.ci/README.md

 [![Build Status](https://gitlab.dune-project.org/copasi/dune-copasi/badges/master/pipeline.svg)](https://gitlab.dune-project.org/copasi/dune-copasi/pipelines)
-[![Build Status](https://travis-ci.org/dune-copasi/dune-copasi.svg?branch=master)](https://travis-ci.org/dune-copasi/dune-copasi)
-[![Build Status](https://ci.appveyor.com/api/projects/status/e7w7u5dt50kue5sb/branch/master?svg=true)](https://ci.appveyor.com/project/SoilRos/dune-copasi-3gv18/branch/master)
+[![Build Status](https://github.com/dune-copasi/dune-copasi/workflows/CI%20Builds/badge.svg?branch=master)](https://github.com/dune-copasi/dune-copasi/actions?query=branch%3Amaster+)
 
-## How does this CI works?
+## How does the CI works?
 
-We have 3 Continous Integration services:
+We have 2 Continous Integration services:
   - [GitLab](https://docs.gitlab.com/ee/ci/)
-  - [Travis](https://travis-ci.org/)
-  - [AppVeyor](https://www.appveyor.com/)
+  - [GitHub](https://github.com/dune-copasi/dune-copasi/actions)
 
-The reason for this is because only one could not tackle all three platforms we
-want to reach. That is:
-  - Linux
-  - macOS
-  - Windows
-
-Sice the last two CI are better ingegrated with GitHub, we have set a repository
-there which mirrors all modifications made in the main repository.
+For this, we have set up a main repository and a mirror:
 
   - Main repository: https://gitlab.dune-project.org/copasi/dune-copasi
   - Mirror repository: https://github.com/dune-copasi/dune-copasi
 
 The main idea here is that they, the different CI, follow almost the same
 instructions in the different stages. In all the cases, the scripts expect
-to have defined `DUNECONTROL` and `DUNE_OPTIONS_FILE` variables for running
-`dunecontrol` and for the configuration options.
+configuration options defined in the main directory `dune-copasi.opts`.
+
+Their files are defined in the default places:
+
+  - [../.gitlab-ci.yml](../.gitlab-ci.yml)
+  - [../.github/workflow/ci.yml](../.github/workflow/ci.yml)
+
+### Stage: Setup Precopiled Dependecies
+
+In the case of GitHub, we use the precopiled libraries provided by the
+[`sme_deps_common`](https://github.com/spatial-model-editor/sme_deps_common).
+The script [`setup_static_deps`](setup_static_deps) obtains the target OS
+from the `dune-copasi.opts`, downloads the respective files, and expand them
+on the cmake install prefix.
 
-### Stage: Setup
+```bash
+./setup_static_deps $PDW/../dune-copasi.opts
+```
 
-In this stage, we configure and install all the dependencies that `dune-copasi`
-requires. In this case, Travis and Appveyor use the script
-[`setup.sh`](setup.sh) while gitlab uses the dependencies docker image in the
-container registry. The latter only updated for the `master` branch by the
-docker script [`dependencies.dockerfile`](../docker/dependencies.dockerfile).
-This makes the GitLab CI run faster as all the dependencies are already
-installed.
+### Stage: Setup Dune Dependecies
 
-### Stage: Build
+In this stage, we configure and install the dune dependencies that `dune-copasi`
+requires. In both cases, the CIs use the script [`setup_dune`](setup_dune), but
+in order to generate faster results in GitLab, this stage is only updated for the
+`master` branch by the docker file [`Dockerfile`](../docker/dune-copasi.dockerfile)
+with target `setup-env`.
 
-This stage builds `dune-copasi` following the [`build.sh`](build.sh) script
-which in turs run the `dunecontrol` command for the project.
-This stage always should be run.
+```bash
+./setup_dune $PDW/../dune-copasi.opts
+```
 
-### Stage: Unit Tests
+### Stage: Build, Install, and Package
 
-This stage builds and runs the unit tests by running the
-[`unit_tests.sh`](unit_tests.sh) script. `ctests` runs all tests with the tag
-`unit`. This stage always should be run.
+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.
 
-### Stage: System Tests
+```bash
+./install $PDW/../dune-copasi.opts
+```
 
-This stage runs all the system tests tagged with `DUNE_SYSTEMTEST` when running
-the [`system_tests.sh`](system_tests.sh) script. Since most of the system tests
-are generated by `dune-testools`, which is optional, this stage will only make
-sense when `dune-testools` is installed in the setup stage. Currently, this i 
-not feasible for windows due to the python environment setup.
+### Stage: Testing
 
+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.
+
+
+```bash
+./test $PDW/../dune-copasi.opts
+```
 
 ## CI Link & Badge
 For getting them replace `<branch>` for the specific branch you want:
 
 ### GitLab CI
   - Link: https://gitlab.dune-project.org/copasi/dune-copasi/pipelines
-  - Badge: [https://gitlab.dune-project.org/copasi/dune-copasi/badges/`<branch>`/pipeline.svg](https://gitlab.dune-project.org/copasi/dune-copasi/badges/master/pipeline.svg)
-### Travis
-  - Link: https://travis-ci.org/SoilRos/dune-copasi
-  - Bagage [https://travis-ci.org/dune-copasi/dune-copasi.svg?branch=`<branch>`](https://travis-ci.org/dune-copasi/dune-copasi/branches)
-### AppVeyor
-  - Link: [https://ci.appveyor.com/project/SoilRos/dune-copasi/branch/`<branch>`](https://ci.appveyor.com/project/SoilRos/dune-copasi-3gv18/branch/master)
-  - Badge: [https://ci.appveyor.com/api/projects/status/e7w7u5dt50kue5sb/branch/`<branch>`?svg=true](https://ci.appveyor.com/api/projects/status/e7w7u5dt50kue5sb/branch/master?svg=true)
-
-
+  - Badge: https://gitlab.dune-project.org/copasi/dune-copasi/badges/`<branch>`/pipeline.svg
+### GitHub Actions
+  - Link: https://github.com/dune-copasi/dune-copasi/actions?query=branch%3A`<branch>`+
+  - Badge: https://github.com/dune-copasi/dune-copasi/workflows/CI%20Builds/badge.svg?branch=`<branch>`

.ci/build.sh

-# build script for all CIs
-
-# make sure we get the right mingw64 version of g++ on appveyor
-PATH=/mingw64/bin:$PATH
-echo "PATH=$PATH"
-echo "MSYSTEM: $MSYSTEM"
-echo "DUNECONTROL: ${DUNECONTROL}"
-echo "DUNE_OPTIONS_FILE: ${DUNE_OPTIONS_FILE}"
-cat ${DUNE_OPTIONS_FILE}
-echo "PWD: $PWD"
-
-which g++
-which python
-which cmake
-g++ --version
-gcc --version
-cmake --version
-
-${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --only=dune-copasi all
\ No newline at end of file

.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

.ci/dune-logging.patch

 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 693bab6..dd4ffae 100644
+index 693bab6..770ba85 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -136,7 +136,6 @@ the command \"git submodule update --init --recursive\" in the dune-logging sour
-   target_compile_definitions(
+@@ -145,7 +145,7 @@ the command \"git submodule update --init --recursive\" in the dune-logging sour
      dune-logging-fmt
-     PRIVATE FMT_EXPORT
--    INTERFACE $<$<NOT:$<STREQUAL:$<TARGET_PROPERTY:TYPE>,STATIC_LIBRARY>>:FMT_SHARED>
-     PUBLIC DUNE_LOGGING_VENDORED_FMT=1
+     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

+#!/usr/bin/env bash
+
+# build and install
+
+# variables from DUNE_OPTIONS_FILE
+#   (optional) CMAKE_FLAGS
+#   (optional) SUDOCMD
+#   (optional) CPACK_GENERATORS
+#   (optional) CPACK_PACKAGE_DIRECTORY
+
+set +e
+
+# set colors for better print
+GREEN=$(tput setaf 2 :-"" 2>/dev/null)
+RESET=$(tput sgr0 :-"" 2>/dev/null)
+
+set -e
+
+# options file may be passed as argument
+[ ! -z "$1" ] && DUNE_OPTIONS_FILE="$1"
+
+# load dune opts
+CMAKE_FLAGS="$(. ${DUNE_OPTIONS_FILE}; eval echo \$CMAKE_FLAGS)"
+SUDOCMD="$(. ${DUNE_OPTIONS_FILE}; eval echo \$SUDOCMD)"
+
+# load useful functions
+CALL_DIR=$PWD
+SCRIPT_PATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+source $SCRIPT_PATH/util
+
+SOURCEDIR=${SCRIPT_PATH}/..
+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
+}
+
+# set up verbose output in case of failure
+ONFAILURE_PROG="git gcc g++ python pip python3 pip3 cmake $SUDOCMD"
+ONFAILURE_VARS="PATH SUDOCMD DUNE_OPTIONS_FILE CMAKE_FLAGS"
+ONFAILURE_CMD="ls cleanup"
+
+trap onfailure EXIT
+
+[[ -d ${BUILD_PATH} ]] && ONFAILURE_MESSAGE+="run this script where no folder 'build-cmake' exists\n" && exit 1
+mkdir $BUILD_PATH && cd $BUILD_PATH
+
+echo "cmake $CMAKE_FLAGS $SOURCEDIR"
+eval cmake $CMAKE_FLAGS $SOURCEDIR
+
+$SUDOCMD cmake --build $BUILD_PATH --target install
+
+for generator in $CPACK_GENERATORS; do
+  cpack -G $generator -B $CPACK_PACKAGE_DIRECTORY CPackConfig.cmake
+done
+
+trap cleanup EXIT

.ci/setup.sh

-# dependencies setup script for Travis and AppVeyor CI
-
-DUNE_VERSION="2.7"
-
-# make sure we get the right mingw64 version of g++ on appveyor
-PATH=/mingw64/bin:$PATH
-echo "PATH=$PATH"
-echo "MSYSTEM: $MSYSTEM"
-echo "DUNECONTROL: ${DUNECONTROL}"
-echo "DUNE_OPTIONS_FILE: ${DUNE_OPTIONS_FILE}"
-cat ${DUNE_OPTIONS_FILE}
-echo "PWD: $PWD"
-
-which g++
-g++ --version
-
-which gcc
-gcc --version
-
-which python
-python --version
-
-which python3
-python3 --version
-
-which pip
-pip --version
-
-which pip3
-pip3 --version
-
-which cmake
-cmake --version
-
-
-# download Dune dependencies
-for repo in core/dune-common core/dune-geometry core/dune-grid core/dune-istl core/dune-localfunctions staging/dune-functions staging/dune-uggrid
-do
-  git clone -b releases/$DUNE_VERSION --depth 1 --recursive https://gitlab.dune-project.org/$repo.git
-done
-for repo in dune-logging dune-typetree dune-pdelab dune-multidomaingrid
-do
-  git clone -b support/dune-copasi-v0.3 --depth 1 --recursive https://gitlab.dune-project.org/copasi/$repo.git
-done
-
-# python virtual environment does not work in windows yet
-if [[ ! $MSYSTEM ]]; then
-	git clone -b releases/$DUNE_VERSION https://gitlab.dune-project.org/quality/dune-testtools.git
-fi
-
-# on windows, symlinks from git repos don't work
-# msys git replaces symlinks with a text file containing the linked file location
-# so here we identify all such files, and replace them with the linked file
-# note msys defines MSYSTEM variable: use this to check if we are on msys/windows
-if [[ $MSYSTEM ]]; then
-	rootdir=$(pwd)
-		for repo in $(ls -d dune-*/)
-		do
-			echo "repo: $repo"
-			cd $rootdir/$repo
-			for f in $(git ls-files -s | awk '/120000/{print $4}')
-			do
-				dname=$(dirname "$f")
-				fname=$(basename "$f")
-				relf=$(cat $f)
-				src="$rootdir/$repo/$dname/$relf"
-				dst="$rootdir/$repo/$dname/$fname"
-				echo "  - copying $src --> $dst"
-				cp $src $dst
-			done
-		done
-	cd $rootdir
-fi
-
-# patch cmake macro to avoid build failure when fortran compiler not found, e.g. on osx
-cd dune-common
-wget https://gist.githubusercontent.com/lkeegan/059984b71f8aeb0bbc062e85ad7ee377/raw/e9c7af42c47fe765547e60833a72b5ff1e78123c/cmake-patch.txt
-echo '' >> cmake-patch.txt
-git apply cmake-patch.txt
-# another patch for missing header in cmake install list
-git apply ../dune-copasi/.ci/dune-common.patch
-cd ../
-
-cd dune-logging
-git apply ../dune-copasi/.ci/dune-logging.patch
-cd ../
-
-ls
-
-# python virtual environment does not work in windows yet
-if [[ ! $MSYSTEM ]]; then
-	${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --module=dune-testtools all
-fi
-
-for repo in dune-testtools dune-logging dune-pdelab dune-multidomaingrid
-do
-  ${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --module=$repo all
-done

.ci/setup_dune

+#!/usr/bin/env bash
+
+# build and install dune dependences
+
+# variables from DUNE_OPTIONS_FILE
+#   (optional) SETUP_DUNE_TESTTOOLS
+#   (optional) SUDOCMD
+#   (optional) DUNE_VENDOR_FMT
+
+set +e
+
+# set colors for better print
+GREEN=$(tput setaf 2 :-"" 2>/dev/null)
+RESET=$(tput sgr0 :-"" 2>/dev/null)
+
+set -e
+
+# options file may be passed as argument
+[ ! -z "$1" ] && DUNE_OPTIONS_FILE="$1"
+
+# load dune options
+SETUP_DUNE_TESTTOOLS="$(. ${DUNE_OPTIONS_FILE}; eval echo \$SETUP_DUNE_TESTTOOLS)"
+SUDOCMD="$(. ${DUNE_OPTIONS_FILE}; eval echo \$SUDOCMD)"
+DUNE_VENDOR_FMT="$(. ${DUNE_OPTIONS_FILE}; eval echo \$DUNE_VENDOR_FMT)"
+
+# load useful functions
+CALL_DIR=$PWD
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+source $SCRIPT_DIR/util
+
+print_opts_file() {
+  cat "${DUNE_OPTIONS_FILE}"
+}
+
+print_cmake_error() {
+  $DUNECONTROL --opts=${DUNE_OPTIONS_FILE} --only=dune-$module bexec "echo \$PWD > /tmp/setup-dune/module_builddir"
+  BUILD_PATH=$(cat /tmp/setup-dune/module_builddir)
+  cat "${BUILD_PATH}/CMakeFiles/CMakeError.log"
+}
+
+cleanup() {
+  rm -rf /tmp/setup-dune
+}
+
+# set up verbose output in case of failure
+ONFAILURE_PROG="git gcc g++ python pip python3 pip3 cmake wget $SUDOCMD"
+ONFAILURE_VARS="PATH MSYSTEM SUDOCMD SETUP_DUNE_TESTTOOLS DUNE_OPTIONS_FILE"
+ONFAILURE_VARS+=" CMAKE_FLAGS CMAKE_INSTALL_PREFIX DUNE_VENDOR_FMT REPO BRANCH PATCHES RECURSIVE BUILD_PATH"
+ONFAILURE_CMD="ls cleanup"
+
+trap onfailure EXIT
+
+[[ -d /tmp/setup-dune ]] && ONFAILURE_MESSAGE+="run this script where no folder '/tmp/setup-dune' exists\n" && exit 1
+mkdir /tmp/setup-dune && cd /tmp/setup-dune
+
+# setup dune repositories, branches, and patches
+for module in common geometry grid istl localfunctions; do
+  eval SETUP_dune_${module}_BRANCH=\"releases/2.7\"
+  eval SETUP_dune_${module}_REPO=\"https://gitlab.dune-project.org/core/dune-${module}.git\"
+done
+
+for module in logging functions uggrid; do
+  eval SETUP_dune_${module}_BRANCH=\"releases/2.7\"
+  eval SETUP_dune_${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-v1.0.0\"
+  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_multidomaingrid_BRANCH="releases/2.7"
+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+=" ${PWD}/cmake-patch.txt"
+
+# hardcoded **ordered** dependencies
+MODULES="common logging uggrid geometry grid localfunctions istl typetree functions pdelab multidomaingrid"
+if [[ "$SETUP_DUNE_TESTTOOLS" =~ ^(ON|on|1|yes|YES|true|TRUE)$ ]]; then
+	MODULES+=" testtools"
+fi
+
+[ -z $DUNE_OPTIONS_FILE ] && ONFAILURE_MESSAGE+="Dune options file is not set!\n" && exit 1
+
+# get cmake flags
+unset CMAKE_FLAGS
+if test "x$DUNE_OPTIONS_FILE" != "x"; then
+  CMAKE_FLAGS="$(. $DUNE_OPTIONS_FILE; eval echo \$CMAKE_FLAGS)"
+fi
+
+# get install prefix
+for flag in $CMAKE_FLAGS; do
+  [[ ${flag#-D} == CMAKE_INSTALL_PREFIX* ]] && CMAKE_INSTALL_PREFIX=${flag#-DCMAKE_INSTALL_PREFIX}
+done
+
+# remove "=" or ":PATH=" prefix
+CMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX#=}
+CMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX#:PATH=}
+# remove quotations
+CMAKE_INSTALL_PREFIX=$(echo $CMAKE_INSTALL_PREFIX | tr -d "'")
+
+[ -z $CMAKE_INSTALL_PREFIX ] && ONFAILURE_MESSAGE+="Options file **shall** provide a CMAKE_INSTALL_PREFIX\n" && exit 1
+
+if command -v $CMAKE_INSTALL_PREFIX/bin/dunecontrol &> /dev/null; then
+  ONFAILURE_MESSAGE+="An installation of 'dunecontrol' was already found in '$CMAKE_INSTALL_PREFIX'\n"
+  ONFAILURE_MESSAGE+="A new setup **must** not override an old installation\n"
+  exit 1
+fi
+
+# install prefix **must** be included on the cmake prefix
+CMAKE_PREFIX_PATH=
+for flag in $CMAKE_FLAGS; do
+  [[ ${flag#-D} == CMAKE_PREFIX_PATH* ]] && CMAKE_PREFIX_PATH+=" $flag"
+done
+unset CMAKE_FLAGS
+
+# check if install prefix is included on cmake prefix path
+if [[ "$CMAKE_PREFIX_PATH" != *${CMAKE_INSTALL_PREFIX}* ]]; then
+  ONFAILURE_MESSAGE+="\n"
+  ONFAILURE_MESSAGE+="CMAKE_INSTALL_PREFIX must be contained in CMAKE_PREFIX_PATH\n"
+  ONFAILURE_MESSAGE+="otherwise cmake projects cannot find installed modules. e.g.\n"
+  ONFAILURE_MESSAGE+="\n"
+  ONFAILURE_MESSAGE+="  CMAKE_FLAGS+=\" -DCMAKE_PREFIX_PATH='${CMAKE_INSTALL_PREFIX}'\"\n"
+  ONFAILURE_MESSAGE+="\n"
+  exit 1
+fi
+
+# download dune dependencies
+for module in $MODULES; do
+
+  echo ""
+  echo $GREEN "============================ Setting up dune-$module ============================" $RESET
+  echo ""
+  REPO="$(eval echo \$SETUP_dune_${module}_REPO)"
+  BRANCH="$(eval echo \$SETUP_dune_${module}_BRANCH)"
+  PATCHES="$(eval echo \$SETUP_dune_${module}_PATCHES)"
+  RECURSIVE="$(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
+
+  # on windows, symlinks from git repos don't work
+  # msys git replaces symlinks with a text file containing the linked file location
+  # so here we identify all such files, and replace them with the linked file
+  # note msys defines MSYSTEM variable: use this to check if we are on msys/windows
+  if [[ $MSYSTEM ]]; then
+    cd dune-$module
+    set +e
+    for f in $(git ls-files -s | awk '/120000/{print $4}'); do
+      dname=$(dirname "$f")
+      fname=$(basename "$f")
+      relf=$(cat $f)
+      src="$PWD/$dname/$relf"
+      dst="$PWD/$dname/$fname"
+      echo "  - copying $src --> $dst"
+      cp $src $dst
+    done
+    set -e
+    cd ..
+  fi
+
+  # apply patches
+  if [[ ! -z $PATCHES ]]; then
+    echo "Applying patches: $PATCHES"
+    # change line ending to DOS if OS is windows
+    [[ $MSYSTEM ]] && dos2unix $PATCHES
+    git -C dune-$module apply -v $PATCHES
+  fi
+  echo ""
+
+  if [ "$module" = "common" ]; then
+    DUNECONTROL=./dune-common/bin/dunecontrol
+  else
+    DUNECONTROL=$CMAKE_INSTALL_PREFIX/bin/dunecontrol
+  fi
+
+  # control path must be explicitely set on windows when dune-common is installed
+  export DUNE_CONTROL_PATH=$PWD
+
+  # configure, build, and install module
+  $DUNECONTROL --opts=${DUNE_OPTIONS_FILE} --only=dune-$module all
+  $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
+  $DUNECONTROL --opts=${DUNE_OPTIONS_FILE} --only=dune-$module bexec "echo \$PWD > /tmp/setup-dune/module_builddir"
+
+  # remove build and sources
+  BUILD_PATH=$(cat /tmp/setup-dune/module_builddir)
+  rm -rf $BUILD_PATH
+  rm -rf dune-$module
+done
+
+trap cleanup EXIT

.ci/setup_static_deps

+#!/usr/bin/env bash
+
+# download and install other dependences (from sme by Liam)
+
+# variables from DUNE_OPTIONS_FILE
+#   OS_TARGET=linux|osx|win32|win64
+#   CMAKE_INSTALL_PREFIX
+#   (optional) SUDOCMD
+
+set -e
+
+# options file may be passed as argument
+[ ! -z "$1" ] && DUNE_OPTIONS_FILE="$1"
+
+# load dune options
+CMAKE_FLAGS="$(. ${DUNE_OPTIONS_FILE}; eval echo \$CMAKE_FLAGS)"
+SUDOCMD="$(. ${DUNE_OPTIONS_FILE}; eval echo \$SUDOCMD)"
+OS_TARGET="$(. ${DUNE_OPTIONS_FILE}; eval echo \$OS_TARGET)"
+
+# load useful functions
+CALL_DIR=$PWD
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+source $SCRIPT_DIR/util
+
+prefix_content() {
+  ls "${CMAKE_INSTALL_PREFIX}"
+}
+
+cleanup() {
+  rm -rf /tmp/setup-static-deps
+}
+
+# set up verbose output in case of failure
+ONFAILURE_PROG="git gcc g++ python pip python3 pip3 cmake wget curl $SUDOCMD"
+ONFAILURE_VARS="SUDOCMD OSTYPE OS_TARGET CMAKE_INSTALL_PREFIX CMAKE_FLAGS CMAKE_PREFIX_PATH VERBOSE_TAR"
+ONFAILURE_CMD="ls prefix_content cleanup"
+
+trap onfailure EXIT
+
+[[ -d /tmp/setup-static-deps ]] && ONFAILURE_MESSAGE+="run this script where no folder '/tmp/setup-static-deps' exists\n" && exit 1
+mkdir /tmp/setup-static-deps && cd /tmp/setup-static-deps
+
+if [[ ! "$OS_TARGET" =~ ^(linux|osx|win32|win64)$ ]]; then
+    ONFAILURE_MESSAGE+="'$OS_TARGET' is not a known OS target\n"
+    exit 1
+fi
+
+echo "Downloading static libs for OS_TARGET: ${OS_TARGET}"
+DEPS_URL="https://github.com/spatial-model-editor/sme_deps_common/releases/cgal5.2/download/sme_deps_common_${OS_TARGET}.tgz"
+if command -v wget &> /dev/null; then
+  wget -nv $DEPS_URL | sed 's/^/  /'
+elif command -v curl &> /dev/null; then
+  curl -L $DEPS_URL >> sme_deps_common_${OS_TARGET}.tgz | sed 's/^/  /'
+else
+  ONFAILURE_MESSAGE+="'wget' not 'curl' was not found."
+  exit 1
+fi
+VERBOSE_TAR=$(tar xvf sme_deps_common_${OS_TARGET}.tgz 2>&1)
+
+[ -z "$CMAKE_INSTALL_PREFIX" ] && ONFAILURE_MESSAGE+="Install prefix is empty\n" && exit 1
+
+echo ""
+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}"
+else
+   $SUDOCMD mv opt/smelibs/* "${CMAKE_INSTALL_PREFIX}"
+fi
+
+# set the following flags in your dune opts file
+  # CMAKE_FLAGS+=" -DGMPXX_INCLUDE_DIR:PATH='"${CMAKE_INSTALL_PREFIX}"/include' "
+  # CMAKE_FLAGS+=" -DGMPXX_LIB:FILEPATH='"${CMAKE_INSTALL_PREFIX}"/lib/libgmpxx.a' "
+  # CMAKE_FLAGS+=" -DGMP_LIB:FILEPATH='"${CMAKE_INSTALL_PREFIX}"/lib/libgmp.a' "
+  # CMAKE_FLAGS+=" -Dfmt_ROOT='"${CMAKE_INSTALL_PREFIX}"' "
+  # CMAKE_FLAGS+=" -DCMAKE_DISABLE_FIND_PACKAGE_QuadMath=TRUE"
+  # CMAKE_FLAGS+=" -DF77=true"
+
+  # be careful when adding several prefix paths, they have to be
+  # set in a semicolon separated list 
+  # CMAKE_FLAGS+=" -DCMAKE_PREFIX_PATH='${CMAKE_PREFIX_PATH}' "
+
+# ...or if you are using the dune-copasi.opts
+  # export DUNE_COPASI_USE_STATIC_DEPS="ON"
+
+trap cleanup EXIT

.ci/system_tests.sh

-# system tests script for all CIs
-
-# make sure we get the right mingw64 version of g++ on appveyor
-PATH=/mingw64/bin:$PATH
-echo "PATH=$PATH"
-echo "MSYSTEM: $MSYSTEM"
-echo "DUNECONTROL: ${DUNECONTROL}"
-echo "DUNE_OPTIONS_FILE: ${DUNE_OPTIONS_FILE}"
-cat ${DUNE_OPTIONS_FILE}
-echo "PWD: $PWD"
-
-which g++
-which python
-which cmake
-g++ --version
-gcc --version
-cmake --version
-
-${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --only=dune-copasi make --target build_system_tests
-${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --only=dune-copasi bexec ctest -j4 -L "DUNE_SYSTEMTEST" --output-on-failure
\ No newline at end of file

.ci/test

+#!/usr/bin/env bash
+
+# unit tests script for all CIs
+
+# input
+#   DUNE_OPTIONS_FILE absolute path to options file
+
+set +e
+
+# set colors for better print
+GREEN=$(tput setaf 2 :-"" 2>/dev/null)
+RESET=$(tput sgr0 :-"" 2>/dev/null)
+
+set -e
+
+# options file may be passed as argument
+[ ! -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
+
+
+print_opts_file() {
+  cat "${DUNE_OPTIONS_FILE}"
+}
+
+print_cmake_error() {
+  cat "${BUILD_PATH}/CMakeFiles/CMakeError.log"
+}
+
+cleanup() {
+  echo "removig intermediate results"
+  rm -rf "${BUILD_PATH}"
+}
+
+# set up verbose output in case of failure
+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"
+
+trap onfailure EXIT
+
+echo $GREEN "============================ Unit Tests ============================" $RESET
+
+BUILD_PATH=/tmp/build-unit-tests
+[[ -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
+  DEBUG_CMAKE_FLAGS="$(. $DUNE_OPTIONS_FILE; eval echo \$CMAKE_FLAGS)"
+fi
+
+echo "cmake $DEBUG_CMAKE_FLAGS $SOURCEDIR"
+eval cmake $DEBUG_CMAKE_FLAGS $SOURCEDIR
+cmake --build . --target build_unit_tests
+ctest -j4 -L "unit" --output-on-failure
+
+echo $GREEN "============================ System Tests ============================" $RESET
+
+BUILD_PATH=/tmp/build-system-tests
+[[ -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 $SOURCEDIR"
+eval cmake $RELEASE_CMAKE_FLAGS $SOURCEDIR
+cmake --build . --target build_system_tests
+ctest -j4 -L "DUNE_SYSTEMTEST" --output-on-failure
+
+trap cleanup EXIT

.ci/unit_tests.sh

-# unit tests script for all CIs
-
-# make sure we get the right mingw64 version of g++ on appveyor
-PATH=/mingw64/bin:$PATH
-echo "PATH=$PATH"
-echo "MSYSTEM: $MSYSTEM"
-echo "DUNECONTROL: ${DUNECONTROL}"
-echo "DUNE_OPTIONS_FILE: ${DUNE_OPTIONS_FILE}"
-cat ${DUNE_OPTIONS_FILE}
-echo "PWD: $PWD"
-
-which g++
-which python
-which cmake
-g++ --version
-gcc --version
-cmake --version
-
-${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --only=dune-copasi make --target build_unit_tests
-${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --only=dune-copasi bexec ctest -j4 -L "unit" --output-on-failure
\ No newline at end of file

.ci/util

+#!/usr/bin/env bash
+
+# This is a helper function to diagnose error on different systems.
+# Use `onfailure` function together with the `trap` command:
+#
+#   trap onfailure EXIT
+#
+#   # some custom script
+#
+#   trap - EXIT
+
+# lets assume no symlink is used
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+
+# default executables to check binary folder and version on failure
+[ -z "$ONFAILURE_PROG" ] && ONFAILURE_PROG='bash'
+
+# default variables to expand on failure
+[ -z "$ONFAILURE_VARS" ] && ONFAILURE_VARS="PATH"
+
+# default commands to run on failure
+[ -z "$ONFAILURE_CMD" ] && ONFAILURE_CMD="pwd"
+
+# default exit message on failure
+[ -z "$ONFAILURE_MESSAGE" ] && ONFAILURE_MESSAGE="A failure has been produced when executing:\n\t'${0} ${@}'\n\n"
+
+onfailure() {
+
+  FAILURE_TYPE="$?"
+
+  # do not exit this function even on case of failures
+  set +e
+
+  RED=$(tput setaf 1 :-"" 2>/dev/null)
+  GREEN=$(tput setaf 2 :-"" 2>/dev/null)
+  YELLOW=$(tput setaf 3 :-"" 2>/dev/null)
+  RESET=$(tput sgr0 :-"" 2>/dev/null)
+
+  echo "${YELLOW}*************************** On Failure: Commands ****************************" $RESET >&2
+  for i in $(echo $ONFAILURE_CMD); do
+    echo "[${YELLOW}${i}${RESET}]:" >&2
+    FUNC="$($i 2>&1)" >&2
+    if [ -z "$FUNC" ]; then
+      echo $RED "NOT OUTPUT" $RESET | sed 's/^/  /' >&2
+    else
+      echo "$FUNC" | sed 's/^/  /' >&2
+    fi
+    echo "" >&2
+  done
+
+  echo "${YELLOW}*************************** On Failure: Executables Info **************************" $RESET >&2
+  for i in $(echo $ONFAILURE_PROG); do
+    echo "[${YELLOW}${i}${RESET}]:" >&2
+    if command -v $i &> /dev/null; then
+      EXEC_PATH=$(which $i 2>&1)
+      VERSION="$($EXEC_PATH --version 2>&1)"
+      echo "  which:" >&2
+      echo "$EXEC_PATH" | sed 's/^/    /' >&2
+      echo "  version:"
+      echo "$VERSION" | sed 's/^/    /' >&2
+    else
+      echo $RED "NOT FOUND" $RESET | sed 's/^/  /' >&2
+    fi
+    echo "" >&2
+  done
+
+  echo "${YELLOW}*************************** On Failure: Variables *********************************" $RESET >&2
+  for i in $(echo $ONFAILURE_VARS); do
+    echo "[${YELLOW}${i}${RESET}]:" >&2
+    VAR=$(eval echo "\$$i")
+    if [ -z "$VAR" ]; then
+      echo $RED "NOT FOUND" $RESET | sed 's/^/  /' >&2
+    else
+      echo "$VAR" | sed 's/^/  /' >&2
+    fi
+    echo "" >&2
+  done
+
+  echo "${YELLOW}*************************** On Failure: Message **************************" $RESET >&2
+
+  echo $RED "" >&2
+  echo "EXIT CODE: $FAILURE_TYPE" $RESET | sed 's/^/  /' >&2
+  echo "" $YELLOW >&2
+  printf "$ONFAILURE_MESSAGE" $RESET | sed 's/^/  /' >&2
+
+	exit $FAILURE_TYPE
+}

.dockerignore

+# inception
+.dockerignore
+Dockerfile
+doc/Dockerfile
+
+# build folders
+build-cmake/
+
+#### Docusaurus ####
+
+# Dependencies
+doc/docusaurus/node_modules
+
+# Production
+doc/docusaurus/build
+
+# Generated files
+doc/docusaurus/.docusaurus
+doc/docusaurus/.cache-loader
+
+doc/docusaurus/npm-debug.log*
+doc/docusaurus/yarn-debug.log*
+doc/docusaurus/yarn-error.log*

.github/workflows/ci.yml

+name: CI Builds
+
+on: push
+
+env:
+  DUNE_COPASI_USE_STATIC_DEPS: 'ON'
+  DUNE_COPASI_SD_EXECUTABLE: 'ON'
+
+jobs:
+  linux:
+    name: Linux
+    runs-on: ubuntu-16.04
+    env:
+      CMAKE_INSTALL_PREFIX: '/opt/smelibs'
+      TERM: 'xterm-256color'
+    defaults:
+      run:
+        shell: bash
+    steps:
+    - name: Set OS
+      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
+    - 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/*
+
+  macos:
+    name: MacOS
+    runs-on: macos-10.15
+    env:
+      CMAKE_INSTALL_PREFIX: '/opt/smelibs'
+      MACOSX_DEPLOYMENT_TARGET: '10.14'
+      DUNE_USE_FALLBACK_FILESYSTEM: 'ON'
+      TERM: 'xterm-256color'
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v2
+      - 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/*
+
+  win64:
+    name: Windows 64-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: MINGW64
+          update: true
+          install: mingw-w64-x86_64-gcc mingw-w64-x86_64-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/*
+
+  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

@@ -3,6 +3,8 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+build-cmake/
+
 python/dune/copasi/cli/cmake_variables.py
 
 #### Docusaurus ####

.gitlab-ci.yml

@@ -3,8 +3,6 @@
 stages:
   - setup
   - build
-  - unit_tests
-  - system_tests
   - deploy
 
 .default_tags: &default_tags
@@ -16,11 +14,14 @@ stages:
     - "dind"
 
 .global_variables: &global_variables
-  DUNE_OPTIONS_FILE: /duneci/dune.opts
   DUNECONTROL: dunecontrol
-  BASE_IMAGE_VERSION: v1.0
+  BASE_IMAGE_VERSION: v1.0.0
+  DUNE_COPASI_SD_EXECUTABLE: 'ON'
+  CPACK_GENERATORS: 'DEB'
+  CPACK_PACKAGE_DIRECTORY: $CI_PROJECT_DIR/tmp
 
 .docker_variables: &docker_variables
+  DOCKER_BUILDKIT: 1
   DOCKER_IMAGE: docker:19.03.1
   DOCKER_HOST: tcp://docker:2375/
   DOCKER_DRIVER: overlay2
@@ -30,41 +31,29 @@ stages:
   <<: *global_variables
   TOOLCHAIN: gcc-8-17
   DUNECI_OS: debian
-  DUNECI_BASE_IMAGE: ${CI_REGISTRY}/docker/ci/debian:10
-  DUNE_COPASI_BASE_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
-  DEPLOY_LATEST: "true"
+  BASE_IMAGE: debian:10
+  DEPENDENCIES_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
 
 .debian_clang: &debian_clang
   <<: *global_variables
   TOOLCHAIN: clang-6-17
   DUNECI_OS: debian
-  DUNECI_BASE_IMAGE: ${CI_REGISTRY}/docker/ci/debian:10
-  DUNE_COPASI_BASE_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
-
-.ubuntu_gcc: &ubuntu_gcc
-  <<: *global_variables
-  TOOLCHAIN: gcc-7-17
-  DUNECI_OS: ubuntu
-  DUNECI_BASE_IMAGE: ${CI_REGISTRY}/docker/ci/ubuntu:18.04
-  DUNE_COPASI_BASE_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
-
-.ubuntu_clang: &ubuntu_clang
-  <<: *global_variables
-  TOOLCHAIN: clang-6-17
-  DUNECI_OS: ubuntu
-  DUNECI_BASE_IMAGE: ${CI_REGISTRY}/docker/ci/ubuntu:18.04
-  DUNE_COPASI_BASE_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
+  BASE_IMAGE: debian:10
+  DEPENDENCIES_IMAGE: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${TOOLCHAIN}-${BASE_IMAGE_VERSION}
+  MASTER_IMAGE: "true"
 
 .setup: &setup
   image: ${DOCKER_IMAGE}
   stage: setup
   script:
     - echo "$CI_REGISTRY_PASSWORD" | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY/copasi/dune-copasi
-    - docker build -f docker/dependencies.dockerfile
-        --build-arg BASE_IMAGE=${DUNECI_BASE_IMAGE}
+    - docker build
+        --build-arg BASE_IMAGE=${BASE_IMAGE}
         --build-arg TOOLCHAIN=${TOOLCHAIN}
-        -t ${DUNE_COPASI_BASE_IMAGE} .
-    - docker push ${DUNE_COPASI_BASE_IMAGE}
+        --build-arg BUILDKIT_INLINE_CACHE=1
+        --target setup-env
+        -t ${DEPENDENCIES_IMAGE} .
+    - docker push ${DEPENDENCIES_IMAGE}
     - docker logout $CI_REGISTRY/copasi/dune-copasi
   rules:
     - if: '$REBUILD_BASE_IMAGE'
@@ -74,60 +63,49 @@ stages:
   <<: *dind_docker_tags
 
 .build: &build
-  image: ${DUNE_COPASI_BASE_IMAGE}
+  image: ${DEPENDENCIES_IMAGE}
   stage: build
   script:
-    - cd ..
-    - bash dune-copasi/.ci/build.sh
-  artifacts:
-    paths:
-      - build-cmake
-    expire_in: 30 mins
-  <<: *default_tags
-
-.unit_tests: &unit_tests
-  image: ${DUNE_COPASI_BASE_IMAGE}
-  stage: unit_tests
-  script:
-    - echo 'CMAKE_FLAGS+=" -DCMAKE_BUILD_TYPE=Debug"' >> /duneci/cmake-flags/dune_copasi.opts
-    - cd ..
-    - bash dune-copasi/.ci/unit_tests.sh
-  artifacts:
-    paths:
-      - build-cmake/test
-    expire_in: 1 day
+    - ./.ci/install /duneci/dune.opts
+    - ./.ci/test /duneci/dune.opts
+    - mkdir -p packages
+    - mv tmp/dune-copasi-*-Runtime.deb packages/dune-copasi-runtime.deb
   <<: *default_tags
-
-.system_tests: &system_tests
-  image: ${DUNE_COPASI_BASE_IMAGE}
-  stage: system_tests
-  script:
-    - cd ..
-    - bash dune-copasi/.ci/system_tests.sh
   artifacts:
     paths:
-      - cd ..
-      - build-cmake/test
-    expire_in: 1 day
-  <<: *default_tags
+      - packages
+    expire_in: 1h
 
 .deploy: &deploy
   image: ${DOCKER_IMAGE}
   stage: deploy
   script:
+    # login into registry
     - echo "$CI_REGISTRY_PASSWORD" | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY/copasi/dune-copasi
     - DOCKER_TAG="${DUNECI_OS}-${TOOLCHAIN}-${CI_COMMIT_REF_NAME}"
-    - docker build -f docker/dune-copasi.dockerfile
-      --build-arg BASE_IMAGE=${DUNE_COPASI_BASE_IMAGE}
-      --build-arg BRANCH=${CI_COMMIT_REF_NAME}
-      -t $CI_REGISTRY/copasi/dune-copasi/dune-copasi:${DOCKER_TAG} .
-    - docker push $CI_REGISTRY/copasi/dune-copasi/dune-copasi:${DOCKER_TAG}
+    - DOCKER_DEPLOY_IMAGE=$CI_REGISTRY/copasi/dune-copasi/dune-copasi:${DOCKER_TAG}
+    # set directory to get packages from the image
+    - mkdir -p $CI_PROJECT_DIR/packages
+    # build final production image using packages from artifacts
+    - docker build
+      --build-arg PRODUCTION_BASE_IMAGE=${BASE_IMAGE}
+      --file docker/deploy.dockerfile
+      --tag ${DOCKER_DEPLOY_IMAGE} .
+    # push images into registry
+    - docker push ${DOCKER_DEPLOY_IMAGE}
+    # set alternative and simpler names
     - |
-      if [ "$CI_COMMIT_BRANCH" == "latest" && $DEPLOY_LATEST ]; then
-        docker tag $CI_REGISTRY/copasi/dune-copasi/dune-copasi:${DOCKER_TAG} $CI_REGISTRY/copasi/dune-copasi/dune-copasi:latest
-        docker push $CI_REGISTRY/copasi/dune-copasi/dune-copasi:latest
+      if [[ ! -z "${MASTER_IMAGE}" ]]; then
+        DOCKER_TAG=${CI_REGISTRY}/copasi/dune-copasi/dune-copasi:${CI_COMMIT_REF_NAME}
+        docker tag ${DOCKER_DEPLOY_IMAGE} ${DOCKER_TAG}
+        docker push ${DOCKER_TAG}
+        if [[ "$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}
+        fi
       fi
-    - docker logout $CI_REGISTRY/copasi/dune-copasi
+    - docker logout ${CI_REGISTRY}/copasi/dune-copasi
   rules:
     - if: '$CI_COMMIT_TAG'
     - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'
@@ -148,63 +126,13 @@ build:debian_gcc:
   dependencies:
     - setup:debian_gcc
 
-unit_tests:debian_gcc:
-  variables:
-    <<: *debian_gcc
-  <<: *unit_tests
-  dependencies:
-    - build:debian_gcc
-
-system_tests:debian_gcc:
-  variables:
-    <<: *debian_gcc
-  <<: *system_tests
-  dependencies:
-    - build:debian_gcc
-
 deploy:debian_gcc:
   variables:
     <<: *docker_variables
     <<: *debian_gcc
   <<: *deploy
   dependencies:
-    - system_tests:debian_gcc
-
-# # ubuntu gcc
-# setup:ubuntu_gcc:
-#   variables:
-#     <<: *docker_variables
-#     <<: *ubuntu_gcc
-#   <<: *setup
-
-# build:ubuntu_gcc:
-#   variables:
-#     <<: *ubuntu_gcc
-#   <<: *build
-#   dependencies:
-#     - setup:ubuntu_gcc
-
-# unit_tests:ubuntu_gcc:
-#   variables:
-#     <<: *ubuntu_gcc
-#   <<: *unit_tests
-#   dependencies:
-#     - build:ubuntu_gcc
-
-# system_tests:ubuntu_gcc:
-#   variables:
-#     <<: *ubuntu_gcc
-#   <<: *system_tests
-#   dependencies:
-#     - build:ubuntu_gcc
-
-# deploy:ubuntu_gcc:
-#   variables:
-#     <<: *docker_variables
-#     <<: *ubuntu_gcc
-#   <<: *deploy
-#   dependencies:
-#     - system_tests:ubuntu_gcc
+    - build:debian_gcc
 
 # debian clang
 setup:debian_clang:
@@ -220,53 +148,10 @@ build:debian_clang:
   dependencies:
     - setup:debian_clang
 
-unit_tests:debian_clang:
-  variables:
-    <<: *debian_clang
-  <<: *unit_tests
-  dependencies:
-    - build:debian_clang
-
-system_tests:debian_clang:
-  variables:
-    <<: *debian_clang
-  <<: *system_tests
-  dependencies:
-    - build:debian_clang
-
 deploy:debian_clang:
   variables:
     <<: *docker_variables
     <<: *debian_clang
   <<: *deploy
   dependencies:
-    - system_tests:debian_clang
-
-# # ubuntu clang
-# setup:ubuntu_clang:
-#   <<: *ubuntu_clang
-#   <<: *setup
-
-# build:ubuntu_clang:
-#   <<: *ubuntu_clang
-#   <<: *build
-#   dependencies:
-#     - setup:ubuntu_clang
-
-# unit_tests:ubuntu_clang:
-#   <<: *ubuntu_clang
-#   <<: *unit_tests
-#   dependencies:
-#     - build:ubuntu_clang
-
-# system_tests:ubuntu_clang:
-#   <<: *ubuntu_clang
-#   <<: *system_tests
-#   dependencies:
-#     - build:ubuntu_clang
-
-# deploy:ubuntu_clang:
-#   <<: *ubuntu_clang
-#   <<: *deploy
-#   dependencies:
-#     - system_tests:ubuntu_clang
+    - build:debian_clang

.gitmodules

-[submodule "dune/copasi/common/ghc"]
-	path = ext/ghc
-	url = https://github.com/gulrak/filesystem

.travis.yml

-language: cpp
-matrix:
-  include:
-    # linux build
-    - os: linux
-      dist: xenial
-      compiler: gcc
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-9
-            - python-dev
-            - python-pip
-            - python-virtualenv
-            - python3
-            - python3-dev
-            - python3-pip
-            - python3-venv
-
-    # mac build
-    - os: osx
-      osx_image: xcode10.3
-      compiler: clang
-
-before_install:
-  # DUNE will only compile for 10.14 - uses some C++17 not available in earlier osx versions...
-  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then export MACOSX_DEPLOYMENT_TARGET=10.14; fi
-  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 100; fi
-  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-9 100; fi
-  - gcc --version
-  - g++ --version
-  # download muparser, gmp and libtiff as static libraries
-  - wget "https://github.com/spatial-model-editor/sme_deps_common/releases/latest/download/sme_deps_common_$TRAVIS_OS_NAME.tgz"
-  - sudo tar xzvf sme_deps_common_$TRAVIS_OS_NAME.tgz -C /
-  - cd ..
-install:
-  - echo 'CMAKE_FLAGS+=" -G '"'"'Unix Makefiles'"'"' "' >> dune.opts
-  - echo 'CMAKE_FLAGS+=" -DCMAKE_CXX_STANDARD=17"' >> dune.opts
-  - echo 'CMAKE_FLAGS+=" -DDUNE_PYTHON_VIRTUALENV_SETUP=1 -DDUNE_PYTHON_ALLOW_GET_PIP=1 "' >> dune.opts
-  - echo 'CMAKE_FLAGS+=" -DDUNE_PYTHON_VIRTUALENV_PATH='"$PWD"'/ext/dune-python-venv"' >> dune.opts
-  - echo 'CMAKE_FLAGS+=" -DCMAKE_DISABLE_FIND_PACKAGE_QuadMath=TRUE -DBUILD_TESTING=OFF"' >> dune.opts
-  - echo 'CMAKE_FLAGS+=" -DDUNE_USE_ONLY_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release"' >> dune.opts
-  - echo 'CMAKE_FLAGS+=" -DF77=true -DCMAKE_PREFIX_PATH=/opt/smelibs"' >> dune.opts
-  - echo 'CMAKE_FLAGS+=" -Dmuparser_INCLUDE_DIR:PATH=/opt/smelibs/include -Dmuparser_LIBRARIES:FILEPATH=opt/smelibs/lib/libmuparser.a"' >> dune.opts
-  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then echo 'CMAKE_FLAGS+=" -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3"' >> dune.opts; fi
-  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then echo 'CMAKE_FLAGS+=" -DUSE_FALLBACK_FILESYSTEM=ON"' >> dune.opts ; fi
-  - echo 'MAKE_FLAGS="-j2 VERBOSE=1"' >> dune.opts
-  - export DUNE_OPTIONS_FILE="dune.opts"
-  - export DUNECONTROL=./dune-common/bin/dunecontrol
-  - echo "${DUNE_OPTIONS_FILE}"
-  # setup dependencies
-  - bash dune-copasi/.ci/setup.sh
-script:
-  - bash dune-copasi/.ci/build.sh
-after_script:
-  - bash dune-copasi/.ci/unit_tests.sh
-  - bash dune-copasi/.ci/system_tests.sh
-  # check dependencies of executable
-  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then otool -L $TRAVIS_BUILD_DIR/build-cmake/src/dune_copasi_md; fi
-  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then ldd $TRAVIS_BUILD_DIR/build-cmake/src/dune_copasi_md; fi
-
-notifications:
-email: false
\ No newline at end of file

.vscode/settings.json

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

CHANGELOG.md

@@ -28,6 +28,46 @@ Types of changes
 
 ## [Unreleased] ([git-diff][Unreleased-diff])
 
+## [1.0.0] ([git-diff][1.0.0-diff]) - 2021-02-11
+### Added
+- Custom membrane flux !30
+- Skip intersection methods in local operators !36
+- Parameters to control Newton's method !30
+- Stepper interface to snap solution to a specific time !45
+- Provide help message when executables are not used correctly !49
+- Produce Debian Packages on the CI !49
+- Installation is now divided on three components: `Runtime|Library|Development` !49
+- Define a recommended dune options file [`dune-copasi.opts`](dune-copasi.opts) !49
+- Versioned documentation !49
+- Dependency on `pkg-config` !52
+### Changed
+- TIFF images are clamped instead of zeroed when evaluated outside its domain !47
+- Produce versioned documentation !49
+- Travis and Appveyor are replaced for GitHub Actions on `Linux|MacOS|Windows` !49
+- Increment CMake required version to 3.13 !49
+- Installed CMake project is now consumable by other CMake projects !49
+- 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
+- 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
+- `dune-logging` and `dune-multidomaingrid` no longer require a COPASI namespace fork !53
+### Removed
+- Automatic flux between compartment components with same name !30
+- Jacobian operator is managed by the stepper instead of the model !39
+- Jacobian tests are improved and extended to cover more cases !39
+- CMake module to find muparser, use `pkg-config` instead !52
+### Fixed
+- Finished and documented Installation procedure !49
+- Wrong rounding on y pixels on TIFF file reads !47
+- Improper vector allocation in multidomain intersections !39
+- Final timestep reduction to reach `end_time` failed in adaptive stepper !43
+- Infinite loop when final adaptive step failed !45
+- Binary executables are now installed !49
+- Support for shared libraries !54
+
 ## [0.3.0] ([git-diff][0.3.0-diff]) - 2020-10-07
 ### Added
 - User documentation !28
@@ -79,10 +119,14 @@ 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/v0.3.0...master
+[Unreleased-diff]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v1.0.0...master
+[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
 [0.2.0-diff]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v0.1.0...v0.2.0
 
+[Unreleased]: https://gitlab.dune-project.org/copasi/dune-copasi/-/tree/master
+
+[1.0.0]: https://gitlab.dune-project.org/copasi/dune-copasi/-/releases/v1.0.0
 [0.3.0]: https://gitlab.dune-project.org/copasi/dune-copasi/-/releases/v0.3.0
 [0.2.0]: https://gitlab.dune-project.org/copasi/dune-copasi/-/releases/v0.2.0
 [0.1.0]: https://gitlab.dune-project.org/copasi/dune-copasi/-/releases/v0.1.0