Merge branch 'config_as_options'

CHANGELOG.md

@@ -11,12 +11,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### Changed
 
-- removed explicit use of build script. Requires removing "build" script entry
+- The project-specific configuration is not part of the `ROOT` file, the formerly 
+  used `isadof.cfg` is obsolete and no longer supported.
+- Removed explicit use of build script. Requires removing "build" script entry
   from ROOT files.
-- lipics support is now official, requires document option "document_comment_latex=true"
+- Support for the `lipics` LaTeX style is now official. This requires document 
-  in the ROOT file.
+  option `document_comment_latex=true` in the ROOT file.
 - Isabelle/DOF is now a proper Isabelle component that should be installed using the
-  "isabelle components" command. The installation script is now only an convenience 
+  `isabelle components` command. The installation script is now only a convenience
   means for installing the required AFP entries.
 
 ## 1.2.0 - 2022-03-26

README.md

@@ -7,7 +7,7 @@ online.](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF
 
 ## Pre-requisites
 
-Isabelle/DOF has three major pre-requisites:
+Isabelle/DOF has three major prerequisites:
 
 * **Isabelle:** Isabelle/DOF requires [Isabelle 2021-1](http://isabelle.in.tum.de/website-Isabelle2021-1/).
   Please download the Isabelle 2021-1 distribution for your operating
@@ -20,16 +20,18 @@ Isabelle/DOF has three major pre-requisites:
   provide a script that only installs the two entries required by
   Isabelle/DOF into the local Isabelle/DOF directory. You can use this
   script 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.
   
 ## Installation
 
 Isabelle/DOF is provided as a Isabelle component. After installing the
-pre-requisites the Isabelle/Archive needs to be unpacked and
+prerequisites the Isabelle/Archive needs to be unpacked and
 registered.  Change into the directory you unpacked Isabelle/DOF (this
 should be the directory containing this `README.md` file) and execute
 
@@ -78,7 +80,7 @@ Isabelle projects that use DOF need to be created using
 foo@bar:~$ isabelle mkroot_DOF
 ```
 
-The ``mkroot_DOF`` command takes the same parameter as the standard
+The ``dof_mkroot`` command takes the same parameter as the standard
 ``mkroot`` command of Isabelle. Thereafter, the normal Isabelle
 command for building documents can be used.
 
@@ -87,7 +89,7 @@ selected and using the ``-t`` option, different LaTeX setups
 can be selected. For example,
 
 ```console
-foo@bar:~$ isabelle mkroot_DOF -o scholarly_paper -t scrartcl
+foo@bar:~$ isabelle dof_mkroot -o scholarly_paper -t scrartcl
 ```
 
 creates a setup using the scholarly_paper ontology and the article
@@ -97,31 +99,21 @@ The help (option ``-h``) show a list of all supported ontologies and
 document templates:
 
 ```console
-foo@bar:~$ isabelle mkroot_DOF -h
+foo@bar:~$ isabelle dof_mkroot -h
-
+Usage: isabelle dof_mkroot [OPTIONS] [DIRECTORY]
-Usage: isabelle mkroot_DOF [OPTIONS] [DIR]
 
   Options are:
-    -h           print this help text and exit
+    -I           init Mercurial repository and add generated files
-    -n NAME      alternative session name (default: DIR base name)
+    -n NAME      alternative session name (default: directory base name)
-    -o ONTOLOGY  (default: scholarly_paper)
+    -o ONTOLOGY  ontology (default: scholarly_paper)
-       Available ontologies:
+    -t TEMPLATE  tempalte (default: scrartcl)
-       * cenelec_50128
-       * mathex
-       * scholarly_paper
-    -t TEMPLATE   (default: scrartcl)
-       Available document templates:
-       * lncs
-       * scrartcl
-       * scrreprt
-       * scrreprt-modern
 
-  Prepare session root DIR (default: current directory).
+  Prepare session root directory (default: current directory).
 ```
 
 ## Releases
 
-For releases, signed archives including a PDF version of the Isabelle/DOF manual are
+For releases, signed archives including a PDF version of the Isabelle/DOF manual
 are available:
 
 * Isabelle/DOF 1.2.0/Isabelle2021

etc/options

@@ -2,18 +2,18 @@
 
 section "Isabelle/DOF"
 
-public option dof_document_class : string = "scrreprt-modern"
+public option dof_template : string = "scrreprt-modern"
-  -- "Default document class for Isabelle/DOF documents"
+  -- "Default document template for Isabelle/DOF documents"
-
-public option dof_presentation_ontologies : string = "technical_report scholarly_paper"
-  -- "ontologies (separated by blanks)"
 
+public option dof_ontologies : string = "Isabelle_DOF.technical_report Isabelle_DOF.scholarly_paper"
+  -- "Isabelle/DOF ontologies (separated by blanks)"
 
 option dof_version : string = "Unreleased" 
   -- "Isabelle/DOF version" 
      (* "Unreleased" for development, semantic version for releases *)
 
 option dof_isabelle : string = "2021-1" 
+option dof_afp : string = "afp-2021-12-28"
 
 option dof_latest_version : string = "1.2.0"    
 option dof_latest_isabelle : string = "Isabelle2021"

etc/settings

@@ -1,25 +1,5 @@
 # -*- shell-script -*- :mode=shellscript:
 
 ISABELLE_DOF_HOME="$COMPONENT"
-ISABELLE_TOOLS="$ISABELLE_TOOLS":"$ISABELLE_DOF_HOME/src/Tools"
 ISABELLE_DOCS="$ISABELLE_DOF_HOME/doc":"$ISABELLE_DOCS"
 
-# Isabelle/DOF Version Information
-DOF_VERSION="Unreleased"    # "Unreleased" for development, semantic version for releases 
-DOF_DATE="00/00/00"
-DOF_LATEST_VERSION="1.2.0"    
-DOF_LATEST_ISABELLE="Isabelle2021"
-DOF_LATEST_DOI="10.5281/zenodo.6385695"
-DOF_GENERIC_DOI="10.5281/zenodo.3370482"
-#
-# Isabelle and AFP Configuration
-ISABELLE_VERSION="Isabelle2021-1"
-ISABELLE_URL="https://isabelle.in.tum.de/website-Isabelle2021-1/"
-AFP_DATE="afp-2021-12-28"
-AFP_URL="https://www.isa-afp.org/release/"$AFP_DATE".tar.gz"
-#
-# Isabelle/DOF Repository Configuration
-DOF_URL="https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF"
-DOF_ARTIFACT_DIR="releases/Isabelle_DOF/Isabelle_DOF"
-DOF_ARTIFACT_HOST="artifacts.logicalhacking.com"
-#

examples/CENELEC_50128/mini_odo/ROOT

@@ -1,9 +1,9 @@
 session "mini_odo" = "Isabelle_DOF" +
-  options [document = pdf, document_output = "output", document_build = dof]
+  options [document = pdf, document_output = "output", document_build = dof,
+           dof_ontologies = "technical_report cenelec_50128", dof_template = "scrreprt-modern"]
   theories
     "mini_odo"
   document_files
-    "isadof.cfg"
     "preamble.tex"
     "root.bib"
     "root.mst"
@@ -12,3 +12,4 @@ session "mini_odo" = "Isabelle_DOF" +
     "figures/odometer.jpeg"
     "figures/three-phase-odo.pdf"
     "figures/wheel-df.png"
+

examples/CENELEC_50128/mini_odo/document/isadof.cfg

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

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

@@ -256,7 +256,7 @@ enforcing a sequence of text-elements that must belong to the corresponding clas
 To start using \<^isadof>, one creates an Isabelle project (with the name 
 \inlinebash{IsaDofApplications}):
 \begin{bash}
-  isabelle mkroot_DOF -o scholarly_paper -t lncs -d  IsaDofApplications
+  isabelle dof_mkroot -o scholarly_paper -t lncs IsaDofApplications
 \end{bash}
 where the \inlinebash{-o scholarly_paper} specifies the ontology for writing scientific articles and 
 \inlinebash{-t lncs} specifies the use of Springer's \LaTeX-configuration for the Lecture Notes in 

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

@@ -1,10 +1,10 @@
 session "2018-cicm-isabelle_dof-applications" = "Isabelle_DOF" + 
   options  [document = pdf, document_output = "output", document_build = dof,
+   dof_ontologies = "scholarly_paper", dof_template = lncs, 
    quick_and_dirty = true]
   theories
     IsaDofApplications
   document_files
-    "isadof.cfg"
     "root.bib"
     "authorarchive.sty"
     "preamble.tex"

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

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

examples/scholarly_paper/2020-iFM-CSP/ROOT

@@ -1,8 +1,8 @@
 session "2020-iFM-csp" = "Isabelle_DOF" +
-  options [document = pdf, document_output = "output", document_build = dof]
+  options [document = pdf, document_output = "output", document_build = dof,
+  dof_ontologies = "scholarly_paper", dof_template = scrartcl]
   theories
     "paper"
   document_files
-    "isadof.cfg"
     "root.bib"
     "preamble.tex"

examples/scholarly_paper/2020-iFM-CSP/document/isadof.cfg

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

examples/technical_report/Isabelle_DOF-Manual/03_GuidedTour.thy

@@ -54,7 +54,7 @@ text\<open>
 Depending on your operating system and depending if you put Isabelle's  \<^boxed_bash>\<open>bin\<close> directory
 in your  \<^boxed_bash>\<open>PATH\<close>, you will need to invoke  \<^boxed_bash>\<open>isabelle\<close> using its
 full qualified path, \<^eg>:
-@{boxed_bash [display]\<open>ë\prompt{}ë /usr/local/Isabelleë\isabelleversionë/bin/isabelle version
+@{boxed_bash [display]\<open>ë\prompt{}ë /usr/local/Isabelleë\isabelleversion/bin/isabelleë version
 ë\isabellefullversionë\<close>}
 \<close>
 
@@ -115,14 +115,16 @@ session and all example documents, execute:
 subsection*[first_project::technical]\<open>Creating an \<^isadof> Project\<close>
 text\<open>
   \<^isadof> provides its own variant of Isabelle's 
-  \<^boxed_bash>\<open>mkroot\<close> tool, called \<^boxed_bash>\<open>mkroot_DOF\<close>\index{mkroot\_DOF}:
+  \<^boxed_bash>\<open>mkroot\<close> tool, called \<^boxed_bash>\<open>dof_mkroot\<close>\index{mkroot\_DOF}:
-@{boxed_bash [display]\<open>ë\prompt{}ë isabelle mkroot_DOF myproject
+@{boxed_bash [display]\<open>ë\prompt{}ë isabelle dof_mkroot myproject
 
 Preparing session "myproject" iëën "myproject"
   creating "myproject/ROOT"
-  creating "myproject/document/root.tex"
+  creating "myproject/myproject.thy"
+  creating "myproject/document/preamble.tex"
+
+Now use the following commanëëd line to build the session:
 
-Now use the following coëëmmand line to build the session:
   isabelle build -D myproject\<close>}
   The created project uses the default configuration (the ontology for writing academic papers 
   (scholarly\_paper) using a report layout based on the article class (\<^boxed_latex>\<open>scrartcl\<close>) of 
@@ -139,21 +141,24 @@ The directory  \<^boxed_bash>\<open>myproject\<close> contains the following fil
 .1 .
 .2 myproject.
 .3 document.
-.4 isadof.cfg\DTcomment{\<^isadof> configuration}.
 .4 preamble.tex\DTcomment{Manual \<^LaTeX>-configuration}.
+.3 myproject.thy\DTcomment{Example theory file}.
 .3 ROOT\DTcomment{Isabelle build-configuration}.
 }
 \end{minipage}
 \end{center}
-The \<^isadof> configuration (\<^boxed_bash>\<open>isadof.cfg\<close>) specifies the required
+
-ontologies and the document template using a YAML syntax.\<^footnote>\<open>Isabelle power users will recognize that 
+The main two configuration files\<^footnote>\<open>Isabelle power users will recognize that
 \<^isadof>'s document setup does not make use of a file \<^boxed_bash>\<open>root.tex\<close>: this file is 
-replaced by built-in document templates.\<close> The main two configuration files for 
+replaced by built-in document templates.\<close>  for users are: 
-users are:
 \<^item> The file \<^boxed_bash>\<open>ROOT\<close>\<^index>\<open>ROOT\<close>, which defines the Isabelle session. New theory files as well as new 
   files required by the document generation (\<^eg>, images, bibliography database using \<^BibTeX>, local
   \<^LaTeX>-styles) need to be registered in this file. For details of Isabelle's build system, please 
-  consult the Isabelle System Manual~@{cite "wenzel:system-manual:2020"}.
+  consult the Isabelle System Manual~@{cite "wenzel:system-manual:2020"}. In addition to the 
+  standard features of, this file also contains \<^isadof> specific configurations:
+  \<^item>  \<^boxed_bash>\<open>dof_ontologies\<close> a list of (fully qualified) ontologies, separated by spaces, used 
+     by the project. 
+  \<^item>  \<^boxed_bash>\<open>dof_template\<close> the document template.
 \<^item> The file \<^boxed_bash>\<open>preamble.tex\<close>\<^index>\<open>preamble.tex\<close>, which allows users to add additional 
   \<^LaTeX>-packages or to add/modify \<^LaTeX>-commands. 
 \<close>
@@ -166,31 +171,21 @@ text\<open>
     obtains and adds the necessary \<^LaTeX> class file. 
     This is due to licensing restrictions).\<close>
 text\<open> 
-  This can be configured by using the command-line options of \<^boxed_bash>\<open>mkroot_DOF\<close>. In 
+  This can be configured by using the command-line options of \<^boxed_bash>\<open>dof_mkroot\<close>. In 
   Particular, \<^boxed_bash>\<open>-o\<close> allows selecting the ontology and \<^boxed_bash>\<open>-t\<close> allows selecting 
-  the document template. The built-in help (using  \<^boxed_bash>\<open>-h\<close>) shows all available options 
+  the document template. The built-in help (using  \<^boxed_bash>\<open>-h\<close>) shows all available options: 
-  as well as a complete list of the available document templates and ontologies: 
 
-  @{boxed_bash [display]\<open>ë\prompt{}ë isabelle mkroot_DOF -h
+  @{boxed_bash [display]\<open>ë\prompt{}ë isabelle dof_mkroot -h
 
-Usage: isabelle mkroot_DOF [OPTIONS] [DIR]
+Usage: isabelle dof_mkroot [OPTIONS] [DIRECTORY]
 
   Options are:
-    -h           print this hëëelp text and exëëit
+    -I           init Mercurial repository and add generated files
-    -n NAME      alternative session name (default: DIR base name)
+    -n NAME      alternative session name (default: directory base name)
-    -o ONTOLOGY  (default: scholarly_paper)
+    -o ONTOLOGY  ontology (default: scholarly_paper)
-       Available ontologies:
+    -t TEMPLATE  tempalte (default: scrartcl)
-       * CENELEC_50128
-       * scholarly_paper
-       * technical_report
-    -t TEMPLATE   (default: scrartcl)
-       Available document templates:
-       * lncs
-       * scrartcl
-       * scrreprt-modern
-       * scrreprt
 
-  Prepare session root DIR (default: current directory). \<close>}
+  Prepare session root directory (default: current directory).\<close>}
 
 \<close>
 

examples/technical_report/Isabelle_DOF-Manual/04_RefMan.thy

@@ -1236,7 +1236,7 @@ section*[infrastructure::technical]\<open>Technical Infrastructure\<close>
 text\<open> 
   The list of fully supported (\<^ie>, supporting both interactive ontological modeling and 
   document generation) ontologies and the list of supported document templates can be 
-  obtained by calling \<^boxed_bash>\<open>isabelle mkroot_DOF -h\<close> (see \<^technical>\<open>first_project\<close>).
+  obtained by calling \<^boxed_bash>\<open>isabelle dof_mkroot -h\<close> (see \<^technical>\<open>first_project\<close>).
   Note that the postfix \<^boxed_bash>\<open>-UNSUPPORTED\<close> denotes experimental ontologies or templates 
   for which further manual setup steps might be required or that are not fully tested. Also note 
   that the \<^LaTeX>-class files required by the templates need to be already installed on your 
@@ -1360,14 +1360,7 @@ text\<open>
 \usepackage{isabelle,isabellesym,amssymb} % Required (by Isabelle)
 \usepackage{amsmath}           % Used by some ontologies  
 \bibliographystyle{abbrv}
-\IfFileExists{DOF-core.sty}{}{ % Required by Isabelle/DOF
+\input{dof-common} % setup shared between all Isabelle/DOF templates
-  \PackageError{DOF-core}{The doëëcument preparation 
-   requires the Isabelle/DOF framework.}{For further help, see 
-   ë\url{\dofurl}ë
-}
-\input{ontologies}             % This will include the document specific 
-                               % ontologies from isadof.cfg
-\IfFileExists{preamble.tex}{\input{preamble.tex}}{}  
 \usepackage{graphicx}          % Required for images. 
 \usepackage[caption]{subfig}
 \usepackage[size=footnotesize]{caption}
@@ -1393,7 +1386,7 @@ text\<open>
 
 subsubsection\<open>Getting Started\<close>
 text\<open>
-  In general, we recommend creating a test project (\<^eg>, using \<^boxed_bash>\<open>isabelle mkroot_DOF\<close>)
+  In general, we recommend creating a test project (\<^eg>, using \<^boxed_bash>\<open>isabelle dof_mkroot\<close>)
   to develop new document templates or ontology representations. The default setup of the \<^isadof>
   build system generated a \<^path>\<open>output/document\<close> directory with a self-contained \<^LaTeX>-setup. In 
   this directory, you can directly use \<^LaTeX> on the main file, called \<^path>\<open>root.tex\<close>:

examples/technical_report/Isabelle_DOF-Manual/ROOT

@@ -1,10 +1,10 @@
 session "Isabelle_DOF-Manual" = "Isabelle_DOF" + 
   options  [document = pdf, document_output = "output", document_build = dof,
+    dof_ontologies = "technical_report cenelec_50128", dof_template = "scrreprt-modern",
     quick_and_dirty = true]
   theories
     "Isabelle_DOF-Manual"
   document_files
-    "isadof.cfg"
     "root.bib"
     "root.mst"
     "preamble.tex"

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

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

examples/technical_report/TR_my_commented_isabelle/ROOT

@@ -1,11 +1,11 @@
 session "TR_MyCommentedIsabelle" = "Isabelle_DOF" +
   options [document = pdf, document_output = "output", document_build = dof,
+           dof_ontologies = "technical_report", dof_template = scrreprt,
     quick_and_dirty = true]
   theories
     "TR_MyCommentedIsabelle"
   document_files
     "root.bib"
-    "isadof.cfg"
     "preamble.tex"
     "prooftree.sty"
     "figures/markup-demo.png"

examples/technical_report/TR_my_commented_isabelle/document/isadof.cfg

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

install-afp

@@ -30,6 +30,7 @@
 #set -e
 shopt -s nocasematch
 
+
 print_help()
 {
     echo "Usage: isabelle env ./install-afp [OPTION] "
@@ -58,8 +59,8 @@ check_isabelle_version() {
         echo "    version of Isabelle and rerun the install script, providing the"
         echo "    the \"isabelle\" command as argument."
         echo "    Isabelle ($ISABELLE_VERSION) can be obtained from:"
-        echo "    $ISABELLE_URL"
+        echo "    https://isabelle.in.tum.de/website-$ISABELLE_VERSION/"
-        echo 
+        echo ""
         read -p "    Still continue (y/N)? " -n 1 -r
         echo 
         if [[ $REPLY =~ ^[Yy]$ ]];
@@ -128,8 +129,18 @@ do
     shift
 done
 
+if [ -z ${ISABELLE_TOOL+x} ];
+then
+    print_help
+    exit 1
+fi
+
 ACTUAL_ISABELLE_VERSION=`$ISABELLE_TOOL version`
 
+ISABELLE_VERSION="Isabelle$($ISABELLE_TOOL options -g dof_isabelle)"
+AFP_DATE="$($ISABELLE_TOOL options -g dof_afp)"
+AFP_URL="https://www.isa-afp.org/release/"$AFP_DATE".tar.gz"
+
 echo ""
 echo "Isabelle/DOF Installer"
 echo "======================"

src/DOF/latex/DOF-COL.sty

@@ -14,8 +14,7 @@
 
 \NeedsTeXFormat{LaTeX2e}\relax
 \ProvidesPackage{DOF-COL}
-  [<isadofltxversion>%
+  [00/00/0000 Document-Type Support Framework for Isabelle.]
-  Document-Type Support Framework for Isabelle.]
 
 \RequirePackage{DOF-core}
 

src/DOF/latex/DOF-amssymb.sty

@@ -14,8 +14,7 @@
 
 \NeedsTeXFormat{LaTeX2e}\relax
 \ProvidesPackage{DOF-amssymb}
-  [<isadofltxversion>%
+  [00/00/0000 Document-Type Support Framework for Isabelle (amssymb wrapper for lualatex/pdflatex).]
-  Document-Type Support Framework for Isabelle (amssymb wrapper for lualatex/pdflatex).]
 
 \usepackage{ifxetex,ifluatex}
 \ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex

src/DOF/latex/DOF-core.sty

@@ -14,8 +14,7 @@
 
 \NeedsTeXFormat{LaTeX2e}\relax
 \ProvidesPackage{DOF-core}
-  [<isadofltxversion>%
+  [00/00/0000 Document-Type Support Framework for Isabelle.]
-  Document-Type Support Framework for Isabelle.]
 
 \RequirePackage{keycommand}
 \RequirePackage{environ}
@@ -24,19 +23,7 @@
 \RequirePackage{etoolbox}
 \RequirePackage{fp}
 
-\newcommand{\isabelleurl}{UNDEFINED}
+\RequirePackage{dof-config}
-\newcommand{\dofurl}{UNDEFINED}
-\newcommand{\dof@isabelleversion}{UNDEFINED}
-\newcommand{\isabellefullversion}{UNDEFINED\xspace}
-\newcommand{\dof@version}{UNDEFINED}
-\newcommand{\dof@artifacturl}{UNDEFINED}
-\newcommand{\doflatestversion}{UNDEFINED}
-\newcommand{\isadoflatestdoi}{UNDEFINED}
-\newcommand{\isadofgenericdoi}{UNDEFINED}
-\newcommand{\isabellelatestversion}{Isabelle2019}
-
-%%% CONFIG %%%
-
 \newcommand{\isabelleversion}{\dof@isabelleversion\xspace}
 \newcommand{\dofversion}{\dof@version\xspace}
 \newcommand{\isadofversion}{\dofversion/\isabelleversion}

src/Tools/mkroot_DOF

@@ -1,150 +0,0 @@
-#/usr/bin/env bash
-# Copyright (c) 2019 University of Exeter
-#               2018-2019 University of Paris-Saclay
-#               2018-2019 The University of Sheffield
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions
-# are met:
-# 1. Redistributions of source code must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-# 2. Redistributions in binary form must reproduce the above copyright
-#    notice, this list of conditions and the following disclaimer in
-#    the documentation and/or other materials provided with the
-#    distribution.
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
-# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
-# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
-# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
-# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-# POSSIBILITY OF SUCH DAMAGE.
-#
-# SPDX-License-Identifier: BSD-2-Clause
-#
-# DESCRIPTION: prepare session root directory with DOF setup
-
-## diagnostics
-
-PRG="$(basename "$0")"
-
-function usage()
-{
-  echo
-  echo "Usage: isabelle $PRG [OPTIONS] [DIR]"
-  echo
-  echo "  Options are:"
-  echo "    -h           print this help text and exit"
-  echo "    -n NAME      alternative session name (default: DIR base name)"
-  echo "    -o ONTOLOGY  (default: $DEFAULT_ONTOLOGY)"
-  echo "       Available ontologies:"
-  for t in "$ISABELLE_DOF_HOME/src/ontologies"/*/*.sty; do
-    if [[ $t =~ DOF-(.*).sty$ ]]; then
-      echo "       * ${BASH_REMATCH[1]}"
-    fi
-  done
-  echo "    -t TEMPLATE   (default: $DEFAULT_TEMPLATE)"
-  echo "       Available document templates:"
-  for t in "$ISABELLE_DOF_HOME/src/document-templates/"*.tex; do
-    if [[ $t =~ root-(.*).tex$ ]]; then
-      echo "       * ${BASH_REMATCH[1]}"
-    fi
-  done
-  echo
-  echo "  Prepare session root DIR (default: current directory)."
-  echo
-  exit 1
-}
-
-function fail()
-{
-  echo "$1" >&2
-  exit 2
-}
-
-
-## process command line
-
-# options
-
-NAME=""
-DEFAULT_TEMPLATE="scrartcl"
-DEFAULT_ONTOLOGY="scholarly_paper"
-
-TEMPLATE="$DEFAULT_TEMPLATE"
-ONTOLOGY=""
-
-while getopts "t:o:n:dh" OPT
-do
-  case "$OPT" in
-    h)
-      usage
-      exit 1
-      ;;
-    n)
-      NAME="$OPTARG"
-      ;;
-    o)
-      if [ ! -f "$ISABELLE_DOF_HOME/src/ontologies"/*/DOF-$OPTARG.sty ]; then
-          echo "ERROR: Ontology $OPTARG not available!"
-          exit 1
-      fi
-      ONTOLOGY="$ONTOLOGY $OPTARG"
-      ;;
-    t)
-      TEMPLATE="$OPTARG"
-      if [ ! -f "$ISABELLE_DOF_HOME/src/document-templates/root-$TEMPLATE.tex" ]; then
-          echo "ERROR: Template $TEMPLATE not available!"
-          exit 1
-      fi
-      ;;
-    \?)
-      usage
-      exit 0
-      ;;
-  esac
-done
-
-shift $(($OPTIND - 1))
-
-ONTOLOGY="${ONTOLOGY:-$DEFAULT_ONTOLOGY}"
-
-# args
-
-if [ "$#" -eq 0 ]; then
-  DIR="."
-elif [ "$#" -eq 1 ]; then
-  DIR="$1"
-  shift
-else
-  usage
-fi
-
-if [ -z "$NAME" ]; then
-  NAME="$DIR"
-fi
-
-$ISABELLE_TOOL mkroot -n "$NAME" "$DIR"
-echo "    \"preamble.tex\"" >> "$DIR"/ROOT
-sed -i -e "s/root.tex/isadof.cfg/" "$DIR"/ROOT
-sed -i -e "s/HOL/Isabelle_DOF/" "$DIR"/ROOT
-sed -i -e "s/\"output\"\]/\"output\", document_build = dof\]/" "$DIR"/ROOT
-rm -f "$DIR"/document/root.tex
-  
-# Creating isadof.cfg
-echo "Template: $TEMPLATE" > "$DIR"/document/isadof.cfg
-for o in $ONTOLOGY; do
-  echo "Ontology: $o" >> "$DIR"/document/isadof.cfg;
-done
-
-# Creating praemble.tex
-TITLE=$(echo "$NAME" | tr _ - | tr -d '\\')
-AUTHOR=$(echo "By $USER" | tr _ - | tr -d '\\')
-echo "%% This is a placeholder for user-specific configuration and packages." >> "$DIR"/document/preamble.tex
-echo "\\title{$TITLE}{}{}{}{}{}{}" >> "$DIR"/document/preamble.tex
-echo "\\author{$AUTHOR}{}{}{}{}{}" >> "$DIR"/document/preamble.tex

src/document-templates/dof-common.tex

@@ -0,0 +1,34 @@
+%% 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 lncs class.
+%%
+%% All customization and/or additional packages should be added to the file
+%% preamble.tex.
+
+\usepackage{isabelle}
+\usepackage{isabellesym}
+\IfFileExists{DOF-core.sty}{}{%
+  \PackageError{DOF-core}{Isabelle/DOF not installed. 
+    This is a Isabelle/DOF project. The document preparation requires
+    the Isabelle/DOF component for Isabelle.
+  }{For further help, see the Isabelle/DOF manual.}
+}
+\title{No Title Given}
+\title{No Author Given}
+\input{ontologies}
+\IfFileExists{preamble.tex}{\input{preamble.tex}}{}%
+\isabellestyle{it}

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

@@ -12,8 +12,6 @@
 %%
 %%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
 
-%%   <isadofltxversion>
-
 %% Warning: Do Not Edit!
 %% =====================
 %% This is the root file for the Isabelle/DOF using the eptcs class. 
@@ -26,25 +24,17 @@
 
 \documentclass[submission,copyright,creativecommons]{eptcs}
 \bibliographystyle{eptcs}% the mandatory bibstyle
+
 \usepackage[T1]{fontenc}
 \usepackage[utf8]{inputenc}
 \usepackage[USenglish]{babel}
-\usepackage{isabelle}
+
-%\usepackage{underscore}
+\input{dof-common}
-\usepackage{xcolor}
+
-\usepackage{isabellesym}
 \usepackage{amsmath}
 \usepackage{DOF-amssymb}
 \usepackage[numbers, sort&compress, sectionbib]{natbib}
-\IfFileExists{DOF-core.sty}{}{%
+\usepackage{xcolor}
-  \PackageError{DOF-core}{Isabelle/DOF not installed. 
-    This is a Isabelle_DOF project. The document preparation requires
-    the Isabelle_DOF framework. Please obtain the framework by cloning
-    the Isabelle_DOF component from:
-    <isadofurl>
-  }{For further help, see <isadofurl>}
-}
-
 \newcommand{\subtitle}[1]{%
   \PackageError{DOF-eptcs-UNSUPPORTED}
                {The LaTeX class eptcs does not support subtitles.}
@@ -54,7 +44,6 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % provide an alternative definition of 
 % begin: scholarly_paper.author
-\RequirePackage{DOF-core}
 \newcommand{\dofeptcsinstitute}[1]{\mbox{}\\\protect\scriptsize%
   \protect\begin{tabular}[t]{@{\protect\footnotesize}c@{}}%
     #1%
@@ -80,15 +69,15 @@
 \makeatother
 % end: scholarly_paper.author
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\input{ontologies}
 
-\IfFileExists{preamble.tex}{\input{preamble.tex}}{}%
+
 \begin{document}
-
 \maketitle
 \input{session}
 % optional bibliography
-\IfFileExists{root.bib}{{\bibliography{root}}}{}
+\IfFileExists{root.bib}{%
+    \bibliography{root}
+}{}
 \end{document}
 
 %%% Local Variables:

src/document-templates/root-lipics-v2021.tex

@@ -12,8 +12,6 @@
 %%
 %%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
 
-%%   <isadofltxversion>
-
 %% Warning: Do Not Edit!
 %% =====================
 %% This is the root file for the Isabelle/DOF using the lipics class.
@@ -29,20 +27,9 @@
 
 \documentclass[a4paper,UKenglish,cleveref, autoref,thm-restate]{lipics-v2021}
 \bibliographystyle{plainurl}% the mandatory bibstyle
-\usepackage{isabelle}
-\usepackage{isabellesym}
-% \usepackage{amsmath}
-% \usepackage{DOF-amssymb}
 \usepackage[numbers, sort&compress, sectionbib]{natbib}
-\IfFileExists{DOF-core.sty}{}{%
-  \PackageError{DOF-core}{Isabelle/DOF not installed. 
-    This is a Isabelle_DOF project. The document preparation requires
-    the Isabelle_DOF component from:
-    <isadofurl>
-  }{For further help, see <isadofurl>}
-}
-
 
+\input{dof-common}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % provide an alternative definition of 
@@ -68,21 +55,21 @@
 \makeatother
 % end: scholarly_paper.author
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\input{ontologies}
 \renewcommand{\DOFauthor}{}
 \renewcommand{\DOFinstitute}{}
 \expandafter\newcommand\csname 2authand\endcsname{}
 \expandafter\newcommand\csname 3authand\endcsname{}
 \expandafter\newcommand\csname 4authand\endcsname{}
 
-\IfFileExists{preamble.tex}{\input{preamble.tex}}{}%
+
 \begin{document}
-
-
 \maketitle
 \input{session}
 % optional bibliography
-\IfFileExists{root.bib}{{\small\bibliography{root}}}{}
+\IfFileExists{root.bib}{%
+\small  
+  \bibliography{root}
+}{}
 \end{document}
 
 %%% Local Variables:

src/document-templates/root-lncs.tex

@@ -12,8 +12,6 @@
 %%
 %%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
 
-%%   <isadofltxversion>
-
 %% Warning: Do Not Edit!
 %% =====================
 %% This is the root file for the Isabelle/DOF using the lncs class.
@@ -26,21 +24,12 @@
 \usepackage[T1]{fontenc}
 \usepackage[utf8]{inputenc}
 \usepackage[USenglish]{babel}
+\input{dof-common}
 \bibliographystyle{splncs04}
-\usepackage{isabelle}
-\usepackage{xcolor}
-\usepackage{isabellesym}
 \usepackage{amsmath}
 \usepackage{DOF-amssymb}
-\IfFileExists{DOF-core.sty}{}{%
+
-  \PackageError{DOF-core}{Isabelle/DOF not installed. 
+\usepackage{xcolor}
-    This is a Isabelle_DOF project. The document preparation requires
-    the Isabelle_DOF component from:
-    <isadofurl>
-  }{For further help, see <isadofurl>}
-}
-\input{ontologies}
-\IfFileExists{preamble.tex}{\input{preamble.tex}}{}%
 \usepackage{graphicx}
 \usepackage{hyperref}
 \setcounter{tocdepth}{3} 
@@ -53,8 +42,7 @@
 } % more detailed digital TOC (aka bookmarks)
 \sloppy
 \allowdisplaybreaks[4]
-\urlstyle{rm}
+
-\isabellestyle{it}
 \usepackage[caption]{subfig}
 \usepackage[size=footnotesize]{caption}
 

src/document-templates/root-scrartcl.tex

@@ -12,8 +12,6 @@
 %%
 %%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
 
-%%   <isadofltxversion>
-
 %% Warning: Do Not Edit!
 %% =====================
 %% This is the root file for the Isabelle/DOF using the scrartcl class.
@@ -23,26 +21,21 @@
 
 \RequirePackage{ifvtex}
 \documentclass[abstract=true,fontsize=11pt,DIV=12,paper=a4]{scrartcl}
+
 \usepackage[T1]{fontenc}
 \usepackage[utf8]{inputenc}
+\usepackage[english]{babel}
+
 \usepackage{textcomp}
 \bibliographystyle{abbrvnat}
-\usepackage[english]{babel}
 \RequirePackage[caption]{subfig}
-\usepackage{isabelle}
+
-\usepackage{isabellesym}
+\input{dof-common}
-\IfFileExists{DOF-core.sty}{}{%
+
-  \PackageError{DOF-core}{Isabelle/DOF not installed. 
-    This is a Isabelle_DOF project. The document preparation requires
-    the Isabelle_DOF component from:
-    <isadofurl>
-  }{For further help, see <isadofurl>}
-}
-\input{ontologies}
-\IfFileExists{preamble.tex}{\input{preamble.tex}}{}%
 \usepackage{amsmath}
 \usepackage{DOF-amssymb}
 \usepackage[numbers, sort&compress, sectionbib]{natbib}
+\usepackage{xcolor}
 \usepackage{graphicx}
 \usepackage{hyperref}
 \setcounter{tocdepth}{3} 
@@ -55,15 +48,12 @@
 } % more detailed digital TOC (aka bookmarks)
 \sloppy
 \allowdisplaybreaks[4]
-\urlstyle{rm}
-\isabellestyle{it}
 
 \newenvironment{frontmatter}{}{}
 
 \begin{document}
 \begin{frontmatter}
   \maketitle
-  % \tableofcontents
 \end{frontmatter}
 \input{session}
 % optional bibliography

src/document-templates/root-scrreprt-modern.tex

@@ -12,8 +12,6 @@
 %%
 %%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
 
-%%   <isadofltxversion>
-
 %% Warning: Do Not Edit!
 %% =====================
 %% This is the root file for the Isabelle/DOF using the scrreprt class with 
@@ -27,13 +25,18 @@
 \documentclass[fontsize=11pt,paper=a4,open=right,twoside,abstract=true]{scrreprt}
 \usepackage[T1]{fontenc}
 \usepackage[utf8]{inputenc}
+\usepackage[english]{babel}
+
 \usepackage{textcomp}
 \bibliographystyle{abbrvnat}
-\usepackage[varqu,varl]{zi4}% inconsolata typewriter
+\usepackage{amsthm}
-\usepackage{amsmath,amsthm}
 \usepackage{newtxsf}
+
+\input{dof-common}
+
+\usepackage{amsmath}
+\usepackage{DOF-amssymb}
 \renewcommand\familydefault{\sfdefault}
-\usepackage{xcolor}
 \colorlet{DOFsectioncolor}{blue!60!black}
 \addtokomafont{chapterentrypagenumber}{\color{DOFsectioncolor}}
 \addtokomafont{chapterentry}{\color{DOFsectioncolor}}
@@ -45,25 +48,15 @@
 \addtokomafont{paragraph}{\color{DOFsectioncolor}}
 \addtokomafont{subparagraph}{\color{DOFsectioncolor}}
 
-\usepackage[english]{babel}
 \RequirePackage[caption]{subfig}
-\usepackage{isabelle}
-\usepackage{isabellesym}
 \renewcommand{\isastyletext}{\normalsize\normalfont\sffamily}
 \renewcommand{\isastyletxt}{\normalfont\sffamily}
 \renewcommand{\isastylecmt}{\normalfont\sffamily}
-\IfFileExists{DOF-core.sty}{}{%
+
-  \PackageError{DOF-core}{Isabelle/DOF not installed. 
-    This is a Isabelle_DOF project. The document preparation requires
-    the Isabelle_DOF component from:
-    <isadofurl>
-  }{For further help, see <isadofurl>}
-}
-\input{ontologies}
-\IfFileExists{preamble.tex}{\input{preamble.tex}}{}%
 \usepackage{amsmath}
 \usepackage{DOF-amssymb}
 \usepackage[numbers, sort&compress, sectionbib]{natbib}
+\usepackage{xcolor}
 \usepackage{graphicx}
 \usepackage{hyperref}
 \setcounter{tocdepth}{2} 
@@ -76,8 +69,6 @@
 } % more detailed digital TOC (aka bookmarks)
 \sloppy
 \allowdisplaybreaks[4]
-\urlstyle{sf}
-\isabellestyle{it}
 
 \newenvironment{frontmatter}{}{}
 

src/document-templates/root-scrreprt.tex

@@ -12,8 +12,6 @@
 %%
 %%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
 
-%%   <isadofltxversion>
-
 %% Warning: Do Not Edit!
 %% =====================
 %% This is the root file for the Isabelle/DOF using the scrreprt class.
@@ -25,24 +23,18 @@
 \documentclass[fontsize=11pt,paper=a4,open=right,twoside,abstract=true]{scrreprt}
 \usepackage[T1]{fontenc}
 \usepackage[utf8]{inputenc}
+\usepackage[english]{babel}
+
 \usepackage{textcomp}
 \bibliographystyle{abbrvnat}
-\usepackage[english]{babel}
 \RequirePackage[caption]{subfig}
-\usepackage{isabelle}
+
-\usepackage{isabellesym}
+\input{dof-common}
-\IfFileExists{DOF-core.sty}{}{%
+
-  \PackageError{DOF-core}{Isabelle/DOF not installed. 
-    This is a Isabelle_DOF project. The document preparation requires
-    the Isabelle_DOF component from:
-    <isadofurl>
-  }{For further help, see <isadofurl>}
-}
-\input{ontologies}
-\IfFileExists{preamble.tex}{\input{preamble.tex}}{}%
 \usepackage{amsmath}
 \usepackage{DOF-amssymb}
 \usepackage[numbers, sort&compress, sectionbib]{natbib}
+\usepackage{xcolor}
 \usepackage{graphicx}
 \usepackage{hyperref}
 \setcounter{tocdepth}{2} 
@@ -55,10 +47,6 @@
 } % more detailed digital TOC (aka bookmarks)
 \sloppy
 \allowdisplaybreaks[4]
-\urlstyle{rm}
-\isabellestyle{it}
-
-\newenvironment{frontmatter}{}{}
 
 \begin{document}
 \renewcommand{\chapterautorefname}{Chapter}
@@ -67,10 +55,8 @@
 \renewcommand{\subsubsectionautorefname}{Section}
 \newcommand{\subtableautorefname}{\tableautorefname}
 \newcommand{\subfigureautorefname}{\figureautorefname}
-\begin{frontmatter}
 \maketitle
 \tableofcontents
-\end{frontmatter}
 \input{session}
 % optional bibliography
 \IfFileExists{root.bib}{{\bibliography{root}}}{}

src/document-templates/root-svjour3-UNSUPPORTED.tex

@@ -12,8 +12,6 @@
 %%
 %%   SPDX-License-Identifier: LPPL-1.3c+ OR BSD-2-Clause
 
-%%   <isadofltxversion>
-
 %% Warning: Do Not Edit!
 %% =====================
 %% This is the root file for the Isabelle/DOF using the scrartcl class.
@@ -26,24 +24,16 @@
 \documentclass[]{svjour3}
 \usepackage[T1]{fontenc}
 \usepackage[utf8]{inputenc}
+\usepackage[english]{babel}
 \usepackage{mathptmx}
 \bibliographystyle{abbrvnat}
-\usepackage[USenglish]{babel}
+
-\usepackage{isabelle}
+\input{dof-common}
-\usepackage{xcolor}
+
-\usepackage{isabellesym}
 \usepackage{amsmath}
 \usepackage{DOF-amssymb}
 \usepackage[numbers, sort&compress, sectionbib]{natbib}
-\IfFileExists{DOF-core.sty}{}{%
+\usepackage{xcolor}
-  \PackageError{DOF-core}{Isabelle/DOF not installed. 
-    This is a Isabelle_DOF project. The document preparation requires
-    the Isabelle_DOF component from:
-    <isadofurl>
-  }{For further help, see <isadofurl>}
-}
-\input{ontologies}
-\IfFileExists{preamble.tex}{\input{preamble.tex}}{}%
 \usepackage{graphicx}
 \usepackage{hyperref}
 \setcounter{tocdepth}{3} 
@@ -56,8 +46,6 @@
 } % more detailed digital TOC (aka bookmarks)
 \sloppy
 \allowdisplaybreaks[4]
-\urlstyle{rm}
-\isabellestyle{it}
 \usepackage[caption]{subfig}
 \usepackage[size=footnotesize]{caption}
 

src/ontologies/CENELEC_50128/DOF-CENELEC_50128.sty

@@ -14,8 +14,7 @@
 
 \NeedsTeXFormat{LaTeX2e}\relax
 \ProvidesPackage{DOF-cenelec_50128}
-  [<isadofltxversion>%
+  [00/00/0000 Document-Type Support Framework for Isabelle (CENELEC 50128).]
-  Document-Type Support Framework for Isabelle (CENELEC 50128).]
 
 \RequirePackage{DOF-COL}
 \usepackage{etex}

src/ontologies/scholarly_paper/DOF-scholarly_paper-thm.sty

@@ -13,8 +13,7 @@
 
 \NeedsTeXFormat{LaTeX2e}\relax
 \ProvidesPackage{DOF-scholarly_paper-thm}
-  [<isadofltxversion>%
+  [00/00/0000 Document-Type Support Framework for Isabelle (LNCS).]
-  Document-Type Support Framework for Isabelle (LNCS).]
 
 \RequirePackage{amsthm}
 

src/ontologies/technical_report/DOF-technical_report.sty

@@ -13,8 +13,7 @@
 
 \NeedsTeXFormat{LaTeX2e}\relax
 \ProvidesPackage{DOF-technical_report}
-  [<isadofltxversion>%
+  [00/00/0000 Document-Type Support Framework for Isabelle (LNCS).]
-  Document-Type Support Framework for Isabelle (LNCS).]
 
 \RequirePackage[force]{DOF-scholarly_paper}
 \RequirePackage{ifthen}

src/scala/dof_document_build.scala

@@ -31,13 +31,14 @@
 package isabelle_dof
 
 import isabelle._
+import java.io.{File => JFile}
 
 
 object DOF_Document_Build
 {
   class Engine extends Document_Build.Bash_Engine("dof")
   {
-    override def use_build_script: Boolean = true
+    // override def use_build_script: Boolean = true
 
     override def prepare_directory(
       context: Document_Build.Context,
@@ -59,7 +60,49 @@ object DOF_Document_Build
       }
       val dof_home= Path.explode(Isabelle_System.getenv_strict("ISABELLE_DOF_HOME"));
       // print(context.options.string("dof_url"));
-      Isabelle_System.copy_file(dof_home + Path.explode("src/scripts/build"), directory.doc_dir);
+      
+      // copy Isabelle/DOF LaTeX templates
+      val template_dir = dof_home + Path.explode("src/document-templates/")
+      // TODO: error handling in case 1) template does not exist or 2) root.tex does already exist
+      Isabelle_System.copy_file(template_dir + Path.explode("root-"+context.options.string("dof_template")+".tex"), 
+                                directory.doc_dir+Path.explode("root.tex"))
+      Isabelle_System.copy_file(template_dir + Path.explode("dof-common.tex"), 
+                                directory.doc_dir)
+
+      // copy Isabelle/DOF LaTeX styles 
+      val doc_jdir = new JFile(directory.doc_dir.implode)
+      val styles = File.find_files(new JFile(dof_home.implode),((f:JFile) => f.getName().endsWith(".sty")), true)
+      for (sty <- styles) { 
+        Isabelle_System.copy_file(sty, doc_jdir)
+      }
+
+      // create ontology.sty
+      val regex = """^.*\.""".r
+      val ltx_styles =  context.options.string("dof_ontologies").split(" +").map(s => regex.replaceAllIn(s,""))
+      File.write(directory.doc_dir+Path.explode("ontologies.tex"),
+      ltx_styles.mkString("\\usepackage{DOF-","}\n\\usepackage{DOF-","}\n"))
+
+      // 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{\dofurl}{""" + context.options.string("dof_url") + """}
+\newcommand{\dof@isabelleversion}{""" + context.options.string("dof_isabelle") + """}
+\newcommand{\isabellefullversion}{""" + context.options.string("dof_isabelle") + """\xspace}
+\newcommand{\dof@version}{""" + context.options.string("dof_version") + """}
+\newcommand{\dof@artifacturl}{""" + context.options.string("dof_artifact_dir") + """}
+\newcommand{\doflatestversion}{""" + context.options.string("dof_latest_version") + """}
+\newcommand{\isadoflatestdoi}{""" + context.options.string("dof_latest_doi") + """}
+\newcommand{\isadofgenericdoi}{""" + context.options.string("dof_generic_doi") + """}
+\newcommand{\isabellelatestversion}{""" + context.options.string("dof_latest_isabelle") + """}
+""")
+ /*
+      sed -i -e "s|<isadofurl>|$DOF_URL|" *.sty
+    sed -i -e "s|<isadofurl>|$DOF_URL|" *.tex
+    LTX_VERSION="$DOF_DATE $DOF_VERSION/$ISABELLE_SHORT_VERSION"
+    sed -i -e "s|<isadofltxversion>|$LTX_VERSION|" *.tex
+    sed -i -e "s|<isadofltxversion>|$LTX_VERSION|" *.sty
+  */
+  //    Isabelle_System.copy_file(dof_home + Path.explode("src/scripts/build"), directory.doc_dir);
 
       directory
     }

src/scala/dof_mkroot.scala

@@ -1,3 +1,34 @@
+/*
+ * Copyright (c) 
+ *               2021-2022 The University of Exeter. 
+ *               2021-2022 The University of Paris-Saclay. 
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in
+ *    the documentation and/or other materials provided with the
+ *    distribution.
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ * COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+ * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+ * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ *
+ * SPDX-License-Identifier: BSD-2-Clause
+ */
+
+
 /*  Author:     Makarius
 
 Prepare session root directory for Isabelle/DOF.
@@ -7,7 +38,6 @@ package isabelle_dof
 
 import isabelle._
 
-
 object DOF_Mkroot
 {
   /** mkroot **/
@@ -17,45 +47,133 @@ object DOF_Mkroot
     session_dir: Path = Path.current,
     session_parent: String = "",
     init_repos: Boolean = false,
-    title: String = "",
+    template: String = "",
-    author: String = "",
+    ontologies: List[String] = List(),
     progress: Progress = new Progress): Unit =
   {
-    Mkroot.mkroot(session_name = session_name, session_dir = session_dir,
+    Isabelle_System.make_directory(session_dir)
-      session_parent = session_parent, init_repos = init_repos,
+
-      title = title, author = author, progress = progress)
+    val name = proper_string(session_name) getOrElse session_dir.absolute_file.getName
+    val parent = proper_string(session_parent) getOrElse Isabelle_System.getenv("ISABELLE_LOGIC")
+
+    val root_path = session_dir + Sessions.ROOT
+    if (root_path.file.exists) error("Cannot overwrite existing " + root_path)
+
+    val document_path = session_dir + Path.explode("document")
+    if (document_path.file.exists) error("Cannot overwrite existing " + document_path)
+
+    progress.echo("\nPreparing session " + quote(name) + " in " + session_dir)
+
+
+    /* ROOT */
+
+    progress.echo("  creating " + root_path)
+
+    File.write(root_path,
+      "session " + Mkroot.root_name(name) + " = " + Mkroot.root_name(parent) + """ +
+  options [document = pdf, document_output = "output", document_build = dof, dof_ontologies = """" 
+       + ontologies.mkString(" ") + """", dof_template = """ + Mkroot.root_name(template) 
+       + """, document_comment_latex=true] 
+(*theories [document = false]
+    A
+    B*)
+  theories
+    """ + Mkroot.root_name(name) + """    
+  document_files
+    "preamble.tex"
+""")
+
+    val thy = session_dir + Path.explode(name+".thy")
+    progress.echo("  creating " + thy)
+    File.write(thy,
+      "theory\n  " + name + "\nimports\n  " + ontologies.mkString("\n  ") +  """
+begin
+  
+end
+""")
+
+
+
+    val preamble_tex = session_dir + Path.explode("document/preamble.tex")
+    progress.echo("  creating " + preamble_tex)
+    Isabelle_System.make_directory(preamble_tex.dir)
+    File.write(preamble_tex,"""%% This is a placeholder for user-specific configuration and packages.""")
+
+    /* Mercurial repository */
+
+    if (init_repos) {
+      progress.echo("  \nInitializing Mercurial repository " + session_dir)
+
+      val hg = Mercurial.init_repository(session_dir)
+
+      val hg_ignore = session_dir + Path.explode(".hgignore")
+      File.write(hg_ignore,
+"""syntax: glob
+
+*~
+*.marks
+*.orig
+*.rej
+.DS_Store
+.swp
+
+syntax: regexp
+
+^output/
+""")
+
+      hg.add(List(root_path, preamble_tex, hg_ignore))
     }
 
 
+    /* notes */
+
+    {
+      val print_dir = session_dir.implode
+      progress.echo("""
+Now use the following command line to build the session:
+
+  isabelle build -D """ +
+        (if (Bash.string(print_dir) == print_dir) print_dir else quote(print_dir)) + "\n")
+    }
+  }
+
 
   /** Isabelle tool wrapper **/
 
   val isabelle_tool = Isabelle_Tool("dof_mkroot", "prepare session root directory for Isabelle/DOF",
     Scala_Project.here, args =>
   {
-    var author = ""
     var init_repos = false
-    var title = ""
+    var help = false
     var session_name = ""
+    var session_parent = "Isabelle_DOF"
+    var ontologies:List[String] = List()
+    var template = "scrartcl"
 
     val getopts = Getopts("""
 Usage: isabelle dof_mkroot [OPTIONS] [DIRECTORY]
 
   Options are:
-    -A LATEX     provide author in LaTeX notation (default: user name)
     -I           init Mercurial repository and add generated files
-    -T LATEX     provide title in LaTeX notation (default: session name)
     -n NAME      alternative session name (default: directory base name)
+    -o ONTOLOGY  ontology (default: scholarly_paper)
+    -t TEMPLATE  tempalte (default: scrartcl)
 
   Prepare session root directory (default: current directory).
 """,
-      "A:" -> (arg => author = arg),
       "I" ->  (arg => init_repos = true),
-      "T:" -> (arg => title = arg),
+      "n:" -> (arg => session_name = arg),
-      "n:" -> (arg => session_name = arg))
+      "o:"  -> (arg => ontologies = ontologies :+ arg),
+      "t:"  -> (arg => template = arg),
+      "h"  -> (arg => help = true)
+    )
 
     val more_args = getopts(args)
 
+    ontologies = if (ontologies.isEmpty) List("scholarly_paper") else ontologies
+  
+    if (help) {getopts.usage()} else {()}
     val session_dir =
       more_args match {
         case Nil => Path.current
@@ -63,7 +181,7 @@ Usage: isabelle dof_mkroot [OPTIONS] [DIRECTORY]
         case _ => getopts.usage()
       }
 
-    mkroot(session_name = session_name, session_dir = session_dir, init_repos = init_repos,
+    mkroot(session_parent=session_parent, session_name = session_name, session_dir = session_dir, init_repos = init_repos,
-      author = author, title = title, progress = new Console_Progress)
+      ontologies = ontologies, template = template, progress = new Console_Progress)
   })
 }

src/scala/dof_tools.scala

@@ -1,8 +1,34 @@
-/*  Author:     Makarius
+/*
-
+ * Copyright (c) 
-Isabelle/DOF command-line tools.
+ *               2021-2022 The University of Exeter. 
+ *               2021-2022 The University of Paris-Saclay. 
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in
+ *    the documentation and/or other materials provided with the
+ *    distribution.
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+ * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+ * COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+ * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+ * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ *
+ * SPDX-License-Identifier: BSD-2-Clause
  */
 
+ 
 package isabelle_dof
 
 import isabelle._

src/scripts/build

@@ -1,160 +0,0 @@
-#!/usr/bin/env bash
-# Copyright (c) 2019 University of Exeter
-#               2018-2019 University of Paris-Saclay
-#               2018-2019 The University of Sheffield
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions
-# are met:
-# 1. Redistributions of source code must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-# 2. Redistributions in binary form must reproduce the above copyright
-#    notice, this list of conditions and the following disclaimer in
-#    the documentation and/or other materials provided with the
-#    distribution.
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
-# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
-# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
-# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
-# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-# POSSIBILITY OF SUCH DAMAGE.
-#
-# SPDX-License-Identifier: BSD-2-Clause
-
-set -e
-OUTFORMAT=${1:-pdf}
-NAME=${2:-root}
-
-ROOT_NAME="root_$NAME"
-
-install_dof_tex(){
-    cp $ISABELLE_DOF_HOME/src/document-templates/* .
-    cp $ISABELLE_DOF_HOME/src/DOF/*/*.sty .
-    cp $ISABELLE_DOF_HOME/src/ontologies/*/*.sty . 
-    
-    ISABELLE_SHORT_VERSION=`echo $ISABELLE_VERSION | sed -e 's/:.*$//'`
-    sed -i -e "s|%%% CONFIG %%%| \
-      \\\\renewcommand{\\\\dof@isabelleversion}{$ISABELLE_SHORT_VERSION} \
-      \\\\renewcommand{\\\\isabellelatestversion}{$DOF_LATEST_ISABELLE} \
-      \\\\renewcommand{\\\\isabellefullversion}{$ISABELLE_VERSION\\\\xspace} \
-      \\\\renewcommand{\\\\dof@version}{$DOF_VERSION} \
-      \\\\renewcommand{\\\\doflatestversion}{$DOF_LATEST_VERSION} \
-      \\\\renewcommand{\\\\isadoflatestdoi}{$DOF_LATEST_DOI} \
-      \\\\renewcommand{\\\\isadofgenericdoi}{$DOF_GENERIC_DOI} \
-      \\\\renewcommand{\\\\isabelleurl}{$ISABELLE_URL} \
-      \\\\renewcommand{\\\\dofurl}{$DOF_URL} \
-      \\\\renewcommand{\\\\dof@artifacturl}{https://$DOF_ARTIFACT_HOST/$DOF_ARTIFACT_DIR}|" \
-      "DOF-core.sty"
-
-    
-    sed -i -e "s|<isadofurl>|$DOF_URL|" *.sty
-    sed -i -e "s|<isadofurl>|$DOF_URL|" *.tex
-    LTX_VERSION="$DOF_DATE $DOF_VERSION/$ISABELLE_SHORT_VERSION"
-    sed -i -e "s|<isadofltxversion>|$LTX_VERSION|" *.tex
-    sed -i -e "s|<isadofltxversion>|$LTX_VERSION|" *.sty
-}
-
-[ ! -f "$DIR/$ROOT_NAME.tex" ] && ROOT_NAME="root"
-
-if [ -f "$DIR/$ROOT_NAME.tex" ]; then 
-    >&2 echo ""
-    >&2 echo "Error: Found root file ($DIR/$ROOT_NAME.tex)"
-    >&2 echo "====="
-    >&2 echo "Isabelle/DOF does not use the Isabelle root file setup. Please check"
-    >&2 echo "your project setup. Your $DIR/isadof.cfg should define a Isabelle/DOF"
-    >&2 echo "template and your project should not include a root file."
-    >&2 echo ""
-    exit 1
-fi
-
-if [ ! -f isadof.cfg ]; then 
-    >&2 echo ""
-    >&2 echo "Error: Isabelle/DOF document setup not correct"
-    >&2 echo "====="
-    >&2 echo "Could not find isadof.cfg. Please upgrade your Isabelle/DOF document"
-    >&2 echo "setup manually."
-    exit 1
-fi
-
-TEMPLATE=""
-ONTOLOGY="core"
-CONFIG="isadof.cfg"
-while IFS= read -r line;do
-    fields=($(printf "%s" "$line"|cut -d':' -f1- | tr ':' ' '))
-    if [[ "${fields[0]}" = "Template" ]]; then 
-	TEMPLATE="${fields[1]}"
-    fi                      
-    if [[ "${fields[0]}" = "Ontology" ]]; then 
-	ONTOLOGY="$ONTOLOGY ${fields[1]}"
-    fi
-done < $CONFIG
-
-for o in $ONTOLOGY; do
-  >&2 echo "\usepackage{DOF-$o}" >> ontologies.tex;
-done
-
-install_dof_tex
-
-ROOT="root-$TEMPLATE.tex"
-if [ ! -f $ROOT ]; then 
-    >&2 echo ""
-    >&2 echo "Error: Isabelle/DOF document setup not correct"
-    >&2 echo "====="
-    >&2 echo "Could not find root file ($ROOT)."
-    >&2 echo "Please upgrade your Isabelle/DOF document setup manually."
-    exit 1
-fi
-
-cp $ROOT root.tex
-
-# delete outdated aux files from previous runs
-rm -f *.aux 
-
-sed -i -e 's/<@>/@/g' *.tex 
-
-$ISABELLE_PDFLATEX root && \
-{ [ ! -f "$ROOT_NAME.bib" ] || $ISABELLE_BIBTEX root; } && \
-{ [ ! -f "$ROOT_NAME.idx" ] || $ISABELLE_MAKEINDEX root; } && \
-$ISABELLE_PDFLATEX root && \
-$ISABELLE_PDFLATEX root
-
-MISSING_CITATIONS=`grep 'Warning.*Citation' root.log | awk '{print $5}' | sort  -u`
-if [ "$MISSING_CITATIONS" != "" ]; then
-    >&2 echo ""
-    >&2 echo "ERROR (Isabelle/DOF): document referencing inconsistent due to missing citations: "
-    >&2 echo "$MISSING_CITATIONS"
-    exit 1
-fi
-DANGLING_REFS=`grep 'Warning.*Refer' root.log | awk '{print $4}' | sort  -u`
-if [ "$DANGLING_REFS" != "" ]; then
-    >&2 echo ""
-    >&2 echo "ERROR (Isabelle/DOF): document referencing inconsistent due to dangling references:"
-    >&2 echo "$DANGLING_REFS"
-    >&2 echo ""
-    exit 1
-fi
-if [ -f "root.blg" ]; then 
-    >&2 echo "BibTeX Warnings:"
-    >&2 echo "================"
-    >&2 grep Warning  root.blg | sed -e 's/Warning--//'
-    >&2 echo ""
-fi
->&2 echo "Layout Glitches:"
->&2 echo "================"
->&2 echo -n "Number of overfull hboxes: "
->&2 grep 'Overfull .hbox' root.log | wc -l
->&2 echo -n "Number of underfull hboxes: "
->&2 grep 'Underfull .hbox' root.log | wc -l
->&2 echo -n "Number of overfull vboxes: "
-grep 'Overfull .vbox' root.log | wc -l
->&2 echo -n "Number of underfull vboxes: "
-grep 'Underfull .vbox' root.log | wc -l
->&2 echo ""
-
-exit 0