simp_trace_new depth=10]] *)
-  apply (induct "length xs")
-  apply (subst (asm) zero_reorient)
-  apply(subst(asm) length_0_conv)
-   apply (subst List.append_Nil2)
-   apply (subst HOL.simp_thms(6))
-  apply (rule TrueI)
-     apply (subst List.append_Nil2)
-  apply (subst HOL.simp_thms(6))
-  apply (rule TrueI)
-  done
-
-lemma conj_test : "A \<and> B \<and> C \<longrightarrow> B \<and> A"
-  apply (rule impI)
-  apply (rule conjI)
-  apply (drule conjunct2)
-   apply (drule conjunct1)
-   apply assumption
-    apply (drule conjunct1)
-  apply assumption
-  done
-
-declare[[show_sorts]]
-declare[[ML_print_depth = 20]]
-
-ML\<open>
-val full = true
-val thm = @{thm "test"}
-val hyps = Thm.hyps_of thm
-val prems = Thm.prems_of thm
-val reconstruct_proof = Thm.reconstruct_proof_of thm
-val standard_proof = Proof_Syntax.standard_proof_of
-          {full = full, expand_name = Thm.expand_name thm} thm
-val term_of_proof = Proof_Syntax.term_of_proof standard_proof
-\<close>
-
-lemma identity_conc' : "conc xs Empty = xs"
-  using [[simp_trace]]
-  using[[simp_trace_depth_limit=8]]
-  using [[unify_trace_simp]]
-  using[[unify_trace_types]]
-  using [[unify_trace_bound=0]]
-  (* using [[simp_trace_new depth=10]] *)
-  apply (induct xs)
-   apply (subst c1)
-   apply (rule refl)
-  apply (subst c2)
-  apply (rule_tac s="xs" and P="\<lambda>X. Seq x1 X = Seq x1 xs" in subst)
-   apply (rule sym)
-   apply assumption
-  apply (rule refl)
-  done
-
-declare[[show_sorts = false]]
-
-ML\<open> (*See: *) \<^file>\<open>~~/src/HOL/Proofs/ex/Proof_Terms.thy\<close>\<close>
-ML\<open>
-  val thm = @{thm "identity_conc'"};
-
-  (*proof body with digest*)
-  val body = Proofterm.strip_thm_body (Thm.proof_body_of thm);
-
-  (*proof term only*)
-  val prf = Proofterm.proof_of body;
-
-  (*clean output*)
-  Pretty.writeln (Proof_Syntax.pretty_proof \<^context> prf);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> false thm);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> true thm);
-
-  (*all theorems used in the graph of nested proofs*)
-  val all_thms =
-    Proofterm.fold_body_thms
-      (fn {name, ...} => insert (op =) name) [body] [];
-\<close>
-
-term*\<open>@{thm \<open>Reification_Test.identity_conc\<close>}\<close>
-value*\<open>proof @{thm \<open>Reification_Test.identity_conc\<close>}\<close>
-
-lemma cons_list' : "a#xs = [a]@xs"
-  using [[simp_trace]]
-  apply (subst List.append.append_Cons)
-  apply (subst List.append.append_Nil)
-  apply (rule refl)
-  done
-
-ML\<open> (*See: *) \<^file>\<open>~~/src/HOL/Proofs/ex/Proof_Terms.thy\<close>\<close>
-ML\<open>
-  val thm = @{thm "cons_list'"};
-
-  (*proof body with digest*)
-  val body = Proofterm.strip_thm_body (Thm.proof_body_of thm);
-
-  (*proof term only*)
-  val prf = Proofterm.proof_of body;
-
-  (*clean output*)
-  Pretty.writeln (Proof_Syntax.pretty_proof \<^context> prf);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> false thm);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> true thm);
-
-  (*all theorems used in the graph of nested proofs*)
-  val all_thms =
-    Proofterm.fold_body_thms
-      (fn {name, ...} => insert (op =) name) [body] [];
-\<close>
-
-declare[[show_sorts = false]]
-declare[[ML_print_depth = 20]]
-
-ML\<open> (*See: *) \<^file>\<open>~~/src/HOL/Proofs/ex/Proof_Terms.thy\<close>\<close>
-ML\<open>
-  val thm = @{thm "test"};
-
-  (*proof body with digest*)
-  val body = Proofterm.strip_thm_body (Thm.proof_body_of thm);
-
-  (*proof term only*)
-  val prf = Proofterm.proof_of body;
-
-  (*clean output*)
-  Pretty.writeln (Proof_Syntax.pretty_proof \<^context> prf);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> false thm);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> true thm);
-
-  (*all theorems used in the graph of nested proofs*)
-  val all_thms =
-    Proofterm.fold_body_thms
-      (fn {name, ...} => insert (op =) name) [body] [];
-\<close>
-
-prf test
-full_prf test
-term*\<open>@{thm \<open>Reification_Test.test\<close>}\<close>
-value*\<open>proof @{thm \<open>Reification_Test.test\<close>}\<close>
-term*\<open>@{thms-of \<open>Reification_Test.test\<close>}\<close>
-value*\<open>@{thms-of \<open>Reification_Test.test\<close>}\<close>
-
-ML\<open> (*See: *) \<^file>\<open>~~/src/HOL/Proofs/ex/Proof_Terms.thy\<close>\<close>
-ML\<open>
-  val thm = @{thm test2};
-
-  (*proof body with digest*)
-  val body = Proofterm.strip_thm_body (Thm.proof_body_of thm);
-
-  (*proof term only*)
-  val prf = Proofterm.proof_of body;
-
-  (*clean output*)
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> false thm);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> true thm);
-
-  (*all theorems used in the graph of nested proofs*)
-  val all_thms =
-    Proofterm.fold_body_thms
-      (fn {name, ...} => insert (op =) name) [body] [];
-\<close>
-
-prf test2
-full_prf test2
-term*\<open>@{thm \<open>Reification_Test.test2\<close>}\<close>
-value*\<open>proof @{thm \<open>Reification_Test.test2\<close>}\<close>
-
-ML\<open> (*See: *) \<^file>\<open>~~/src/HOL/Proofs/ex/Proof_Terms.thy\<close>\<close>
-ML\<open>
-  val thm = @{thm test3};
-
-  (*proof body with digest*)
-  val body = Proofterm.strip_thm_body (Thm.proof_body_of thm);
-
-  (*proof term only*)
-  val prf = Proofterm.proof_of body;
-
-  (*clean output*)
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> false thm);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> true thm);
-
-  (*all theorems used in the graph of nested proofs*)
-  val all_thms =
-    Proofterm.fold_body_thms
-      (fn {name, ...} => insert (op =) name) [body] [];
-\<close>
-
-prf test3
-full_prf test3
-term*\<open>@{thm \<open>Reification_Test.test3\<close>}\<close>
-value*\<open>@{thm \<open>Reification_Test.test3\<close>}\<close>
-
-ML\<open> (*See: *) \<^file>\<open>~~/src/HOL/Proofs/ex/Proof_Terms.thy\<close>\<close>
-ML\<open>
-  val thm = @{thm test4};
-
-  (*proof body with digest*)
-  val body = Proofterm.strip_thm_body (Thm.proof_body_of thm);
-
-  (*proof term only*)
-  val prf = Proofterm.proof_of body;
-
-  (*clean output*)
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> false thm);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> true thm);
-
-  (*all theorems used in the graph of nested proofs*)
-  val all_thms =
-    Proofterm.fold_body_thms
-      (fn {name, ...} => insert (op =) name) [body] [];
-\<close>
-
-prf test4
-full_prf test4
-term*\<open>@{thm \<open>Reification_Test.test4\<close>}\<close>
-value*\<open>@{thm \<open>Reification_Test.test4\<close>}\<close>
-
-ML\<open> (*See: *) \<^file>\<open>~~/src/HOL/Proofs/ex/Proof_Terms.thy\<close>\<close>
-ML\<open>
-  val thm = @{thm Pure.symmetric};
-
-  (*proof body with digest*)
-  val body = Proofterm.strip_thm_body (Thm.proof_body_of thm);
-
-  (*proof term only*)
-  val prf = Proofterm.proof_of body;
-
-  (*clean output*)
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> false thm);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> true thm);
-
-  (*all theorems used in the graph of nested proofs*)
-  val all_thms =
-    Proofterm.fold_body_thms
-      (fn {name, ...} => insert (op =) name) [body] [];
-\<close>
-
-prf symmetric
-full_prf symmetric
-term*\<open>@{thm \<open>Pure.symmetric\<close>}\<close>
-value*\<open>proof @{thm \<open>Pure.symmetric\<close>}\<close>
-
-ML\<open>
-val full = true
-val thm = @{thm "Groups.minus_class.super"}
-val standard_proof = Proof_Syntax.standard_proof_of
-          {full = full, expand_name = Thm.expand_name thm} thm
-val term_of_proof = Proof_Syntax.term_of_proof standard_proof
-\<close>
-
-ML\<open>
-val thm = Proof_Context.get_thm \<^context> "Groups.minus_class.super"
-val prop = Thm.prop_of thm
-val proof = Thm.proof_of thm
-\<close>
-
-prf Groups.minus_class.super
-full_prf Groups.minus_class.super
-term*\<open>@{thm \<open>Groups.minus_class.super\<close>}\<close>
-value*\<open>@{thm \<open>Groups.minus_class.super\<close>}\<close>
-
-(*ML\<open>
-val full = true
-val thm = @{thm "Homotopy.starlike_imp_contractible"}
-val standard_proof = Proof_Syntax.standard_proof_of
-          {full = full, expand_name = Thm.expand_name thm} thm
-val term_of_proof = Proof_Syntax.term_of_proof standard_proof
-\<close>
-
-ML\<open>
-val thm = Proof_Context.get_thm \<^context> "Homotopy.starlike_imp_contractible"
-val prop = Thm.prop_of thm
-val proof = Thm.proof_of thm
-\<close>
-
-prf Homotopy.starlike_imp_contractible
-full_prf Homotopy.starlike_imp_contractible
-term*\<open>@{thm \<open>Homotopy.starlike_imp_contractible\<close>}\<close>
-value*\<open>@{thm \<open>Homotopy.starlike_imp_contractible\<close>}\<close>*)
-
-(* stefan bergofer phd thesis example proof construction 2.3.2 *)
-
-lemma stefan_example : "(\<exists>x. \<forall>y. P x y) \<longrightarrow> (\<forall>y. \<exists>x. P x y)"
-  apply (rule impI)
-  apply(rule allI)
-  apply (erule exE)
-   apply(rule exI)
-  apply(erule allE)
-  apply (assumption)
-  done
-
-ML\<open> (*See: *) \<^file>\<open>~~/src/HOL/Proofs/ex/Proof_Terms.thy\<close>\<close>
-ML\<open>
-  val thm = @{thm stefan_example};
-
-  (*proof body with digest*)
-  val body = Proofterm.strip_thm_body (Thm.proof_body_of thm);
-
-  (*proof term only*)
-  val prf = Proofterm.proof_of body;
-
-  (*clean output*)
-  Pretty.writeln (Proof_Syntax.pretty_proof \<^context> prf);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> false thm);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> true thm);
-
-  (*all theorems used in the graph of nested proofs*)
-  val all_thms =
-    Proofterm.fold_body_thms
-      (fn {name, ...} => insert (op =) name) [body] [];
-\<close>
-ML\<open>
-val thy = \<^theory>;
-  val prf =
-    Proof_Syntax.read_proof thy true false
-      "mp \<cdot> _ \<cdot> _ \<bullet> (impI \<cdot> _ \<cdot> _ \<bullet> (conjI \<cdot> _ \<cdot> _ ))";
-      (*"conjI \<cdot> _ \<cdot> _ ";*)
-      (*"(\<^bold>\<lambda>(H: _) Ha: _. conjI \<cdot> _ \<cdot> _ \<bullet> Ha \<bullet> H)";*)
-(*val t = Proofterm.reconstruct_proof thy \<^prop>\<open>(A \<longrightarrow> B) \<Longrightarrow> A \<Longrightarrow> B\<close> prf*)
-(*  val thm =  
-    Proofterm.reconstruct_proof thy \<^prop>\<open>A \<Longrightarrow> B\<close> prf
-    |> Proof_Checker.thm_of_proof thy
-    |> Drule.export_without_context
-val pretty =  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> true thm);*)
-\<close>
-
-extract_type
-  "typeof (Trueprop P) \<equiv> typeof P"
-
-realizers
-  impI (P, Q): "\<lambda>pq. pq"
-    "\<^bold>\<lambda>(c: _) (d: _) P Q pq (h: _). allI \<cdot> _ \<bullet> c \<bullet> (\<^bold>\<lambda>x. impI \<cdot> _ \<cdot> _ \<bullet> (h \<cdot> x))"
-find_consts name:"MinProof"
-
-ML_val \<open>
-  val thy = \<^theory>;
-  val prf =
-    Proof_Syntax.read_proof thy true false
-      "impI \<cdot> _ \<cdot> _ \<bullet> \
-      \   (\<^bold>\<lambda>H: _. \
-      \     conjE \<cdot> _ \<cdot> _ \<cdot> _ \<bullet> H \<bullet> \
-      \       (\<^bold>\<lambda>(H: _) Ha: _. conjI \<cdot> _ \<cdot> _ \<bullet> Ha \<bullet> H))";
-  val thm =
-    Proofterm.reconstruct_proof thy \<^prop>\<open>A \<and> B \<longrightarrow> B \<and> A\<close> prf
-    |> Proof_Checker.thm_of_proof thy
-    |> Drule.export_without_context;
-val pretty =  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> true thm);
-\<close>
-ML_file "~~/src/Provers/classical.ML"
-lemma testtest : "A \<and> B \<longrightarrow> B \<and> A"
-  apply (rule impI)
-  apply (erule conjE)
-  apply(erule conjI)
-  apply assumption
-  done
-
-ML\<open> (*See: *) \<^file>\<open>~~/src/HOL/Proofs/ex/Proof_Terms.thy\<close>\<close>
-ML\<open>
-  val thm = @{thm testtest};
-
-  (*proof body with digest*)
-  val body = Proofterm.strip_thm_body (Thm.proof_body_of thm);
-
-  (*proof term only*)
-  val prf = Proofterm.proof_of body;
-
-  (*clean output*)
-  Pretty.writeln (Proof_Syntax.pretty_proof \<^context> prf);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> false thm);
-  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> true thm);
-
-  (*all theorems used in the graph of nested proofs*)
-  val all_thms =
-    Proofterm.fold_body_thms
-      (fn {name, ...} => insert (op =) name) [body] [];
-\<close>
-
-ML\<open>
-val thy = \<^theory>
-val prf =
-    Proof_Syntax.read_proof thy true false
-      "impI \<cdot> _ \<cdot> _ \<bullet> \
-      \   (\<^bold>\<lambda>H: _. \
-      \     conjE \<cdot> _ \<cdot> _ \<cdot> _ \<bullet> H \<bullet> \
-      \       (\<^bold>\<lambda>(H: _) Ha: _. conjI \<cdot> _ \<cdot> _ \<bullet> Ha \<bullet> H))";
-\<close>
-
-ML\<open>
-val thy = \<^theory>
-val prf =
-    Proof_Syntax.read_proof thy true false
-      "\<^bold>\<lambda>(H: A \<and> B). conjE \<cdot> A \<cdot> B \<cdot> A \<and> B \<bullet> H";
-(*  val thm =
-    Proofterm.reconstruct_proof thy \<^prop>\<open>A \<Longrightarrow> B \<Longrightarrow> B \<and> A\<close> prf
-    |> Proof_Checker.thm_of_proof thy
-    |> Drule.export_without_context;
-val pretty =  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> true thm);*)
-\<close>
-ML\<open>
-val thy = \<^theory>
-val prf =
-    Proof_Syntax.read_proof thy true false
-      "\<^bold>\<lambda>(H: _) Ha: _. conjI \<cdot> _ \<cdot> _ \<bullet> Ha \<bullet> H";
-  val thm =
-    Proofterm.reconstruct_proof thy \<^prop>\<open>A \<Longrightarrow> B \<Longrightarrow> B \<and> A\<close> prf
-    |> Proof_Checker.thm_of_proof thy
-    |> Drule.export_without_context;
-val pretty =  Pretty.writeln (Proof_Syntax.pretty_standard_proof_of \<^context> true thm);
-\<close>
- 
-end

Isabelle_DOF-Proofs/Very_Deep_DOF.thy

@@ -1,19 +0,0 @@
-theory Very_Deep_DOF
-  imports "Isabelle_DOF-Proofs.Very_Deep_Interpretation"
-
-begin
-
-(* tests *)
-term "@{typ  ''int => int''}"  
-term "@{term ''Bound 0''}"  
-term "@{thm  ''refl''}"  
-term "@{docitem  ''<doc_ref>''}"
-ML\<open>   @{term "@{docitem  ''<doc_ref>''}"}\<close>
-
-term "@{typ  \<open>int \<Rightarrow> int\<close>}"  
-term "@{term \<open>\<forall>x. P x \<longrightarrow> Q\<close>}"  
-term "@{thm  \<open>refl\<close>}"  
-term "@{docitem  \<open>doc_ref\<close>}"
-ML\<open>   @{term "@{docitem  \<open>doc_ref\<close>}"}\<close>
-
-end

Isabelle_DOF-Proofs/Very_Deep_Interpretation.thy

@@ -1,237 +0,0 @@
-theory Very_Deep_Interpretation
-  imports "Isabelle_DOF.Isa_COL"
-          Metalogic_ProofChecker.ProofTerm
-
-begin
-
-subsection\<open> Syntax \<close>
-
-\<comment> \<open>and others in the future : file, http, thy, ...\<close> 
-
-(* Delete shallow interpretation notations (mixfixes) of the term anti-quotations,
-  so we can use them for the deep interpretation *)
-no_notation "Isabelle_DOF_typ" ("@{typ _}")
-no_notation "Isabelle_DOF_term" ("@{term _}")
-no_notation "Isabelle_DOF_thm" ("@{thm _}")
-no_notation "Isabelle_DOF_file" ("@{file _}")
-no_notation "Isabelle_DOF_thy" ("@{thy _}")
-no_notation "Isabelle_DOF_docitem" ("@{docitem _}")
-no_notation "Isabelle_DOF_docitem_attr" ("@{docitemattr (_) :: (_)}")
-no_notation "Isabelle_DOF_trace_attribute" ("@{trace'_-attribute _}")
-
-consts Isabelle_DOF_typ :: "string \<Rightarrow> typ" ("@{typ _}")
-consts Isabelle_DOF_term :: "string \<Rightarrow> term" ("@{term _}")
-datatype "thm" = Isabelle_DOF_thm string ("@{thm _}") | Thm_content ("proof":proofterm)
-datatype "thms_of" = Isabelle_DOF_thms_of string ("@{thms-of _}")
-datatype "file" = Isabelle_DOF_file string  ("@{file _}")
-datatype "thy" = Isabelle_DOF_thy string  ("@{thy _}")
-consts Isabelle_DOF_docitem      :: "string \<Rightarrow> 'a"                ("@{docitem _}")
-datatype "docitem_attr" = Isabelle_DOF_docitem_attr string  string ("@{docitemattr (_) :: (_)}")
-consts Isabelle_DOF_trace_attribute :: "string \<Rightarrow> (string * string) list" ("@{trace'_-attribute _}")
-
-subsection\<open> Semantics \<close>
-
-ML\<open>
-structure Meta_ISA_core = 
-struct
-
-fun ML_isa_check_trace_attribute thy (term, _, pos) s =
-  let
-    val oid = (HOLogic.dest_string term
-                  handle TERM(_,[t]) => error ("wrong term format: must be string constant: " 
-                                               ^ Syntax.string_of_term_global thy t ))
-    val _ = DOF_core.get_instance_global oid thy
-  in SOME term end
-
-fun reify_typ (Type (s, typ_list)) =
-      \<^Const>\<open>Ty\<close> $ HOLogic.mk_literal s $ HOLogic.mk_list \<^Type>\<open>typ\<close> (map reify_typ typ_list)
-  | reify_typ (TFree (name, sort)) =
-      \<^Const>\<open>Tv\<close> $(\<^Const>\<open>Free\<close> $ HOLogic.mk_literal name)
-      $ (HOLogic.mk_set \<^typ>\<open>class\<close> (map HOLogic.mk_literal sort))
-  | reify_typ (TVar (indexname, sort)) =
-      let val (name, index_value) = indexname
-      in  \<^Const>\<open>Tv\<close>
-          $ (\<^Const>\<open>Var\<close>
-             $ HOLogic.mk_prod (HOLogic.mk_literal name, HOLogic.mk_number \<^Type>\<open>int\<close> index_value))
-          $ (HOLogic.mk_set \<^typ>\<open>class\<close> (map HOLogic.mk_literal sort)) end
-
-fun ML_isa_elaborate_typ (thy:theory) _ _ term_option _ =
-  case term_option of
-      NONE => error("Wrong term option. You must use a defined term")
-    | SOME term => let 
-                     val typ_name = HOLogic.dest_string term
-                     val typ = Syntax.read_typ_global thy typ_name
-                   in reify_typ typ end
-
-fun reify_term (Const (name, typ)) =\<^Const>\<open>Ct\<close> $ HOLogic.mk_literal name $ reify_typ typ
-  | reify_term (Free (name, typ)) =
-      \<^Const>\<open>Fv\<close> $ (\<^Const>\<open>Free\<close> $ HOLogic.mk_literal name) $ reify_typ typ
-  | reify_term (Var (indexname, typ)) =
-      let val (name, index_value) = indexname
-      in  \<^Const>\<open>Fv\<close>
-          $ (\<^Const>\<open>Var\<close>
-             $ HOLogic.mk_prod (HOLogic.mk_literal name, HOLogic.mk_number \<^Type>\<open>int\<close> index_value))
-          $ reify_typ typ end
-  | reify_term (Bound i) = \<^Const>\<open>Bv\<close> $ HOLogic.mk_nat i
-  | reify_term (Abs (_, typ, term)) = \<^Const>\<open>Abs\<close> $ reify_typ typ $ reify_term term
-  | reify_term (Term.$ (t1, t2)) = \<^Const>\<open>App\<close> $ reify_term t1 $ reify_term t2
-
-fun ML_isa_elaborate_term (thy:theory) _ _ term_option _ =
-  case term_option of
-      NONE => error("Wrong term option. You must use a defined term")
-    | SOME term => let 
-                     val term_name = HOLogic.dest_string term
-                     val term = Syntax.read_term_global thy term_name
-                   in reify_term term end
-
-fun reify_proofterm (PBound i) =\<^Const>\<open>PBound\<close> $ (HOLogic.mk_nat i)
-  | reify_proofterm (Abst (_, typ_option, proof)) =
-      \<^Const>\<open>Abst\<close> $ reify_typ (the typ_option) $ reify_proofterm proof
-  | reify_proofterm (AbsP (_, term_option, proof)) =
-      \<^Const>\<open>AbsP\<close> $ reify_term (the term_option) $ reify_proofterm proof
-  | reify_proofterm (op % (proof, term_option)) =
-      \<^Const>\<open>Appt\<close> $ reify_proofterm proof $ reify_term (the term_option)
-  | reify_proofterm (op %% (proof1, proof2)) =
-      \<^Const>\<open>AppP\<close> $ reify_proofterm proof1 $ reify_proofterm proof2
-  | reify_proofterm (Hyp term) = \<^Const>\<open>Hyp\<close> $ (reify_term term)
-  | reify_proofterm (PAxm (_, term, typ_list_option)) =
-      let 
-          val tvars = rev (Term.add_tvars term [])
-          val meta_tvars = map (fn ((name, index_value), sort) =>
-                HOLogic.mk_prod
-                  (\<^Const>\<open>Var\<close>                    
-                   $ HOLogic.mk_prod
-                      (HOLogic.mk_literal name, HOLogic.mk_number \<^Type>\<open>int\<close> index_value)
-                       , HOLogic.mk_set \<^typ>\<open>class\<close> (map HOLogic.mk_literal sort))) tvars
-          val meta_typ_list = 
-            HOLogic.mk_list @{typ "tyinst"} (map2 (fn x => fn y => HOLogic.mk_prod (x, y))
-                                              meta_tvars (map reify_typ (the typ_list_option)))
-      in \<^Const>\<open>PAxm\<close> $ reify_term term $ meta_typ_list end
-  | reify_proofterm (PClass (typ, class)) =
-      \<^Const>\<open>OfClass\<close> $ reify_typ typ $ HOLogic.mk_literal class
-  | reify_proofterm (PThm ({prop = prop, types = types, ...}, _)) =
-      let
-        val tvars = rev (Term.add_tvars prop [])
-        val meta_tvars = map (fn ((name, index_value), sort) =>
-                HOLogic.mk_prod
-                  (\<^Const>\<open>Var\<close>                    
-                  $ HOLogic.mk_prod
-                      (HOLogic.mk_literal name, HOLogic.mk_number \<^Type>\<open>int\<close> index_value)
-                  , HOLogic.mk_set \<^typ>\<open>class\<close> (map HOLogic.mk_literal sort))) tvars
-        val meta_typ_list = 
-            HOLogic.mk_list \<^typ>\<open>tyinst\<close> (map2 (fn x => fn y => HOLogic.mk_prod (x, y))
-                                          meta_tvars (map reify_typ (the types)))
-      in \<^Const>\<open>PAxm\<close> $ reify_term prop $ meta_typ_list end
-
-fun ML_isa_elaborate_thm (thy:theory) _ _ term_option pos =
-  case term_option of
-      NONE => ISA_core.err ("Malformed term annotation") pos
-    | SOME term =>
-        let
-          val thm_name = HOLogic.dest_string term
-          val _ = writeln ("In ML_isa_elaborate_thm thm_name: " ^ \<^make_string> thm_name)
-          val thm = Proof_Context.get_thm (Proof_Context.init_global thy) thm_name
-          val _ = writeln ("In ML_isa_elaborate_thm thm: " ^ \<^make_string> thm)
-          val body = Proofterm.strip_thm_body (Thm.proof_body_of thm);
-          val prf = Proofterm.proof_of body;
-          (* Proof_Syntax.standard_proof_of reconstructs the proof and seems to rewrite
-             the option arguments (with a value NONE) of the proof datatype constructors,
-             at least for PAxm, with "SOME (typ/term)",
-             allowing us the use the projection function "the".
-             Maybe the function can deal with
-             all the option types of the proof datatype constructors *)
-          val proof = Proof_Syntax.standard_proof_of
-                                   {full = true, expand_name = Thm.expand_name thm} thm
-          val _ = writeln ("In ML_isa_elaborate_thm proof: " ^ \<^make_string> proof)
-          (* After a small discussion with Simon Roßkopf, It seems preferable to use
-             Thm.reconstruct_proof_of instead of Proof_Syntax.standard_proof_of
-             whose operation is not well known.
-             Thm.reconstruct_proof_of seems sufficient to have a reifiable PAxm
-             in the metalogic. *)
-          val proof' = Thm.reconstruct_proof_of thm 
-        (*in \<^Const>\<open>Thm_content\<close> $ reify_proofterm prf end*)        
-        (*in \<^Const>\<open>Thm_content\<close> $ reify_proofterm proof end*)
-        in \<^Const>\<open>Thm_content\<close> $ reify_proofterm proof end
-
-
-fun ML_isa_elaborate_thms_of (thy:theory) _ _ term_option pos =
-  case term_option of
-      NONE => ISA_core.err ("Malformed term annotation") pos
-    | SOME term =>
-        let
-          val thm_name = HOLogic.dest_string term
-          val thm = Proof_Context.get_thm (Proof_Context.init_global thy) thm_name
-          val body = Proofterm.strip_thm_body (Thm.proof_body_of thm)
-          val all_thms_name = Proofterm.fold_body_thms (fn {name, ...} => insert (op =) name) [body] []
-          (*val all_thms = map (Proof_Context.get_thm (Proof_Context.init_global thy)) all_thms_name*)
-          (*val all_proofs = map (Proof_Syntax.standard_proof_of
-                                   {full = true, expand_name = Thm.expand_name thm}) all_thms*)
-        (*in HOLogic.mk_list \<^Type>\<open>thm\<close> (map (fn proof => \<^Const>\<open>Thm_content\<close> $ reify_proofterm proof) all_proofs) end*)
-        in HOLogic.mk_list \<^typ>\<open>string\<close> (map HOLogic.mk_string all_thms_name) end
-
-fun ML_isa_elaborate_trace_attribute (thy:theory) _ _ term_option pos =
-case term_option of
-    NONE => ISA_core.err ("Malformed term annotation") pos
-  | SOME term => 
-      let
-        val oid = HOLogic.dest_string term
-        val traces = ISA_core.compute_attr_access (Context.Theory thy) "trace" oid NONE pos
-        fun conv (\<^Const>\<open>Pair \<^typ>\<open>doc_class rexp\<close> \<^typ>\<open>string\<close>\<close>
-                    $ (\<^Const>\<open>Atom \<^typ>\<open>doc_class\<close>\<close> $ (\<^Const>\<open>mk\<close> $ s)) $ S) =
-          let val s' =  DOF_core.get_onto_class_name_global (HOLogic.dest_string s) thy 
-          in \<^Const>\<open>Pair \<^typ>\<open>string\<close> \<^typ>\<open>string\<close>\<close> $ HOLogic.mk_string s' $ S end
-        val traces' = map conv (HOLogic.dest_list traces)
-      in HOLogic.mk_list \<^Type>\<open>prod \<^typ>\<open>string\<close> \<^typ>\<open>string\<close>\<close> traces' end
-
-end; (* struct *)
-
-\<close>
-
-ML\<open>
-val ty1 = Meta_ISA_core.reify_typ @{typ "int"}
-val ty2 = Meta_ISA_core.reify_typ @{typ "int \<Rightarrow> bool"}
-val ty3 = Meta_ISA_core.reify_typ @{typ "prop"}
-val ty4 = Meta_ISA_core.reify_typ @{typ "'a list"}
-\<close>
-
-ML\<open>
-val t1 = Meta_ISA_core.reify_term @{term "1::int"}
-val t2 = Meta_ISA_core.reify_term @{term "\<lambda>x. x = 1"}
-val t3 = Meta_ISA_core.reify_term @{term "[2, 3::int]"}
-\<close>
-
-subsection\<open> Isar - Setup\<close>
-(* Isa_transformers declaration for Isabelle_DOF term anti-quotations (typ, term, thm, etc.).
-   They must be declared in the same theory file as the one of the declaration
-   of Isabelle_DOF term anti-quotations !!! *)
-setup\<open>
-[(\<^type_name>\<open>thm\<close>, ISA_core.ML_isa_check_thm, Meta_ISA_core.ML_isa_elaborate_thm)
- , (\<^type_name>\<open>thms_of\<close>, ISA_core.ML_isa_check_thm, Meta_ISA_core.ML_isa_elaborate_thms_of)
- , (\<^type_name>\<open>file\<close>, ISA_core.ML_isa_check_file, ISA_core.ML_isa_elaborate_generic)]
-|> fold (fn (n, check, elaborate) => fn thy =>
-let val ns = Sign.tsig_of thy |> Type.type_space
-    val name = n
-    val {pos, ...} = Name_Space.the_entry ns name
-    val bname = Long_Name.base_name name
-    val binding = Binding.make (bname, pos)
-                   |> Binding.prefix_name DOF_core.ISA_prefix
-                   |> Binding.prefix false bname
-in  DOF_core.add_isa_transformer binding ((check, elaborate) |> DOF_core.make_isa_transformer) thy
-end)
-#>
-([(\<^const_name>\<open>Isabelle_DOF_typ\<close>, ISA_core.ML_isa_check_typ, Meta_ISA_core.ML_isa_elaborate_typ)
-  ,(\<^const_name>\<open>Isabelle_DOF_term\<close>, ISA_core.ML_isa_check_term, Meta_ISA_core.ML_isa_elaborate_term)
-  ,(\<^const_name>\<open>Isabelle_DOF_docitem\<close>,
-      ISA_core.ML_isa_check_docitem, ISA_core.ML_isa_elaborate_generic)
-  ,(\<^const_name>\<open>Isabelle_DOF_trace_attribute\<close>,
-      ISA_core.ML_isa_check_trace_attribute, ISA_core.ML_isa_elaborate_trace_attribute)]
-|> fold (fn (n, check, elaborate) => fn thy =>
-let val ns = Sign.consts_of thy |> Consts.space_of
-    val name = n
-    val {pos, ...} = Name_Space.the_entry ns name
-    val bname =  Long_Name.base_name name
-    val binding = Binding.make (bname, pos)
-in  DOF_core.add_isa_transformer binding ((check, elaborate) |> DOF_core.make_isa_transformer) thy
-end))
-\<close>
-end

Isabelle_DOF-Unit-Tests/AssnsLemmaThmEtc.thy

@@ -1,237 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019      The University of Exeter 
- *               2018-2019 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-chapter\<open>Testing Freeform and Formal Elements from the scholarly-paper Ontology\<close>
-
-theory 
-  AssnsLemmaThmEtc
-imports 
-  "Isabelle_DOF-Ontologies.Conceptual"  
-  "Isabelle_DOF.scholarly_paper"
-  "Isabelle_DOF_Unit_Tests_document"
-  TestKit
-begin
-
-section\<open>Test Objective\<close>
-
-text\<open>Testing Core Elements for \<^theory>\<open>Isabelle_DOF.scholarly_paper\<close> wrt. to 
-existance, controlability via implicit and explicit default classes, and potential 
-LaTeX Layout.\<close>
-
-text\<open>Current status:\<close>
-print_doc_classes
-print_doc_items
-
-
-section\<open>An Example for use-before-declaration of Formal Content\<close>
-
-text*[aa::F, properties = "[@{term ''True''}]"]
-\<open>Our definition of the HOL-Logic has the following properties:\<close>
-assert*\<open>F.properties @{F \<open>aa\<close>} = [@{term ''True''}]\<close>
-
-text\<open>For now, as the term annotation is not bound to a meta logic which will translate
-\<^term>\<open>[@{term ''True''}]\<close> to \<^term>\<open>[True]\<close>, we can not use the HOL \<^const>\<open>True\<close> constant
-in the assertion.\<close>
-
-ML\<open> @{term_ "[@{term \<open>True \<longrightarrow> True \<close>}]"}; (* with isa-check *)  \<close>
-
-ML\<open> 
-    (* Checking the default classes which should be in a neutral(unset) state. *)
-    (* Note that in this state, the "implicit default" is "math_content". *) 
-    @{assert} (Config.get_global @{theory} Definition_default_class = "");
-    @{assert} (Config.get_global @{theory} Lemma_default_class = "");
-    @{assert} (Config.get_global @{theory} Theorem_default_class = "");
-    @{assert} (Config.get_global @{theory} Proposition_default_class = "");
-    @{assert} (Config.get_global @{theory} Premise_default_class = "");
-    @{assert} (Config.get_global @{theory} Corollary_default_class = "");
-    @{assert} (Config.get_global @{theory} Consequence_default_class = "");
-    @{assert} (Config.get_global @{theory} Assumption_default_class = "");
-    @{assert} (Config.get_global @{theory} Hypothesis_default_class = "");
-    @{assert} (Config.get_global @{theory} Consequence_default_class = "");
-    @{assert} (Config.get_global @{theory} Assertion_default_class = "");
-    @{assert} (Config.get_global @{theory} Proof_default_class = "");
-    @{assert} (Config.get_global @{theory} Example_default_class = "");
-\<close>
-
-
-Definition*[e1]\<open>Lorem ipsum dolor sit amet, ... \<close>
-text\<open>Note that this should yield a warning since \<^theory_text>\<open>Definition*\<close>  uses as "implicit default" the class
-    \<^doc_class>\<open>math_content\<close> which has no \<^term>\<open>text_element.level\<close> set, however in this context,
-    it is required to be a positive number since it is \<^term>\<open>text_element.referentiable\<close> . 
-    This is intended behaviour in order to give the user a nudge to be more specific.\<close> 
-
-text\<open>A repair looks like this:\<close>
-declare [[Definition_default_class = "definition"]]
-
-text\<open>Now, define a forward reference to the formal content: \<close>
-
-declare_reference*[e1bisbis::"definition"]
-
-text\<open>... which makes it possible to refer in a freeform definition to its formal counterpart
-which will appear textually later. With this pragmatics, an "out-of-    order-presentation" 
-can be achieved within \<^theory>\<open>Isabelle_DOF.scholarly_paper\<close> for the most common cases.\<close>
-
-
-(*<*) (* PDF references to definition* not implemented *)
-Definition*[e1bis::"definition", short_name="\<open>Nice lemma.\<close>"]
-   \<open>Lorem ipsum dolor sit amet, ... 
-    This is formally defined as follows in @{definition (unchecked) "e1bisbis"}\<close>
-definition*[e1bisbis, status=formal] e :: int where "e = 2"
-(*>*)
-section\<open>Tests for Theorems, Assertions, Assumptions, Hypothesis, etc.\<close>
-
-declare [[Theorem_default_class     = "theorem",
-          Premise_default_class     = "premise",
-          Hypothesis_default_class  = "hypothesis",
-          Assumption_default_class  = "assumption",
-          Conclusion_default_class  = "conclusion",
-          Consequence_default_class = "consequence",
-          Assertion_default_class   = "assertion",
-          Corollary_default_class   = "corollary",
-          Proof_default_class       = "math_proof",
-          Conclusion_default_class  = "conclusion_stmt"]]
-
-Theorem*[e2]\<open>... suspendisse non arcu malesuada mollis, nibh morbi, ... \<close>
-
-theorem*[e2bis::"theorem", status=formal] f : "e = 1+1" unfolding e_def by simp
-
-(*<*) (* @{theorem "e2bis"} breaks LaTeX generation ... *)
-Lemma*[e3,level="Some 2"]
-\<open>... phasellus amet id massa nunc, pede suscipit repellendus, ... @{theorem "e2bis"} \<close>
-(*>*) 
-Proof*[d10, short_name="\<open>Induction over Tinea pedis.\<close>"]\<open>Freeform Proof\<close>
-
-lemma*[dfgd::"lemma"] q: "All (\<lambda>x. X \<and> Y \<longrightarrow> True)" oops
-text-assert-error\<open>@{lemma dfgd} \<close>\<open>Undefined instance:\<close> \<comment> \<open>oops‘ed objects are not referentiable.\<close>
-
-text\<open>... in ut tortor eleifend augue pretium consectetuer...  
-     Lectus accumsan velit ultrices, ...\<close>
-
-Proposition*[d2::"proposition"]\<open>"Freeform Proposition"\<close> 
-
-Assumption*[d3] \<open>"Freeform Assertion"\<close>
-
-Premise*[d4]\<open>"Freeform Premise"\<close> 
-
-Corollary*[d5]\<open>"Freeform Corollary"\<close> 
-
-Consequence*[d6::scholarly_paper.consequence]\<open>"Freeform Consequence"\<close> \<comment> \<open>longname just for test\<close>
-
-(*<*)
-declare_reference*[ababa::scholarly_paper.assertion]
-Assertion*[d7]\<open>Freeform Assumption with forward reference to the formal  
-               @{assertion (unchecked) ababa}.\<close>  
-assert*[ababa::assertion] "3 < (4::int)"
-assert*[ababab::assertion] "0 < (4::int)"
-(*>*)
-
-Conclusion*[d8]\<open>"Freeform Conclusion"\<close>
-
-Hypothesis*[d9]\<open>"Freeform Hypothesis"\<close> 
-
-Example*[d11::math_example]\<open>"Freeform Example"\<close> 
-
-text\<open>An example for the ontology specification character of the short-cuts such as 
-@{command  "assert*"}: in the following, we use the same notation referring to a completely
-different class. "F" and "assertion" have only in common that they posses the attribute
-@{const [names_short] \<open>properties\<close>}: \<close>
-
-section\<open>Exhaustive Scholarly\_paper Test\<close>
-
-subsection\<open>Global Structural Elements\<close>
-(* maybe it is neither necessary nor possible to test these here... title is unique in
-   a document, for example. To be commented out of needed. *)
-text*[tt1::scholarly_paper.title]\<open>Lectus accumsan velit ultrices, ...\<close> 
-text*[tt2::scholarly_paper.author]\<open>Lectus accumsan velit ultrices, ...\<close>  
-text*[tt3::scholarly_paper.article]\<open>Lectus accumsan velit ultrices, ...\<close> 
-text*[tt4::scholarly_paper.annex]\<open>Lectus accumsan velit ultrices, ...\<close>  
-text*[tt5::scholarly_paper.abstract]\<open>Lectus accumsan velit ultrices, ...\<close>  
-text*[tt6::scholarly_paper.subtitle]\<open>Lectus accumsan velit ultrices, ...\<close> 
-text*[tt7::scholarly_paper.bibliography]\<open>Lectus accumsan velit ultrices, ...\<close>        
-text*[tt8::scholarly_paper.introduction]\<open>Lectus accumsan velit ultrices, ...\<close> 
-text*[tt9::scholarly_paper.related_work]\<open>Lectus accumsan velit ultrices, ...\<close>        
-text*[tt11::scholarly_paper.text_section]\<open>Lectus accumsan velit ultrices, ...\<close>        
-text*[tt12::scholarly_paper.background ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tt13::scholarly_paper.conclusion ]\<open>Lectus accumsan velit ultrices, ...\<close>
-
-subsection\<open>Technical Content Specific Elements\<close>
-
-text*[tu1::scholarly_paper.axiom    ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu1bis::scholarly_paper.math_content, mcc="axm"   ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu2::scholarly_paper.lemma    ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu3::scholarly_paper.example  ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu4::scholarly_paper.premise  ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu5::scholarly_paper.theorem  ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu6::scholarly_paper.assertion]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu7::scholarly_paper.corollary]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu9::scholarly_paper.technical]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu10::scholarly_paper.assumption ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu13::scholarly_paper.definition ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu15::scholarly_paper.experiment ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu16::scholarly_paper.hypothesis ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu17::scholarly_paper.math_proof ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu18::scholarly_paper.consequence]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu19::scholarly_paper.math_formal]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu20::scholarly_paper.proposition]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu21::scholarly_paper.math_content    ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu22::scholarly_paper.math_example    ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu23::scholarly_paper.conclusion_stmt ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu24::scholarly_paper.math_motivation ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu25::scholarly_paper.tech_definition ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu28::scholarly_paper.eng_example     ]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tt10::scholarly_paper.tech_example]\<open>Lectus accumsan velit ultrices, ...\<close>        
-text*[tu8::scholarly_paper.tech_code]        \<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu27::scholarly_paper.engineering_content]\<open>Lectus accumsan velit ultrices, ...\<close>
-text*[tu14::scholarly_paper.evaluation ]\<open>Lectus accumsan velit ultrices, ...\<close>
-
-text\<open> @{axiom tu1} @{lemma tu2} @{example tu3} @{premise tu4} @{theorem tu5} @{assertion tu6} 
-      @{technical tu9} @{assumption             tu10 }  @{definition             tu13 }
-      @{experiment      tu15 } @{hypothesis      tu16 } @{math_proof      tu17 }
-      @{consequence     tu18 } @{math_formal     tu19 } @{proposition     tu20 }
-      @{math_content    tu21 } @{math_example    tu22 } @{conclusion_stmt tu23 }
-      @{math_motivation tu24 } @{tech_definition tu25 } @{eng_example     tu28 }
-      @{tech_example    tt10 } @{tech_code       tu8 }  @{engineering_content tu27 }
-      @{evaluation      tu14 }
-    \<close>
-
-subsection\<open>The Use in Macros\<close>
-
-Lemma*[ttu2::scholarly_paper.lemma    ]\<open>Lectus accumsan velit ultrices, ...\<close>
-Example*[ttu3::scholarly_paper.math_example  ]\<open>Lectus accumsan velit ultrices, ...\<close>
-Premise*[ttu4::scholarly_paper.premise  ]\<open>Lectus accumsan velit ultrices, ...\<close>
-Theorem*[ttu5::scholarly_paper.theorem  ]\<open>Lectus accumsan velit ultrices, ...\<close>
-Assertion*[ttu6::scholarly_paper.assertion]\<open>Lectus accumsan velit ultrices, ...\<close>
-Corollary*[ttu7::scholarly_paper.corollary]\<open>Lectus accumsan velit ultrices, ...\<close>
-Assumption*[ttu10::scholarly_paper.assumption ]\<open>Lectus accumsan velit ultrices, ...\<close>
-Definition*[ttu13::scholarly_paper.definition ]\<open>Lectus accumsan velit ultrices, ...\<close>
-Hypothesis*[ttu16::scholarly_paper.hypothesis ]\<open>Lectus accumsan velit ultrices, ...\<close>
-Proof*[ttu17::scholarly_paper.math_proof ]\<open>Lectus accumsan velit ultrices, ...\<close>
-Consequence*[ttu18::scholarly_paper.consequence]\<open>Lectus accumsan velit ultrices, ...\<close>
-Proposition*[ttu20::scholarly_paper.proposition]\<open>Lectus accumsan velit ultrices, ...\<close>
-Conclusion*[ttu23::scholarly_paper.conclusion_stmt ]\<open>Lectus accumsan velit ultrices, ...\<close>
-(* Definition*[ttu25::scholarly_paper.tech_definition ]\<open>Lectus accumsan velit ultrices, ...\<close> 
-   interesting modeling bug.
-*)
-(*Example*[ttu28::scholarly_paper.eng_example     ]\<open>Lectus accumsan velit ultrices, ...\<close>
-   interesting modeling bug.
-*)  
-text\<open> @{lemma ttu2} @{math_example ttu3} @{premise ttu4} @{theorem ttu5} @{assertion ttu6} 
-      @{assumption ttu10 }  @{definition ttu13 }
-      @{hypothesis      ttu16 } @{math_proof      ttu17 }
-      @{consequence     ttu18 } @{proposition     ttu20 }
-      @{math_content    tu21 }  @{conclusion_stmt ttu23 }
-      @ \<open>{eng_example     ttu28 }\<close>
-      @ \<open>{tech_example    tt10 }\<close>  
-    \<close>
-
-end

Isabelle_DOF-Unit-Tests/Attributes.thy

@@ -1,233 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019      The University of Exeter 
- *               2018-2019 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-theory 
-  Attributes
-  imports 
-  "Isabelle_DOF_Unit_Tests_document"
-  "Isabelle_DOF-Ontologies.Conceptual"
-  Concept_MonitorTest1
-begin
-ML\<open>@{assert} (1 = 1)\<close>
-section\<open>Elementar Creation of Doc-items and Access of their Attibutes\<close>
-
-text\<open>Current status:\<close>
-print_doc_classes
-print_doc_items
-
-(* this corresponds to low-level accesses : *)
-ML\<open>  
-val docitem_tab = DOF_core.get_instances \<^context>
-val isa_transformer_tab = DOF_core.get_isa_transformers \<^context>
-val docclass_tab = DOF_core.get_onto_classes @{context};
-\<close>
-ML\<open>
-map fst (Name_Space.dest_table docitem_tab);
-Name_Space.dest_table docclass_tab;
-
-\<close>
-
-
-
-find_theorems (60) name:"Conceptual.M." 
-
-value [simp]"M.trace(M.make undefined [] ())"
-value "M.ok(M.make undefined_AAA [] ())"
-value "M.trace(M.make undefined_AAA [] ())"
-value "M.tag_attribute(M.make undefined_AAA [] ())"
-
-
-value "M.ok(M.make 0 [] ())"
-(*
-value "ok(M.make undefined [] ())"
-value "ok(M.make 0 [] undefined)"
-*)
-
-value [simp] \<open> M.ok 
-                   (Conceptual.M.trace_update (\<lambda>x. [])
-                    (Conceptual.M.tag_attribute_update (\<lambda>x. 0)
-                     (Conceptual.M.ok_update (\<lambda>x. ())
-                   (undefined::M)) 
-                   ))\<close>
-
-value [simp] \<open> M.ok 
-                   (Conceptual.M.trace_update (\<lambda>x. [])
-                    (Conceptual.M.tag_attribute_update (\<lambda>x. 0)
-                     (Conceptual.M.ok_update (\<lambda>x. ())
-                   (undefined::M)) 
-                   ))\<close>
-value  \<open> M.ok 
-                   (Conceptual.M.trace_update (\<lambda>x. [])
-                    (Conceptual.M.tag_attribute_update (\<lambda>x. 0)
-                     (Conceptual.M.ok_update (\<lambda>x. ())
-                   (AAAA::M)) 
-                   ))\<close>
-
-
-value  \<open> M.ok 
-                   (Conceptual.M.trace_update (\<lambda>x. [])
-                    (Conceptual.M.tag_attribute_update (\<lambda>x. 0)
-                     (Conceptual.M.ok_update (\<lambda>x. ())
-                   (M.make XX1 XX2 XX3::M)) 
-                   ))\<close>
-
-
-text\<open>A text item containing standard theorem antiquotations and complex meta-information.\<close>
-(* crashes in batch mode ... 
-text*[dfgdfg::B, Conceptual.B.x ="''f''", y = "[''sdf'']"]\<open> Lorem ipsum ...  @{thm refl} \<close>
-*)
-text*[dfgdfg::B]\<open> Lorem ipsum ...  @{thm refl} \<close>
-
-text\<open>document class declarations lead also HOL-type declarations (relevant for ontological links).\<close>
-typ "C"
-typ "D"
-text\<open> ... as well as HOL-constant declarations (relevant for monitor rexps and tracres.).\<close>
-term "C"
-
-text\<open>Voila what happens on the ML level:\<close>
-ML\<open>val Type("Conceptual.B.B_ext",[Type("Conceptual.C.C_ext",t)]) = @{typ "C"};
-   val \<^typ>\<open>D\<close> = DOF_core.get_onto_class_cid \<^theory> "Conceptual.D"
-                    |> snd ;
-   val \<^typ>\<open>E\<close> = DOF_core.get_onto_class_cid \<^theory> "Conceptual.E"
-                    |> snd;
-  \<close>
-
-text*[dfgdfg2::C, z = "None"]\<open> Lorem ipsum ... @{thm refl} \<close> 
-
-text*[omega::E, x = "''def''"]\<open> Lorem ipsum ... @{thm refl} \<close> 
-
-text\<open> As mentioned in @{docitem \<open>dfgdfg\<close>} \<close>
-
-text\<open>Here is a simulation what happens on the level of the (HOL)-term representation:\<close>
-typ \<open>'a A_scheme\<close>
-typ \<open>A\<close>
-term "A.x (undefined\<lparr>A.x := 3\<rparr>)"
-term "B.x ((undefined::C)\<lparr>B.y := [''sdf'']\<rparr>)"
-term "C.z ((undefined::C)\<lparr>B.y := [''sdf''], z:= Some undefined\<rparr>)"
-
-ML\<open>
-val SOME {def_occurrence = "Conceptual.A", long_name = "Conceptual.A.x", typ = t, def_pos} 
-    = DOF_core.get_attribute_info  "Conceptual.A" "x" @{theory};
-DOF_core.get_attribute_info  "Conceptual.B" "x" @{theory};
-DOF_core.get_attribute_info  "Conceptual.B" "y" @{theory};
-DOF_core.get_attribute_info  "Conceptual.C" "x" @{theory};
-val SOME {def_occurrence = "Conceptual.C", long_name = "Conceptual.B.y", typ = t', def_pos}
-    = DOF_core.get_attribute_info  "Conceptual.C" "y" @{theory};
-    (* this is the situation where an attribute is defined in C, but due to inheritance
-       from B, where it is firstly declared which results in a different long_name. *)
-DOF_core.get_attribute_info  "Conceptual.C" "z" @{theory};
-\<close>
-
-
-ML\<open>
-DOF_core.value_of "sdf" \<^theory>;
-DOF_core.value_of "sdfg" \<^theory>;
-DOF_core.value_of "dfgdfg" \<^theory>;
-DOF_core.value_of "omega" \<^theory>;
-\<close>
-
-text\<open>A not too trivial test: default y -> [].
-     At creation :  x -> "f", y -> "sdf".
-     The latter wins at access time.
-     Then @{term "t"}: creation of a multi inheritance object omega,
-     triple updates, the last one wins.\<close>
-ML\<open>val s = map HOLogic.dest_string (HOLogic.dest_list @{docitem_attribute y::dfgdfg});
-   val t = HOLogic.dest_string (@{docitem_attribute x::omega});  \<close>
-
-
-
-
-section\<open>Mutation of Attibutes in DocItems\<close>
-
-ML\<open> val Const("Groups.zero_class.zero", @{typ "int"}) =  @{docitem_attribute a2::omega} \<close>
-
-update_instance*[omega::E, a2+="1"]
-
-ML\<open> val (s as Const("Groups.one_class.one", @{typ "int"}))=  @{docitem_attribute a2 :: omega} \<close>
-
-update_instance*[omega::E, a2+="6"]
-
-ML\<open> @{docitem_attribute a2::omega};
-    val s =  HOLogic.dest_number @{docitem_attribute a2::omega} \<close>
-
-type_synonym ALFACENTAURI = E
-
-update_instance*[omega::E, x+="''inition''"]
-
-ML\<open> val s = HOLogic.dest_string ( @{docitem_attribute x::omega}) \<close>
-                            
-update_instance*[omega::E, y+="[''defini'',''tion'']"]
-
-update_instance*[omega::E, y+="[''en'']"]
-
-ML\<open> val s =  map HOLogic.dest_string (HOLogic.dest_list @{docitem_attribute y::omega}); \<close>
-
-subsection\<open> Example text antiquotation:\<close>
-text\<open> @{docitem_attribute y::omega}  \<close>
-
-
-section\<open>Simulation of a Monitor\<close>
-
-declare[[free_class_in_monitor_checking]]
-
-
-ML\<open>val monitor_infos = DOF_core.get_monitor_infos \<^context>\<close>
-figure*[fig_C::figure, 
-        relative_width="90",
-        file_src="''figures/A.png''"]
-       \<open> The C train \ldots \<close>
-
-
-ML\<open>val monitor_infos = DOF_core.get_monitor_infos \<^context>\<close>
-
-
-
-declare[[free_class_in_monitor_checking = false]]
-
-text\<open>Resulting trace of figs1 as ML antiquotation: \<close>
-
-text\<open>Resulting trace of figs as text antiquotation:\<close>
-
-
-
-section\<open>A Complex Evaluation involving Automatas\<close>
-
-text\<open>Test trace\_attribute term antiquotation:\<close>
-
-notation Star  ("\<lbrace>(_)\<rbrace>\<^sup>*" [0]100)
-notation Plus  (infixr "||" 55)
-notation Times (infixr "~~" 60)
-notation Atom  ("\<lfloor>_\<rfloor>" 65)
-
-definition example_expression where "example_expression \<equiv> \<lbrace>\<lfloor>''Conceptual.A''\<rfloor> || \<lfloor>''Conceptual.F''\<rfloor>\<rbrace>\<^sup>*"
-
-no_notation Star  ("\<lbrace>(_)\<rbrace>\<^sup>*" [0]100)
-no_notation Plus  (infixr "||" 55)
-no_notation Times (infixr "~~" 60)
-no_notation Atom  ("\<lfloor>_\<rfloor>" 65)
-
-value* \<open> DA.accepts (na2da (rexp2na example_expression)) (map fst @{trace_attribute \<open>aaa\<close>}) \<close>
-
-definition word_test  :: "'a list \<Rightarrow> 'a rexp \<Rightarrow> bool" (infix "is-in" 60)
-  where " w is-in rexp \<equiv>  DA.accepts (na2da (rexp2na rexp)) (w)"
-
-value* \<open> (map fst @{trace_attribute \<open>aaa\<close>}) is-in example_expression \<close>
-
-
-(*<*)
-text\<open>Final Status:\<close>
-print_doc_items
-print_doc_classes 
-
-end
-(*>*)

Isabelle_DOF-Unit-Tests/COL_Test.thy

@@ -1,59 +0,0 @@
-theory 
-  COL_Test
-imports 
-  "Isabelle_DOF_Unit_Tests_document"
-begin
-
-
-print_doc_items
-print_doc_classes
-
-section\<open>General Heading COL Elements\<close> 
-
-chapter*[S1::"chapter"]\<open>Chapter\<close>
-text*[S1'::"chapter"]\<open>Chapter\<close>
-
-section*[S2::"section"]\<open>Section\<close>
-text*[S2'::"section"]\<open>Section\<close>
-
-subsection*[S3::"subsection"]\<open>Subsection\<close>
-text*[S3'::"subsection"]\<open>Subsection\<close>
-
-subsubsection*[S4::"subsubsection"]\<open>Subsubsection\<close>
-text*[S4'::"subsubsection"]\<open>Subsubsection\<close>
-
-paragraph*[S5::"paragraph"]\<open>PAragraph\<close>
-text*[S5'::"paragraph"]\<open>Paragraph\<close>
-
-
-section\<open>General Figure COL Elements\<close> 
-
-figure*[fig1_test,relative_width="95",file_src="''figures/A.png''"]
-       \<open> This is the label text  \<^term>\<open>\<sigma>\<^sub>i+2\<close> \<close>  
-
-(*<*) (* text* with type figure not supported *)
-text*[fig2_test::figure, relative_width="95",file_src="''figures/A.png''"
-]\<open> This is the label text\<close>
-
-text\<open>check @{figure fig1_test} cmp to @{figure fig2_test}\<close>
-(*>*)
-
-
-(* And a side-chick ... *)
-
-text*[inlinefig::float, 
-      main_caption="\<open>The Caption.\<close>"]
-     \<open>@{theory_text [display, margin = 5] \<open>lemma A :: "a \<longrightarrow> b"\<close>}\<close>
-
-text*[dupl_graphics::float, 
-      main_caption="\<open>The Caption.\<close>"]
-\<open>
-@{fig_content (width=40, height=35, caption="This is a left test") "figures/A.png"
-}\<^hfill>@{fig_content (width=40, height=35, caption="This is a right \<^term>\<open>\<sigma>\<^sub>i + 1\<close> test") "figures/B.png"} 
-\<close>
-
-
-
-end
-(*>*)
-

Isabelle_DOF-Unit-Tests/Cenelec_Test.thy

@@ -1,70 +0,0 @@
-theory 
-  Cenelec_Test
-imports 
-  "Isabelle_DOF_Unit_Tests_document"
-  "Isabelle_DOF-Ontologies.CENELEC_50128"
-begin
-
-declare[[strict_monitor_checking = true]]
-declare[[invariants_checking = true]]
-declare[[invariants_checking_with_tactics = true]]
-
-print_doc_items
-print_doc_classes
-
-open_monitor*[SIL0Test::monitor_SIL0]
-
-text*[sqap_instance::SQAP, sil="SIL0", written_by="Some RQM", fst_check="Some VER", snd_check="Some VAL"]\<open>\<close>
-text*[sqavr_instance::SQAVR, sil= "SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[scmp_instance::SCMP, sil="SIL0", written_by="Some CM", fst_check="Some VER", snd_check="Some VAL"]\<open>\<close>
-text*[svp_instance::SVP, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[svap_instance::SVAP, sil="SIL0", written_by="Some VAL", fst_check="Some VER", snd_check="None"]\<open>\<close>
-text*[swrs_instance::SWRS, sil="SIL0", written_by="Some RQM", fst_check="Some VER", snd_check="Some VAL"]\<open>\<close>
-text*[oswts_instance::OSWTS, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swrvr_instance::SWRVR, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swas_instance::SWAS, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swds_instance::SWDS, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swis_instance::SWIS, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swits_instance::SWITS, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swhits_instance::SWHITS, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swadvr_instance::SWADVR, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swcds_instance::SWCDS, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swcts_instance::SWCTS, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swcdvr_instance::SWCDVR, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swscd_instance::SWSCD, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swctr_instance::SWCTR, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swscvr_instance::SWSCVR, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[switr_instance::SWITR, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swhaitr_instance::SWHAITR, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swivr_instance::SWIVR, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[oswtr_instance::OSWTR, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swvalr_instance::SWVALR, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[tvalr_instance::TVALR, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swvrn_instance::SWVRN, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[ars_instance::ARS, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[app_instance::APP, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[ats_instance::ATS, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[aad_instance::AAD, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[apvr_instance::APVR, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[atr_instance::ATR, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[socoada_instance::SOCOADA, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[adavr_instance::ADAVR, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swrdp_instance::SWRDP, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swdm_instance::SWDM, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swdrn_instance::SWDRN, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swdr_instance::SWDR, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swdvr_instance::SWDVR, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swmp_instance::SWMP, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swcr_instance::SWCR, sil="SIL0", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swmr_instance::SWMR, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swmvr_instance::SWMVR, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swap_instance::SWAP, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-text*[swar_instance::SWAR, sil="SIL0", nlvl="R", written_by="Some VER", fst_check="None", snd_check="Some VAL"]\<open>\<close>
-
-close_monitor*[SIL0Test]
-
-declare[[strict_monitor_checking = true]]
-declare[[invariants_checking = true]]
-declare[[invariants_checking_with_tactics = true]]
-
-end 

Isabelle_DOF-Unit-Tests/Concept_Example_Low_Level_Invariant.thy

@@ -1,162 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2023 The University of Exeter 
- *               2018-2023 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-chapter\<open>Testing hand-programmed (low-level) Invariants\<close>
-
-theory Concept_Example_Low_Level_Invariant
-  imports 
-  "Isabelle_DOF_Unit_Tests_document"
-  "Isabelle_DOF-Ontologies.Conceptual" (* we use the generic "Conceptual" ontology *)
-  TestKit
-begin
-
-section\<open>Test Purpose.\<close>
-text\<open> Via @{ML "DOF_core.add_ml_invariant"} it is possible to attach user-defined
-      ML-code to classes which is executed at each creation or modification of 
-      class instances. We test exection  of creation  and updates. \<close>
-
-text\<open>Consult the status of the DOF engine:\<close>
-print_doc_classes
-print_doc_items
-
-
-section\<open>Example: Standard Class Invariant\<close>
-
-
-text\<open>Watch out: The current programming interface to document class invariants is pretty low-level:
-\<^item> No inheritance principle
-\<^item> No high-level notation in HOL
-\<^item> Typing on ML level is assumed to be correct.
-The implementor of an ontology must know what he does ...
-\<close>
-
-text\<open>Setting a sample invariant, which simply produces some side-effect:\<close>
-
-setup\<open>
-fn thy =>
-let val ctxt = Proof_Context.init_global thy
-    val cid_long = DOF_core.get_onto_class_name_global "A" thy
-    val bind = Binding.name "Sample_Echo"
-    val exec = (fn oid =>  fn {is_monitor = b} => fn ctxt => 
-                  (writeln ("sample echo : "^oid); true))
-in DOF_core.add_ml_invariant bind (DOF_core.make_ml_invariant (exec, cid_long)) thy end
-\<close>
-
-text\<open>The checker \<open>exec\<close> above is set. Just used to provoke output: "sample echo : b"\<close>
-text*[b::A, x = "5"] \<open> Lorem ipsum dolor sit amet, ... \<close>
-
-text\<open>Setting a sample invariant, referring to attribute value "x":\<close>
-setup\<open>
-fn thy =>
-let fun check_A_invariant oid {is_monitor:bool} ctxt =
-      let val term =  ISA_core.compute_attr_access ctxt "x" oid NONE @{here} 
-          val (@{typ "int"},x_value) = HOLogic.dest_number term
-      in  if x_value > 5 then error("class A invariant violation") else true end
-    val cid_long = DOF_core.get_onto_class_name_global "A" thy    
-    val bind = Binding.name "Check_A_Invariant"
-in DOF_core.add_ml_invariant bind (DOF_core.make_ml_invariant (check_A_invariant, cid_long)) thy end
-\<close>
-
-(* borderline test *)
-text*[d0::A, x = "5"]            \<open>Lorem ipsum dolor sit amet, ...\<close>
-text-assert-error[d1::A, x = "6"]\<open>Lorem ipsum dolor sit amet, ...\<close>\<open>class A invariant violation\<close>
-
-subsection*[d::A, x = "4"] \<open> Lorem ipsum dolor sit amet, ... \<close>
-
-(* invariant still valid *)
-update_instance*[d::A, x += "1"]
-
-(* invariant no longer holds*)
-update_instance-assert-error[d::A, x += "1"]\<open>class A invariant violation\<close>
-
-
-section\<open>Example: Monitor Class Invariant\<close>
-
-text\<open>Of particular interest are class invariants attached to monitor classes: since the
-latter manage a trace-attribute, a class invariant on them can assure a global form of consistency. 
-It is possible to express:
-\<^item> that attributes of a document element must satisfy particular conditions depending on the
-  prior document elements --- as long they have been observed in a monitor.
-\<^item> non-regular properties on a trace not expressible in a regular expression 
-  (like balanced ness of opening and closing text elements)
-\<^item> etc.
-\<close>
-
-text\<open>A simple global trace-invariant is expressed in the following: it requires
-that instances of class C occur more often as those of class D; note that this is meant
-to take sub-classing into account:
-\<close>
-
-setup\<open>
-fn thy =>
-let fun check_M_invariant oid {is_monitor} ctxt =
-      let val term =  ISA_core.compute_attr_access ctxt "trace" oid NONE @{here} 
-          fun conv (\<^Const>\<open>Pair \<^typ>\<open>doc_class rexp\<close> \<^typ>\<open>string\<close>\<close>
-                      $ (\<^Const>\<open>Atom \<^typ>\<open>doc_class\<close>\<close> $ (\<^Const>\<open>mk\<close> $ s)) $ S) =
-            let val s' =  DOF_core.get_onto_class_name_global' (HOLogic.dest_string s) thy
-            in (s', HOLogic.dest_string S) end
-          val string_pair_list = map conv (HOLogic.dest_list term) 
-          val cid_list = map fst string_pair_list
-          val ctxt' = Proof_Context.init_global(Context.theory_of ctxt)
-          fun is_C x = DOF_core.is_subclass ctxt' x "Conceptual.C"
-          fun is_D x = DOF_core.is_subclass ctxt' x "Conceptual.D"
-          val n = length (filter is_C cid_list)
-          val m = length (filter is_D cid_list)
-      in  if m > n then error("class M invariant violation") else true end
-    val cid_long = DOF_core.get_onto_class_name_global "M" thy
-    val binding = Binding.name "Check_M_Invariant"
-in DOF_core.add_ml_invariant binding (DOF_core.make_ml_invariant (check_M_invariant, cid_long)) thy end
-\<close>
-
-
-section\<open>Example: Monitor Class Invariant\<close>
-
-open_monitor*[struct::M]
-                                   
-subsection*[a::A, x = "3"]       \<open> Lorem ipsum dolor sit amet, ... \<close>
-
-text*[c1::C, x = "''beta''"]     \<open> ... suspendisse non arcu malesuada mollis, nibh morbi, ...  \<close>
-
-text*[d1::E, a1 = "X3"]          \<open> ... phasellus amet id massa nunc, pede suscipit repellendus, ... \<close>
-    
-text*[c2:: C, x = "''delta''"]   \<open> ... in ut tortor eleifend augue pretium consectetuer...  \<close>
-
-subsection*[f::E]                \<open> Lectus accumsan velit ultrices, ... \<close>
-
-
-text-assert-error[f2::E]         \<open> Lectus accumsan velit ultrices, ... \<close>\<open>class M invariant violation\<close>
-
-
-ML\<open>val ctxt = @{context}
-   val term = ISA_core.compute_attr_access 
-                  (Context.Proof ctxt) "trace" "struct" NONE @{here} ;
-   fun conv (Const(@{const_name "Pair"},_) $ Const(s,_) $ S) = (s, HOLogic.dest_string S)
-   fun conv' (\<^Const>\<open>Pair \<^typ>\<open>doc_class rexp\<close> \<^typ>\<open>string\<close>\<close>
-                      $ (\<^Const>\<open>Atom \<^typ>\<open>doc_class\<close>\<close> $ (\<^Const>\<open>mk\<close> $ s)) $ S) =
-     let val s' =  DOF_core.get_onto_class_name_global' 
-                                     (HOLogic.dest_string s)
-                                     (Proof_Context.theory_of ctxt)
-     in (s', HOLogic.dest_string S) end
-   val string_pair_list = map conv' (HOLogic.dest_list term);
-   @{assert} (string_pair_list = 
-                     [("Conceptual.A", "a"), ("Conceptual.C", "c1"), 
-                      ("Conceptual.E", "d1"), ("Conceptual.C", "c2"),
-                      ("Conceptual.E", "f")])
-  \<close>
-
-
-close_monitor*[struct]
-
-
-end 
-  

Isabelle_DOF-Unit-Tests/Concept_High_Level_Invariants.thy

@@ -1,280 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2023 The University of Exeter 
- *               2018-2023 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-chapter\<open>High-level Class Invariants\<close>
-
-theory Concept_High_Level_Invariants
-  imports "Isabelle_DOF.Isa_DOF"
-          "Isabelle_DOF_Unit_Tests_document"
-          TestKit
-begin
-
-section\<open>Test Purpose.\<close>
-text\<open>
-  Without invariants, ontological classes as such are too liberal in many situations.
-  Similarly to UML constraints, invariants or hand-programmed checking functions
-  can be added in ODL ontologies in order to constrain class instances or
-  (via monitor traces) impose structural constraints over an entire document.
-
-  While hand-programmed checking functions were tested in test-case 
-  \<^verbatim>\<open>Concept_Example_Low_Level_Invariant\<close>, in this text case, we test 
-  high-level invariants, i.e. data-constraints speicified as executable 
-  HOL-predicates in the @{theory_text \<open>invariant\<close>} clause of ODL definitions.
-
-  To enable the checking of the invariants, the \<open>invariants_checking\<close>
-  theory attribute must be set:\<close>
-
-
-section\<open>The Scenario.\<close>
-
-text\<open> This is merely an example that shows that the generated invariants
-      fit nicely together; i.e. allow for sensible consistency and invariant
-      preservation proofs related to ontological matchings. \<close>
-
-
-text\<open>Using HOL, we can define a mapping between two ontologies.
-  It is called ontology matching or ontology alignment.
-  Here is an example which show how to map two classes.
-  HOL also allows us to map the invariants (ontological rules) of the classes!\<close>
-
-text\<open>
-  Ontological classes as described so far are too liberal in many situations.
-  There is a first high-level syntax implementation for class invariants.
-  These invariants can be checked when an instance of the class is defined.
-  To enable the checking of the invariants, the \<open>invariants_checking\<close>
-  theory attribute must be set:\<close>
-
-
-declare[[invariants_strict_checking = true]]
-
-text\<open>For example, let's define the following two classes:\<close>
-
-doc_class class_inv1 =
-  int1 :: "int"
-  invariant inv1 :: "int1 \<sigma> \<ge> 3"
-
-doc_class class_inv2 = class_inv1 +
-  int2 :: "int"
-  invariant inv2 :: "int2 \<sigma> < 2"
-
-text\<open>The  symbol \<^term>\<open>\<sigma>\<close> is reserved and references the future instance class.
-  By relying on the implementation of the Records
-  in Isabelle/HOL~@{cite "wenzel:isabelle-isar:2020"},
-  one can reference an attribute of an instance using its selector function.
-  For example, \<^term>\<open>int1 \<sigma>\<close> denotes the value
-  of the \<^term>\<open>int1\<close> attribute
-  of the future instance of the class @{doc_class class_inv1}.
-  Now let's define two instances, one of each class:\<close>
-
-text*[testinv1::class_inv1, int1=4]\<open>lorem ipsum...\<close>
-update_instance*[testinv1::class_inv1, int1:="3"]
-(* When not commented, should violated the invariant:
-update_instance*[testinv1::class_inv1, int1:=1]
-*)
-
-text*[testinv2::class_inv2, int1=3, int2=1]\<open>lorem ipsum...\<close>
-
-text\<open>
-  The value of each attribute defined for the instances is checked against their classes invariants.
-  As the class @{doc_class class_inv2} is a subsclass of the class @{doc_class class_inv1},
-  it inherits @{doc_class class_inv1} invariants.
-  Hence the \<^term>\<open>int1\<close> invariant is checked when the instance @{docitem testinv2} is defined.\<close>
-
-text\<open>Test invariant for attributes of attributes: \<close>
-
-doc_class inv_test1 =
-  a :: int
-
-doc_class inv_test2 =
-  b :: "inv_test1"
-  c:: int
-  invariant inv_test2 :: "c \<sigma> = 1"
-  invariant inv_test2' :: "a (b \<sigma>) = 2"
-
-doc_class inv_test3 = inv_test1 +
-  b :: "inv_test1"
-  c:: int
-  invariant inv_test3 :: "a \<sigma> = 2"
-  invariant inv_test3' :: "a (b \<sigma>) = 2"
-
-doc_class inv_test4 = inv_test2 +
-  d :: "inv_test3"
-  invariant inv_test4 :: "a (inv_test2.b \<sigma>) = 2"
-  invariant inv_test4' :: "a (d \<sigma>) = 2"
-
-text*[inv_test1_instance::inv_test1, a=2]\<open>\<close>
-text*[inv_test3_instance::inv_test3, a=2, b="@{inv_test1 \<open>inv_test1_instance\<close>}" ]\<open>\<close>
-text*[inv_test4_instance::inv_test4, b="@{inv_test1 \<open>inv_test1_instance\<close>}"
-                                   , c=1, d="@{inv_test3 \<open>inv_test3_instance\<close>}"]\<open>\<close>
-
-text\<open>To support invariant on attributes in attributes
-and invariant on attributes of the superclasses,
-we check that the type of the attribute of the subclass is ground:\<close>
-ML\<open>
-val Type(st, [ty]) = \<^typ>\<open>inv_test1\<close>
-val Type(st', [ty']) = \<^typ>\<open>'a inv_test1_scheme\<close>
-val t = ty = \<^typ>\<open>unit\<close>
-\<close>
-
-text\<open>Now assume the following ontology:\<close>
-
-doc_class title =
-  short_title :: "string option" <= "None"
-
-doc_class author =
-  email :: "string" <= "''''"
-
-datatype classification = SIL0 | SIL1 | SIL2 | SIL3 | SIL4
-
-doc_class abstract =
-  keywordlist :: "string list" <= "[]"
-  safety_level :: "classification" <= "SIL3"
-
-doc_class text_section =
-  authored_by :: "author set" <= "{}"
-  level :: "int option" <= "None"
-
-type_synonym notion = string
-
-doc_class introduction = text_section +
-  authored_by :: "author set"  <= "UNIV" 
-  uses :: "notion set"
-  invariant author_finite :: "finite (authored_by \<sigma>)"
-  and force_level :: "(level \<sigma>) \<noteq> None \<and> the (level \<sigma>) > 1"
-
-doc_class claim = introduction +
-  based_on :: "notion list"
-
-doc_class technical = text_section +
-  formal_results :: "thm list" 
-
-doc_class "definition" = technical +
-  is_formal :: "bool"
-  property  :: "term list" <= "[]" 
-
-datatype kind = expert_opinion | argument | "proof"
-
-doc_class result = technical +
-  evidence :: kind
-  property :: "thm list" <= "[]"
-  invariant has_property :: "evidence \<sigma> = proof \<longleftrightarrow> property \<sigma> \<noteq> []"
-
-doc_class example = technical +
-  referring_to :: "(notion + definition) set" <= "{}"
-
-doc_class conclusion = text_section +
-  establish :: "(claim \<times> result) set"
-  invariant establish_defined :: "\<forall> x. x \<in> Domain (establish \<sigma>)
-                                           \<longrightarrow> (\<exists> y \<in> Range (establish \<sigma>). (x, y) \<in> establish \<sigma>)"
-
-text\<open>Next we define some instances (docitems): \<close>
-
-declare[[invariants_checking_with_tactics = true]]
-
-text*[church::author, email="\<open>church@lambda.org\<close>"]\<open>\<close>
-
-text\<open>We can also reference instances of classes defined in parent theories:\<close>
-text*[church'::scholarly_paper.author, email="\<open>church'@lambda.org\<close>"]\<open>\<close>
-
-text*[resultProof::result, evidence = "proof", property="[@{thm \<open>HOL.refl\<close>}]"]\<open>\<close>
-text*[resultArgument::result, evidence = "argument"]\<open>\<close>
-
-text\<open>The invariants \<^theory_text>\<open>author_finite\<close> and \<^theory_text>\<open>establish_defined\<close> can not be checked directly
-  and need a little help.
-  We can set the \<open>invariants_checking_with_tactics\<close> theory attribute to help the checking.
-  It will enable a basic tactic, using unfold and auto:\<close>
-
-declare[[invariants_checking_with_tactics = true]]
-
-text*[curry::author, email="\<open>curry@lambda.org\<close>"]\<open>\<close>
-
-text*[introduction2::introduction, authored_by = "{@{author \<open>church\<close>}}", level = "Some 2"]\<open>\<close>
-(* When not commented, should violated the invariant:
-update_instance*[introduction2::Introduction
-                  , authored_by := "{@{Author \<open>church\<close>}}"
-                  , level := "Some 1"]
-*)
-text\<open>Use of the instance @{docitem_name "church'"}
-     to instantiate a \<^doc_class>\<open>scholarly_paper.introduction\<close> class:\<close>
-text*[introduction2'::scholarly_paper.introduction,
-      main_author = "Some @{scholarly_paper.author \<open>church'\<close>}", level = "Some 2"]\<open>\<close>
-
-value*\<open>@{scholarly_paper.author \<open>church'\<close>}\<close>
-value*\<open>@{author \<open>church\<close>}\<close>
-value*\<open>@{Concept_High_Level_Invariants.author \<open>church\<close>}\<close>
-
-value*\<open>@{instances_of \<open>scholarly_paper.author\<close>}\<close>
-value*\<open>@{instances_of \<open>author\<close>}\<close>
-value*\<open>@{instances_of \<open>Concept_High_Level_Invariants.author\<close>}\<close>
-
-text*[introduction3::introduction, authored_by = "{@{author \<open>church\<close>}}", level = "Some 2"]\<open>\<close>
-text*[introduction4::introduction, authored_by = "{@{author \<open>curry\<close>}}", level = "Some 4"]\<open>\<close>
-
-text*[resultProof2::result, evidence = "proof", property="[@{thm \<open>HOL.sym\<close>}]"]\<open>\<close>
-
-text\<open>Then we can evaluate expressions with instances:\<close>
-
-term*\<open>authored_by @{introduction \<open>introduction2\<close>} = authored_by @{introduction \<open>introduction3\<close>}\<close>
-value*\<open>authored_by @{introduction \<open>introduction2\<close>} = authored_by @{introduction \<open>introduction3\<close>}\<close>
-value*\<open>authored_by @{introduction \<open>introduction2\<close>} = authored_by @{introduction \<open>introduction4\<close>}\<close>
-
-value*\<open>@{introduction \<open>introduction2\<close>}\<close>
-
-value*\<open>{@{author \<open>curry\<close>}} = {@{author \<open>church\<close>}}\<close>
-
-term*\<open>property @{result \<open>resultProof\<close>} = property @{result \<open>resultProof2\<close>}\<close>
-value*\<open>property @{result \<open>resultProof\<close>} = property @{result \<open>resultProof2\<close>}\<close>
-
-value*\<open>evidence @{result \<open>resultProof\<close>} = evidence @{result \<open>resultProof2\<close>}\<close>
-
-declare[[invariants_checking_with_tactics = false]]
-
-declare[[invariants_strict_checking = false]]
-
-text\<open>Invariants can have term anti-quotations\<close>
-doc_class invA =
-a :: int
-
-text*[invA_inst::invA, a = 3]\<open>\<close>
-
-doc_class invB = invA +
-b :: int
-invariant a_pos :: "a \<sigma> \<ge> 0"
-
-text*[invB_inst::invB, a = 3]\<open>\<close>
-
-doc_class invC =
-c :: invB
-invariant a_invB_pos :: "a (c \<sigma>) \<ge> a @{invA \<open>invA_inst\<close>}"
-
-text*[invC_inst::invC, c = "@{invB \<open>invB_inst\<close>}"]\<open>\<close>
-
-text\<open>Bug:
-With the polymorphic class implementation, invariants type inference is to permissive:
-\<close>
-doc_class invA' =
-a :: int
-
-doc_class invB' = invA' +
-b :: int
-invariant a_pos :: "a \<sigma> \<ge> 0"
-
-doc_class ('a, 'b) invC' =
-c :: invB'
-d :: "'a list"
-e :: "'b list"
-invariant a_pos :: "a \<sigma> \<ge> 0"
-text\<open>The \<^const>\<open>a\<close> selector in the \<^const>\<open>a_pos_inv\<close> invariant of the class \<^doc_class>\<open>('a, 'b) invC'\<close>
-should be rejected as the class does not have nor inherit an \<^const>\<open>a\<close> attribute
-\<close>
-end

Isabelle_DOF-Unit-Tests/Concept_MonitorTest1.thy

@@ -1,127 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2023 The University of Exeter 
- *               2018-2023 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-chapter\<open>Testing Nested Monitors\<close>
-
-theory 
-  Concept_MonitorTest1
-  imports 
-  "Isabelle_DOF_Unit_Tests_document"
-  "Isabelle_DOF-Ontologies.Conceptual" (* we use the generic "Conceptual" ontology *)
-  TestKit
-begin
-
-section\<open>Test Purpose.\<close>
-text\<open> Creation of document parts that are controlled by (nested, locally defined) monitors. \<close>
-
-open_monitor*[aaa::Conceptual.M]  
-text*[test::A]\<open>For Test and Validation\<close>
-
-text\<open>Defining some document elements to be referenced in later on in another theory: \<close>
-text*[sdf]         \<open> Lorem ipsum ... \<close>         \<comment> \<open>anonymous reference, ignored by monitor.\<close>
-text*[sdfg :: F]   \<open> Lorem ipsum ...\<close>          \<comment> \<open>causes just warnings for invariant violations  
-                                                   due to non-strict checking mode\<close>
-close_monitor*[aaa]                            \<comment> \<open>causes warning: accept clause 1 
-                                                   not in final state .\<close>
-
-section\<open>A Local Monitor Class Definition\<close>
-
-doc_class test_monitor_free =
-  tmhd :: int
-doc_class test_monitor_head =
-  tmhd :: int
-doc_class test_monitor_A = test_monitor_head +
-  tmA :: int
-doc_class test_monitor_B = test_monitor_A +
-  tmB :: int
-doc_class test_monitor_C = test_monitor_A +
-  tmC :: int
-doc_class test_monitor_D = test_monitor_B +
-  tmD :: int
-doc_class test_monitor_E = test_monitor_D +
-  tmE :: int
-
-doc_class monitor_M =
-  tmM :: int
-  rejects "test_monitor_A"
-  accepts "test_monitor_head ~~ test_monitor_B ~~ test_monitor_C"
-
-section\<open>A more Complex Monitoring Example \<close>
-
-text\<open>Consult the status of the DOF engine:\<close>
-print_doc_classes
-print_doc_items
-
-
-
-declare[[free_class_in_monitor_checking]]
-
-open_monitor*[test_monitor_M::monitor_M]
-
-text*[testFree::test_monitor_free]\<open>...\<close>
-
-open_monitor*[test_monitor_M2::monitor_M]
-
-declare[[strict_monitor_checking]]
-text-assert-error[test_monitor_A1::test_monitor_A]\<open>\<close> 
-                  \<open>accepts clause 1 of monitor Concept_MonitorTest1.test_monitor_M rejected\<close>
-declare[[strict_monitor_checking=false]]
-text*[test_monitor_A1::test_monitor_A]\<open>\<close> \<comment> \<open>the same in non-strict monitor checking.\<close>
-declare[[free_class_in_monitor_strict_checking]]
-text-assert-error[testFree2::test_monitor_free]\<open>\<close>
-                  \<open>accepts clause 1 of monitor Concept_MonitorTest1.test_monitor_M not enabled\<close>
-declare[[free_class_in_monitor_strict_checking=false]]
-text*[test_monitor_head1::test_monitor_head]\<open>\<close>
-text*[testFree3::test_monitor_free]\<open>\<close>
-text*[test_monitor_B1::test_monitor_B]\<open>\<close>
-text*[testFree4::test_monitor_free]\<open>\<close>
-text*[test_monitor_D1::test_monitor_D]\<open>\<close>
-text*[testFree5::test_monitor_free]\<open>\<close>
-text*[test_monitor_C1::test_monitor_C]\<open>\<close>
-text*[testFree6::test_monitor_free]\<open>\<close>
-
-close_monitor*[test_monitor_M2]
-
-close_monitor*[test_monitor_M]
-
-declare[[free_class_in_monitor_checking = false]]
-
-text\<open>Consult the final status of the DOF engine:\<close>
-print_doc_classes
-print_doc_items
-
-ML\<open>
-val (oid, DOF_core.Instance {value, ...}) =
-    Name_Space.check (Context.Proof \<^context>) (DOF_core.get_instances \<^context>) ("aaa", Position.none)
-\<close>
-term*\<open>map fst @{trace_attribute \<open>test_monitor_M\<close>}\<close>
-value*\<open>map fst @{trace_attribute \<open>test_monitor_M\<close>}\<close>
-
-ML\<open>@{assert} ([("Conceptual.A", "test"), ("Conceptual.F", "sdfg")] =  @{trace_attribute aaa})       \<close>
-
-
-open_monitor*[test_monitor_M3::monitor_M]
-
-declare[[strict_monitor_checking]]
-text-assert-error[test_monitor_A2::test_monitor_A]\<open>\<close> 
-                  \<open>accepts clause 1 of monitor Concept_MonitorTest1.test_monitor_M3 rejected\<close>
-declare[[strict_monitor_checking=false]]
-text*[test_monitor_A3::test_monitor_A]\<open>\<close> \<comment> \<open>the same in non-strict monitor checking.\<close>
-declare[[free_class_in_monitor_strict_checking]]
-text-assert-error[testFree7::test_monitor_free]\<open>\<close>
-                  \<open>accepts clause 1 of monitor Concept_MonitorTest1.test_monitor_M3 not enabled\<close>
-declare[[free_class_in_monitor_strict_checking=false]]
-
-
-end 
-  

Isabelle_DOF-Unit-Tests/Concept_MonitorTest2.thy

@@ -1,68 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2023 The University of Exeter 
- *               2018-2023 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-chapter\<open>Testing Nested Monitors\<close>
-
-theory 
-  Concept_MonitorTest2
-  imports
-  Concept_MonitorTest1
-begin
-
-section\<open>Test Purpose.\<close>
-text\<open> Creation of document parts that are controlled by (nested, locally defined) monitors. \<close>
-
-doc_class test_monitor_B =
-  tmB :: int
-
-doc_class monitor_M =
-  tmM :: int
-  rejects "Concept_MonitorTest1.test_monitor_B"
-  accepts "test_monitor_E ~~ test_monitor_C"
-
-doc_class test_monitor_head =
-  tmhd :: int
-
-declare[[free_class_in_monitor_checking]]
-
-declare[[free_class_in_monitor_strict_checking]]
-text-assert-error[test_monitor_head1::test_monitor_head]\<open>\<close>
-                  \<open>accepts clause 1 of monitor Concept_MonitorTest1.test_monitor_M3 not enabled\<close>
-declare[[free_class_in_monitor_strict_checking=false]]
-text*[test_monitor_head2::Concept_MonitorTest1.test_monitor_head]\<open>\<close>
-
-open_monitor*[test_monitor_M3::monitor_M]
-
-text*[test_monitor_head3::Concept_MonitorTest1.test_monitor_head]\<open>\<close>
-text*[testFree3::test_monitor_free]\<open>\<close>
-declare[[strict_monitor_checking]]
-text-assert-error[test_monitor_B1::test_monitor_B]\<open>\<close>
-                  \<open>accepts clause 1 of monitor Concept_MonitorTest2.test_monitor_M3 rejected\<close>
-declare[[strict_monitor_checking=false]]
-text*[testFree4::test_monitor_free]\<open>\<close>
-declare[[strict_monitor_checking]]
-text-assert-error[test_monitor_D1::test_monitor_D]\<open>\<close>
-                  \<open>accepts clause 1 of monitor Concept_MonitorTest2.test_monitor_M3 rejected\<close>
-declare[[strict_monitor_checking=false]]
-text*[testFree5::test_monitor_free]\<open>\<close>
-text*[test_monitor_E1::test_monitor_E]\<open>\<close>
-text*[test_monitor_C1::test_monitor_C]\<open>\<close>
-text*[testFree6::test_monitor_free]\<open>\<close>
-
-close_monitor*[Concept_MonitorTest1.test_monitor_M3]
-
-close_monitor*[test_monitor_M3]
-
-declare[[free_class_in_monitor_checking = false]]
-
-end

Isabelle_DOF-Unit-Tests/Concept_OntoReferencing.thy

@@ -1,177 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2023 The University of Exeter 
- *               2018-2023 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-chapter\<open>Creating and Referencing Ontological Instances\<close>
-
-theory   Concept_OntoReferencing
-  imports   "TestKit"
-            "Isabelle_DOF_Unit_Tests_document"
-            "Isabelle_DOF-Ontologies.Conceptual" 
-begin
-
-section\<open>Test Purpose.\<close>
-text\<open> Creation of ontological instances along the \<^theory>\<open>Isabelle_DOF-Ontologies.Conceptual\<close> 
-Ontology. Emphasis is put on type-safe (ontologically consistent) referencing of text, code and
-proof elements. Some tests cover also the critical cases concerning name spaces of oid's. \<close>
-
-section\<open>Setting up a monitor.\<close>
-text\<open>\<^theory>\<open>Isabelle_DOF-Ontologies.Conceptual\<close> provides a monitor \<^typ>\<open>M\<close>  enforcing a 
-     particular document structure. Here, we say: From now on, this structural rules are 
-     respected wrt. all \<^theory_text>\<open>doc_classes M\<close> is enabled for.\<close>
-
-open_monitor*[struct::M]  
-
-section\<open>Defining Text Elements and Referring to them... \<close>
-
-text\<open> This uses elements of two ontologies, notably 
-      \<^theory>\<open>Isabelle_DOF-Ontologies.Conceptual\<close> and \<^theory>\<open>Isabelle_DOF.Isa_COL\<close>.\<close>
-
-(*<*)
-
-title*[ag::title, short_title="Some\<open>ooups.\<close>"]\<open>Lorem ipsum dolor sit amet ...\<close>
-subtitle*[af::subtitle, abbrev = "Some\<open>ooups-oups.\<close>"]\<open>Lorem ipsum dolor sit amet ...\<close>
-chapter*[a0::A, x = "3"]   \<open> Lorem ipsum dolor sit amet ... \<close>
-section*[a::A, x = "3"]         \<open> Lorem ipsum dolor sit amet, ... \<close>
-subsection*[ab::A, x = "3"]     \<open> Lorem ipsum dolor sit amet, ... 
-                                  As mentioned in the @{title \<open>ag\<close>}... \<close> \<comment> \<open>old-style and ...\<close>
-subsubsection*[ac::A, x = "3"]  \<open> Lorem ipsum dolor sit amet, ... 
-                                  As mentioned in the \<^title>\<open>ag\<close>\<close>    \<comment> \<open>new-style references to
-                                                                          ontological instances 
-                                                                          assigned to text 
-                                                                          elements ...\<close>
-
-
-text\<open>Meta-Objects are typed, and references have to respect this : \<close>
-text-assert-error[ad]\<open> \<^title>\<open>a\<close> \<close>    \<open>reference ontologically inconsistent\<close>
-text-assert-error[ae]\<open> \<^title>\<open>af\<close> \<close>\<open>reference ontologically inconsistent\<close> 
-                       \<comment> \<open>erroneous reference: please consider class hierarchy!\<close>
-(*>*)
-
-text\<open>References to Meta-Objects can be forward-declared:\<close>
-
-text-assert-error[ae1]\<open>@{C \<open>c1\<close>}\<close>\<open>Undefined instance:\<close>
-
-declare_reference*[c1::C]     \<comment> \<open>forward declaration\<close>
-
-text-assert-error\<open>@{C \<open>c1\<close>} \<close>\<open>Instance declared but not defined, try option unchecked\<close>
-
-text\<open>@{C (unchecked) \<open>c1\<close>} \<close>
-
-text*[a1::A, level="Some 0", x = 3]\<open>... phasellus amet id massa nunc, ...\<close>
-text*[c1::C, x = "''beta''"] \<open> ... suspendisse non arcu malesuada mollis, nibh morbi, ...  \<close>
-
-text-assert-error[c1::C, x = "''gamma''"] 
-                             \<open> ... suspendisse non arcu malesuada mollis, nibh morbi, ...  \<close>
-                             \<open>Duplicate instance declaration\<close>
-
-\<comment> \<open>Referencing from a text context:\<close>
-text*[d::D, a1 = "X3"] \<open> ... phasellus amet id massa nunc, pede suscipit repellendus, 
-                         ... @{C "c1"} or @{C \<open>c1\<close>} or \<^C>\<open>c1\<close>
-                             similar to @{thm "refl"} and \<^thm>"refl"\<close>  \<comment> \<open>ontological and built-in
-                                                                          references\<close>
-
-text\<open>Not only text-elements are "ontology-aware", proofs and code can this be too !\<close>
-
-\<comment> \<open>Referencing from and to a ML-code context:\<close>
-
-ML*[c4::C, z = "Some @{A \<open>a1\<close>}"]\<open>
-fun fac x = if x  = 0  then 1 else x * (fac(x-1))
-val v = \<^value_>\<open>A.x (the (z @{C \<open>c4\<close>}))\<close> |> HOLogic.dest_number |> snd |> fac
-\<close>
-
-definition*[a2::A, x=5, level="Some 1"] xx' where "xx' \<equiv> A.x @{A \<open>a1\<close>}" if "A.x @{A \<open>a1\<close>} = 5"
-
-lemma*[e5::E] testtest : "xx + A.x @{A \<open>a1\<close>} = yy + A.x @{A \<open>a1\<close>} \<Longrightarrow> xx = yy" by simp
-
-doc_class cc_assumption_test =
-a :: int
-text*[cc_assumption_test_ref::cc_assumption_test]\<open>\<close>
-
-definition tag_l :: "'a \<Rightarrow> 'b \<Rightarrow> 'b" where "tag_l \<equiv> \<lambda>x y. y"
-
-lemma* tagged : "tag_l @{cc_assumption_test \<open>cc_assumption_test_ref\<close>} AA \<Longrightarrow> AA"
-  by (simp add: tag_l_def)
-
-find_theorems name:tagged "(_::cc_assumption_test \<Rightarrow> _ \<Rightarrow> _) _ _ \<Longrightarrow>_"
-
-declare_reference-assert-error[c1::C]\<open>Duplicate instance declaration\<close>     \<comment> \<open>forward declaration\<close>
-
-declare_reference*[e6::E] 
-(*<*)  (* pdf GENERATION NEEDS TO BE IMPLEMENTED IN FRONT AND BACKEND *)
-text\<open>This is the answer to the "OutOfOrder Presentation Problem": @{E (unchecked) \<open>e6\<close>} \<close>
-
-definition*[e6::E] facu :: "nat \<Rightarrow> nat" where "facu arg = undefined"
-
-text\<open>As shown in @{E \<open>e5\<close>} following from  @{E \<open>e6\<close>}\<close> 
-
-
-text\<open>As shown in @{C \<open>c4\<close>}\<close>
-(*>*)
-
-
-
-text\<open>Ontological information ("class instances") is mutable: \<close>
-
-update_instance*[d::D, a1 := X2]
-(*<*)
-text\<open> ... in ut tortor ... @{docitem \<open>a\<close>} ... @{A \<open>a\<close>} ... \<close> \<comment> \<open>untyped or typed referencing \<close>
-(*>*)
-text-assert-error[ae::text_element]\<open>the function @{C [display] "c4"} \<close>\<open>referred text-element is no macro!\<close>
-
-text*[c2::C, x = "\<open>delta\<close>"]  \<open> ... in ut tortor eleifend augue pretium consectetuer.  \<close>
-
-text\<open>Note that both the notations @{term "''beta''"} and @{term "\<open>beta\<close>"} are possible;
-the former is a more ancient format only supporting pure ascii, while the latter also supports
-fancy unicode such as: @{term "\<open>\<beta>\<^sub>i''\<close>"} \<close>
-
-text*[f::F] \<open> Lectus accumsan velit ultrices, ... \<close>
-  
-theorem some_proof : "True" by simp
-
-text\<open>This is an example where we add a theorem into a kind of "result-list" of the doc-item f.\<close>
-update_instance*[f::F,r:="[@{thm ''Concept_OntoReferencing.some_proof''}]"]
-(*<*)
-text\<open> ..., mauris amet, id elit aliquam aptent id,  ... @{docitem \<open>a\<close>} \<close>
-(*>*)
-text\<open>Here we add and maintain a link that is actually modeled as m-to-n relation ...\<close>
-update_instance*[f::F,b:="{(@{A  \<open>a\<close>}::A,@{C  \<open>c1\<close>}::C), 
-                           (@{A  \<open>a\<close>},   @{C  \<open>c2\<close>})}"] 
-
-section\<open>Closing the Monitor and testing the Results.\<close>
-
-close_monitor*[struct]
-
-text\<open>And the trace of the monitor is:\<close>
-ML\<open>val trace = @{trace_attribute struct}\<close>
-ML\<open>@{assert} (trace = 
-   [("Conceptual.A", "a0"), ("Conceptual.A", "a"), ("Conceptual.A", "ab"),
-    ("Conceptual.A", "ac"), ("Conceptual.A", "a1"),
-    ("Conceptual.C", "c1"), ("Conceptual.D", "d"), ("Conceptual.C", "c4"),
-    ("Conceptual.A", "a2"), ("Conceptual.E", "e5"), 
-    ("Conceptual.E", "e6"), ("Conceptual.C", "c2"), ("Conceptual.F", "f")]) \<close>
-
-
-text\<open>Note that the monitor \<^typ>\<open>M\<close> of the ontology \<^theory>\<open>Isabelle_DOF-Ontologies.Conceptual\<close> does
-     not observe the common entities of \<^theory>\<open>Isabelle_DOF.Isa_COL\<close>, but just those defined in the 
-     accept- clause of \<^typ>\<open>M\<close>.\<close>
-
-text\<open>One final check of the status DOF core: observe that no new classes have been defined,
-     just a couple of new document elements have been introduced.\<close>
-
-print_doc_classes
-print_doc_items
-
-
-
-end 
-