.ci/README.md

@@ -50,8 +50,8 @@ with target `setup-env`.
 This stage builds, installs and optionally packages `dune-copasi` following the
 [`install`](install) script. Similar to the others, this script expects the options
 file which in turs run `cmake` and its targets. If the environmental variables
-`CPACK_GENERATORS` and `CPACK_PACKAGE_DIRECTORY`, the script will package the
-library with the given generators.
+`CPACK_GENERATORS` and `CPACK_PACKAGE_DIRECTORY` are set, the script will package the
+library with the given generators (e.g. debian packages).
 
 ```bash
 ./install $PDW/../dune-copasi.opts
@@ -61,10 +61,7 @@ library with the given generators.
 
 This stage builds and runs the unit and system tests by using the
 [`test`](test) script. `ctests` runs all tests with the tag
-`unit` and `DUNE_SYSTEMTEST`. Most of the system tests
-are generated by `dune-testools`, so its availability depends whether
-`dune-testtools` is installed. In any case, performing this stage is very
-important because it checks whether the library is findable by CMake.
+`unit` and `system`.
 
 
 ```bash

.ci/dune-common.patch

-diff --git a/cmake/modules/DuneMacros.cmake b/cmake/modules/DuneMacros.cmake
-index 1c9b0412..778c9a92 100644
---- a/cmake/modules/DuneMacros.cmake
-+++ b/cmake/modules/DuneMacros.cmake
-@@ -977,8 +977,6 @@ endif()
-     configure_file(config.h.cmake ${CMAKE_CURRENT_BINARY_DIR}/config.h)
-   endif()
- 
--  include(CPack)
--
-   feature_summary(WHAT ALL)
- 
-   # check if CXX flag overloading has been enabled
-diff --git a/dune/common/std/CMakeLists.txt b/dune/common/std/CMakeLists.txt
-index 40004d3c..94a2d7ac 100644
---- a/dune/common/std/CMakeLists.txt
-+++ b/dune/common/std/CMakeLists.txt
-@@ -1,6 +1,7 @@
- install(
-   FILES
-   apply.hh
-+  functional.hh
-   make_array.hh
-   memory.hh
-   optional.hh

.ci/dune-logging.patch

-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 693bab6..770ba85 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -145,7 +145,7 @@ the command \"git submodule update --init --recursive\" in the dune-logging sour
-     dune-logging-fmt
-     PUBLIC
-       $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/dune/vendor/fmt>
--      $<INSTALL_INTERFACE:dune/vendor/fmt>
-+      $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/dune/vendor/fmt>
-     )
- 
- endif()

.ci/install

@@ -2,11 +2,15 @@
 
 # build and install
 
+# used env variables
+# DUNE_OPTIONS_FILE
+#   (optional) CPACK_GENERATORS
+#   (optional) CPACK_PACKAGE_DIRECTORY
+#   (optional) CODE_CHECKER_REPORT_PATH
+
 # variables from DUNE_OPTIONS_FILE
 #   (optional) CMAKE_FLAGS
 #   (optional) SUDOCMD
-#   (optional) CPACK_GENERATORS
-#   (optional) CPACK_PACKAGE_DIRECTORY
 
 set +e
 
@@ -24,21 +28,16 @@ CMAKE_FLAGS="$(. ${DUNE_OPTIONS_FILE}; eval echo \$CMAKE_FLAGS)"
 SUDOCMD="$(. ${DUNE_OPTIONS_FILE}; eval echo \$SUDOCMD)"
 
 # load useful functions
-CALL_DIR=$PWD
 SCRIPT_PATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 source $SCRIPT_PATH/util
 
-SOURCEDIR=${SCRIPT_PATH}/..
+SOURCEDIR=`readlink -f ${SCRIPT_PATH}/..`
 BUILD_PATH=/tmp/dune-copasi-build
 
 print_opts_file() {
   cat "${DUNE_OPTIONS_FILE}"
 }
 
-print_cmake_error() {
-  cat "${BUILD_PATH}/src/CMakeFiles/multidomain-exec.dir/build.make"
-}
-
 cleanup() {
   echo "removig intermediate results"
   rm -rf $BUILD_PATH
@@ -55,12 +54,18 @@ trap onfailure EXIT
 mkdir $BUILD_PATH && cd $BUILD_PATH
 
 echo "cmake $CMAKE_FLAGS $SOURCEDIR"
-eval cmake $CMAKE_FLAGS $SOURCEDIR
+eval CMAKE_EXPORT_COMPILE_COMMANDS=ON cmake $CMAKE_FLAGS $SOURCEDIR
 
-$SUDOCMD cmake --build $BUILD_PATH --target install
+if test "x$CODE_CHECKER_REPORT_PATH" != "x"; then
+  CodeChecker analyze $BUILD_PATH/compile_commands.json --config ${SOURCEDIR}/.codechecker.json --output $CODE_CHECKER_REPORT_PATH
+  CodeChecker parse --config ${SOURCEDIR}/.codechecker.json --trim-path-prefix ${SOURCEDIR} -e codeclimate $CODE_CHECKER_REPORT_PATH > $CODE_CHECKER_REPORT_PATH/gl-code-quality-report.json
+else
+  $SUDOCMD cmake --build $BUILD_PATH --target install
 
-for generator in $CPACK_GENERATORS; do
-  cpack -G $generator -B $CPACK_PACKAGE_DIRECTORY CPackConfig.cmake
-done
+  for generator in $CPACK_GENERATORS; do
+    cpack -G $generator -B $CPACK_PACKAGE_DIRECTORY CPackConfig.cmake
+  done
+fi
 
+cd $SCRIPT_PATH
 trap cleanup EXIT

.ci/setup_dune

@@ -5,7 +5,6 @@
 # variables from DUNE_OPTIONS_FILE
 #   (optional) SETUP_DUNE_TESTTOOLS
 #   (optional) SUDOCMD
-#   (optional) DUNE_VENDOR_FMT
 
 set +e
 
@@ -21,7 +20,6 @@ set -e
 # load dune options
 SETUP_DUNE_TESTTOOLS="$(. ${DUNE_OPTIONS_FILE}; eval echo \$SETUP_DUNE_TESTTOOLS)"
 SUDOCMD="$(. ${DUNE_OPTIONS_FILE}; eval echo \$SUDOCMD)"
-DUNE_VENDOR_FMT="$(. ${DUNE_OPTIONS_FILE}; eval echo \$DUNE_VENDOR_FMT)"
 
 # load useful functions
 CALL_DIR=$PWD
@@ -45,7 +43,7 @@ cleanup() {
 # set up verbose output in case of failure
 ONFAILURE_PROG="git gcc g++ python pip python3 pip3 cmake wget $SUDOCMD"
 ONFAILURE_VARS="PATH MSYSTEM SUDOCMD SETUP_DUNE_TESTTOOLS DUNE_OPTIONS_FILE"
-ONFAILURE_VARS+=" CMAKE_FLAGS CMAKE_INSTALL_PREFIX DUNE_VENDOR_FMT REPO BRANCH PATCHES RECURSIVE BUILD_PATH"
+ONFAILURE_VARS+=" CMAKE_FLAGS CMAKE_INSTALL_PREFIX REPO BRANCH PATCHES RECURSIVE BUILD_PATH"
 ONFAILURE_CMD="ls cleanup"
 
 trap onfailure EXIT
@@ -55,53 +53,34 @@ mkdir /tmp/setup-dune && cd /tmp/setup-dune
 
 # setup dune repositories, branches, and patches
 for module in common geometry grid istl localfunctions; do
-  eval SETUP_dune_${module}_BRANCH=\"releases/2.7\"
+  eval SETUP_dune_${module}_BRANCH=\"master\"
   eval SETUP_dune_${module}_REPO=\"https://gitlab.dune-project.org/core/dune-${module}.git\"
 done
 
-for module in logging functions uggrid; do
-  eval SETUP_dune_${module}_BRANCH=\"releases/2.7\"
+for module in functions uggrid typetree; do
+  eval SETUP_dune_${module}_BRANCH=\"master\"
   eval SETUP_dune_${module}_REPO=\"https://gitlab.dune-project.org/staging/dune-${module}.git\"
 done
 
-for module in typetree pdelab
-do
-  eval SETUP_dune_${module}_BRANCH=\"support/dune-copasi-latest\"
-  eval SETUP_dune_${module}_REPO=\"https://gitlab.dune-project.org/copasi/dune-${module}.git\"
-done
-
-SETUP_dune_testtools_BRANCH="releases/2.7"
-SETUP_dune_testtools_REPO="https://gitlab.dune-project.org/quality/dune-testtools.git"
+SETUP_dune_pdelab_BRANCH="feature/dune-assembler/main-multithreaded"
+SETUP_dune_pdelab_REPO="https://gitlab.dune-project.org/pdelab/dune-pdelab.git"
 
-SETUP_dune_multidomaingrid_BRANCH="releases/2.7"
+SETUP_dune_multidomaingrid_BRANCH="master"
 SETUP_dune_multidomaingrid_REPO="https://gitlab.dune-project.org/extensions/dune-multidomaingrid.git"
 
-cat ${SCRIPT_DIR}/dune-common.patch >> "${PWD}/dune-common.patch"
-
-SETUP_dune_common_PATCHES="${SCRIPT_DIR}/dune-common.patch"
-
-SETUP_dune_logging_RECURSIVE="$DUNE_VENDOR_FMT"
-
-echo "Downloading patches"
-
-PATCH_URL="https://gist.githubusercontent.com/lkeegan/059984b71f8aeb0bbc062e85ad7ee377/raw/e9c7af42c47fe765547e60833a72b5ff1e78123c/cmake-patch.txt"
-if command -v wget &> /dev/null; then
-  wget -O cmake-patch.txt $PATCH_URL
-elif command -v curl &> /dev/null; then
-  curl $PATCH_URL --output cmake-patch.txt
-else
-  ONFAILURE_MESSAGE+="'wget' not 'curl' was not found."
-  exit 1
-fi
-
-echo '' >> cmake-patch.txt
-SETUP_dune_common_PATCHES+=" ${PWD}/cmake-patch.txt"
+SETUP_dune_common_BRANCH="1b79c9e4fe055ffa79e30b5b76989c4ebe30c606"
+SETUP_dune_geometry_BRANCH="d45c81e18d940b4a0f755e64b9f3b67638508ada"
+SETUP_dune_grid_BRANCH="70cd26d527b30ca2961e53b00f113f295f021f22"
+SETUP_dune_uggrid_BRANCH="dec73a978754c6959dc9b8c34278979e9f6ba5bc"
+SETUP_dune_istl_BRANCH="64f5f5184143f7a401b5e68a2ba76d9d3dd22570"
+SETUP_dune_localfunctions_BRANCH="920cc8544401adde20b2fd6603a2050b810a4e31"
+SETUP_dune_functions_BRANCH="664f68c63444ffd31537a57c5b12a6c40ed03da9"
+SETUP_dune_multidomaingrid_BRANCH="7d04696469d62b36239d3d1101d9ac71ff247137"
+SETUP_dune_typetree_BRANCH="962308509de2e67732afe5fe7e9c816ee16eec30"
+SETUP_dune_pdelab_BRANCH="73f4c866b55f02c7b4bd0319bf304c5b01956bf3"
 
 # hardcoded **ordered** dependencies
-MODULES="common logging uggrid geometry grid localfunctions istl typetree functions pdelab multidomaingrid"
-if [[ "$SETUP_DUNE_TESTTOOLS" =~ ^(ON|on|1|yes|YES|true|TRUE)$ ]]; then
-	MODULES+=" testtools"
-fi
+MODULES="common geometry uggrid grid typetree localfunctions istl functions multidomaingrid pdelab"
 
 [ -z $DUNE_OPTIONS_FILE ] && ONFAILURE_MESSAGE+="Dune options file is not set!\n" && exit 1
 
@@ -160,7 +139,8 @@ for module in $MODULES; do
   RECURSIVE="$(eval echo \$SETUP_dune_${module}_RECURSIVE)"
 
   [[ "$RECURSIVE" =~ ^(ON|on|1|yes|YES|true|TRUE)$ ]] && RECURSIVE_ARG="--recursive"
-  git clone -b $BRANCH --depth 1 $RECURSIVE_ARG $REPO
+  git clone $RECURSIVE_ARG $REPO
+  git -C dune-$module checkout $BRANCH
 
   # on windows, symlinks from git repos don't work
   # msys git replaces symlinks with a text file containing the linked file location
@@ -201,11 +181,11 @@ for module in $MODULES; do
   export DUNE_CONTROL_PATH=$PWD
 
   # configure, build, and install module
-  $DUNECONTROL --opts=${DUNE_OPTIONS_FILE} --only=dune-$module all
+  $DUNECONTROL --opts=${DUNE_OPTIONS_FILE} --only=dune-$module configure
   $SUDOCMD $DUNECONTROL --opts=${DUNE_OPTIONS_FILE} --only=dune-$module bexec cmake --build . --target install
 
   # we want to know where the build dir is located
-  # since it could be ant complex path, we write the path from dunecontrol into a file
+  # since it could be a complex path, we write the path from dunecontrol into a file
   $DUNECONTROL --opts=${DUNE_OPTIONS_FILE} --only=dune-$module bexec "echo \$PWD > /tmp/setup-dune/module_builddir"
 
   # remove build and sources

.ci/setup_static_deps

@@ -3,7 +3,7 @@
 # download and install other dependences (from sme by Liam)
 
 # variables from DUNE_OPTIONS_FILE
-#   OS_TARGET=linux|osx|win32|win64
+#   OS_TARGET=linux|osx|win32-mingw|win64-mingw
 #   CMAKE_INSTALL_PREFIX
 #   (optional) SUDOCMD
 
@@ -40,13 +40,13 @@ trap onfailure EXIT
 [[ -d /tmp/setup-static-deps ]] && ONFAILURE_MESSAGE+="run this script where no folder '/tmp/setup-static-deps' exists\n" && exit 1
 mkdir /tmp/setup-static-deps && cd /tmp/setup-static-deps
 
-if [[ ! "$OS_TARGET" =~ ^(linux|osx|win32|win64)$ ]]; then
+if [[ ! "$OS_TARGET" =~ ^(linux|osx|win32-mingw|win64-mingw)$ ]]; then
     ONFAILURE_MESSAGE+="'$OS_TARGET' is not a known OS target\n"
     exit 1
 fi
 
 echo "Downloading static libs for OS_TARGET: ${OS_TARGET}"
-DEPS_URL="https://github.com/spatial-model-editor/sme_deps_common/releases/latest/download/sme_deps_common_${OS_TARGET}.tgz"
+DEPS_URL="https://github.com/spatial-model-editor/sme_deps_common/releases/download/2024.01.23/sme_deps_common_${OS_TARGET}.tgz"
 if command -v wget &> /dev/null; then
   wget -nv $DEPS_URL | sed 's/^/  /'
 elif command -v curl &> /dev/null; then
@@ -65,9 +65,9 @@ echo "Moving libs to install prefix: ${CMAKE_INSTALL_PREFIX}"
 # copy libs to desired location
 $SUDOCMD mkdir -p "${CMAKE_INSTALL_PREFIX}"
 if [[ "$OS_TARGET" == *"win"* ]]; then
-   $SUDOCMD mv smelibs/* "${CMAKE_INSTALL_PREFIX}"
+   $SUDOCMD mv c/smelibs /c/
 else
-   $SUDOCMD mv opt/smelibs/* "${CMAKE_INSTALL_PREFIX}"
+   $SUDOCMD mv opt/* /opt/
 fi
 
 # set the following flags in your dune opts file
@@ -79,7 +79,7 @@ fi
   # CMAKE_FLAGS+=" -DF77=true"
 
   # be careful when adding several prefix paths, they have to be
-  # set in a semicolon separated list 
+  # set in a semicolon separated list
   # CMAKE_FLAGS+=" -DCMAKE_PREFIX_PATH='${CMAKE_PREFIX_PATH}' "
 
 # ...or if you are using the dune-copasi.opts

.ci/test

@@ -17,12 +17,11 @@ set -e
 [ ! -z "$1" ] && DUNE_OPTIONS_FILE="$1"
 
 # load useful functions
-CALL_DIR=$PWD
 SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 source $SCRIPT_DIR/util
 
-SOURCEDIR=${SCRIPT_DIR}/../test
-
+TEST_SOURCEDIR=${SCRIPT_DIR}/../test
+TUTORIAL_SOURCEDIR=${SCRIPT_DIR}/../doc
 
 print_opts_file() {
   cat "${DUNE_OPTIONS_FILE}"
@@ -41,7 +40,7 @@ cleanup() {
 ONFAILURE_PROG="git gcc g++ python pip python3 pip3 cmake"
 ONFAILURE_VARS="PATH DUNE_OPTIONS_FILE "
 ONFAILURE_VARS+="DEBUG_CMAKE_FLAGS RELEASE_CMAKE_FLAGS"
-ONFAILURE_CMD="ls cleanup"
+ONFAILURE_CMD="pwd ls cleanup"
 
 trap onfailure EXIT
 
@@ -55,8 +54,8 @@ if [[ -n "$DUNE_OPTIONS_FILE" ]]; then
   DEBUG_CMAKE_FLAGS="$(. $DUNE_OPTIONS_FILE; eval echo \$CMAKE_FLAGS)"
 fi
 
-echo "cmake $DEBUG_CMAKE_FLAGS $SOURCEDIR"
-eval cmake $DEBUG_CMAKE_FLAGS $SOURCEDIR
+echo "cmake $DEBUG_CMAKE_FLAGS $TEST_SOURCEDIR"
+eval cmake $DEBUG_CMAKE_FLAGS $TEST_SOURCEDIR
 cmake --build . --target build_unit_tests
 ctest -j4 -L "unit" --output-on-failure
 
@@ -70,9 +69,25 @@ if [[ -n "$DUNE_OPTIONS_FILE" ]]; then
   RELEASE_CMAKE_FLAGS="$(. $DUNE_OPTIONS_FILE; eval echo \$CMAKE_FLAGS)"
 fi
 
-echo "cmake $RELEASE_CMAKE_FLAGS $SOURCEDIR"
-eval cmake $RELEASE_CMAKE_FLAGS $SOURCEDIR
+echo "cmake $RELEASE_CMAKE_FLAGS $TEST_SOURCEDIR"
+eval cmake $RELEASE_CMAKE_FLAGS $TEST_SOURCEDIR
 cmake --build . --target build_system_tests
-ctest -j4 -L "DUNE_SYSTEMTEST" --output-on-failure
+ctest -j4 -L "system" --output-on-failure
+
+echo $GREEN "============================ Tutorial Tests ============================" $RESET
+
+BUILD_PATH=/tmp/build-system-tutorials
+[[ -d ${BUILD_PATH} ]] && ONFAILURE_MESSAGE+="the folder '${BUILD_PATH}' should not exist prior running this script\n" && exit 1
+mkdir $BUILD_PATH && cd $BUILD_PATH
+
+if [[ -n "$DUNE_OPTIONS_FILE" ]]; then
+  RELEASE_CMAKE_FLAGS="$(. $DUNE_OPTIONS_FILE; eval echo \$CMAKE_FLAGS)"
+fi
+
+echo "cmake $RELEASE_CMAKE_FLAGS $TUTORIAL_SOURCEDIR"
+eval cmake $RELEASE_CMAKE_FLAGS $TUTORIAL_SOURCEDIR
+cmake --build . --target build_tutorial_tests
+ctest -j4 -L "tutorial" --output-on-failure
 
+cd $SCRIPT_PATH
 trap cleanup EXIT

.clang-format

 ---
-BasedOnStyle: Mozilla
\ No newline at end of file
+BasedOnStyle: Mozilla
+ColumnLimit: '100'
+
+...

.clang-tidy

+---
+FormatStyle:         file
+UseColor:            true
+HeaderFilterRegex:   'dune/copasi/*'
+
+Checks:              '*,-llvmlibc-*,-fuchsia-*,-modernize-use-trailing-return-type,-llvm-header-guard'

.codechecker.json

+{
+  "analyze": [
+    "--analyzers=clang-tidy",
+    "--file=*/dune-copasi/*.cc"
+  ],
+  "parse": [
+    "--file=*/dune-copasi/*"
+  ]
+}

.gitattributes

+test/data/** filter=lfs diff=lfs merge=lfs -text
+doc/docusaurus/versioned_docs/** filter=lfs diff=lfs merge=lfs -text

.github/workflows/ci.yml

@@ -4,25 +4,45 @@ on: push
 
 env:
   DUNE_COPASI_USE_STATIC_DEPS: 'ON'
-  DUNE_COPASI_SD_EXECUTABLE: 'ON'
+  BUILD_SHARED_LIBS: 'OFF'
+  CMAKE_DISABLE_FIND_PACKAGE_MPI: 'ON'
+  CMAKE_DISABLE_FIND_PACKAGE_parafields: 'ON'
+  DUNE_COPASI_DISABLE_FETCH_PACKAGE_parafields: 'ON'
+  DUNE_ENABLE_PYTHONBINDINGS: 'OFF'
+  DUNE_PDELAB_ENABLE_TRACING: 'OFF'
 
 jobs:
   linux:
     name: Linux
-    runs-on: ubuntu-16.04
+    runs-on: ubuntu-20.04
     env:
       CMAKE_INSTALL_PREFIX: '/opt/smelibs'
+      CMAKE_PREFIX_PATH: '/opt/smelibs'
+      CMAKE_CXX_FLAGS: "'-fvisibility=hidden -D_GLIBCXX_USE_TBB_PAR_BACKEND=0 -DNDEBUG'"
+      MAKE_OPTIONS: "-j4"
+      DUNE_COPASI_GRID_DIMENSIONS: '"2;3"'
+      CC: "clang"
+      CXX: "clang++"
       TERM: 'xterm-256color'
     defaults:
       run:
         shell: bash
     steps:
-    - name: Set OS
+    - name: Add llvm repo for clang 17 & install
       run: |
-        sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 100
-        sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-9 100
-        sudo apt-get install libncurses5-dbg
-    - uses: actions/checkout@v2
+        sudo wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
+        sudo add-apt-repository "deb http://apt.llvm.org/focal/ llvm-toolchain-focal-17 main"
+        sudo apt update -yy
+        sudo apt install -yy clang-17
+    - name: Set clang version
+      run: |
+        sudo update-alternatives --remove-all clang || echo "nothing to remove"
+        sudo update-alternatives --remove-all clang++ || echo "nothing to remove"
+        sudo update-alternatives --install /usr/bin/clang clang /usr/bin/clang-17 100
+        sudo update-alternatives --install /usr/bin/clang++ clang++ /usr/bin/clang++-17 100
+    - uses: actions/checkout@v4
+      with:
+        lfs: true
     - name: Setup static dependencies
       run: ./.ci/setup_static_deps $PWD/dune-copasi.opts
     - name: Setup dune dependencies
@@ -31,23 +51,27 @@ jobs:
       run: ./.ci/install $PWD/dune-copasi.opts
     - name: Build and run tests
       run: ./.ci/test $PWD/dune-copasi.opts
-    # - uses: actions/upload-artifact@v2
-    #   with:
-    #     path: ./artefacts/*
 
   macos:
     name: MacOS
-    runs-on: macos-10.15
+    runs-on: macos-13
     env:
       CMAKE_INSTALL_PREFIX: '/opt/smelibs'
-      MACOSX_DEPLOYMENT_TARGET: '10.14'
-      DUNE_USE_FALLBACK_FILESYSTEM: 'ON'
+      CMAKE_PREFIX_PATH: '/opt/smelibs'
+      MAKE_OPTIONS: "-j3"
+      DUNE_COPASI_GRID_DIMENSIONS: '"2;3"'
+      MACOSX_DEPLOYMENT_TARGET: '11'
       TERM: 'xterm-256color'
     defaults:
       run:
         shell: bash
     steps:
-      - uses: actions/checkout@v2
+      - uses: maxim-lobanov/setup-xcode@v1
+        with:
+          xcode-version: "14.3"
+      - uses: actions/checkout@v4
+        with:
+          lfs: true
       - name: Setup static dependencies
         run: ./.ci/setup_static_deps $PWD/dune-copasi.opts
       - name: Setup dune dependencies
@@ -56,80 +80,31 @@ jobs:
         run: ./.ci/install $PWD/dune-copasi.opts
       - name: Build and run tests
         run: ./.ci/test $PWD/dune-copasi.opts
-      # - uses: actions/upload-artifact@v2
-      #   with:
-      #     path: ./artefacts/*
 
   win64:
     name: Windows 64-bit
-    runs-on: windows-2019
+    runs-on: windows-2022
     env:
       CMAKE_INSTALL_PREFIX: '/c/smelibs'
+      CMAKE_PREFIX_PATH: '/c/smelibs'
+      MAKE_OPTIONS: "-j4"
+      DUNE_COPASI_GRID_DIMENSIONS: '"2;3"'
     defaults:
       run:
         shell: msys2 {0}
     steps:
-      - uses: actions/checkout@v2
       - uses: msys2/setup-msys2@v2
         with:
-          msystem: MINGW64
+          msystem: UCRT64
           update: true
-          install: mingw-w64-x86_64-gcc mingw-w64-x86_64-cmake make git dos2unix
+          install: mingw-w64-ucrt-x86_64-gcc mingw-w64-ucrt-x86_64-cmake make git mingw-w64-ucrt-x86_64-git-lfs dos2unix
+      - name: Clone repo
+        run: pwd && ls && git lfs install && git clone -b ${{ github.head_ref || github.ref_name }} https://github.com/${{ github.repository }} . && git lfs pull && ls
       - name: Setup static dependencies
-        run: ./.ci/setup_static_deps $PWD/dune-copasi.opts
+        run: pwd && ls && ./.ci/setup_static_deps $PWD/dune-copasi.opts
       - name: Setup dune dependencies
         run: ./.ci/setup_dune $PWD/dune-copasi.opts
       - name: Build and Install
         run: ./.ci/install $PWD/dune-copasi.opts
       - name: Build and run tests
         run: ./.ci/test $PWD/dune-copasi.opts
-      # - uses: actions/upload-artifact@v2
-      #   with:
-      #     path: ./artefacts/*
-
-  win32:
-    name: Windows 32-bit
-    runs-on: windows-2019
-    env:
-      CMAKE_INSTALL_PREFIX: '/c/smelibs'
-    defaults:
-      run:
-        shell: msys2 {0}
-    steps:
-      - uses: actions/checkout@v2
-      - uses: msys2/setup-msys2@v2
-        with:
-          msystem: MINGW32
-          update: true
-          install: mingw-w64-i686-gcc mingw-w64-i686-cmake make git dos2unix
-      - name: Setup static dependencies
-        run: ./.ci/setup_static_deps $PWD/dune-copasi.opts
-      - name: Setup dune dependencies
-        run: ./.ci/setup_dune $PWD/dune-copasi.opts
-      - name: Build and Install
-        run: ./.ci/install $PWD/dune-copasi.opts
-      - name: Build and run tests
-        run: ./.ci/test $PWD/dune-copasi.opts
-      # - uses: actions/upload-artifact@v2
-      #   with:
-      #     path: ./artefacts/*
-
-  # release:
-  #   name: Upload Binaries to GitHub Release
-  #   needs: [linux, macos, win64, win32]
-  #   runs-on: ubuntu-18.04
-  #   # upload binaries to github release if commit is tagged
-  #   if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/')
-  #   steps:
-  #     - uses: actions/download-artifact@v2
-  #       with:
-  #         name: artifact
-  #         path: binaries
-  #     - name: Upload binaries to release
-  #       uses: svenstaro/upload-release-action@v2
-  #       with:
-  #         repo_token: ${{ secrets.GITHUB_TOKEN }}
-  #         file: binaries/*
-  #         tag: ${{ github.ref }}
-  #         overwrite: true
-  #         file_glob: true

.gitignore

@@ -4,6 +4,11 @@ __pycache__/
 *$py.class
 
 build-cmake/
+build-em/*
+!build-em/.gitkeep
+dist/
+dune-copasi.js
+dune-copasi.wasm
 
 python/dune/copasi/cli/cmake_variables.py
 
@@ -22,3 +27,13 @@ doc/docusaurus/.cache-loader
 doc/docusaurus/npm-debug.log*
 doc/docusaurus/yarn-debug.log*
 doc/docusaurus/yarn-error.log*
+
+# editor files
+*.swo
+*.swp
+
+test/build/
+
+# editor files
+*.swo
+*.swp

.gitlab-ci.yml

@@ -2,156 +2,310 @@
 
 stages:
   - setup
+  - check
   - build
+  - codequality
   - deploy
 
-.default_tags: &default_tags
-  tags:
-    - "cores:4"
+workflow:
+  auto_cancel:
+    on_new_commit: interruptible
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "push" && $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
+      when: never
+    - when: always
 
-.dind_docker_tags: &dind_docker_tags
-  tags:
-    - "dind"
+default:
+  interruptible: true
+  tags: [dune-copasi]
 
-.global_variables: &global_variables
+variables:
   DUNECONTROL: dunecontrol
-  BASE_IMAGE_VERSION: v1.1.0
-  DUNE_COPASI_SD_EXECUTABLE: 'ON'
-  CPACK_GENERATORS: 'DEB'
-  CPACK_PACKAGE_DIRECTORY: $CI_PROJECT_DIR/tmp
+  CMAKE_GENERATOR: "Ninja"
+  PACKAGE_REGISTRY: ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/generic/dune-copasi
+  MASTER_IMAGE: debian:bookworm
+  BASE_IMAGE_VERSION:
+    value: "v2.0.0"
+    options:
+      - "v2.0.0"        # Main dependecy base image
+      - "v2.0.0-tmp"    # Temporary (one time testing)
+    description: "Key to tag images in the registry. Use '*-tmp' key to try out changes that need to rebild the dependencies image"
+  FORCE_REBUILD_BASE_IMAGE:
+    value: "false"
+    options:
+      - "true"
+      - "false"
+    description: "Force rebuild of base image"
 
 .docker_variables: &docker_variables
   DOCKER_BUILDKIT: 1
-  DOCKER_IMAGE: docker:19.03.1
-  DOCKER_HOST: tcp://docker:2375/
-  DOCKER_DRIVER: overlay2
-  DOCKER_TLS_CERTDIR: ""
-
-.debian_gcc: &debian_gcc
-  <<: *global_variables
-  TOOLCHAIN: gcc-8-17
+
+.debian_base: &debian_base
   DUNECI_OS: debian
-  BASE_IMAGE: debian:10
-  DEPENDENCIES_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
+  BASE_IMAGE: debian:bookworm
 
 .debian_clang: &debian_clang
-  <<: *global_variables
-  TOOLCHAIN: clang-6-17
-  DUNECI_OS: debian
-  BASE_IMAGE: debian:10
+  <<: *debian_base
+  CPACK_GENERATORS: 'DEB'
+  CPACK_PACKAGE_DIRECTORY: $CI_PROJECT_DIR/tmp
+  TOOLCHAIN: clang-17
+  DEPENDENCIES_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
+
+.debian_emscripten: &debian_emscripten
+  <<: *debian_base
+  CPACK_GENERATORS: 'DEB'
+  CPACK_PACKAGE_DIRECTORY: $CI_PROJECT_DIR/tmp
+  TOOLCHAIN: emscripten-3.1.51
   DEPENDENCIES_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
-  MASTER_IMAGE: "true"
 
-.setup: &setup
+.deploy_rules: &deploy_rules
+  rules:
+    - if: '$CI_COMMIT_TAG'
+    - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'
+    - if: '$CI_COMMIT_BRANCH == "latest"'
+
+.build_rules: &build_rules
+  rules:
+    - !reference [.deploy_rules, rules]
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+      changes:
+        - src/**/*
+        - dune/**/*
+        - dune-copasi.opts
+        - cmake
+        - CMakeLists.txt
+        - docker/*.dockerfile
+
+.update_version: &update_version
+  before_script:
+    - |
+     if [ -z "$CI_COMMIT_TAG" ]; then
+        ./util/version_handler.py --replace-prerelease="git${CI_COMMIT_SHORT_SHA:-0}" --replace-build="dune.gitlab.${CI_JOB_ID:-0}" --update-all
+      else
+        ./util/version_handler.py --override-version ${CI_COMMIT_TAG:1} --update-all
+      fi
+
+.setup_exec: &setup_exec
   image: ${DOCKER_IMAGE}
   stage: setup
   script:
-    - echo "$CI_REGISTRY_PASSWORD" | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY/copasi/dune-copasi
-    - docker build
+    - echo "$CI_REGISTRY_PASSWORD" | podman login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY/copasi/dune-copasi
+    - podman build
         --build-arg BASE_IMAGE=${BASE_IMAGE}
         --build-arg TOOLCHAIN=${TOOLCHAIN}
         --build-arg BUILDKIT_INLINE_CACHE=1
         --target setup-env
         -t ${DEPENDENCIES_IMAGE} .
-    - docker push ${DEPENDENCIES_IMAGE}
-    - docker logout $CI_REGISTRY/copasi/dune-copasi
+    - podman push ${DEPENDENCIES_IMAGE}
+    - podman logout $CI_REGISTRY/copasi/dune-copasi
   rules:
-    - if: '$REBUILD_BASE_IMAGE'
-    - if: '$CI_COMMIT_TAG'
-    - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'
-    - if: '$CI_COMMIT_BRANCH == "latest"'
-  <<: *dind_docker_tags
+    - !reference [.deploy_rules, rules]
+    - if: '$FORCE_REBUILD_BASE_IMAGE == "true"'
+
+.setup_wasm: &setup_wasm
+  image: ${DOCKER_IMAGE}
+  stage: setup
+  script:
+    - echo "$CI_REGISTRY_PASSWORD" | podman login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY/copasi/dune-copasi
+    - podman build
+        --format docker
+        --build-arg BASE_IMAGE=${BASE_IMAGE}
+        --build-arg BUILDKIT_INLINE_CACHE=1
+        --target setup-env
+        -t ${DEPENDENCIES_IMAGE}
+        -f docker/emscripten.dockerfile .
+    - podman push ${DEPENDENCIES_IMAGE}
+    - podman logout $CI_REGISTRY/copasi/dune-copasi
+  rules:
+    - !reference [.deploy_rules, rules]
+    - if: '$FORCE_REBUILD_BASE_IMAGE == "true"'
 
 .build: &build
   image: ${DEPENDENCIES_IMAGE}
   stage: build
+  <<: *update_version
   script:
-    - ./.ci/install /duneci/dune.opts
-    - ./.ci/test /duneci/dune.opts
+    - ./.ci/install dune-copasi.opts
+    - ./.ci/test dune-copasi.opts
     - mkdir -p packages
     - mv tmp/dune-copasi-*-Runtime.deb packages/dune-copasi-runtime.deb
-  <<: *default_tags
   artifacts:
     paths:
       - packages
     expire_in: 1h
+  rules:
+    - !reference [.build_rules, rules]
+
+.codequality: &codequality
+  image: ${DEPENDENCIES_IMAGE}
+  stage: codequality
+  script:
+    - CODE_CHECKER_REPORT_PATH=$CI_PROJECT_DIR/code_checker_report ./.ci/install dune-copasi.opts
+  artifacts:
+    reports:
+      codequality: $CI_PROJECT_DIR/code_checker_report/gl-code-quality-report.json
+  rules:
+    - !reference [.build_rules, rules]
 
 .deploy: &deploy
   image: ${DOCKER_IMAGE}
   stage: deploy
   script:
     # login into registry
-    - echo "$CI_REGISTRY_PASSWORD" | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY/copasi/dune-copasi
+    - echo "$CI_REGISTRY_PASSWORD" | podman login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY/copasi/dune-copasi
     - DOCKER_TAG="${DUNECI_OS}-${TOOLCHAIN}-${CI_COMMIT_REF_NAME}"
     - DOCKER_DEPLOY_IMAGE=$CI_REGISTRY/copasi/dune-copasi/dune-copasi:${DOCKER_TAG}
-    # set directory to get packages from the image
+    # set directory to get packages within the image (prepared by build job)
     - mkdir -p $CI_PROJECT_DIR/packages
     # build final production image using packages from artifacts
-    - docker build
+    - podman build
       --build-arg PRODUCTION_BASE_IMAGE=${BASE_IMAGE}
       --file docker/deploy.dockerfile
       --tag ${DOCKER_DEPLOY_IMAGE} .
     # push images into registry
-    - docker push ${DOCKER_DEPLOY_IMAGE}
-    # set alternative and simpler names
+    - podman push ${DOCKER_DEPLOY_IMAGE}
+    # set alternative and simpler names for a master image
     - |
-      if [[ ! -z "${MASTER_IMAGE}" ]]; then
+      if [[ "${MASTER_IMAGE}" == "${BASE_IMAGE}" ]]; then
         DOCKER_TAG=${CI_REGISTRY}/copasi/dune-copasi/dune-copasi:${CI_COMMIT_REF_NAME}
-        docker tag ${DOCKER_DEPLOY_IMAGE} ${DOCKER_TAG}
-        docker push ${DOCKER_TAG}
+        podman tag ${DOCKER_DEPLOY_IMAGE} ${DOCKER_TAG}
+        podman push ${DOCKER_TAG}
         if [[ "$CI_COMMIT_BRANCH" == "latest" ]]; then
           DOCKER_TAG=${CI_REGISTRY}/copasi/dune-copasi/dune-copasi:latest
-          docker tag ${DOCKER_DEPLOY_IMAGE} ${DOCKER_TAG}
-          docker push ${DOCKER_TAG}
+          podman tag ${DOCKER_DEPLOY_IMAGE} ${DOCKER_TAG}
+          podman push ${DOCKER_TAG}
         fi
       fi
-    - docker logout ${CI_REGISTRY}/copasi/dune-copasi
+    - podman logout ${CI_REGISTRY}/copasi/dune-copasi
   rules:
-    - if: '$CI_COMMIT_TAG'
-    - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'
-    - if: '$CI_COMMIT_BRANCH == "latest"'
-  <<: *dind_docker_tags
+    - !reference [.deploy_rules, rules]
 
-# debian gcc
-setup:debian_gcc:
+codespell:
   variables:
-    <<: *docker_variables
-    <<: *debian_gcc
-  <<: *setup
+    <<: *debian_clang
+  stage: check
+  image: ${DEPENDENCIES_IMAGE}
+  script:
+  - codespell
+    --skip="./doc/docusaurus/yarn.lock,./.git/**/*"
+    --ignore-words-list="warn"
 
-build:debian_gcc:
+config_format:
   variables:
-    <<: *debian_gcc
-  <<: *build
-  dependencies:
-    - setup:debian_gcc
+    <<: *debian_clang
+  stage: check
+  image: ${DEPENDENCIES_IMAGE}
+  script:
+  - ./util/validate_json.py  -j doc/docusaurus/docs/assets/config_opts.json -s util/config_opts_schema.json
 
-deploy:debian_gcc:
+setup_exec:debian_clang:
   variables:
     <<: *docker_variables
-    <<: *debian_gcc
-  <<: *deploy
+    <<: *debian_clang
+  <<: *setup_exec
+
+build_exec:debian_clang:
+  variables:
+    DUNE_COPASI_DISABLE_FETCH_PACKAGE_parafields: 'OFF'
+    <<: *debian_clang
+  <<: *build
   dependencies:
-    - build:debian_gcc
+    - setup_exec:debian_clang
 
-# debian clang
-setup:debian_clang:
+codequality:debian_clang:
   variables:
-    <<: *docker_variables
     <<: *debian_clang
-  <<: *setup
+  <<: *codequality
+  dependencies:
+    - setup_exec:debian_clang
 
-build:debian_clang:
+deploy_deb:debian_clang:
+  image: ${DEPENDENCIES_IMAGE}
   variables:
     <<: *debian_clang
-  <<: *build
+  stage: deploy
+  script:
+    - |
+      VERSION=$(./util/version_handler.py)
+      curl --header "JOB-TOKEN: ${CI_JOB_TOKEN}" --upload-file packages/dune-copasi-runtime.deb "${PACKAGE_REGISTRY}/${VERSION}/dune-copasi-runtime.deb"
   dependencies:
-    - setup:debian_clang
+    - build_exec:debian_clang
+  rules:
+    - !reference [.deploy_rules, rules]
 
-deploy:debian_clang:
+deploy_docker:debian_clang:
   variables:
     <<: *docker_variables
     <<: *debian_clang
   <<: *deploy
   dependencies:
-    - build:debian_clang
+    - build_exec:debian_clang
+
+setup_wasam:debian_emscripten:
+  variables:
+    <<: *docker_variables
+    <<: *debian_emscripten
+  <<: *setup_wasm
+
+build_wasm:debian_emscripten:
+  variables:
+    CPACK_PACKAGE_DIRECTORY: $CI_PROJECT_DIR/tmp
+    <<: *debian_emscripten
+  dependencies:
+    - setup_wasam:debian_emscripten
+  image: ${DEPENDENCIES_IMAGE}
+  stage: build
+  <<: *update_version
+  script:
+    - source /duneci/modules/emsdk/emsdk_env.sh && ./.ci/install $DUNE_OPTS_FILE
+    - mkdir -p packages
+    - mv /duneci/install/bin/dune-copasi.js /duneci/install/bin/dune-copasi.wasm packages
+  artifacts:
+    paths:
+      - packages
+    expire_in: 1h
+  rules:
+    - !reference [.build_rules, rules]
+
+deploy_wasm:debian_emscripten:
+  image: ${DEPENDENCIES_IMAGE}
+  variables:
+    <<: *debian_emscripten
+  stage: deploy
+  <<: *update_version
+  dependencies:
+    - build_wasm:debian_emscripten
+  rules:
+    - !reference [.deploy_rules, rules]
+  script:
+    - |
+      cd npm
+      mv $CI_PROJECT_DIR/packages/dune-copasi.* .
+      echo "@copasi:registry=https://${CI_SERVER_HOST}/api/v4/projects/${CI_PROJECT_ID}/packages/npm/" > .npmrc
+      echo "//${CI_SERVER_HOST}/api/v4/projects/${CI_PROJECT_ID}/packages/npm/:_authToken=${CI_JOB_TOKEN}" >> .npmrc
+      if [ -z "$CI_COMMIT_TAG" ]; then
+        npm publish --tag canary
+      else
+        npm publish --tag latest
+        echo "//registry.npmjs.org/:_authToken=${NPM_TOKEN}" > .npmrc
+        npm publish --tag latest --access public
+      fi
+
+deploy:documentation:
+  image: ${DEPENDENCIES_IMAGE}
+  variables:
+    <<: *debian_emscripten
+    GIT_STRATEGY: none
+  stage: deploy
+  script:
+    - curl -s --head --request GET https://${CI_COMMIT_REF_SLUG}--dune-copasi.netlify.app | grep "HTTP/2 404" 2> /dev/null || EXIT=$?
+    - test ${EXIT} -eq 1
+  environment:
+    name: documentation/${CI_COMMIT_REF_NAME}
+    url: https://${CI_COMMIT_REF_SLUG}--dune-copasi.netlify.app
+  allow_failure: true
+  rules:
+    - !reference [.deploy_rules, rules]
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+      changes:
+        - doc/**/*

.gitlab/merge_request_templates/MR_from_task.md

@@ -12,7 +12,7 @@ _Fill this in_
 - [ ] Added/Updated tests
 - [ ] Added/Updated documentation
 - [ ] Pipelines passing <!-- please check for new warnings -->
-<!-- change all occurences of <branch> for your branch name and uncomment
+<!-- change all occurrences of <branch> for your branch name and uncomment
    - [ ] [![Build Status](https://gitlab.dune-project.org/copasi/dune-copasi/badges/<branch>/pipeline.svg)](https://gitlab.dune-project.org/copasi/dune-copasi/pipelines)
    - [ ] [![Build Status](https://travis-ci.org/dune-copasi/dune-copasi.svg?branch=<branch>)](https://travis-ci.org/dune-copasi/dune-copasi/branches)
    - [ ] [https://ci.appveyor.com/api/projects/status/e7w7u5dt50kue5sb/branch/<branch>?svg=true](https://ci.appveyor.com/api/projects/status/e7w7u5dt50kue5sb/branch/<branch>?svg=true)
@@ -41,7 +41,7 @@ Briefly explain __how__ you achieved the proposal of the task.
 MR are supposed to evolve with code.
 
 IMPORTANT: Make sure to set the merge request as Work In Progress (WIP) or Draft
-until you want to get the MR to be reviewed by a mantainer.
+until you want to get the MR to be reviewed by a maintainer.
 
 It is not necessary to fill everything while the MR is in WIP. Feel free to fill
 the required information as you get the feature ready by editing the initial

.vscode/settings.json

-{
-  "cmake.configureOnOpen": true
-}
\ No newline at end of file

CHANGELOG.md

@@ -28,6 +28,119 @@ Types of changes
 
 ## [Unreleased] ([git-diff][Unreleased-diff])
 
+## [2.0.0] ([git-diff][2.0.0-diff]) - 2024-03-26
+
+_**Note**: This version is a complete re-write of the library based on a custom version of PDELab tailored for this module. Thus, this changelog does not make much sense in comparison to version [1.1.0]. Instead, the following entries are written with respect to the first refactor from [1.1.0] made on !83._
+
+### Refactor
+
+* Allows different parser backends: [muparser](https://beltoforion.de/en/muparser/), [exprtk](https://github.com/ArashPartow/exprtk), and [SymEngine](https://github.com/symengine/symengine) !83
+* Adds constants, (lambda) function, and [random fields](https://github.com/parafields/parafields-core) definitions within the parsers !83
+* Re-implementation of local operator: huge performance improvements !83
+* Adds tensor cross-diffusion, storage, velocity, and external boundary terms !83
+* Allows for volume coupling between compartments !83
+* Splits the subdomain and the compartment concepts. Now compartments with no entities or no components are perfectly possible !83
+* Uses new basis functions from dune-pdelab that allows native usage of multi-domains (branch: features/dune-assembler/main) !83
+* Extends compatibility of tiff images to different bit sizes !83
+* Adds monitoring (info, warning and error) of variables with new generic reduce operators !83
+* Switches logging from dune-logging to [spdlog](https://github.com/gabime/spdlog) !83
+* Designed to be thread-safe, although is not entirely yet implemented !83
+* Adds tracing capabilities with [perfetto](https://perfetto.dev/) !83
+* Allows Selection of between direct and sparse solvers, and matrix free operators !83
+* Allows to print matrix layout in a SVG file !83
+* Unifies the executable for different dimensions and different degrees of freedom layouts !83
+* Improves command line interface !83
+
+### Added
+ - Docusaurus now upgrades latest `canary` wasm binary automatically !186
+ - Hierarchical ISTL solvers and preconditioners in a dynamic registry !156
+ - Initial web interface for Wasm executable !170
+ - Deploy NPM packages to GitLab registry !179
+ - Tutorial and test on Cardiac Electrophysiology simulations !157
+ - Grid cell data !175
+ - Push CI artifacts to the GitLab registry !169 !173
+ - Test more complicated cases !158
+ - Job to build Wasm binaries in the CI !150
+ - Math expressions with only numbers as scientific notation don't need a parser !154
+ - Allow underscores in parser function arguments !152
+ - Make multi-threading optional !149
+ - Compile 2D and 3D in GitHub Actions !141
+ - Customization point on grid axis names !139
+ - Diagnostic information on SymEngine compilation failure !134
+ - Test on pattern generation !132
+ - Multi-threaded assembly !98
+ - Allow arbitrary number of functions in ExprTk !148
+ - Codequality check on the CI !123
+ - LLVM visitor for SymEngine !121
+ - Throw meaningful error message when config file is empty !119
+ - Diagnostic information on ExprTk compilation failure !115
+ - Command line help information !107 !120 !138
+ - Interpolation for 1D functions !102
+ - Initial value to reuction operations !100
+ - Code spelling to the CI !88
+ - Helper constraints for function spaces !87
+ - Support libc++ and reduce minimum required standard from C++23 to C++20 !84
+ - Show error when config file does not exist !86
+ - ~~Doxygen documentation is now deployed to Netlify !73~~ (reverted on !176)
+### Changed
+ - Update docusaurus documentation to latest changes !176 !178 !88
+ - Math parsers now can only take move only functions !187
+ - Reduce operations now receive one less argument !184
+ - Reorganize files and add `DiffusionReaction` namespace !183
+ - Use grid leaf view instead of level 0 grid view for grid cell data !177
+ - Author email address !181
+ - Improve support for Wasm binaries !170 !182
+ - Move configuration options to a JSON file and use schema validator on it !174
+ - Use Debian Bookworm in the CI !171
+ - Conditinally test possion config if ExprTk is available !168
+ - Use (faster) integer based multi-domain grid !165
+ - Simplify CMake usage !161 !162 !163
+ - Improve version handler !159
+ - Improve local basis cache to also handle intersections !145
+ - Improve log error on failure !136
+ - How to use constraints !135
+ - Update docusaurus to version `3.0.0` !124
+ - Cleanup of the build system files !118
+ - Cleanup the CI installation scripts !110
+ - Make options consistent with respect to file inputs `--*.path=/path/to/file` !109
+ - Use `PDELab::Execution` to express (possible) concurrency !108
+ - Use newer commit on `parafields-core` !105
+ - Improve implementation of muParser and ExprTk parsers !96
+ - Update docusaurus to version `2.0.0-alpha.75` !72
+### Fixed
+ - Missing CMake installation of Hierarchical ISTL solvers (from !156) !183
+ - Boundary constraints were handled incorrectly !167
+ - Coloring option for multi-threading was swapped with micro-locks !166
+ - Remove wrong definition of maximum number of ExpTk functions !130
+ - Wrong definition for SuiteSparse library !144
+ - Missing user in Dockerfile !153 !155
+ - ~~Freeze `dune-grid` dependency !147~~ (reverted by !164)
+ - Use the keyword `no_value` to identify special values in the parsers !140
+ - Inheritance of `parser_context.parser_type` !133
+ - Entries per row estimate for pattern creation !127
+ - Use `NDEBUG` compiler definition on release build !131
+ - Compatibility issue with {fmt} 10.2 !125
+ - Duplicated output on reduction algorithms !117
+ - Testing in the CI !114
+ - Correct construction on parser contexts !116
+ - Compatibility with XCode and Msys !111
+ - Consistent use of `struct` across different headers !104
+ - Unused function keywords on SymEngine where throwing unnecessary errors !101
+ - Deprecation warning on SVG writer !97
+ - Compile final executable with different parsers !95
+ - CMake problems on target installation !94
+ - Support for {fmt} >= 9.0.0 !90 !91 !93 !129
+ - Docker image now uses `dune-copas` executable instead of `dune-copasi-[sd|md]` !91
+ - CI jobs now passes since the re-write !89
+ - Solver on linear problems was wrongly reused !85
+### Removed
+ - Unused header files from version [1.1.0] !183
+ - Dependency on `dune-testtools` !122
+ - Inherited `parafield-core` tests !112
+ - Fallback for `std::filesystem` !94
+###  Security
+ - Update `follow-redirects` in web documentation !126
+
 ## [1.1.0] ([git-diff][1.1.0-diff]) - 2021-04-29
 ### Added
  - Dune options file receives `CMAKE_OPTIONS` and `MAKE_OPTIONS` !60
@@ -66,7 +179,7 @@ Types of changes
 - Vendor GHC with CMake instead of git submodules !49
 - Increase vendored GHC version to 10.5 !49 & !51
 - Force GHC usage whenever c++ filesystem cannot be found, else, optional !49
-- CI scripts are improved to simplfy usage !49
+- CI scripts are improved to simplify usage !49
 - Simplify build and usage on docker containers !49
 - Drastically reduce size of final docker container !49
 - Improve performance on cases with no interaction between all species !43
@@ -136,7 +249,8 @@ Types of changes
 - [Semantic Versioning](https://semver.org/spec/v2.0.0.html)
 - Solver for reaction-diffusion systems in multiple compartments.
 
-[Unreleased-diff]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v1.1.0...master
+[Unreleased-diff]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v2.0.0...master
+[2.0.0-diff]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v1.1.0...v2.0.0
 [1.1.0-diff]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v1.0.0...v1.1.0
 [1.0.0-diff]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v0.3.0...v1.0.0
 [0.3.0-diff]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v0.2.0...v0.3.0

CMakeLists.txt

-cmake_minimum_required(VERSION 3.13)
+cmake_minimum_required(VERSION 3.16 FATAL_ERROR)
 project(dune-copasi CXX)
 
-include(GNUInstallDirs)
-
-cmake_policy(SET CMP0074 NEW)
-if(POLICY CMP0087)
-  cmake_policy(SET CMP0087 OLD)
-endif()
-
-# define cmake options
-option(DUNE_COPASI_SD_EXECUTABLE
-       "Build SingleDomain executable by default"
-       OFF
-)
-option(DUNE_COPASI_SD_LIBRARY
-       "Include precompiled SingleDomain objects in dune-copasi library (optional)"
-       ${DUNE_COPASI_SD_EXECUTABLE}
-)
-option(DUNE_COPASI_MD_EXECUTABLE
-       "Build MultiDimain executable by default"
-       ON
-)
-option(DUNE_COPASI_MD_LIBRARY
-       "Include precompiled MultiDimain objects in dune-copasi library (optional)"
-       ${DUNE_COPASI_MD_EXECUTABLE}
-)
-option(DUNE_COPASI_COMPILE_3D
-      "Compile 3D cases in libraries and executables"
-      OFF
-)
-
 ########## Setup dependencies ##########
 
 # find dune dependencies
@@ -45,157 +16,109 @@ dune_project()
 # make sure to find and install our own cmake modules
 add_subdirectory(cmake/modules)
 
-# find specific dune-copasi dependencies
-find_package(muparser REQUIRED)
-find_package(TIFF REQUIRED)
-find_package(Filesystem)
+########## Include other scripts  ##########
 
-# if standard C++ filesystem is not found, using a fallback is mandatory
-include(CMakeDependentOption)
-cmake_dependent_option(DUNE_USE_FALLBACK_FILESYSTEM
-    "Use bundled std::filesystem alternative (enable this for macOS older than 10.15)" OFF
-    "Filesystem_FOUND" ON
-)
+# include header files
+add_subdirectory(dune)
 
-if(DUNE_USE_FALLBACK_FILESYSTEM)
-  # let's use ghc_filesystem
-  find_package(ghc_filesystem QUIET)
-
-  # ... library not installed, we provide it from git
-  if (NOT ghc_filesystem_FOUND)
-    include(FetchContent)
-    message("-- Declaring GHC Filesystem")
-    FetchContent_Declare(
-      ghc_filesystem
-      GIT_REPOSITORY https://github.com/gulrak/filesystem.git
-      GIT_TAG        0f6f0af4b42480ad5e0e4c033e5c37659842c252
-    )
-
-    if(NOT ghc_filesystem_POPULATED)
-      message("-- Populating GHC Filesystem")
-      FetchContent_Populate(ghc_filesystem)
-      add_subdirectory("${ghc_filesystem_SOURCE_DIR}" "${ghc_filesystem_BINARY_DIR}")
-    endif()
-  endif()
-endif()
+# source files for final libraries and executables
+add_subdirectory(src)
 
-########## Setup dependency target ##########
-
-# create a target to gather all dependencies
-add_library(dune-copasi-deps INTERFACE)
-target_link_libraries(dune-copasi-deps INTERFACE muparser::muparser ${DUNE_LIBS})
-
-# get properties defined by dune macros
-get_property(all_incs GLOBAL PROPERTY ALL_PKG_INCS)
-get_property(all_defs GLOBAL PROPERTY ALL_PKG_DEFS)
-get_property(all_opts GLOBAL PROPERTY ALL_PKG_OPTS)
-get_property(all_libs GLOBAL PROPERTY ALL_PKG_LIBS)
-
-# ...apply them to the dependency target
-target_include_directories(dune-copasi-deps INTERFACE ${all_incs})
-target_compile_definitions(dune-copasi-deps INTERFACE ${all_defs})
-target_compile_options(dune-copasi-deps INTERFACE ${all_opts})
-target_link_libraries(dune-copasi-deps INTERFACE ${all_libs})
-
-# Set up filesystem. Where do we get it from?
-if(DUNE_USE_FALLBACK_FILESYSTEM)
-  # and add ghc_filesystem to our filesystem target
-  target_link_libraries(dune-copasi-deps INTERFACE ghcFilesystem::ghc_filesystem)
-  target_compile_definitions(dune-copasi-deps INTERFACE DUNE_USE_FALLBACK_FILESYSTEM)
-else()
-  # ... else we don't need a back up. Link agaist standard library
-  target_link_libraries(dune-copasi-deps INTERFACE std::filesystem)
-endif()
+# documentation files
+add_subdirectory(doc)
 
-########## Create main targets ##########
+########## Setup config file ##########
 
-# create main library target
-add_library(dune-copasi)
-set_target_properties(dune-copasi PROPERTIES LIBRARY_OUTPUT_NAME dunecopasi)
-set_target_properties(dune-copasi PROPERTIES ARCHIVE_OUTPUT_NAME dunecopasi)
-target_link_libraries(dune-copasi PUBLIC dune-copasi-deps PRIVATE TIFF::TIFF)
+# include targets file in config file
+set(DUNE_CUSTOM_PKG_CONFIG_SECTION "${DUNE_CUSTOM_PKG_CONFIG_SECTION}
+set(DUNE_COPASI_GRID_DIMENSIONS ${DUNE_COPASI_GRID_DIMENSIONS})
+set(DUNE_COPASI_PARSER_LIST ${DUNE_COPASI_PARSER_LIST})
+# ensure dune cmake modules are found and used
+set(PREVIOUS_CMAKE_MODULE_PATH \${CMAKE_MODULE_PATH})
+list(PREPEND CMAKE_MODULE_PATH \"\${dune-copasi_MODULE_PATH}\")
 
-# create executable targets
-if(DUNE_COPASI_SD_EXECUTABLE)
-  add_executable(singledomain-exec)
-endif()
-if(DUNE_COPASI_MD_EXECUTABLE)
-  add_executable(multidomain-exec)
-endif()
+include(CMakeFindDependencyMacro)
+")
 
-########## Include other scripts  ##########
+foreach(module ${ALL_DEPENDENCIES})
+  if(${${module}_FOUND})
+    set(DUNE_CUSTOM_PKG_CONFIG_SECTION "${DUNE_CUSTOM_PKG_CONFIG_SECTION}
+find_dependency(${module} REQUIRED)
+list(APPEND CMAKE_MODULE_PATH \"\${${module}_MODULE_PATH}\")")
+  endif()
+endforeach()
 
-# include header files
-add_subdirectory(dune)
 
-# include main library set up
-add_subdirectory(lib)
+if(TARGET MPI::MPI_C)
+  set(DUNE_CUSTOM_PKG_CONFIG_SECTION "${DUNE_CUSTOM_PKG_CONFIG_SECTION}
+find_dependency(MPI 3.0 REQUIRED COMPONENTS C)")
+endif()
 
-# source files for final libraries and executables
-add_subdirectory(src)
+set(DUNE_CUSTOM_PKG_CONFIG_SECTION "${DUNE_CUSTOM_PKG_CONFIG_SECTION}
+find_dependency(TIFF REQUIRED)
+find_dependency(spdlog REQUIRED)
+find_dependency(fmt REQUIRED)
+find_dependency(TBB CONFIG REQUIRED)")
 
-# documentation files
-add_subdirectory(doc)
+if(TARGET METIS::METIS)
+  set(DUNE_CUSTOM_PKG_CONFIG_SECTION "${DUNE_CUSTOM_PKG_CONFIG_SECTION}
+find_dependency(METIS REQUIRED)")
+endif()
 
-# finalize the dune project: Generate and install config.h, cmake target and version file
-finalize_dune_project(GENERATE_CONFIG_H_CMAKE)
-target_compile_definitions(dune-copasi INTERFACE HAVE_DUNE_COPASI_CONFIG_H)
+if(TARGET Dune::Wrapper::SymEngine)
+  set(DUNE_CUSTOM_PKG_CONFIG_SECTION "${DUNE_CUSTOM_PKG_CONFIG_SECTION}
+find_dependency(SymEngine 0.8.0 REQUIRED)
+add_library(Dune::Wrapper::SymEngine INTERFACE IMPORTED)
+target_link_libraries(Dune::Wrapper::SymEngine INTERFACE \${SYMENGINE_LIBRARIES})
+target_include_directories(Dune::Wrapper::SymEngine INTERFACE \${SYMENGINE_INCLUDE_DIRS})")
+endif()
 
-# install generated config in build and install directories
-file(COPY "${CMAKE_CURRENT_BINARY_DIR}/config.h"
-     DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/dune/copasi"
-)
-install(FILES "${CMAKE_CURRENT_BINARY_DIR}/dune/copasi/config.h"
-        COMPONENT Development
-        DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/dune/copasi"
-)
+if(TARGET muparser::muparser)
+  set(DUNE_CUSTOM_PKG_CONFIG_SECTION "${DUNE_CUSTOM_PKG_CONFIG_SECTION}
+find_dependency(muparser REQUIRED)")
+endif()
 
-# If the FC.h file is generated (dune-common<=2.7), install into build and install directories
-file(TOUCH "${CMAKE_CURRENT_BINARY_DIR}/FC.h")
-file(COPY "${CMAKE_CURRENT_BINARY_DIR}/FC.h"
-     DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/dune/copasi"
-)
+if(TARGET parafields::parafields)
+  set(DUNE_CUSTOM_PKG_CONFIG_SECTION "${DUNE_CUSTOM_PKG_CONFIG_SECTION}
+find_dependency(parafields REQUIRED)")
+endif()
 
-install(FILES "${CMAKE_CURRENT_BINARY_DIR}/dune/copasi/FC.h"
-        COMPONENT Development
-        DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/dune/copasi"
-)
+if(TARGET SuiteSparse::UMFPACK)
+  set(DUNE_CUSTOM_PKG_CONFIG_SECTION "${DUNE_CUSTOM_PKG_CONFIG_SECTION}
+find_dependency(SuiteSparse REQUIRED COMPONENTS UMFPACK)")
+endif()
 
-# taget configuration for downstream projects
-install(TARGETS dune-copasi-deps dune-copasi
-        EXPORT dune-copasi-targets
-        LIBRARY DESTINATION "${DUNE_INSTALL_LIBDIR}/cmake/dune-copasi"
-          COMPONENT Libraries
-          NAMELINK_COMPONENT Development
-        ARCHIVE DESTINATION "${DUNE_INSTALL_LIBDIR}/cmake/dune-copasi"
-          COMPONENT Development
-)
+if(TARGET SuperLU::SuperLU)
+  set(DUNE_CUSTOM_PKG_CONFIG_SECTION "${DUNE_CUSTOM_PKG_CONFIG_SECTION}
+find_dependency(SuperLU REQUIRED)")
+endif()
+
+set(DUNE_CUSTOM_PKG_CONFIG_SECTION "${DUNE_CUSTOM_PKG_CONFIG_SECTION}
 
+list(REMOVE_DUPLICATES CMAKE_MODULE_PATH)
+get_filename_component(_dir \"\${CMAKE_CURRENT_LIST_FILE}\" PATH)
+include(\"\${_dir}/dune-copasi-installed-targets.cmake\")
+# restore previous CMAKE_MODULE_PATH
+set(CMAKE_MODULE_PATH \${PREVIOUS_CMAKE_MODULE_PATH})
+unset(PREVIOUS_CMAKE_MODULE_PATH)
+")
 
+# finalize the dune project: Generate and install config headers, cmake targets and version files
+finalize_dune_project()
 
 # export targets to be used with installed tree
 install(EXPORT dune-copasi-targets
-        FILE dune-copasi-targets.cmake
-        NAMESPACE dune-copasi::
+        FILE dune-copasi-installed-targets.cmake
+        NAMESPACE Dune::
         COMPONENT Development
         DESTINATION "${DUNE_INSTALL_LIBDIR}/cmake/dune-copasi"
 )
 
 # export targets to be used with build tree
 export(EXPORT dune-copasi-targets
-       FILE "${CMAKE_CURRENT_BINARY_DIR}/dune-copasi-targets.cmake"
-       NAMESPACE dune-copasi::
+       FILE "${CMAKE_CURRENT_BINARY_DIR}/dune-copasi-installed-targets.cmake"
+       NAMESPACE Dune::
 )
-
-# create read-only targets
-add_library(dune-copasi::dune-copasi ALIAS dune-copasi)
-if(TARGET singledomain-exec)
-  add_executable(dune-copasi::singledomain-exec ALIAS singledomain-exec)
-endif()
-if(TARGET multidomain-exec)
-  add_executable(dune-copasi::multidomain-exec ALIAS multidomain-exec)
-endif()
-
 # include tests as a sub project
 include(CTest)
 if(BUILD_TESTING)

CODE_OF_CONDUCT.md

@@ -60,7 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-*santiago.ospina at uni-heidelberg.de*.
+*dune-copasi at dune-project.org*.
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the
@@ -126,4 +126,3 @@ enforcement ladder](https://github.com/mozilla/diversity).
 For answers to common questions about this code of conduct, see the FAQ at
 https://www.contributor-covenant.org/faq. Translations are available at
 https://www.contributor-covenant.org/translations.
-

CONTRIBUTING.md

@@ -5,7 +5,7 @@ When contributing to `dune-copasi`, first discuss the change you wish to make vi
 Try to do this before anything else. This will greately improve both your and
 our experience working together :-). We follow the
 [GitLab Workflow](https://about.gitlab.com/blog/2016/10/25/gitlab-workflow-an-overview/)
-in our software development cycle and we expet you to be part of it. In short,
+in our software development cycle and we expect you to be part of it. In short,
 contributing single features can be summarized by following these steps:
 
 1. **ISSUE**: Create an issue in our
@@ -16,15 +16,15 @@ contributing single features can be summarized by following these steps:
 2. In the created issue, discuss with others the whole idea of your proposal.
    This is important because you may get input from someone that know the
    software on how to do it effectively, and poimting out considerations you may
-   have missed. It also syncronizes ideas so that changes are more easily
+   have missed. It also synchronizes ideas so that changes are more easily
    accepted.
 3. **CODE**: Implement what you proposed :-) in a new branch.
 4. Create a [Merge Request (MR)](https://docs.gitlab.com/ee/gitlab-basics/add-merge-request.html)
    using suitable template. Mark the MR as
-   [*Work In Progres* (WIP)](https://docs.gitlab.com/ee/user/project/merge_requests/work_in_progress_merge_requests.html)
+   [*Work In Progress* (WIP)](https://docs.gitlab.com/ee/user/project/merge_requests/work_in_progress_merge_requests.html)
    until is sent to review for approval. MR differ from issues in that MR
    discuss *how* to implement the idea rather than the idea itself. A MR is
-   filled of technical details that ensure that the *task* idea is fullfiled.
+   filled of technical details that ensure that the *task* idea is fulfilled.
 5. **COMMIT**: In the MR, discuss with others the details of your
    implementation. If discussions show that your proposal has to be modified to
    be accepted, push new commits and update the MR with the new technical
@@ -42,4 +42,3 @@ contributing single features can be summarized by following these steps:
    assigning a maintainer to review your modification.
 
 Check out our [code of conduct](CODE_OF_CONDUCT.md), please follow it in our interactions.
-