Merge branch 'Isabelle_dev'

.woodpecker/README.md

@@ -15,4 +15,4 @@ It may also contain additional tools and script that are useful for preparing a
 * pdflatex
   * [browser_info](https://artifacts.logicalhacking.com/ci/Isabelle_DOF/Isabelle_DOF/main/latest/pdflatex/browser_info/Unsorted/)
   * [aux files](https://artifacts.logicalhacking.com/ci/Isabelle_DOF/Isabelle_DOF/main/latest/pdflatex/)
-* [Isabelle_DOF-Unreleased_Isabelle2021-1.tar.xz](https://artifacts.logicalhacking.com/ci/Isabelle_DOF/Isabelle_DOF/main/latest/Isabelle_DOF-Unreleased_Isabelle2021-1.tar.xz)
+* [Isabelle_DOF-Unreleased_Isabelle2022.tar.xz](https://artifacts.logicalhacking.com/ci/Isabelle_DOF/Isabelle_DOF/main/latest/Isabelle_DOF-Unreleased_Isabelle2022.tar.xz)

.woodpecker/build.yml

@@ -1,6 +1,6 @@
 pipeline:
   build:
-    image: docker.io/logicalhacking/isabelle2021-1
+    image: docker.io/logicalhacking/isabelle2022
     commands:
       - export ARTIFACT_DIR=$CI_WORKSPACE/.artifacts/$CI_REPO/$CI_BRANCH/$CI_BUILD_NUMBER/$LATEX
       - mkdir -p $ARTIFACT_DIR
@@ -16,7 +16,7 @@ pipeline:
       - cd ../..
       - ln -s * latest
   archive:
-    image: docker.io/logicalhacking/isabelle2021-1
+    image: docker.io/logicalhacking/isabelle2022
     commands:
       - export ARTIFACT_DIR=$CI_WORKSPACE/.artifacts/$CI_REPO/$CI_BRANCH/$CI_BUILD_NUMBER/$LATEX
       - mkdir -p $ARTIFACT_DIR

CHANGELOG.md

@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### Changed
 
+- Updated Isabelle version to Isabelle 2022
+
 ## [1.3.0] - 2022-07-08
 
 ### Changed

README.md

@@ -1,46 +1,32 @@
 # [Isabelle/DOF](https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF): Document Preparation Setup
 
 Isabelle/DOF is a novel Document Ontology Framework on top of Isabelle.
-Isabelle/DOF allows for both conventional typesetting as well as formal
+Isabelle/DOF allows for both conventional typesetting and formal development.
-development. The manual for [Isabelle/DOF 1.3.0/Isabelle2021-1 is available
+The manual for [Isabelle/DOF 1.3.0/Isabelle2021-1 is available
 online.](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.3.0_Isabelle2021-1.pdf)
 
 ## Pre-requisites
 
 Isabelle/DOF has three major prerequisites:
 
-* **Isabelle:** Isabelle/DOF requires [Isabelle 2021-1](http://isabelle.in.tum.de/website-Isabelle2021-1/).
+* **Isabelle:** Isabelle/DOF requires [Isabelle
-  Please download the Isabelle 2021-1 distribution for your operating
+  2022](http://isabelle.in.tum.de/website-Isabelle2022/). Please download the
-  system from the [Isabelle
+  Isabelle 2022 distribution for your operating system from the [Isabelle
-  website](http://isabelle.in.tum.de/website-Isabelle2021-1/).
+  website](http://isabelle.in.tum.de/website-Isabelle2022/).
-* **AFP:** Isabelle/DOF requires two entries from the [Archive of
+* **AFP:** Isabelle/DOF requires two entries from the [Archive of Formal Proofs
-  Formal Proofs (AFP)](https://www.isa-afp.org/). Please install the
+  (AFP)](https://www.isa-afp.org/).  Please install the AFP following the
-  AFP following the instructions given at
+  instructions given at <https://www.isa-afp.org/using.html>.
-  <https://www.isa-afp.org/using.html>. For your convenience, we also
-  provide a script that only installs the two entries required by
-  Isabelle/DOF into the local Isabelle/DOF directory. First, Isabelle/DOF
-  needs to be registered as an Isabelle component:
-  
-  ```console
-  foo@bar:~$ isabelle components -u `pwd`
-  ```  
-
-  Thereafter, the AFP entries can be installed as follows:
-  
-  ```console
-  foo@bar:~$ isabelle env ./install-afp
-  ```  
-
 * **LaTeX:** Isabelle/DOF requires a modern LaTeX installation, i.e., at least
-  [TeX Live 2022](https://www.tug.org/texlive/) with all available updates applied.
+  [TeX Live 2022](https://www.tug.org/texlive/) with all available updates
+  applied.
   
 ## Installation
 
 Isabelle/DOF is provided as an Isabelle component. After installing the
 prerequisites, change into the directory containing Isabelle/DOF (this should be
 the directory containing this `README.md` file) and execute (if you executed
-this command already during the installation of the pre-requisites, you 
+this command already during the installation of the prerequisites, you can skip
-can skip it now):
+it now):
 
 ```console
 foo@bar:~$ isabelle components -u `pwd`
@@ -58,25 +44,24 @@ This will compile Isabelle/DOF and run the example suite.
 
 ### Opening an Example
 
-If you want to work with or extend one of the examples, e.g., you can
+If you want to work with or extend one of the examples, e.g., you can open it
-open it similar to any standard Isabelle theory:
+similar to any standard Isabelle theory:
 
 ```console
 isabelle jedit -d . -l Isabelle_DOF examples/scholarly_paper/2018_cicm/IsaDofApplications.thy
 ```
 
-This will open an example of a scientific paper using the pre-compiled
+This will open an example of a scientific paper using the pre-compiled session
-session ``Isabelle_DOF``, i.e., you will not be able to edit the
+``Isabelle_DOF``, i.e., you will not be able to edit the ontology definitions.
-ontology definitions. If you want to edit the ontology definition,
+If you want to edit the ontology definition, just open the theory file with the
-just open the theory file with the default HOL session:
+default HOL session:
 
 ```console
 isabelle jedit -d . -l HOL examples/scholarly_paper/2018_cicm/IsaDofApplications.thy
 ```
 
 While this gives you more flexibility, it might "clutter" your editing
-experience, as a lot of internal theories are loaded into Isabelle's
+experience, as a lot of internal theories are loaded into Isabelle's editor.
-editor.
 
 ### Creating a New Project
 
@@ -87,23 +72,22 @@ Isabelle projects that use DOF need to be created using
 foo@bar:~$ isabelle dof_mkroot
 ```
 
-The ``dof_mkroot`` command takes the same parameter as the standard
+The ``dof_mkroot`` command takes the same parameter as the standard ``mkroot``
-``mkroot`` command of Isabelle. Thereafter, the normal Isabelle
+command of Isabelle. Thereafter, the normal Isabelle command for building
-command for building documents can be used.
+documents can be used.
 
-Using the ``-o`` option, different ontology setups can be
+Using the ``-o`` option, different ontology setups can be selected and using the
-selected and using the ``-t`` option, different LaTeX setups
+``-t`` option, different LaTeX setups can be selected. For example,
-can be selected. For example,
 
 ```console
 foo@bar:~$ isabelle dof_mkroot -o scholarly_paper -t scrartcl
 ```
 
-creates a setup using the scholarly_paper ontology and the article
+creates a setup using the scholarly_paper ontology and the article class from
-class from the KOMA-Script bundle.
+the KOMA-Script bundle.
 
-The help (option ``-h``) show a list of all supported ontologies and
+The help (option ``-h``) show a list of all supported ontologies and document
-document templates:
+templates:
 
 ```console
 foo@bar:~$ isabelle dof_mkroot -h
@@ -128,7 +112,7 @@ are available:
   * [Isabelle_DOF-1.3.0_Isabelle2021-1.tar.xz](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.3.0_Isabelle2021-1.tar.xz)
   * [Isabelle_DOF-1.3.0_Isabelle2021-1.tar.xz.asc](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.3.0_Isabelle2021-1.tar.xz.asc)
 
-### Older Releases 
+### Older Releases
 
 * Isabelle/DOF 1.2.0/Isabelle2021
   * [Isabelle_DOF-1.2.0_Isabelle2021.pdf](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.2.0_Isabelle2021.pdf)
@@ -169,28 +153,32 @@ SPDX-License-Identifier: BSD-2-Clause
 
 ## Publications
 
-* Achim D. Brucker, Idir Ait-Sadoune, Paolo Crisafulli, and Burkhart
+* Achim D. Brucker, Idir Ait-Sadoune, Paolo Crisafulli, and Burkhart Wolff.
-  Wolff. [Using The Isabelle Ontology Framework: Linking the Formal
+  [Using The Isabelle Ontology Framework: Linking the Formal with the
-  with the Informal](https://www.brucker.ch/bibliography/download/2018/brucker.ea-isabelle-ontologies-2018.pdf).
+  Informal](https://www.brucker.ch/bibliography/download/2018/brucker.ea-isabelle-ontologies-2018.pdf).
-  In Conference on Intelligent Computer Mathematics (CICM). Lecture
+  In Conference on Intelligent Computer Mathematics (CICM). Lecture Notes in
-  Notes in Computer Science (11006), Springer-Verlag, 2018.
+  Computer Science (11006), Springer-Verlag, 2018.
   [doi:10.1007/978-3-319-96812-4_3](https://doi.org/10.1007/978-3-319-96812-4_3).
 
 * Achim D. Brucker and Burkhart Wolff. [Isabelle/DOF: Design and
   Implementation](https://www.brucker.ch/bibliography/download/2019/brucker.ea-isabelledof-2019.pdf).
-  In Software Engineering and Formal Methods (SEFM). Lecture Notes in
+  In Software Engineering and Formal Methods (SEFM). Lecture Notes in Computer
-  Computer Science (11724), Springer-Verlag, 2019.
+  Science (11724), Springer-Verlag, 2019.
   [doi:10.1007/978-3-030-30446-1_15](https://doi.org/10.1007/978-3-030-30446-1_15).
 
-* Achim D. Brucker, Burkhart Wolff. [Using Ontologies in Formal Developments Targeting Certification](https://www.brucker.ch/bibliography/download/2019/brucker.ea-ontologies-certification-2019.pdf). In
+* Achim D. Brucker, Burkhart Wolff. [Using Ontologies in Formal Developments
-  Integrated Formal Methods (IFM). Lecture Notes in Computer Science (11918). Springer-Verlag 2019.
+  Targeting
+  Certification](https://www.brucker.ch/bibliography/download/2019/brucker.ea-ontologies-certification-2019.pdf).
+  In Integrated Formal Methods (IFM). Lecture Notes in Computer Science (11918).
+  Springer-Verlag 2019.
   [doi:10.1007/978-3-030-34968-4_4](http://dx.doi.org/10.1007/978-3-030-34968-4_4)  
 
-* Sergio Bezzecchi, Paolo Crisafulli, Charlotte Pichot, and Burkhart Wolff. [Making Agile Development
+* Sergio Bezzecchi, Paolo Crisafulli, Charlotte Pichot, and Burkhart Wolff.
-  Processes fit for V-style Certification Procedures.](https://hal.archives-ouvertes.fr/hal-01702815/document)
+  [Making Agile Development Processes fit for V-style Certification
-   In ERTS 2018. <https://hal.archives-ouvertes.fr/hal-01702815>
+   Procedures.](https://hal.archives-ouvertes.fr/hal-01702815/document). In ERTS
+   2018. <https://hal.archives-ouvertes.fr/hal-01702815>
 
 ## Upstream Repository
 
-The upstream git repository, i.e., the single source of truth, for this project is hosted
+The upstream git repository, i.e., the single source of truth, for this project
-at <https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF>.
+is hosted at <https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF>.

etc/build.props

@@ -8,5 +8,5 @@ sources = \
   src/scala/dof_mkroot.scala \
   src/scala/dof_tools.scala
 services = \
-  isabelle_dof.DOF_Tools \
+  isabelle.dof.DOF_Tools \
-  isabelle_dof.DOF_Document_Build$Engine
+  isabelle.dof.DOF_Document_Build$Engine

etc/options

@@ -12,8 +12,8 @@ option dof_version : string = "Unreleased"
   -- "Isabelle/DOF version" 
      (* "Unreleased" for development, semantic version for releases *)
 
-option dof_isabelle : string = "2021-1" 
+option dof_isabelle : string = "2022" 
-option dof_afp : string = "afp-2021-12-28"
+option dof_afp : string = "afp-2022-10-27"
 
 option dof_latest_version : string = "1.3.0"    
 option dof_latest_isabelle : string = "Isabelle2021-1"

examples/technical_report/TR_my_commented_isabelle/TR_MyCommentedIsabelle.thy

@@ -1,7 +1,7 @@
 (*************************************************************************
  * Copyright (C) 
- *               2019-2021 The University of Exeter 
+ *               2019-2022 The University of Exeter 
- *               2018-2021 The University of Paris-Saclay
+ *               2018-2022 The University of Paris-Saclay
  *               2018      The University of Sheffield
  *
  * License:
@@ -23,7 +23,7 @@ open_monitor*[this::report]
 (*>*)
 
 title*[tit::title]\<open>My Personal, Eclectic Isabelle Programming Manual\<close> 
-subtitle*[stit::subtitle]\<open>Version : Isabelle 2020\<close>
+subtitle*[stit::subtitle]\<open>Version : Isabelle 2022\<close>
 text*[bu::author,     
       email       = "''wolff@lri.fr''",
       affiliation = "\<open>Université Paris-Saclay, LRI, France\<close>"]\<open>Burkhart Wolff\<close>
@@ -1183,7 +1183,7 @@ text\<open> The extensibility of Isabelle as a system framework depends on a num
  \<^item> \<^ML>\<open>Toplevel.theory: (theory -> theory) -> Toplevel.transition -> Toplevel.transition\<close>
    adjoins a theory transformer.
  \<^item> \<^ML>\<open>Toplevel.generic_theory: (generic_theory -> generic_theory) -> Toplevel.transition -> Toplevel.transition\<close>
- \<^item> \<^ML>\<open>Toplevel.theory': (bool -> theory -> theory) -> Toplevel.transition -> Toplevel.transition\<close>
+ \<^item> \<^ML>\<open>Toplevel.theory': (bool -> theory -> theory) -> Toplevel.presentation -> Toplevel.transition -> Toplevel.transition\<close>
  \<^item> \<^ML>\<open>Toplevel.exit: Toplevel.transition -> Toplevel.transition\<close>
  \<^item> \<^ML>\<open>Toplevel.ignored: Position.T -> Toplevel.transition\<close>
  \<^item> \<^ML>\<open>Toplevel.present_local_theory:  (xstring * Position.T) option ->
@@ -1845,6 +1845,7 @@ text\<open>The second part is much more high-level, and can be found under \<^ML
   This is perhaps meant with the fairly cryptic comment:
   "Quasi-inner syntax based on outer tokens: concrete argument syntax of
   attributes, methods etc." at the beginning of this structure.\<close>
+ML\<open>open Args\<close>  
 
 text\<open> Some more combinators
 \<^item>\<^ML>\<open>Args.symbolic : Token.T parser\<close>
@@ -1865,12 +1866,11 @@ Common Isar Syntax
 \<^item>\<^ML>\<open>Args.name_position: (string * Position.T) parser\<close>
 \<^item>\<^ML>\<open>Args.cartouche_inner_syntax: string parser\<close>
 \<^item>\<^ML>\<open>Args.cartouche_input: Input.source parser\<close>
-\<^item>\<^ML>\<open>Args.text_token: Token.T parser \<close>
 
 
 Common Isar Syntax
-\<^item>\<^ML>\<open>Args.text_input: Input.source parser\<close>
+\<^item>\<^ML>\<open>Parse.embedded_input: Input.source parser\<close>
-\<^item>\<^ML>\<open>Args.text      : string parser\<close>
+\<^item>\<^ML>\<open>Parse.embedded      : string parser\<close>
 \<^item>\<^ML>\<open>Args.binding   : Binding.binding parser\<close>
 
 Common Stuff related to Inner Syntax Parsing
@@ -1893,8 +1893,7 @@ Common Isar Syntax
 \<^item>\<^ML>\<open>Args.named_source: (Token.T -> Token.src) -> Token.src parser\<close>
 \<^item>\<^ML>\<open>Args.named_typ   : (string -> typ) -> typ parser\<close>
 \<^item>\<^ML>\<open>Args.named_term : (string -> term) -> term parser\<close>
-\<^item>\<^ML>\<open>Args.text_declaration: (Input.source -> declaration) -> declaration parser\<close>
+\<^item>\<^ML>\<open>Args.embedded_declaration: (Input.source -> declaration) -> declaration parser\<close>
-\<^item>\<^ML>\<open>Args.cartouche_declaration: (Input.source -> declaration) -> declaration parser\<close>
 \<^item>\<^ML>\<open>Args.typ_abbrev  : typ context_parser\<close>
 \<^item>\<^ML>\<open>Args.typ: typ context_parser\<close>
 \<^item>\<^ML>\<open>Args.term: term context_parser\<close>
@@ -1903,8 +1902,6 @@ Common Isar Syntax
 \<^item>\<^ML>\<open>Args.named_source: (Token.T -> Token.src) -> Token.src parser\<close>
 \<^item>\<^ML>\<open>Args.named_typ : (string -> typ) -> typ parser\<close>
 \<^item>\<^ML>\<open>Args.named_term: (string -> term) -> term parser\<close>
-\<^item>\<^ML>\<open>Args.text_declaration: (Input.source -> declaration) -> declaration parser\<close>
-\<^item>\<^ML>\<open>Args.cartouche_declaration: (Input.source -> declaration) -> declaration parser\<close>
 
 Syntax for some major Pure commands in Isar
 \<^item>\<^ML>\<open>Args.prop: term context_parser\<close>
@@ -2132,7 +2129,6 @@ Since Isabelle2018, an own AST is provided for the LaTeX syntax, analogously to
 \<^item>\<^ML>\<open>Latex.string: string -> Latex.text\<close>
 \<^item>\<^ML>\<open>Latex.text: string * Position.T -> Latex.text\<close>
 
-\<^item>\<^ML>\<open>Latex.output_name: string -> string\<close>
 \<^item>\<^ML>\<open>Latex.output_ascii: string -> string\<close>
 \<^item>\<^ML>\<open>Latex.output_symbols: Symbol.symbol list -> string\<close>
                                                                           

install-afp

@@ -35,6 +35,8 @@ print_help()
 {
     echo "Usage: isabelle env ./install-afp [OPTION] "
     echo ""
+    echo "Warning: This tools is deprecated."
+    echo ""
     echo "Run ..."
     echo ""
     echo "  --help, -h                display this help message"
@@ -44,11 +46,29 @@ print_help()
 
 exit_error() {
     echo ""
-    echo "  *** Isabelle/DOF installation FAILED, please check the README.md for help ***"
+    echo "  *** Local AFP installation FAILED, please check the README.md for help ***"
     echo ""
     exit 1
 }
 
+confirm_usage() {
+    echo "* From Isabelle2021-1 on, the recommended method for making the whole AFP "
+    echo "  available to Isabelle is the isabelle components -u command."
+    echo "  For doing so, please follow the instructions at: "
+    echo "  https://www.isa-afp.org/help/"
+    echo ""
+    echo "  Alternatively, you can continue, on your own risk, to install only"
+    echo "  the AFP entries required to run Isabelle/DOF."
+    echo ""
+    read -p "    Still continue (y/N)? " -n 1 -r
+    echo 
+    if [[ $REPLY =~ ^[Yy]$ ]];
+    then 
+        echo "    Continuing installation on your OWN risk."
+    else
+        exit_error
+    fi
+}
 check_isabelle_version() {
     echo "* Checking Isabelle version:"
     if [ "$ISABELLE_VERSION" != "$ACTUAL_ISABELLE_VERSION" ]; then
@@ -149,6 +169,7 @@ AFP_URL="https://www.isa-afp.org/release/"$AFP_DATE".tar.gz"
 echo ""
 echo "Isabelle/DOF AFP Installation Utility"
 echo "====================================="
+confirm_usage
 check_isabelle_version
 check_afp_entries
 echo "* AFP Installation successful."

src/DOF/Isa_COL.thy

@@ -206,7 +206,7 @@ fun check_latex_measure _ src  =
                      handle Fail _ => error ("syntax error in LaTeX measure") )
          in () end
 
-val parse_latex_measure = Args.text_input >> (fn src => (check_latex_measure () (* dummy arg *) src; 
+val parse_latex_measure = Parse.embedded_input >> (fn src => (check_latex_measure () (* dummy arg *) src; 
                                        (fst o Input.source_content) src )  )
 
 end\<close>

src/DOF/Isa_DOF.thy

@@ -1,7 +1,7 @@
 (*************************************************************************
  * Copyright (C) 
- *               2019      The University of Exeter 
+ *               2019-2022 The University of Exeter 
- *               2018-2019 The University of Paris-Saclay
+ *               2018-2022 The University of Paris-Saclay
  *               2018      The University of Sheffield
  *
  * License:
@@ -1965,6 +1965,23 @@ fun document_output {markdown: bool, markup: Latex.text -> Latex.text} meta_args
     val output_text = Document_Output.output_document ctxt {markdown = markdown} text;
   in markup (output_meta @ output_text) end;
 
+    val output_name = (* was available as Latex.output_name in Isabelle 2021-1 and earlier *)
+          translate_string
+          (fn "_" => "UNDERSCORE"
+            | "'" => "PRIME"
+            | "0" => "ZERO"
+            | "1" => "ONE"
+            | "2" => "TWO"
+            | "3" => "THREE"
+            | "4" => "FOUR"
+            | "5" => "FIVE"
+            | "6" => "SIX"
+            | "7" => "SEVEN"
+            | "8" => "EIGHT"
+            | "9" => "NINE"
+            | s => s);
+
+
 fun document_output_reports name {markdown, body} meta_args text ctxt =
   let
     val pos = Input.pos_of text;
@@ -1974,7 +1991,7 @@ fun document_output_reports name {markdown, body} meta_args text ctxt =
          (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;
+      in [XML.Elem (m (output_name name), xml)] end;
   in document_output {markdown = markdown, markup = markup} meta_args text ctxt end;
 
 
@@ -2364,7 +2381,7 @@ val docitem_modes = Scan.optional (Args.parens (Args.$$$ defineN || Args.$$$ unc
                                    {unchecked = false, define= false} (* default *);
 
 
-val docitem_antiquotation_parser = (Scan.lift (docitem_modes -- Args.text_input))
+val docitem_antiquotation_parser = (Scan.lift (docitem_modes -- Parse.embedded_input))
                                    : ({define:bool,unchecked:bool} * Input.source) context_parser;
 
 
@@ -2835,7 +2852,7 @@ fun string_2_theory_text_antiquotation ctxt text =
       end
 
 fun gen_text_antiquotation name reportNcheck compile =
-  Document_Output.antiquotation_raw_embedded name (Scan.lift Args.text_input)
+  Document_Output.antiquotation_raw_embedded name (Scan.lift Parse.embedded_input)
     (fn ctxt => fn text:Input.source =>
       let
         val _ = reportNcheck ctxt text;
@@ -2848,7 +2865,7 @@ fun std_text_antiquotation name (* redefined in these more abstract terms *) =
 
 (* should be the same as (2020):
 fun text_antiquotation name =
-  Thy_Output.antiquotation_raw_embedded name (Scan.lift Args.text_input)
+  Thy_Output.antiquotation_raw_embedded name (Scan.lift Parse.embedded_input)
     (fn ctxt => fn text =>
       let
         val _ = report_text ctxt text;
@@ -2864,7 +2881,7 @@ fun std_theory_text_antiquotation name (* redefined in these more abstract terms
 
 (* should be the same as (2020):
 fun theory_text_antiquotation name =
-  Thy_Output.antiquotation_raw_embedded name (Scan.lift Args.text_input)
+  Thy_Output.antiquotation_raw_embedded name (Scan.lift Parse.embedded_input)
     (fn ctxt => fn text =>
       let
         val keywords = Thy_Header.get_keywords' ctxt;
@@ -2886,12 +2903,11 @@ fun theory_text_antiquotation name =
 
 
 fun environment_delim name =
- ("%\n\\begin{" ^ Latex.output_name name ^ "}\n",
+ ("%\n\\begin{" ^ Monitor_Command_Parser.output_name name ^ "}\n",
-  "\n\\end{" ^ Latex.output_name name ^ "}");
+  "\n\\end{" ^ Monitor_Command_Parser.output_name name ^ "}");
 
 fun environment_block name = environment_delim name |-> XML.enclose;
 
-
 fun enclose_env verbatim ctxt block_env body =
   if Config.get ctxt Document_Antiquotation.thy_output_display
   then if verbatim 
@@ -2902,6 +2918,7 @@ fun enclose_env verbatim ctxt block_env body =
 end
 \<close>
 
+
 ML\<open>
 local 
 val parse_literal = Parse.alt_string || Parse.cartouche

src/DOF/RegExpInterface.thy

@@ -118,7 +118,7 @@ ML\<open>
       fun is_sml_file f = String.isSuffix ".ML" (Path.implode (#path f))
       val files = (map (Generated_Files.check_files_in (Context.proof_of ctxt)) args) 
       val ml_files = filter is_sml_file (map #1 (maps Generated_Files.get_files_in files))
-      val ml_content = map (fn f => Syntax.read_input (#content f)) ml_files
+      val ml_content = map (fn f => Syntax.read_input (Bytes.content (#content f))) ml_files
       fun eval ml_content   = fold (fn sml => (ML_Context.exec 
                                            (fn () => ML_Context.eval_source ML_Compiler.flags sml))) 
                                    ml_content 

src/scala/dof_document_build.scala

@@ -28,10 +28,9 @@
  * SPDX-License-Identifier: BSD-2-Clause
  */
 
-package isabelle_dof
+package isabelle.dof
 
 import isabelle._
-import java.io.{File => JFile}
 
 
 object DOF_Document_Build
@@ -50,31 +49,31 @@ object DOF_Document_Build
       val directory = context.prepare_directory(dir, doc, latex_output)
 
       // produced by alternative presentation hook (workaround for missing Toplevel.present_theory)
-      for (name <- context.document_theories) {
+      for {
+        name <- context.document_theories.iterator
+        entry <- context.session_context.get(name.theory, Export.DOCUMENT_LATEX + "_dof")
+      } {
         val path = Path.basic(Document_Build.tex_name(name))
-        val xml =
+        val xml = YXML.parse_body(entry.text)
-          YXML.parse_body(context.get_export(name.theory, Export.DOCUMENT_LATEX + "_dof").text)
+        File.content(path, xml).output(latex_output(_, file_pos = path.implode_symbolic))
-        if (xml.nonEmpty) {
+          .write(directory.doc_dir)
-          File.Content(path, xml).output(latex_output(_, file_pos = path.implode_symbolic))
-            .write(directory.doc_dir)
-        }
       }
-      val dof_home= Path.explode(Isabelle_System.getenv_strict("ISABELLE_DOF_HOME"));
+      val isabelle_dof_dir = context.session_context.sessions_structure("Isabelle_DOF").dir
       // print(context.options.string("dof_url"));
       
       // copy Isabelle/DOF LaTeX templates
-      val template_dir = dof_home + Path.explode("src/document-templates/")
+      val template_dir = isabelle_dof_dir + Path.explode("document-templates")
       // TODO: error handling in case 1) template does not exist or 2) root.tex does already exist
       val  template = regex.replaceAllIn(context.options.string("dof_template"),"")
       Isabelle_System.copy_file(template_dir + Path.explode("root-"+template+".tex"), 
                                 directory.doc_dir+Path.explode("root.tex"))
 
-      // copy Isabelle/DOF LaTeX styles 
+      // copy Isabelle/DOF LaTeX styles
-      val doc_jdir = new JFile(directory.doc_dir.implode)
+      List(Path.explode("DOF/latex"), Path.explode("ontologies"))
-      val styles = File.find_files(new JFile(dof_home.implode),((f:JFile) => f.getName().endsWith(".sty")), true)
+        .flatMap(dir =>
-      for (sty <- styles) { 
+          File.find_files((isabelle_dof_dir + dir).file,
-        Isabelle_System.copy_file(sty, doc_jdir)
+            file => file.getName.endsWith(".sty"), include_dirs = true))
-      }
+        .foreach(sty => Isabelle_System.copy_file(sty, directory.doc_dir.file))
 
       // create ontology.sty
       val ltx_styles =  context.options.string("dof_ontologies").split(" +").map(s => regex.replaceAllIn(s,""))
@@ -83,7 +82,7 @@ object DOF_Document_Build
 
       // create dof-config.sty
       File.write(directory.doc_dir+Path.explode("dof-config.sty"), """
-\newcommand{\isabelleurl}{https://isabelle.in.tum.de/website-Isabelle2021-1/""" + context.options.string("dof_isabelle") + """}
+\newcommand{\isabelleurl}{https://isabelle.in.tum.de/website-Isabelle2022/""" + context.options.string("dof_isabelle") + """}
 \newcommand{\dofurl}{""" + context.options.string("dof_url") + """}
 \newcommand{\dof@isabelleversion}{""" + context.options.string("dof_isabelle") + """}
 \newcommand{\isabellefullversion}{""" + context.options.string("dof_isabelle") + """\xspace}

src/scala/dof_mkroot.scala

@@ -34,7 +34,7 @@
 Prepare session root directory for Isabelle/DOF.
 */
 
-package isabelle_dof
+package isabelle.dof
 
 import isabelle._
 

src/scala/dof_tools.scala

@@ -29,7 +29,7 @@
  */
 
  
-package isabelle_dof
+package isabelle.dof
 
 import isabelle._
 

src/tests/OutOfOrderPresntn.thy

@@ -244,7 +244,7 @@ fun string_2_theory_text_antiquotation ctxt text =
       end
 
 fun gen_text_antiquotation name reportNcheck compile =
-  Document_Output.antiquotation_raw_embedded name (Scan.lift Args.text_input)
+  Document_Output.antiquotation_raw_embedded name (Scan.lift Parse.embedded_input)
     (fn ctxt => fn text:Input.source =>
       let
         val _ = reportNcheck ctxt text;
@@ -257,7 +257,7 @@ fun std_text_antiquotation name (* redefined in these more abstract terms *) =
 
 (* should be the same as (2020):
 fun text_antiquotation name =
-  Thy_Output.antiquotation_raw_embedded name (Scan.lift Args.text_input)
+  Thy_Output.antiquotation_raw_embedded name (Scan.lift Parse.embedded_input)
     (fn ctxt => fn text =>
       let
         val _ = report_text ctxt text;
@@ -273,7 +273,7 @@ fun std_theory_text_antiquotation name (* redefined in these more abstract terms
 
 (* should be the same as (2020):
 fun theory_text_antiquotation name =
-  Thy_Output.antiquotation_raw_embedded name (Scan.lift Args.text_input)
+  Thy_Output.antiquotation_raw_embedded name (Scan.lift Parse.embedded_input)
     (fn ctxt => fn text =>
       let
         val keywords = Thy_Header.get_keywords' ctxt;