.gitignore

@@ -2,4 +2,3 @@ output
 .afp
 *~
 *#
-Isabelle_DOF-Unit-Tests/latex_test/

.woodpecker/build.yml

@@ -1,29 +1,22 @@
 pipeline:
   build:
-    image: git.logicalhacking.com/lh-docker/lh-docker-isabelle/isabelle2023:latest
-    pull: true
+    image: docker.io/logicalhacking/isabelle2022
     commands:
-      - hg log --limit 2 /root/isabelle
-      - ./.woodpecker/check_dangling_theories
-      - ./.woodpecker/check_external_file_refs
-      - ./.woodpecker/check_quick_and_dirty
       - export ARTIFACT_DIR=$CI_WORKSPACE/.artifacts/$CI_REPO/$CI_BRANCH/$CI_BUILD_NUMBER/$LATEX
       - mkdir -p $ARTIFACT_DIR
       - export `isabelle getenv ISABELLE_HOME_USER`
       - mkdir -p $ISABELLE_HOME_USER/etc
       - echo "ISABELLE_PDFLATEX=\"$LATEX --file-line-error\"" >> $ISABELLE_HOME_USER/etc/settings
-      - isabelle build -x HOL-Proofs -x Isabelle_DOF-Proofs -D . -o browser_info
-      - if [ "$LATEX" = "lualatex" ]; then isabelle build -o 'timeout_scale=2' -D . -o browser_info; else echo "Skipping Isabelle_DOF-Proofs for pdflatex build."; fi
-      - find . -name 'root.tex' -prune -o -name 'output' -type f | xargs latexmk -$LATEX -cd  -quiet -Werror
-      - isabelle components -u .
-      - isabelle dof_mkroot -q DOF_test
+      - isabelle components -u `pwd` 
+      - isabelle build -D . -o browser_info
+      - isabelle dof_mkroot DOF_test
       - isabelle build -D DOF_test
       - cp -r $ISABELLE_HOME_USER/browser_info $ARTIFACT_DIR
       - cd $ARTIFACT_DIR
       - cd ../..
       - ln -s * latest
   archive:
-    image: git.logicalhacking.com/lh-docker/lh-docker-isabelle/isabelle2023:latest
+    image: docker.io/logicalhacking/isabelle2022
     commands:
       - export ARTIFACT_DIR=$CI_WORKSPACE/.artifacts/$CI_REPO/$CI_BRANCH/$CI_BUILD_NUMBER/$LATEX
       - mkdir -p $ARTIFACT_DIR
@@ -45,7 +38,7 @@ pipeline:
         from_secret: artifacts_ssh
       user: artifacts
   notify:
-    image: docker.io/drillster/drone-email
+    image: drillster/drone-email
     settings:
       host: smtp.0x5f.org
       username: woodpecker

.woodpecker/check_dangling_theories

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

.woodpecker/check_external_file_refs

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

.woodpecker/check_quick_and_dirty

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

.woodpecker/mk_release

@@ -83,22 +83,22 @@ build_and_install_manuals()
     if [ "$DIRTY" = "true" ]; then
         if [ -z ${ARTIFACT_DIR+x} ]; then
             echo "  * Quick and Dirty Mode (local build)"
-            $ISABELLE build -d . Isabelle_DOF Isabelle_DOF-Example-I
-            mkdir -p $ISADOF_WORK_DIR/Isabelle_DOF-Example-I/output/
-            cp Isabelle_DOF-Example-I/output/document.pdf \
-               $ISADOF_WORK_DIR/Isabelle_DOF-Example-I/output/
-            mkdir -p $ISADOF_WORK_DIR/Isabelle_DOF/output/
-            cp Isabelle_DOF/output/document.pdf \
-               $ISADOF_WORK_DIR/Isabelle_DOF/output/;
+            $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/Isabelle_DOF-Example-I/output/
-            cp $ARTIFACT_DIR/browser_info/AFP/Isabelle_DOF-Example-I/document.pdf \
-               $ISADOF_WORK_DIR/Isabelle_DOF-Example-I/output/
+            mkdir -p $ISADOF_WORK_DIR/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/Isabelle_DOF/output/
-            cp $ARTIFACT_DIR/browser_info/AFP/Isabelle_DOF/document.pdf \
-               $ISADOF_WORK_DIR/Isabelle_DOF/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)
@@ -107,13 +107,13 @@ build_and_install_manuals()
     mkdir -p $ISADOF_WORK_DIR/doc
     echo "Isabelle/DOF Manuals!" > $ISADOF_WORK_DIR/doc/Contents
     
-    cp $ISADOF_WORK_DIR/Isabelle_DOF/output/document.pdf \
+    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/Isabelle_DOF-Example-I/output/document.pdf \
-        $ISADOF_WORK_DIR/doc/Isabelle_DOF-Example-I.pdf
-    echo "  Isabelle_DOF-Example-I       Example academic paper" >> $ISADOF_WORK_DIR/doc/Contents
+    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 $ISADOF_WORK_DIR/.afp 
@@ -143,6 +143,7 @@ publish_archive()
     ssh 0x5f.org chmod go+u-w -R www/$DOF_ARTIFACT_HOST/htdocs/$DOF_ARTIFACT_DIR
 }
 
+
 ISABELLE=`which isabelle`
 USE_TAG="false"
 SIGN="false"
@@ -193,8 +194,8 @@ 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_VERSION="Isabelle$($ISABELLE_TOOL options -g dof_isabelle)"
+DOF_VERSION="$($ISABELLE_TOOL options -g dof_version)"
 
 ISABELLE_SHORT_VERSION=`echo $ISABELLE_VERSION | sed -e 's/:.*$//'`
 ISADOF_TAR="Isabelle_DOF-"$DOF_VERSION"_"$ISABELLE_SHORT_VERSION
@@ -220,3 +221,4 @@ fi
 
 rm -rf $BUILD_DIR
 
+exit 0 

CHANGELOG.md

@@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### Changed
 
-- Updated Isabelle version to Isabelle 2023
+- Updated Isabelle version to Isabelle 2022
 
 ## [1.3.0] - 2022-07-08
 

Isabelle_DOF-Example-II/ROOT

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

Isabelle_DOF-Examples-Extra/CC_ISO15408/PikeOS_study/ROOT

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

Isabelle_DOF-Examples-Extra/CC_ISO15408/ROOTS

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

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

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

Isabelle_DOF-Examples-Extra/beamerx/ROOTS

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

Isabelle_DOF-Examples-Extra/beamerx/poster/ROOT

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

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

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

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

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

Isabelle_DOF-Examples-Extra/beamerx/presentation/ROOT

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

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

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

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

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

Isabelle_DOF-Examples-Extra/cytology/ROOT

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

Isabelle_DOF-Examples-Templates/ROOTS

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Isabelle_DOF-Examples-Templates/template-lncs/ROOT

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

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

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

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

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

Isabelle_DOF-Examples-Templates/template-scrartcl/ROOT

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

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

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

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

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

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

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

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

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

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

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

Isabelle_DOF-Examples-Templates/template-scrreprt/ROOT

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Isabelle_DOF-Ontologies/CC_v3_1_R5/DOF-CC_terminology.sty

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

Isabelle_DOF-Ontologies/CENELEC_50128/CENELEC_50128_Documentation.thy

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

Isabelle_DOF-Ontologies/CENELEC_50128/DOF-CENELEC_50128.sty

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

Isabelle_DOF-Ontologies/ROOT

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

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

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

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

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

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

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

Isabelle_DOF-Ontologies/document/lstisadof-manual.sty

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

Isabelle_DOF-Ontologies/document/preamble.tex

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

Isabelle_DOF-Ontologies/document_setup.thy

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

Isabelle_DOF-Ontologies/document_templates.thy

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

Isabelle_DOF-Proofs/ROOT

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

Isabelle_DOF-Proofs/Reification_Test.thy

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

Isabelle_DOF-Proofs/Very_Deep_DOF.thy

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

Isabelle_DOF-Proofs/Very_Deep_Interpretation.thy

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

Isabelle_DOF-Unit-Tests/AssnsLemmaThmEtc.thy

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

Isabelle_DOF-Unit-Tests/COL_Test.thy

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

Isabelle_DOF-Unit-Tests/Cenelec_Test.thy

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

Isabelle_DOF-Unit-Tests/Concept_Example_Low_Level_Invariant.thy

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

Isabelle_DOF-Unit-Tests/Concept_MonitorTest1.thy

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

Isabelle_DOF-Unit-Tests/Concept_MonitorTest2.thy

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

Isabelle_DOF-Unit-Tests/Concept_OntoReferencing.thy

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

Isabelle_DOF-Unit-Tests/Concept_TermAntiquotations.thy

@@ -1,182 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2023 The University of Exeter 
- *               2018-2023 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-chapter\<open>Term Antiquotations\<close>
-
-text\<open>Terms are represented by "Inner Syntax" parsed by an Earley parser in Isabelle.
-For historical reasons, \<^emph>\<open>term antiquotations\<close> are called therefore somewhat misleadingly
-"Inner Syntax Antiquotations". \<close>
-
-theory 
-  Concept_TermAntiquotations
-imports 
-  "Isabelle_DOF_Unit_Tests_document"
-  "Isabelle_DOF-Ontologies.Conceptual"
-   TestKit
-begin
-
-section\<open>Context\<close>
-
-text\<open>Since the syntax chosen for values of doc-class attributes is HOL-syntax --- requiring
-a fast read on the ``What's in Main''-documentation, but not additional knowledge on, say, 
-SML --- an own syntax for references to types, terms, theorems, etc. are necessary. These are 
-the ``Term Antiquotations'' (in earlier papers also called: ``Inner Syntax Antiquotations'').
-
-They are the key-mechanism to denote 
-\<^item> Ontological Links, i.e. attributes refering to document classes defined by the ontology
-\<^item> Ontological F-Links, i.e. attributes referring to formal entities inside Isabelle (such as thm's)
-
-This file contains a number of examples resulting from the 
-@{theory "Isabelle_DOF-Ontologies.Conceptual"} - ontology; the emphasis of this presentation is to 
-present the expressivity of ODL on a paradigmatical example.
-\<close>
-
-
-section\<open>Test Purpose.\<close>
-
-text\<open>Testing Standard Term-Antiquotations and Code-Term-Antiquotations. \<close>
-
-text\<open>Just a check of the status DOF core: observe that no new classes have been defined.\<close>
-
-print_doc_classes
-print_doc_items
-
-
-section\<open>Term-Antiquotations Referring to \<^verbatim>\<open>thm\<close>‘s\<close>
-
-text\<open>Some sample lemma:\<close>
-lemma*[l::E] murks : "Example = @{thm ''refl''}" oops
-
-text-assert-error\<open>... @{E "l"}\<close>\<open>Undefined instance:\<close>   \<comment> \<open>oops retracts the ENTIRE system state,
-                                                          thus also the creation of an instance of E\<close>
-
-lemma*[l::E] local_sample_lemma : 
-       "@{thm \<open>refl\<close>} = @{thm ''refl''}" by simp
-                                                       \<comment> \<open>un-evaluated references are similar to
-                                                           uninterpreted constants. Not much is known
-                                                           about them, but that doesn't mean that we
-                                                           can't prove some basics over them...\<close>
-
-
-lemma*[l2::E] local_sample_lemma2 :
-      "@{thm ''local_sample_lemma''} = @{thm ''local_sample_lemma''}" by simp
-
-
-value*\<open>@{thm ''local_sample_lemma''}\<close>
-value-assert-error\<open> @{thm \<open>Conxept_TermAntiquotations.local_sample_lemma\<close>}\<close>\<open>Undefined fact\<close>
-
-section\<open>Testing the Standard ("Built-in") Term-Antiquotations\<close>
-
-text\<open>Example for a meta-attribute of ODL-type @{typ "file"} with an 
-     appropriate ISA for the file @{file "Concept_TermAntiquotations.thy"}\<close>
-
-
-
-text*[xcv1::A, x=5]\<open>Lorem ipsum ...\<close>
-text*[xcv3::A, x=7]\<open>Lorem ipsum ...\<close>
-
-text\<open>Example for a meta-attribute of ODL-type @{typ "typ"} with an appropriate ISA for the
-     theorem @{thm "refl"}\<close>
-text*[xcv2::C, g="@{thm ''HOL.refl''}"]\<open>Lorem ipsum ...\<close>
-
-text\<open>A warning about the usage of the \<open>docitem\<close> TA:
-The \<open>docitem\<close> TA offers a way to check the reference of class instances
-without checking the instances type.
-So one will be able to reference \<open>docitem\<close>s (class instances) and have them checked,
-without the burden of the type checking required otherwise.
-But it may give rise to unwanted behaviors, due to its polymorphic type.
-It must not be used for certification.
-\<close>
-
-section\<open>Other Built-In Term Antiquotations\<close>
-text-assert-error[ae::text_element]\<open>@{file "non-existing.thy"}\<close>\<open>No such file: \<close>
-text\<open>A text-antiquotation from Main: @{file "TestKit.thy"}\<close>
-
-value-assert-error\<open>@{file \<open>non-existing.thy\<close>}\<close>\<open>No such file: \<close>
-value*\<open>@{file \<open>TestKit.thy\<close>}\<close>
-
-text*[xcv::F, u="@{file ''TestKit.thy''}"]\<open>Lorem ipsum ...\<close>
-
-
-value*\<open>@{term \<open>aa + bb\<close>}\<close>
-value*\<open>@{typ \<open>'a list\<close>}\<close>
-
-
-section\<open>Putting everything together\<close>
-
-text\<open>Major sample: test-item of doc-class \<open>F\<close> with a relational link between class instances, 
-     and links to formal Isabelle items like \<open>typ\<close>, \<open>term\<close> and \<open>thm\<close>. \<close>
-declare[[ML_print_depth = 10000]]
-text*[xcv4::F, r="[@{thm ''HOL.refl''}, 
-                   @{thm \<open>Concept_TermAntiquotations.local_sample_lemma\<close>}]", (* long names required *)
-               b="{(@{A ''xcv1''},@{C \<open>xcv2\<close>})}",  (* notations \<open>...\<close> vs. ''...'' *)
-               s="[@{typ \<open>int list\<close>}]",                        
-               properties = "[@{term \<open>H \<longrightarrow> H\<close>}]"              (* notation \<open>...\<close> required for UTF8*)
-]\<open>Lorem ipsum ...\<close>
-declare[[ML_print_depth = 20]]
-text*[xcv5::G, g="@{thm \<open>HOL.sym\<close>}"]\<open>Lorem ipsum ...\<close>
-
-text\<open>... and here we add a relation between @{docitem \<open>xcv3\<close>} and @{docitem \<open>xcv2\<close>} 
-into the relation \verb+b+ of @{docitem \<open>xcv5\<close>}. Note that in the link-relation,
-a @{typ "C"}-type is required, so if a  @{typ "G"}-type is offered, it is considered illegal
-in \verb+Isa_DOF+ despite the sub-class relation between those classes: \<close>
-update_instance-assert-error[xcv4::F, b+="{(@{docitem ''xcv3''},@{docitem ''xcv5''})}"]
-\<open>Type unification failed\<close>
-
-text\<open>And here is the results of some ML-term antiquotations:\<close>
-ML\<open> @{docitem_attribute b::xcv4} \<close>
-ML\<open> @{docitem xcv4}              \<close>
-ML\<open> @{docitem_name xcv4}         \<close>
-
-text\<open>Now we might need to reference a class instance in a term command and we would like
-Isabelle to check that this instance is indeed an instance of this class.
-Here, we want to reference the instance @{docitem_name "xcv4"} previously defined.
-We can use the term* command which extends the classic term command
-and does the appropriate checking.\<close>
-term*\<open>@{F \<open>xcv4\<close>}\<close>
-
-text\<open>We can also reference an attribute of the instance.
-Here we reference the attribute r of the class F which has the type @{typ \<open>thm list\<close>}.\<close>
-term*\<open>r @{F \<open>xcv4\<close>}\<close>
-
-text\<open>We declare a new text element. Note that the class name contains an underscore "\_".\<close>
-text*[te::text_element]\<open>Lorem ipsum...\<close>
-
-term*\<open>@{text_element \<open>te\<close>}\<close>
-
-text\<open>Terms containing term antiquotations can be checked and evaluated
-using \<^theory_text>\<open>term_\<close> and \<^theory_text>\<open>value_\<close> text antiquotations respectively:
-We can print the term @{term_ \<open>r @{F \<open>xcv4\<close>}\<close>} with \<open>@{term_ \<open>r @{F \<open>xcv4\<close>}\<close>}\<close>
-or get the value of the \<^const>\<open>F.r\<close> attribute of @{docitem \<open>xcv4\<close>} with \<open>@{value_ \<open>r @{F \<open>xcv4\<close>}\<close>}\<close>
-\<^theory_text>\<open>value_\<close> may have an optional argument between square brackets to specify the evaluator but this
-argument must be specified after a default optional argument already defined
-by the text antiquotation implementation.
-So one must use the following syntax if he does not want to specify the first optional argument:
-\<open>@{value_ [] [nbe] \<open>r @{F \<open>xcv4\<close>}\<close>}\<close>. Note the empty brackets.
-
-\<close>
-
-text\<open>There also are \<^theory_text>\<open>term_\<close> and \<^theory_text>\<open>value_\<close> ML antiquotations:
-\<^ML>\<open>@{term_ \<open>r @{F \<open>xcv4\<close>}\<close>}\<close> will return the ML representation of the term \<^term_>\<open>r @{F \<open>xcv4\<close>}\<close>,
-and \<^ML>\<open>@{value_ \<open>r @{F \<open>xcv4\<close>}\<close>}\<close> will return the ML representation
-of the value of the \<^const>\<open>F.r\<close> attribute of @{docitem \<open>xcv4\<close>}.
-\<^theory_text>\<open>value_\<close> may have an optional argument between square brackets to specify the evaluator:
-\<close>
-
-ML\<open>
-val t = @{term_ \<open>r @{F \<open>xcv4\<close>}\<close>}
-val tt = @{value_ [nbe] \<open>r @{F \<open>xcv4\<close>}\<close>}
-\<close>
-
-end
-

Isabelle_DOF-Unit-Tests/Isabelle_DOF_Unit_Tests_document.thy

@@ -1,30 +0,0 @@
-(*<*)
-(*************************************************************************
- * Copyright (C) 
- *               2019-2023 The University of Exeter 
- *               2018-2023 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-theory "Isabelle_DOF_Unit_Tests_document"
-  imports
-    "Isabelle_DOF.technical_report"
-    (* "Isabelle_DOF-Ontologies.CENELEC_50128"  where do we use this - bu *)
-  
-begin
-
-use_template "scrreprt-modern"
-use_ontology "technical_report" (* and "Isabelle_DOF-Ontologies.CENELEC_50128" *)
-(*>*)
-
-title*[title::title]         \<open>The Isabelle/DOF Implementation\<close>
-subtitle*[subtitle::subtitle]\<open>The Unit-Test Suite\<close>
-
-(*<*)
-end
-(*>*)

Isabelle_DOF-Unit-Tests/Latex_Tests.thy

@@ -1,444 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2023 The University of Exeter 
- *               2018-2023 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-chapter\<open>LaTeX Generation Tests\<close>
-
-
-theory   Latex_Tests
-  imports    "TestKit"
-             "Isabelle_DOF_Unit_Tests_document"  
-  keywords   "Figure*"          :: document_body  (* still experimental feature *)
-
-begin
-
-
-section\<open>Test Purpose.\<close>
-text\<open> Testing the generation of LaTeX code. Serves in particular during development. \<close>
-
-text\<open>Output status:\<close>
-print_doc_classes
-print_doc_items
-
-
-section\<open>Elementary Creation of Doc-items and Access of their Attibutes\<close>
-
-
-text\<open>And here a tex - text macro.\<close>
-text\<open>Pythons ReStructuredText (RST). 
-     @{url \<open>https://de.wikipedia.org/wiki/ReStructuredText\<close>}. Tool: Sphinx.
-    \<close>
-
-text*[aaaa::B]\<open>dfg @{thm [display] refl}\<close>
-(*<*)                            
-text-[dfgdfg::B]
-\<open> Lorem ipsum ...  @{thm [display] refl}  Frédéric \textbf{TEST} \verb+sdf+ \<open>dfgdfg\<close>  \<close>
-
-text-latex\<open> Lorem ipsum ...  @{thm [display] refl}  Frédéric \textbf{TEST} \verb+sdf+ \<open>dfgdfg\<close>  \<close>
-text-[asd::B]
-\<open>... and here is its application macro expansion: 
-     @{B [display] "dfgdfg"} 
-     \textbf{TEST}
-     @{cartouche [display] 
-         \<open>text*[dfgdfg::B]
-           \<open> Lorem ipsum ...  @{thm refl} Frederic \textbf{TEST} \verb+sdf+ \<open>dfgdfg\<close>  \<close>
-          \<close>}
-\<close>
-
-text-latex\<open>... and here is its application macro expansion: 
-     @{B [display] "dfgdfg"} 
-     \textbf{TEST}
-     @{cartouche [display] 
-         \<open>text*[dfgdfg::B]
-           \<open> Lorem ipsum ...  @{thm refl}  Fr\'ed\'eric \textbf{TEST} \verb+sdf+ \<open>dfgdfg\<close>  \<close>
-          \<close>}\<close>
-
-text-latex\<open> \<^theory_text>\<open>definition df = ...  
-        \<close>
-       @{ML      [display] \<open> let val x = 3 + 4 in true end 
-                           \<close>}
-
-       @{ML_text [display] \<open> val x = ...  
-                           \<close>}
-
-       @{verbatim [display] \<open> Lorem ipsum ...  @{thm refl} 
-                              Fr\'ed\'eric \textbf{TEST} \verb+sdf+ \<open>dfgdfg\<close> \<close>}
-       @{theory_text [display] \<open>definition df = ... \<lambda>x.  
-                               \<close>}
-       @{cartouche [display]   \<open> @{figure "cfgdfg"}\<close>} \<close>
-(*>*)
-
-text\<open>Final Status:\<close>
-print_doc_items
-print_doc_classes 
-
-section\<open>Experiments on Inline-Textelements\<close>
-text\<open>Std Abbreviations. Inspired by the block *\<open>control spacing\<close> 
-     in @{file \<open>$ISABELLE_HOME/src/Pure/Thy/document_antiquotations.ML\<close>}.
-     We mechanize the table-construction and even attach the LaTeX 
-     quirks to be dumped into the prelude.  \<close>
-
-ML\<open>
-val _ =
-  Theory.setup
-   (   Document_Output.antiquotation_raw \<^binding>\<open>doof\<close> (Scan.succeed ())
-          (fn _ => fn () => Latex.string "\\emph{doof}")
-    #> Document_Output.antiquotation_raw \<^binding>\<open>LATEX\<close> (Scan.succeed ())
-          (fn _ => fn () => Latex.string "\\textbf{LaTeX}") 
-   )
-\<close>
-
-text-latex\<open> \<^doof> \<^LATEX> \<close>
-
-(* the same effect is achieved with : *)
-setup \<open>DOF_lib.define_shortcut (Binding.make("bla",\<^here>)) "\\blabla"\<close>
-(* Note that this assumes that the generated LaTeX macro call "\blabla" is defined somewhere in the
-   target document, for example, in the tex prelude. Note that the "Binding.make" can be avoided
-   using the alternative \<^binding> notation (see above).*)
-
-
-setup\<open>DOF_lib.define_macro (Binding.make("blong",\<^here>)) "\\blong{" "}" (K(K()))\<close>
-
-(*<*)
-text-latex\<open> \<^blong>\<open>asd\<close> outer  \<^blong>\<open>syntax| ! see {syntax, outer}\<close> \<close>
-(*>*)
-
-section\<open>Experimental Code and Test of advanced LaTeX for free-form text units\<close>
-
-ML\<open>
-
-fun report_text ctxt text =
-    let val pos = Input.pos_of text in
-       Context_Position.reports ctxt
-         [(pos, Markup.language_text (Input.is_delimited text)),
-          (pos, Markup.raw_text)]
-    end;
-
-fun report_theory_text ctxt text =
-    let val keywords = Thy_Header.get_keywords' ctxt;
-        val _ = report_text ctxt text;
-        val _ =
-          Input.source_explode text
-          |> Token.tokenize keywords {strict = true}
-          |> maps (Token.reports keywords)
-          |> Context_Position.reports_text ctxt;
-    in () end
-
-fun prepare_text ctxt =
-  Input.source_content #> #1 #> Document_Antiquotation.prepare_lines ctxt;
-(* This also produces indent-expansion and changes space to "\_" and the introduction of "\newline",
-   I believe. Otherwise its in Thy_Output.output_source, the compiler from string to LaTeX.text. *)
-
-fun string_2_text_antiquotation ctxt text = 
-        prepare_text ctxt text
-        |> Document_Output.output_source ctxt
-        |> Document_Output.isabelle ctxt
-
-fun string_2_theory_text_antiquotation ctxt text =
-      let
-        val keywords = Thy_Header.get_keywords' ctxt;
-      in
-        prepare_text ctxt text
-        |> Token.explode0 keywords
-        |> maps (Document_Output.output_token ctxt)
-        |> Document_Output.isabelle ctxt
-      end
-
-fun gen_text_antiquotation name reportNcheck compile =
-  Document_Output.antiquotation_raw_embedded name (Scan.lift Parse.embedded_input)
-    (fn ctxt => fn text:Input.source =>
-      let
-        val _ = reportNcheck ctxt text;
-      in
-        compile ctxt text    
-      end);
-
-fun std_text_antiquotation name (* redefined in these more abstract terms *) =
-    gen_text_antiquotation name report_text string_2_text_antiquotation
-
-(* should be the same as (2020):
-fun text_antiquotation name =
-  Thy_Output.antiquotation_raw_embedded name (Scan.lift Parse.embedded_input)
-    (fn ctxt => fn text =>
-      let
-        val _ = report_text ctxt text;
-      in
-        prepare_text ctxt text
-        |> Thy_Output.output_source ctxt
-        |> Thy_Output.isabelle ctxt
-      end);
-*)
-
-fun std_theory_text_antiquotation name (* redefined in these more abstract terms *) =
-    gen_text_antiquotation name report_theory_text string_2_theory_text_antiquotation
-
-(* should be the same as (2020):
-fun theory_text_antiquotation name =
-  Thy_Output.antiquotation_raw_embedded name (Scan.lift Parse.embedded_input)
-    (fn ctxt => fn text =>
-      let
-        val keywords = Thy_Header.get_keywords' ctxt;
-
-        val _ = report_text ctxt text;
-        val _ =
-          Input.source_explode text
-          |> Token.tokenize keywords {strict = true}
-          |> maps (Token.reports keywords)
-          |> Context_Position.reports_text ctxt;
-      in
-        prepare_text ctxt text
-        |> Token.explode0 keywords
-        |> maps (Thy_Output.output_token ctxt)
-        |> Thy_Output.isabelle ctxt
-        |> enclose_env ctxt "isarbox"
-      end);
-*)
-
-
-
-fun enclose_env ctxt block_env body =
-  if Config.get ctxt Document_Antiquotation.thy_output_display
-  then Latex.environment block_env body
-  else body;
-
-
-fun boxed_text_antiquotation name (* redefined in these more abstract terms *) =
-    gen_text_antiquotation name report_text 
-                           (fn ctxt => string_2_text_antiquotation ctxt
-                                       #> enclose_env ctxt "isarbox")
-
-
-fun boxed_theory_text_antiquotation name (* redefined in these more abstract terms *) =
-    gen_text_antiquotation name report_theory_text 
-                           (fn ctxt => string_2_theory_text_antiquotation ctxt 
-                                        #> enclose_env ctxt "isarbox")
-
-
-(*   #> enclose_env ctxt "isarbox" *)
-
-val _ = Theory.setup
-   (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>); (* is overriding possible ?*)
-
-\<close>
-(*<*)
-text-latex\<open> 
-      @{boxed_cartouche   [display] \<open>definition dfg = \<lambda>x. x\<close>}
-      @{boxed_theory_text [display] \<open>doc_class dfg = \<lambda>x... \<Gamma>\<close>}  \<close>
-(*>*)
-
-
-
-section\<open>Experimental Section for Multiple Figure Content\<close>
-
-ML\<open>
-
-val thy_output_display = Attrib.setup_option_bool ("thy_output_display", \<^here>);
-
-val caption_param = Config.declare_string ("caption", \<^here>) (K "");
-val width_param   = Config.declare_int    ("width", \<^here>)   (K 80);  \<comment> \<open>char per line\<close>
-val scale_param   = Config.declare_int    ("scale", \<^here>)   (K 100); \<comment> \<open>in percent\<close>
-
-Config.put caption_param;
-Config.put_global;
-Config.get ;
-
-(*
-      Latex.string (enclose "[" "]" (String.concat [ label_and_type, ", args={", (commas str_args), "}"]))
-*)
-
-(*
-\begin{figure}[h]
-     \centering
-
-     \includegraphics[scale=0.5]{graph_a}
-     \caption{An example graph}
-
-     \label{fig:x cubed graph}
-\end{figure}
-
-
-\begin{figure}
-     \centering
-
-     \begin{subfigure}[b]{0.3\textwidth}
-
-         \centering
-         \includegraphics[width=\textwidth]{graph1}
-         \caption{$y=x$}
-
-         \label{fig:y equals x}   (* PROBLEM *)
-     \end{subfigure}
-
-     \hfill
-
-     \begin{subfigure}[b]{0.3\textwidth}
-
-         \centering
-         \includegraphics[width=\textwidth]{graph2}
-         \caption{$y=3sinx$}
-
-         \label{fig:three sin x}  (* PROBLEM *)
-     \end{subfigure}
-
-     \hfill
-
-     \begin{subfigure}[b]{0.3\textwidth}
-
-         \centering
-         \includegraphics[width=\textwidth]{graph3}
-         \caption{$y=5/x$}
-
-         \label{fig:five over x} (* PROBLEM *)
-     \end{subfigure}
-
-  \caption{Three simple graphs}
-  \label{fig:three graphs}
-\end{figure}
-
-
-\begin{wrapfigure}{l}{0.5\textwidth}
-
-     \centering
-     \includegraphics[width=1.5cm]{logo.png}
-     \caption{$y=5/x$}
-
-\end{wrapfigure}
-
-*)
-
-datatype figure_type   = single | subfigure | float_embedded
-
-(* to check if this can be done more properly: user-state or attributes ??? *)
-val figure_mode        = Unsynchronized.ref(float_embedded)
-val figure_label       = Unsynchronized.ref(NONE:string option)
-val figure_proportions = Unsynchronized.ref([]:int list)
-(* invariant : !figure_mode = subfigure_embedded ==> length(!figure_proportions) > 1 *)
-
-fun figure_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;
-    let val cap = Config.get ctxt caption_param
-        val cap_txt = if cap = "" then "" else (Library.enclose "\n\\caption{" "}\n" cap)
-                      \<comment> \<open>this is naive. one should add an evaluation of doc antiquotations here\<close>
-        val wdth= Config.get ctxt width_param
-        val wdth_ltx = (if wdth = 100 then "" 
-                       else if 10<=wdth andalso wdth<=99 
-                            then "width=0."^(Int.toString wdth)
-                            else if 1<=wdth then "width=0.0"^(Int.toString wdth)
-                                 else error "width out of range (must be between 1 and 100"
-                       )^"\\textwidth"
-        val scl = Config.get ctxt scale_param
-        val scl_ltx = if scl = 100 then "" 
-                       else if 10<=scl andalso scl<=99 then "scale=0."^(Int.toString scl)
-                            else if 1<=scl then "scale=0.0"^(Int.toString scl)
-                                 else error "scale out of range (must be between 1 and 100"
-        val fig_args = Library.enclose "[" "]" (commas [wdth_ltx,scl_ltx])
-        val _ = writeln cap
-        fun proportion () = "0."^ (Int.toString (100 div List.length(!figure_proportions)))
-                             \<comment> \<open>naive: assumes equal proportions\<close>
-        fun core arg = "\n\\centering\n"
-                       ^"\\includegraphics"
-                       ^fig_args^(Library.enclose "{" "}" arg)
-                       ^cap_txt
-                       \<comment> \<open>add internal labels here\<close>
-        fun pat arg = case !figure_mode of
-                       single => core arg   
-                      |subfigure =>   "\n\\begin{subfigure}[b]{"^proportion ()^"\\textwidth}"
-                                     ^ core arg 
-                                     ^"\n\\end{subfigure}\n"
-                      |float_embedded => "\n\\begin{wrapfigure}{r}{"^wdth_ltx^"}"
-                                         ^ core arg 
-                                         ^"\n\\end{wrapfigure}\n"
-                   
-    in   (Latex.output_ascii_breakable "/" (Input.string_of source))
-        |> pat
-        |> Latex.string
-    end));
-
-val _ = Theory.setup
- (Document_Antiquotation.setup_option \<^binding>\<open>width\<close> 
-       (Config.put width_param o Document_Antiquotation.integer) #>
-  Document_Antiquotation.setup_option \<^binding>\<open>scale\<close> 
-       (Config.put scale_param o Document_Antiquotation.integer) #>
-  Document_Antiquotation.setup_option \<^binding>\<open>caption\<close> 
-       (Config.put caption_param) #>
-  Document_Output.antiquotation_raw_embedded \<^binding>\<open>figure_content\<close> 
-       (figure_antiq Resources.check_file) (K I)
-
- );
-\<close>
-
-(*<*)
-text-latex\<open>
-@{figure_content [width=40, scale=35, caption="This is a test"] "ROOT"}
-\<close>
-(*>*)
-ML\<open>
-
-fun gen_enriched_document_command3 name {body} cid_transform attr_transform markdown
-                                  ((((binding,cid_pos), doc_attrs) : ODL_Meta_Args_Parser.meta_args_t,
-                                     xstring_opt:(xstring * Position.T) option),
-                                    toks:Input.source list)
-= gen_enriched_document_command2 name {body=body} cid_transform attr_transform markdown
-                                  ((((binding,cid_pos), doc_attrs) : ODL_Meta_Args_Parser.meta_args_t,
-                                     xstring_opt:(xstring * Position.T) option),
-                                     toks) \<comment> \<open>Hack : drop second and thrd args.\<close>
-
-val _ =
-  Outer_Syntax.command ("Figure*", @{here}) "multiple figure"
-    (ODL_Meta_Args_Parser.attributes -- Parse.opt_target -- Scan.repeat1 Parse.document_source 
-      >> (Toplevel.theory o (gen_enriched_document_command2 "TTT" {body=true} I I {markdown = true} )));
-
-
-\<close>
-(*
-Figure*[fff::figure,src="\<open>this is a side-by-side\<close>"]
-   \<open>@{figure_content [width=40, scale=35, caption="This is a test"] "ROOT"}\<close> 
-   \<open> \<^doof> \<^LATEX> \<close>  
-   \<open> \<^theory_text>\<open>definition df = ... \<close>
-     @{ML        [display]   \<open> let val x = 3 + 4 in true end\<close>}
-     @{cartouche [display]   \<open> @{figure "cfgdfg"}\<close>}
-   \<close>  
-*)
-
-
-(*<*)
-
-Figure*[figxxx::float,main_caption="\<open>Proofs establishing an Invariant Preservation.\<close>"]
-\<open>  @{fig_content (width=40, height=35, caption="This is a right test") "figures/A.png"}  
-   @{fig_content (width=40, height=35, caption="This is a left \<^term>\<open>\<sigma>\<^sub>i + 1\<close> test") "figures/A.png"} 
-\<close>
-
-
-
-(* proposed syntax for sub-figure labels : text\<open> @{figure "ffff(2)"}\<close> *)
-
-Figure*[figxxxx::float,main_caption="\<open>Proofs establishing an Invariant Preservation.\<close>"]
-\<open>@{boxed_theory_text [display]
-\<open>lemma inv_c2_preserved :  "c2_inv \<sigma> \<Longrightarrow> c1_inv (\<sigma> \<langle>Hardware\<rangle>\<^sub>C\<^sub>o\<^sub>m\<^sub>p\<^sub>u\<^sub>t\<^sub>e\<^sub>r\<^sub>H\<^sub>a\<^sub>r\<^sub>d\<^sub>w\<^sub>a\<^sub>r\<^sub>e)"
-  unfolding c1_inv_def c2_inv_def 
-            Computer_Hardware_to_Hardware_morphism_def
-            Product_to_Component_morphism_def  
-  by (auto simp: comp_def)
-
-lemma Computer_Hardware_to_Hardware_total :
-         "Computer_Hardware_to_Hardware_morphism ` ({X. c2_inv X}) 
-      \<subseteq> ({X::Hardware. c1_inv X})"
-  using inv_c2_preserved by auto\<close>}\<close> 
-
-end
-(*>*)

Isabelle_DOF-Unit-Tests/Ontology_Matching_Example.thy

@@ -1,95 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2023 The University of Exeter 
- *               2018-2023 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-chapter\<open>Ontologys Matching\<close>
-
-theory Ontology_Matching_Example
-  imports TestKit
-          "Isabelle_DOF.Isa_DOF"
-          "Isabelle_DOF_Unit_Tests_document"
-
-begin
-
-section\<open>Test Purpose.\<close>
-text\<open> This is merely an example that shows that the generated invariants 
-      fit nicely together; i.e. allow for sensible consistency and invariant
-      preservation proofs related to ontological matchings. \<close>
-
-section\<open>The Scenario.\<close>
-
-text\<open>Using HOL, we can define a mapping between two ontologies.
-  It is called ontology matching or ontology alignment.
-  Here is an example which show how to map two classes.
-  HOL also allows us to map the invariants (ontological rules) of the classes!\<close>
-
-type_synonym UTF8 = string
-
-definition utf8_to_string
-  where "utf8_to_string xx = xx"
-
-
-doc_class A =
-  first_name  :: UTF8
-  last_name   :: UTF8
-  age         :: nat
-  married_to  :: "string option"
-  invariant a :: "age \<sigma> < 18 \<longrightarrow> married_to \<sigma> = None"
-
-
-doc_class B =
-  name        :: string 
-  adult       :: bool
-  is_married  :: bool
-  invariant b :: "is_married \<sigma> \<longrightarrow> adult \<sigma>"
-
-text\<open>We define the mapping between the two classes,
-  i.e. how to transform the class @{doc_class A} in to the class @{doc_class B}:\<close>
-
-definition A_to_B_morphism
-  where "A_to_B_morphism X =
-        \<lparr> tag_attribute = A.tag_attribute X
-          , name = utf8_to_string (first_name X) @ '' ''  @ utf8_to_string (last_name X)
-          , adult = (age X \<ge> 18)
-          , is_married = (married_to X \<noteq> None) \<rparr>" 
-
-text\<open>Sanity check: Invariants are non-contradictory, i.e. there is a witness.\<close>
-
-lemma inv_a_satisfyable : " Ex (a_inv::A \<Rightarrow> bool)"
-  unfolding a_inv_def
-  apply(rule_tac x ="\<lparr>Ontology_Matching_Example.A.tag_attribute = xxx, 
-                      first_name = yyy, last_name = zzz, age = 17, 
-                      married_to = None\<rparr>" in exI)
-  by auto
-
-text\<open>Now we check that the invariant is preserved through the morphism:\<close>
-
-lemma inv_a_preserved :
-  "a_inv X \<Longrightarrow> b_inv (A_to_B_morphism X)"
-  unfolding a_inv_def b_inv_def A_to_B_morphism_def
-  by auto
-
-text\<open>This also implies that B invariants are non-contradictory: \<close>
-
-lemma inv_b_preserved : "\<exists>x. (b_inv::B \<Rightarrow> bool) x"
-   apply(rule_tac x ="A_to_B_morphism \<lparr>Ontology_Matching_Example.A.tag_attribute = xxx, 
-                                       first_name = yyy, last_name = zzz, age = 17, 
-                                        married_to = None\<rparr>" in exI)
-   by(rule inv_a_preserved,auto simp: a_inv_def)
-
-
-lemma A_morphism_B_total :
-  "A_to_B_morphism ` ({X::A. a_inv X}) \<subseteq> ({X::B. b_inv X})"
-  using inv_a_preserved
-  by auto
-
-end

Isabelle_DOF-Unit-Tests/ROOT

@@ -1,23 +0,0 @@
-session "Isabelle_DOF-Unit-Tests" = "Isabelle_DOF-Ontologies" + 
-  options [document = pdf, document_output = "output", document_build = dof, document_variants = "document:overview=-proof,-ML,-unimportant"]
-  theories
-    "TestKit"
-    "Latex_Tests"
-    "Concept_OntoReferencing"
-    "Concept_Example_Low_Level_Invariant"
-    "Concept_High_Level_Invariants"
-    "Concept_MonitorTest1"
-    "Concept_MonitorTest2"
-    "Concept_TermAntiquotations"
-    "Concept_TermEvaluation"
-    "Attributes"
-    "AssnsLemmaThmEtc" 
-    "Ontology_Matching_Example"
-    "Cenelec_Test"  
-    "OutOfOrderPresntn"
-    "COL_Test"
-    "Test_Polymorphic_Classes"
-  document_files
-    "root.bib"
-    "figures/A.png"
-    "figures/B.png"

Isabelle_DOF-Unit-Tests/TestKit.thy

@@ -1,219 +0,0 @@
-(*************************************************************************
- * Copyright (C) 
- *               2019-2023 The University of Exeter 
- *               2018-2023 The University of Paris-Saclay
- *               2018      The University of Sheffield
- *
- * License:
- *   This program can be redistributed and/or modified under the terms
- *   of the 2-clause BSD-style license.
- *
- *   SPDX-License-Identifier: BSD-2-Clause
- *************************************************************************)
-
-chapter\<open>The Isabelle/DOF TestKit\<close>
-
-theory 
-  TestKit
-imports 
-  "Isabelle_DOF_Unit_Tests_document"
-  "Isabelle_DOF-Ontologies.Conceptual"
-keywords "text-" "text-latex"             :: document_body
-    and  "text-assert-error"              :: document_body
-    and  "update_instance-assert-error"   :: document_body
-    and  "declare_reference-assert-error" :: document_body
-    and  "value-assert-error"             :: document_body
-    and  "definition-assert-error"        :: document_body
-    and  "doc_class-assert-error"        :: document_body
-
-begin
-
-section\<open>Testing Commands (exec-catch-verify - versions of DOF commands)\<close>
-
-ML\<open> 
-
-fun gen_enriched_document_command2 name {body} cid_transform attr_transform markdown
-                                  ((meta_args,
-                                     xstring_opt:(xstring * Position.T) option),
-                                    toks_list:Input.source list) 
-                                  : theory -> theory =
-  let  val toplvl = Toplevel.make_state o SOME
-       val ((binding,cid_pos), doc_attrs) = meta_args
-       val oid = Binding.name_of binding
-       val oid' = if meta_args = ODL_Meta_Args_Parser.empty_meta_args
-                  then "output"
-                  else oid
-       (* as side-effect, generates markup *)
-       fun check_n_tex_text thy toks = let val ctxt = Toplevel.presentation_context (toplvl thy)
-                                      val pos = Input.pos_of toks;
-                                      val _ =   Context_Position.reports ctxt
-                                                [(pos, Markup.language_document (Input.is_delimited toks)),
-                                                 (pos, Markup.plain_text)];
-                                      fun markup xml = let val m = if body then Markup.latex_body 
-                                                                   else Markup.latex_heading
-                                                       in [XML.Elem (m (Latex.output_name name), 
-                                                           xml)] end;
-
-                                      val text = Document_Output.output_document 
-                                                                 (Proof_Context.init_global thy) 
-                                                                 markdown toks
-(*   type file = {path: Path.T, pos: Position.T, content: string} *) 
-
-                                      val strg = XML.string_of (hd (Latex.output text))
-                                      val file = {path = Path.make [oid' ^ "_snippet.tex"],
-                                                  pos = @{here}, 
-                                                  content = Bytes.string strg}
-                                      val dir = Path.append (Resources.master_directory thy) (Path.make ["latex_test"]) 
-                                      val _ = Generated_Files.write_file dir file
-                                      val _ = writeln (strg)
-                                  in  () end \<comment> \<open>important observation: thy is not modified.
-                                                  This implies that several text block can be 
-                                                  processed in parallel in a future, as long
-                                                  as they are associated to one meta arg.\<close>
-       val handle_margs_opt = (if meta_args = ODL_Meta_Args_Parser.empty_meta_args
-              then I
-              else
-          Value_Command.Docitem_Parser.create_and_check_docitem 
-                              {is_monitor = false} {is_inline = false} {define = true}
-                              binding (cid_transform cid_pos) (attr_transform doc_attrs))
-       (* ... generating the level-attribute syntax *)
-  in   handle_margs_opt  #> (fn thy => (app (check_n_tex_text thy) toks_list; thy))
-  end;
-
-val _ =
-  Outer_Syntax.command ("text-", @{here}) "formal comment macro"
-    (ODL_Meta_Args_Parser.attributes -- Parse.opt_target -- Scan.repeat1 Parse.document_source 
-      >> (Toplevel.theory o (gen_enriched_document_command2 "TTT" {body=true} I I {markdown = true} )));
-
-(* copied from Pure_syn for experiments *)
-
-fun output_document2 state markdown txt =
-  let
-    val ctxt = Toplevel.presentation_context state;
-    val pos = Input.pos_of txt;
-    val _ =
-      Context_Position.reports ctxt
-        [(pos, Markup.language_document (Input.is_delimited txt)),
-         (pos, Markup.plain_text)];
-    val txt' = Document_Output.output_document ctxt markdown txt
-    val strg = XML.string_of (hd (Latex.output txt'))
-
-    val _ = writeln (strg)
-  in Document_Output.output_document ctxt markdown txt end;
-
-fun document_command2 markdown (loc, txt) =
-  let fun doc2 state = (case loc of
-                      NONE => ignore (output_document2 state markdown txt)
-                    | SOME (_, pos) =>(ISA_core.err 
-                                           "Illegal target specification -- not a theory context" 
-                                           pos))
-      fun out2 state = output_document2 state markdown txt
-  in  Toplevel.keep doc2  o  Toplevel.present_local_theory loc out2
-  end
-
-fun gen_enriched_document_command3 assert name body trans at md (margs, src_list) thy
- = (gen_enriched_document_command2 name body trans at md  (margs, src_list)  thy)
-   handle ERROR msg => (if assert src_list msg then (writeln ("Correct error: "^msg^": reported.");thy)
-                                               else error"Wrong error reported")
-
-fun error_match src msg = (String.isPrefix (Input.string_of src) msg)
-
-fun  error_match2 [_, src] msg = error_match src msg
-   | error_match2 _ _ = error "Wrong text-assertion-error. Argument format <arg><match> required."
-
-
-val _ =
-  Outer_Syntax.command ("text-assert-error", @{here}) "formal comment macro"
-    (ODL_Meta_Args_Parser.opt_attributes -- Parse.opt_target -- Scan.repeat1 Parse.document_source 
-      >> (Toplevel.theory o (gen_enriched_document_command3 error_match2 "TTT" {body=true}
-                                                            I I {markdown = true} )));
-
-fun update_instance_command (args,src) thy = 
-    (Monitor_Command_Parser.update_instance_command args thy
-     handle ERROR msg => (if error_match src msg 
-                          then (writeln ("Correct error: "^msg^": reported.");thy)
-                          else error"Wrong error reported"))
-val _ =
-  Outer_Syntax.command \<^command_keyword>\<open>update_instance-assert-error\<close>
-                       "update meta-attributes of an instance of a document class"
-                        (ODL_Meta_Args_Parser.attributes_upd -- Parse.document_source
-                         >> (Toplevel.theory o update_instance_command)); 
-
-val _ = 
-  let fun create_and_check_docitem (((binding,cid_pos),doc_attrs),src) thy =
-                  (Value_Command.Docitem_Parser.create_and_check_docitem
-                          {is_monitor = false} {is_inline=true}
-                          {define = false} binding (cid_pos) (doc_attrs) thy)
-                   handle ERROR msg => (if error_match src msg 
-                          then (writeln ("Correct error: "^msg^": reported.");thy)
-                          else error"Wrong error reported")
-  in  Outer_Syntax.command \<^command_keyword>\<open>declare_reference-assert-error\<close>
-                           "declare document reference"
-                           (ODL_Meta_Args_Parser.attributes -- Parse.document_source
-                            >> (Toplevel.theory o create_and_check_docitem))
-  end;
-
-
-val _ =
-  let fun pass_trans_to_value_cmd (args, (((name, modes), t),src)) trans  =
-      let val pos = Toplevel.pos_of trans
-      in trans |> Toplevel.theory
-                  (fn thy => Value_Command.value_cmd {assert=false} args name modes t pos thy
-                   handle ERROR msg => (if error_match src msg 
-                                        then (writeln ("Correct error: "^msg^": reported."); thy)
-                                        else error"Wrong error reported"))
-      end
-  in  Outer_Syntax.command \<^command_keyword>\<open>value-assert-error\<close> "evaluate and print term"
-       (ODL_Meta_Args_Parser.opt_attributes -- 
-          (Value_Command.opt_evaluator 
-           -- Value_Command.opt_modes 
-           -- Parse.term 
-           -- Parse.document_source) 
-        >> (pass_trans_to_value_cmd))
-  end;
-
-val _ =
-  let fun definition_cmd' meta_args_opt decl params prems spec src bool ctxt =
-        Local_Theory.background_theory (Value_Command.meta_args_exec meta_args_opt) ctxt
-        |> (fn ctxt => Definition_Star_Command.definition_cmd decl params prems spec bool ctxt
-        handle ERROR msg => if error_match src msg 
-                             then (writeln ("Correct error: "^msg^": reported.")
-                                  ; pair "Bound 0" @{thm refl}
-                                    |> pair (Bound 0)
-                                    |> rpair ctxt)
-                             else error"Wrong error reported")
-  in
-  Outer_Syntax.local_theory' \<^command_keyword>\<open>definition-assert-error\<close> "constant definition"
-    (ODL_Meta_Args_Parser.opt_attributes --
-      (Scan.option Parse_Spec.constdecl -- (Parse_Spec.opt_thm_name ":" -- Parse.prop) --
-        Parse_Spec.if_assumes -- Parse.for_fixes -- Parse.document_source)
-     >> (fn (meta_args_opt, ((((decl, spec), prems), params), src)) => 
-                                    #2 oo definition_cmd' meta_args_opt decl params prems spec src))
-  end;
-
-
-val _ =
-  let fun add_doc_class_cmd' ((((overloaded, hdr), (parent, attrs)),((rejects,accept_rex),invars)), src) =
-        (fn thy => OntoParser.add_doc_class_cmd {overloaded = overloaded} hdr parent attrs rejects accept_rex invars thy
-         handle ERROR msg => (if error_match src msg 
-                                        then (writeln ("Correct error: "^msg^": reported."); thy)
-                                        else error"Wrong error reported"))
-  in
-  Outer_Syntax.command \<^command_keyword>\<open>doc_class-assert-error\<close> 
-                       "define document class"
-                        ((OntoParser.parse_doc_class -- Parse.document_source)
-                         >> (Toplevel.theory o add_doc_class_cmd'))
-  end
-
-val _ =
-  Outer_Syntax.command ("text-latex", \<^here>) "formal comment (primary style)"
-    (Parse.opt_target -- Parse.document_source >> document_command2 {markdown = true});
-
-\<close>
-
-(* a little auto-test *)
-text-latex\<open>dfg\<close>
-
-text-assert-error[aaaa::A]\<open> @{A \<open>sdf\<close>}\<close>\<open>reference ontologically inconsistent\<close>
-
-end

Isabelle_DOF-Unit-Tests/Test_Polymorphic_Classes.thy

@@ -1,719 +0,0 @@
-theory Test_Polymorphic_Classes
-  imports Isabelle_DOF.Isa_DOF
-          TestKit
-begin
-
-text\<open>The name \<open>text\<close> is reserved by the implementation and refers to the default super class:\<close>
-doc_class-assert-error "text" =
-a::int
-\<open>text: This name is reserved by the implementation\<close>
-
-doc_class title =
-  short_title :: "string option" <= "None"
-
-doc_class Author =
-  email :: "string" <= "''''"
-
-datatype classification = SIL0 | SIL1 | SIL2 | SIL3 | SIL4
-
-doc_class abstract =
-  keywordlist :: "string list" <= "[]"
-  safety_level :: "classification" <= "SIL3"
-
-doc_class text_section =
-  authored_by :: "Author set" <= "{}"
-  level :: "int option" <= "None"
-
-doc_class ('a::one, 'b, 'c) test0 = text_section +
-  testa :: "'a list"
-  testb :: "'b list"
-  testc :: "'c list"
-
-typ\<open>('a, 'b, 'c) test0\<close>
-typ\<open>('a, 'b, 'c, 'd) test0_scheme\<close>
-
-find_consts name:"test0"
-find_theorems name:"test0"
-
-
-doc_class 'a test1 = text_section +
-  test1 :: "'a list"
-   invariant author_finite_test :: "finite (authored_by \<sigma>)"
-   invariant force_level_test :: "(level \<sigma>) \<noteq> None \<and> the (level \<sigma>) > 1"
-
-find_consts name:"test1*inv"
-find_theorems name:"test1*inv"
-
-text*[church::Author, email="\<open>b\<close>"]\<open>\<close>
-text\<open>@{Author "church"}\<close>
-value*\<open>@{Author \<open>church\<close>}\<close>
-
-text\<open>\<^value_>\<open>@{Author \<open>church\<close>}\<close>\<close>
-
-doc_class ('a, 'b) test2 =  "'a test1" +
-  test2 :: "'b list"
-type_synonym ('a, 'b) test2_syn = "('a, 'b) test2"
-
-find_theorems name:"test2"
-
-declare [[invariants_checking_with_tactics]]
-text*[testtest::"('a, int) test2", level = "Some 2", authored_by = "{@{Author \<open>church\<close>}}", test2 = "[1]"]\<open>\<close>
-value*\<open>test2 @{test2 \<open>testtest\<close>}\<close>
-
-text*[testtest2''::"(nat, int) test2", test1 = "[2::nat, 3]", test2 = "[4::int, 5]", level = "Some (2::int)"]\<open>\<close>
-value*\<open>test1 @{test2 \<open>testtest2''\<close>}\<close>
-declare [[invariants_checking_with_tactics = false]]
-
-ML\<open>
-val t = Syntax.parse_term \<^context> "@{test2 \<open>testtest\<close>}"
-
-\<close>
-ML\<open>
-val t = \<^term>\<open>test2.make 8142730 Test_Parametric_Classes_2_test2_authored_by_Attribute_Not_Initialized Test_Parametric_Classes_2_test2_level_Attribute_Not_Initialized Test_Parametric_Classes_2_test2_test1_Attribute_Not_Initialized
-                         Test_Parametric_Classes_2_test2_test2_Attribute_Not_Initialized
-                        \<lparr>authored_by := bot, level := None\<rparr> \<close>
-\<close>
-
-text\<open>test2 = "[1::'a::one]" should be test2 = "[1::int]" because the type of testtest4 is ('a::one, int) test2:\<close>
-text-assert-error[testtest4::"('a::one, int) test2", level = "Some 2", authored_by = "{@{Author \<open>church\<close>}}", test2 = "[1::'a::one]"]\<open>\<close>
-  \<open>Type unification failed\<close>
-text\<open>Indeed this definition fails:\<close>
-definition-assert-error testtest2::"('a::one, int) test2" where "testtest2 \<equiv>
-                  test2.make 11953346 
-                  {@{Author \<open>church\<close>}}
-                  (Some 2)
-                  []
-                  []
-                  \<lparr>authored_by := bot
-                      , level := None, level := Some 2
-                      , authored_by := insert \<lparr>Author.tag_attribute = 11953164, email = []\<rparr> bot
-                      , test2.test2 := [1::('a::one)]\<rparr> "
-\<open>Type unification failed\<close>
-
-text\<open>For now, no more support of type synonyms as parent:\<close>
-doc_class ('a, 'b, 'c) A =
-a :: "'a list"
-b :: "'b list"
-c :: "'c list"
-type_synonym ('a, 'b, 'c) A_syn = "('a, 'b, 'c) A"
-
-doc_class-assert-error ('a, 'b, 'c, 'd) B = "('b, 'c, 'd) A_syn" +
-d ::"'a::one list" <= "[1]"
-\<open>Undefined onto class: "A_syn"\<close>
-
-
-declare[[invariants_checking_with_tactics]]
-
-definition* testauthor0  where "testauthor0 \<equiv> \<lparr>Author.tag_attribute = 5, email = \<open>test_author_email\<close>\<rparr>"
-definition* testauthor :: "Author" where "testauthor \<equiv> \<lparr>Author.tag_attribute = 5, email = \<open>test_author_email\<close>\<rparr>"
-definition* testauthor2 :: "Author" where "testauthor2 \<equiv> \<lparr>Author.tag_attribute = 5, email = \<open>test_author_email\<close>\<rparr> \<lparr>email := \<open>test_author_email_2\<close> \<rparr>"
-definition* testauthor3 :: "Author" where "testauthor3 \<equiv> testauthor \<lparr>email := \<open>test_author_email_2\<close> \<rparr>"
-
-ML\<open>
-val ctxt =  \<^context>
-val input0 = Syntax.read_input "@{Author \<open>church\<close>}"
-val source = Syntax.read_input "\<^term_>\<open>@{Author \<open>church\<close>}\<close>"
-val input = source
-val tt = Document_Output.output_document ctxt {markdown = false} input
-\<close>
-
-doc_class ('a, 'b) elaborate1 =
-a :: "'a list"
-b :: "'b list"
-
-doc_class ('a, 'b) elaborate2 = 
-c :: "('a, 'b) elaborate1 list"
-
-doc_class ('a, 'b) elaborate3 = 
-d :: "('a, 'b) elaborate2 list"
-
-text*[test_elaborate1::"('a::one, 'b) elaborate1", a = "[1]"]\<open>\<close>
-
-term*\<open>@{elaborate1 \<open>test_elaborate1\<close>}\<close>
-value* [nbe]\<open>@{elaborate1 \<open>test_elaborate1\<close>}\<close> 
-
-
-text*[test_elaborate2::"('a::one, 'b) elaborate2", c = "[@{elaborate1 \<open>test_elaborate1\<close>}]"]\<open>\<close>
-
-text*[test_elaborate3::"('a::one, 'b) elaborate3", d = "[@{elaborate2 \<open>test_elaborate2\<close>}]"]\<open>\<close>
-
-term*\<open>(concat o concat) ((map o map) a (map c (elaborate3.d @{elaborate3 \<open>test_elaborate3\<close>})))\<close>
-value*\<open>(concat o concat) ((map o map) a (map c (elaborate3.d @{elaborate3 \<open>test_elaborate3\<close>})))\<close>
-
-
-text\<open>
-The term antiquotation is considered a ground term.
-Then its type here is \<^typ>\<open>'a::one list\<close> with \<open>'a\<close> a fixed-type variable.
-So the following definition only works because the parameter of the class is also \<open>'a\<close>.\<close>
-declare[[ML_print_depth = 10000]]
-doc_class 'a elaborate4 = 
-d :: "'a::one list" <= "(concat o concat) ((map o map) a (map c (elaborate3.d @{elaborate3 \<open>test_elaborate3\<close>})))"
-declare[[ML_print_depth = 20]]
-
-declare[[ML_print_depth = 10000]]
-text*[test_elaborate4::"'a::one elaborate4"]\<open>\<close>
-declare[[ML_print_depth = 20]]
-
-
-text\<open>Bug:
-As the term antiquotation is considered as a ground term,
-its type \<^typ>\<open>'a::one list\<close> conflicts with the type of the attribute \<^typ>\<open>int list\<close>.
-To support the instantiation of the term antiquotation as an \<^typ>\<open>int list\<close>,
-the term antiquotation should have the same behavior as a constant definition,
-which is not the case for now.\<close>
-declare[[ML_print_depth = 10000]]
-doc_class-assert-error elaborate4' = 
-d :: "int list" <= "(concat o concat) ((map o map) a (map c (elaborate3.d @{elaborate3 \<open>test_elaborate3\<close>})))"
-\<open>Type unification failed\<close>
-declare[[ML_print_depth = 20]]
-
-text\<open>The behavior we want to support: \<close>
-
-definition one_list :: "'a::one list" where "one_list \<equiv> [1]"
-
-text\<open>the constant \<^const>\<open>one_list\<close> can be instantiate as an \<^typ>\<open>int list\<close>:\<close>
-doc_class elaborate4'' = 
-d :: "int list" <= "one_list"
-
-declare[[ML_print_depth = 10000]]
-text*[test_elaborate4''::"elaborate4''"]\<open>\<close>
-declare[[ML_print_depth = 20]]
-
-
-term*\<open>concat (map a (elaborate2.c @{elaborate2 \<open>test_elaborate2\<close>}))\<close>
-value*\<open>concat (map a (elaborate2.c @{elaborate2 \<open>test_elaborate2\<close>}))\<close>
-
-text\<open>
-The term antiquotation is considered a ground term.
-Then its type here is \<^typ>\<open>'a::one list\<close> with \<open>'a\<close> a fixed-type variable.
-So the following definition only works because the parameter of the class is also \<open>'a\<close>.\<close>
-declare[[ML_print_depth = 10000]]
-doc_class 'a elaborate5 =
-d :: "'a::one list" <= "concat (map a (elaborate2.c @{elaborate2 \<open>test_elaborate2\<close>}))"
-declare[[ML_print_depth = 20]]
-
-text\<open>Bug: But when defining an instance, as we use a \<open>'b\<close> variable to specify the type
-of the instance (\<^typ>\<open>'b::one elaborate5\<close>, then the unification fails\<close>
-declare[[ML_print_depth = 10000]]
-text-assert-error[test_elaborate5::"'b::one elaborate5"]\<open>\<close>
-\<open>Inconsistent sort constraints for type variable "'b"\<close>
-declare[[ML_print_depth = 20]]
-
-text\<open>Bug:
-The term antiquotation is considered a ground term.
-Then its type here is \<^typ>\<open>'a::one list\<close> with \<open>'a\<close> a fixed-type variable.
-So it is not compatible with the type of the attribute \<^typ>\<open>'a::numeral list\<close>\<close>
-doc_class-assert-error 'a elaborate5' =
-d :: "'a::numeral list" <= "concat (map a (elaborate2.c @{elaborate2 \<open>test_elaborate2\<close>}))"
-\<open>Sort constraint\<close>
-
-text\<open>The behavior we want to support: \<close>
-
-text\<open>the constant \<^const>\<open>one_list\<close> can be instantiate as an \<^typ>\<open>'a::numeral list\<close>:\<close>
-doc_class 'a elaborate5'' = 
-d :: "'a::numeral list" <= "one_list"
-
-
-text*[test_elaborate1a::"('a::one, int) elaborate1", a = "[1]", b = "[2]"]\<open>\<close>
-
-term*\<open>@{elaborate1 \<open>test_elaborate1a\<close>}\<close>
-value* [nbe]\<open>@{elaborate1 \<open>test_elaborate1a\<close>}\<close> 
-
-text*[test_elaborate2a::"('a::one, int) elaborate2", c = "[@{elaborate1 \<open>test_elaborate1a\<close>}]"]\<open>\<close>
-
-text*[test_elaborate3a::"('a::one, int) elaborate3", d = "[@{elaborate2 \<open>test_elaborate2a\<close>}]"]\<open>\<close>
-
-text\<open>
-The term antiquotation is considered a ground term.
-Then its type here is \<^typ>\<open>'a::one list\<close> with \<open>'a\<close> a fixed-type variable.
-So the following definition only works because the parameter of the class is also \<open>'a\<close>.\<close>
-definition* test_elaborate3_embedding ::"'a::one list"
-  where "test_elaborate3_embedding \<equiv> (concat o concat) ((map o map) elaborate1.a (map elaborate2.c (elaborate3.d @{elaborate3 \<open>test_elaborate3a\<close>})))"
-
-text\<open>Bug:
-The term antiquotation is considered a ground term.
-Then its type here is \<^typ>\<open>'a::one list\<close> with \<open>'a\<close> a fixed-type variable.
-So it is not compatible with the specified type of the definition \<^typ>\<open>int list\<close>:\<close>
-definition-assert-error test_elaborate3_embedding'::"int list"
-  where "test_elaborate3_embedding' \<equiv> (concat o concat) ((map o map) elaborate1.a (map elaborate2.c (elaborate3.d @{elaborate3 \<open>test_elaborate3a\<close>})))"
-\<open>Type unification failed\<close>
-
-term*\<open>@{elaborate1 \<open>test_elaborate1a\<close>}\<close>
-value* [nbe]\<open>@{elaborate1 \<open>test_elaborate1a\<close>}\<close>
-
-
-record ('a, 'b) elaborate1' =
-a :: "'a list"
-b :: "'b list"
-
-record ('a, 'b) elaborate2' = 
-c :: "('a, 'b) elaborate1' list"
-
-record ('a, 'b) elaborate3' = 
-d :: "('a, 'b) elaborate2' list"
-
-doc_class 'a one =
-a::"'a list"
-
-text*[test_one::"'a::one one", a = "[1]"]\<open>\<close>
-
-value* [nbe] \<open>@{one \<open>test_one\<close>}\<close>
-
-term*\<open>a @{one \<open>test_one\<close>}\<close>
-
-text\<open>Bug:
-The term antiquotation is considered a ground term.
-Then its type here is \<^typ>\<open>'a::one list\<close> with \<open>'a\<close> a fixed-type variable.
-So it is not compatible with the specified type of the definition \<^typ>\<open>('b::one, 'a::numeral) elaborate1'\<close>
-because the term antiquotation can not be instantiate as a \<^typ>\<open>'b::one list\<close>
-and the \<open>'a\<close> is checked against the \<open>'a::numeral\<close> instance type parameter:\<close>
-definition-assert-error test_elaborate1'::"('b::one, 'a::numeral) elaborate1'"
-  where "test_elaborate1' \<equiv> \<lparr> elaborate1'.a = a @{one \<open>test_one\<close>}, b = [2] \<rparr>"
-\<open>Sort constraint\<close>
-
-text\<open>This is the same behavior as the following:\<close>
-definition-assert-error test_elaborate10::"('b::one, 'a::numeral) elaborate1'"
-  where "test_elaborate10 \<equiv> \<lparr>  elaborate1'.a = [1::'a::one], b = [2] \<rparr>"
-\<open>Sort constraint\<close>
-
-definition-assert-error test_elaborate11::"('b::one, 'c::numeral) elaborate1'"
-  where "test_elaborate11 \<equiv> \<lparr>  elaborate1'.a = [1::'a::one], b = [2] \<rparr>"
-\<open>Type unification failed\<close>
-
-text\<open>So this works:\<close>
-definition* test_elaborate1''::"('a::one, 'b::numeral) elaborate1'"
-  where "test_elaborate1'' \<equiv> \<lparr> elaborate1'.a = a @{one \<open>test_one\<close>}, b = [2] \<rparr>"
-
-term \<open>elaborate1'.a test_elaborate1''\<close>
-value [nbe] \<open>elaborate1'.a test_elaborate1''\<close>
-
-text\<open>But if we embed the term antiquotation in a definition,
-the type unification works:\<close>
-definition* onedef where "onedef \<equiv> @{one \<open>test_one\<close>}"
-
-definition test_elaborate1'''::"('b::one, 'a::numeral) elaborate1'"
-  where "test_elaborate1''' \<equiv> \<lparr>  elaborate1'.a = a onedef, b = [2] \<rparr>"
-
-value [nbe] \<open>elaborate1'.a test_elaborate1'''\<close>
-
-
-definition test_elaborate2'::"(int, 'b::numeral) elaborate2'"
-  where "test_elaborate2' \<equiv> \<lparr> c = [test_elaborate1''] \<rparr>"
-
-definition test_elaborate3'::"(int, 'b::numeral) elaborate3'"
-  where "test_elaborate3' \<equiv> \<lparr> d = [test_elaborate2'] \<rparr>"
-
-
-doc_class 'a test3' =
-test3 :: "int"
-test3' :: "'a list"
-
-text*[testtest30::"'a::one test3'", test3'="[1]"]\<open>\<close>
-text-assert-error[testtest30::"'a test3'", test3'="[1]"]\<open>\<close>
-\<open>Type unification failed: Variable\<close>
-
-find_consts name:"test3'.test3"
-definition testone :: "'a::one test3'" where "testone \<equiv> \<lparr>tag_attribute = 5, test3 = 3, test3' = [1] \<rparr>"
-definition* testtwo :: "'a::one test3'" where "testtwo \<equiv> \<lparr>tag_attribute = 5, test3 = 1, test3' = [1] \<rparr>\<lparr> test3 := 1\<rparr>"
-
-text*[testtest3'::"'a test3'", test3 = "1"]\<open>\<close>
-
-declare [[show_sorts = false]]
-definition* testtest30 :: "'a test3'" where "testtest30 \<equiv> \<lparr>tag_attribute = 12, test3 = 2, test3' = [] \<rparr>"
-update_instance*[testtest3'::"'a test3'", test3 := "2"]
-
-ML\<open>
-val t = @{value_ [nbe] \<open>test3 @{test3' \<open>testtest3'\<close>}\<close>}
-val tt = HOLogic.dest_number t
-\<close>
-
-text\<open>@{value_ [] [nbe] \<open>test3 @{test3' \<open>testtest3'\<close>}\<close>}\<close>
-
-update_instance*[testtest3'::"'a test3'", test3 += "2"]
-
-ML\<open>
-val t = @{value_ [nbe] \<open>test3 @{test3' \<open>testtest3'\<close>}\<close>}
-val tt = HOLogic.dest_number t
-\<close>
-
-value\<open>test3 \<lparr> tag_attribute = 1, test3 = 2, test3' = [2::int, 3] \<rparr>\<close>
-value\<open>test3 \<lparr> tag_attribute = 1, test3 = 2, test3' = [2::int, 3] \<rparr>\<close>
-find_consts name:"test3'.test3"
-
-ML\<open>
-val test_value = @{value_ \<open>@{test3' \<open>testtest3'\<close>}\<close>}
-
-\<close>
-declare [[show_sorts = false]]
-update_instance*[testtest3'::"'a test3'", test3 += "3"]
-declare [[show_sorts = false]]
-value*\<open>test3 @{test3' \<open>testtest3'\<close>}\<close>
-value\<open>test3 \<lparr> tag_attribute = 12, test3 = 5, test3' = AAAAAA\<rparr>\<close>
-
-find_consts name:"test3'.test3"
-
-text*[testtest3''::"int test3'", test3 = "1"]\<open>\<close>
-
-update_instance*[testtest3''::"int test3'", test3' += "[3]"]
-
-value*\<open>test3' @{test3' \<open>testtest3''\<close>}\<close>
-
-update_instance*[testtest3''::"int test3'", test3' := "[3]"]
-
-value*\<open>test3' @{test3' \<open>testtest3''\<close>}\<close>
-
-update_instance*[testtest3''::"int test3'", test3' += "[2,5]"]
-
-value*\<open>test3' @{test3' \<open>testtest3''\<close>}\<close>
-
-definition testeq where "testeq \<equiv> \<lambda>x. x"
-find_consts name:"test3'.ma"
-
-text-assert-error[testtest3''::"int test3'", test3 = "1", test3' = "[3::'a::numeral]"]\<open>\<close>
-  \<open>Type unification failed\<close>
-
-text-assert-error[testtest3''::"int test3'", test3 = "1", test3' = "[3]"]\<open>\<close>
-  \<open>Duplicate instance declaration\<close>
-
-
-declare[[ML_print_depth = 10000]]
-definition-assert-error testest3''' :: "int test3'"
-  where "testest3''' \<equiv> \<lparr> tag_attribute = 12, test3 = 1, test3' = [2]\<rparr>\<lparr> test3' := [3::'a::numeral]\<rparr>"
-\<open>Type unification failed\<close>
-declare[[ML_print_depth = 20]]
-
-value* \<open>test3 @{test3' \<open>testtest3''\<close>}\<close>
-value* \<open>\<lparr> tag_attribute = 12, test3 = 1, test3' = [2]\<rparr>\<lparr> test3' := [3::int]\<rparr>\<close>
-value* \<open>test3 (\<lparr> tag_attribute = 12, test3 = 1, test3' = [2]\<rparr>\<lparr> test3' := [3::int]\<rparr>)\<close>
-term*\<open>@{test3' \<open>testtest3''\<close>}\<close>
-
-ML\<open>val t = \<^term_>\<open>test3 @{test3' \<open>testtest3''\<close>}\<close>\<close>
-
-value\<open>test3 \<lparr> tag_attribute = 12, test3 = 2, test3' =  [2::int ,3]\<rparr>\<close>
-
-find_consts name:"test3'.test3"
-find_consts name:"Isabelle_DOF_doc_class_test3'"
-update_instance*[testtest3''::"int test3'", test3 := "2"]
-ML\<open>
-val t = @{value_ [nbe] \<open>test3 @{test3' \<open>testtest3''\<close>}\<close>}
-val tt = HOLogic.dest_number t |> snd
-\<close>
-
-doc_class 'a testa =
-a:: "'a set"
-b:: "int set"
-
-text*[testtesta::"'a testa", b = "{2}"]\<open>\<close>
-update_instance*[testtesta::"'a testa", b += "{3}"]
-
-ML\<open>
-val t = @{value_ [nbe] \<open>b @{testa \<open>testtesta\<close>}\<close>}
-val tt = HOLogic.dest_set t |> map (HOLogic.dest_number #> snd)
-\<close>
-
-update_instance-assert-error[testtesta::"'a::numeral testa", a := "{2::'a::numeral}"]
-\<open>incompatible classes:'a Test_Polymorphic_Classes.testa:'a::numeral Test_Polymorphic_Classes.testa\<close>
-
-text*[testtesta'::"'a::numeral testa", a = "{2}"]\<open>\<close>
-
-update_instance*[testtesta'::"'a::numeral testa", a += "{3}"]
-
-ML\<open>
-val t = @{value_ [nbe] \<open>a @{testa \<open>testtesta'\<close>}\<close>}
-\<close>
-
-update_instance-assert-error[testtesta'::"'a::numeral testa", a += "{3::int}"]
-  \<open>Type unification failed\<close>
-
-definition-assert-error testtesta'' :: "'a::numeral testa"
-  where "testtesta'' \<equiv> \<lparr>tag_attribute = 5, a = {1}, b = {1} \<rparr>\<lparr> a := {1::int}\<rparr>"
-\<open>Type unification failed\<close>
-
-update_instance*[testtesta'::"'a::numeral testa", b := "{3::int}"]
-ML\<open>
-val t = @{value_ [nbe] \<open>b @{testa \<open>testtesta'\<close>}\<close>}
-\<close>
-
-value* [nbe] \<open>b @{testa \<open>testtesta'\<close>}\<close>
-
-definition testtesta'' :: "'a::numeral testa"
-  where "testtesta'' \<equiv> \<lparr>tag_attribute = 5, a = {1}, b = {1} \<rparr>\<lparr> b := {2::int}\<rparr>"
-
-value [nbe]\<open>b testtesta''\<close>
-
-doc_class 'a test3 =
-test3 :: "'a list"
-type_synonym 'a test3_syn = "'a test3"
-
-text*[testtest3::"int test3", test3 = "[1]"]\<open>\<close>
-update_instance*[testtest3::"int test3", test3 := "[2]"]
-ML\<open>
-val t = \<^term_>\<open>test3 @{test3 \<open>testtest3\<close>}\<close>
-val tt = \<^value_>\<open>test3 @{test3 \<open>testtest3\<close>}\<close> |> HOLogic.dest_list |> map HOLogic.dest_number
-\<close>
-
-update_instance*[testtest3::"int test3", test3 += "[3]"]
-value*\<open>test3 @{test3 \<open>testtest3\<close>}\<close>
-
-
-doc_class ('a, 'b) test4 =  "'a test3" +
-  test4 :: "'b list"
-
-definition-assert-error testtest0'::"('a::one, int) test4" where "testtest0' \<equiv>
-                  test4.make 11953346 
-                  [] [1::('a::one)]"
-\<open>Type unification failed\<close>
-
-definition-assert-error testtest0''::"('a, int) test4" where "testtest0'' \<equiv>
-                  test4.make 11953346 
-                   [1] Test_Parametric_Classes_2_test4_test4_Attribute_Not_Initialized"
-\<open>Type unification failed\<close>
-
-text\<open>Must fail because the equivalent definition
-\<open>testtest0'\<close> below fails
-due to the constraint in the where [1::('a::one)] is not an \<^typ>\<open>int list\<close>
-but an \<^typ>\<open>'a::one list\<close> list \<close>
-text-assert-error[testtest0::"('a::one, int) test4", test4 = "[1::'a::one]"]\<open>\<close>
-\<open>Type unification failed\<close>
-update_instance-assert-error[testtest0::"('a::one, int) test4"]
-  \<open>Undefined instance: "testtest0"\<close>
-
-value-assert-error\<open>@{test4 \<open>testtest0\<close>}\<close>\<open>Undefined instance: "testtest0"\<close>
-
-definition testtest0''::"('a, int) test4" where "testtest0'' \<equiv>
-                  \<lparr> tag_attribute = 11953346, test3 = [], test4 =  [1]\<rparr>\<lparr>test4 := [2]\<rparr>"
-
-definition testtest0'''::"('a, int) test4" where "testtest0''' \<equiv>
-                  \<lparr> tag_attribute = 11953346, test3 = [], test4 =  [1]\<rparr>\<lparr>test4 := [2]\<rparr>"
-
-
-value [nbe] \<open>test3 testtest0''\<close>
-
-type_synonym notion = string
-
-doc_class Introduction = text_section +
-  authored_by :: "Author set"  <= "UNIV" 
-  uses :: "notion set"
-  invariant author_finite :: "finite (authored_by \<sigma>)"
-  and force_level :: "(level \<sigma>) \<noteq> None \<and> the (level \<sigma>) > 1"
-
-doc_class claim = Introduction +
-  based_on :: "notion list"
-
-doc_class technical = text_section +
-  formal_results :: "thm list" 
-
-doc_class "definition" = technical +
-  is_formal :: "bool"
-  property  :: "term list" <= "[]" 
-
-datatype kind = expert_opinion | argument | "proof"
-
-doc_class result = technical +
-  evidence :: kind
-  property :: "thm list" <= "[]"
-  invariant has_property :: "evidence \<sigma> = proof \<longleftrightarrow> property \<sigma> \<noteq> []"
-
-doc_class example = technical +
-  referring_to :: "(notion + definition) set" <= "{}"
-
-doc_class conclusion = text_section +
-  establish :: "(claim \<times> result) set"
-  invariant establish_defined :: "\<forall> x. x \<in> Domain (establish \<sigma>)
-                                           \<longrightarrow> (\<exists> y \<in> Range (establish \<sigma>). (x, y) \<in> establish \<sigma>)"
-
-text\<open>Next we define some instances (docitems): \<close>
-
-declare[[invariants_checking_with_tactics = true]]
-
-text*[church1::Author, email="\<open>church@lambda.org\<close>"]\<open>\<close>
-
-text*[resultProof::result, evidence = "proof", property="[@{thm \<open>HOL.refl\<close>}]"]\<open>\<close>
-text*[resultArgument::result, evidence = "argument"]\<open>\<close>
-
-text\<open>The invariants \<^theory_text>\<open>author_finite\<close> and \<^theory_text>\<open>establish_defined\<close> can not be checked directly
-  and need a little help.
-  We can set the \<open>invariants_checking_with_tactics\<close> theory attribute to help the checking.
-  It will enable a basic tactic, using unfold and auto:\<close>
-
-declare[[invariants_checking_with_tactics = true]]
-
-text*[curry::Author, email="\<open>curry@lambda.org\<close>"]\<open>\<close>
-text*[introduction2::Introduction, authored_by = "{@{Author \<open>church\<close>}}", level = "Some 2"]\<open>\<close>
-(* When not commented, should violated the invariant:
-update_instance*[introduction2::Introduction
-                  , authored_by := "{@{Author \<open>church\<close>}}"
-                  , level := "Some 1"]
-*)
-
-text*[introduction_test_parsed_elaborate::Introduction, authored_by = "authored_by @{Introduction \<open>introduction2\<close>}", level = "Some 2"]\<open>\<close>
-term*\<open>authored_by @{Introduction \<open>introduction_test_parsed_elaborate\<close>}\<close>
-value*\<open>authored_by @{Introduction \<open>introduction_test_parsed_elaborate\<close>}\<close>
-text*[introduction3::Introduction, authored_by = "{@{Author \<open>church\<close>}}", level = "Some 2"]\<open>\<close>
-text*[introduction4::Introduction, authored_by = "{@{Author \<open>curry\<close>}}", level = "Some 4"]\<open>\<close>
-
-text*[resultProof2::result, evidence = "proof", property="[@{thm \<open>HOL.sym\<close>}]"]\<open>\<close>
-
-text\<open>Then we can evaluate expressions with instances:\<close>
-
-term*\<open>authored_by @{Introduction \<open>introduction2\<close>} = authored_by @{Introduction \<open>introduction3\<close>}\<close>
-value*\<open>authored_by @{Introduction \<open>introduction2\<close>} = authored_by @{Introduction \<open>introduction3\<close>}\<close>
-value*\<open>authored_by @{Introduction \<open>introduction2\<close>} = authored_by @{Introduction \<open>introduction4\<close>}\<close>
-
-value*\<open>@{Introduction \<open>introduction2\<close>}\<close>
-
-value*\<open>{@{Author \<open>curry\<close>}} = {@{Author \<open>church\<close>}}\<close>
-
-term*\<open>property @{result \<open>resultProof\<close>} = property @{result \<open>resultProof2\<close>}\<close>
-value*\<open>property @{result \<open>resultProof\<close>} = property @{result \<open>resultProof2\<close>}\<close>
-
-value*\<open>evidence @{result \<open>resultProof\<close>} = evidence @{result \<open>resultProof2\<close>}\<close>
-
-declare[[invariants_checking_with_tactics = false]]
-
-declare[[invariants_strict_checking = false]]
-
-doc_class test_A =
-   level :: "int option"
-   x :: int
-
-doc_class test_B =
-   level :: "int option"
-   x :: "string"                            (* attributes live in their own name-space *)
-   y :: "string list"          <= "[]"      (* and can have arbitrary type constructors *)
-                                            (* LaTeX may have problems with this, though *)
-
-text\<open>We may even use type-synonyms for class synonyms ...\<close>
-type_synonym test_XX = test_B
-
-doc_class test_C0 = test_B +                           
-   z :: "test_A option"             <= None      (* A LINK, i.e. an attribute that has a type
-                                               referring to a document class. Mathematical
-                                               relations over document items can be modeled. *)
-   g :: "thm"                               (* a reference to the proxy-type 'thm' allowing
-
-                                               to denote references to theorems inside attributes *)
-
-
-doc_class test_C = test_B +
-   z :: "test_A option"             <= None      (* A LINK, i.e. an attribute that has a type
-                                               referring to a document class. Mathematical
-                                               relations over document items can be modeled. *)
-   g :: "thm"                               (* a reference to the proxy-type 'thm' allowing
-
-                                               to denote references to theorems inside attributes *)
-
-datatype enum = X1 | X2 | X3                (* we add an enumeration type ... *)
- 
-
-doc_class test_D = test_B +
-   x  :: "string"              <= "\<open>def \<longrightarrow>\<close>" (* overriding default *)
-   a1 :: enum                  <= "X2"      (* class - definitions may be mixed 
-                                               with arbitrary HOL-commands, thus 
-                                               also local definitions of enumerations *)
-   a2 :: int                   <= 0
-
-doc_class test_E = test_D +
-   x :: "string"              <= "''qed''"  (* overriding default *)
-
-doc_class test_G = test_C +
-   g :: "thm"  <= "@{thm \<open>HOL.refl\<close>}"  (* warning overriding attribute expected*)
-
-doc_class 'a test_F  =     
-   properties  :: "term list"
-   r           :: "thm list"
-   u           :: "file"
-   s           :: "typ list"
-   b           :: "(test_A \<times> 'a test_C_scheme) set"  <= "{}"       (* This is a relation link, roughly corresponding
-                                                 to an association class. It can be used to track
-                                                 claims to result - relations, for example.*) 
-   b'          :: "(test_A \<times> 'a test_C_scheme) list"  <= "[]"
-   invariant br :: "r \<sigma> \<noteq> [] \<and> card(b \<sigma>) \<ge> 3"
-        and  br':: "r \<sigma> \<noteq> [] \<and> length(b' \<sigma>) \<ge> 3"
-        and  cr :: "properties \<sigma> \<noteq> []"
-
-lemma*[l::test_E] local_sample_lemma : 
-       "@{thm \<open>refl\<close>} = @{thm ''refl''}" by simp
-                                                       \<comment> \<open>un-evaluated references are similar to
-                                                           uninterpreted constants. Not much is known
-                                                           about them, but that doesn't mean that we
-                                                           can't prove some basics over them...\<close>
-
-text*[xcv1::test_A, x=5]\<open>Lorem ipsum ...\<close>
-text*[xcv2::test_C, g="@{thm ''HOL.refl''}"]\<open>Lorem ipsum ...\<close>
-text*[xcv3::test_A, x=7]\<open>Lorem ipsum ...\<close>
-
-text\<open>Bug: For now, the implementation is no more compatible with the docitem term-antiquotation:\<close>
-text-assert-error[xcv10::"unit test_F", r="[@{thm ''HOL.refl''}, 
-                   @{thm \<open>local_sample_lemma\<close>}]", (* long names required *)
-               b="{(@{docitem ''xcv1''},@{docitem \<open>xcv2\<close>})}",  (* notations \<open>...\<close> vs. ''...'' *)
-               s="[@{typ \<open>int list\<close>}]",                        
-               properties = "[@{term \<open>H \<longrightarrow> H\<close>}]"              (* notation \<open>...\<close> required for UTF8*)
-]\<open>Lorem ipsum ...\<close>\<open>Type unification failed\<close>
-
-text*[xcv11::"unit test_F", r="[@{thm ''HOL.refl''}, 
-                   @{thm \<open>local_sample_lemma\<close>}]", (* long names required *)
-               b="{(@{test_A ''xcv1''},@{test_C \<open>xcv2\<close>})}",  (* notations \<open>...\<close> vs. ''...'' *)
-               s="[@{typ \<open>int list\<close>}]",                        
-               properties = "[@{term \<open>H \<longrightarrow> H\<close>}]"              (* notation \<open>...\<close> required for UTF8*)
-]\<open>Lorem ipsum ...\<close>
-
-value*\<open>b @{test_F \<open>xcv11\<close>}\<close>
-
-typ\<open>unit test_F\<close>
-
-text*[xcv4::"unit test_F", r="[@{thm ''HOL.refl''}, 
-                   @{thm \<open>local_sample_lemma\<close>}]", (* long names required *)
-               b="{(@{test_A ''xcv1''},@{test_C \<open>xcv2\<close>})}",  (* notations \<open>...\<close> vs. ''...'' *)
-               s="[@{typ \<open>int list\<close>}]",                        
-               properties = "[@{term \<open>H \<longrightarrow> H\<close>}]"              (* notation \<open>...\<close> required for UTF8*)
-]\<open>Lorem ipsum ...\<close>
-
-value*\<open>b @{test_F \<open>xcv4\<close>}\<close>
-
-text*[xcv5::test_G, g="@{thm \<open>HOL.sym\<close>}"]\<open>Lorem ipsum ...\<close>
-
-update_instance*[xcv4::"unit test_F", b+="{(@{test_A ''xcv3''},@{test_C ''xcv2''})}"]
-
-update_instance-assert-error[xcv4::"unit test_F", b+="{(@{test_A ''xcv3''},@{test_G ''xcv5''})}"]
-  \<open>Type unification failed: Clash of types\<close>
-                
-
-
-typ\<open>unit test_G_ext\<close>
-typ\<open>\<lparr>test_G.tag_attribute :: int\<rparr>\<close>
-text*[xcv6::"\<lparr>test_G.tag_attribute :: int\<rparr> test_F", b="{(@{test_A ''xcv3''},@{test_G ''xcv5''})}"]\<open>\<close>
-
-
-text\<open>\<open>lemma*\<close>, etc. do not support well polymorphic classes term antiquotations.
-For now only embedded term-antiquotation in a definition could work:\<close>
-definition* testtest_level where "testtest_level \<equiv> the (text_section.level @{test2 \<open>testtest2''\<close>})"
-lemma*[e5::E] testtest : "xx + testtest_level = yy + testtest_level \<Longrightarrow> xx = yy" by simp
-
-text\<open>Indeed this fails:\<close>
-(*lemma*[e6::E] testtest : "xx + the (level @{test2 \<open>testtest2''\<close>}) = yy + the (level @{test2 \<open>testtest2''\<close>}) \<Longrightarrow> xx = yy" by simp*)
-
-text\<open>Bug: Checking of \<^theory_text>\<open>text*\<close> type against \<^theory_text>\<open>declare_reference*\<close> is not done.
-Should be compatible with type unification mechanism. See the record package\<close>
-doc_class 'a AAA_test =
-aaa::"'a list"
-
-doc_class 'a BBB_test =
-bbb::"'a list"
-
-declare_reference*[aaa_test::"'a::one AAA_test"]
-text\<open>@{AAA_test (unchecked) \<open>aaa_test\<close>}\<close>
-
-text\<open>\<open>aaa_test\<close> should fail and trigger an error because its type was \<^typ>\<open>'a::one AAA_test\<close>
-    in the \<^theory_text>\<open>declare_reference*\<close> command:\<close>
-(*text*[aaa_test::"'a::one BBB_test"]\<open>\<close>*)
-
-text*[aaa_test::"int AAA_test"]\<open>\<close>
-
-text\<open>\<open>aaa_test'\<close> should fail and trigger an error because its type \<^typ>\<open>string AAA_test\<close>
-    is not compatible with its type  \<^typ>\<open>'a::one AAA_test\<close> declared in
-    the \<^theory_text>\<open>declare_reference*\<close> command:\<close>
-text*[aaa_test'::"string AAA_test"]\<open>\<close>
-
-
-end

Isabelle_DOF-Unit-Tests/document/root.bib

@@ -1,6 +0,0 @@
-@Manual{	  wenzel:isabelle-isar:2020,
-  title		= {The Isabelle/Isar Reference Manual},
-  author	= {Makarius Wenzel},
-  year		= 2020,
-  note		= {Part of the Isabelle distribution.}
-}

Isabelle_DOF/ROOT

@@ -1,59 +0,0 @@
-chapter AFP
-
-session "Isabelle_DOF" (AFP) = "Functional-Automata" + 
-  options [document = pdf, document_output = "output", document_build = dof, timeout = 300]
-  sessions
-    "Regular-Sets"
-  directories 
-    "thys"
-    "thys/manual"
-    "ontologies"
-    "ontologies/scholarly_paper"
-    "ontologies/technical_report"
-  theories [document = false]
-    "ontologies/ontologies"
-    "ontologies/technical_report/technical_report"
-    "ontologies/scholarly_paper/scholarly_paper"
-    "thys/RegExpInterface"
-    "thys/Isa_DOF"
-    "thys/Isa_COL"
-  theories [document = true]
-    "thys/manual/M_00_Frontmatter"
-    "thys/manual/M_01_Introduction"
-    "thys/manual/M_02_Background"
-    "thys/manual/M_03_GuidedTour"
-    "thys/manual/M_04_Document_Ontology"
-    "thys/manual/M_05_Proofs_Ontologies"
-    "thys/manual/M_06_RefMan"
-    "thys/manual/M_07_Implementation"
-    "thys/manual/Isabelle_DOF_Manual"
-  document_files
-    "root.bib"
-    "dof_session.tex"
-    "root.mst"
-    "preamble.tex"
-    "lstisadof-manual.sty" 
-    "figures/cicm2018-combined.png"
-    "figures/document-hierarchy.pdf"
-    "figures/Dogfood-figures.png"
-    "figures/Dogfood-II-bgnd1.png"
-    "figures/Dogfood-III-bgnd-text_section.png"
-    "figures/Dogfood-IV-jumpInDocCLass.png"
-    "figures/Dogfood-V-attribute.png"
-    "figures/Dogfood-VI-linkappl.png"
-    "figures/isabelle-architecture.pdf"
-    "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"
-    "figures/doc-mod-generic.pdf"
-    "figures/doc-mod-isar.pdf"
-    "figures/doc-mod-onto-docinst.pdf"
-    "figures/doc-mod-DOF.pdf"
-    "figures/doc-mod-term-aq.pdf"
-    "figures/ThisPaperWithPreviewer.png"
-  export_classpath
-
-

Isabelle_DOF/document/dof_session.tex

@@ -1,9 +0,0 @@
-\input{M_00_Frontmatter.tex}
-\input{M_01_Introduction.tex}
-\input{M_02_Background.tex}
-\input{M_03_GuidedTour.tex}
-\input{M_04_Document_Ontology.tex}
-\input{M_05_Proofs_Ontologies.tex}
-\input{M_06_RefMan.tex}
-\input{M_07_Implementation.tex}
-\input{Isabelle_DOF_Manual.tex}

Isabelle_DOF/document/lstisadof-manual.sty

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

Isabelle_DOF/document/root.bib

@@ -1,573 +0,0 @@
-@STRING{pub-springer={Springer} }
-@STRING{pub-springer:adr="" }
-@STRING{s-lncs	= "LNCS" }
-
-@Misc{		  w3c:ontologies:2015,
-  author	= {W3C},
-  title		= {Ontologies},
-  organisation	= {W3c},
-  url		= {https://www.w3.org/standards/semanticweb/ontology},
-  year		= 2015
-}
-
-@
-Book{            books/daglib/0032976,
-  added-at      = {2014-03-12T00:00:00.000+0100},
-  author        = {Euzenat, J{\~A}<7D>r{\~A}<7D>me and Shvaiko, Pavel},
-  biburl        = {https://www.bibsonomy.org/bibtex/28d5372a81f181d9d5a761ca12209cf39/dblp},    
-  interhash     = {fc55a5b84d114e38db0a0303cc1bd7da},
-  intrahash     = {8d5372a81f181d9d5a761ca12209cf39},
-  isbn          = {978-3-642-38720-3},
-  keywords      = {dblp},
-  pages         = {I-XVII, 1--511},
-  publisher     = {Springer}, 
-  timestamp     = {2015-06-18T09:49:52.000+0200},
-  title         = {Ontology Matching, Second Edition.},
-  year          = 2013,
-  doi           = {10.1007/978-3-642-38721-0}
-} 
-
-@Misc{            atl,
-  title         = {{ATL} -- A model transformation technology},
-  url           = {https://www.eclipse.org/atl/},
-  author        = {{Eclipse Foundation}},
-} 
-
-@InProceedings{   BGPP95,
-  author        = {Yamine A{\"{\i}}t Ameur and Frederic Besnard and Patrick Girard and Guy Pierra and Jean{-}Claude
-                  Potier},
-  title         = {Formal Specification and Metaprogramming in the {EXPRESS} Language}, 
-  booktitle     = {The 7th International Conference on Software Engineering and Knowledge Engineering (SEKE)},
-  pages         = {181--188},
-  publisher     = {Knowledge Systems Institute},
-  year          = 1995
-}
-
-@Misc{		  ibm:doors:2019,
-  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		= 2022,
-  note		= {Part of the Isabelle distribution.}
-}
-
-@InCollection{	  brucker.ea:isabelledof:2019,
-  abstract	= {DOF is a novel framework for defining ontologies and
-		  enforcing them during document development and evolution. A
-		  major goal of DOF is the integrated development of formal
-		  certification documents (e. g., 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 the formal methods
-		  framework Isabelle/HOL. A particular emphasis is put on a
-		  deep integration into Isabelle{\^a}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. Isabelle/DOF 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 collabo- ratively, while ensuring their
-		  consistency, and the impact of changes (in the formal and
-		  the semi-formal content) is tracked automatically.},
-  keywords	= {Ontology, Formal Document Development, CERtification, DOF,
-		  Isabelle/DOF},
-  location	= {Oslo},
-  author	= {Achim D. Brucker and Burkhart Wolff},
-  booktitle	= {Software Engineering and Formal Methods (SEFM)},
-  language	= {USenglish},
-  url		= {https://www.brucker.ch/bibliography/abstract/brucker.ea-isabelledof-2019},
-  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},
-  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},
-  public	= {yes}
-}
-
-@InCollection{	  brucker.ea:deep-ontologies:2023,
-  author	= {Achim D. Brucker and Idir Ait-Sadoune and Nicolas Meric and Burkhart Wolff},
-  booktitle	= {9th International Conference on Rigorous State-Based Methods (ABZ 2023)},
-  language	= {USenglish},
-  publisher	= {Springer-Verlag},
-  address	= {Heidelberg},
-  series	= {Lecture Notes in Computer Science},
-  number	= {14010},
-  title		= {{U}sing {D}eep {O}ntologies in {F}ormal {S}oftware {E}ngineering},
-  year    = {2023},
-  abstract = {Isabelle/DOF is an ontology framework on top of Isabelle Isabelle/DOF allows for the 
-              formal development of ontologies as well as continuous conformity-checking of 
-              integrated documents annotated by ontological data. An integrated document may 
-              contain text, code, definitions, proofs and user-programmed constructs supporting a 
-              wide range of Formal Methods. Isabelle/DOF is designed to leverage traceability in  
-              integrated documents by supporting navigation in Isabelle’s IDE as well as the 
-              document generation process.
-                 In this paper we extend Isabelle/DOF with annotations of terms, a pervasive 
-              data-structure underlying Isabelle used to syntactically rep- resent expressions 
-              and formulas. Rather than introducing an own pro- gramming language for meta-data, 
-              we use Higher-order Logic (HOL) for expressions, data-constraints, ontological 
-              invariants, and queries via code-generation and reflection. This allows both for 
-              powerful query languages and logical reasoning over ontologies in, for example, 
-              ontological mappings. Our application examples cover documents targeting formal 
-              certifications such as CENELEC, Common Criteria, etc.}
-}
-
-@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.},
-  keywords	= {Isabelle/Isar, HOL, Ontologies},
-  location	= {Hagenberg, Austria},
-  author	= {Achim D. Brucker and Idir Ait-Sadoune and Paolo Crisafulli
-		  and Burkhart Wolff},
-  booktitle	= {Conference on Intelligent Computer Mathematics (CICM)},
-  language	= {USenglish},
-  publisher	= {Springer-Verlag},
-  address	= {Heidelberg},
-  series	= {Lecture Notes in Computer Science},
-  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},
-  classification= {conference},
-  areas		= {formal methods, software},
-  categories	= {isadof},
-  public	= {yes},
-  year		= {2018},
-  doi		= {10.1007/978-3-319-96812-4_3},
-  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}
-}
-
-@Booklet{	  cc:cc-part3:2006,
-  bibkey	= {cc:cc-part3:2006},
-  key		= {Common Criteria},
-  institution	= {Common Criteria},
-  language	= {USenglish},
-  month		= sep,
-  year		= 2006,
-  public	= {yes},
-  title		= {Common Criteria for Information Technology Security
-		  Evaluation (Version 3.1), {Part} 3: Security assurance
-		  components},
-  note		= {Available as document
-		  \href{http://www.commoncriteriaportal.org/public/files/CCPART3V3.1R1.pdf}
-		  {CCMB-2006-09-003}},
-  number	= {CCMB-2006-09-003},
-  acknowledgement={brucker, 2007-04-24}
-}
-
-@Book{		  nipkow.ea:isabelle:2002,
-  author	= {Tobias Nipkow and Lawrence C. Paulson and Markus Wenzel},
-  title		= {Isabelle/HOL---A Proof Assistant for Higher-Order Logic},
-  publisher	= pub-springer,
-  address	= pub-springer:adr,
-  series	= s-lncs,
-  volume	= 2283,
-  doi		= {10.1007/3-540-45949-9},
-  abstract	= {This book is a self-contained introduction to interactive
-		  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.
-		  
-		  1. Elementary Techniques shows how to model functional
-		  programs in higher-order logic. Early examples involve
-		  lists and the natural numbers. Most proofs are two steps
-		  long, consisting of induction on a chosen variable followed
-		  by the auto tactic. But even this elementary part covers
-		  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/\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
-		  languages. 3. Advanced Material describes a variety of
-		  other topics. Among these are the real numbers, records and
-		  overloading. Advanced techniques are described involving
-		  induction and recursion. A whole chapter is devoted to an
-		  extended example: the verification of a security protocol. },
-  year		= 2002,
-  acknowledgement={brucker, 2007-02-19},
-  bibkey	= {nipkow.ea:isabelle:2002},
-  tags		= {noTAG},
-  clearance	= {unclassified},
-  timestap	= {2008-05-26}
-}
-
-@InProceedings{wenzel:asynchronous:2014,
-  author	= {Makarius Wenzel},
-  title		= {Asynchronous User Interaction and Tool Integration in
-		  {Isabelle}/{PIDE}},
-  booktitle	= {ITP},
-  pages		= {515--530},
-  year		= 2014,
-  crossref	= {klein.ea:interactive:2014},
-  doi		= {10.1007/978-3-319-08970-6_33},
-  timestamp	= {Sun, 21 May 2017 00:18:59 +0200},
-  abstract	= { Historically, the LCF tradition of interactive theorem
-		  proving was tied to the read-eval-print loop, with
-		  sequential and synchronous evaluation of prover commands
-		  given on the command-line. This user-interface technology
-		  was adequate when R. Milner introduced his LCF proof
-		  assistant in the 1970-ies, but it severely limits the
-		  potential of current multicore hardware and advanced IDE
-		  front-ends.
-		  
-		  Isabelle/PIDE breaks this loop and retrofits the
-		  read-eval-print phases into an asynchronous model of
-		  document-oriented proof processing. Instead of feeding a
-		  sequence of individual commands into the prover process,
-		  the primary interface works via edits over a family of
-		  document versions. Execution is implicit and managed by the
-		  prover on its own account in a timeless and stateless
-		  manner. Various aspects of interactive proof checking are
-		  scheduled according to requirements determined by the
-		  front-end perspective on the proof document, while making
-		  adequate use of the CPU resources on multicore hardware on
-		  the back-end.
-		  
-		  Recent refinements of Isabelle/PIDE provide an explicit
-		  concept of asynchronous print functions over existing proof
-		  states. This allows to integrate long-running or
-		  potentially non-terminating tools into the document-model.
-		  Applications range from traditional proof state output
-		  (which may consume substantial time in interactive
-		  development) to automated provers and dis-provers that
-		  report on existing proof document content (e.g.
-		  Sledgehammer, Nitpick, Quickcheck in Isabelle/HOL).
-		  Moreover, it is possible to integrate query operations via
-		  additional GUI panels with separate input and output (e.g.
-		  for Sledgehammer or find-theorems). Thus the Prover IDE
-		  provides continuous proof processing, augmented by add-on
-		  tools that help the user to continue writing proofs. }
-}
-
-@Proceedings{	  klein.ea:interactive:2014,
-  editor	= {Gerwin Klein and Ruben Gamboa},
-  title		= {Interactive Theorem Proving - 5th International
-		  Conference, {ITP} 2014, Held as Part of the Vienna Summer
-		  of Logic, {VSL} 2014, Vienna, Austria, July 14-17, 2014.
-		  Proceedings},
-  series	= s-lncs,
-  volume	= 8558,
-  publisher	= pub-springer,
-  year		= 2014,
-  doi		= {10.1007/978-3-319-08970-6}
-}
-
-@InProceedings{	  bezzecchi.ea:making:2018,
-  title		= {Making Agile Development Processes fit for V-style
-		  Certification Procedures},
-  author	= {Bezzecchi, S. and Crisafulli, P. and Pichot, C. and Wolff,
-		  B.},
-  booktitle	= {{ERTS'18}},
-  abstract	= {We present a process for the development of safety and
-		  security critical components in transportation systems
-		  targeting a high-level certification (CENELEC 50126/50128,
-		  DO 178, CC ISO/IEC 15408).
-		  
-		  The process adheres to the objectives of an ``agile
-		  development'' in terms of evolutionary flexibility and
-		  continuous improvement. Yet, it enforces the overall
-		  coherence of the development artifacts (ranging from proofs
-		  over tests to code) by a particular environment (CVCE).
-		  
-		  In particular, the validation process is built around a
-		  formal development based on the interactive theorem proving
-		  system Isabelle/HOL, by linking the business logic of the
-		  application to the operating system model, down to code and
-		  concrete hardware models thanks to a series of refinement
-		  proofs.
-		  
-		  We apply both the process and its support in CVCE to a
-		  case-study that comprises a model of an odometric service
-		  in a railway-system with its corresponding implementation
-		  integrated in seL4 (a secure kernel for which a
-		  comprehensive Isabelle development exists). Novel
-		  techniques implemented in Isabelle enforce the coherence of
-		  semi-formal and formal definitions within to specific
-		  certification processes in order to improve their
-		  cost-effectiveness. },
-  pdf		= {https://www.lri.fr/~wolff/papers/conf/2018erts-agile-fm.pdf},
-  year		= 2018,
-  series	= {ERTS Conference Proceedings},
-  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},
-  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
-}
-
-@Misc{		  biendarra.ea:defining:2019,
-  title		= {Defining (Co)datatypes and Primitively (Co)recursive
-		  Functions in Isabelle/HOL},
-  author	= {Julian Biendarra and Jasmin Christian Blanchette and
-		  Martin Desharnais and Lorenz Panny and Andrei Popescu and
-		  Dmitriy Traytel},
-  note		= {\url{https://isabelle.in.tum.de/doc/datatypes.pdf}},
-  year		= 2019
-}
-
-@Misc{		  kraus:defining:2020,
-  title		= {Defining Recursive Functions in Isabelle/HOL},
-  author	= {Alexander Kraus},
-  note		= {\url{https://isabelle.in.tum.de/doc/functions.pdf}},
-  year		= 2020
-}
-
-@Misc{		  nipkow:whats:2020,
-  title		= {What's in Main},
-  author	= {Tobias Nipkow},
-  note		= {\url{https://isabelle.in.tum.de/doc/main.pdf}},
-  year		= 2020
-}
-
-@InProceedings{	  wenzel:system:2014,
-  author	= {Makarius Wenzel},
-  title		= {System description: Isabelle/{jEdit} in 2014},
-  booktitle	= {UITP},
-  pages		= {84--94},
-  year		= 2014,
-  doi		= {10.4204/EPTCS.167.10}
-}
-
-@InProceedings{	  barras.ea:pervasive:2013,
-  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
-		  and Burkhart Wolff},
-  title		= {Pervasive Parallelism in Highly-Trustable Interactive
-		  Theorem Proving Systems},
-  booktitle	= {MKM},
-  pages		= {359--363},
-  year		= 2013,
-  doi		= {10.1007/978-3-642-39320-4_29}
-}
-
-@Article{	  faithfull.ea:coqoon:2018,
-  author	= {Faithfull, Alexander and Bengtson, Jesper and Tassi,
-		  Enrico and Tankink, Carst},
-  title		= {Coqoon},
-  journal	= {Int. J. Softw. Tools Technol. Transf.},
-  issue_date	= {April 2018},
-  volume	= 20,
-  number	= 2,
-  month		= apr,
-  year		= 2018,
-  issn		= {1433-2779},
-  pages		= {125--137},
-  numpages	= 13,
-  doi		= {10.1007/s10009-017-0457-2},
-  acmid		= 3204223,
-  publisher	= {Springer-Verlag},
-  address	= {Berlin, Heidelberg}
-}
-
-@InProceedings{	  abrial:steam-boiler:1996,
-  author	= {Abrial, Jean-Raymond},
-  title		= {Steam-Boiler Control Specification Problem},
-  booktitle	= {Formal Methods for Industrial Applications, Specifying and
-		  Programming the Steam Boiler Control (the Book Grow out of
-		  a Dagstuhl Seminar, June 1995).},
-  year		= 1996,
-  isbn		= {3-540-61929-1},
-  pages		= {500--509},
-  numpages	= 10,
-  url		= {http://dl.acm.org/citation.cfm?id=647370.723886},
-  acmid		= 723886,
-  publisher	= {Springer-Verlag},
-  address	= {London, UK, UK}
-}
-
-@TechReport{	  bsi:50128:2014,
-  type		= {Standard},
-  key		= {BS EN 50128:2011},
-  month		= apr,
-  year		= 2014,
-  series	= {British Standards Publication},
-  title		= {BS EN 50128:2011: Railway applications -- Communication,
-		  signalling and processing systems -- Software for railway
-		  control and protecting systems},
-  institution	= {Britisch Standards Institute (BSI)},
-  keywords	= {CENELEC},
-  abstract	= {This European Standard is part of a group of related
-		  standards. The others are EN 50126-1:1999 "Railway
-		  applications -- The specification and demonstration of
-		  Reliability, Availability, Maintainability and Safety
-		  (RAMS) -- Part 1: Basic requirements and generic process --
-		  and EN 50129:2003 "Railway applications -- Communication,
-		  signalling and processing systems -- Safety related
-		  electronic systems for signalling". EN 50126-1 addresses
-		  system issues on the widest scale, while EN 50129 addresses
-		  the approval process for individual systems which can exist
-		  within the overall railway control and protection system.
-		  This European Standard concentrates on the methods which
-		  need to be used in order to provide software which meets
-		  the demands for safety integrity which are placed upon it
-		  by these wider considerations. This European Standard
-		  provides a set of requirements with which the development,
-		  deployment and maintenance of any safety-related software
-		  intended for railway control and protection applications
-		  shall comply. It defines requirements concerning
-		  organisational structure, the relationship between
-		  organisations and division of responsibility involved in
-		  the development, deployment and maintenanceactivities.}
-}
-
-@Article{	  kraus.ea:regular-sets-afp:2010,
-  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
-		  proof development},
-  issn		= {2150-914x}
-}
-
-@Article{	  nipkow.ea:functional-Automata-afp:2004,
-  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},
-		  Formal proof development},
-  issn		= {2150-914x}
-}
-
-@Booklet{	  kohm:koma-script:2019,
-  author	= {Markus Kohm},
-  title		= {{KOMA-Script}: a versatile {\LaTeXe{}} bundle},
-  year		= 2019
-}
-
-@Booklet{	  wenzel:system-manual:2020,
-  author	= {Makarius Wenzel},
-  title		= {The {Isabelle} System Manual},
-  year		= 2020,
-  note		= {Part of the Isabelle distribution.}
-}
-
-@Booklet{	  chervet:keycommand:2010,
-  author	= {Florent Chervet},
-  title		= {The free and open source keycommand package: key-value
-		  interface for commands and environments in {\LaTeX}.},
-  year		= 2010
-}
-
-@Book{		  knuth:texbook:1986,
-  author	= {Knuth, Donald E.},
-  title		= {The TeXbook},
-  year		= 1986,
-  isbn		= 0201134470,
-  publisher	= {Addison-Wesley Professional}
-}
-
-@Book{		  mittelbach.ea:latex:1999,
-  author	= {Mittelbach, Frank and Goossens, Michel and Braams,
-		  Johannes and Carlisle, David and Rowley, Chris},
-  title		= {The LaTeX Companion},
-  year		= 2004,
-  edition	= {2nd},
-  publisher	= {Addison-Wesley Longman Publishing Co., Inc.},
-  address	= {Boston, MA, USA}
-}
-
-@Book{		  eijkhout:latex-cs:2012,
-  author	= {Victor Eijkhout},
-  title		= {The Computer Science of TeX and LaTeX},
-  publisher = {Texas Advanced Computing Center},
-  year		= 2012
-}

Isabelle_DOF/etc/build.props

@@ -1,10 +0,0 @@
-title = Isabelle/DOF
-module = $ISABELLE_HOME_USER/DOF/isabelle_dof.jar
-no_build = false
-requirements = \
-  env:ISABELLE_SCALA_JAR
-sources = \
-  scala/dof.scala \
-  scala/dof_document_build.scala 
-services = \
-  isabelle.dof.DOF_Document_Build$Engine

Isabelle_DOF/latex/styles/DOF-COL.sty

@@ -1,38 +0,0 @@
-%% 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
-
-\NeedsTeXFormat{LaTeX2e}\relax
-\ProvidesPackage{DOF-COL}
-  [00/00/0000 Document-Type Support Framework for Isabelle.]
-
-\RequirePackage{DOF-core}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% begin: float*
-\NewEnviron{isamarkupfloat*}[1][]{\isaDof[env={float},#1]{\BODY}}
-\newisadof{IsaUNDERSCORECOLDOTfloat}%
-[label=,type=%
-,IsaUNDERSCORECOLDOTfloatDOTplacement=%
-,IsaUNDERSCORECOLDOTfloatDOTfloatUNDERSCOREkind=%
-,IsaUNDERSCORECOLDOTfloatDOTmainUNDERSCOREcaption=%
-,IsaUNDERSCORECOLDOTfloatDOTspawnUNDERSCOREcolumns=enum False True%
-][1]{%
-  \begin{figure}
-    #1
-    \caption{\commandkey{IsaUNDERSCORECOLDOTfloatDOTmainUNDERSCOREcaption}}
-    \label{\commandkey{label}}%
-  \end{figure}
-}
-% end: float*
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Isabelle_DOF/ontologies/scholarly_paper/DOF-scholarly_paper.sty

@@ -1,259 +0,0 @@
-%% 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
-
-\NeedsTeXFormat{LaTeX2e}\relax
-\ProvidesPackage{DOF-scholarly_paper}
-  [2021/03/22 Unreleased/Isabelle2021%
-  Document-Type Support Framework for Isabelle (LNCS).]
-
-\RequirePackage{DOF-COL}
-\RequirePackage{ifthen}
-
-\RequirePackage{ifthen}
-\newboolean{DOF@scholarlypaper@force}
-\DeclareOption{force}{\setboolean{DOF@scholarlypaper@force}{true}}
-
-\ProcessOptions\relax
-
-\ifthenelse{\boolean{DOF@scholarlypaper@force}}{%
-}{%
-\@ifclassloaded{llncs}%
-  {}%
-  {%
-    \@ifclassloaded{scrartcl}%
-    {%
-      \RequirePackage{amsthm}
-      \newcommand{\institute}[1]{}%
-      \newcommand{\inst}[1]{}%
-      \newcommand{\orcidID}[1]{}%
-      \newcommand{\email}[1]{}%
-    }%
-    {%
-      \@ifclassloaded{lipics-v2021}%
-      {%
-        \RequirePackage{amsthm}
-        \newcommand{\institute}[1]{}%
-        \newcommand{\inst}[1]{}%
-        \newcommand{\orcidID}[1]{}%
-        \newcommand{\email}[1]{}%
-      }%
-      {%
-        {%
-          \@ifclassloaded{svjour3}%
-          {%
-              \newcommand{\inst}[1]{}%
-          }%
-          {%
-            \PackageError{DOF-scholarly_paper}
-                        {Scholarly Paper only supports LNCS or scrartcl as document class.}
-                        {}\stop%
-          }%
-        }%
-      }%
-    }
-  }
-}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% begin: title*
-\NewEnviron{isamarkuptitle*}[1][]{\isaDof[env={title},#1]{\BODY}}
-\newisadof{titleDOTscholarlyUNDERSCOREpaperDOTtitle}%
-[label=,type=%
-,scholarlyUNDERSCOREpaperDOTtitleDOTshortUNDERSCOREtitle=%
-][1]{%
-  \immediate\write\@auxout{\noexpand\title{#1}}%
-}
-% end: title*
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% begin: subtitle*
-\NewEnviron{isamarkupsubtitle*}[1][]{\isaDof[env={subtitle},#1]{\BODY}}
-\newisadof{subtitleDOTscholarlyUNDERSCOREpaperDOTsubtitle}%
-[label=,type=%
-,scholarlyUNDERSCOREpaperDOTsubtitleDOTabbrev=%
-][1]{%
-  \immediate\write\@auxout{\noexpand\subtitle{#1}}%
-}
-% end: subtitle*
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% begin: scholarly_paper.author
-\def\dof@author{}%
-\def\dof@affiliation{}%
-
-\newcommand{\DOFauthor}{\author{\dof@author}}
-\newcommand{\DOFinstitute}{\institute{\dof@affiliation}}
-
-\AtBeginDocument{%
-  \DOFauthor
-  \DOFinstitute
-}
-
-\def\leftadd#1#2{\expandafter\leftaddaux\expandafter{#1}{#2}{#1}}
-\def\leftaddaux#1#2#3{\gdef#3{#1#2}}
-
-\newcounter{dof@cnt@author}
-\newcommand{\addauthor}[1]{%
-  \ifthenelse{\equal{\dof@author}{}}{%
-    \gdef\dof@author{#1}%
-  }{%
-    \leftadd\dof@author{\protect\and #1}%
-  }
-}
-
-\newcommand{\addaffiliation}[1]{%
-  \ifthenelse{\equal{\dof@affiliation}{}}{%
-    \gdef\dof@affiliation{#1}%
-  }{%
-    \leftadd\dof@affiliation{\protect\and #1}%
-  }
-}
-
-\NewEnviron{isamarkupauthor*}[1][]{\isaDof[env={text},#1]{\BODY}}
-\provideisadof{textDOTscholarlyUNDERSCOREpaperDOTauthor}%
-[label=,type=%
-,scholarlyUNDERSCOREpaperDOTauthorDOTemail=%
-,scholarlyUNDERSCOREpaperDOTauthorDOTaffiliation=%
-,scholarlyUNDERSCOREpaperDOTauthorDOTorcid=%
-,scholarlyUNDERSCOREpaperDOTauthorDOThttpUNDERSCOREsite=%
-][1]{%
-  \stepcounter{dof@cnt@author}
-  \def\dof@a{\commandkey{scholarlyUNDERSCOREpaperDOTauthorDOTaffiliation}}
-  \ifthenelse{\equal{\commandkey{scholarlyUNDERSCOREpaperDOTauthorDOTorcid}}{}}{%
-    \protected@write\@auxout{}{\string\addauthor{#1\string\inst{\thedof@cnt@author}}}%
-  }{%
-    \protected@write\@auxout{}{\string\addauthor{#1\string\inst{\thedof@cnt@author}\string\orcidID{\commandkey{scholarlyUNDERSCOREpaperDOTauthorDOTorcid}}}}%
-  }
-  \protected@write\@auxout{}{\string\addaffiliation{\dof@a\\\string\email{\commandkey{scholarlyUNDERSCOREpaperDOTauthorDOTemail}}}}%
-}
-% end: scholarly_paper.author
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% begin: scholarly_paper.abstract
-\providecommand{\keywords}[1]{\mbox{}\\[2ex]\mbox{}\noindent{\textbf{Keywords:}} #1}
-\NewEnviron{isamarkupabstract*}[1][]{\isaDof[env={text},#1]{\BODY}}
-\newisadof{textDOTscholarlyUNDERSCOREpaperDOTabstract}%
-[label=,type=%
-,scholarlyUNDERSCOREpaperDOTabstractDOTkeywordlist=%
-][1]{%
-  \begin{isamarkuptext}%
-    \begin{abstract}%
-      #1%
-      \ifthenelse{\equal{\commandkey{scholarlyUNDERSCOREpaperDOTabstractDOTkeywordlist}}{}}{}{%     
-        \keywords{\commandkey{scholarlyUNDERSCOREpaperDOTabstractDOTkeywordlist}}%
-      }%
-    \end{abstract}%
-  \end{isamarkuptext}%
-}
-
-%\RequirePackage{amsthm}
-%\newtheorem{example}{Example}
-%\newtheorem{assumption}{Assumption}
-%\newtheorem{definition}{Definition}
-%\newtheorem{theorem}{Theorem} 
-\newtheorem{defn}{Definition} 
-\providecommand{\defnautorefname}{Definition} 
-\NewEnviron{isamarkupDefinition*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{axm}{Axiom}
-\providecommand{\axmautorefname}{Axiom}
-\NewEnviron{isamarkupAxiom*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{theom}{Theorem}
-\providecommand{\theomautorefname}{Theorem}
-\NewEnviron{isamarkupTheorem*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{lemm}{Lemma}
-\providecommand{\lemmautorefname}{Lemma}
-\NewEnviron{isamarkupLemma*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{corr}{Corollary}
-\providecommand{\corrautorefname}{Corollary}
-\NewEnviron{isamarkupCorollary*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{prpo}{Proposition}
-\providecommand{\prpoautorefname}{Proposition}
-\NewEnviron{isamarkupProposition*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{rulE}{Rule}
-\providecommand{\rulEautorefname}{Rule}
-\NewEnviron{isamarkupRule*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{assn}{Assertion}    
-\providecommand{\assnautorefname}{Assertion}    
-\NewEnviron{isamarkupAssertion*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{hypt}{Hypothesis}
-\providecommand{\hyptautorefname}{Hypothesis}
-\NewEnviron{isamarkupHypothesis*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{assm}{Assumption}
-\providecommand{\assmautorefname}{Assumption}
-\NewEnviron{isamarkupAssumption*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{prms}{Premise}
-\providecommand{\prmsautorefname}{Premise}
-\NewEnviron{isamarkupPremise*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{cons}{Consequence}
-\providecommand{\consautorefname}{Consequence}
-\NewEnviron{isamarkupConsequence*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{concUNDERSCOREstmt}{Conclusion}
-\providecommand{\concUNDERSCOREstmtautorefname}{Conclusion}
-\NewEnviron{isamarkupConclusion*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{prfUNDERSCOREstmt}{Proof}
-\providecommand{\prfUNDERSCOREstmtautorefname}{Proof}
-\NewEnviron{isamarkupProof*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{explUNDERSCOREstmt}{Example}
-\providecommand{\explUNDERSCOREstmtautorefname}{Example}
-\NewEnviron{isamarkupExample*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{rmrk}{Remark}
-\providecommand{\rmrkautorefname}{Remark}
-\NewEnviron{isamarkupRemark*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{notn}{Notation}
-\providecommand{\notnautorefname}{Notation}
-\NewEnviron{isamarkupNotation*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-\newtheorem{tmgy}{Terminology}
-\providecommand{\tmgyautorefname}{Terminology}
-\NewEnviron{isamarkupTerminology*}[1][]{\isaDof[env={text},#1,type={scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}]{\BODY}}
-
-\newisadof{textDOTscholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontent}%
-[label=,type=%
- , scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTshortUNDERSCOREname ={}%
- , scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc     = % 
- , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel         =%
- , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTreferentiable =%
- , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTvariants      =%
- , scholarlyUNDERSCOREpaperDOTtextUNDERSCOREsectionDOTmainUNDERSCOREauthor  =%
- , scholarlyUNDERSCOREpaperDOTtextUNDERSCOREsectionDOTfixmeUNDERSCORElist   =%
- , IsaUNDERSCORECOLDOTtextUNDERSCOREelementDOTlevel                =%
- , scholarlyUNDERSCOREpaperDOTtechnicalDOTdefinitionUNDERSCORElist =%
- , scholarlyUNDERSCOREpaperDOTtechnicalDOTstatus          =%
- ]
- [1]
- {%
-    \begin{isamarkuptext}%
-      \ifthenelse{\equal{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTshortUNDERSCOREname}} {} }  
-        {%
-         \begin{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}\label{\commandkey{label}}
-           #1
-         \end{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}
-        }{%
-         \begin{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}[\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTshortUNDERSCOREname}]\label{\commandkey{label}} 
-           #1 
-         \end{\commandkey{scholarlyUNDERSCOREpaperDOTmathUNDERSCOREcontentDOTmcc}}
-        }
-    \end{isamarkuptext}%
- } 
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%% Miscellaneous
-\usepackage{xspace}
-\newcommand{\ie}{i.\,e.\xspace}
-\newcommand{\eg}{e.\,g.\xspace}
-\newcommand{\etc}{etc}
-
-