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

@@ -1,4 +1,4 @@
 output
+*.template.sty
 .afp
 *~
-*#

.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

@@ -1,55 +0,0 @@
-pipeline:
-  build:
-    image: docker.io/logicalhacking/isabelle2022
-    commands:
-      - 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 -D . -o browser_info
-      - isabelle components -u .
-      - isabelle build -D . -o browser_info
-      - isabelle dof_mkroot -q DOF_test
-      - isabelle build -D DOF_test
-      - cp -r $ISABELLE_HOME_USER/browser_info $ARTIFACT_DIR
-      - cd $ARTIFACT_DIR
-      - cd ../..
-      - ln -s * latest
-  archive:
-    image: docker.io/logicalhacking/isabelle2022
-    commands:
-      - export ARTIFACT_DIR=$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: 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/mk_release

@@ -1,224 +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-Manual 2018-cicm-isabelle_dof-applications
-            mkdir -p $ISADOF_WORK_DIR/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/output/
-            cp examples/scholarly_paper/2018-cicm-isabelle_dof-applications/output/document.pdf \
-               $ISADOF_WORK_DIR/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/output/
-            mkdir -p $ISADOF_WORK_DIR/examples/technical_report/Isabelle_DOF-Manual/output/
-            cp examples/technical_report/Isabelle_DOF-Manual/output/document.pdf \
-               $ISADOF_WORK_DIR/examples/technical_report/Isabelle_DOF-Manual/output/;
-        else
-            echo "  * Quick and Dirty Mode (running on CI)"
-            mkdir -p $ISADOF_WORK_DIR/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/output/
-            cp $ARTIFACT_DIR/browser_info/Unsorted/2018-cicm-isabelle_dof-applications/document.pdf \
-               $ISADOF_WORK_DIR/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/output/
- 
-            mkdir -p $ISADOF_WORK_DIR/examples/technical_report/Isabelle_DOF-Manual/output/
-            cp $ARTIFACT_DIR/browser_info/Unsorted/Isabelle_DOF-Manual/document.pdf \
-               $ISADOF_WORK_DIR/examples/technical_report/Isabelle_DOF-Manual/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/examples/technical_report/Isabelle_DOF-Manual/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/examples/scholarly_paper/2018-cicm-isabelle_dof-applications/output/document.pdf \
-        $ISADOF_WORK_DIR/doc/2018-cicm-isabelle_dof-applications.pdf
-    echo "  2018-cicm-isabelle_dof-applications       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
-
-exit 0 

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 2022
-
-## [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

LICENSE

@@ -1,6 +1,6 @@
 Copyright (C) 2018-2019 The University of Sheffield
-              2019-2022 The University of Exeter
-              2018-2022 The University of Paris-Saclay
+              2019-2019 The University of Exeter
+              2018-2019 The University of Paris-Saclay
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -1,67 +1,67 @@
 # [Isabelle/DOF](https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF): Document Preparation Setup
 
 Isabelle/DOF is a novel Document Ontology Framework on top of Isabelle.
-Isabelle/DOF allows for both conventional typesetting and formal development.
-The manual for [Isabelle/DOF 1.3.0/Isabelle2021-1 is available
-online.](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.3.0_Isabelle2021-1.pdf)
+Isabelle/DOF allows for both conventional typesetting as well as formal
+development.
 
 ## Pre-requisites
 
-Isabelle/DOF has three major prerequisites:
+Isabelle/DOF has two major pre-requisites:
+
+* **Isabelle:** Isabelle/DOF requires [Isabelle 2018](http://isabelle.in.tum.de/website-Isabelle2018/).
+  Please download the Isabelle 2018 distribution for your operating
+  system from the [Isabelle website](http://isabelle.in.tum.de/website-Isabelle2018/).
+* **LaTeX:** Isabelle/DOF requires a modern pdfTeX-engine supporting the \expanded{}-primitive. This
+  is, for example, included in the [TeXLive 2019](https://www.tug.org/texlive/) (or later)
+  distribution. Please follow the [TeXLive installation instructions](https://www.tug.org/texlive/acquire-netinstall.html)
+  for installing TeXLive.
 
-* **Isabelle:** Isabelle/DOF requires [Isabelle
-  2022](https://isabelle.in.tum.de/website-Isabelle2022/). Please download the
-  Isabelle 2022 distribution for your operating system from the [Isabelle
-  website](https://isabelle.in.tum.de/website-Isabelle2022/).
-* **AFP:** Isabelle/DOF requires several entries from the [Archive of Formal Proofs
-  (AFP)](https://www.isa-afp.org/).  Please install the AFP following the
-  instructions given at <https://www.isa-afp.org/using.html>.
-* **LaTeX:** Isabelle/DOF requires a modern LaTeX installation, i.e., at least
-  [TeX Live 2022](https://www.tug.org/texlive/) with all available updates
-  applied.
-  
 ## Installation
 
-Isabelle/DOF is provided as an Isabelle component. After installing the
-prerequisites, change into the directory containing Isabelle/DOF (this should be
-the directory containing this `README.md` file) and execute (if you executed
-this command already during the installation of the prerequisites, you can skip
-it now):
+In most case, the DOF-plugin can be installed as follows:
 
 ```console
-foo@bar:~$ isabelle components -u .
+foo@bar:~$ ./install
 ```
 
-The final step for the installation is:
+If a specific Isabelle version should be used (i.e., not the default
+one), the full path to the ``isabelle`` command needs to be passed as
+using the ``--isabelle`` command line argument of the ``install`` script:
 
 ```console
-foo@bar:~$ isabelle build -D .
+foo@bar:~$ ./install --isabelle /usr/local/Isabelle2018/bin/isabelle
 ```
 
-This will compile Isabelle/DOF and run the example suite.
+For further command line options of the installer, please use the
+built-in help:
+
+```console
+foo@bar:~$ ./install --help
+```
 
 ## Usage
 
 ### Opening an Example
 
-If you want to work with or extend one of the examples, e.g., you can open it
-similar to any standard Isabelle theory:
+If you want to work with or extend one of the examples, e.g., you can
+open it similar to any standard Isabelle theory:
 
 ```console
 isabelle jedit -d . -l Isabelle_DOF examples/scholarly_paper/2018_cicm/IsaDofApplications.thy
 ```
 
-This will open an example of a scientific paper using the pre-compiled session
-``Isabelle_DOF``, i.e., you will not be able to edit the ontology definitions.
-If you want to edit the ontology definition, just open the theory file with the
-default HOL session:
+This will open an example of a scientific paper using the pre-compiled
+session ``Isabelle_DOF``, i.e., you will not be able to edit the
+ontology definitions. If you want to edit the ontology definition,
+just open the theory file with the default HOL session:
 
 ```console
 isabelle jedit -d . -l HOL examples/scholarly_paper/2018_cicm/IsaDofApplications.thy
 ```
 
 While this gives you more flexibility, it might "clutter" your editing
-experience, as a lot of internal theories are loaded into Isabelle's editor.
+experience, as a lot of internal theories are loaded into Isabelle's
+editor.
 
 ### Creating a New Project
 
@@ -69,72 +69,50 @@ The DOF-plugin provides an alternative to Isabelle's ``mkroot`` command.
 Isabelle projects that use DOF need to be created using
 
 ```console
-foo@bar:~$ isabelle dof_mkroot
+foo@bar:~$ isabelle mkroot_DOF
 ```
 
-The ``dof_mkroot`` command takes the same parameter as the standard ``mkroot``
-command of Isabelle. Thereafter, the normal Isabelle command for building
-documents can be used.
+The ``mkroot_DOF`` command takes the same parameter as the standard
+``mkroot`` command of Isabelle. Thereafter, the normal Isabelle
+command for building documents can be used.
 
-Using the ``-o`` option, different ontology setups can be selected and using the
-``-t`` option, different LaTeX setups can be selected. For example,
+Using the ``-o`` option, different ontology setups can be
+selected and using the ``-t`` option, different LaTeX setups 
+can be selected. For example,
 
 ```console
-foo@bar:~$ isabelle dof_mkroot -o scholarly_paper -t scrartcl
+foo@bar:~$ isabelle mkroot_DOF -o scholarly_paper -t scrartcl
 ```
 
-creates a setup using the scholarly_paper ontology and the article class from
-the KOMA-Script bundle.
+creates a setup using the scholarly_paper ontology and the article
+class from the KOMA-Script bundle.
 
-The help (option ``-h``) show a list of all supported ontologies and document
-templates:
+The help (option ``-h``) show a list of all supported ontologies and
+document templates:
 
 ```console
-foo@bar:~$ isabelle dof_mkroot -h
+foo@bar:~$ isabelle mkroot_DOF -h
 
-Usage: isabelle dof_mkroot [OPTIONS] [DIRECTORY]
+Usage: isabelle mkroot_DOF [OPTIONS] [DIR]
 
   Options are:
-    -I           init Mercurial repository and add generated files
-    -h           print help
-    -n NAME      alternative session name (default: directory base name)
-    -o NAMES     list of ontologies, separated by blanks
-                 (default: "technical_report scholarly_paper")
-    -q           quiet mode: less verbosity
-    -t NAME      template (default: "scrreprt-modern")
+    -h           print this help text and exit
+    -n NAME      alternative session name (default: DIR base name)
+    -o ONTOLOGY  (default: scholarly_paper)
+       Available ontologies:
+       * cenelec_50128
+       * mathex
+       * scholarly_paper
+    -t TEMPLATE   (default: scrartcl)
+       Available document templates:
+       * lncs
+       * scrartcl
+       * scrreprt
+       * scrreprt-modern
 
-  Create session root directory for Isabelle/DOF (default: current directory).
+  Prepare session root DIR (default: current directory).
 ```
 
-## Releases
-
-For releases, signed archives including a PDF version of the Isabelle/DOF manual
-are available:
-
-* Isabelle/DOF 1.3.0/Isabelle2021-1
-  * [Isabelle_DOF-1.3.0_Isabelle2021-1.pdf](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.3.0_Isabelle2021-1.pdf)
-  * [Isabelle_DOF-1.3.0_Isabelle2021-1.tar.xz](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.3.0_Isabelle2021-1.tar.xz)
-  * [Isabelle_DOF-1.3.0_Isabelle2021-1.tar.xz.asc](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.3.0_Isabelle2021-1.tar.xz.asc)
-
-### Older Releases
-
-* Isabelle/DOF 1.2.0/Isabelle2021
-  * [Isabelle_DOF-1.2.0_Isabelle2021.pdf](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.2.0_Isabelle2021.pdf)
-  * [Isabelle_DOF-1.2.0_Isabelle2021.tar.xz](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.2.0_Isabelle2021.tar.xz)
-  * [Isabelle_DOF-1.2.0_Isabelle2021.tar.xz.asc](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.2.0_Isabelle2021.tar.xz.asc)
-* Isabelle/DOF 1.1.0/Isabelle2021
-  * [Isabelle_DOF-1.1.0_Isabelle2021.pdf](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.1.0_Isabelle2021.pdf)
-  * [Isabelle_DOF-1.1.0_Isabelle2021.tar.xz](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.1.0_Isabelle2021.tar.xz)
-  * [Isabelle_DOF-1.1.0_Isabelle2021.tar.xz.asc](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.1.0_Isabelle2021.tar.xz.asc)
-* Isabelle/DOF 1.1.0/Isabelle2020
-  * [Isabelle_DOF-1.1.0_Isabelle2020.pdf](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.1.0_Isabelle2020.pdf)
-  * [Isabelle_DOF-1.1.0_Isabelle2020.tar.xz](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.1.0_Isabelle2020.tar.xz)
-  * [Isabelle_DOF-1.1.0_Isabelle2020.tar.xz.asc](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.1.0_Isabelle2020.tar.xz.asc)
-* Isabelle/DOF 1.0.0/Isabelle2019
-  * [Isabelle_DOF-1.0.0_Isabelle2019.pdf](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.0.0_Isabelle2019.pdf)
-  * [Isabelle_DOF-1.0.0_Isabelle2019.tar.xz](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.0.0_Isabelle2019.tar.xz)
-  * [Isabelle_DOF-1.0.0_Isabelle2019.tar.xz.asc](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.0.0_Isabelle2019.tar.xz.asc)
-
 ## Team
 
 Main contacts:
@@ -147,7 +125,6 @@ Main contacts:
 * Idir Ait-Sadoune
 * Paolo Crisafulli
 * Chantal Keller
-* Nicolas Méric
 
 ## License
 
@@ -157,32 +134,18 @@ SPDX-License-Identifier: BSD-2-Clause
 
 ## Publications
 
-* Achim D. Brucker, Idir Ait-Sadoune, Paolo Crisafulli, and Burkhart Wolff.
-  [Using The Isabelle Ontology Framework: Linking the Formal with the
-  Informal](https://www.brucker.ch/bibliography/download/2018/brucker.ea-isabelle-ontologies-2018.pdf).
-  In Conference on Intelligent Computer Mathematics (CICM). Lecture Notes in
-  Computer Science (11006), Springer-Verlag, 2018.
-  [doi:10.1007/978-3-319-96812-4_3](https://doi.org/10.1007/978-3-319-96812-4_3).
+* Achim D. Brucker, Idir Ait-Sadoune, Paolo Crisafulli, and Burkhart
+  Wolff. [Using The Isabelle Ontology Framework: Linking the Formal
+  with the Informal](https://www.brucker.ch/bibliography/download/2018/brucker.ea-isabelle-ontologies-2018.pdf).
+  In Conference on Intelligent Computer Mathematics (CICM). Lecture
+  Notes in Computer Science (11006), Springer-Verlag, 2018.
 
 * Achim D. Brucker and Burkhart Wolff. [Isabelle/DOF: Design and
   Implementation](https://www.brucker.ch/bibliography/download/2019/brucker.ea-isabelledof-2019.pdf).
-  In Software Engineering and Formal Methods (SEFM). Lecture Notes in Computer
-  Science (11724), Springer-Verlag, 2019.
-  [doi:10.1007/978-3-030-30446-1_15](https://doi.org/10.1007/978-3-030-30446-1_15).
+  In Software Engineering and Formal Methods (SEFM). Lecture Notes in
+  Computer Science, Springer-Verlag, 2019.
 
-* Achim D. Brucker, Burkhart Wolff. [Using Ontologies in Formal Developments
-  Targeting
-  Certification](https://www.brucker.ch/bibliography/download/2019/brucker.ea-ontologies-certification-2019.pdf).
-  In Integrated Formal Methods (IFM). Lecture Notes in Computer Science (11918).
-  Springer-Verlag 2019.
-  [doi:10.1007/978-3-030-34968-4_4](http://dx.doi.org/10.1007/978-3-030-34968-4_4)  
+## Master Repository
 
-* Sergio Bezzecchi, Paolo Crisafulli, Charlotte Pichot, and Burkhart Wolff.
-  [Making Agile Development Processes fit for V-style Certification
-   Procedures.](https://hal.archives-ouvertes.fr/hal-01702815/document). In ERTS
-   2018. <https://hal.archives-ouvertes.fr/hal-01702815>
-
-## Upstream Repository
-
-The upstream git repository, i.e., the single source of truth, for this project
-is hosted at <https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF>.
+The master git repository for this project is hosted
+<https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF>.

etc/build.props

@@ -1,13 +0,0 @@
-title = Isabelle/DOF
-module = $ISABELLE_HOME_USER/DOF/isabelle_dof.jar
-no_build = false
-requirements = \
-  env:ISABELLE_SCALA_JAR
-sources = \
-  src/scala/dof.scala \
-  src/scala/dof_document_build.scala \
-  src/scala/dof_mkroot.scala \
-  src/scala/dof_tools.scala
-services = \
-  isabelle.dof.DOF_Tools \
-  isabelle.dof.DOF_Document_Build$Engine

etc/settings

@@ -1,4 +0,0 @@
-# -*- shell-script -*- :mode=shellscript:
-
-ISABELLE_DOF_HOME="$COMPONENT"
-ISABELLE_DOCS="$ISABELLE_DOF_HOME/doc:$ISABELLE_DOCS"

examples/CC_ISO15408/PikeOS_study/PikeOS_ST.thy

@@ -1,90 +0,0 @@
-theory PikeOS_ST (*Security Target *)
-
-imports "../../../src/ontologies/CC_v3.1_R5/CC_v3_1_R5"
-        (*  Isabelle_DOF.CC_v3_1_R5 in the future.  *)
-
-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 toe_def} is the operating system PikeOS version 3.4 
-   running on the microprocessor family x86 hosting different applications. 
-   The @{docitem toe_def} 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 @{definition \<open>toe\<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

examples/CENELEC_50128/mini_odo/ROOT

@@ -1,11 +1,11 @@
 session "mini_odo" = "Isabelle_DOF" +
-  options [document = pdf, document_output = "output", document_build = dof]
-  sessions 
-    "Physical_Quantities"
+  options [document = pdf, document_output = "output"]
   theories
     "mini_odo"
   document_files
+    "isadof.cfg"
     "preamble.tex"
+    "build"
     "root.bib"
     "root.mst"
     "lstisadof.sty"
@@ -13,4 +13,3 @@ session "mini_odo" = "Isabelle_DOF" +
     "figures/odometer.jpeg"
     "figures/three-phase-odo.pdf"
     "figures/wheel-df.png"
-

examples/CENELEC_50128/mini_odo/document/build

@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+# Copyright (c) 2018-2019 The University of Sheffield. All rights reserved.
+#               2018 The University of Paris-Saclay. All rights reserved.
+#
+# 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
+if [ ! -f $ISABELLE_HOME_USER/DOF/document-template/build_lib.sh ]; then
+    echo ""
+    echo "Error: Isabelle/DOF not installed"
+    echo "====="
+    echo "This is a Isabelle/DOF project. The document preparation requires"
+    echo "the Isabelle/DOF framework. Please obtain the framework by cloning"
+    echo "the Isabelle/DOF git repository, i.e.: "
+    echo "    git clone https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF"
+    echo "You can install the framework as follows:"
+    echo "    cd Isabelle_DOF/document-generator"
+    echo "    ./install"
+    echo ""
+    exit 1
+fi
+
+cp $ISABELLE_HOME_USER/DOF/document-template/build_lib.sh .
+source build_lib.sh

examples/CENELEC_50128/mini_odo/document/isadof.cfg

@@ -0,0 +1,3 @@
+Template: scrreprt-modern
+Ontology: technical_report
+Ontology: cenelec_50128

examples/CENELEC_50128/mini_odo/document/lstisadof.sty

@@ -1,16 +1,3 @@
-%% Copyright (C) 2018 The University of Sheffield
-%%               2018 The University of Paris-Saclay
-%%               2019 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
 
 \definecolor{OliveGreen}    {cmyk}{0.64,0,0.95,0.40}
 \definecolor{BrickRed}      {cmyk}{0,0.89,0.94,0.28}

examples/CENELEC_50128/mini_odo/document/preamble.tex

@@ -1,17 +1,3 @@
-%% Copyright (C) 2018 The University of Sheffield
-%%               2018 The University of Paris-Saclay
-%%               2019 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
-
 %% This is a placeholder for user-specific configuration and packages.
 \usepackage{listings}
 \usepackage{lstisadof}
@@ -19,6 +5,8 @@
 \usepackage{paralist}
 \usepackage{numprint}
 \newcommand{\fixIsarList}{\vspace{-\topsep}\vspace{-\baselineskip}\mbox{}\\[0pt]\noindent}
+\newcommand{\eg}{e.\,g.}
+\newcommand{\ie}{i.\,e.}
 \author{}
 \title{}
 

examples/CENELEC_50128/mini_odo/mini_odo.thy

@@ -1,65 +1,27 @@
-(*************************************************************************
- * 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  
+  imports  
   "Isabelle_DOF.CENELEC_50128" 
   "Isabelle_DOF.technical_report"
-  "Physical_Quantities.SI" "Physical_Quantities.SI_Pretty"
 begin
-use_template "scrreprt-modern"
-use_ontology technical_report and 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>
+chapter*[casestudy::technical]\<open>A Case-Study: 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 
+  odometry function of a train. This software 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. 
+  physical model of the environment, the physical and architectural model of the odometer 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 safety critical embedded system.
 
   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 
@@ -70,8 +32,7 @@ text\<open>
   development.
 \<close>
 
-section\<open>A CENELEC-conform development as an \<^emph>\<open>Integrated Source\<close>\<close>
-
+section\<open>System Requirements Specification 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 
@@ -85,9 +46,9 @@ text\<open>
   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}
+  \begin{wrapfigure}[8]{l}{3.9cm}
     \centering
-    \vspace{-.5cm}
+    \vspace{-.7cm}
     \includegraphics[width=3.4cm]{figures/wheel-df}
     \caption{Motion sensing via an odometer.}
     \label{wheel-df}
@@ -100,23 +61,17 @@ text\<open>
 
   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>
+  particular, we need to make the following assumptions explicit:\vspace{-.3cm}
+  \<^item>  that the wheel is perfectly circular with a given, constant radius,
+  \<^item>  that the slip between the trains wheel and the track negligible,
+  \<^item>  the distance between all teeth of a wheel is the same and constant, and  
+  \<^item>  the sampling rate of positions is a given constant.
 
-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
+  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
@@ -125,53 +80,57 @@ text\<open>
 \<close>
 
 subsection\<open>Capturing ``System Architecture.''\<close>
-
-figure*["three-phase"::figure,relative_width="70",src="''figures/three-phase-odo''"]
-\<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>. 
+  \begin{figure}
+    \centering
+    \includegraphics[width=.70\textwidth]{figures/three-phase-odo}
+    \begin{picture}(0,0)
+      \put(-112,44){\includegraphics[width=.30\textwidth]{figures/odometer}}
+    \end{picture}
+  \caption{An odometer with three sensors \inlineisar{C1}, \inlineisar{C2}, and \inlineisar{C3}.}\label{three-phase} 
+\end{figure}
+  The requirements analysis also contains a sub-document \<^emph>\<open>system architecture description\<close> 
+  (CENELEC notion) that contains technical drawing of the odometer, a timing diagrams 
+  (see \autoref{three-phase}), and tables describing the encoding of the position 
+  for the possible signal transitions of the sensors \inlineisar{C1}, \inlineisar{C2}, and $C3.$ 
 \<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
+  The requirements analysis also contains a sub-document \<^emph>\<open>functions and interfaces\<close> 
+  (CENELEC notion) 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 $N_{\text{avg}}$ samples''
+  where the speed refers to the physical speed of the train and $N_{\text{avg}}$ a parameter of the
   sub-system configuration. \<close>
 
 (*<*)
-declare_reference*["df-numerics-encshaft"::figure] 
+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 
+  however, certain interface parameters like \inlineisar*Odometric_Position_TimeStamp*
+  (a counter on the number of samplings) and \inlineisar*Relative_Position* 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 
+  For our case-study, we assume maximum deviation of the \inlineisar*Relative_Position* 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",src="''figures/df-numerics-encshaft''"]
 \<open>Real distance vs. discrete distance vs. shaft-encoder sequence\<close>
 
 
 subsection\<open>Capturing the ``Software Design Spec'' (Resume).\<close>
 text\<open>
+\enlargethispage{\baselineskip}
   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), 
+  recovery, another one, fatal, signaling, \eg, a defect of the receiver hardware), 
   calculating the relative position, speed and acceleration.
 \<close>
 
@@ -189,123 +148,88 @@ text\<open>
   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 
+ \<open>formal enrichment\<close>. For example, from the assumptions in the architecture follow 
+ the definitions:
+\begin{isar}
+definition teeth_per_wheelturn::nat  ("tpw") where "tpw \<equiv> SOME x. x > 0"
+definition wheel_diameter::real ("w$_d$") where "w$_d$ \<equiv> SOME x. x > 0" 
+definition wheel_circumference::real ("w$_{\text{circ}}$") where "w$_{\text{circ}}$ \<equiv> pi * w$_d$"
+definition \<delta>s$_{\text{res}}$::real where "\<delta>s$_{\text{res}}$ \<equiv> w$_{\text{circ}}$ / (2 * 3 * tpw)"
+\end{isar}
+  Here, \inlineisar{real} 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. \inlineisar{SOME} is the
+  Hilbert choice operator from HOL; the definitions of the model parameters admit all possible positive values as uninterpreted
+  constants. Our perfect-wheel assumption is translated into a calculation of the circumference of the 
+  wheel, while \inlineisar{\<delta>s<bsub>res<esub>}, 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 
+\begin{isar}
+type_synonym distance_function = "real\<Rightarrow>real"  
+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)" 
+\end{isar}
+which permits to constrain the central observable \inlineisar|distance_function| 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> . 
+reliable measurements over a \inlineisar|distance_function df|. 
 
 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>}
-
+\begin{isar}
+definition normally_behaved_distance_function :: "(real \<Rightarrow> real) \<Rightarrow> bool"
+    where  normally_behaved_distance_function df = 
+            ( \<forall> t. df(t) \<in> \<real>$_{\ge 0}$  \<and>  (\<forall> t \<in> \<real>$_{\le 0}$. df(t) = 0)  
+             \<and> df differentiable on$_{\text{R}}$ \<and> (Speed df)differentiable on$_{\text{R}}$ 
+             \<and> (Accel df)differentiable on$_{\ensuremath{R}}$ 
+             \<and> (\<forall> t. (Speed df) t \<in> {-Speed$_{\text{Max}}$ .. Speed$_{\text{Max}}$})  
+             \<and> (\<forall> t. (Accel df) t \<in> {-\<bar>Accel$_{\text{Max}}$\<bar> .. \<bar>Accel$_{\text{Max}}$\<bar>}))
+\end{isar}
 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>}
-
+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 \inlineisar+shaft_encoder_state+ (a triple with the sensor values 
+\inlineisar{C1}, \inlineisar{C2}, \inlineisar{C3})  were formalized as types, while tables were defined as recursive functions:
+\enlargethispage{2\baselineskip}\begin{isar}
+fun phase$_0$ :: "nat \<Rightarrow> shaft_encoder_state"   where 
+   "phase$_0$ (0) =  \<lparr> C1 = False, C2 = False, C3 = True \<rparr>" 
+  |"phase$_0$ (1) =  \<lparr> C1 = True,  C2 = False, C3 = True \<rparr>" 
+  |"phase$_0$ (2) =  \<lparr> C1 = True,  C2 = False, C3 = False\<rparr>" 
+  |"phase$_0$ (3) =  \<lparr> C1 = True,  C2 = True,  C3 = False\<rparr>" 
+  |"phase$_0$ (4) =  \<lparr> C1 = False, C2 = True,  C3 = False\<rparr>" 
+  |"phase$_0$ (5) =  \<lparr> C1 = False, C2 = True,  C3 = True \<rparr>" 
+  |"phase$_0$ x   =  phase$_0$(x - 6)"         
+definition Phase ::"nat\<Rightarrow>shaft_encoder_state" where Phase(x) = phase$_0$(x-1)
+\end{isar}
+We now define shaft encoder sequences as
+translations of distance functions:
+\begin{isar}
+definition encoding::"distance_function\<Rightarrow>nat\<Rightarrow>real\<Rightarrow>shaft_encoder_state" 
+  where "encoding df init$_{\text{pos}}$ \<equiv> \<lambda>x. Phase(nat\<lfloor>df(x) / \<delta>s$_{\text{res}}$\<rfloor> + init$_{\text{pos}}$)"
+\end{isar}
+where \inlineisar+init$_{\text{pos}}$+ is the initial position of the wheel. 
+\inlineisar+sampling+'s were constructed from encoding sequences over discretized time points:
+\begin{isar}
+definition $\!\!$sampling::"distance$\!$_function\<Rightarrow>nat\<Rightarrow>real\<Rightarrow>nat\<Rightarrow>shaft$\!$_encoder$\!$_state" 
+  where "sampling df init$_{\text{pos}}$ \<delta>t \<equiv> \<lambda>n::nat. encoding df init$_{\text{pos}}$ (n * \<delta>t)"
+\end{isar}
+The sampling interval \inlineisar+\<delta>t+ (the inverse of the sampling frequency) is a critical
 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.
+  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 1m for
+\inlineisar+w$_d$+, 100 for \inlineisar+tpw+, 80km/h \inlineisar+Speed$_{\text{Max}}$+,
+and 14400Hz for the sampling frequency, results in an odometer resolution of 2.3mm,  
+a maximum distance of 9878km, and a maximal system up-time of 123.4 hours.
 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>.
+the maximally allowed difference between \inlineisar+df(n*\<delta>t)+ and 
+\inlineisar+sampling df init$_{\text{pos}}$ \<delta>t n+ for all \inlineisar+init$_{\text{pos}}$ \<in>{0..5}+.
 \<close>
 (*<*)
 ML\<open>val two_thirty2 = 1024 * 1024 * 1024 * 4;
@@ -315,50 +239,41 @@ ML\<open>val two_thirty2 = 1024 * 1024 * 1024 * 4;
 
 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 
+properties of the device. For example, the \inlineisar+Phase+-table excludes situations in which 
+all sensors \inlineisar{C1}, \inlineisar{C2}, and \inlineisar{C3} 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
+shown by a very small Isabelle case-distinction proof that this safety requirement follows indeed from the 
+above definitions:
+\begin{isar}
+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
+\end{isar}
+for all positions \inlineisar+x+. Similarly, it is proved that the table is indeed
+cyclic: \inlineisar+ phase$_0$ x = phase$_0$(x mod 6)+ and locally injective:
+\inlineisar+\<forall>x<6. \<forall>y<6. phase$_0$ x = phase$_0$ y \<longrightarrow> x = y+.
+These lemmas, building the ``theory of an odometer,'' culminate in a theorem 
 that we would like to present in more detail.
+\begin{isar}
+theorem minimal_sampling :
+  assumes * : normally_behaved_distance_function df
+    and  ** : \<delta>t * Speed$_{\text{Max}}$ < \<delta>s$_{\text{res}}$
+  shows \<forall> \<delta>X\<le>\<delta>t. 0<\<delta>X \<longrightarrow> 
+             \<exists>f. retracting (f::nat\<Rightarrow>nat) \<and> 
+                 sampling df init$_{\text{pos}}$ \<delta>X = (sampling df init$_{\text{pos}}$ \<delta>t) o f
 
-   @{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
+\end{isar}
+This theorem states for \inlineisar+normally_behaved_distance_function+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'' 
+some \inlineisar$df$ 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 
+Of particular interest is the second assumption, labelled ``\inlineisar|**|,'' which  
+establishes a lower bound from \inlineisar+w$_{\text{circ}}$+, \inlineisar+tpw+, 
+\inlineisar+Speed$_{\text{Max}}$+ 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 
@@ -372,7 +287,6 @@ standard~@{cite "bsi:50128:2014"}, 7.2.4.22 and are usually addressed in an own
 \<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 
@@ -384,144 +298,125 @@ text\<open>
 
 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
+  \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 
+  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
+  of the concept ``traceability'' in paragraphs 3.1.46 (a notion referenced 31 times in the standard), 
+  which we translated directly into:
+\begin{isar}
+Definition*[traceability::concept]<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>
+\end{isar}
+  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
+\begin{isar}
+text*[...]<open>  ... to assure <@>{concept traceability} for 
+  <@>{requirement bitwiseAND}, we prove ... <close>
+\end{isar}
+  The presentation of this document element inside \isadof is immediately hyperlinked against the 
+  \inlineisar+Definition*+ 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 = 
+\begin{isar}
+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         *) | ...
+\end{isar}
+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>:
+\begin{isar}
+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 
+\end{isar}
+  In contrast to the standard, we can parameterize \inlineisar+formal_proof+ 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. 
+  world of systems attempting to assure traceability, 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.  
+  We introduce central concept of a \<^emph>\<open>requirement\<close> as an ODL \inlineisar*doc_class* 
+  based on some generic basic library \inlineisar*text_element* providing basic layout attributes.
+\begin{isar}
+doc_class requirement = text_element +
+   long_name    :: "string option"
+   is_concerned :: "role set"
+\end{isar}
+where the \inlineisar*roles* are exactly the ones defined in the previous section and represent 
+the groups of stakeholders in the CENELEC process. Therefore, the \inlineisar+is_concerned+-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>
+\begin{isar}
+doc_class sub_requirement = 
+   decomposes :: "requirement"
+   relates_to :: "requirement set"
+\end{isar}\<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> 
-
+consider the following statement @{cite "bsi:50128:2014"}, pp. 25.:\vspace{-1.5mm}
 \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>}
-
+\end{quote}\vspace{-1.5mm}
+The terms \<^emph>\<open>judgment\<close> and \<^emph>\<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 judgment, \eg, by 
+the following concept:
+\begin{isar}
+doc_class judgement =    
+   refers_to       :: requirement
+   evidence        :: "vnt_technique list"
+   status          :: status
+   is_concerned    :: "role set" <= "{VER,ASR,VAL}" 
+\end{isar}
 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>}
+There are different views possible here: an alternative would be to define \inlineisar+evidence+
+as ontological concept with  \inlineisar+vnt_technique+'s (rather than an attribute of judgement) 
+and consider the basis of judgments as a relation between requirements and relation:
+\begin{isar}
+doc_class judgement =    
+   based_on        :: "(requirement \<times> evidence) set"
+   status          :: status
+   is_concerned    :: "role set" <= "{VER,ASR,VAL}" 
+\end{isar}
 
 More experimentation will be needed to find out what kind of ontological modeling is most
 adequate for developers in the context of \isadof. 
@@ -533,66 +428,60 @@ text\<open>From the variety of different possibilities for adding CENELEC annota
 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
+text\<open>In our case, the SR-team early on detected a property necessary
+for error-detection of the device (c.f. @{docitem verific}):
+\enlargethispage{2\baselineskip}\begin{isar}
+text*[encoder_props::requirement]<open> The requirement specification team ...
+    C1 & C2 & C3  = 0   (bitwise logical AND operation)
+    C1 | C2 | C3  = 1   (bitwise logical OR operation) <close>
+\end{isar}
+After the Isabelle proofs shown in @{docitem 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 
+\begin{isar}
+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$_0$"}.<close>
+\end{isar}
+The references \inlineisar|<@>{...}|, 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). 
+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 \inlineisar+df+, and any representable 
+and valid sampling sequence that can be constructed for \inlineisar+df+, 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.
+\begin{isar}
+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$_{\text{odo}}$) - (\<delta>s$_{\text{res}}$ * pos)\<bar> \<le> \<delta>s$_{\text{res}}$))
 
-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
+update_instance*[R5::safety_requirement,
+       formal_definition:="[<@>{thm <open>Odometric_Position_Count_precise_def<close>}]"]    
+\end{isar}
+By \inlineisar+update_instance*+, we book the property \inlineisar+Position_Count_precise_def+ as
+\inlineisar+safety_requirement+, a specific sub-class of \inlineisar+requirement+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
+the condition labelled ``\inlineisar|**|'' 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 
+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,
@@ -607,71 +496,65 @@ different PDF versions and for each version, document specific consistency guara
 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
+\inlineisar+SRAC+ (CENELEC for: safety-related application condition; ontologically, this is a
+derived class from \inlineisar+requirement+.) and add the definition of the predicate into the
 document instance as described in the previous section.\<close>
 
 
 
+
+text\<open>\appendix\<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"}
+\<^item> \inlineisar|<@>{thm refl}|: @{thm refl}
+\<^item> \inlineisar|<@>{thm [source] refl}|: @{thm [source] refl}
+\<^item> \inlineisar|<@>{thm[mode=Rule] conjI}|: @{thm[mode=Rule] conjI}
+\<^item> \inlineisar|<@>{file "mini_odo.thy"}|: @{file "mini_odo.thy"}
+\<^item> \inlineisar|<@>{value "3+4::int"}|: @{value "3+4::int"}
+\<^item> \inlineisar|<@>{const hd}|: @{const hd}
+\<^item> \inlineisar|<@>{theory HOL.List}|: @{theory HOL.List}
+\<^item> \inlineisar|<@>{term "3"}|: @{term "3"}
+\<^item> \inlineisar|<@>{type bool}|: @{type bool}
+\<^item> \inlineisar|<@>{term [show_types] "f x = a + x"}|: @{term [show_types] "f x = a + x"}
 \<close>
 
-text\<open>Examples for declaration of typed doc-classes "assumption" (sic!) and "hypothesis" (sic!!),
+text\<open>Examples for declaration of typed doc-items "assumption" and "hypothesis",
      concepts defined in the underlying ontology @{theory "Isabelle_DOF.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*[ass1::assumption, long_name="Some ''assumption one''"] \<open> The subsystem Y is safe. \<close>
+text*[hyp1::hypothesis] \<open> P not equal NP \<close>
   
-text\<open>  
-   A real example fragment fsrom a larger project, declaring a text-element as a
-   "safety-related application condition", a concept defined in the 
-   @{theory "Isabelle_DOF.CENELEC_50128"} ontology:\<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.CENELEC_50128"} ontology:\<close>  
 
-text*[hyp2::hypothesis]\<open>Under the assumption @{assumption \<open>ass2\<close>} we establish the following: ... \<close>
+text*[hyp2::hypothesis]\<open>Under the assumption @{assumption \<open>ass1\<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*[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*[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*[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*[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 (unchecked) \<open>t10\<close>}, 
-                         @{test_result (define) \<open>t10\<close>} \<close>
-text \<open> the               @{test_result \<open>t10\<close>}                      
-       as well as the    @{SRAC \<open>ass122\<close>}\<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 @{docref (unchecked) \<open>t10\<close>}, 
+                         @{docref (define) \<open>t10\<close>} \<close>
+text \<open> the               @{docref \<open>t10\<close>}                      
+       as well as the    @{docref \<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
 (*>*)

examples/ROOTS

@@ -1,3 +1,4 @@
 scholarly_paper
 technical_report
+math_exam
 CENELEC_50128

examples/cytology/Cytology.thy

@@ -1,90 +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 :: "\<lambda>\<sigma>::eucaryotic_cells. \<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 [] 3 []))\<close>
-
-value \<open>has_nucleus_inv(eucaryotic_cells.make X Y Z Z Z [] 3 [])\<close>
-
-value \<open>has_nucleus_inv(eucaryotic_cells.make X Y Z Z Z [] 3 
-                         [upcast\<^sub>n\<^sub>u\<^sub>c\<^sub>l\<^sub>e\<^sub>u\<^sub>s (nucleus.make a b c d [])])\<close>
-
-
-
-end

examples/math_exam/MathExam/MathExam.thy

@@ -0,0 +1,98 @@
+(*<*)
+theory MathExam
+  imports "Isabelle_DOF.math_exam"
+    HOL.Real
+begin
+(*>*)   
+(* open_monitor*[exam::MathExam]  *)
+
+section*[header::Header,examSubject= "[algebra]", 
+            date="''02-05-2018''", timeAllowed="90::int"] \<open>Exam number 1\<close>
+text\<open>
+\begin{itemize}
+\item Use black ink or black ball-point pen. 
+\item Draw diagrams in pencil.
+\item Answer all questions in the spaces provided.
+\end{itemize}
+\<close>
+
+text*[idir::Author, affiliation="''CentraleSupelec''", 
+         email="''idir.aitsadoune@centralesupelec.fr''"]
+        \<open>Idir AIT SADOUNE\<close>
+  
+  
+figure*[figure::figure, spawn_columns=False,
+        relative_width="80", 
+        src="''figures/Polynomialdeg5''"] 
+        \<open>A Polynome.\<close>
+
+
+subsubsection*[exo1 :: Exercise, content="[q1::Task,q2::Task]"]\<open>Exercise 1\<close>
+text\<open>
+Here are the first four lines of a number pattern.
+\begin{itemize}
+\item Line 1 : @{term "1*6 + 2*4 = 2*7"}
+\item Line 2 : @{term "2*7 + 2*5 = 3*8"}
+\item Line 3 : @{term "3*8 + 2*6 = 4*9"}
+\item Line 4 : @{term "4*9 + 2*7 = 5*10"} 
+\end{itemize}
+\<close>
+
+declare [[show_sorts=false]]  
+subsubsection*[exo2 :: Exercise, content="[q1::Task,q2::Task]"]\<open>Exercise 2\<close> 
+  
+text\<open>Find the roots of the polynome:
+@{term "(x^3) - 6 * x^2 + 5 * x + 12"}.
+Note the intermediate steps in the following fields and submit the solution.\<close>
+text\<open>
+\begin{Form}[action={http://your-web-server.com/path/receiveform.cgi}]
+\begin{tabular}{l}
+    From @{term "(x^3) - 6 * x^2 + 5 * x + 12"}  \\\\  
+    \TextField{have 1} \\\\  
+    \TextField{have 2} \\\\  
+    \TextField{have 3} \\\\
+    \TextField{finally show} \\\\
+    \CheckBox[width=1em]{Has the polynomial as many solutions as its degree ? } \\\\
+    \Submit{Submit}\\
+\end{tabular}
+\end{Form}
+\<close>
+
+(* a bit brutal, as long as lemma* does not yet work *)
+(*<*)
+lemma check_polynome :
+  fixes x::real 
+  shows "(x^3) - 6 * x^2 + 5 * x + 12 = (x-4) * (x+1) * (x - 3)"
+        
+proof -
+  have * : "(x-4) * (x+1) * (x - 3) = (x-4) * ((x+1) * (x-3))"
+         by simp
+  have ** : "... = (x-4) * (x^2 - 2*x - 3)"
+    apply(auto simp: right_diff_distrib add.commute semiring_normalization_rules(1)[symmetric])
+    by (simp add: semiring_normalization_rules(29))
+  have *** : "... = x^3 - 6 * x^2 + 5 * x + 12"
+    apply(auto simp: right_diff_distrib left_diff_distrib add.commute semiring_normalization_rules(1)[symmetric])
+    by (simp add: numeral_3_eq_3 semiring_normalization_rules(29))
+  show ?thesis
+    by(simp only: * ** ***)
+qed
+(*>*)
+
+text*[a1::Answer_Formal_Step]\<open>First Step: Fill in term and justification\<close>
+text*[a2::Answer_Formal_Step]\<open>Next Step: Fill in term and justification\<close>
+text*[a3::Answer_Formal_Step]\<open>Next Step: Fill in term and justification\<close>
+text*[a4::Answer_Formal_Step]\<open>Next Step: Fill in term and justification\<close>
+  
+text*[q1::Task, local_grade="oneStar", mark="1::int", type="formal"] 
+\<open>Complete Line 10 :  @{term "10*x + 2*y =  11*16"}\<close>
+
+subsubsection*[exo3 :: Exercise, content="[q1::Task,q2::Task]"]\<open>Exercise 3\<close>  
+
+text*[q2::Task, local_grade="threeStars", mark="3::int", type="formal"] 
+\<open>Prove that  @{term "n*(n+5) + 2*(n+3) "} is always the product of two numbers 
+   with a difference of 5.
+\<close> 
+(* this does not work on the level of the LaTeX output for known restrictions of the Toplevel. *)
+(* close_monitor*[exam :: MathExam] *)
+
+end

examples/math_exam/MathExam/ROOT

@@ -0,0 +1,10 @@
+session "MathExam" = "Isabelle_DOF" +
+  options [document = pdf, document_output = "output"]
+  theories
+    MathExam
+  document_files
+    "preamble.tex"
+    "isadof.cfg"
+    "preamble.tex"
+    "build"
+    "figures/Polynomialdeg5.png"

examples/math_exam/MathExam/document/build

@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+# Copyright (c) 2018-2019 The University of Sheffield. All rights reserved.
+#               2018 The University of Paris-Saclay. All rights reserved.
+#
+# 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
+if [ ! -f $ISABELLE_HOME_USER/DOF/document-template/build_lib.sh ]; then
+    echo ""
+    echo "Error: Isabelle/DOF not installed"
+    echo "====="
+    echo "This is a Isabelle/DOF project. The document preparation requires"
+    echo "the Isabelle/DOF framework. Please obtain the framework by cloning"
+    echo "the Isabelle/DOF git repository, i.e.: "
+    echo "    git clone https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF"
+    echo "You can install the framework as follows:"
+    echo "    cd Isabelle_DOF/document-generator"
+    echo "    ./install"
+    echo ""
+    exit 1
+fi
+
+cp $ISABELLE_HOME_USER/DOF/document-template/build_lib.sh .
+source build_lib.sh

examples/math_exam/MathExam/document/isadof.cfg

@@ -0,0 +1,2 @@
+Template: scrartcl
+Ontology: math_exam

examples/math_exam/MathExam/document/preamble.tex

@@ -0,0 +1,18 @@
+%% 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. 
+
+\title{<TITLE>}
+\author{<AUTHOR>}
+

examples/math_exam/ROOTS

@@ -0,0 +1 @@
+MathExam

examples/scholarly_paper/2018-cicm-isabelle_dof-applications/IsaDofApplications.thy

@@ -1,80 +1,51 @@
-(*************************************************************************
- * 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 "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>
-
 (*>*)
 
-title*[tit::title]       \<open>Using the Isabelle Ontology Framework\<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>
+text*[adb:: author,
+      email="''a.brucker@sheffield.ac.uk''",
+      orcid="''0000-0002-6355-1200''",
+      affiliation="''The University of Sheffield, Sheffield, UK''"]\<open>Achim D. Brucker\<close>
+text*[idir::author,
+      email       = "''idir.aitsadoune@centralesupelec.fr''",
+      affiliation = "''CentraleSupelec, Paris, France''"]\<open>Idir Ait-Sadoune\<close>
+text*[paolo::author,
+      email      = "''paolo.crisafulli@irt-systemx.fr''",
+      affiliation= "''IRT-SystemX, Paris, France''"]\<open>Paolo Crisafulli\<close>
+text*[bu::author,
+      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. 
+text*[abs::abstract,
+      keywordlist="[''Ontology'',''Ontological Modeling'',''Isabelle/DOF'']"]\<open>
+While Isabelle is mostly known as part of Isabelle/HOL (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. 
 
-   %% If you consider citing this paper, please refer to 
-   %% @{cite "brucker.ea:isabelle-ontologies:2018"}.
+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. 
 \<close>
 
 section*[intro::introduction]\<open> Introduction \<close>  
-text*[introtext::introduction, level = "Some 1"]\<open> 
+text*[introtext::introduction]\<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
@@ -82,7 +53,7 @@ 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 
+\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
@@ -96,22 +67,22 @@ describing \<^emph>\<open>attributes\<close> of the concept, as well as \<^emph>
 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
+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>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 in case of 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>   
+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
+Isabelle/HOL 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>
 
@@ -123,29 +94,29 @@ 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 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>}
+text*[plan::introduction]\<open> The plan of the paper is follows: we start by introducing  the underlying 
+Isabelel sytem (@{docitem (unchecked) \<open>bgrnd\<close>}) followed by presenting the 
+essentials of  \isadof and its ontology language (@{docitem (unchecked) \<open>isadof\<close>}). 
+It follows @{docitem (unchecked) \<open>ontomod\<close>}, where we present three application 
+scenarios from the point of view of the ontology modeling. In @{docitem_ref (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>  
+conclusions  and discuss related work in @{docitem_ref (unchecked) \<open>conclusion\<close>}. \<close>  
 
-section*[bgrnd::text_section,main_author="Some(@{docitem ''bu''}::author)"]
+section*[bgrnd::text_section,main_author="Some(@{docitem ''adb''}::author)"]
         \<open> Background: The Isabelle System \<close>
-text*[background::introduction, level="Some 1"]\<open>
+text*[background::introduction]\<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
+``\textsl{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"} 
+  \<^emph>\<open>systems\<close>.}''~@{cite "wenzel.ea:building:2007"} 
 
 The current system framework offers moreover the following features:
 
@@ -162,24 +133,24 @@ figure*[architecture::figure,relative_width="100",src="''figures/isabelle-archit
      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>}
+text*[blug::introduction]\<open> The Isabelle system architecture shown in @{docitem_ref \<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 
+resides in the SML structure \texttt{Context}. 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, 
+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 \inlineisar+section+ \<^dots>, 
-\inlineisar+subsection+ \<^dots>, \inlineisar+text+ \<^dots>, etc.
+which is based on literate specification commands such as \inlineisar+section+ \ldots, 
+\inlineisar+subsection+ \ldots, \inlineisar+text+ \ldots, etc.
 Thus, a user can add a simple text:
 \begin{isar}
   text\<Open>This is a description.\<Close>
 \end{isar}
 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. 
+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>:
 \begin{isar}
   text\<Open>According to the reflexivity axiom \at{thm refl}, we obtain in \<Gamma> 
@@ -194,45 +165,45 @@ For the antiquotation \inlineisar+\at{value "fac 5"}+  we assume the usual defin
 \inlineisar+fac+ in HOL.
 \<close>
 
-text*[anti::introduction, level = "Some 1"]\<open> Thus, antiquotations can refer to formal content, can be type-checked before being 
+text*[anti]\<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(@{docitem ''adb''}::author)"]\<open> \<^isadof> \<close>
+section*[isadof::technical,main_author="Some(@{docitem ''adb''}::author)"]\<open> \isadof \<close>
    
-text\<open> An \<^isadof> document consists of three components: 
+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
+  importing the ontology definition. \isadof provides an own family of text-element
   commands such as \inlineisar+title*+, \inlineisar+section*+,  \inlineisar+text*+, 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 
+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 
+ 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 
+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 
+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>. 
+\eg, HTML, and increases the risk of arcane error-messages in generated \LaTeX{}. 
 
- The \<^isadof> ontology specification language consists basically on a notation for
+ 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 
+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, 
@@ -247,7 +218,7 @@ The HOL-types inside the document specification language support built-in types
 \inlineisar+typ+'s,  \inlineisar+term+'s, and \inlineisar+thm+'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.
+\isadof for consistency.
 
 Document classes can have a \inlineisar+where+ clause containing a regular 
 expression over class names. Classes with such a \inlineisar+where+ were called \<^emph>\<open>monitor classes\<close>.
@@ -256,10 +227,10 @@ 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 must belong to the corresponding classes. 
 
-To start using \<^isadof>, one creates an Isabelle project (with the name 
+To start using \isadof, one creates an Isabelle project (with the name 
 \inlinebash{IsaDofApplications}):
 \begin{bash}
-  isabelle dof_mkroot -o scholarly_paper -t lncs IsaDofApplications
+  isabelle mkroot_DOF -o scholarly_paper -t lncs -d  IsaDofApplications
 \end{bash}
 where the \inlinebash{-o scholarly_paper} specifies the ontology for writing scientific articles and 
 \inlinebash{-t lncs} specifies the use of Springer's \LaTeX-configuration for the Lecture Notes in 
@@ -270,8 +241,8 @@ article in PDF using the  following command:
 \end{bash}
 \<close>
 
-section*[ontomod::text_section]\<open> Modeling Ontologies in \<^isadof> \<close> 
-text\<open> In this section, we will use the \<^isadof> document ontology language
+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
@@ -279,11 +250,11 @@ 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 
+\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>.
+of \isadof.
 
 
 \begin{figure}
@@ -314,18 +285,18 @@ with the usual text-elements of a scientific paper. The attributes \inlineisar+s
 Our model prescribes an optional \inlineisar+main_author+ 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 \inlineisar+author+ is a HOL-type internally generated by \<^isadof> framework and can therefore
+Since \inlineisar+author+ is a HOL-type internally generated by \isadof framework and can therefore
 appear in the \inlineisar+main_author+ attribute of the \inlineisar+text_section+ 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 
+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. \<close>
 
 figure*[fig1::figure,spawn_columns=False,relative_width="95",src="''figures/Dogfood-Intro''"]
-       \<open> Ouroboros I: This paper from inside \<^dots> \<close>  
+       \<open> Ouroboros I: This paper from inside \ldots \<close>  
 
-text\<open> @{figure \<open>fig1\<close>} shows the corresponding view in the Isabelle/PIDE of thqqe present paper.
-Note that the text uses \<^isadof>'s own text-commands containing the meta-information provided by
+text\<open> @{docitem \<open>fig1\<close>} shows the corresponding view in the Isabelle/PIDE of thqqe 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 \inlineisar+introduction+'s, which we define as the extension of
 \inlineisar+text_section+ which is intended to capture common infrastructure:
@@ -407,15 +378,15 @@ doc_class figure   = text_section +
 
 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 
+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,spawn_columns=False,relative_width="85",src="''figures/Dogfood-figures''"]
-       \<open> Ouroboros II: figures \<^dots> \<close>
+       \<open> Ouroboros II: figures \ldots \<close>
 
-text\<open> The document class \inlineisar+figure+ --- supported by the \<^isadof> text command 
+text\<open> The document class \inlineisar+figure+ --- supported by the \isadof text command 
 \inlineisar+figure*+ --- makes it possible to express the pictures and diagrams in this paper 
-such as @{figure \<open>fig_figures\<close>}.
+such as @{docitem_ref \<open>fig_figures\<close>}.
 \<close>
          
 subsection*[math_exam::example]\<open> The Math-Exam Scenario \<close> 
@@ -427,12 +398,12 @@ during the exam and the preparation requires a very rigorous process, as the fre
 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 
+\<^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 
+\<^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. 
+\<^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
@@ -506,7 +477,7 @@ 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 \autoref{fig:onto-exam-monitor}). 
-In our scenario this sample proofs are completely \<^emph>\<open>intern\<close>, \<^ie>, not exposed to the 
+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.
 \begin{figure}
 \begin{isar}
@@ -532,15 +503,15 @@ doc_class MathExam=
   
 declare_reference*["fig_qcm"::figure]
 
-text\<open> Using the \<^LaTeX> package hyperref, it is possible to conceive an interactive 
+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 
+(see @{docitem_ref (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,spawn_columns=False,
         relative_width="90",src="''figures/InteractiveMathSheet''"]
-        \<open> A Generated QCM Fragment \<^dots> \<close>  
+        \<open> A Generated QCM Fragment \ldots \<close>  
 
 subsection*[cenelec_onto::example]\<open> The Certification Scenario following CENELEC \<close>
 text\<open> Documents to be provided in formal certifications (such as CENELEC
@@ -615,7 +586,7 @@ doc_class srac = ec  +
    
 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>
+and @{example \<open>cenelec_onto\<close>} with Isabelle/PIDE instrumented by \isadof. \<close>
 
 subsection*[scholar_pide::example]\<open> A Scholarly Paper \<close>  
 text\<open> In \autoref{fig-Dogfood-II-bgnd1} and \autoref{fig-bgnd-text_section} we show how
@@ -648,7 +619,7 @@ figure*[figDogfoodVIlinkappl::figure,relative_width="80",src="''figures/Dogfood-
        \<open> Exploring an attribute (hyperlinked to the class). \<close> 
 subsection*[cenelec_pide::example]\<open> CENELEC  \<close>
 declare_reference*[figfig3::figure]  
-text\<open> The corresponding view in @{docitem (unchecked) \<open>figfig3\<close>} shows core part of a document,  
+text\<open> The corresponding view in @{docitem_ref (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>
@@ -657,20 +628,20 @@ figure*[figfig3::figure,relative_width="80",src="''figures/antiquotations-PIDE''
 \<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 
+text\<open> The subsequent sample in @{docitem_ref (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", src="''figures/srac-definition''"]
-        \<open> Defining a SRAC reference \<^dots> \<close>
+        \<open> Defining a SRAC reference \ldots \<close>
 figure*[figfig7::figure, relative_width="80", src="''figures/srac-as-es-application''"]
         \<open> Using a SRAC as EC document reference. \<close>
        
-text\<open> Now we reference in @{figure (unchecked) \<open>figfig7\<close>} this safety-related condition; 
+text\<open> Now we reference in @{docitem_ref (unchecked) \<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. 
+\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. 
@@ -693,20 +664,22 @@ The control of monitors is done by the commands:
 \<^item> \inlineisar+close_monitor* + <doc-class> 
 \<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>
+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
+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,
+\<^item> \isadof and its ontology language  are a strongly typed language that allows
+  for referring (albeit not reasoning) to entities of Isabelle/HOL, 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 
+\<^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.
@@ -725,27 +698,27 @@ 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"},
+large group of ontology editors (\eg, Prot{\'e}g{\'e}~@{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>,
+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
+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
+for Prot{\'e}g{\'e} 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 
+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 
+  For the moment, \isadof is conceived as an 
+  add-on for Isabelle/HOL; 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 

examples/scholarly_paper/2018-cicm-isabelle_dof-applications/ROOT

@@ -1,13 +1,13 @@
 session "2018-cicm-isabelle_dof-applications" = "Isabelle_DOF" + 
-  options [document = pdf, document_output = "output", document_build = dof, quick_and_dirty = true]
+  options  [document = pdf, document_output = "output", quick_and_dirty = true]
   theories
     IsaDofApplications
   document_files
+    "isadof.cfg"
     "root.bib"
-    "authorarchive.sty"
     "preamble.tex"
+    "build"
     "lstisadof.sty"
-    "vector_iD_icon.pdf"
     "figures/isabelle-architecture.pdf"
     "figures/Dogfood-Intro.png"
     "figures/InteractiveMathSheet.png"

examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/authorarchive.sty

@@ -1,339 +0,0 @@
-%% Copyright (C) 2008-2019 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}
-  [0000/00/00 Unreleased v1.1.1+%
-  Self-archiving information for scientific publications.]
-%
-\PassOptionsToPackage{hyphens}{url}
-%
-\RequirePackage{ifthen}
-\RequirePackage[inline]{enumitem}
-\RequirePackage{graphicx}
-\RequirePackage{eso-pic}
-\RequirePackage{intopdf}
-\RequirePackage{kvoptions}
-\RequirePackage{hyperref}
-\RequirePackage{calc}
-\RequirePackage{qrcode}
-\RequirePackage{hvlogos}
-%
-%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*
-
-% Provide command for dynamic configuration seutp
-\def\authorsetup{\kvsetkeys{AA}}
-
-% Load local configuration
-\InputIfFileExists{authorarchive.config}{}{}
-
-
-\newlength\AA@x
-\newlength\AA@y
-\newlength\AA@width
-
-\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}
-
-\newboolean{AA@bibExists}
-\setboolean{AA@bibExists}{false}
-\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}}{}
-
-\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]{\href{https://orcid.org/#1}{%
-      \textsuperscript{\,\includegraphics[height=2\fontcharht\font`A]{vector_iD_icon}}}}
-  \else\relax\fi%
-%  
-  \ifthenelse{\equal{\AA@publisher}{UNKNOWN PUBLISHER}}{%
-    \setkeys{AA}{publisher=Springer-Verlag}
-  }{}
-  \renewcommand{\authorcrfont}{\scriptsize}
-  \@ifclasswith{llncs}{a4paper}{%
-    \ExplSyntaxOn
-    \@ifundefined{pdfmanagement_add:nnn}{%
-      \pdfpagesattr{/CropBox [92 114 523 780]}%
-    }{%
-      \pdfmanagement_add:nnn {Pages}{CropBox}{[92~114~523~780]}
-    }%
-    \ExplSyntaxOff
-    \renewcommand{\authorat}[1]{\put(\LenToUnit{\AA@x},40){#1}}%
-  }{%
-    \ExplSyntaxOn
-    \@ifundefined{pdfmanagement_add:nnn}{%
-      \pdfpagesattr{/CropBox [92 65 523 731]}% LNCS page: 152x235 mm
-    }{%
-      \pdfmanagement_add:nnn {Pages}{CropBox}{[92~62~523~731]}
-    }%
-    \ExplSyntaxOff
-    \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}
-  \pdfpagesattr{/CropBox [70 65 526.378 748.15]} % TODO
-  \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,
-  pdfauthor     = {\@author},
-  pdftitle      = {\@title},
-}
-
-\@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 \attachandlink{\AA@bibBibTeX}[application/x-bibtex]{BibTeX entry of this paper}{\BibTeX}%
-            }{%
-              \IfFileExists{\AA@bibBibTeXLong}{%
-                \item \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 \attachandlink{\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 \attachandlink{\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 \attachandlink{\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}}}
-}

examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/build

@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+# Copyright (c) 2018-2019 The University of Sheffield. All rights reserved.
+#               2018 The University of Paris-Saclay. All rights reserved.
+#
+# 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
+if [ ! -f $ISABELLE_HOME_USER/DOF/document-template/build_lib.sh ]; then
+    echo ""
+    echo "Error: Isabelle/DOF not installed"
+    echo "====="
+    echo "This is a Isabelle/DOF project. The document preparation requires"
+    echo "the Isabelle/DOF framework. Please obtain the framework by cloning"
+    echo "the Isabelle/DOF git repository, i.e.: "
+    echo "    git clone https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF"
+    echo "You can install the framework as follows:"
+    echo "    cd Isabelle_DOF/document-generator"
+    echo "    ./install"
+    echo ""
+    exit 1
+fi
+
+cp $ISABELLE_HOME_USER/DOF/document-template/build_lib.sh .
+source build_lib.sh

examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/isadof.cfg

@@ -0,0 +1,2 @@
+Template: scrartcl
+Ontology: scholarly_paper

examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/lstisadof.sty

@@ -1,16 +1,3 @@
-%% Copyright (C) 2018 The University of Sheffield
-%%               2018 The University of Paris-Saclay
-%%               2019 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
 
 \definecolor{OliveGreen}    {cmyk}{0.64,0,0.95,0.40}
 \definecolor{BrickRed}      {cmyk}{0,0.89,0.94,0.28}

examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/preamble.tex

@@ -22,6 +22,7 @@
 \usepackage{listings}
 \usepackage{lstisadof}
 \usepackage{xspace}
+\usepackage[draft]{fixme}
 
 \lstloadlanguages{bash}
 \lstdefinestyle{bash}{language=bash,
@@ -52,19 +53,27 @@
 \usepackage[caption]{subfig}
 \usepackage[size=footnotesize]{caption}
 
+\newcommand{\ie}{i.e.}
+\newcommand{\eg}{e.g.}
 
-\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}
+
+\subject{Example of an Academic Paper\footnote{%
+  This document is an example setup for writing academic paper. While
+  it is optimized for Springer's LNCS class, it uses a Koma Script
+  LaTeX class to avoid the need for distributing \texttt{llncs.cls},
+  which would violate Springer's copyright. This example has been
+  published at CICM 2018:
+    \protect\begin{quote}
+      Achim D. Brucker, Idir Ait-Sadoune, Paolo Crisafulli, and
+      Burkhart Wolff. Using The Isabelle Ontology Framework: Linking
+      the Formal with the Informal. In Conference on Intelligent
+      Computer Mathematics (CICM). Lecture Notes in Computer Science
+      (11006), Springer-Verlag, 2018. 
+    \protect\end{quote}
+    Note that the content of this example is not updated and, hence,
+    might not be correct with respect to the latest version of
+    \isadof{}. 
+    }}
 
 
 \title{<TITLE>}

examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/root.bib

@@ -108,7 +108,7 @@
   volume        = 2283,
   doi           = {10.1007/3-540-45949-9},
   abstract      = {This book is a self-contained introduction to interactive
-                  proof in higher-order logic HOL, using the proof
+                  proof in higher-order logic (\acs{hol}), using the proof
                   assistant Isabelle2002. It is a tutorial for potential
                   users rather than a monograph for researchers. The book has
                   three parts.
@@ -121,7 +121,7 @@
                   such advanced topics as nested and mutual recursion. 2.
                   Logic and Sets presents a collection of lower-level tactics
                   that you can use to apply rules selectively. It also
-                  describes Isabelle/HOL's treatment of sets, functions
+                  describes Isabelle/\acs{hol}'s treatment of sets, functions
                   and relations and explains how to define sets inductively.
                   One of the examples concerns the theory of model checking,
                   and another is drawn from a classic textbook on formal
@@ -279,21 +279,3 @@
   year = {2018}
 }
 
-@incollection{brucker.ea:isabelle-ontologies:2018,
-  abstract = {While Isabelle is mostly known as part of Isabelle/HOL (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 Isabelle/DOF, a novel Document Ontology Framework on top of Isabelle. Isabelle/DOF allows for conventional typesetting \emph{as well} as formal development. We show how to model document ontologies inside Isabelle/DOF, how to use the resulting meta-information for enforcing a certain document structure, and discuss ontology-specific IDE support.},
-  address = {Heidelberg},
-  author = {Achim D. Brucker and Idir Ait-Sadoune and Paolo Crisafulli and Burkhart Wolff},
-  booktitle = {Conference on Intelligent Computer Mathematics (CICM)},
-  doi = {10.1007/978-3-319-96812-4_3},
-  keywords = {Isabelle/Isar, HOL, Ontologies},
-  language = {USenglish},
-  location = {Hagenberg, Austria},
-  number = {11006},
-  pdf = {https://www.brucker.ch/bibliography/download/2018/brucker.ea-isabelle-ontologies-2018.pdf},
-  publisher = {Springer-Verlag},
-  series = {Lecture Notes in Computer Science},
-  title = {Using The Isabelle Ontology Framework: Linking the Formal with the Informal},
-  url = {https://www.brucker.ch/bibliography/abstract/brucker.ea-isabelle-ontologies-2018},
-  year = {2018}
-}
-

examples/scholarly_paper/2020-iFM-CSP/ROOT

@@ -1,7 +0,0 @@
-session "2020-iFM-csp" = "Isabelle_DOF" +
-  options [document = pdf, document_output = "output", document_build = dof]
-  theories
-    "paper"
-  document_files
-    "root.bib"
-    "preamble.tex"

examples/scholarly_paper/2020-iFM-CSP/document/preamble.tex

@@ -1,8 +0,0 @@
-%% This is a placeholder for user-specific configuration and packages.
-
-\usepackage{stmaryrd}
-
-\title{<TITLE>}
-\author{<AUTHOR>}
-
-

examples/scholarly_paper/ROOTS

@@ -1,2 +1 @@
 2018-cicm-isabelle_dof-applications
-2020-iFM-CSP

examples/technical_report/Isabelle_DOF-Manual/00_Frontmatter.thy

@@ -1,143 +1,44 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2022 The University of Exeter 
- *               2018-2022 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 "00_Frontmatter"
   imports "Isabelle_DOF.technical_report"
 begin
 
-
-section\<open>Local Document Setup.\<close>
-text\<open>Introducing document specific abbreviations and macros:\<close>
-
-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>
-
-text\<open>Note that these setups assume that the associated \<^LaTeX> macros 
-     are defined, \<^eg>, in the document prelude. \<close>
-
-define_macro* index  \<rightleftharpoons> \<open>\index{\<close> _ \<open>}\<close>
-define_macro* bindex \<rightleftharpoons> \<open>\bindex{\<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>(* 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>
-
 open_monitor*[this::report] 
 
 (*>*)
 
-title*[title::title]         \<open>Isabelle/DOF\<close> 
+title*[title::title]\<open>Isabelle/DOF\<close> 
 subtitle*[subtitle::subtitle]\<open>User and Implementation Manual\<close> 
-author*[  adb,
-          email       ="\<open>a.brucker@exeter.ac.uk\<close>",
-          orcid       ="\<open>0000-0002-6355-1200\<close>",
-          http_site   ="\<open>https://www.brucker.ch/\<close>",
-          affiliation ="\<open>University of Exeter, Exeter, UK\<close>"]\<open>Achim D. Brucker\<close>
-author*[  bu,
-          email       = "\<open>wolff@lri.fr\<close>",
-          affiliation = "\<open>Université Paris-Saclay, LRI, Paris, France\<close>"]\<open>Burkhart Wolff\<close>
+text*[adb:: author,
+      email="\<open>a.brucker@exeter.ac.uk\<close>",
+      orcid="\<open>0000-0002-6355-1200\<close>",
+      http_site="\<open>https://www.brucker.ch/\<close>",
+      affiliation="\<open>University of Exeter, Exeter, UK\<close>"]\<open>Achim D. Brucker\<close>
+text*[bu::author,
+      email       = "\<open>wolff@lri.fr\<close>",
+      affiliation = "\<open>Université Paris-Saclay, LRI, Paris, France\<close>"]\<open>Burkhart Wolff\<close>
  
-abstract*[abs, keywordlist="[\<open>Ontology\<close>, \<open>Ontological Modeling\<close>, \<open>Document Management\<close>, 
-                             \<open>Formal Document Development\<close>,\<open>Document Authoring\<close>,\<open>Isabelle/DOF\<close>]"]
-\<open>   \<^isadof> provides an implementation of \<^dof> on top of Isabelle/HOL. 
-    \<^dof> itself is a novel framework for \<^emph>\<open>defining\<close> ontologies
-    and \<^emph>\<open>enforcing\<close> them during document development and document
-    evolution. \<^isadof> targets use-cases such as mathematical texts referring
-    to a theory development or technical reports requiring a particular structure.
-    A major application of \<^dof> is the integrated development of
-    formal certification documents (\<^eg>, for Common Criteria or CENELEC
-    50128) that require consistency across both formal and informal
-    arguments. 
+text*[abs::abstract,
+      keywordlist="[''Ontology'', ''Ontological Modeling'', ''Document Management'', 
+                    ''Formal Document Development'', ''Document Authoring'', ''Isabelle/DOF'']"]
+\<open> \isadof provides an implementation of \dof on top of Isabelle/HOL. 
+  \dof itself is a novel framework for \<^emph>\<open>defining\<close> ontologies
+  and \<^emph>\<open>enforcing\<close> them during document development and document
+  evolution. A major goal of \dof is the integrated development of
+  formal certification documents (\eg, for Common Criteria or CENELEC
+  50128) that require consistency across both formal and informal
+  arguments.
 
-    \<^isadof> is integrated into Isabelle's IDE, which
-    allows for smooth ontology development as well as immediate
-    ontological feedback during the editing of a document.
-    Its checking facilities leverage the collaborative 
-    development of documents required to be consistent with an
-    underlying ontological structure.
-    
-    In this user-manual, we give an in-depth presentation of the design
-    concepts of \<^dof>'s Ontology Definition Language (ODL) and describe
-    comprehensively its major commands. Many examples show typical best-practice
-    applications of the system.
+  \isadof is integrated into Isabelle's IDE, which
+  allows for smooth ontology development as well as immediate
+  ontological feedback during the editing of a document.
   
-    It is an unique feature of  \<^isadof>  that ontologies may be used to control
-    the link between formal and informal content in documents in a machine
-    checked way. These links can connect both text elements and formal
-    modeling elements such as terms, definitions, code  and logical formulas,
-    altogether \<^emph>\<open>integrated\<close> in a state-of-the-art interactive theorem prover.
-
+  In this paper, we give an in-depth presentation of the design
+  concepts of \dof's Ontology Definition Language (ODL) and key
+  aspects of the technology of its implementation.  \isadof is the
+  first ontology language supporting machine-checked
+  links between the formal and informal parts in an LCF-style
+  interactive theorem proving environment.
 \<close>
 
 (*<*) 

examples/technical_report/Isabelle_DOF-Manual/01_Introduction.thy

@@ -1,16 +1,3 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2021 The University of Exeter 
- *               2018-2021 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 "01_Introduction"
   imports "00_Frontmatter"
@@ -23,7 +10,7 @@ The linking of the \<^emph>\<open>formal\<close> to the \<^emph>\<open>informal\
 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
+\<^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 
@@ -33,8 +20,8 @@ have to follow a structure.  In practice, large groups of developers have to pro
 set of documents where the consistency is notoriously difficult to maintain. In particular, 
 certifications are centered around the \<^emph>\<open>traceability\<close> of requirements throughout the entire 
 set of documents. While technical solutions for the traceability problem exists (most notably:
-DOORS~@{cite "ibm:doors:2019"}), they are weak in the treatment of formal entities (such as formulas 
-and their logical contexts).
+DOORS~\cite{doors}), they are weak in the treatment of formal entities (such as formulas and their 
+logical contexts).
 
 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
@@ -42,21 +29,20 @@ In general, an ontology is a formal explicit description of \<^emph>\<open>conce
 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.
 
-To address this challenge, we present the Document Ontology Framework (\<^dof>) and an 
-implementation of \<^dof> called \<^isadof>. \<^dof> is designed for building scalable and user-friendly 
-tools on top of interactive theorem provers. \<^isadof> is an instance of this novel framework, 
-implemented as extension of Isabelle/HOL, to \<^emph>\<open>model\<close> typed ontologies and to \<^emph>\<open>enforce\<close> them 
-during document evolution. Based on Isabelle's infrastructures, ontologies may refer to types, 
-terms, proven theorems, code, or established assertions. Based on a novel adaption of the Isabelle 
-IDE (called PIDE, @{cite "wenzel:asynchronous:2014"}), 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 
+To adress this challenge, we present developed the Document Ontology Framework (\dof). \dof is 
+designed for building scalable and user-friendly tools on top of interactive theorem provers, 
+and an implementation of DOF called \isadof. \isadof is a novel framework, extending of 
+Isabelle/HOL, 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 in case of document evolution, 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 
+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/HOL 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 
+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>
 
 subsubsection\<open>How to Read This Manual\<close>
@@ -69,41 +55,50 @@ declare_reference*[isadof_developers::text_section]
 text\<open>
 This manual can be read in different ways, depending on what you want to accomplish. We see three
 different main user groups: 
-\<^enum> \<^emph>\<open>\<^isadof> users\<close>, \<^ie>, users that just want to edit a core document, be it for a paper or a 
+\<^enum> \<^emph>\<open>\isadof users\<close>, \ie, users that just want to edit a core document, be it for a paper or a 
   technical report, using a given ontology. These users should focus on 
-  @{docitem (unchecked) \<open>isadof_tour\<close>} and, depending on their knowledge of Isabelle/HOL, also
-  @{docitem (unchecked) \<open>background\<close>}. 
-\<^enum> \<^emph>\<open>Ontology developers\<close>, \<^ie>,  users that want to develop new ontologies or modify existing 
+  @{docitem_ref (unchecked) \<open>isadof_tour\<close>} and, depending on their knowledge of Isabelle/HOL, also
+  @{docitem_ref (unchecked) \<open>background\<close>}. 
+\<^enum> \<^emph>\<open>Ontology developers\<close>, \ie,  users that want to develop new ontologies or modify existing 
   document ontologies. These users should, after having gained acquaintance as a user, focus 
-  on @{docitem (unchecked) \<open>isadof_ontologies\<close>}. 
-\<^enum> \<^emph>\<open>\<^isadof> developers\<close>, \<^ie>, users that want to extend or modify \<^isadof>, \<^eg>, by adding new 
-  text-elements. These users should read @{docitem (unchecked) \<open>isadof_developers\<close>}
+  on @{docitem_ref (unchecked) \<open>isadof_ontologies\<close>}. 
+\<^enum> \<^emph>\<open>\isadof developers\<close>, \ie, users that want to extend or modify \isadof, \eg, by adding new 
+  text-elements. These users should read @{docitem_ref (unchecked) \<open>isadof_developers\<close>}
 \<close>
 
 subsubsection\<open>Typographical Conventions\<close>
 text\<open>
-  We acknowledge that understanding \<^isadof> and its implementation in all details requires
+  We acknowledge that understanding \isadof and its implementation in all details requires
   separating multiple technological layers or languages. To help the reader with this, we 
   will type-set the different languages in different styles. In particular, we will use 
-  \<^item> a light-blue background for input written in Isabelle's Isar language, \<^eg>:
-    @{boxed_theory_text [display]
-    \<open>lemma refl: "x = x" 
-  by simp\<close>}
-  \<^item> a green background for examples of generated document fragments (\<^ie>, PDF output):
-    @{boxed_pdf [display] \<open>The axiom refl\<close>}
-  \<^item> a red background for (S)ML-code:
-    @{boxed_sml [display] \<open>fun id x = x\<close>}
+  \<^item> a light-blue background for input written in Isabelle's Isar language, \eg:
+    \begin{isar}
+    lemma refl: "x = x" 
+      by simp
+    \end{isar}
+  \<^item> a green background for examples of generated document fragments (\ie, PDF output):
+    \begin{out}
+    The axiom refl
+    \end{out}
+  \<^item> a red background for For (S)ML-code:
+    \begin{sml}
+    fun id x = x
+    \end{sml}
   \<^item> a yellow background for \LaTeX-code:
-    @{boxed_latex [display] \<open>\newcommand{\refl}{$x = x$}\<close>}
+    \begin{ltx}
+    \newcommand{\refl}{$x = x$}
+    \end{ltx}
   \<^item> a grey background for shell scripts and interactive shell sessions:
-    @{boxed_bash [display]\<open>ë\prompt{}ë ls
-CHANGELOG.md  CITATION  examples  install  LICENSE  README.md  ROOTS  src\<close>}
+    \begin{bash}
+    ë\prompt{}ë ls
+    CHANGELOG.md  CITATION  examples  install  LICENSE  README.md  ROOTS  src
+   \end{bash}
 \<close>
 
-subsubsection\<open>How to Cite \<^isadof>\<close>
+subsubsection\<open>How to Cite \isadof\<close>
 text\<open>
-  If you use or extend \<^isadof> in your publications, please use 
-  \<^item> for the \<^isadof> system~@{cite "brucker.ea:isabelle-ontologies:2018"}:
+  If you use or extend \isadof in your publications, please use 
+  \<^item> for the \isadof system~@{cite "brucker.ea:isabelle-ontologies:2018"}:
     \begin{quote}\small
       A.~D. Brucker, I.~Ait-Sadoune, P.~Crisafulli, and B.~Wolff. Using the {Isabelle} ontology 
       framework: Linking the formal with the informal. In \<^emph>\<open>Conference on Intelligent Computer 
@@ -111,30 +106,21 @@ text\<open>
       Heidelberg, 2018. \href{https://doi.org/10.1007/978-3-319-96812-4\_3}
       {10.1007/978-3-319-96812-4\_3}.
     \end{quote}
-    A \<^BibTeX>-entry is available at: 
-    \<^url>\<open>https://www.brucker.ch/bibliography/abstract/brucker.ea-isabelle-ontologies-2018\<close>. 
-  \<^item> for the implementation of \<^isadof>~@{cite "brucker.ea:isabelledof:2019"}:
+    A \BibTeX-entry is available at: 
+    \url{https://www.brucker.ch/bibliography/abstract/brucker.ea-isabelle-ontologies-2018}. 
+  \<^item> for the implementation of \isadof~@{cite "brucker.ea:isabelledof:2019"}:
     \begin{quote}\small
-      A.~D. Brucker and B.~Wolff. \<^isadof>: Design and implementation. In P.C.~{\"O}lveczky and 
-      G.~Sala{\"u}n, editors, \<^emph>\<open>Software Engineering and Formal Methods (SEFM)\<close>, number 11724 in
-      Lecture Notes in Computer Science. Springer-Verlag, Heidelberg, 2019.
-      \href{https://doi.org/10.1007/978-3-030-30446-1_15}{10.1007/978-3-030-30446-1\_15}.
-    \end{quote}
-    A \<^BibTeX>-entry is available at: 
-    \<^url>\<open>https://www.brucker.ch/bibliography/abstract/brucker.ea-isabelledof-2019\<close>.
-  \<^item> for an application of \<^isadof> in the context of certifications:
-    \begin{quote}\small
-     A.~D. Brucker and B.~Wolff.
-     Using Ontologies in Formal Developments Targeting Certification. 
-     In W. Ahrendt and S. Tarifa, editors. \<^emph>\<open>Integrated Formal Methods (IFM)\<close>, number 11918.
-     Lecture Notes in Computer Science. Springer-Verlag, Heidelberg, 2019.
-     \href{https://doi.org/10.1007/978-3-030-34968-4\_4}.
+      A.~D. Brucker and B.~Wolff. \isadof: Design and implementation. In P.~{\"O}lveczky and 
+      G.~Sala{\"u}n, editors, \<^emph>\<open>Software Engineering and Formal Methods (SEFM)\<close>, Lecture Notes 
+      in Computer Science. Springer-Verlag, Heidelberg, 2019.
     \end{quote}
+    A \BibTeX-entry is available at: 
+    \url{https://www.brucker.ch/bibliography/abstract/brucker.ea-isabelledof-2019}.
 \<close>
 subsubsection\<open>Availability\<close>
 text\<open>
   The implementation of the framework is available at 
-  \url{\dofurl}. The website also provides links to the latest releases. \<^isadof> is licensed 
+  \url{\dofurl}. The website also provides links to the latest releases. \isadof is licensed 
   under a 2-clause BSD license (SPDX-License-Identifier: BSD-2-Clause).
 \<close>
 

examples/technical_report/Isabelle_DOF-Manual/02_Background.thy

@@ -1,16 +1,3 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2022 The University of Exeter 
- *               2018-2022 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 "02_Background"
   imports "01_Introduction"
@@ -26,7 +13,7 @@ figure*[architecture::figure,relative_width="95",src="''figures/isabelle-archite
      the IDE (right-hand side). \<close>
 
 text*[bg::introduction]\<open>
-While Isabelle is widely perceived as an interactive theorem 
+While Isabelle @{cite "nipkow.ea:isabelle:2002"} 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 ``\<^emph>\<open>generic system framework of Isabelle/Isar underlying recent versions of Isabelle.  
@@ -37,31 +24,29 @@ with explicit infrastructure for building derivative systems.\<close>''~@{cite "
 
 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> a prover IDE (PIDE) framework~@{cite "wenzel:asynchronous:2014"} with various front-ends 
 \<^item> documentation-generation,
 \<^item> code generators for various target languages,
 \<^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>
-text\<open>
-The Isabelle system architecture shown in @{docitem \<open>architecture\<close>} comes with many layers, 
+
+
+The Isabelle system architecture shown in @{docitem_ref \<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 \<^boxed_sml>\<open>Context\<close>. 
+foresees a \<^emph>\<open>Nano-Kernel\<close> (our terminology) which resides in the SML structure \inlinesml{Context}. 
 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 
+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>
 
-section*[dof::introduction]\<open>The Document Model Required by \<^dof>\<close>
+section*[dof::introduction]\<open>The Document Model Required by \dof\<close>
 text\<open>
   In this section, we explain the assumed document model underlying our Document Ontology Framework 
-  (\<^dof>) in general. In particular we discuss the concepts 
-   \<^emph>\<open>integrated document\<close>\<^bindex>\<open>integrated document\<close>, \<^emph>\<open>sub-document\<close>\<^bindex>\<open>sub-document\<close>,  
-  \<^emph>\<open>text-element\<close>\<^bindex>\<open>text-element\<close>, and \<^emph>\<open>semantic macros\<close>\<^bindex>\<open>semantic macros\<close> occurring 
-  inside text-elements. Furthermore, we assume two different levels of parsers 
-  (for \<^emph>\<open>outer\<close> and \<^emph>\<open>inner syntax\<close>) where the inner-syntax is basically a typed \<open>\<lambda>\<close>-calculus 
-  and some Higher-order Logic (HOL)\<^bindex>\<open>HOL\<close>.
+  (\dof) in general. In particular we discuss the concepts \<^emph>\<open>integrated document\<close>, \<^emph>\<open>sub-document\<close>, 
+  \<^emph>\<open>text-element\<close> and \<^emph>\<open>semantic macros\<close> occurring inside text-elements. Furthermore, we assume two 
+  different levels of parsers (for \<^emph>\<open>outer\<close> and \<^emph>\<open>inner syntax\<close>) where the inner-syntax is basically 
+  a typed \inlineisar|\<lambda>|-calculus and some Higher-order Logic (HOL).
 \<close>
 
 (*<*)
@@ -70,136 +55,105 @@ declare_reference*["fig:dependency"::text_section]
 
 
 text\<open>
-  The Isabelle Framework is based on a \<^emph>\<open>document-centric view\<close>\<^bindex>\<open>document-centric view\<close> of 
-  a document, treating the input in its integrality as set of (user-programmable) \<^emph>\<open>document element\<close> 
-  that may mutually depend on and link to each other; A \<^emph>\<open>document\<close> in our sense is what is configured in a set of 
-  \<^verbatim>\<open>ROOT\<close>- and \<^verbatim>\<open>ROOTS\<close>-files.
-
-  Isabelle assumes a hierarchical document model\<^index>\<open>document model\<close>, \<^ie>, an \<^emph>\<open>integrated\<close> document 
-  consist of a hierarchy of \<^emph>\<open>sub-documents\<close>  (files); dependencies are restricted to be
-  acyclic at this level. 
+  We assume a hierarchical document model\index{document model}, \ie, an \<^emph>\<open>integrated\<close> document 
+  consist of a hierarchy \<^emph>\<open>sub-documents\<close>  (files) that can depend acyclically on each other. 
   Sub-documents can have different document types in order to capture documentations consisting of 
   documentation, models, proofs, code of various forms and other technical artifacts.  We call the 
-  main sub-document type, for historical reasons, \<^emph>\<open>theory\<close>-files.  A theory file\<^bindex>\<open>theory!file\<close>
-  consists of a \<^emph>\<open>header\<close>\<^bindex>\<open>header\<close>, a \<^emph>\<open>context definition\<close>\<^index>\<open>context\<close>, and a body 
-  consisting of a sequence of document elements called
-  \<^emph>\<open>command\<close>s (see @{figure (unchecked) "fig:dependency"}). Even
-  the header consists of a sequence of commands used for introductory text elements not depending on 
-  any context. The context-definition contains an \<^boxed_theory_text>\<open>import\<close> and a 
-  \<^boxed_theory_text>\<open>keyword\<close> section, for example:
-@{boxed_theory_text [display]\<open>
-  theory Example         \<comment>\<open>Name of the 'theory'\<close>
-    imports              \<comment>\<open>Declaration of 'theory' dependencies\<close>
-      Main               \<comment>\<open>Imports a library called 'Main'\<close>
-    keywords             \<comment>\<open>Registration of keywords defined locally\<close>
-      requirement        \<comment>\<open>A command for describing requirements\<close> \<close>}
-  where \<^boxed_theory_text>\<open>Example\<close> is the abstract name of the text-file, \<^boxed_theory_text>\<open>Main\<close> 
-  refers to an imported theory (recall that the import relation must be acyclic) and 
-  \<^boxed_theory_text>\<open>keywords\<close> are used to separate commands from each other.
-\<close>
+  main sub-document type, for historical reasons, \<^emph>\<open>theory\<close>-files.  A theory file\bindex{theory!file}
+  consists of a \<^emph>\<open>header\<close>\bindex{header}, a \<^emph>\<open>context definition\<close>\index{context}, and a body 
+  consisting of a sequence of \<^emph>\<open>command\<close>s (see @{figure (unchecked) "fig:dependency"}). Even the header consists 
+  of a sequence of commands used for introductory text elements not depending on any context.  
+  The context-definition contains an \inlineisar{import} and a 
+  \inlineisar{keyword} section, for example:
+\begin{isar}
+"  theory Example         (* Name of the 'theory'                     *)
+"    imports              (* Declaration of 'theory' dependencies     *)
+"      Main               (* Imports a library called 'Main'          *)
+"    keywords             (* Registration of keywords defined locally *)
+"      requirement        (* A command for describing requirements    *)
+\end{isar}
+  where \inlineisar{Example} is the abstract name of the text-file,
+  \inlineisar{Main} refers to an imported theory (recall that the import
+  relation must be acyclic) and \inlineisar{keywords} are used to
+  separate commands from each other.
 
-text\<open> A text-element \<^index>\<open>text-element\<close> may look like this:
+  We distinguish fundamentally two different syntactic levels:
+  \<^item> the \emph{outer-syntax}\bindex{syntax!outer}\index{outer syntax|see {syntax, outer}} (\ie, the 
+    syntax for commands) is processed by a lexer-library and parser combinators built on top, and
+  \<^item> the \emph{inner-syntax}\bindex{syntax!inner}\index{inner syntax|see {syntax, inner}} (\ie, the 
+    syntax for \inlineisar|\<lambda>|-terms in HOL) with its own parametric polymorphism type 
+    checking.
 
-  @{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>}
-... so it is a command \<^theory_text>\<open>text\<close> followed by an argument (here in  \<open>\<open> ... \<close>\<close> parenthesis) which 
-contains characters and a special notation for semantic macros \<^bindex>\<open>semantic macros\<close> 
-(here \<^theory_text>\<open>@{term "fac 5"}).\<close>
-\<close>
 
-text\<open>While we concentrate in this manual on \<^theory_text>\<open>text\<close>-document elements --- this is the main
-use of \<^dof> in its current stage --- it is important to note that there are actually three
-families of ``ontology aware'' document elements with analogous 
-syntax to standard ones. The difference is a bracket with meta-data of the form:
-@{theory_text [display,indent=5, margin=70] 
-\<open>
-text*[label::classid, attr\<^sub>1=E\<^sub>1, ... attr\<^sub>n=E\<^sub>n]\<open> some semi-formal text \<close>
-ML*[label::classid, attr\<^sub>1=E\<^sub>1, ... attr\<^sub>n=E\<^sub>n]\<open> some SML code \<close>
-value*[label::classid, attr\<^sub>1=E\<^sub>1, ... attr\<^sub>n=E\<^sub>n]\<open> some annotated \<lambda>-term \<close>
-\<close>}
-
-Depending on the family, we will speak about \<^emph>\<open>(formal) text-contexts\<close>,\<^index>\<open>formal text-contexts\<close> 
-\<^emph>\<open>(ML) code-contexts\<close>\<^index>\<open>code-contexts\<close> and \<^emph>\<open>term-contexts\<close>\<^index>\<open>term-contexts\<close> if we refer 
-to sub-elements inside the \<open>\<open>...\<close>\<close> cartouches of these command families. Note that the Isabelle
-framework allows for nesting cartouches that permits to support switching into a different
-context. In general, this has also the effect that the evaluation of antiquotations changes.
-\<^footnote>\<open>In the literature, this concept has been referred to \<open>Cascade-Syntax\<close> and was used in the 
-Centaur-system and is existing in some limited form in some Emacs-implementations these days. \<close>  
-\<close>
-text\<open>
   On the semantic level, we assume a validation process for an integrated document, where the 
-  semantics of a command is a transformation \<open>\<theta> \<rightarrow> \<theta>\<close> for some system state \<open>\<theta>\<close>.
-  This document model can be instantiated depending on  the text-code-, or term-contexts.
-  For common text elements, \<^eg>, \<^theory_text>\<open>section\<open>...\<close>\<close> or \<^theory_text>\<open>text\<open>...\<close>\<close>, 
-  users can add informal text to a sub-document using a text command:
-  @{boxed_theory_text [display] \<open>text\<open>This is a description.\<close>\<close> }
+  semantics of a command is a transformation \inlineisar+\<theta> \<rightarrow> \<theta>+ for some system state 
+  \inlineisar+\<theta>+. This document model can be instantiated with outer-syntax commands for common 
+  text elements, \eg, \inlineisar+section{*...*}+ or \inlineisar+text{*...*}+.  Thus, users can add 
+  informal text to a sub-document using a text command:
+  \begin{isar}
+    text\<Open>This is a description.\<Close>
+  \end{isar}
   This will type-set the corresponding text in, for example, a PDF document.  However, this 
-  translation is not necessarily one-to-one: text elements can be enriched by formal, \<^ie>, 
-  machine-checked content via \<^emph>\<open>semantic macros\<close>, called antiquotations\<^bindex>\<open>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 \<open>fac 5\<close>} the result @{value \<open>fac 5\<close>}.\<close>\<close>
-  }
-which is represented in the final document (\<^eg>, a PDF) by:
-@{boxed_pdf [display]
-\<open>According to the $\emph{reflexivity}$ axiom $\mathrm{x = x}$, we obtain in $\Gamma$ 
-for $\operatorname{fac} \text{\textrm{5}}$ the result $\text{\textrm{120}}$.\<close>
- }
-
-  Semantic macros are partial functions of type \<open>\<theta> \<rightarrow> text\<close>; since they can use the
+  translation is not necessarily one-to-one: text elements can be enriched by formal, \ie, 
+  machine-checked content via \emph{semantic macros}, called antiquotations\bindex{antiquotation}:
+\begin{isar}
+text\<Open>According to the reflexivity axiom <@>{thm refl}, we obtain in \<Gamma> 
+      for <@>{term "fac 5"} the result <@>{value "fac 5"}.\<Close>
+\end{isar}
+which is represented in the final document (\eg, a PDF) by:
+\begin{out}
+According to the reflexivity axiom $\mathrm{x = x}$, we obtain in $\Gamma$ for $\operatorname{fac} \text{\textrm{5}}$ the result $\text{\textrm{120}}$.
+\end{out}
+  Semantic macros are partial functions of type \inlineisar+\<theta> \<rightarrow> text+; since they can use the
   system state, they can perform all sorts of specific checks or evaluations (type-checks, 
   executions of code-elements, references to text-elements or proven theorems such as 
-  \<open>refl\<close>, which is the reference to the axiom of reflexivity).
+  \inlineisar+refl+, which is the reference to the axiom of reflexivity).
 
   Semantic macros establish \<^emph>\<open>formal content\<close> inside informal content; they can be 
   type-checked before being displayed and can be used for calculations before being 
   typeset. They represent the device for linking the formal with the informal. 
 \<close>
 
-
-
 figure*["fig:dependency"::figure,relative_width="70",src="''figures/document-hierarchy''"]
        \<open>A Theory-Graph in the Document Model. \<close>
 
-section*[bgrnd21::introduction]\<open>Implementability of the Document Model in other ITP's\<close>
+section*[bgrnd21::introduction]\<open>Implementability of the Required Document Model.\<close>
 text\<open> 
-  Batch-mode checkers for \<^dof> can be implemented in all systems of the LCF-style prover family, 
-  \<^ie>, systems with a type-checked \<open>term\<close>, and abstract \<open>thm\<close>-type for theorems 
-  (protected by a kernel).  This includes, \<^eg>, ProofPower, HOL4, HOL-light, Isabelle, or Coq
-  and its derivatives. \<^dof> is, however, designed for fast interaction in an IDE. If a user wants
+  Batch-mode checkers for \dof can be implemented in all systems of the LCF-style prover family, 
+  \ie, systems with a type-checked \inlinesml{term}, and abstract \inlinesml{thm}-type for
+  theorems (protected by a kernel).  This includes, \eg, ProofPower, HOL4, HOL-light, Isabelle, or 
+  Coq and its derivatives. \dof is, however, designed for fast interaction in an IDE. If a user wants
   to benefit from this experience, only Isabelle and Coq have the necessary infrastructure of 
-  asynchronous proof-processing and support by a PIDE~@{cite "wenzel:asynchronous:2014" and 
-  "wenzel:system:2014" and "barras.ea:pervasive:2013" and "faithfull.ea:coqoon:2018"} which 
-  in many features over-accomplishes the required  features of \<^dof>. For example, current Isabelle 
-  versions offer cascade-syntaxes (different syntaxes and even parser-technologies which can be 
-  nested along the \<open>\<open>...\<close>\<close> barriers), while \<^dof> actually only requires a two-level syntax model.
+  asynchronous proof-processing and support by a PIDE~@{cite "DBLP:conf/itp/Wenzel14" and 
+  "DBLP:journals/corr/Wenzel14" and "DBLP:conf/mkm/BarrasGHRTWW13"
+  and "Faithfull:2018:COQ:3204179.3204223"} which in many features over-accomplishes the required 
+  features of \dof. For example, current Isabelle versions offer cascade-syntaxes (different 
+  syntaxes and even parser-technologies which can be nested along the 
+  \inlineisar+\<Open> ... \<Close> + barriers, while \dof actually only requires a two-level 
+  syntax model.
 \<close>
 
 figure*["fig:dof-ide"::figure,relative_width="95",src="''figures/cicm2018-combined''"]\<open> 
-     The \<^isadof> IDE (left) and the corresponding PDF (right), showing the first page
-      of~@{cite "brucker.ea:isabelle-ontologies:2018"}.\<close>
+     The \isadof IDE (left) and the corresponding PDF (right), showing the first page
+      of~\cite{brucker.ea:isabelle-ontologies:2018}.\<close>
 
 text\<open> 
-  We call the present implementation of \<^dof> on the Isabelle platform  \<^isadof> . 
+  We call the present implementation of \dof on the Isabelle platform  \isadof. 
   @{docitem "fig:dof-ide"} shows  a screen-shot of an introductory paper on 
-  \<^isadof>~@{cite "brucker.ea:isabelle-ontologies:2018"}: the \<^isadof> PIDE can be seen on the left, 
+  \isadof~@{cite "brucker.ea:isabelle-ontologies:2018"}: the \isadof PIDE can be seen on the left, 
   while the generated presentation in PDF is shown on the right.
 
-  Isabelle provides, beyond the features required for \<^dof>, a lot of additional benefits. 
-  Besides UTF8-support for characters used in text-elements, Isabelle offers built-in already a 
-  mechanism for user-programmable antiquotations \<^index>\<open>antiquotations\<close> which we use to implement
-  semantic macros  \<^index>\<open>semantic macros\<close> in \<^isadof> (We will actually use these two terms
-  as synonym in the context of \<^isadof>). Moreover, \<^isadof> allows for the asynchronous 
-  evaluation and checking of the document content~@{cite "wenzel:asynchronous:2014" and 
-  "wenzel:system:2014" and "barras.ea:pervasive:2013"} and is dynamically extensible. Its PIDE 
-  provides a  \<^emph>\<open>continuous build, continuous check\<close>  functionality, syntax highlighting, and 
-  auto-completion. It also provides infrastructure for displaying meta-information (\<^eg>, binding 
-  and type annotation) as pop-ups, while hovering over sub-expressions.  A fine-grained dependency 
-  analysis allows the processing of individual parts of theory files asynchronously, allowing 
-  Isabelle to interactively process large (hundreds of theory files) documents.  Isabelle can group 
-  sub-documents into sessions, \<^ie>, sub-graphs of the document-structure that can be ``pre-compiled'' 
-  and loaded instantaneously, \<^ie>, without re-processing, which is an important means to scale up. \<close>
+  Isabelle provides, beyond the features required for \dof, a lot of additional benefits. For 
+  example, it also allows the asynchronous evaluation and checking of the document 
+  content~@{cite "DBLP:conf/itp/Wenzel14" and "DBLP:journals/corr/Wenzel14" and
+  "DBLP:conf/mkm/BarrasGHRTWW13"} and is dynamically extensible. Its PIDE provides a 
+  \<^emph>\<open>continuous build, continuous check\<close>  functionality, syntax highlighting, and auto-completion. 
+  It also provides infrastructure for displaying meta-information (\eg, binding and type annotation)
+  as pop-ups, while hovering over sub-expressions.  A fine-grained dependency analysis allows the 
+  processing of individual parts of theory files asynchronously, allowing Isabelle to interactively
+  process large (hundreds of theory files) documents.  Isabelle can group sub-documents into sessions,
+  \ie, sub-graphs of the document-structure that can be ``pre-compiled'' and loaded
+  instantaneously, \ie, without re-processing. \<close>
 
 (*<*) 
 end

examples/technical_report/Isabelle_DOF-Manual/05_Implementation.thy

@@ -1,16 +1,3 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2022 University of Exeter 
- *               2018-2022 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 "05_Implementation"
   imports "04_RefMan"
@@ -18,22 +5,22 @@ begin
 (*>*)
 
 
-chapter*[isadof_developers::text_section]\<open>Extending \<^isadof>\<close>
+chapter*[isadof_developers::text_section]\<open>Extending \isadof\<close>
 text\<open>
-  In this chapter, we describe the basic implementation aspects of \<^isadof>, which is based on 
+  In this chapter, we describe the basic implementation aspects of \isadof, which is based on 
   the following design-decisions:
-  \<^item> the entire \<^isadof> is a ``pure add-on,'' \<^ie>, we deliberately resign the possibility to 
-    modify Isabelle itself,
-  \<^item> we made a small exception to this rule: the \<^isadof> package modifies in its installation 
-    about 10 lines in the \LaTeX-generator (\path{src/patches/thy_output.ML}),
+  \<^item> the entire \isadof is a ``pure add-on,'' \ie, we deliberately resign on the possibility to 
+    modify Isabelle itself.
+  \<^item> we made a small exception to this rule: the \isadof package modifies in its installation 
+    about 10 lines in the \LaTeX-generator (\path{src/patches/thy_output.ML}).
   \<^item> we decided to make the markup-generation by itself to adapt it as well as possible to the 
-    needs of tracking the linking in documents,
-  \<^item> \<^isadof> is deeply integrated into the Isabelle's IDE (PIDE) to give immediate feedback during 
+    needs of tracking the linking in documents.
+  \<^item> \isadof is deeply integrated into the Isabelle's IDE (PIDE) to give immediate feedback during 
     editing and other forms of document evolution.
 \<close>
 text\<open>
   Semantic macros, as required by our document model, are called \<^emph>\<open>document antiquotations\<close>
-  in the Isabelle literature~@{cite "wenzel:isabelle-isar:2020"}. While Isabelle's code-antiquotations 
+  in the Isabelle literature~@{cite "wenzel:isabelle-isar:2019"}. While Isabelle's code-antiquotations 
   are an old concept going back to Lisp and having found via SML and OCaml their ways into modern 
   proof systems, special annotation syntax inside documentation comments have their roots in 
   documentation generators such as Javadoc. Their use, however, as a mechanism to embed 
@@ -41,57 +28,61 @@ text\<open>
   IDE support.
 \<close>
 
-section\<open>\<^isadof>: A User-Defined Plugin in Isabelle/Isar\<close>
-text\<open> 
+section\<open>\isadof: A User-Defined Plugin in Isabelle/Isar\<close>
+text\<open>
   A plugin in Isabelle starts with defining the local data and registering it in the framework. As 
   mentioned before, contexts are structures with independent cells/compartments having three
-  primitives \<^boxed_sml>\<open>init\<close>,  \<^boxed_sml>\<open>extend\<close> and  \<^boxed_sml>\<open>merge\<close>. Technically this is done by 
-  instantiating a functor  \<^boxed_sml>\<open>Generic_Data\<close>, and the following fairly typical code-fragment 
-  is drawn from \<^isadof>:
+  primitives \inlinesml+init+, \inlinesml+extend+ and \inlinesml+merge+. Technically this is done by 
+  instantiating a functor \inlinesml+Generic_Data+, and the following fairly typical code-fragment 
+  is drawn from \isadof:
 
-@{boxed_sml [display]
-\<open>structure Data = Generic_Data
+\begin{sml}
+structure Data = Generic_Data
 (  type T = docobj_tab * docclass_tab * ...
    val empty  = (initial_docobj_tab, initial_docclass_tab, ...) 
+   val extend = I
    fun merge((d1,c1,...),(d2,c2,...)) = (merge_docobj_tab  (d1,d2,...), 
                                          merge_docclass_tab(c1,c2,...))
-);\<close>}
-  where the table  \<^boxed_sml>\<open>docobj_tab\<close> manages document class instances
-  and \<^boxed_sml>\<open>docclass_tab\<close> the environment for class definitions
-  (inducing the inheritance relation). Other tables capture, \eg, 
+);
+\end{sml}
+  where the table \inlinesml+docobj_tab+ manages document classes and \inlinesml+docclass_tab+ the 
+  environment for class definitions (inducing the inheritance relation). Other tables capture, \eg, 
   the class invariants, inner-syntax antiquotations. Operations follow the MVC-pattern, where 
   Isabelle/Isar provides the controller part. A typical model operation has the type:
 
-@{boxed_sml [display]
-\<open>val opn :: <args_type> -> Context.generic -> Context.generic\<close>}
+\begin{sml}
+val opn :: <args_type> -> Context.generic -> Context.generic
+\end{sml}
   representing a transformation on system contexts. For example, the operation of declaring a local 
   reference in the context is presented as follows:
 
-@{boxed_sml [display]
-\<open>fun declare_object_local oid ctxt  =
+\begin{sml}
+fun declare_object_local oid ctxt  =
 let fun decl {tab,maxano} = {tab=Symtab.update_new(oid,NONE) tab,
                              maxano=maxano}
 in  (Data.map(apfst decl)(ctxt)
   handle Symtab.DUP _ =>
               error("multiple declaration of document reference"))
-end\<close>}
-  where \<^boxed_sml>\<open>Data.map\<close> is the update function resulting from the instantiation of the 
-  functor  \<^boxed_sml>\<open>Generic_Data\<close>. This code fragment uses operations from a library structure 
-   \<^boxed_sml>\<open>Symtab\<close> that were used to update the appropriate table for document objects in
+end
+\end{sml}                                            
+  where \inlineisar+Data.map+ is the update function resulting from the instantiation of the 
+  functor \inlinesml|Generic_Data|. This code fragment uses operations from a library structure 
+  \inlinesml+Symtab+ that were used to update the appropriate table for document objects in
   the plugin-local state. Possible exceptions to the update operation were mapped to a system-global 
   error reporting function.
 
   Finally, the view-aspects were handled by an API for parsing-combinators. The library structure 
-   \<^boxed_sml>\<open>Scan\<close> provides the operators:
+  \inlinesml+Scan+ provides the operators:
 
-@{boxed_sml [display]
-\<open>op ||     : ('a -> 'b) * ('a -> 'b) -> 'a -> 'b
+\begin{sml}
+op ||     : ('a -> 'b) * ('a -> 'b) -> 'a -> 'b
 op --     : ('a -> 'b * 'c) * ('c -> 'd * 'e) -> 'a -> ('b * 'd) * 'e
 op >>     : ('a -> 'b * 'c) * ('b -> 'd) -> 'a -> 'd * 'c
 op option : ('a -> 'b * 'a) -> 'a -> 'b option * 'a
-op repeat : ('a -> 'b * 'a) -> 'a -> 'b list * 'a \<close>}
+op repeat : ('a -> 'b * 'a) -> 'a -> 'b list * 'a 
+\end{sml}                                            
   for alternative, sequence, and piping, as well as combinators for option and repeat. Parsing 
-  combinators have the advantage that they can be integrated into standard programs, 
+  combinators have the advantage that they can be smoothlessly integrated into standard programs, 
   and they enable the dynamic extension of the grammar. There is a more high-level structure 
   \inlinesml{Parse} providing specific combinators for the command-language Isar:
 
@@ -106,25 +97,26 @@ val attributes =(Parse.$$$ "[" |-- (reference
                    |--(Parse.enum ","attribute)))[]))--| Parse.$$$ "]"              
 \end{sml}                                            
 
-  The ``model'' \<^boxed_sml>\<open>declare_reference_opn\<close> and ``new'' \<^boxed_sml>\<open>attributes\<close> parts were 
+  The ``model'' \inlineisar+declare_reference_opn+ and ``new'' \inlineisar+attributes+ parts were 
   combined via the piping operator and registered in the Isar toplevel:
 
-@{boxed_sml [display]
-\<open>fun declare_reference_opn (((oid,_),_),_) =
+\begin{sml}
+  fun declare_reference_opn (((oid,_),_),_) =
                  (Toplevel.theory (DOF_core.declare_object_global oid))
   val _ = Outer_Syntax.command <@>{command_keyword "declare_reference"}
           "declare document reference"
-          (attributes >> declare_reference_opn);\<close>}
+          (attributes >> declare_reference_opn);
+\end{sml}
 
   Altogether, this gives the extension of Isabelle/HOL with Isar syntax and semantics for the 
   new \emph{command}:
 
-@{boxed_theory_text [display]\<open>
+\begin{isar}
 declare_reference [lal::requirement, alpha="main", beta=42]
-\<close>}
+\end{isar}
 
   The construction also generates implicitly some markup information; for example, when hovering
-  over the \<^boxed_theory_text>\<open>declare_reference\<close> command in the IDE, a popup window with the text: 
+  over the \inlineisar|declare_reference| command in the IDE, a popup window with the text: 
   ``declare document reference'' will appear.
 \<close>
 
@@ -134,116 +126,139 @@ text\<open>
   principle: based on a number of combinators, new user-defined antiquotation syntax and semantics
   can be added to the system that works on the internal plugin-data freely. For example, in
 
-@{boxed_sml [display]
-\<open>val _ = Theory.setup(
+\begin{sml}
+val _ = Theory.setup(
           Thy_Output.antiquotation <@>{binding docitem} 
                                    docitem_antiq_parser 
                                    (docitem_antiq_gen default_cid) #>
           ML_Antiquotation.inline  <@>{binding docitem_value} 
-                                   ML_antiq_docitem_value)\<close>}
-  the text antiquotation \<^boxed_sml>\<open>docitem\<close> is declared and bounded to a parser for the argument 
+                                   ML_antiq_docitem_value)
+\end{sml}
+  the text antiquotation \inlineisar+docitem+ is declared and bounded to a parser for the argument 
   syntax and the overall semantics. This code defines a generic antiquotation to be used in text 
   elements such as
 
-@{boxed_theory_text [display]\<open>
-text\<open>as defined in @{docitem \<open>d1\<close>} ...\<close>
-\<close>}
+\begin{isar}
+text\<Open>as defined in <@>{docitem \<Open>d1\<Close>} ...\<Close>
+\end{isar}
 
-  The subsequent registration \<^boxed_sml>\<open>docitem_value\<close> binds code to a ML-antiquotation usable 
+  The subsequent registration \inlineisar+docitem_value+ binds code to a ML-antiquotation usable 
   in an ML context for user-defined extensions; it permits the access to the current ``value'' 
-  of document element, \<^ie>, a term with the entire update history.
+  of document element, \ie; a term with the entire update history.
 
   It is possible to generate antiquotations \emph{dynamically}, as a consequence of a class 
-  definition in ODL. The processing of the ODL class \<^typ>\<open>definition\<close> also \emph{generates}
-  a text antiquotation \<^boxed_theory_text>\<open>@{"definition" \<open>d1\<close>}\<close>, which works similar to 
-  \<^boxed_theory_text>\<open>@{docitem \<open>d1\<close>}\<close> except for an additional type-check that assures that 
-  \<^boxed_theory_text>\<open>d1\<close> is a reference to a definition. These type-checks support the subclass hierarchy.
+  definition in ODL. The processing of the ODL class \inlineisar+d$$efinition+ also \emph{generates}
+  a text antiquotation \inlineisar+<@>{definition \<Open>d1\<Close>}+, which works similar to 
+  \inlineisar+<@>{docitem \<Open>d1\<Close>}+ except for an additional type-check that assures that 
+  \inlineisar+d1+ is a reference to a definition. These type-checks support the subclass hierarchy.
 \<close>
 
 section\<open>Implementing Second-level Type-Checking\<close>
-
 text\<open>
   On expressions for attribute values, for which we chose to use HOL syntax to avoid that users 
   need to learn another syntax, we implemented an own pass over type-checked terms. Stored in the 
-  late-binding table \<^boxed_sml>\<open>ISA_transformer_tab\<close>, we register for each inner-syntax-annotation 
+  late-binding table \inlineisar+ISA_transformer_tab+, we register for each inner-syntax-annotation 
   (ISA's), a function of type
 
-@{boxed_sml [display]
-\<open>   theory -> term * typ * Position.T -> term option\<close>}
+\begin{sml}
+   theory -> term * typ * Position.T -> term option
+\end{sml}
 
-  Executed in a second pass of term parsing, ISA's may just return \<^boxed_theory_text>\<open>None\<close>. This is 
-  adequate for ISA's just performing some checking in the logical context \<^boxed_theory_text>\<open>theory\<close>; 
+  Executed in a second pass of term parsing, ISA's may just return \inlineisar+None+. This is 
+  adequate for ISA's just performing some checking in the logical context \inlineisar+theory+; 
   ISA's of this kind report errors  by exceptions. In contrast, \<^emph>\<open>transforming\<close> ISA's will 
   yield a term; this is adequate, for example, by replacing a string-reference to some term denoted 
   by it. This late-binding table is also used to generate standard inner-syntax-antiquotations from 
-  a \<^boxed_theory_text>\<open>doc_class\<close>.
+  a \inlineisar+doc_class+.
 \<close>
 
 section\<open>Programming Class Invariants\<close>
 text\<open>
-  See \<^technical>\<open>sec:low_level_inv\<close>.
+  For the moment, there is no high-level syntax for the definition of class invariants. A 
+  formulation, in SML, of the first class-invariant in @{docref "sec:class_inv"} is straight-forward:
+
+\begin{sml}
+fun check_result_inv oid {is_monitor:bool} ctxt =
+  let val kind = compute_attr_access ctxt "kind" oid <@>{here} <@>{here} 
+      val prop = compute_attr_access ctxt "property" oid <@>{here} <@>{here} 
+      val tS = HOLogic.dest_list prop
+  in  case kind_term of
+       <@>{term "proof"} => if not(null tS) then true
+                          else error("class result invariant violation") 
+      | _ => false
+  end
+ val _ = Theory.setup (DOF_core.update_class_invariant 
+                                "tiny_cert.result" check_result_inv)
+\end{sml}
+
+  The \inlinesml{setup}-command (last line) registers the \inlineisar+check_result_inv+ function 
+  into the \isadof kernel, which activates any creation or modification of an instance of
+  \inlineisar+result+.  We cannot replace \inlineisar+compute_attr_access+ by the corresponding 
+  antiquotation \inlineisar+<@>{docitem_value kind::oid}+, since \inlineisar+oid+ is
+  bound to a variable here and can therefore not be statically expanded.
 \<close>
 
 section\<open>Implementing Monitors\<close>
-
 text\<open>
   Since monitor-clauses have a regular expression syntax, it is natural to implement them as 
-  deterministic automata. These are stored in the  \<^boxed_sml>\<open>docobj_tab\<close> for monitor-objects 
-  in the \<^isadof> component. We implemented the functions:
+  deterministic automata. These are stored in the  \inlineisar+docobj_tab+ for monitor-objects 
+  in the \isadof component. We implemented the functions:
 
-@{boxed_sml [display]
-\<open>  val  enabled : automaton -> env -> cid list
-   val  next    : automaton -> env -> cid -> automaton\<close>}
-  where \<^boxed_sml>\<open>env\<close> is basically a map between internal automaton states and class-id's 
-  (\<^boxed_sml>\<open>cid\<close>'s). An automaton is said to be \<^emph>\<open>enabled\<close> for a class-id, 
-  iff it either occurs in its accept-set or its reject-set (see @{docitem "sec:monitors"}). During 
+\begin{sml}
+   val  enabled : automaton -> env -> cid list
+   val  next    : automaton -> env -> cid -> automaton
+\end{sml}
+  where \inlineisar+env+ is basically a map between internal automaton states and class-id's 
+  (\inlineisar+cid+'s). An automaton is said to be \<^emph>\<open>enabled\<close> for a class-id, 
+  iff it either occurs in its accept-set or its reject-set (see @{docref "sec:monitors"}). During 
   top-down document validation, whenever a text-element is encountered, it is checked if a monitor 
-  is \emph{enabled} for this class; in this case, the \<^boxed_sml>\<open>next\<close>-operation is executed. The 
-  transformed automaton recognizing the rest-language is stored in \<^boxed_sml>\<open>docobj_tab\<close> if
-  possible;
-  % TODO: clarify the notion of rest-language
-  otherwise, if \<^boxed_sml>\<open>next\<close> fails, an error is reported. The automata implementation
-  is, in large parts, generated from a formalization of functional automata~\cite{nipkow.ea:functional-Automata-afp:2004}.
+  is \emph{enabled} for this class; in this case, the \inlineisar+next+-operation is executed. The 
+  transformed automaton recognizing the rest-language is stored in \inlineisar+docobj_tab+ if
+  possible; otherwise, if \inlineisar+next+ fails, an error is reported. The automata implementation 
+  is, in large parts, generated from a formalization of functional automata~\cite{Functional-Automata-AFP}.
 \<close>
 
-section\<open>The \<^LaTeX>-Core of \<^isadof>\<close>
+section\<open>The \LaTeX-Core of \isadof\<close>
 text\<open>
-  The \<^LaTeX>-implementation of \<^isadof> heavily relies on the 
-  ``keycommand''~@{cite "chervet:keycommand:2010"} package. In fact, the core \<^isadof> \<^LaTeX>-commands
+  The \LaTeX-implementation of \isadof heavily relies on the 
+  ``keycommand''~@{cite "chervet:keycommand:2010"} package. In fact, the core \isadof \LaTeX-commands
   are just wrappers for the corresponding commands from the keycommand package:
 
-@{boxed_latex [display]
-\<open>\newcommand\newisadof[1]{%
+\begin{ltx}
+\newcommand\newisadof[1]{%
   \expandafter\newkeycommand\csname isaDof.#1\endcsname}%
 \newcommand\renewisadof[1]{%
   \expandafter\renewkeycommand\csname isaDof.#1\endcsname}%
 \newcommand\provideisadof[1]{%
-  \expandafter\providekeycommand\csname isaDof.#1\endcsname}%\<close>}
+  \expandafter\providekeycommand\csname isaDof.#1\endcsname}%
+\end{ltx}
 
-  The \<^LaTeX>-generator of \<^isadof> maps each \<^boxed_theory_text>\<open>doc_item\<close> to an \<^LaTeX>-environment (recall
-  @{docitem "text-elements"}). As generic \<^boxed_theory_text>\<open>doc_item\<close>s are derived from the text element, 
-  the environment \inlineltx|isamarkuptext*| builds the core of \<^isadof>'s \<^LaTeX> implementation. 
-  For example, the @{docitem "ass123"} from page \pageref{ass123} is mapped to
+  The \LaTeX-generator of \isadof maps each \inlineisar{doc_item} to an \LaTeX-environment (recall
+  @{docref "text-elements"}). As generic \inlineisar{doc_item} are derived from the text element, 
+  the enviornment \inlineltx|{isamarkuptext*}| builds the core of \isadof's \LaTeX{} implementation. 
+  For example, the @{docref "ass123"} from page \pageref{ass123} is mapped to
 
-@{boxed_latex [display]
-\<open>\begin{isamarkuptext*}%
+\begin{ltx}
+\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>}
+\end{isamarkuptext*}
+\end{ltx}
 
-This environment is mapped to a plain \<^LaTeX> command via (again, recall @{docitem "text-elements"}):
-@{boxed_latex [display]
-\<open> \NewEnviron{isamarkuptext*}[1][]{\isaDof[env={text},#1]{\BODY}} \<close>}
+This environment is mapped to a plain \LaTeX command via (again, recall @{docref "text-elements"}):
+\begin{ltx}
+  \NewEnviron{isamarkuptext*}[1][]{\isaDof[env={text},#1]{\BODY}}
+\end{ltx}
 
-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>:
+For the command-based setup, \isadof provides a dispatcher that selects the most specific 
+implementation for a given \inlineisar|doc_class|:
 
-@{boxed_latex [display]
-\<open>%% The Isabelle/DOF dispatcher:
+\begin{ltx}
+%% The Isabelle/DOF dispatcher:
 \newkeycommand+[\|]\isaDof[env={UNKNOWN},label=,type={dummyT},args={}][1]{%
   \ifcsname isaDof.\commandkey{type}\endcsname%
       \csname isaDof.\commandkey{type}\endcsname%
@@ -264,7 +279,8 @@ implementation for a given \<^boxed_theory_text>\<open>doc_class\<close>:
         definition for "\commandkey{env}" available either.}%
       \fi%
   \fi%
-}\<close>}
+}
+\end{ltx}
 \<close>
 
 (*<*)

examples/technical_report/Isabelle_DOF-Manual/Isabelle_DOF-Manual.thy

@@ -1,28 +1,11 @@
-(*************************************************************************
- * 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 "Isabelle_DOF-Manual"
   imports "05_Implementation"
 begin
-use_template "scrreprt-modern"
-use_ontology "technical_report" and "CENELEC_50128"
 close_monitor*[this]
 check_doc_global
-text\<open>Resulting trace in \<^verbatim>\<open>doc_item\<close> ''this'': \<close>
+text\<open>Resulting trace in doc\_item ''this'': \<close>
 ML\<open>@{trace_attribute this}\<close>
-
- 
 end
 (*>*) 
 

examples/technical_report/Isabelle_DOF-Manual/ROOT

@@ -1,12 +1,14 @@
 session "Isabelle_DOF-Manual" = "Isabelle_DOF" + 
-  options [document = pdf, document_output = "output", document_build = dof, quick_and_dirty = true]
+  options  [document = pdf, document_output = "output", quick_and_dirty = true]
   theories
     "Isabelle_DOF-Manual"
   document_files
+    "isadof.cfg"
     "root.bib"
     "root.mst"
     "preamble.tex"
-    "lstisadof-manual.sty" 
+    "build"
+    "lstisadof-manual.sty"
     "figures/antiquotations-PIDE.png"
     "figures/cicm2018-combined.png"
     "figures/cicm2018-dof.png"
@@ -19,15 +21,13 @@ session "Isabelle_DOF-Manual" = "Isabelle_DOF" +
     "figures/Dogfood-Intro.png"
     "figures/Dogfood-IV-jumpInDocCLass.png"
     "figures/Dogfood-V-attribute.png"
-    "figures/Dogfood-VI-linkappl.png"
+    "figures/IsaArchGlobal.png"
+    "figures/IsaArchInteract.png"
+    "figures/IsaArch.odp"
     "figures/isabelle-architecture.pdf"
     "figures/isabelle-architecture.svg"
     "figures/isadof.png"
+    "figures/PIDE-interaction.pdf"
     "figures/srac-as-es-application.png"
     "figures/srac-definition.png"
     "figures/Isabelle_DOF-logo.pdf"
-    "figures/header_CSP_pdf.png"
-    "figures/header_CSP_source.png"
-    "figures/definition-use-CSP-pdf.png"
-    "figures/definition-use-CSP.png"
-    "figures/MyCommentedIsabelle.png"

examples/technical_report/Isabelle_DOF-Manual/document/build

@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+# Copyright (c) 2018-2019 The University of Sheffield. All rights reserved.
+#               2018 The University of Paris-Saclay. All rights reserved.
+#
+# 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
+if [ ! -f $ISABELLE_HOME_USER/DOF/document-template/build_lib.sh ]; then
+    echo ""
+    echo "Error: Isabelle/DOF not installed"
+    echo "====="
+    echo "This is a Isabelle/DOF project. The document preparation requires"
+    echo "the Isabelle/DOF framework. Please obtain the framework by cloning"
+    echo "the Isabelle/DOF git repository, i.e.: "
+    echo "    git clone https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF"
+    echo "You can install the framework as follows:"
+    echo "    cd Isabelle_DOF/document-generator"
+    echo "    ./install"
+    echo ""
+    exit 1
+fi
+
+cp $ISABELLE_HOME_USER/DOF/document-template/build_lib.sh .
+source build_lib.sh

examples/technical_report/Isabelle_DOF-Manual/document/isadof.cfg

@@ -0,0 +1,4 @@
+Template: scrreprt-modern
+Ontology: technical_report
+Ontology: cenelec_50128
+

examples/technical_report/Isabelle_DOF-Manual/document/lstisadof-manual.sty

@@ -1,16 +1,3 @@
-%% 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}
@@ -80,17 +67,116 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %% <isar>
+\newcommand{\subscr}[1]{\ensuremath{_{\text{#1}}}}
+\newcommand{\supscr}[1]{\ensuremath{^{\text{#1}}}}
+\lstdefinestyle{isar}{%
+  language=%
+  ,basicstyle=\ttfamily%
+  ,showspaces=false%
+  ,showlines=false%
+  ,columns=flexible%
+  ,keepspaces
+  ,morecomment=[s]{(*}{*)}%
+  % ,moredelim=*[s][\rmfamily]{\{*}{*\}}%
+  ,moredelim = **[is][\beginlstdelim{\{*}{*\}}{black}]{\{*}{*\}}
+  ,showstringspaces=false%
+  ,moredelim=*[is][\supscr]{<bsup>}{<esup>}%
+  ,moredelim=*[is][\subscr]{<bsub>}{<esub>}%
+  ,literate={%
+    {...}{\,\ldots\,}3%
+    {<Open>}{\ensuremath{\isacartoucheopen}}1%
+    {<open>}{\ensuremath{\isacartoucheopen}}1%
+    %{<@>}{@}1%
+    {"}{}0%
+    {é}{\'e}1%
+    {~}{\ }1%
+    {::}{:\!:}1%
+    {<Close>}{\ensuremath{\isacartoucheclose}}1%
+    {<close>}{\ensuremath{\isacartoucheclose}}1%
+    {\\<Gamma>}{\ensuremath{\Gamma}}1%
+    {\\<theta>}{\ensuremath{\theta}}1%
+    {\\<times>}{\ensuremath{\times}}1%
+    {\\<equiv>}{\ensuremath{\equiv}}1%
+    {\\<sigma>}{\ensuremath{\sigma}}1%
+    {\\<geq>}{\ensuremath{\geq}}1%
+    {level0}{level\textsubscript{0}}6%
+    {\\<Rightarrow>}{\ensuremath{\Rightarrow}}1%
+    {\\<rightarrow>}{\ensuremath{\rightarrow}}1%
+    {\\<longrightarrow>}{\ensuremath{\rightarrow}}1%
+    {\\<and>}{\ensuremath{\land}}1%  
+    {\\<or>}{\ensuremath{\lor}}1%
+    {\\<lfloor>}{\ensuremath{\lfloor}}1%
+    {\\<rfloor>}{\ensuremath{\rfloor}}1%  
+    %{\\<lparr>}{\ensuremath{\lparr}}1% 
+    %{\\<rparr>}{\ensuremath{\rparr}}1%
+    {\\<le>}{\ensuremath{\le}}1%
+    {\\<delta>}{\ensuremath{\delta}}1%
+    {\\<lambda>}{\ensuremath{\lambda}}1%
+    {\\<bar>}{\ensuremath{\vert}}1%
+    {\<sigma>}{\ensuremath{\sigma}}1%
+    {\\<lparr>}{\ensuremath{\isasymlparr}}1%  
+    {\\<rparr>}{\ensuremath{\isasymrparr}}1% 
+    {\\<leftrightarrow>}{\ensuremath{\leftrightarrow}}1%
+    {\{*}{\raise.3ex\hbox{$\scriptscriptstyle\langle$}}1%
+    {*\}}{\raise.3ex\hbox{$\scriptscriptstyle\rangle$}}1%
+    {\\<open>}{\raise.3ex\hbox{$\scriptscriptstyle\langle$}}1%
+    {\\<Open>}{\raise.3ex\hbox{$\scriptscriptstyle\langle$}}1%
+    {\\<close>}{\raise.3ex\hbox{$\scriptscriptstyle\rangle$}}1%
+    {\\<Close>}{\raise.3ex\hbox{$\scriptscriptstyle\rangle$}}1%
+    {\\<forall>}{\ensuremath{\forall}}1%
+    {\\<exists>}{\ensuremath{\exists}}1%
+    {\\<in>}{\ensuremath{\in}}1%
+    {\\<delta>}{\ensuremath{\delta}}1%
+    {\\<real>}{\ensuremath{\mathbb{R}}}1%
+    {\\<noteq>}{\ensuremath{\neq}}1%
+    {\\<exists>}{\ensuremath{\exists}}1%
+    {\\<Forall>}{\ensuremath{\bigwedge\,}}1%
+    {<string>}{<\ensuremath{\text{\textit{string}}}>}9%
+    {\\<lbrakk>}{\ensuremath{\mathopen{\lbrack\mkern-3mu\lbrack}}}1%
+    {\\<lbrace>}{\ensuremath{\mathopen{\lbrace\mkern-4.5mu\mid}}}1%
+    {\\<rbrakk>}{\ensuremath{\mathclose{\rbrack\mkern-3mu\rbrack}}}1%
+    {\\<rbrace>}{\ensuremath{\mathclose{\mid\mkern-4.5mu\rbrace}}}1%
+  }%
+  % % Defining "tags" (text-antiquotations) based on 1-keywords
+   ,tag=**[s]{@\{}{\}}%
+   ,tagstyle=\color{CornflowerBlue}%
+   ,markfirstintag=true%
+   ,keywordstyle=\bfseries%
+   ,keywords={}
+   % Defining 2-keywords
+   ,keywordstyle=[2]{\color{Blue!60}\bfseries}%
+   ,alsoletter={*,-}
+   ,morekeywords=[2]{case, then, show, theory, begin, end, ML,section,subsection,paragraph,chapter,text}%
+   %,moredelim=[s][\textit]{<}{>}
+   % Defining 3-keywords
+   ,keywordstyle=[3]{\color{OliveGreen!60}\bfseries}%
+   ,morekeywords=[3]{doc_class,declare_reference,update_instance*,
+     open_monitor*,  close_monitor*, declare_reference*,section*,text*,title*,abstract*}%
+   % Defining 4-keywords
+   ,keywordstyle=[4]{\color{black!60}\bfseries}%
+   ,morekeywords=[4]{where, imports, keywords}%
+   % Defining 5-keywords
+   ,keywordstyle=[5]{\color{BrickRed!70}\bfseries}%
+   ,morekeywords=[5]{datatype, by, fun, Definition*, definition,
+     type_synonym, typedecl, 
+     consts, assumes, and, shows, proof, next, qed, lemma, theorem}%
+   % Defining 6-keywords
+   ,keywordstyle=[6]{\itshape}%
+   ,morekeywords=[6]{meta-args, ref, expr, class_id}%
+  % 
+}%
+%% 
+
 \providecolor{isar}{named}{blue}
-\renewcommand{\isacommand}[1]{\textcolor{OliveGreen!60}{\ttfamily\bfseries #1}}
-\newcommand{\inlineisarbox}[1]{#1}
-\NewTColorBox[]{isarbox}{}{
+\def\inlineisar{\lstinline[style=isar,breaklines=true,mathescape,breakatwhitespace=true]}
+\newtcblisting{isar}[1][]{%
+      listing only%
      ,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
      % ,before skip=10pt
      % ,after skip=10pt
      ,enlarge top by=0mm
@@ -98,7 +184,13 @@
      ,overlay={\node[draw,fill=isar!60!black,xshift=0pt,anchor=north
        east,font=\bfseries\footnotesize\color{white}]
                 at (frame.north east) {Isar};}
-}
+     ,listing options={
+          style=isar
+          ,basicstyle=\small\ttfamily
+         ,mathescape
+         ,#1
+      }
+  }%
 %% </isar>
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
@@ -184,7 +276,6 @@
 \lstdefinestyle{lltx}{language=[AlLaTeX]TeX,
   ,basicstyle=\ttfamily%
   ,showspaces=false%
-  ,escapechar=ë
   ,showlines=false%
   ,morekeywords={newisadof}
  %  ,keywordstyle=\bfseries%

examples/technical_report/Isabelle_DOF-Manual/document/preamble.tex

@@ -6,22 +6,23 @@
 %%   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.
+%%   version 1 of the License, or any later version.
 %%   OR
 %%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
+%%  
+%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
 
 %% This is a placeholder for user-specific configuration and packages. 
 \usepackage{etex}
-\ifdef{\reserveinserts}{\reserveinserts{28}}{} 
+\reserveinserts{28}
+
 \usepackage{dirtree}
 \renewcommand*\DTstylecomment{\ttfamily\itshape}
 \usepackage{textcomp}
 \usepackage{xcolor}
 \usepackage{lstisadof-manual}
 \usepackage{xspace}
-\IfFileExists{hvlogos.sty}{\usepackage{hvlogos}}{\newcommand{\TeXLive}{\TeX Live}\newcommand{\BibTeX}{Bib\TeX}}
+\usepackage{dtk-logos}
 \usepackage{railsetup}
 \setcounter{secnumdepth}{2}
 \usepackage{index}
@@ -29,20 +30,20 @@
 %\makeindex
 %\AtEndDocument{\printindex}
 
-\newcommand{\dof}{DOF\xspace}
-\newcommand{\isactrlemph}{*}
-
+\newcommand{\ie}{i.e.}
+\newcommand{\eg}{e.g.}
 \newcommand{\path}[1]{\texttt{\nolinkurl{#1}}}
 \title{<TITLE>}
 \author{<AUTHOR>}
 
+\newcommand{\dof}{DOF\xspace}
 \renewcommand{\listofSRACs}{\relax}
 \renewcommand{\listofECs}{\relax}
 \pagestyle{headings}
 
 \uppertitleback{
-Copyright \copyright{} 2019--2022 University of Exeter, UK\\
-\phantom{Copyright \copyright{}} 2018--2022 Universit\'e Paris-Saclay, France\\
+Copyright \copyright{} 2019\phantom{--2019} University of Exeter, UK\\
+\phantom{Copyright \copyright{}} 2018--2019 Universit\'e Paris-Saclay, France\\
 \phantom{Copyright \copyright{}} 2018--2019 The University of Sheffield, UK\\
 
 \smallskip
@@ -76,14 +77,13 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 }
 
 \lowertitleback{%
-This manual describes \isadof version \isadofversion.  The latest official 
-release is \isadoflatestversion{} (\href{https://doi.org/\isadoflatestdoi}{doi:\isadoflatestdoi}). 
-The DOI \href{https://doi.org/\isadofgenericdoi}{\isadofgenericdoi} will allways point to the latest 
-release.  The latest development version as well as official releases are available at 
+This manual describes \isadof version \isadofversion.  
+
+The latest development version as well as previous releases are available at 
 \url{\dofurl}.
 
 \paragraph*{Contributors.} We would like to thank the following contributors to \isadof 
-(in alphabetical order): Idir Ait-Sadoune, Paolo Crisafulli, and Nicolas M{\'e}ric.
+(in alphabetical order): Idir Ait-Sadoune, Paolo Crisafulli, and Chantal Keller.
 
 \paragraph*{Acknowledgments.} This work has been partially supported by IRT SystemX, Paris-Saclay, 
 France, and therefore granted with public funds of the Program ``Investissements d'Avenir.''
@@ -109,7 +109,7 @@ France, and therefore granted with public funds of the Program ``Investissements
   \hfill
   \begin{minipage}{8cm}
     \raggedleft\normalsize
-    Laboratoire des Methodes Formelles (LMF)\\
+    Laboratoire en Recherche en Informatique (LRI)\\
     Universit\'e Paris-Saclay\\
     91405 Orsay Cedex\\
     France
@@ -118,3 +118,4 @@ France, and therefore granted with public funds of the Program ``Investissements
 }
 
 \AtBeginDocument{\isabellestyle{literal}\newcommand{\lstnumberautorefname}{Line}}
+\renewcommand{\isacommand}[1]{\textcolor{OliveGreen!60}{\ttfamily\bfseries #1}}

examples/technical_report/Isabelle_DOF-Manual/document/root.bib

@@ -3,27 +3,33 @@
 @STRING{s-lncs	= "LNCS" }
 
 @Misc{		  w3c:ontologies:2015,
-  author	= {W3C},
+  author        = {W3C},
   title		= {Ontologies},
   organisation	= {W3c},
   url		= {https://www.w3.org/standards/semanticweb/ontology},
   year		= 2015
 }
 
-@Misc{		  ibm:doors:2019,
-  author	= {IBM},
+@Misc{		  doors,
+  author        = {IBM},
   title		= {{IBM} Engineering Requirements Management {DOORS} Family},
   note		= {\url{https://www.ibm.com/us-en/marketplace/requirements-management}},
   year		= 2019
 }
 
-@Manual{	  wenzel:isabelle-isar:2020,
-  title		= {The Isabelle/Isar Reference Manual},
-  author	= {Makarius Wenzel},
-  year		= 2020,
-  note		= {Part of the Isabelle distribution.}
+@Manual{ wenzel:isabelle-isar:2019,
+  title =        {The Isabelle/Isar Reference Manual},
+  author =    {Makarius Wenzel},
+  OPTorganization = {},
+  OPTaddress =   {},
+  OPTedition =   {},
+  OPTmonth =     {},
+  year =      {2019},
+  note =      {Part of the Isabelle distribution.},
+  OPTannote =    {}
 }
 
+
 @InCollection{	  brucker.ea:isabelledof:2019,
   abstract	= {DOF is a novel framework for defining ontologies and
 		  enforcing them during document development and evolution. A
@@ -41,7 +47,7 @@
 		  ontological feedback during the editing of a document.
 		  
 		  In this paper, we give an in-depth presentation of the
-		  design concepts of DOF's Ontology Definition Language
+		  design concepts of DOF{\^a}s Ontology Definition Language
 		  (ODL) and key aspects of the technology of its
 		  implementation. Isabelle/DOF is the first ontology language
 		  supporting machine-checked links between the formal and
@@ -60,16 +66,14 @@
   publisher	= {Springer-Verlag},
   address	= {Heidelberg},
   series	= {Lecture Notes in Computer Science},
-  number	= {11724},
   isbn		= {3-540-25109-X},
-  doi		= {10.1007/978-3-030-30446-1_15},
-  editor	= {Peter C. {\"O}lveczky and Gwen Sala{\"u}n},
+  editor	= {Peter {\"O}lveczky and Gwen Sala{\"u}n},
   pdf		= {https://www.brucker.ch/bibliography/download/2019/brucker.ea-isabelledof-2019.pdf},
   title		= {{Isabelle/DOF}: Design and Implementation},
   classification= {conference},
   areas		= {formal methods, software},
   categories	= {isadof},
-  year		= {2019},
+  year		= 2019,
   public	= {yes}
 }
 
@@ -103,7 +107,7 @@
   publisher	= {Springer-Verlag},
   address	= {Heidelberg},
   series	= {Lecture Notes in Computer Science},
-  number	= {11006},
+  number	= 11006,
   url		= {https://www.brucker.ch/bibliography/abstract/brucker.ea-isabelle-ontologies-2018},
   title		= {Using the {Isabelle} Ontology Framework: Linking the
 		  Formal with the Informal},
@@ -111,35 +115,16 @@
   areas		= {formal methods, software},
   categories	= {isadof},
   public	= {yes},
-  year		= {2018},
-  doi		= {10.1007/978-3-319-96812-4_3},
+  year		= 2018,
   pdf		= {https://www.brucker.ch/bibliography/download/2018/brucker.ea-isabelle-ontologies-2018.pdf}
 }
 
-@InCollection{	  taha.ea:philosophers:2020,
-  keywords	= {CSP, Isabelle/HOL, Process-Algebra,Formal Verification, Refinement},
-  author	= {Safouan Taha  and Burkhart Wolff and Lina Ye},
-  booktitle	= {International Conference on Integrated Formal Methods (IFM)},
-  language	= {USenglish},
-  publisher	= {Springer-Verlag},
-  address	= {Heidelberg},
-  series	= {Lecture Notes in Computer Science},
-  number	= {to appear},
-  title		= {Philosophers may dine --- definitively!},
-  classification= {conference},
-  areas		= {formal methods, software},
-  public	= {yes},
-  year		= {2020}
-}
-
-
-
 @Book{		  boulanger:cenelec-50128:2015,
   author	= {Boulanger, Jean-Louis},
   title		= {{CENELEC} 50128 and {IEC} 62279 Standards},
   publisher	= {Wiley-ISTE},
   year		= 2015,
-  address	= {Boston}
+  address	= {Boston},
 }
 
 @Booklet{	  cc:cc-part3:2006,
@@ -199,7 +184,7 @@
   timestap	= {2008-05-26}
 }
 
-@InProceedings{wenzel:asynchronous:2014,
+@InProceedings{	  wenzel:asynchronous:2014,
   author	= {Makarius Wenzel},
   title		= {Asynchronous User Interaction and Tool Integration in
 		  {Isabelle}/{PIDE}},
@@ -257,7 +242,7 @@
   volume	= 8558,
   publisher	= pub-springer,
   year		= 2014,
-  doi		= {10.1007/978-3-319-08970-6}
+  doi		= {10.1007/978-3-319-08970-6},
 }
 
 @InProceedings{	  bezzecchi.ea:making:2018,
@@ -299,37 +284,39 @@
   location	= {Toulouse}
 }
 
-@InCollection{	  wenzel.ea:building:2007,
-  abstract	= {We present the generic system framework of
-		  Isabelle/Isarunderlying 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 tactical 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 systems. To demonstrate the technical
-		  potential of the framework, we apply it to a concrete
-		  formalmethods tool: the HOL-Z 3.0 environment, which is
-		  geared towards the analysis of Z specifications and formal
-		  proof of forward-refinements.},
-  author	= {Makarius Wenzel and Burkhart Wolff},
-  booktitle	= {TPHOLs 2007},
-  editor	= {Klaus Schneider and Jens Brandt},
-  language	= {USenglish},
+@InCollection{    wenzel.ea:building:2007,
+  abstract      = {We present the generic system framework of
+                  Isabelle/Isarunderlying 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 tactical 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 systems. To demonstrate the technical
+                  potential of the framework, we apply it to a concrete
+                  formalmethods tool: the HOL-Z 3.0 environment, which is
+                  geared towards the analysis of Z specifications and formal
+                  proof of forward-refinements.},
+  author        = {Makarius Wenzel and Burkhart Wolff},
+  booktitle     = {TPHOLs 2007},
+  editor        = {Klaus Schneider and Jens Brandt},
+  language      = {USenglish},
   acknowledgement={none},
-  pages		= {352--367},
-  publisher	= pub-springer,
-  address	= pub-springer:adr,
-  number	= 4732,
-  series	= s-lncs,
-  title		= {Building Formal Method Tools in the {Isabelle}/{Isar}
-		  Framework},
-  doi		= {10.1007/978-3-540-74591-4_26},
-  year		= 2007
+  pages         = {352--367},
+  publisher     = pub-springer,
+  address       = pub-springer:adr,
+  number        = 4732,
+  series        = s-lncs,
+  title         = {Building Formal Method Tools in the {Isabelle}/{Isar}
+                  Framework},
+  doi           = {10.1007/978-3-540-74591-4_26},
+  year          = 2007
 }
 
-@Misc{		  biendarra.ea:defining:2019,
+%%%%%%%%%%%%%%%%%%%%%%
+
+@Misc{		  datarefman19,
   title		= {Defining (Co)datatypes and Primitively (Co)recursive
 		  Functions in Isabelle/HOL},
   author	= {Julian Biendarra and Jasmin Christian Blanchette and
@@ -339,30 +326,43 @@
   year		= 2019
 }
 
-@Misc{		  kraus:defining:2020,
+@Misc{		  functions19,
   title		= {Defining Recursive Functions in Isabelle/HOL},
   author	= {Alexander Kraus},
   note		= {\url{https://isabelle.in.tum.de/doc/functions.pdf}},
-  year		= 2020
+  year		= 2019
 }
 
-@Misc{		  nipkow:whats:2020,
+@Misc{		  nipkowMain19,
   title		= {What's in Main},
   author	= {Tobias Nipkow},
   note		= {\url{https://isabelle.in.tum.de/doc/main.pdf}},
-  year		= 2020
+  year		= 2019
 }
 
-@InProceedings{	  wenzel:system:2014,
+@InProceedings{	  DBLP:conf/itp/Wenzel14,
+  author	= {Makarius Wenzel},
+  title		= {Asynchronous User Interaction and Tool Integration in
+		  Isabelle/PIDE},
+  booktitle	= {Interactive Theorem Proving (ITP)},
+  pages		= {515--530},
+  year		= 2014,
+  doi		= {10.1007/978-3-319-08970-6_33},
+  timestamp	= {Sun, 21 May 2017 00:18:59 +0200},
+  biburl	= {https://dblp.org/rec/bib/conf/itp/Wenzel14},
+  bibsource	= {dblp computer science bibliography, https://dblp.org}
+}
+
+@InProceedings{	  DBLP:journals/corr/Wenzel14,
   author	= {Makarius Wenzel},
   title		= {System description: Isabelle/{jEdit} in 2014},
   booktitle	= {UITP},
   pages		= {84--94},
   year		= 2014,
-  doi		= {10.4204/EPTCS.167.10}
+  doi		= {10.4204/EPTCS.167.10},
 }
 
-@InProceedings{	  barras.ea:pervasive:2013,
+@InProceedings{	  DBLP:conf/mkm/BarrasGHRTWW13,
   author	= {Bruno Barras and Lourdes Del Carmen
 		  Gonz{\'{a}}lez{-}Huesca and Hugo Herbelin and Yann
 		  R{\'{e}}gis{-}Gianas and Enrico Tassi and Makarius Wenzel
@@ -372,10 +372,10 @@
   booktitle	= {MKM},
   pages		= {359--363},
   year		= 2013,
-  doi		= {10.1007/978-3-642-39320-4_29}
+  doi		= {10.1007/978-3-642-39320-4_29},
 }
 
-@Article{	  faithfull.ea:coqoon:2018,
+@Article{	  Faithfull:2018:COQ:3204179.3204223,
   author	= {Faithfull, Alexander and Bengtson, Jesper and Tassi,
 		  Enrico and Tankink, Carst},
   title		= {Coqoon},
@@ -388,12 +388,55 @@
   issn		= {1433-2779},
   pages		= {125--137},
   numpages	= 13,
+  url		= {https://doi.org/10.1007/s10009-017-0457-2},
   doi		= {10.1007/s10009-017-0457-2},
   acmid		= 3204223,
   publisher	= {Springer-Verlag},
   address	= {Berlin, Heidelberg}
 }
 
+@InCollection{	  brucker.wolff19:isadof-design-impl:2019,
+  abstract	= {DOF is a novel framework for \emph{defining} ontologies
+		  and \emph{enforcing} them during document development and
+		  document evolution. A major goal of DOF is the integrated
+		  development of formal certification documents (\eg, for
+		  Common Criteria or CENELEC 50128) that require consistency
+		  across both formal and informal arguments.
+		  
+		  To support a consistent development of formal and informal
+		  parts of a document, we provide Isabelle/DOF, an
+		  implementation of DOF on top of Isabelle/HOL. \isadof is
+		  integrated into Isabelle's IDE, which allows for smooth
+		  ontology development as well as immediate ontological
+		  feedback during the editing of a document.
+		  
+		  In this paper, we give an in-depth presentation of the
+		  design concepts of DOF's Ontology Definition Language (ODL)
+		  and key aspects of the technology of its implementation.
+		  \isadof is the first ontology language supporting
+		  machine-checked links between the formal and informal parts
+		  in an LCF-style interactive theorem proving environment.
+		  
+		  Sufficiently annotated, large documents can easily be
+		  developed collaboratively, while \emph{ensuring their
+		  consistency}, and the impact of changes (in the formal and
+		  the semi-formal content) is tracked automatically.},
+  address	= {Heidelberg},
+  author	= {Achim D. Brucker and Burkhart Wolff},
+  booktitle	= {International Conference on Software Engineering and
+		  Formal Methods (SEFM)},
+  doi		= {10.1007/978-3-319-96812-4_3},
+  keywords	= {Isabelle, HOL, Ontologies, Certification},
+  language	= {USenglish},
+  location	= {Oslo, Norway},
+  number	= {TO APPEAR},
+  pdf		= {https://www.lri.fr/~wolff/papers/conf/2019-sefm-isa_dof-framework.pdf},
+  publisher	= {Springer-Verlag},
+  series	= {Lecture Notes in Computer Science},
+  title		= {{I}sabelle/{DOF}: {D}esign and {I}mplementation},
+  year		= 2019
+}
+
 @InProceedings{	  abrial:steam-boiler:1996,
   author	= {Abrial, Jean-Raymond},
   title		= {Steam-Boiler Control Specification Problem},
@@ -445,24 +488,25 @@
 		  the development, deployment and maintenanceactivities.}
 }
 
-@Article{	  kraus.ea:regular-sets-afp:2010,
+
+@Article{	  Regular-Sets-AFP,
   author	= {Alexander Krauss and Tobias Nipkow},
   title		= {Regular Sets and Expressions},
   journal	= {Archive of Formal Proofs},
   month		= may,
   year		= 2010,
-  note		= {\url{https://isa-afp.org/entries/Regular-Sets.html}, Formal
+  note		= {\url{http://isa-afp.org/entries/Regular-Sets.html}, Formal
 		  proof development},
   issn		= {2150-914x}
 }
 
-@Article{	  nipkow.ea:functional-Automata-afp:2004,
+@Article{	  Functional-Automata-AFP,
   author	= {Tobias Nipkow},
   title		= {Functional Automata},
   journal	= {Archive of Formal Proofs},
   month		= mar,
   year		= 2004,
-  note		= {\url{https://isa-afp.org/entries/Functional-Automata.html},
+  note		= {\url{http://isa-afp.org/entries/Functional-Automata.html},
 		  Formal proof development},
   issn		= {2150-914x}
 }
@@ -473,11 +517,11 @@
   year		= 2019
 }
 
-@Booklet{	  wenzel:system-manual:2020,
+@Booklet{	  wenzel:system-manual:2019,
   author	= {Makarius Wenzel},
   title		= {The {Isabelle} System Manual},
-  year		= 2020,
-  note		= {Part of the Isabelle distribution.}
+  year		= 2019,
+  note          = {Part of the Isabelle distribution.}
 }
 
 @Booklet{	  chervet:keycommand:2010,
@@ -508,6 +552,5 @@
 @Book{		  eijkhout:latex-cs:2012,
   author	= {Victor Eijkhout},
   title		= {The Computer Science of TeX and LaTeX},
-  publisher = {Texas Advanced Computing Center},
-  year		= 2012
+  year		= 2012,
 }

examples/technical_report/TR_my_commented_isabelle/ROOT

@@ -1,17 +1,18 @@
 session "TR_MyCommentedIsabelle" = "Isabelle_DOF" +
-  options [document = pdf, document_output = "output", document_build = dof, quick_and_dirty = true]
+  options [document = pdf, document_output = "output",quick_and_dirty = true]
   theories
     "TR_MyCommentedIsabelle"
   document_files
     "root.bib"
+    "isadof.cfg"
     "preamble.tex"
     "prooftree.sty"
+    "build"
     "figures/markup-demo.png"
     "figures/text-element.pdf"
     "figures/isabelle-architecture.pdf"
     "figures/pure-inferences-I.pdf"
     "figures/pure-inferences-II.pdf"
     "figures/document-model.pdf"
-    "figures/MyCommentedIsabelle.png"
 
 

examples/technical_report/TR_my_commented_isabelle/document/build

@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+# Copyright (c) 2018-2019 The University of Sheffield. All rights reserved.
+#               2018 The University of Paris-Saclay. All rights reserved.
+#
+# 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
+if [ ! -f $ISABELLE_HOME_USER/DOF/document-template/build_lib.sh ]; then
+    echo ""
+    echo "Error: Isabelle/DOF not installed"
+    echo "====="
+    echo "This is a Isabelle/DOF project. The document preparation requires"
+    echo "the Isabelle/DOF framework. Please obtain the framework by cloning"
+    echo "the Isabelle/DOF git repository, i.e.: "
+    echo "    git clone https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF"
+    echo "You can install the framework as follows:"
+    echo "    cd Isabelle_DOF/document-generator"
+    echo "    ./install"
+    echo ""
+    exit 1
+fi
+
+cp $ISABELLE_HOME_USER/DOF/document-template/build_lib.sh .
+source build_lib.sh

examples/technical_report/TR_my_commented_isabelle/document/isadof.cfg

@@ -0,0 +1,2 @@
+Template: scrreprt
+Ontology: technical_report

examples/technical_report/TR_my_commented_isabelle/document/preamble.tex

@@ -5,16 +5,16 @@
 %%   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.
+%%   version 1 of the License, or any later version.
 %%   OR
 %%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
+%%  
+%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
 
 %% This is a placeholder for user-specific configuration and packages. 
 
-\renewcommand{\isasymtheta}{\texorpdfstring{\isamath{\vartheta}}{ϑ}}
 \usepackage{prooftree}
 \title{<TITLE>}
 \author{<AUTHOR>}
-
+\newcommand{\eg}{e.\,g.}
+\newcommand{\ie}{i.\,e.}

install

@@ -0,0 +1,284 @@
+#!/usr/bin/env bash
+# Copyright (c) 2018-2019 The University of Sheffield.
+#               2019-2019 The University of Exeter. 
+#               2018-2019 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
+
+# get global configuration  
+source .config
+
+print_help()
+{
+    echo "Usage: install [OPTION] "
+    echo ""
+    echo "Run ..."
+    echo ""
+    echo "  --help, -h                display this help message"
+    echo "  --isabelle, -i isabelle   isabelle command used for installation"
+    echo "                            (default: $ISABELLE)"
+    echo "  --skip-patch-and-afp, -s  skip installation of Isabelle/DOF patch for" 
+    echo "                            Isabelle and required AFP entries. "
+    echo "                            USE AT YOUR OWN RISK (default: $SKIP)"
+}
+
+
+
+exit_error() {
+    echo ""
+    echo "  *** Isabelle/DOF installation FAILED, please check the README.md for help ***"
+    echo ""
+    exit 1
+}
+
+check_isabelle_version() {
+    echo "* Checking Isabelle version:"
+    if [ "$ISABELLE_VERSION" != "$ACTUAL_ISABELLE_VERSION" ]; then
+        echo "  WARNING:"
+        echo "    The version of Isabelle (i.e., $ACTUAL_ISABELLE_VERSION) you are using"
+        echo "                        IS NOT SUPPORTED"
+        echo "    by the current version of Isabelle/DOF. Please install a supported"
+        echo "    version of Isabelle and rerun the install script, providing the"
+        echo "    the \"isabelle\" command as argument."
+        echo "    Isabelle ($ISABELLE_VERSION) can be obtained from:"
+        echo "    $ISABELLE_URL"
+        echo 
+        read -p "    Still continue (y/N)? " -n 1 -r
+        echo 
+        if [[ $REPLY =~ ^[Yy]$ ]];
+        then 
+            echo "    Continuing installation on your OWN risk."
+        else
+            exit_error
+        fi
+     else
+        echo "  Success: found supported Isabelle version ($ISABELLE_VERSION)"
+    fi
+}
+
+check_pdftex() {
+    echo "* Checking (La)TeX installation:"
+    OLDDIR=`pwd`
+    DIR=`mktemp -d`
+    cd $DIR; 
+    pdftex -interaction=nonstopmode \\expanded{Success}\\end > /dev/null
+    if [ $? -eq 0 ]; then
+        echo "  Success: pdftex supports \\expanded{} primitive."
+    else 
+        cd $OLDDIR
+        echo "  WARNING:"
+        echo "    The version of pdf(La)TeX you are using is outdated (and does"
+        echo "    not support the \\expanded primitive). It is not supported by the"
+        echo "    current version of Isabelle/DOF. Please install a supported TeX"
+        echo "    distribution (e.g., TeXLive 2019 or later)."
+        echo 
+        read -p "    Still continue (y/N)? " -n 1 -r
+        echo 
+        if [[ $REPLY =~ ^[Yy]$ ]];
+        then 
+            echo "    Continuing installation on your OWN risk."
+        else
+            exit_error
+        fi
+    fi
+    cd $OLDDIR
+}
+
+check_afp_entries() {
+    echo "* Checking availability of AFP entries:"
+    missing=""
+    required="Regular-Sets Functional-Automata"
+    for afp in $required; do 
+        res=`$ISABELLE build -n $afp 2>/dev/null || true`
+        if [ "$res" != "" ]; then 
+            echo "  Success: found APF entry $afp."
+        else
+            echo "  Warning: could not find AFP entry $afp."
+            missing="$missing $afp"
+       fi
+    done
+    if [ "$missing" != "" ]; then 
+        echo "           Trying to install AFP (this might take a few *minutes*) ...."
+	extract=""
+	for e in $missing; do
+	    extract="$extract $AFP_DATE/thys/$e"
+	done
+	mkdir -p .afp
+        if curl -s -L $AFP_URL | tar zxf - -C .afp $extract; then 
+            for e in $missing; do 
+                echo "           Registering $e in $ISABELLE_HOME_USER/ROOTS"
+		touch $ISABELLE_HOME_USER/ROOTS
+		grep -q $PWD/.afp/$AFP_DATE/thys/$e $ISABELLE_HOME_USER/ROOTS || echo "$PWD/.afp/$AFP_DATE/thys/$e" >> $ISABELLE_HOME_USER/ROOTS 
+            done
+            echo "           AFP installation successful."
+        else
+            echo "  FAILURE: could not find AFP entries: $missing."
+            echo "    Please obtain the AFP from"
+            echo "    $AFP_URL"
+            echo "    and follow the following instructions:"
+            echo "    https://www.isa-afp.org/using.html"
+            exit_error
+        fi
+    fi
+}
+
+check_isa_dof_patch() {
+    echo "* Check availability of Isabelle/DOF patch:"
+    src="src/patches/thy_output.ML"
+    dst="$ISABELLE_HOME/src/Pure/Thy/thy_output.ML"
+     
+    if command -v cmp > /dev/null 2>&1 && cmp -s "$src" "$dst" ; then
+        echo "  Success: latest Isabelle/DOF patch already applied"
+        if isabelle process -e 'Thy_Output.set_meta_args_parser' &> /dev/null ; then
+            true
+        else
+            echo "  Warning: Isabelle/HOL needs to be rebuild to activate patch."
+        fi
+    else
+        command -v cmp >/dev/null 2>&1 || echo "  Warning: cmp not available, cannot check if patch is already applied."
+        echo "  Warning: Isabelle/DOF patch is not available or outdated."
+        echo "           Trying to patch system ...."
+        if [ ! -f "$dst.backup-by-isadof-installer" ]; then
+            cp -f "$dst" "$dst.backup-by-isadof-installer" || true;
+        fi
+	if (cp -f $src $dst) &> /dev/null; then 
+	    echo "       Applied patch successfully, Isabelle/HOL will be rebuilt during"
+	    echo "       the next start of Isabelle."
+	else
+            echo "  FAILURE: Could not apply Isabelle/DOF patch."
+            echo "    Please copy $src to $dst, e.g.:"
+            echo "       cp -f $src $dst"
+            echo "    and rebuild Isabelle/HOL."
+            exit_error
+	fi
+    fi
+}
+
+check_old_installation(){
+    echo "* Searching for existing installation:"
+    if [[ -d "$ISABELLE_HOME_USER/DOF" ]]; then
+        echo "  Found old installation, moving it to $ISABELLE_HOME_USER/DOF.bak."
+        rm -rf "$ISABELLE_HOME_USER/DOF.bak"
+        mv "$ISABELLE_HOME_USER/DOF" "$ISABELLE_HOME_USER/DOF.bak"
+    else
+        echo "  No old installation found."
+    fi
+
+}
+
+install_and_register(){
+    echo "* Installing Isabelle/DOF"
+
+    DIR="$ISABELLE_HOME_USER/DOF/Tools"
+    echo "  - Installing Tools in $DIR"
+    mkdir -p "$DIR"
+    cp $GEN_DIR/Tools/* "$DIR"
+    chmod 755 "$DIR"/*
+
+    DIR="$ISABELLE_HOME_USER/DOF/document-template"
+    echo "  - Installing document templates in $DIR"
+    mkdir -p "$DIR"
+    cp $GEN_DIR/scripts/* "$DIR"
+    cp $GEN_DIR/document-templates/* "$DIR"
+    cp $GEN_DIR/DOF/*/*.sty "$DIR"
+    
+    ISABELLE_SHORT_VERSION=`echo $ISABELLE_VERSION | sed -e 's/:.*$//'`
+    sed -i -e "s|%%% CONFIG %%%| \
+      \\\\renewcommand{\\\\dof@isabelleversion}{$ISABELLE_SHORT_VERSION} \
+      \\\\renewcommand{\\\\isabellefullversion}{$ISABELLE_VERSION\\\\xspace} \
+      \\\\renewcommand{\\\\dof@version}{$DOF_VERSION} \
+      \\\\renewcommand{\\\\isabelleurl}{$ISABELLE_URL} \
+      \\\\renewcommand{\\\\dofurl}{$DOF_URL} \
+      \\\\renewcommand{\\\\dof@artifacturl}{https://$DOF_ARTIFACT_HOST/$DOF_ARTIFACT_DIR}|" \
+      "$DIR/DOF-core.sty"
+
+    DIR="$ISABELLE_HOME_USER/DOF/latex"
+    echo "  - Installing LaTeX styles in $DIR"
+    mkdir -p "$DIR"
+    cp $GEN_DIR/ontologies/*/*.sty "$DIR"
+    
+    DIR="$ISABELLE_HOME_USER/etc"
+    echo "  - Registering Isabelle/DOF"
+    mkdir -p "$DIR"
+    if [[ $ISABELLE_TOOLS = *DOF* ]]; then
+        echo "    * Tools already registered in $DIR/settings"
+    else
+        echo "    * Registering tools in $DIR/settings"
+        echo 'ISABELLE_TOOLS=$ISABELLE_TOOLS:$ISABELLE_HOME_USER/DOF/Tools' \
+             >> "$DIR/settings"
+    fi
+    sed -i -e "s|<isadofurl>|$DOF_URL|" $ISABELLE_HOME_USER/DOF/*/*
+    grep -q $PWD\$ $ISABELLE_HOME_USER/ROOTS || echo "$PWD" >> $ISABELLE_HOME_USER/ROOTS 
+}
+
+
+ISABELLE=`which isabelle`
+SKIP="false"
+while [ $# -gt 0 ]
+do
+    case "$1" in
+        --isabelle|-i)
+            ISABELLE="$2";
+            shift;;
+        --skip-patch-and-afp|-s)
+            SKIP="true";;
+        --help|-h)
+            print_help
+            exit 0;;
+        *)  print_help
+            exit 1;;
+    esac
+    shift
+done
+
+
+ACTUAL_ISABELLE_VERSION=`$ISABELLE version`
+GEN_DIR=src
+PROG=`echo $0 | sed 's|.*/||'`;
+VARS=`$ISABELLE getenv ISABELLE_HOME_USER ISABELLE_HOME ISABELLE_TOOLS`
+for i in $VARS; do 
+	export "$i"
+done
+
+echo ""
+echo "Isabelle/DOF Installer"
+echo "======================"
+check_isabelle_version
+check_pdftex
+if [ "$SKIP" = "true" ]; then
+  echo "* Warning: skipping installation of Isabelle patch and AFP entries."
+else
+  check_isa_dof_patch
+  check_afp_entries
+fi
+check_old_installation
+install_and_register
+echo "* Installation successful. Enjoy Isabelle/DOF, you can build the session"
+echo "  Isabelle_DOF and all example documents by executing:"
+echo "  $ISABELLE build -D ."
+exit 0

install-afp

@@ -1,179 +0,0 @@
-#!/usr/bin/env bash
-# Copyright (c) 2018-2019 The University of Sheffield.
-#               2019-2020 The University of Exeter. 
-#               2018-2020 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: isabelle env ./install-afp [OPTION] "
-    echo ""
-    echo "Warning: This tools is deprecated."
-    echo ""
-    echo "Run ..."
-    echo ""
-    echo "  --help, -h                display this help message"
-}
-
-
-
-exit_error() {
-    echo ""
-    echo "  *** Local AFP installation FAILED, please check the README.md for help ***"
-    echo ""
-    exit 1
-}
-
-confirm_usage() {
-    echo "* From Isabelle2021-1 on, the recommended method for making the whole AFP "
-    echo "  available to Isabelle is the isabelle components -u command."
-    echo "  For doing so, please follow the instructions at: "
-    echo "  https://www.isa-afp.org/help/"
-    echo ""
-    echo "  Alternatively, you can continue, on your own risk, to install only"
-    echo "  the AFP entries required to run Isabelle/DOF."
-    echo ""
-    read -p "    Still continue (y/N)? " -n 1 -r
-    echo 
-    if [[ $REPLY =~ ^[Yy]$ ]];
-    then 
-        echo "    Continuing installation on your OWN risk."
-    else
-        exit_error
-    fi
-}
-check_isabelle_version() {
-    echo "* Checking Isabelle version:"
-    if [ "$ISABELLE_VERSION" != "$ACTUAL_ISABELLE_VERSION" ]; then
-        echo "  WARNING:"
-        echo "    The version of Isabelle (i.e., $ACTUAL_ISABELLE_VERSION) you are using"
-        echo "                        IS NOT SUPPORTED"
-        echo "    by the current version of Isabelle/DOF. Please install a supported"
-        echo "    version of Isabelle and rerun the install script, providing the"
-        echo "    the \"isabelle\" command as argument."
-        echo "    Isabelle ($ISABELLE_VERSION) can be obtained from:"
-        echo "    https://isabelle.in.tum.de/website-$ISABELLE_VERSION/"
-        echo ""
-        read -p "    Still continue (y/N)? " -n 1 -r
-        echo 
-        if [[ $REPLY =~ ^[Yy]$ ]];
-        then 
-            echo "    Continuing installation on your OWN risk."
-        else
-            exit_error
-        fi
-     else
-        echo "  Success: found supported Isabelle version ($ISABELLE_VERSION)"
-    fi
-}
-
-check_afp_entries() {
-    echo "* Checking availability of AFP entries:"
-    missing=""
-    required="Regular-Sets Functional-Automata Physical_Quantities"
-    for afp in $required; do 
-        res=`$ISABELLE_TOOL build -n $afp 2>/dev/null || true`
-        if [ "$res" != "" ]; then 
-            echo "  Success: found APF entry $afp."
-        else
-            echo "  Warning: could not find AFP entry $afp."
-            missing="$missing $afp"
-       fi
-    done
-    if [ "$missing" != "" ]; then 
-        echo "           Trying to install AFP (this might take a few *minutes*) ...."
-	extract=""
-	for e in $missing; do
-	    extract="$extract $AFP_DATE/thys/$e"
-	done
-	mkdir -p .afp
-        if curl -s -L $AFP_URL | tar zxf - -C .afp $extract; then 
-            for e in $missing; do 
-                echo "           Registering $e"
-                $ISABELLE_TOOL components -u "$PWD/.afp/$AFP_DATE/thys/$e"
-            done
-            echo "           AFP installation successful."
-        else
-            echo "  FAILURE: could not find AFP entries: $missing."
-            echo "    Please obtain the AFP from"
-            echo "    $AFP_URL"
-            echo "    and follow the following instructions:"
-            echo "    https://www.isa-afp.org/using.html"
-            exit_error
-        fi
-    fi
-}
-
-while [ $# -gt 0 ]
-do
-    case "$1" in
-        --help|-h)
-            print_help
-            exit 0;;
-        *)  print_help
-            exit 1;;
-    esac
-    shift
-done
-
-if [ -z ${ISABELLE_TOOL+x} ];
-then
-    print_help
-    exit 1
-fi
-
-ACTUAL_ISABELLE_VERSION=`$ISABELLE_TOOL version`
-
-ISABELLE_VERSION="Isabelle$($ISABELLE_TOOL dof_param -b isabelle_version)"
-
-if [ ${ISABELLE_VERSION} = "Isabelle" ];
-then
-   echo "Error: cannot find Isabelle/DOF configuration, please check that you"
-   echo "       registered Isabelle/DOF as an Isabelle component, e.g., using" 
-   echo "       isabelle components -u ."
-   exit 1
-fi
-
-
-
-AFP_DATE="$($ISABELLE_TOOL dof_param -b afp_version)"
-AFP_URL="https://www.isa-afp.org/release/"$AFP_DATE".tar.gz"
-
-echo ""
-echo "Isabelle/DOF AFP Installation Utility"
-echo "====================================="
-confirm_usage
-check_isabelle_version
-check_afp_entries
-echo "* AFP Installation successful."
-echo "  You should now be able to enjoy Isabelle/DOF by building its session"
-echo "  and all example documents by executing:"
-echo "  $ISABELLE_TOOL build -D ."
-exit 0

src/DOF/Assert.thy

@@ -0,0 +1,69 @@
+section \<open> Little theory implementing the an assertion command in Isabelle/HOL. \<close>
+text\<open>This command is useful for certification documents allowing to validate 
+     corner-cases of (executable) definitions. \<close>
+
+theory Assert
+  imports Main
+      keywords "assert" ::thy_decl
+
+begin
+  
+subsection\<open>Core\<close>
+  
+ML\<open>
+local 
+(* Reimplementation needed because not exported from ML structure Value_Command *)
+fun value_maybe_select some_name =
+  case some_name
+    of NONE => Value_Command.value
+     | SOME name => Value_Command.value_select name;
+in
+(* Reimplementation needed because not exported from ML structure Value_Command *)
+val opt_modes =
+  Scan.optional (@{keyword "("} |-- Parse.!!! (Scan.repeat1 Parse.name --| @{keyword ")"})) [];
+
+(* Reimplementation needed because not exported from ML structure Value_Command *)
+val opt_evaluator =
+  Scan.option (@{keyword "["} |-- Parse.name --| @{keyword "]"})
+
+(* Reimplementation  structure Value_Command due to tiny modification of value_cmd. *)
+fun assert_cmd some_name modes raw_t ctxt (* state*) =
+  let
+   (* val ctxt = Toplevel.context_of state; *)
+    val t = Syntax.read_term ctxt raw_t;
+    val t'  = value_maybe_select some_name ctxt t;
+    val ty' = Term.type_of t';
+    val ty' = case ty' of @{typ "bool"} => ty' | _ =>  error "Assertion expressions must be boolean.";
+    val t'  = case t'  of @{term "True"} => t' | _ =>  error "Assertion failed.";
+    val ctxt' = Variable.auto_fixes t' ctxt;
+    val p = Print_Mode.with_modes modes (fn () =>
+      Pretty.block [Pretty.quote (Syntax.pretty_term ctxt' t'), Pretty.fbrk,
+        Pretty.str "::", Pretty.brk 1, Pretty.quote (Syntax.pretty_typ ctxt' ty')]) ();
+  in Pretty.writeln p end;
+
+val _ =
+  Outer_Syntax.command @{command_keyword assert} "evaluate and print term"
+    (opt_evaluator -- opt_modes -- Parse.term
+      >> (fn ((some_name, modes), t) =>   
+            Toplevel.keep ( (assert_cmd some_name modes t) o Toplevel.context_of) ));
+end
+\<close>
+
+
+
+subsection\<open> Test: \<close> 
+(*    
+ assert ""
+ assert "3 = 4"
+ assert "False"
+ assert "5 * 5 = 25"
+*)
+
+subsection\<open>Example\<close>
+
+assert "True \<and> True "
+
+assert "(5::int) * 5 = 25 "
+  
+end  
+  

src/DOF/AssertLong.thy

@@ -0,0 +1,57 @@
+theory AssertLong
+  imports Main
+      keywords "assert" ::thy_decl
+
+begin
+  
+
+  
+  
+ML\<open>
+
+fun value_maybe_select some_name =
+  case some_name
+    of NONE => Value_Command.value
+     | SOME name => Value_Command.value_select name;
+
+val TT = Unsynchronized.ref (HOLogic.boolT);
+
+fun value_cmd2 some_name modes raw_t state =
+  let
+    val ctxt = Toplevel.context_of state;
+    val t = Syntax.read_term ctxt raw_t;
+    val t' = value_maybe_select some_name ctxt t;
+    val ty' = Term.type_of t';
+    val t' = case ty' of @{typ "bool"} => t' | _ =>  error "Assertion expressions must be boolean.";
+    val t' = case t' of @{term "True"} => t' | _ =>  error "Assertion failed.";
+    val ctxt' = Variable.auto_fixes t' ctxt;
+    val p = Print_Mode.with_modes modes (fn () =>
+      Pretty.block [Pretty.quote (Syntax.pretty_term ctxt' t'), Pretty.fbrk,
+        Pretty.str "::", Pretty.brk 1, Pretty.quote (Syntax.pretty_typ ctxt' ty')]) ();
+  in Pretty.writeln p end;
+
+\<close>
+ML\<open>value_cmd2\<close>
+definition ASSERT :: "bool \<Rightarrow> bool" where "ASSERT p == (p=True)"
+ML\<open>val x = @{code "ASSERT"}\<close> 
+ML\<open>
+val opt_modes =
+  Scan.optional (@{keyword "("} |-- Parse.!!! (Scan.repeat1 Parse.name --| @{keyword ")"})) [];
+
+val opt_evaluator =
+  Scan.option (@{keyword "["} |-- Parse.name --| @{keyword "]"})
+
+val _ =
+  Outer_Syntax.command @{command_keyword assert} "evaluate and print term"
+    (opt_evaluator -- opt_modes -- Parse.term
+      >> (fn ((some_name, modes), t) => 
+             let val _ = writeln t in
+              (* Toplevel.keep (Value_Command.value_cmd some_name modes (enclose "ASSERT(" ")" t)) *)
+                Toplevel.keep (value_cmd2 some_name modes t) 
+             end));
+\<close>    
+
+assert "True"
+assert "True \<and> True "
+ML\<open>!TT ;
+      @{term "True"}\<close>

src/DOF/Isa_COL.thy

@@ -1,37 +1,56 @@
-(*************************************************************************
- * 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>The Document Ontology Common Library for the Isabelle Ontology Framework\<close>
 
-text\<open> Building a fundamental infrastructure for common document elements such as
-      Structuring Text-Elements (the top classes), Figures, (Tables yet todo)
-
-      The COL provides a number of ontological "macros" like "section*" which 
-      automatically set a number of class-attributes in particular ways without 
-      user-interference. 
-    \<close> 
-
+text\<open> Offering 
+\<^item> ...
+\<^item> 
+\<^item> LaTeX support. \<close> 
+  
+ 
 theory Isa_COL   
   imports  Isa_DOF  
-  keywords "title*"        "subtitle*"      
-           "chapter*"      "section*"   
-           "subsection*"   "subsubsection*" 
-           "paragraph*"    "subparagraph*"         
-           "figure*"       "side_by_side_figure*" :: document_body 
-
 begin
   
-section\<open>Basic Text and Text-Structuring Elements\<close>
+   
+section\<open> Library of Standard Text Ontology \<close>
+
+
+
+
+datatype placement = pl_h  | (*here*) 
+                     pl_t  | (*top*)
+                     pl_b  | (*bottom*)
+                     pl_ht | (*here ->  top*) 
+                     pl_hb   (*here ->  bottom*)
+
+
+doc_class figure   = 
+   relative_width   :: "int" (* percent of textwidth *)    
+   src              :: "string"
+   placement        :: placement 
+   spawn_columns    :: bool <= True 
+
+doc_class side_by_side_figure = figure +
+   anchor           :: "string"
+   caption          :: "string"
+   relative_width2  :: "int" (* percent of textwidth *)    
+   src2             :: "string"
+   anchor2          :: "string"
+   caption2         :: "string"
+
+
+doc_class figure_group = 
+   (*  trace :: "doc_class rexp list" <= "[]" automatically generated since monitor clause *)
+   caption          :: "string"
+   rejects             figure_group   (* this forbids recursive figure-groups not supported
+                                        by the current LaTeX style-file. *)
+   accepts             "\<lbrace>figure\<rbrace>\<^sup>+"
+
+
+
+(* dito the future table *)
+
+(* dito the future monitor: table - block *)
+
 
 text\<open> The attribute @{term "level"} in the subsequent enables doc-notation support section* etc.
 we follow LaTeX terminology on levels 
@@ -42,606 +61,43 @@ we follow LaTeX terminology on levels
 \<^enum>             subsubsection = Some 3
 \<^enum>             ... 
 
-for scholarly paper: invariant level > 0. \<close>
+for scholarly paper: invariant level > 0 \<close>
 
-doc_class text_element =     
+doc_class text_element = 
    level         :: "int  option"    <=  "None" 
    referentiable :: bool <= "False"
    variants      :: "String.literal set" <= "{STR ''outline'', STR ''document''}" 
 
-doc_class "chapter" = text_element +
-   level         :: "int  option"    <=  "Some 0" 
-doc_class "section" = text_element +
-   level         :: "int  option"    <=  "Some 1" 
-doc_class "subsection" = text_element +
-   level         :: "int  option"    <=  "Some 2" 
-doc_class "subsubsection" = text_element +
-   level         :: "int  option"    <=  "Some 3" 
+section\<open>Some attempt to model standardized links to Standard Isabelle Formal Content\<close>
 
+doc_class assertions = 
+    properties :: "term list"
+  
+doc_class "thms" =
+    properties :: "thm list"
 
-subsection\<open>Ontological Macros\<close>
+doc_class formal_item = 
+    item :: "(assertions + thms)"
 
-ML\<open> 
+doc_class definitions =
+    requires    :: "formal_item list"
+    establishes :: "thms list"
 
-structure Onto_Macros =
-struct
-local open ODL_Meta_Args_Parser in
-(* *********************************************************************** *)
-(* Ontological Macro Command Support                                       *)
-(* *********************************************************************** *)
+doc_class formal_content =
+    style :: "string option"
+    accepts "\<lbrace>formal_item\<rbrace>\<^sup>+"
 
-(* {markdown = true} sets the parsing process such that in the text-core markdown elements are
-   accepted. *)
 
- 
-fun enriched_text_element_cmd level =
-   let fun transform doc_attrs = case level of 
-                  NONE => doc_attrs 
-                | SOME(NONE)   => (("level",@{here}),"None")::doc_attrs
-                | SOME(SOME x) => (("level",@{here}),"Some("^ Int.toString x ^"::int)")::doc_attrs
-   in Monitor_Command_Parser.gen_enriched_document_cmd {inline=true} I transform end; 
-
-(*
-val enriched_document_command_macro = 
-    let fun transform_cid X = (writeln (@{make_string} X); X)
-    in  gen_enriched_document_command {inline=true} transform_cid I end;
-*)
-
-
-local 
-fun transform_cid thy NONE X = X
-   |transform_cid thy (SOME ncid) NONE =  (SOME(ncid,@{here}))
-   |transform_cid thy (SOME cid) (SOME (sub_cid,pos)) =
-                             let val cid_long  = DOF_core.read_cid_global thy cid
-                                 val sub_cid_long =  DOF_core.read_cid_global thy sub_cid
-                             in  if DOF_core.is_subclass_global thy  sub_cid_long cid_long
-                                 then (SOME (sub_cid,pos))
-                                 else (* (SOME (sub_cid,pos)) *)
-                                      (*  BUG : check reveals problem of Definition* misuse.  *)
-                                        error("class "^sub_cid_long^
-                                              " must be sub-class of "^cid_long) 
-                             end  
-in
-
-fun enriched_formal_statement_command ncid (S: (string * string) list) =
-   let fun transform_attr doc_attrs = (map (fn(cat,tag) => ((cat,@{here}),tag)) S) @ 
-                                      (("formal_results",@{here}),"([]::thm list)")::doc_attrs
-   in  fn margs => fn thy =>
-          Monitor_Command_Parser.gen_enriched_document_cmd {inline=true} 
-                                    (transform_cid thy ncid) transform_attr margs thy 
-   end;
-
-fun enriched_document_cmd_exp ncid (S: (string * string) list) =
-   (* expands ncid into supertype-check. *)
-   let fun transform_attr attrs = (map (fn(cat,tag) => ((cat,@{here}),tag)) S) @ attrs
-   in  fn margs => fn thy =>
-         Monitor_Command_Parser.gen_enriched_document_cmd {inline=true} (transform_cid thy ncid)
-                                                                            transform_attr margs thy
-   end;
-end (* local *)
-
-
-fun heading_command (name, pos) descr level =
-  Monitor_Command_Parser.document_command (name, pos) descr
-    {markdown = false, body = true} (enriched_text_element_cmd level);
-
-val _ = heading_command \<^command_keyword>\<open>title*\<close> "section heading" NONE;
-val _ = heading_command \<^command_keyword>\<open>subtitle*\<close> "section heading" NONE;
-val _ = heading_command \<^command_keyword>\<open>chapter*\<close> "section heading" (SOME (SOME 0));
-val _ = heading_command \<^command_keyword>\<open>section*\<close> "section heading" (SOME (SOME 1));
-val _ = heading_command \<^command_keyword>\<open>subsection*\<close> "subsection heading" (SOME (SOME 2));
-val _ = heading_command \<^command_keyword>\<open>subsubsection*\<close> "subsubsection heading" (SOME (SOME 3));
-val _ = heading_command \<^command_keyword>\<open>paragraph*\<close> "paragraph heading" (SOME (SOME 4));
-val _ = heading_command \<^command_keyword>\<open>subparagraph*\<close> "subparagraph heading" (SOME (SOME 5));
-
-end 
-end
-\<close>
-
-section\<open> Library of Standard Text Ontology \<close>
-
-datatype placement = pl_h  | (*here*) 
-                     pl_t  | (*top*)
-                     pl_b  | (*bottom*)
-                     pl_ht | (*here ->  top*) 
-                     pl_hb   (*here ->  bottom*)
-
-ML\<open>(Symtab.defined (#docclass_tab(DOF_core.get_data_global @{theory}))) "side_by_side_figure"\<close>
-
-print_doc_classes
-
-
-doc_class figure   = 
-   relative_width   :: "int"  (* percent of textwidth *)    
-   src              :: "string"
-   placement        :: placement  
-   spawn_columns    :: bool <= True 
-
-doc_class figure2   =  figure +
-   caption          :: string
-
-
-doc_class side_by_side_figure = figure +
-   anchor           :: "string"
-   caption          :: "string"
-   relative_width2  :: "int"  (* percent of textwidth *)    
-   src2             :: "string"
-   anchor2          :: "string"
-   caption2         :: "string"
-
-print_doc_classes
-
-doc_class figure_group = 
-   (*  trace :: "doc_class rexp list" <= "[]" automatically generated since monitor clause *)
-   caption          :: "string"
-   rejects             figure_group   (* this forbids recursive figure-groups not supported
-                                        by the current LaTeX style-file. *)
-   accepts             "\<lbrace>figure\<rbrace>\<^sup>+"
-
-print_doc_classes
-
-
-
-section\<open>Layout Trimming Commands (with syntactic checks)\<close>
-
-ML\<open> 
-local
-
-val scan_cm = Scan.ahead (Basic_Symbol_Pos.$$$ "c" |-- Basic_Symbol_Pos.$$$ "m" ) ;
-val scan_pt = Scan.ahead (Basic_Symbol_Pos.$$$ "p" |-- Basic_Symbol_Pos.$$$ "t" ) ;
-val scan_blank = Scan.repeat (   Basic_Symbol_Pos.$$$ " "
-                              || Basic_Symbol_Pos.$$$ "\t" 
-                              || Basic_Symbol_Pos.$$$ "\n");
-
-in
-
-val scan_latex_measure = (scan_blank
-                          |-- Scan.option (Basic_Symbol_Pos.$$$ "-")
-                          |-- Symbol_Pos.scan_nat 
-                          |-- (Scan.option ((Basic_Symbol_Pos.$$$ ".") |-- Symbol_Pos.scan_nat))
-                          |-- scan_blank
-                          |-- (scan_cm || scan_pt)
-                          |-- scan_blank
-                         ) ;
-           
-fun check_latex_measure _ src  = 
-         let val _ = ((Scan.catch scan_latex_measure (Symbol_Pos.explode(Input.source_content src)))
-                     handle Fail _ => error ("syntax error in LaTeX measure") )
-         in () end
-
-val parse_latex_measure = Parse.embedded_input >> (fn src => (check_latex_measure () (* dummy arg *) src; 
-                                       (fst o Input.source_content) src )  )
-
-end\<close>
-
-
-
-setup\<open> DOF_lib.define_macro \<^binding>\<open>vs\<close>  "\\vspace{" "}" (check_latex_measure) \<close> 
-setup\<open> DOF_lib.define_macro \<^binding>\<open>hs\<close>  "\\hspace{" "}" (check_latex_measure) \<close> 
-
-(*<*)
-
-text\<open>Tests: \<^vs>\<open>-0.14cm\<close>\<close>
-
-ML\<open> check_latex_measure @{context} (Input.string "-0.14 cm") \<close>
-define_macro* vs2 \<rightleftharpoons> \<open>\vspace{\<close> _ \<open>}\<close> (check_latex_measure) (* checkers NYI on Isar-level *)
-define_macro* hs2 \<rightleftharpoons> \<open>\hspace{\<close> _ \<open>}\<close> (* works fine without checker.*)
-
-(*>*)
-
-subsection\<open>Figures\<close>
-
-ML\<open>open Args\<close>
-
-ML\<open>
-(* *********************************************************************** *)
-(* Ontological Macro Command Support                                       *)
-(* *********************************************************************** *)
-
-val _ = Onto_Macros.heading_command \<^command_keyword>\<open>figure*\<close> "figure" NONE;
-val _ = Onto_Macros.heading_command \<^command_keyword>\<open>side_by_side_figure*\<close> "multiple figures" NONE;
-\<close>
-
-(*<*)
-(*
-ML\<open>ML_Context.expression\<close>
-fun setup source =
-  ML_Context.expression (Input.pos_of source)
-    (ML_Lex.read "Theory.setup (" @ ML_Lex.read_source source @ ML_Lex.read ")")
-  |> Context.theory_map;
-setup\<open>\<close>
-
-*)
-(*>*)
-
-subsubsection\<open>Figure Content\<close>
-text\<open>The intermediate development goal is to separate the ontological, top-level construct 
-\<open>figure*\<close>, which will remain a referentiable, ontological document unit, from the more versatile
-\<^emph>\<open>import\<close> of a figure. The hope is that this opens the way for more orthogonality and
-abstraction from the LaTeX engine.
-\<close>
-
-ML\<open>
-
-type fig_content =   {relative_width  : int, (* percent of textwidth, default 100 *)
-                      scale           : int, (* percent, default 100 *)
-                      caption         : Input.source (* default empty *)}
-
-val mt_fig_content = {relative_width  = 100,
-                      scale           = 100,    
-                      caption         = Input.empty }: fig_content
-
-(* doof wie 100 m feldweg. *)
-fun upd_relative_width key {relative_width,scale,caption } : fig_content = 
-            {relative_width = key,scale = scale,caption = caption}: fig_content
-
-fun upd_scale key  {relative_width,scale,caption } : fig_content = 
-            {relative_width = relative_width,scale = key,caption = caption}: fig_content
-
-fun upd_caption key {relative_width,scale,caption} : fig_content = 
-            {relative_width = relative_width,scale = scale,caption= key}: fig_content
-
-
-val widthN     = "width"
-val scaleN     = "scale" 
-val captionN   = "caption";
-
-fun fig_content_modes (ctxt, toks) = 
-       let val (y, toks') = ((((Scan.optional 
-                      (Args.parens 
-                         (Parse.list1
-                           (   (Args.$$$ widthN |-- Args.$$$ "=" -- Parse.int
-                                >> (fn (_, k) => upd_relative_width k))   
-                            || (Args.$$$ scaleN |-- Args.$$$ "=" -- Parse.int
-                                >> (fn (_, k) => upd_scale k))    
-                            || (Args.$$$ captionN |-- Args.$$$ "=" -- Parse.document_source
-                                >> (fn (_, k) => upd_caption k))    
-                      ))) [K mt_fig_content]) 
-                      : (fig_content -> fig_content) list parser)
-                      >> (foldl1 (op #>)))
-                      : (fig_content -> fig_content) parser)
-                      (toks)
-        in (y, (ctxt, toks')) end
-
-fun document_antiq (check: Proof.context -> Path.T option -> Input.source -> Path.T) =
-  Args.context -- Scan.lift Parse.path_input >> (fn (ctxt, source) =>
-   (check ctxt NONE source;
-    Latex.string (Latex.output_ascii_breakable "/" (Input.string_of source))
-    |> Latex.macro "isatt"));
-
-
-fun fig_content_antiquotation name scan =
-  (Document_Output.antiquotation_raw_embedded name 
-    (scan : ((fig_content -> fig_content) * Input.source) context_parser)
-    (fn ctxt => 
-      (fn (cfg_trans,file:Input.source) =>
-          let val {relative_width,scale,caption} = cfg_trans mt_fig_content
-              val _      = if relative_width < 0 orelse scale<0 then error("negative parameter.") 
-                                                                else ()
-              val wdth_s = if relative_width = 100 then ""
-                           else "width="^Real.toString((Real.fromInt relative_width) 
-                                              / (Real.fromInt 100))^"\textwidth" 
-              val scale_s= if scale = 100 then ""
-                           else "scale="^Real.toString((Real.fromInt scale) / (Real.fromInt 100))
-              val arg    = enclose "[" "]" (commas [wdth_s,scale_s])
-              val lab    = Document_Output.output_document ctxt {markdown = false} caption
-              val path   = Resources.check_file ctxt NONE file
-              val _      = writeln("file "^Path.file_name path)  
-                  (* ToDo: must be declared source of type png or jpeg or pdf, ... *)
-          in  file 
-              |> (Latex.string o Input.string_of)
-              |> (XML.enclose ("\\includegraphics"^arg^"{") "}")
-              |> (fn X => X @ Latex.macro "capture" lab)
-          end
-      )
-    ));
-
-val _ = fig_content_antiquotation 
-        : binding 
-         -> ((fig_content -> fig_content) * Input.source) context_parser 
-         -> theory -> theory
-
-val _ = Theory.setup 
-           (   fig_content_antiquotation \<^binding>\<open>fig_content\<close> 
-                                         (fig_content_modes -- Scan.lift(Parse.path_input)))
-
-\<close>
-
-subsection\<open>Tables\<close>
-(* TODO ! ! ! *)
-(* dito the future monitor: table - block *)
-(* some studies *)
-
-text\<open>Tables are (sub) document-elements represented inside the documentation antiquotation
-language. The used technology is similar to the existing railroad-diagram support 
-(cf. \<^url>\<open>https://isabelle.in.tum.de/doc/isar-ref.pdf\<close>, Sec. 4.5). 
-
-However, tables are not directly based on the idiosyncrasies of Knuth-based language design ---
-
-However, tables come with a more abstract structure model than conventional typesetting in the 
-LaTeX tradition. It is based of the following principles:
-  \<^item> The core unit of a table is a \<^emph>\<open>cell\<close> having a \<^emph>\<open>configuration\<close>, i.e. a
-    number of attributes specifying its width, height, borderline, etc. 
-    A cell may be \<^emph>\<open>elementary\<close>, i.e. containing structured text or \<^emph>\<open>compound\<close>, 
-    i.e. containing a sub-table.
-  \<^item> A \<^emph>\<open>table\<close> contains either a list of \<^emph>\<open>rows\<close> or a list of \<^emph>\<open>columns\<close>, which are both
-    lists of cells.
-  \<^item> The tables, rows and columns posses own configurations.
-  \<^item> Concerning the layout, \<^emph>\<open>propagation\<close>  laws of configurations control that 
-    information flows top-down from tables to rows or columns, from rows/columns to cells,
-    from left to right within rows and from top to bottom in columns; propagation produces
-    the desired presentation effect of tables that cells appear somewhat uniform in it. 
-  \<^item> Since rows are lists of cells, configurations are also a list of attributes.
-    Attributes of the same kind may appear repeatedly. If the sub-list of attributes 
-    of the same kind is shorter than the list of cells it is referring to, than
-    the last element in this sub-list is duplicated as many times as necessary. This feature
-    of configuration propagation is called \<^emph>\<open>filling\<close>.
-  \<^item> Lists of rows and lists of cells consists of the same number of cells.
-  \<^item> Since propagation and filling induce a congruence relation on table trees, a normalisation
-    process is a necessary pre-requisite for the compilation to LaTeX.
-\<close>
-
-ML\<open>
-local
-
-fun mk_line st1 st2 [a] =  [a @ Latex.string st2]
-   |mk_line st1 st2 (a::S) = [a @ Latex.string st1] @ mk_line st1 st2 S;
-
-(* tab attributes for global setup *)
-
-type cell_config =   {cell_placing    : string list, 
-                      cell_height     : string list,
-                      cell_width      : string list,
-                      cell_bgnd_color : string list,
-                      cell_line_color : string list,
-                      cell_line_width : string list}
-
-val mt_cell_config = {cell_placing   = [],
-                      cell_height    = [],    
-                      cell_width     = [],    
-                      cell_bgnd_color= [], 
-                      cell_line_color= [], 
-                      cell_line_width= [] }: cell_config
-
-(* doof wie 100 m feldweg. *)
-fun upd_cell_placing key 
-            {cell_placing,cell_height,cell_width, cell_bgnd_color,   
-             cell_line_color,cell_line_width} : cell_config = 
-            {cell_placing   = cell_placing @ [key],  cell_height    = cell_height,    
-             cell_width     = cell_width,            cell_bgnd_color= cell_bgnd_color, 
-             cell_line_color= cell_line_color,       cell_line_width= cell_line_width } 
-            : cell_config
-
-fun upd_cell_height num 
-            {cell_placing,cell_height,cell_width, cell_bgnd_color,   
-             cell_line_color,cell_line_width} : cell_config = 
-            {cell_placing   = cell_placing ,  cell_height    = cell_height @ [num],    
-             cell_width     = cell_width,     cell_bgnd_color= cell_bgnd_color, 
-             cell_line_color= cell_line_color,cell_line_width= cell_line_width } 
-            : cell_config
-
-fun upd_cell_width num 
-            {cell_placing,cell_height,cell_width, cell_bgnd_color,   
-             cell_line_color,cell_line_width} : cell_config = 
-            {cell_placing   = cell_placing ,   cell_height    = cell_height,    
-             cell_width     = cell_width@[num],cell_bgnd_color= cell_bgnd_color, 
-             cell_line_color= cell_line_color, cell_line_width= cell_line_width } 
-            : cell_config
-
-fun upd_cell_bgnd_color str 
-            {cell_placing,cell_height,cell_width, cell_bgnd_color,   
-             cell_line_color,cell_line_width} : cell_config = 
-            {cell_placing   = cell_placing ,   cell_height    = cell_height,    
-             cell_width     = cell_width,      cell_bgnd_color= cell_bgnd_color@[str], 
-             cell_line_color= cell_line_color, cell_line_width= cell_line_width } 
-            : cell_config
-
-fun upd_cell_line_color str 
-            {cell_placing,cell_height,cell_width, cell_bgnd_color,   
-             cell_line_color,cell_line_width} : cell_config = 
-            {cell_placing   = cell_placing ,         cell_height    = cell_height,    
-             cell_width     = cell_width,            cell_bgnd_color= cell_bgnd_color, 
-             cell_line_color= cell_line_color@[str], cell_line_width= cell_line_width } 
-            : cell_config
-
-fun upd_cell_line_width num 
-            {cell_placing,cell_height,cell_width, cell_bgnd_color,   
-             cell_line_color,cell_line_width} : cell_config = 
-            {cell_placing    = cell_placing ,   cell_height     = cell_height,    
-             cell_width      = cell_width,      cell_bgnd_color = cell_bgnd_color, 
-             cell_line_color = cell_line_color, cell_line_width = cell_line_width@[num] } 
-            : cell_config
-
-(*global default configs *)
-val (tab_cell_placing, tab_cell_placing_setup)
-     = Attrib.config_string \<^binding>\<open>tab_cell_placing\<close> (K "center");
-val (tab_cell_height, tab_cell_height_setup)
-     = Attrib.config_string \<^binding>\<open>tab_cell_height\<close> (K "0.0cm");
-val (tab_cell_width, tab_cell_width_setup)
-     = Attrib.config_string \<^binding>\<open>tab_cell_width\<close> (K "0.0cm");
-val (tab_cell_bgnd_color, tab_cell_bgnd_color_setup)
-     = Attrib.config_string \<^binding>\<open>tab_cell_bgnd_height\<close> (K "white");
-val (tab_cell_line_color, tab_cell_line_color_setup)
-     = Attrib.config_string \<^binding>\<open>tab_cell_line_color\<close> (K "black");
-val (tab_cell_line_width, tab_cell_line_width_setup)
-     = Attrib.config_string \<^binding>\<open>tab_cell_line_height\<close> (K "0.0cm");
-
-fun default_cell_config ctxt = {cell_placing    = [Config.get ctxt tab_cell_placing],
-                                cell_height     = [Config.get ctxt tab_cell_height],    
-                                cell_width      = [Config.get ctxt tab_cell_width],    
-                                cell_bgnd_color = [Config.get ctxt tab_cell_bgnd_color], 
-                                cell_line_color = [Config.get ctxt tab_cell_line_color], 
-                                cell_line_width = [Config.get ctxt tab_cell_line_width]}
-                              : cell_config
-
-
-val _ = Theory.setup(   tab_cell_placing_setup
-                     #> tab_cell_height_setup
-                     #> tab_cell_width_setup
-                     #> tab_cell_bgnd_color_setup
-                     #> tab_cell_line_color_setup
-                     #> tab_cell_line_width_setup
-                    )
-
-
-(*syntax for local tab specifier *)
-val cell_placingN    = "cell_placing"
-val cell_heightN     = "cell_height" 
-val cell_widthN      = "cell_width"
-val cell_bgnd_colorN = "cell_bgnd_color" 
-val cell_line_colorN = "cell_line_color"
-val cell_line_widthN = "cell_line_width" 
-
-val placing_scan = Args.$$$ "left" || Args.$$$ "center" || Args.$$$ "right" 
-
-val color_scan   =   Args.$$$ "none" || Args.$$$ "red" || Args.$$$ "green"                   
-                  || Args.$$$ "blue" || Args.$$$ "black"
-
-(*
-
-val _ = Scan.lift 
-
-fun lift scan (st, xs) =
-  let val (y, xs') = scan xs
-  in (y, (st, xs')) end;
-
-*)
-
-fun tabitem_modes (ctxt, toks) = 
-       let val (y, toks') = ((((Scan.optional 
-                      (Args.parens 
-                         (Parse.list1
-                           (   (Args.$$$ cell_placingN |-- Args.$$$ "=" -- placing_scan
-                                >> (fn (_, k) => upd_cell_placing k))   
-                            || (Args.$$$ cell_heightN |-- Args.$$$ "=" -- parse_latex_measure
-                                >> (fn (_, k) => upd_cell_height k))    
-                            || (Args.$$$ cell_widthN |-- Args.$$$ "=" -- parse_latex_measure
-                                >> (fn (_, k) => upd_cell_width k))    
-                            || (Args.$$$ cell_bgnd_colorN |-- Args.$$$ "=" -- color_scan
-                                >> (fn (_, k) => upd_cell_bgnd_color k))
-                            || (Args.$$$ cell_line_colorN |-- Args.$$$ "=" -- color_scan
-                                >> (fn (_, k) => upd_cell_line_color k))
-                            || (Args.$$$ cell_line_widthN |-- Args.$$$ "=" -- parse_latex_measure
-                                >> (fn (_, k) => upd_cell_line_width k))
-                      ))) [K (default_cell_config (Context.the_proof ctxt))]) 
-                      : (cell_config -> cell_config) list parser)
-                      >> (foldl1 (op #>)))
-                      : (cell_config -> cell_config) parser)
-                      (toks)
-        in (y, (ctxt, toks')) end
-
-
-datatype table_tree  = mk_tab    of cell_config * cell_group
-                     | mk_cell   of cell_config * Input.source
-   and   cell_group  = mk_row    of cell_config * table_tree list
-                     | mk_column of cell_config * table_tree list
-                                             
-
-
-val tab_config_parser =  tabitem_modes : ((cell_config -> cell_config) ) context_parser
-val table_parser =  tab_config_parser -- Scan.repeat1(Scan.repeat1(Scan.lift Args.cartouche_input))
-
-fun table_antiquotation name scan =
-  Document_Output.antiquotation_raw_embedded name 
-    scan
-    (fn ctxt => 
-      (fn (cfg_trans,content:Input.source list list) =>
-          let val cfg = cfg_trans mt_cell_config
-              val _ = writeln ("XXX"^ @{make_string} cfg)
-              fun check _ = ()  (* ToDo *)
-              val _  = check content
-          in  content 
-              |> (map(map (Document_Output.output_document ctxt {markdown = false})
-                  #> mk_line "&" "\\\\"
-                  #> List.concat )
-                  #> List.concat)
-              |> XML.enclose "\\table[allerhandquatsch]{" "}"
-          end
-      )
-    );
-
-fun cell_antiquotation name scan =
-    Document_Output.antiquotation_raw_embedded name 
-    scan
-    (fn ctxt => 
-      (fn (cfg_trans,content:Input.source) => 
-          let val cfg = cfg_trans mt_cell_config
-              val _ = writeln ("XXX"^ @{make_string} cfg) 
-          in  content |> Document_Output.output_document ctxt {markdown = false}
-          end
-      )
-    )
-
-fun row_antiquotation name scan =
-    Document_Output.antiquotation_raw_embedded name 
-    scan
-    (fn ctxt => 
-      (fn (cfg_trans,content:Input.source list) => 
-          let val cfg = cfg_trans mt_cell_config
-              val _ = writeln ("XXX"^ @{make_string} cfg) 
-          in  content |> (map (Document_Output.output_document ctxt {markdown = false})
-                          #> List.concat)
-          end
-      )
-    )
-
-fun column_antiquotation name scan =
-    Document_Output.antiquotation_raw_embedded name 
-    scan
-    (fn ctxt => 
-      (fn (cfg_trans,content:Input.source list) => 
-          let val cfg = cfg_trans mt_cell_config
-              val _ = writeln ("XXX"^ @{make_string} cfg) 
-          in  content |> (map (Document_Output.output_document ctxt {markdown = false})
-                          #> List.concat)
-          end
-      )
-    )
-
-in
-
-val _ = Theory.setup 
-           (   table_antiquotation  \<^binding>\<open>table_inline\<close> 
-                                    table_parser
-            #> table_antiquotation  \<^binding>\<open>subtab\<close> table_parser
-            #> cell_antiquotation   \<^binding>\<open>cell\<close>   
-                                    (tab_config_parser--Scan.lift Args.cartouche_input)
-            #> row_antiquotation    \<^binding>\<open>row\<close>  
-                                    (tab_config_parser--Scan.repeat1(Scan.lift Args.cartouche_input))  
-            #> column_antiquotation \<^binding>\<open>column\<close> 
-                                    (tab_config_parser--Scan.repeat1(Scan.lift Args.cartouche_input))
-           );
-
-end
-\<close>
-
-text\<open> @{file "../ROOT"} \<close>
-define_shortcut* clearpage \<rightleftharpoons> \<open>\clearpage{}\<close>
-                 hf \<rightleftharpoons> \<open>\hfill\<close> 
-                 br \<rightleftharpoons> \<open>\break\<close> 
-
-
-declare[[tab_cell_placing="left",tab_cell_height="18.0cm"]]
+doc_class concept = 
+    tag        :: "string"   <= "''''"
+    properties :: "thm list" <= "[]"
 
 section\<open>Tests\<close>
-(*<*)
-
-text\<open> @{fig_content   [display] (scale = 80, width=80, caption=\<open>this is \<^term>\<open>\<sigma>\<^sub>i+2\<close> \<dots>\<close>) 
-                      \<open>../../examples/scholarly_paper/2018-cicm-isabelle_dof-applications/document/figures/isabelle-architecture.pdf\<close>}\<close>
-text\<open> @{table_inline  [display] (cell_placing = center,cell_height =\<open>12.0cm\<close>,
-                                 cell_height =\<open>13pt\<close>,  cell_width = \<open>12.0cm\<close>,
-                                 cell_bgnd_color=black,cell_line_color=red,cell_line_width=\<open>12.0cm\<close>)
-          \<open>\<open>\<^cell>\<open>dfg\<close> \<^col>\<open>dfg\<close> \<^row>\<open>dfg\<close> @{cell (cell_height =\<open>12.0cm\<close>) \<open>abracadabra\<close>}\<close>
-           \<open>\<open>1\<close>  \<open>2\<close>  \<open>3\<sigma>\<close>\<close>
-          \<close>}
-      \<^cell>\<open>dfg\<close>  @{row \<open>is technical\<close> \<open> \<open>\<sigma> * a\<^sub>4\<close> \<close>}\<close>
-(*>*)
 
 ML\<open>@{term "side_by_side_figure"};
-   @{typ "doc_class rexp"}; 
-   DOF_core.SPY;
-
+@{typ "doc_class rexp"}; 
+DOF_core.SPY;
 \<close>
 
-text\<open>@{term_ \<open>3 + 4::int\<close>} @{value_ \<open>3 + 4::int\<close>} \<close>
+
 end

src/DOF/RegExp.thy

@@ -0,0 +1,93 @@
+theory RegExp
+imports "Functional-Automata.Execute"
+begin
+
+term Atom
+value "Star (Times(Plus (Atom(CHR ''a'')) (Atom(CHR ''b''))) (Atom(CHR ''c'')))"
+
+notation Star  ("\<lbrace>(_)\<rbrace>\<^sup>*" [0]100)
+notation Plus  (infixr "||" 55)
+notation Times (infixr "~~" 60)
+notation Atom  ("\<lfloor>_\<rfloor>" 65)
+
+(*
+datatype 'a rexp = Empty                         ("<>")
+                 | Atom 'a                       ("\<lfloor>_\<rfloor>" 65)
+                 | Alt  "('a rexp)" "('a rexp)"  (infixr "||" 55)
+                 | Conc "('a rexp)" "('a rexp)"  (infixr "~~" 60)
+                 | Star "('a rexp)"              ("\<lbrace>(_)\<rbrace>\<^sup>*" [0]100)          
+*)
+
+definition rep1 :: "'a rexp \<Rightarrow> 'a rexp" ("\<lbrace>(_)\<rbrace>\<^sup>+")
+  where "\<lbrace>A\<rbrace>\<^sup>+ \<equiv>  A ~~ \<lbrace>A\<rbrace>\<^sup>*"
+    
+definition opt :: "'a rexp \<Rightarrow> 'a rexp" ("\<lbrakk>(_)\<rbrakk>")
+   where "\<lbrakk>A\<rbrakk> \<equiv>  A || One"
+                   
+value "Star (Conc(Alt (Atom(CHR ''a'')) (Atom(CHR ''b''))) (Atom(CHR ''c'')))"
+text\<open>or better equivalently:\<close>
+value "\<lbrace>(\<lfloor>CHR ''a''\<rfloor> || \<lfloor>CHR ''b''\<rfloor>) ~~ \<lfloor>CHR ''c''\<rfloor>\<rbrace>\<^sup>*"
+
+section\<open>Definition of a semantic function: the ``language'' of the regular expression\<close>
+text\<open> This is just a reminder - already defined in @{theory Regular_Exp} as @{term lang}.\<close>
+
+text\<open>In the following, we give a semantics for our regular expressions, which so far have
+just been a term language (i.e. abstract syntax). The semantics is a ``denotational semantics'',
+i.e. we give a direct meaning for regular expressions in some universe of ``denotations''. 
+
+This universe of denotations is in our concrete case:\<close>
+
+definition enabled :: "('a,'\<sigma> set)da  \<Rightarrow> '\<sigma> set \<Rightarrow> 'a list \<Rightarrow>  'a list" 
+  where   "enabled A \<sigma> = filter (\<lambda>x. next A x \<sigma> \<noteq> {}) "
+
+text\<open>Now the denotational semantics for regular expression can be defined on a post-card:\<close>
+
+fun              L :: "'a rexp => 'a lang"
+  where L_Emp :   "L Zero        = {}"
+       |L_One:    "L One         = {[]}"
+       |L_Atom:   "L (\<lfloor>a\<rfloor>)       = {[a]}"
+       |L_Un:     "L (el || er)  = (L el) \<union> (L er)"
+       |L_Conc:   "L (el ~~ er)  = {xs@ys | xs ys. xs \<in> L el \<and> ys \<in> L er}"
+       |L_Star:   "L (Star e)    = Regular_Set.star(L e)"
+
+
+text\<open>A more useful definition is the \<close>
+fun       L\<^sub>s\<^sub>u\<^sub>b :: "'a::order rexp => 'a lang"
+  where   L\<^sub>s\<^sub>u\<^sub>b_Emp:    "L\<^sub>s\<^sub>u\<^sub>b Zero        = {}"
+         |L\<^sub>s\<^sub>u\<^sub>b_One:    "L\<^sub>s\<^sub>u\<^sub>b One         = {[]}"
+         |L\<^sub>s\<^sub>u\<^sub>b_Atom:   "L\<^sub>s\<^sub>u\<^sub>b (\<lfloor>a\<rfloor>)       = {z . \<forall>x. x \<le> a \<and> z=[x]}"
+         |L\<^sub>s\<^sub>u\<^sub>b_Un:     "L\<^sub>s\<^sub>u\<^sub>b (el || er)  = (L\<^sub>s\<^sub>u\<^sub>b el) \<union> (L\<^sub>s\<^sub>u\<^sub>b er)"
+         |L\<^sub>s\<^sub>u\<^sub>b_Conc:   "L\<^sub>s\<^sub>u\<^sub>b (el ~~ er)  = {xs@ys | xs ys. xs \<in> L\<^sub>s\<^sub>u\<^sub>b el \<and> ys \<in> L\<^sub>s\<^sub>u\<^sub>b er}"
+         |L\<^sub>s\<^sub>u\<^sub>b_Star:   "L\<^sub>s\<^sub>u\<^sub>b (Star e)    = Regular_Set.star(L\<^sub>s\<^sub>u\<^sub>b e)"
+
+
+definition XX where "XX = (rexp2na example_expression)"
+definition YY where "YY = na2da(rexp2na example_expression)"
+(* reminder from execute *)
+value "NA.accepts (rexp2na example_expression) [0,1,1,0,0,1]"
+value "DA.accepts (na2da (rexp2na example_expression)) [0,1,1,0,0,1]"
+
+definition zero where "zero = (0::nat)"
+definition one where "one = (1::nat)"
+
+typ "'a set"
+
+
+export_code  zero one Suc Int.nat  nat_of_integer int_of_integer  
+             Zero One     Atom     Plus  Times  Star      
+             rexp2na      na2da    enabled
+             NA.accepts   DA.accepts  
+
+             example_expression
+
+             in SML
+                                 
+      
+      module_name RegExpChecker file "RegExpChecker.sml"
+
+SML_file "RegExpChecker.sml"
+
+no_notation Atom ("\<lfloor>_\<rfloor>")  
+
+
+end

src/DOF/RegExpChecker.sml

@@ -0,0 +1,339 @@
+structure RegExpChecker : sig
+  type 'a equal
+  type num
+  type int
+  datatype nat = Zero_nat | Suc of nat
+  type 'a set
+  datatype 'a rexp = Zero | Onea | Atom of 'a | Plus of 'a rexp * 'a rexp |
+    Times of 'a rexp * 'a rexp | Star of 'a rexp
+  val nat : int -> nat
+  val accepts : 'a * (('b -> 'a -> 'a) * ('a -> bool)) -> 'b list -> bool
+  val acceptsa :
+    'a equal -> 'a * (('b -> 'a -> 'a set) * ('a -> bool)) -> 'b list -> bool
+  val na2da :
+    'a equal ->
+      'a * (('b -> 'a -> 'a set) * ('a -> bool)) ->
+        'a set * (('b -> 'a set -> 'a set) * ('a set -> bool))
+  val rexp2na :
+    'a equal ->
+      'a rexp ->
+        bool list * (('a -> bool list -> (bool list) set) * (bool list -> bool))
+  val one : nat
+  val zero : nat
+  val enabled :
+    'a set * (('b -> 'a set -> 'a set) * ('a set -> bool)) ->
+      'a set -> 'b list -> 'b list
+  val example_expression : nat rexp
+  val nat_of_integer : IntInf.int -> nat
+  val int_of_integer : IntInf.int -> int
+end = struct
+
+fun equal_boola p true = p
+  | equal_boola p false = not p
+  | equal_boola true p = p
+  | equal_boola false p = not p;
+
+type 'a equal = {equal : 'a -> 'a -> bool};
+val equal = #equal : 'a equal -> 'a -> 'a -> bool;
+
+val equal_bool = {equal = equal_boola} : bool equal;
+
+fun eq A_ a b = equal A_ a b;
+
+fun equal_lista A_ [] (x21 :: x22) = false
+  | equal_lista A_ (x21 :: x22) [] = false
+  | equal_lista A_ (x21 :: x22) (y21 :: y22) =
+    eq A_ x21 y21 andalso equal_lista A_ x22 y22
+  | equal_lista A_ [] [] = true;
+
+fun equal_list A_ = {equal = equal_lista A_} : ('a list) equal;
+
+datatype num = One | Bit0 of num | Bit1 of num;
+
+datatype int = Zero_int | Pos of num | Neg of num;
+
+datatype nat = Zero_nat | Suc of nat;
+
+datatype 'a set = Set of 'a list | Coset of 'a list;
+
+datatype 'a rexp = Zero | Onea | Atom of 'a | Plus of 'a rexp * 'a rexp |
+  Times of 'a rexp * 'a rexp | Star of 'a rexp;
+
+fun dup (Neg n) = Neg (Bit0 n)
+  | dup (Pos n) = Pos (Bit0 n)
+  | dup Zero_int = Zero_int;
+
+fun plus_nat (Suc m) n = plus_nat m (Suc n)
+  | plus_nat Zero_nat n = n;
+
+val one_nat : nat = Suc Zero_nat;
+
+fun nat_of_num (Bit1 n) = let
+                            val m = nat_of_num n;
+                          in
+                            Suc (plus_nat m m)
+                          end
+  | nat_of_num (Bit0 n) = let
+                            val m = nat_of_num n;
+                          in
+                            plus_nat m m
+                          end
+  | nat_of_num One = one_nat;
+
+fun nat (Pos k) = nat_of_num k
+  | nat Zero_int = Zero_nat
+  | nat (Neg k) = Zero_nat;
+
+fun uminus_int (Neg m) = Pos m
+  | uminus_int (Pos m) = Neg m
+  | uminus_int Zero_int = Zero_int;
+
+fun plus_num (Bit1 m) (Bit1 n) = Bit0 (plus_num (plus_num m n) One)
+  | plus_num (Bit1 m) (Bit0 n) = Bit1 (plus_num m n)
+  | plus_num (Bit1 m) One = Bit0 (plus_num m One)
+  | plus_num (Bit0 m) (Bit1 n) = Bit1 (plus_num m n)
+  | plus_num (Bit0 m) (Bit0 n) = Bit0 (plus_num m n)
+  | plus_num (Bit0 m) One = Bit1 m
+  | plus_num One (Bit1 n) = Bit0 (plus_num n One)
+  | plus_num One (Bit0 n) = Bit1 n
+  | plus_num One One = Bit0 One;
+
+val one_int : int = Pos One;
+
+fun bitM One = One
+  | bitM (Bit0 n) = Bit1 (bitM n)
+  | bitM (Bit1 n) = Bit1 (Bit0 n);
+
+fun sub (Bit0 m) (Bit1 n) = minus_int (dup (sub m n)) one_int
+  | sub (Bit1 m) (Bit0 n) = plus_int (dup (sub m n)) one_int
+  | sub (Bit1 m) (Bit1 n) = dup (sub m n)
+  | sub (Bit0 m) (Bit0 n) = dup (sub m n)
+  | sub One (Bit1 n) = Neg (Bit0 n)
+  | sub One (Bit0 n) = Neg (bitM n)
+  | sub (Bit1 m) One = Pos (Bit0 m)
+  | sub (Bit0 m) One = Pos (bitM m)
+  | sub One One = Zero_int
+and plus_int (Neg m) (Neg n) = Neg (plus_num m n)
+  | plus_int (Neg m) (Pos n) = sub n m
+  | plus_int (Pos m) (Neg n) = sub m n
+  | plus_int (Pos m) (Pos n) = Pos (plus_num m n)
+  | plus_int Zero_int l = l
+  | plus_int k Zero_int = k
+and minus_int (Neg m) (Neg n) = sub n m
+  | minus_int (Neg m) (Pos n) = Neg (plus_num m n)
+  | minus_int (Pos m) (Neg n) = Pos (plus_num m n)
+  | minus_int (Pos m) (Pos n) = sub m n
+  | minus_int Zero_int l = uminus_int l
+  | minus_int k Zero_int = k;
+
+fun list_ex p [] = false
+  | list_ex p (x :: xs) = p x orelse list_ex p xs;
+
+fun bex (Set xs) p = list_ex p xs;
+
+fun snd (x1, x2) = x2;
+
+fun fst (x1, x2) = x1;
+
+fun next a = fst (snd a);
+
+fun foldl f a [] = a
+  | foldl f a (x :: xs) = foldl f (f a x) xs;
+
+fun foldl2 f xs a = foldl (fn aa => fn b => f b aa) a xs;
+
+fun delta a = foldl2 (next a);
+
+fun filter p [] = []
+  | filter p (x :: xs) = (if p x then x :: filter p xs else filter p xs);
+
+fun membera A_ [] y = false
+  | membera A_ (x :: xs) y = eq A_ x y orelse membera A_ xs y;
+
+fun member A_ x (Coset xs) = not (membera A_ xs x)
+  | member A_ x (Set xs) = membera A_ xs x;
+
+fun removeAll A_ x [] = []
+  | removeAll A_ x (y :: xs) =
+    (if eq A_ x y then removeAll A_ x xs else y :: removeAll A_ x xs);
+
+fun inserta A_ x xs = (if membera A_ xs x then xs else x :: xs);
+
+fun insert A_ x (Coset xs) = Coset (removeAll A_ x xs)
+  | insert A_ x (Set xs) = Set (inserta A_ x xs);
+
+fun fold f (x :: xs) s = fold f xs (f x s)
+  | fold f [] s = s;
+
+fun sup_set A_ (Coset xs) a = Coset (filter (fn x => not (member A_ x a)) xs)
+  | sup_set A_ (Set xs) a = fold (insert A_) xs a;
+
+val bot_set : 'a set = Set [];
+
+fun sup_seta A_ (Set xs) = fold (sup_set A_) xs bot_set;
+
+fun map f [] = []
+  | map f (x21 :: x22) = f x21 :: map f x22;
+
+fun image f (Set xs) = Set (map f xs);
+
+fun deltaa A_ a [] p = insert A_ p bot_set
+  | deltaa A_ aa (a :: w) p =
+    sup_seta A_ (image (deltaa A_ aa w) (next aa a p));
+
+fun null [] = true
+  | null (x :: xs) = false;
+
+fun start a = fst a;
+
+fun fin a = snd (snd a);
+
+fun accepts a = (fn w => fin a (delta a w (start a)));
+
+fun acceptsa A_ a w = bex (deltaa A_ a w (start a)) (fin a);
+
+fun or x =
+  (fn (ql, (dl, fl)) => fn (qr, (dr, fr)) =>
+    ([], ((fn a => fn b =>
+            (case b
+              of [] =>
+                sup_set (equal_list equal_bool)
+                  (image (fn aa => true :: aa) (dl a ql))
+                  (image (fn aa => false :: aa) (dr a qr))
+              | true :: s => image (fn aa => true :: aa) (dl a s)
+              | false :: s => image (fn aa => false :: aa) (dr a s))),
+           (fn a =>
+             (case a of [] => fl ql orelse fr qr | true :: s => fl s
+               | false :: s => fr s)))))
+    x;
+
+fun is_empty (Set xs) = null xs;
+
+fun na2da A_ a =
+  (insert A_ (start a) bot_set,
+    ((fn aa => fn q => sup_seta A_ (image (next a aa) q)),
+      (fn q => bex q (fin a))));
+
+fun atom A_ a =
+  ([true],
+    ((fn b => fn s =>
+       (if equal_lista equal_bool s [true] andalso eq A_ b a
+         then insert (equal_list equal_bool) [false] bot_set else bot_set)),
+      (fn s => equal_lista equal_bool s [false])));
+
+fun conc x =
+  (fn (ql, (dl, fl)) => fn (qr, (dr, fr)) =>
+    (true :: ql,
+      ((fn a => fn b =>
+         (case b of [] => bot_set
+           | true :: s =>
+             sup_set (equal_list equal_bool)
+               (image (fn aa => true :: aa) (dl a s))
+               (if fl s then image (fn aa => false :: aa) (dr a qr)
+                 else bot_set)
+           | false :: s => image (fn aa => false :: aa) (dr a s))),
+        (fn a =>
+          (case a of [] => false
+            | left :: s =>
+              left andalso (fl s andalso fr qr) orelse
+                not left andalso fr s)))))
+    x;
+
+fun plus x =
+  (fn (q, (d, f)) =>
+    (q, ((fn a => fn s =>
+           sup_set (equal_list equal_bool) (d a s)
+             (if f s then d a q else bot_set)),
+          f)))
+    x;
+
+val epsilon :
+  bool list * (('a -> bool list -> (bool list) set) * (bool list -> bool))
+  = ([], ((fn _ => fn _ => bot_set), null));
+
+fun star a = or epsilon (plus a);
+
+fun rexp2na A_ Zero = ([], ((fn _ => fn _ => bot_set), (fn _ => false)))
+  | rexp2na A_ Onea = epsilon
+  | rexp2na A_ (Atom a) = atom A_ a
+  | rexp2na A_ (Plus (r, s)) = or (rexp2na A_ r) (rexp2na A_ s)
+  | rexp2na A_ (Times (r, s)) = conc (rexp2na A_ r) (rexp2na A_ s)
+  | rexp2na A_ (Star r) = star (rexp2na A_ r);
+
+fun apsnd f (x, y) = (x, f y);
+
+val one : nat = one_nat;
+
+val zero : nat = Zero_nat;
+
+fun enabled a sigma = filter (fn x => not (is_empty (next a x sigma)));
+
+val example_expression : nat rexp =
+  let
+    val r0 = Atom Zero_nat;
+    val r1 = Atom one_nat;
+  in
+    Times (Star (Plus (Times (r1, r1), r0)), Star (Plus (Times (r0, r0), r1)))
+  end;
+
+fun sgn_integer k =
+  (if ((k : IntInf.int) = (0 : IntInf.int)) then (0 : IntInf.int)
+    else (if IntInf.< (k, (0 : IntInf.int)) then (~1 : IntInf.int)
+           else (1 : IntInf.int)));
+
+fun divmod_integer k l =
+  (if ((k : IntInf.int) = (0 : IntInf.int))
+    then ((0 : IntInf.int), (0 : IntInf.int))
+    else (if ((l : IntInf.int) = (0 : IntInf.int)) then ((0 : IntInf.int), k)
+           else (apsnd o (fn a => fn b => IntInf.* (a, b)) o sgn_integer) l
+                  (if (((sgn_integer k) : IntInf.int) = (sgn_integer l))
+                    then IntInf.divMod (IntInf.abs k, IntInf.abs l)
+                    else let
+                           val (r, s) =
+                             IntInf.divMod (IntInf.abs k, IntInf.abs l);
+                         in
+                           (if ((s : IntInf.int) = (0 : IntInf.int))
+                             then (IntInf.~ r, (0 : IntInf.int))
+                             else (IntInf.- (IntInf.~ r, (1 : IntInf.int)),
+                                    IntInf.- (IntInf.abs l, s)))
+                         end)));
+
+fun nat_of_integer k =
+  (if IntInf.<= (k, (0 : IntInf.int)) then Zero_nat
+    else let
+           val (l, j) = divmod_integer k (2 : IntInf.int);
+           val la = nat_of_integer l;
+           val lb = plus_nat la la;
+         in
+           (if ((j : IntInf.int) = (0 : IntInf.int)) then lb
+             else plus_nat lb one_nat)
+         end);
+
+fun times_num (Bit1 m) (Bit1 n) =
+  Bit1 (plus_num (plus_num m n) (Bit0 (times_num m n)))
+  | times_num (Bit1 m) (Bit0 n) = Bit0 (times_num (Bit1 m) n)
+  | times_num (Bit0 m) (Bit1 n) = Bit0 (times_num m (Bit1 n))
+  | times_num (Bit0 m) (Bit0 n) = Bit0 (Bit0 (times_num m n))
+  | times_num One n = n
+  | times_num m One = m;
+
+fun times_int (Neg m) (Neg n) = Pos (times_num m n)
+  | times_int (Neg m) (Pos n) = Neg (times_num m n)
+  | times_int (Pos m) (Neg n) = Neg (times_num m n)
+  | times_int (Pos m) (Pos n) = Pos (times_num m n)
+  | times_int Zero_int l = Zero_int
+  | times_int k Zero_int = Zero_int;
+
+fun int_of_integer k =
+  (if IntInf.< (k, (0 : IntInf.int))
+    then uminus_int (int_of_integer (IntInf.~ k))
+    else (if ((k : IntInf.int) = (0 : IntInf.int)) then Zero_int
+           else let
+                  val (l, j) = divmod_integer k (2 : IntInf.int);
+                  val la = times_int (Pos (Bit0 One)) (int_of_integer l);
+                in
+                  (if ((j : IntInf.int) = (0 : IntInf.int)) then la
+                    else plus_int la one_int)
+                end));
+
+end; (*struct RegExpChecker*)

src/DOF/RegExpInterface.thy

@@ -1,23 +1,7 @@
-(*************************************************************************
- * 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>The High-Level Interface to the Automata-Library\<close>
 
 theory RegExpInterface
-  imports "Functional-Automata.Execute"
-  keywords
-  "reflect_ML_exports" :: thy_decl
-
+imports "Functional-Automata.Execute"
 begin
 
 
@@ -68,13 +52,13 @@ This universe of denotations is in our concrete case:\<close>
 
 text\<open>Now the denotational semantics for regular expression can be defined on a post-card:\<close>
 
-fun       Lang :: "'a rexp => 'a lang"
-  where   L_Emp :   "Lang Zero        = {}"
-         |L_One:    "Lang One         = {[]}"
-         |L_Atom:   "Lang (\<lfloor>a\<rfloor>)       = {[a]}"
-         |L_Un:     "Lang (el || er)  = (Lang el) \<union> (Lang er)"
-         |L_Conc:   "Lang (el ~~ er)  = {xs@ys | xs ys. xs \<in> Lang el \<and> ys \<in> Lang er}"
-         |L_Star:   "Lang (Star e)    = Regular_Set.star(Lang e)"
+fun       L :: "'a rexp => 'a lang"
+  where   L_Emp :   "L Zero        = {}"
+         |L_One:    "L One         = {[]}"
+         |L_Atom:   "L (\<lfloor>a\<rfloor>)       = {[a]}"
+         |L_Un:     "L (el || er)  = (L el) \<union> (L er)"
+         |L_Conc:   "L (el ~~ er)  = {xs@ys | xs ys. xs \<in> L el \<and> ys \<in> L er}"
+         |L_Star:   "L (Star e)    = Regular_Set.star(L e)"
 
 
 text\<open>A more useful definition is the sub-language - definition\<close>
@@ -93,6 +77,7 @@ definition YY where "YY = na2da(rexp2na example_expression)"
 value "NA.accepts (rexp2na example_expression) [0,1,1,0,0,1]"
 value "DA.accepts (na2da (rexp2na example_expression)) [0,1,1,0,0,1]"
 
+
 section\<open>HOL - Adaptions and Export to SML\<close>
 
 definition enabled :: "('a,'\<sigma> set)da  \<Rightarrow> '\<sigma> set \<Rightarrow> 'a list \<Rightarrow>  'a list" 
@@ -102,57 +87,29 @@ definition enabled :: "('a,'\<sigma> set)da  \<Rightarrow> '\<sigma> set \<Right
 definition zero where "zero = (0::nat)"
 definition one where "one = (1::nat)"
 
-export_code   zero one Suc Int.nat  nat_of_integer int_of_integer  (* for debugging *)
+
+export_code  zero one Suc Int.nat  nat_of_integer int_of_integer  (* for debugging *)
              example_expression                                   (* for debugging *)
 
              Zero One     Atom     Plus  Times  Star              (* regexp abstract syntax *)
 
              rexp2na      na2da    enabled                        (* low-level automata interface *)
              NA.accepts   DA.accepts  
-             in SML   module_name RegExpChecker 
-
-subsection\<open>Infrastructure for Reflecting exported SML code\<close>
-ML\<open>
-  fun reflect_local_ML_exports args trans =  let
-    fun eval_ML_context ctxt = let 
-      fun is_sml_file f = String.isSuffix ".ML" (Path.implode (#path f))
-      val files = (map (Generated_Files.check_files_in (Context.proof_of ctxt)) args) 
-      val ml_files = filter is_sml_file (map #1 (maps Generated_Files.get_files_in files))
-      val ml_content = map (fn f => Syntax.read_input (Bytes.content (#content f))) ml_files
-      fun eval ml_content   = fold (fn sml => (ML_Context.exec 
-                                           (fn () => ML_Context.eval_source ML_Compiler.flags sml))) 
-                                   ml_content 
-    in 
-      (eval ml_content #> Local_Theory.propagate_ml_env) ctxt
-    end
-  in
-    Toplevel.generic_theory eval_ML_context trans
-  end
-
-
-  val files_in_theory =
-    (Parse.underscore >> K [] || Scan.repeat1 Parse.path_binding) --
-      Scan.option (\<^keyword>\<open>(\<close> |-- Parse.!!! (\<^keyword>\<open>in\<close> 
-                     |-- Parse.theory_name --| \<^keyword>\<open>)\<close>));
-
-  val _ =
-    Outer_Syntax.command \<^command_keyword>\<open>reflect_ML_exports\<close> 
-      "evaluate generated Standard ML files"
-      (Parse.and_list1 files_in_theory  >> (fn args => reflect_local_ML_exports args));
-\<close>
-
-
-
-reflect_ML_exports _
-
 
+             in SML  module_name RegExpChecker 
+                     file "RegExpChecker.sml"                     (* writing it to a file *)
+                                                                  
+(* potentially susceptible to race conditions ... *)                                                                 
+SML_file "RegExpChecker.sml"                                      (* reads and eval generated file  
+                                                                     into SML toplevel  *)
+SML_export \<open>structure RegExpChecker = RegExpChecker\<close>              (* copies from SML toplevel into 
+                                                                     Isabelle/ML toplevel *)
 
 section\<open>The Abstract Interface For Monitor Expressions\<close>
 text\<open>Here comes the hic : The reflection of the HOL-Automata module into an SML module 
 with an abstract interface hiding some generation artefacts like the internal states 
 of the deterministic automata ...\<close>
 
-
 ML\<open> 
 
 structure RegExpInterface : sig
@@ -178,7 +135,7 @@ local open RegExpChecker in
 
   type automaton = state * ((Int.int -> state -> state) * (state -> bool))
 
-  val add_atom = fold_aterms (fn Const (c as (_, \<^Type>\<open>rexp _\<close>)) => insert (op=) c | _=> I);
+  val add_atom = fold_aterms (fn Const(c as(_,Type(@{type_name "rexp"},_)))=> insert (op=) c |_=>I);
   fun alphabet termS  =  rev(map fst (fold add_atom termS []));
   fun ext_alphabet env termS  =  
          let val res = rev(map fst (fold add_atom termS [])) @ env;
@@ -187,14 +144,14 @@ local open RegExpChecker in
                      else ()
          in res end;
 
-  fun conv \<^Const_>\<open>Regular_Exp.rexp.Zero _\<close> _ = Zero
-     |conv \<^Const_>\<open>Regular_Exp.rexp.One _\<close> _ = Onea 
-     |conv \<^Const_>\<open>Regular_Exp.rexp.Times _ for X Y\<close> env = Times(conv X env, conv Y env)
-     |conv \<^Const_>\<open>Regular_Exp.rexp.Plus _ for X Y\<close> env = Plus(conv X env, conv Y env)
-     |conv \<^Const_>\<open>Regular_Exp.rexp.Star _ for X\<close> env = Star(conv X env)
-     |conv \<^Const_>\<open>RegExpInterface.opt _ for X\<close> env = Plus(conv X env, Onea)
-     |conv \<^Const_>\<open>RegExpInterface.rep1 _ for X\<close> env = Times(conv X env, Star(conv X env))
-     |conv (Const (s, \<^Type>\<open>rexp _\<close>)) env =
+  fun conv (Const(@{const_name "Regular_Exp.rexp.Zero"},_)) _ = Zero
+     |conv (Const(@{const_name "Regular_Exp.rexp.One"},_)) _ = Onea 
+     |conv (Const(@{const_name "Regular_Exp.rexp.Times"},_) $ X $ Y) env = Times(conv X env, conv Y env)
+     |conv (Const(@{const_name "Regular_Exp.rexp.Plus"},_) $ X $ Y) env = Plus(conv X env, conv Y env)
+     |conv (Const(@{const_name "Regular_Exp.rexp.Star"},_) $ X) env = Star(conv X env)
+     |conv (Const(@{const_name "RegExpInterface.opt"},_) $ X) env = Plus(conv X env, Onea)
+     |conv (Const(@{const_name "RegExpInterface.rep1"},_) $ X) env = Times(conv X env, Star(conv X env))
+     |conv (Const (s, Type(@{type_name "rexp"},_))) env = 
                let val n = find_index (fn x => x = s) env 
                    val _ = if n<0 then error"conversion error of regexp."  else ()
                in  Atom(n) end
@@ -239,4 +196,3 @@ end  (* struct *)
 no_notation Atom ("\<lfloor>_\<rfloor>")  
 
 end
-  

src/DOF/latex/DOF-COL.sty

@@ -6,15 +6,16 @@
 %%   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.
+%%   version 1 of the License, or any later version.
 %%   OR
 %%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
+%%  
+%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
 
 \NeedsTeXFormat{LaTeX2e}\relax
 \ProvidesPackage{DOF-COL}
-  [00/00/0000 Document-Type Support Framework for Isabelle.]
+  [0000/00/00 Unreleased v0.0.0+%
+  Document-Type Support Framework for Isabelle.]
 
 \RequirePackage{DOF-core}
 
@@ -54,7 +55,6 @@
 \newisadof{side_by_side_figure.Isa_COL.side_by_side_figure}%
 [label=,type=%
 ,Isa_COL.figure.relative_width=%
-,Isa_COL.figure.placement=%
 ,Isa_COL.figure.src=%
 ,Isa_COL.side_by_side_figure.anchor=%
 ,Isa_COL.side_by_side_figure.caption=%

src/DOF/latex/DOF-amssymb.sty

@@ -1,25 +0,0 @@
-%% Copyright (C) 2021 University of Exeter
-%%               2021 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-amssymb}
-  [00/00/0000 Document-Type Support Framework for Isabelle (amssymb wrapper for lualatex/pdflatex).]
-
-\usepackage{ifxetex,ifluatex}
-\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
-  \usepackage{amssymb}
-\else % if luatex or xetex
-  \usepackage{unicode-math}
-  \usepackage{latexsym}
-\fi

src/DOF/latex/DOF-core.sty

@@ -6,43 +6,36 @@
 %%   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.
+%%   version 1 of the License, or any later version.
 %%   OR
 %%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
+%%  
+%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
 
 \NeedsTeXFormat{LaTeX2e}\relax
 \ProvidesPackage{DOF-core}
-  [00/00/0000 Document-Type Support Framework for Isabelle.]
-
-\usepackage[T1]{fontenc}
-\usepackage[utf8]{inputenc}
-\usepackage[english,USenglish]{babel}
+  [0000/00/00 Unreleased v0.0.0+%
+  Document-Type Support Framework for Isabelle.]
 
 \RequirePackage{keycommand}
 \RequirePackage{environ}
 \RequirePackage{graphicx}
-\RequirePackage{xcolor}
 \RequirePackage{xspace}
 \RequirePackage{etoolbox}
 \RequirePackage{fp}
-\usepackage{amsmath}
-\usepackage{DOF-amssymb}
 
-\usepackage{isabelle}
-\usepackage{isabellesym}
+\newcommand{\isabelleurl}{UNDEFINED}
+\newcommand{\dofurl}{UNDEFINED}
+\newcommand{\dof@isabelleversion}{UNDEFINED}
+\newcommand{\isabellefullversion}{UNDEFINED\xspace}
+\newcommand{\dof@version}{UNDEFINED}
+\newcommand{\dof@artifacturl}{UNDEFINED}
 
-\isabellestyle{it}
+%%% CONFIG %%%
 
-
-
-
-\RequirePackage{dof-config}
 \newcommand{\isabelleversion}{\dof@isabelleversion\xspace}
 \newcommand{\dofversion}{\dof@version\xspace}
-\newcommand{\isadofversion}{\dofversion/\isabelleversion}
-\newcommand{\isadoflatestversion}{\doflatestversion/\isabellelatestversion}
+\newcommand{\isadofversion}{\dofversion/\isabelleversion\xspace}
 \newcommand{\isadofdir}{Isabelle_DOF-\dof@version_\dof@isabelleversion}
 \newcommand{\isadofdirn}{Isabelle\_DOF-\dof@version\_\dof@isabelleversion}
 \newcommand{\isadofarchive}{\isadofdir.tar.xz}
@@ -156,12 +149,5 @@
 % begin: label and ref
 \newisadof{label}[label=,type=][1]{\label{#1}}
 \newisadof{ref}[label=,type=][1]{\autoref{#1}}
-\newisadof{macroDef}[label=,type=][1]{MMM \label{#1}}        %% place_holder
-\newisadof{macroExp}[label=,type=][1]{MMM \autoref{#1}}   %% place_holder
 % end: label and ref
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-\title{No Title Given}
-\author{No Author Given}
-\input{ontologies}
-\IfFileExists{preamble.tex}{\input{preamble.tex}}{}%

src/ROOT

@@ -1,19 +1,16 @@
 session "Isabelle_DOF" = "Functional-Automata" + 
-  options [document = pdf, document_output = "output", document_build = dof]
+  options [document = pdf, document_output = "output"]
   sessions
     "Regular-Sets"
-  directories 
-    "DOF"
-    "ontologies"
-    "ontologies/CENELEC_50128"
-    "ontologies/Conceptual"
-    "ontologies/scholarly_paper"
-    "ontologies/small_math"
-    "ontologies/technical_report"
-    "ontologies/CC_v3_1_R5"
   theories
     "DOF/Isa_DOF"
     "ontologies/ontologies"
-  export_classpath
-
 
+session "Isabelle_DOF-tests" = "Isabelle_DOF" + 
+  options [document = false]
+  theories
+    "tests/AssnsLemmaThmEtc" 
+    "tests/Concept_ExampleInvariant"
+    "tests/Concept_Example"
+    "tests/InnerSyntaxAntiquotations"
+    "tests/Attributes"

src/ROOTS

@@ -1 +0,0 @@
-tests

src/Tools/mkroot_DOF

@@ -0,0 +1,150 @@
+#/usr/bin/env bash
+# Copyright (c) 2019 University of Exeter
+#               2018-2019 University of Paris-Saclay
+#               2018-2019 The University of Sheffield
+#
+# 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
+#
+# DESCRIPTION: prepare session root directory with DOF setup
+
+## diagnostics
+
+PRG="$(basename "$0")"
+
+function usage()
+{
+  echo
+  echo "Usage: isabelle $PRG [OPTIONS] [DIR]"
+  echo
+  echo "  Options are:"
+  echo "    -h           print this help text and exit"
+  echo "    -n NAME      alternative session name (default: DIR base name)"
+  echo "    -o ONTOLOGY  (default: $DEFAULT_ONTOLOGY)"
+  echo "       Available ontologies:"
+  for t in "$ISABELLE_HOME_USER/DOF/latex/"*.sty; do
+    if [[ $t =~ DOF-(.*).sty$ ]]; then
+      echo "       * ${BASH_REMATCH[1]}"
+    fi
+  done
+  echo "    -t TEMPLATE   (default: $DEFAULT_TEMPLATE)"
+  echo "       Available document templates:"
+  for t in "$ISABELLE_HOME_USER/DOF/document-template/"*.tex; do
+    if [[ $t =~ root-(.*).tex$ ]]; then
+      echo "       * ${BASH_REMATCH[1]}"
+    fi
+  done
+  echo
+  echo "  Prepare session root DIR (default: current directory)."
+  echo
+  exit 1
+}
+
+function fail()
+{
+  echo "$1" >&2
+  exit 2
+}
+
+
+## process command line
+
+# options
+
+NAME=""
+DEFAULT_TEMPLATE="scrartcl"
+DEFAULT_ONTOLOGY="scholarly_paper"
+
+TEMPLATE="$DEFAULT_TEMPLATE"
+ONTOLOGY="$DEFAULT_ONTOLOGY"
+
+while getopts "t:o:n:dh" OPT
+do
+  case "$OPT" in
+    h)
+      usage
+      exit 1
+      ;;
+    n)
+      NAME="$OPTARG"
+      ;;
+    o)
+      if [ ! -f "$ISABELLE_HOME_USER/DOF/latex/DOF-$OPTARG.sty" ]; then
+          echo "ERROR: Ontology $OPTARG not available!"
+          exit 1
+      fi
+      ONTOLOGY="$ONTOLOGY $OPTARG"
+      ;;
+    t)
+      TEMPLATE="$OPTARG"
+      if [ ! -f "$ISABELLE_HOME_USER/DOF/document-template/root-$TEMPLATE.tex" ]; then
+          echo "ERROR: Template $TEMPLATE not available!"
+          exit 1
+      fi
+      ;;
+    \?)
+      usage
+      exit 0
+      ;;
+  esac
+done
+
+shift $(($OPTIND - 1))
+
+
+# args
+
+if [ "$#" -eq 0 ]; then
+  DIR="."
+elif [ "$#" -eq 1 ]; then
+  DIR="$1"
+  shift
+else
+  usage
+fi
+
+if [ -z "$NAME" ]; then
+  NAME="$DIR"
+fi
+
+$ISABELLE_TOOL mkroot -n "$NAME" "$DIR"
+echo "    \"preamble.tex\"" >> "$DIR"/ROOT
+echo "    \"build\"" >> "$DIR"/ROOT
+sed -i -e "s/root.tex/isadof.cfg/" "$DIR"/ROOT
+sed -i -e "s/HOL/Isabelle_DOF/" "$DIR"/ROOT
+rm -f "$DIR"/document/root.tex
+  
+# Creating isadof.cfg
+echo "Template: $TEMPLATE" > "$DIR"/document/isadof.cfg
+cp "$ISABELLE_HOME_USER/DOF/document-template/build" "$DIR"/document/
+for o in $ONTOLOGY; do
+  echo "Ontology: $o" >> "$DIR"/document/isadof.cfg;
+done
+
+# Creating praemble.tex
+TITLE=$(echo "$NAME" | tr _ - | tr -d '\\')
+AUTHOR=$(echo "By $USER" | tr _ - | tr -d '\\')
+echo "%% This is a placeholder for user-specific configuration and packages." >> "$DIR"/document/preamble.tex
+echo "\\title{$TITLE}{}{}{}{}{}{}" >> "$DIR"/document/preamble.tex
+echo "\\author{$AUTHOR}{}{}{}{}{}" >> "$DIR"/document/preamble.tex

src/document-templates/root-eptcs-UNSUPPORTED.tex

@@ -1,16 +1,16 @@
-%% Copyright (c) 2019-2022 University of Exeter
-%%               2018-2022 University of Paris-Saclay
+%% Copyright (c) 2019 University of Exeter
+%%               2018-2019 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.
+%%   version 1 of the License, or any later version.
 %%   OR
 %%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
+%%  
+%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
 
 %% Warning: Do Not Edit!
 %% =====================
@@ -23,11 +23,28 @@
 %% preamble.tex. 
 
 \documentclass[submission,copyright,creativecommons]{eptcs}
-
-\usepackage{DOF-core}
 \bibliographystyle{eptcs}% the mandatory bibstyle
-
+\usepackage[T1]{fontenc}
+\usepackage[utf8]{inputenc}
+\usepackage[USenglish]{babel}
+\usepackage{isabelle}
+%\usepackage{underscore}
+\usepackage{xcolor}
+\usepackage{isabellesym}
+\usepackage{amsmath}
+\usepackage{amssymb}
 \usepackage[numbers, sort&compress, sectionbib]{natbib}
+\IfFileExists{DOF-core.sty}{}{%
+  \PackageError{DOF-core}{Isabelle/DOF not installed. 
+    This is a Isabelle_DOF project. The document preparation requires
+    the Isabelle_DOF framework. Please obtain the framework by cloning
+    the Isabelle_DOF git repository, i.e.: 
+         "git clone <isadofurl>"
+    You can install the framework as follows:
+         "cd Isabelle_DOF/document-generator && ./install"}{%
+    For further help, see <isadofurl>}
+}
+
 \newcommand{\subtitle}[1]{%
   \PackageError{DOF-eptcs-UNSUPPORTED}
                {The LaTeX class eptcs does not support subtitles.}
@@ -37,6 +54,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % provide an alternative definition of 
 % begin: scholarly_paper.author
+\RequirePackage{DOF-core}
 \newcommand{\dofeptcsinstitute}[1]{\mbox{}\\\protect\scriptsize%
   \protect\begin{tabular}[t]{@{\protect\footnotesize}c@{}}%
     #1%
@@ -62,15 +80,15 @@
 \makeatother
 % end: scholarly_paper.author
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\input{ontologies}
 
-
+\IfFileExists{preamble.tex}{\input{preamble.tex}}{}%
 \begin{document}
+
 \maketitle
 \input{session}
 % optional bibliography
-\IfFileExists{root.bib}{%
-    \bibliography{root}
-}{}
+\IfFileExists{root.bib}{{\bibliography{root}}}{}
 \end{document}
 
 %%% Local Variables:

src/document-templates/root-lipics-v2019-UNSUPPORTED.tex

@@ -1,33 +1,47 @@
-%% Copyright (c) 2019-2022 University of Exeter
-%%               2018-2022 University of Paris-Saclay
+%% Copyright (c) 2019 University of Exeter
+%%               2018-2019 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.
+%%   version 1 of the License, or any later version.
 %%   OR
 %%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
+%%  
+%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
 
 %% Warning: Do Not Edit!
 %% =====================
 %% This is the root file for the Isabelle/DOF using the lipics class.
-%% Note that lipics cannot is *not* distributed as part of Isabelle/DOF; 
-%% you need to download lipics.cls from 
+%% Note that lipics cannot be distributed as part of Isabelle/DOF; you need
+%% to download lipics.cls from 
 %% https://www.dagstuhl.de/en/publications/lipics/instructions-for-authors/
 %% and add it manually to the praemble.tex and the ROOT file.
 %%
 %% All customization and/or additional packages should be added to the file
 %% preamble.tex.
 
-\documentclass[a4paper,UKenglish,cleveref, autoref,thm-restate]{lipics-v2021}
+\documentclass[a4paper,USenglish,cleveref, autoref]{lipics-v2019}
 \bibliographystyle{plainurl}% the mandatory bibstyle
+\usepackage{isabelle}
+\usepackage{isabellesym}
+% \usepackage{amsmath}
+% \usepackage{amssymb}
 \usepackage[numbers, sort&compress, sectionbib]{natbib}
+\IfFileExists{DOF-core.sty}{}{%
+  \PackageError{DOF-core}{Isabelle/DOF not installed. 
+    This is a Isabelle_DOF project. The document preparation requires
+    the Isabelle_DOF framework. Please obtain the framework by cloning
+    the Isabelle_DOF git repository, i.e.: 
+         "git clone <isadofurl>"
+    You can install the framework as follows:
+         "cd Isabelle_DOF/document-generator && ./install"}{%
+    For further help, see <isadofurl>}
+}
+
 
-\usepackage{DOF-core}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % provide an alternative definition of 
@@ -53,21 +67,24 @@
 \makeatother
 % end: scholarly_paper.author
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\input{ontologies}
 \renewcommand{\DOFauthor}{}
 \renewcommand{\DOFinstitute}{}
 \expandafter\newcommand\csname 2authand\endcsname{}
 \expandafter\newcommand\csname 3authand\endcsname{}
 \expandafter\newcommand\csname 4authand\endcsname{}
 
-
+\IfFileExists{preamble.tex}{\input{preamble.tex}}{}%
 \begin{document}
+
+
 \maketitle
 \input{session}
 % optional bibliography
 \IfFileExists{root.bib}{%
-\small  
+{\small  
   \bibliography{root}
-}{}
+}}{}
 \end{document}
 
 %%% Local Variables:

src/document-templates/root-lncs.tex

@@ -1,29 +1,52 @@
-%% Copyright (c) 2019-2022 University of Exeter
-%%               2018-2022 University of Paris-Saclay
+%% Copyright (c) 2019 University of Exeter
+%%               2018-2019 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.
+%%   version 1 of the License, or any later version.
 %%   OR
 %%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
+%%  
+%%   SPDX-License-Identifier: LPPL-1.0+ OR BSD-2-Clause
 
 %% Warning: Do Not Edit!
 %% =====================
 %% This is the root file for the Isabelle/DOF using the lncs class.
+%% Note that lncs cannot be distributed as part of Isabelle/DOF; you need
+%% to download lncs.cls from 
+%% https://www.springer.com/gp/computer-science/lncs/conference-proceedings-guidelines
+%% and add it manually to the praemble.tex and the ROOT file.
 %%
 %% All customization and/or additional packages should be added to the file
 %% preamble.tex.
 
 \RequirePackage{ifvtex}
 \documentclass{llncs}
-\usepackage{DOF-core}
-\bibliographystyle{splncs04}
-
+\usepackage[T1]{fontenc}
+\usepackage[utf8]{inputenc}
+\usepackage[USenglish]{babel}
+\usepackage{isabelle}
+\usepackage{xcolor}
+\usepackage{isabellesym}
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage[numbers, sort&compress, sectionbib]{natbib}
+\IfFileExists{DOF-core.sty}{}{%
+  \PackageError{DOF-core}{Isabelle/DOF not installed. 
+    This is a Isabelle_DOF project. The document preparation requires
+    the Isabelle_DOF framework. Please obtain the framework by cloning
+    the Isabelle_DOF git repository, i.e.: 
+         "git clone <isadofurl>"
+    You can install the framework as follows:
+         "cd Isabelle_DOF/document-generator && ./install"}{%
+    For further help, see <isadofurl>}
+}
+\input{ontologies}
+\IfFileExists{preamble.tex}{\input{preamble.tex}}{}%
+\usepackage{graphicx}
 \usepackage{hyperref}
 \setcounter{tocdepth}{3} 
 \hypersetup{%
@@ -35,7 +58,8 @@
 } % more detailed digital TOC (aka bookmarks)
 \sloppy
 \allowdisplaybreaks[4]
-
+\urlstyle{rm}
+\isabellestyle{it}
 \usepackage[caption]{subfig}
 \usepackage[size=footnotesize]{caption}
 
@@ -50,6 +74,17 @@
 \renewcommand{\floatpagefraction}{0.7}        % require fuller float pages
 \renewcommand{\dblfloatpagefraction}{0.7}     % require fuller float pages
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%% Overrides the (rightfully issued) warning by Koma Script that \rm
+%%% etc. should not be used (they are deprecated since more than a
+%%% decade)
+  \DeclareOldFontCommand{\rm}{\normalfont\rmfamily}{\mathrm}
+  \DeclareOldFontCommand{\sf}{\normalfont\sffamily}{\mathsf}
+  \DeclareOldFontCommand{\tt}{\normalfont\ttfamily}{\mathtt}
+  \DeclareOldFontCommand{\bf}{\normalfont\bfseries}{\mathbf}
+  \DeclareOldFontCommand{\it}{\normalfont\itshape}{\mathit}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 \begin{document}
 \selectlanguage{USenglish}%
 \renewcommand{\bibname}{References}%
@@ -65,10 +100,17 @@
 
 
 
-  \maketitle
+\maketitle
 \input{session}
 % optional bibliography
-\IfFileExists{root.bib}{{\small\bibliography{root}}}{}
+\IfFileExists{root.bib}{%
+{\small   \renewcommand{\doi}[1]{}
+  \newcommand{\urlprefix}{}
+
+  \bibliographystyle{spmpscinat}
+  
+  \bibliography{root}
+}}{}
 \end{document}
 
 %%% Local Variables:

src/document-templates/root-scrartcl.tex

@@ -1,16 +1,16 @@
-%% Copyright (c) 2019-2022 University of Exeter
-%%               2018-2022 University of Paris-Saclay
+%% Copyright (c) 2019 University of Exeter
+%%               2018-2019 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.
+%%   version 1 of the License, or any later version.
 %%   OR
 %%   The 2-clause BSD-style license.
-%%
-%%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
+%%  
+%%   SPDX-License-Identifier: LPPL-1
 
 %% Warning: Do Not Edit!
 %% =====================
@@ -20,17 +20,31 @@
 %% preamble.tex.
 
 \RequirePackage{ifvtex}
-\documentclass[abstract=true,fontsize=11pt,DIV=12,paper=a4]{scrartcl}
-
-\usepackage{DOF-core}
-
+\documentclass[fontsize=11pt,DIV=12,paper=a4]{scrartcl}
+\usepackage[T1]{fontenc}
+\usepackage[utf8]{inputenc}
 \usepackage{textcomp}
 \bibliographystyle{abbrvnat}
+\usepackage[english]{babel}
 \RequirePackage[caption]{subfig}
-
-
+\usepackage{isabelle}
+\usepackage{isabellesym}
+\IfFileExists{DOF-core.sty}{}{%
+  \PackageError{DOF-core}{Isabelle/DOF not installed. 
+    This is a Isabelle_DOF project. The document preparation requires
+    the Isabelle_DOF framework. Please obtain the framework by cloning
+    the Isabelle_DOF git repository, i.e.: 
+         "git clone <isadofurl>"
+    You can install the framework as follows:
+         "cd Isabelle_DOF/document-generator && ./install"}{%
+    For further help, see <isadofurl>}
+}
+\input{ontologies}
+\IfFileExists{preamble.tex}{\input{preamble.tex}}{}%
+\usepackage{amsmath}
+\usepackage{amssymb}
 \usepackage[numbers, sort&compress, sectionbib]{natbib}
-
+\usepackage{graphicx}
 \usepackage{hyperref}
 \setcounter{tocdepth}{3} 
 \hypersetup{%
@@ -42,16 +56,30 @@
 } % more detailed digital TOC (aka bookmarks)
 \sloppy
 \allowdisplaybreaks[4]
-
+\urlstyle{rm}
+\isabellestyle{it}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%% Overrides the (rightfully issued) warning by Koma Script that \rm
+%%% etc. should not be used (they are deprecated since more than a
+%%% decade)
+  \DeclareOldFontCommand{\rm}{\normalfont\rmfamily}{\mathrm}
+  \DeclareOldFontCommand{\sf}{\normalfont\sffamily}{\mathsf}
+  \DeclareOldFontCommand{\tt}{\normalfont\ttfamily}{\mathtt}
+  \DeclareOldFontCommand{\bf}{\normalfont\bfseries}{\mathbf}
+  \DeclareOldFontCommand{\it}{\normalfont\itshape}{\mathit}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \newenvironment{frontmatter}{}{}
 
 \begin{document}
 \begin{frontmatter}
   \maketitle
+  \tableofcontents
 \end{frontmatter}
 \input{session}
 % optional bibliography
-\IfFileExists{root.bib}{{\bibliography{root}}}{}
+\IfFileExists{root.bib}{%
+    \bibliography{root}
+}{}
 \end{document}
 
 %%% Local Variables: