Santiago Ospina De Los Ríos · Liam Keegan · Santiago Ospina De Los Ríos · Liam Keegan · Santiago Ospina De Los Ríos · Liam Keegan
--- a/.ci/README.md
+++ b/.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/SoilRos/dune-copasi.svg?branch=master)](https://travis-ci.org/SoilRos/dune-copasi)
-[![Build status](https://ci.appveyor.com/api/projects/status/6605joy2w17qvca8/branch/master?svg=true)](https://ci.appveyor.com/project/SoilRos/dune-copasi/branch/master)
+[![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)

 ## How does this CI works?

-We have 3 Continous Integration services: 
+We have 3 Continous Integration services:
  - [GitLab](https://docs.gitlab.com/ee/ci/)
  - [Travis](https://travis-ci.org/)
  - [AppVeyor](https://www.appveyor.com/)

-The reason for this is because only one could not tackle all three platforms we want 
-to reach. That is:
+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.
+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.

  - Main repository: https://gitlab.dune-project.org/copasi/dune-copasi
-  - Mirror repository: https://github.com/SoilRos/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. 
+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.

 ### Stage: Setup

-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.
+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: Build

-This stage builds `dune-copasi` following the [`build.sh`](build.sh) script which in turs run the 
-`dunecontrol` command for the project.
+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.

 ### Stage: Unit Tests

-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 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.

 ### Stage: System Tests

-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 is 
+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.


@@ -62,9 +65,9 @@ For getting them replace `<branch>` for the specific branch you want:
  - 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
-  - Badge: [https://travis-ci.org/SoilRos/dune-copasi.svg?branch=`<branch>`](https://travis-ci.org/SoilRos/dune-copasi.svg?branch=master)
+  - 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/branch/master)
-  - Badge: [https://ci.appveyor.com/api/projects/status/6605joy2w17qvca8/branch/`<branch>`?svg=true](https://ci.appveyor.com/api/projects/status/6605joy2w17qvca8/branch/master?svg=true)
+  - 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)


--- a/.ci/setup.sh
+++ b/.ci/setup.sh
@@ -40,12 +40,12 @@ do
 done
 for repo in dune-logging dune-typetree dune-pdelab dune-multidomaingrid
 do
-  git clone -b support/dune-copasi --depth 1 --recursive https://gitlab.dune-project.org/copasi/$repo.git
+  git clone -b support/dune-copasi-v0.3 --depth 1 --recursive https://gitlab.dune-project.org/copasi/$repo.git
 done

 # python virtual environment does not work in windows yet
 if [[ ! $MSYSTEM ]]; then
-	git clone -b feature/allow-multidomain-vtk-compare-to-have-same-thresholds https://gitlab.dune-project.org/quality/dune-testtools.git
+	git clone -b releases/$DUNE_VERSION https://gitlab.dune-project.org/quality/dune-testtools.git
 fi

 # on windows, symlinks from git repos don't work
@@ -95,4 +95,4 @@ fi
 for repo in dune-testtools dune-logging dune-pdelab dune-multidomaingrid
 do
  ${DUNECONTROL} --opts=${DUNE_OPTIONS_FILE} --module=$repo all
-done
\ No newline at end of file
+done
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,20 @@ __pycache__/
 *.py[cod]
 *$py.class

-python/dune/copasi/cli/cmake_variables.py
\ No newline at end of file
+python/dune/copasi/cli/cmake_variables.py
+
+#### 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*
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -7,84 +7,74 @@ stages:
  - system_tests
  - deploy

-.docker_variables: &docker_variables
-  image: docker:19.03.1
-  variables:
-    DOCKER_HOST: tcp://docker:2375/
-    DOCKER_DRIVER: overlay2
-    DOCKER_TLS_CERTDIR: ""
+.default_tags: &default_tags
  tags:
-    - "dind"
+    - "cores:4"

-.general_definitions: &general_definitions
+.dind_docker_tags: &dind_docker_tags
  tags:
-    - "cores:4"
+    - "dind"
+
+.global_variables: &global_variables
+  DUNE_OPTIONS_FILE: /duneci/dune.opts
+  DUNECONTROL: dunecontrol
+  BASE_IMAGE_VERSION: v1.0
+
+.docker_variables: &docker_variables
+  DOCKER_IMAGE: docker:19.03.1
+  DOCKER_HOST: tcp://docker:2375/
+  DOCKER_DRIVER: overlay2
+  DOCKER_TLS_CERTDIR: ""

-# OS setup
 .debian_gcc: &debian_gcc
-  <<: *general_definitions
-  image: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:debian-gcc-8-17
-  before_script:
-    - DUNECI_TOOLCHAIN="gcc-8-17"
-    - DUNECI_OS="debian"
-    - DUNECI_BASE_IMAGE=${CI_REGISTRY}/docker/ci/debian:10
-    - DUNE_COPASI_BASE_IMAGE=${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${DUNECI_TOOLCHAIN}
-    - export DUNE_OPTIONS_FILE=/duneci/dune.opts
-    - export DUNECONTROL=dunecontrol
+  <<: *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"

 .debian_clang: &debian_clang
-  <<: *general_definitions
-  image: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:debian-clang-7-libcpp-17
-  before_script:
-    - DUNECI_TOOLCHAIN="clang-7-libcpp-17"
-    - DUNECI_OS="debian"
-    - DUNECI_BASE_IMAGE=${CI_REGISTRY}/docker/ci/debian:10
-    - DUNE_COPASI_BASE_IMAGE=${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${DUNECI_TOOLCHAIN}
-    - export DUNE_OPTIONS_FILE=/duneci/dune.opts
-    - export DUNECONTROL=dunecontrol
+  <<: *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
-  <<: *general_definitions
-  image: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:ubuntu-gcc-7-17
-  before_script:
-    - DUNECI_TOOLCHAIN="gcc-7-17"
-    - DUNECI_OS="ubuntu"
-    - DUNECI_BASE_IMAGE=${CI_REGISTRY}/docker/ci/ubuntu:18.04
-    - DUNE_COPASI_BASE_IMAGE=${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${DUNECI_TOOLCHAIN}
-    - export DUNE_OPTIONS_FILE=/duneci/dune.opts
-    - export DUNECONTROL=dunecontrol
+  <<: *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
-  <<: *general_definitions
-  image: ${CI_REGISTRY}/copasi/dune-copasi/dependencies:ubuntu-clang-6-17
-  before_script:
-    - DUNECI_TOOLCHAIN="clang-6-17"
-    - DUNECI_OS="ubuntu"
-    - DUNECI_BASE_IMAGE=${CI_REGISTRY}/docker/ci/ubuntu:18.04
-    - DUNE_COPASI_BASE_IMAGE=${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${DUNECI_TOOLCHAIN}
-    - export DUNE_OPTIONS_FILE=/duneci/dune.opts
-    - export DUNECONTROL=dunecontrol
-
-# Stages
+  <<: *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}
+
 .setup: &setup
-  <<: *docker_variables
+  image: ${DOCKER_IMAGE}
  stage: setup
  script:
-    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY/copasi/dune-copasi
+    - echo "$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}
-        -t ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${DUNECI_TOOLCHAIN} .
-    - docker push ${CI_REGISTRY}/copasi/dune-copasi/dependencies:${DUNECI_OS}-${DUNECI_TOOLCHAIN}
+        --build-arg TOOLCHAIN=${TOOLCHAIN}
+        -t ${DUNE_COPASI_BASE_IMAGE} .
+    - docker push ${DUNE_COPASI_BASE_IMAGE}
    - docker logout $CI_REGISTRY/copasi/dune-copasi
-
-  only:
-    variables:
-      # Run job if branch is master, job is scheduled or the variable REBUILD_BASE_IMAGE is defined
-      - $CI_COMMIT_BRANCH == "master"
-      - $CI_PIPELINE_SOURCE == "schedule"
-      - $REBUILD_BASE_IMAGE
+  rules:
+    - if: '$REBUILD_BASE_IMAGE'
+    - if: '$CI_COMMIT_TAG'
+    - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'
+    - if: '$CI_COMMIT_BRANCH == "latest"'
+  <<: *dind_docker_tags

 .build: &build
+  image: ${DUNE_COPASI_BASE_IMAGE}
  stage: build
  script:
    - cd ..
@@ -93,8 +83,10 @@ stages:
    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
@@ -104,8 +96,10 @@ stages:
    paths:
      - build-cmake/test
    expire_in: 1 day
+  <<: *default_tags

 .system_tests: &system_tests
+  image: ${DUNE_COPASI_BASE_IMAGE}
  stage: system_tests
  script:
    - cd ..
@@ -115,104 +109,135 @@ stages:
      - cd ..
      - build-cmake/test
    expire_in: 1 day
+  <<: *default_tags

 .deploy: &deploy
-  <<: *docker_variables
+  image: ${DOCKER_IMAGE}
  stage: deploy
  script:
-    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY/copasi/dune-copasi
+    - echo "$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 $CI_REGISTRY/copasi/dune-copasi/dune-copasi:${DUNECI_OS}-${DUNECI_TOOLCHAIN}-${CI_COMMIT_REF_NAME} .
-    - docker push $CI_REGISTRY/copasi/dune-copasi/dune-copasi:${DUNECI_OS}-${DUNECI_TOOLCHAIN}-${CI_COMMIT_REF_NAME}
+      --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}
+    - |
+      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
+      fi
    - docker logout $CI_REGISTRY/copasi/dune-copasi
-  only:
-    - master
+  rules:
+    - if: '$CI_COMMIT_TAG'
+    - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'
+    - if: '$CI_COMMIT_BRANCH == "latest"'
+  <<: *dind_docker_tags

 # debian gcc
 setup:debian_gcc:
-  <<: *debian_gcc
+  variables:
+    <<: *docker_variables
+    <<: *debian_gcc
  <<: *setup

 build:debian_gcc:
-  <<: *debian_gcc
+  variables:
+    <<: *debian_gcc
  <<: *build
  dependencies:
    - setup:debian_gcc

 unit_tests:debian_gcc:
-  <<: *debian_gcc
+  variables:
+    <<: *debian_gcc
  <<: *unit_tests
  dependencies:
    - build:debian_gcc

 system_tests:debian_gcc:
-  <<: *debian_gcc
+  variables:
+    <<: *debian_gcc
  <<: *system_tests
  dependencies:
    - build:debian_gcc

 deploy:debian_gcc:
-  <<: *debian_gcc
+  variables:
+    <<: *docker_variables
+    <<: *debian_gcc
  <<: *deploy
  dependencies:
    - system_tests:debian_gcc

 # # ubuntu gcc
 # setup:ubuntu_gcc:
-#   <<: *ubuntu_gcc
+#   variables:
+#     <<: *docker_variables
+#     <<: *ubuntu_gcc
 #   <<: *setup

 # build:ubuntu_gcc:
-#   <<: *ubuntu_gcc
+#   variables:
+#     <<: *ubuntu_gcc
 #   <<: *build
 #   dependencies:
 #     - setup:ubuntu_gcc

 # unit_tests:ubuntu_gcc:
-#   <<: *ubuntu_gcc
+#   variables:
+#     <<: *ubuntu_gcc
 #   <<: *unit_tests
 #   dependencies:
 #     - build:ubuntu_gcc

 # system_tests:ubuntu_gcc:
-#   <<: *ubuntu_gcc
+#   variables:
+#     <<: *ubuntu_gcc
 #   <<: *system_tests
 #   dependencies:
 #     - build:ubuntu_gcc

 # deploy:ubuntu_gcc:
-#   <<: *ubuntu_gcc
+#   variables:
+#     <<: *docker_variables
+#     <<: *ubuntu_gcc
 #   <<: *deploy
 #   dependencies:
 #     - system_tests:ubuntu_gcc

 # debian clang
 setup:debian_clang:
-  <<: *debian_clang
+  variables:
+    <<: *docker_variables
+    <<: *debian_clang
  <<: *setup

 build:debian_clang:
-  <<: *debian_clang
+  variables:
+    <<: *debian_clang
  <<: *build
  dependencies:
    - setup:debian_clang

 unit_tests:debian_clang:
-  <<: *debian_clang
+  variables:
+    <<: *debian_clang
  <<: *unit_tests
  dependencies:
    - build:debian_clang

 system_tests:debian_clang:
-  <<: *debian_clang
+  variables:
+    <<: *debian_clang
  <<: *system_tests
  dependencies:
    - build:debian_clang

 deploy:debian_clang:
-  <<: *debian_clang
+  variables:
+    <<: *docker_variables
+    <<: *debian_clang
  <<: *deploy
  dependencies:
    - system_tests:debian_clang
@@ -244,4 +269,4 @@ deploy:debian_clang:
 #   <<: *ubuntu_clang
 #   <<: *deploy
 #   dependencies:
-#     - system_tests:ubuntu_clang
\ No newline at end of file
+#     - system_tests:ubuntu_clang
--- a/.gitlab/merge_request_templates/MR_from_task.md
+++ b/.gitlab/merge_request_templates/MR_from_task.md
@@ -2,28 +2,34 @@
 _Fill this in_

 ### Is there something that needs to be double checked?
-<!-- Is there something a reviewer should look out for _especially_? -->
+<!-- Is there something a reviewer should be aware of or needs to be discussed? -->
 _Fill this in_

 ### Can this MR be accepted?
- [ ] Implemented ...
-   - [ ] ...
- [ ] Added/Updated tests:
-   - [ ] ...
+
+- [ ] I've read [`contribution guide`](../../CONTRIBUTING.md)
+- [ ] Implemented <!-- Break down the list of new features if possible -->
+- [ ] Added/Updated tests
 - [ ] Added/Updated documentation
 - [ ] Pipelines passing <!-- please check for new warnings -->
-   <!-- change all occurences of <branch> for your branch name -->
+<!-- change all occurences 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/SoilRos/dune-copasi.svg?branch=<branch>)](https://travis-ci.org/SoilRos/dune-copasi/branches)
-   - [ ] [![Build status](https://ci.appveyor.com/api/projects/status/6605joy2w17qvca8/branch/<branch>?svg=true)](https://ci.appveyor.com/project/SoilRos/dune-copasi/history)
+   - [ ] [![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)
+ -->
 - [ ] Delete branch option set <!-- unless there's a good reason -->
- [ ] Added entry to `CHANGELOG.md`
+- [ ] [Fast-forwaded git merge](https://ariya.io/2013/09/fast-forward-git-merge) is possible
+   <!-- If fast-forward git merge is not possible, rebase this branch onto the
+      target branch (e.g. master). If you do not know how to do it, ask
+      maintainer's help or try it out by yourself (just try to keep a copy of
+      your changes somewhere else since rebasing changes history and things can
+      get messy for newcomers) -->
+- [ ] Added entry to [`CHANGELOG.md`](../../CHANGELOG.md)

 ### Related issues

-Closes #
 <!-- For automatic closing, do not forget the commas between issue numbers-->
-
+Closes #

 <!--
 PLEASE READ THIS!
@@ -32,6 +38,12 @@ A Merge Request should be associated to a certain task or issue.
 Its changes are supposed to be merged into the master branch.

 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.

-IMPORTANT: Make sure to set the merge request WIP if you are not finished yet.
+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
+post.
 -->
--- a/.gitmodules
+++ b/.gitmodules
+[submodule "dune/copasi/common/ghc"]
+	path = ext/ghc
+	url = https://github.com/gulrak/filesystem
--- a/.travis.yml
+++ b/.travis.yml
@@ -32,8 +32,8 @@ before_install:
  - gcc --version
  - g++ --version
  # download muparser, gmp and libtiff as static libraries
-  - wget "https://github.com/lkeegan/libsbml-static/releases/latest/download/libsbml-static-$TRAVIS_OS_NAME.tgz"
-  - sudo tar xzvf libsbml-static-$TRAVIS_OS_NAME.tgz -C /
+  - 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
@@ -42,9 +42,10 @@ install:
  - echo 'CMAKE_FLAGS+=" -DDUNE_PYTHON_VIRTUALENV_PATH='"$PWD"'/ext/dune-python-venv"' >> dune.opts
  - echo 'CMAKE_FLAGS+=" -DCMAKE_DISABLE_FIND_PACKAGE_QuadMath=TRUE -DBUILD_TESTING=OFF"' >> dune.opts
  - echo 'CMAKE_FLAGS+=" -DDUNE_USE_ONLY_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release"' >> dune.opts
-  - echo 'CMAKE_FLAGS+=" -DF77=true -DCMAKE_PREFIX_PATH=/opt/libs"' >> dune.opts
-  - echo 'CMAKE_FLAGS+=" -Dmuparser_INCLUDE_DIR:PATH=/opt/libs/include -Dmuparser_LIBRARIES:FILEPATH=opt/libs/lib/libmuparser.a"' >> dune.opts
+  - echo 'CMAKE_FLAGS+=" -DF77=true -DCMAKE_PREFIX_PATH=/opt/smelibs"' >> dune.opts
+  - echo 'CMAKE_FLAGS+=" -Dmuparser_INCLUDE_DIR:PATH=/opt/smelibs/include -Dmuparser_LIBRARIES:FILEPATH=opt/smelibs/lib/libmuparser.a"' >> dune.opts
  - if [ "$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

--- a/CHANGELOG.md
+++ b/CHANGELOG.md
 # Changelog
+
 All notable changes to this project will be documented in this file.

 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
@@ -25,14 +26,37 @@ Types of changes
    Security      in case of vulnerabilities.
 -->

-## [Unreleased]
+## [Unreleased] ([git-diff][Unreleased-diff])
+
+## [0.3.0] ([git-diff][0.3.0-diff]) - 2020-10-07
+### Added
+- User documentation !28
+- Scape VTK write by omitting `[writer]` section !24
+- Added Explicit and Diagonally Runge-Kutta time solvers !25
+- 3D simulations are now possible !27
+### Changed
+- Improved errors when a config file is incorrect !25
+- Update meaningful logging values on the test ini file !25
+- Clean up logger output !25
+- Time stepping is now done outside the model class !25
+- Writer might write on different files on request !25
+- Move read/write responsibility to model state !25
+- States are now independent from models !25
+- Output files changed its name scheme !25
+- Configuration file changed its structure (see git diff on tests) !25
+### Removed
+- Coefficient mapper and its use on local operators !25
+- Remove the operator map of objects within the model class !25
+### Fixed
+- Violation of the One-Definition-Rule due to external linkage of `LocalOperatorApply` lambdas !23
+- Error on the gaussian equation used on comparisons !23

-## [0.2.0] - 2020-02-20
+## [0.2.0] ([git-diff][0.2.0-diff]) - 2020-02-20
 ### Added
 - Code documentation
 - Data Context concept for factories
 - Factory concept for arbitrary object instantiation
- Add factories for finite element and finite element mas
+- Add factories for finite element and finite element map
 - Brief installation instructions
 - Models can interpolate grid functions
 - Grid utilities to recognize and mark tripes of entities
@@ -55,6 +79,10 @@ Types of changes
 - [Semantic Versioning](https://semver.org/spec/v2.0.0.html)
 - Solver for reaction-diffusion systems in multiple compartments.

-[Unreleased]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v0.2.0...master
-[0.2.0]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v0.1.0...0.2.0
-[0.1.0]: https://gitlab.dune-project.org/copasi/dune-copasi/-/tags/v0.1.0
\ No newline at end of file
+[Unreleased-diff]: https://gitlab.dune-project.org/copasi/dune-copasi/compare/v0.3.0...master
+[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
+
+[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
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -24,6 +24,14 @@ dune_project()

 dune_enable_all_packages()

+set(USE_FALLBACK_FILESYSTEM no CACHE BOOL "Use bundled std::filesystem alternative (enable this for macOS older than 10.15)")
+if(USE_FALLBACK_FILESYSTEM)
+  add_subdirectory(ext/ghc)
+  install(FILES ext/ghc/include/ghc/filesystem.hpp
+          COMPONENT Development
+          DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/ghc")
+endif()
+
 add_subdirectory(src)
 add_subdirectory(dune)
 add_subdirectory(lib)
@@ -35,4 +43,4 @@ add_subdirectory(test)
 add_subdirectory(cmake/modules)

 # finalize the dune project, e.g. generating config.h etc.
-finalize_dune_project(GENERATE_CONFIG_H_CMAKE)
\ No newline at end of file
+finalize_dune_project(GENERATE_CONFIG_H_CMAKE)
--- a/CODE_OF_CONDUCT.md
+++ b/CODE_OF_CONDUCT.md
+# Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+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*.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+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.
+
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
+# Contributing
+
+When contributing to `DuneCopasi`, first discuss the change you wish to make via the
+[issue tracker](https://gitlab.dune-project.org/copasi/dune-copasi/-/issues).
+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,
+contributing single features can be summarized by following these steps:
+
+1. **ISSUE**: Create an issue in our
+   [Gitlab repository](https://gitlab.dune-project.org/copasi/dune-copasi)
+   containing a proposal for your modification. We call this a *task*. If your
+   proposal has a major change, create a *meta-task*, which should divide the
+   proposal in several tasks. Use a suitable issue template for your proposal.
+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
+   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)
+   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.
+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
+   details.
+6. If applicable, create a
+   [unit test](https://en.wikipedia.org/wiki/Unit_testing) that proves that your
+   implementation has the expected behavior. Ensure that the created test is
+   being run by the [Gitlab CI](https://docs.gitlab.com/ee/ci/pipelines.html).
+7. **TEST**: Once implementation and test are finished, ensure that your MR is
+   passing the different [pipelines](https://gitlab.dune-project.org/copasi/dune-copasi/-/tree/master/.ci).
+8. Update the [CHANGELOG](CHANGELOG.md) with changes to the interface. It
+   must include a link to the associated MR and a short description that
+   summarizes the changes.
+9. **REVIEW**: Send the MR to review for approval unmarking the WIP and
+   assigning a maintainer to review your modification.
+
+Check out our [code of conduct](CODE_OF_CONDUCT.md), please follow it in our interactions.
+
--- a/README.md
+++ b/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/SoilRos/dune-copasi.svg?branch=master)](https://travis-ci.org/SoilRos/dune-copasi)
-[![Build status](https://ci.appveyor.com/api/projects/status/6605joy2w17qvca8/branch/master?svg=true)](https://ci.appveyor.com/project/SoilRos/dune-copasi/history)
+[![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)
+[![Netlify Status](https://api.netlify.com/api/v1/badges/6fc6d371-87df-49b5-8e72-e1873fa5d54b/deploy-status)](https://app.netlify.com/sites/dune-copasi/deploys)

-# dune-copasi
+# DuneCopasi

 Solver for reaction-diffusion systems in multiple compartments

@@ -11,230 +12,8 @@ Solver for reaction-diffusion systems in multiple compartments
 * Neumann flux at the interface of compartments for variables with
   the same name on the two compartments
 * Easy to modify configuration file
- * Initial conditions can be a TIFF file or a math expression
- * Solved using the finite element or finite volume method
+ * Initial conditions can be a TIFF file or/and a math expression
+ * Using the finite element
 * Output in the VTK format
- * Currently it only supports 2D simulations

-This project is made under the umbrella of the
-[*Distributed and Unified Numerics Environment* `DUNE`](https://www.dune-project.org/) and the
-[*Biochemical System Simulator* `COPASI`](http://copasi.org/).
-Altought the rationale of the design is always driven by biochemical process (e.g. cell biology),
-this software is not limited to this scope and can be used for other processes involving reaction-diffusion systems.
-
-## Graphical User Interface for SBML files
-
-For those working in bio-informatics there exist a grafical user interface for [`SBML`](https://en.wikipedia.org/wiki/SBML) files!
-The GUI is able to convert non-spatial SBML models of bio-chemical reactions into
-2D spatial models, and to simulate them with `dune-copasi`:
-
-https://github.com/lkeegan/spatial-model-editor
-
-## Installation
-
-This requires that you have installed the following packages before the actual installation of `dune-copasi`.
-
-| Software | Version/Branch | Comments |
-| ---------| -------------- | -------- |
-| [CMake](https://cmake.org/) | 3.1 |
-| C++ compiler | [C++17](https://en.wikipedia.org/wiki/List_of_compilers#C++_compilers) |
-| [libTIFF](http://www.libtiff.org/) | 3.6.1 |
-| [muParser](https://beltoforion.de/article.php?a=muparser) | 2.2.5 |
-| [dune-common](https://gitlab.dune-project.org/copasi/dune-common) | releases/2.7 | https://gitlab.dune-project.org/core/dune-common
-| [dune-geometry](https://gitlab.dune-project.org/core/dune-geometry) | releases/2.7 | https://gitlab.dune-project.org/core/dune-geometry
-| [dune-grid](https://gitlab.dune-project.org/core/dune-grid) | releases/2.7 | https://gitlab.dune-project.org/core/dune-grid
-| [dune-uggrid](https://gitlab.dune-project.org/staging/dune-uggrid) | releases/2.7 | https://gitlab.dune-project.org/staging/dune-uggrid
-| [dune-istl](https://gitlab.dune-project.org/core/dune-istl) | releases/2.7 | https://gitlab.dune-project.org/core/dune-istl
-| [dune-localfunctions](https://gitlab.dune-project.org/core/dune-localfunctions) | releases/2.7 | https://gitlab.dune-project.org/core/dune-localfunctions
-| [dune-functions](https://gitlab.dune-project.org/staging/dune-functions) | releases/2.7 | https://gitlab.dune-project.org/staging/dune-functions
-| [dune-logging](https://gitlab.dune-project.org/staging/dune-logging) | support/dune-copasi (recursive) | https://gitlab.dune-project.org/copasi/dune-logging
-| [dune-typetree](https://gitlab.dune-project.org/copasi/dune-typetree) | support/dune-copasi | https://gitlab.dune-project.org/copasi/dune-typetree
-| [dune-pdelab](https://gitlab.dune-project.org/copasi/dune-pdelab) | support/dune-copasi | https://gitlab.dune-project.org/copasi/dune-pdelab
-| [dune-multidomaingrid](https://gitlab.dune-project.org/copasi/dune-multidomaingrid) | support/dune-copasi | https://gitlab.dune-project.org/copasi/dune-multidomaingrid
-
-The first four can be obtained by your prefered package manager in unix-like operating systems. e.g.
-
-```bash
-# if you are in a debian/ubuntu OS
-apt update
-apt install cmake gcc g++ libtiff-dev libmuparser-dev git
-
-# if you are in a macOS
-xcode-select --install # Apple Command Line Tools
-brew update
-brew install cmake gcc libtiff muparser git
-```
-
-Now, the dune modules (including `dune-copasi`) can be all checkout in a same folder and be installed in one go.
-
-```bash
-# prepare a folder to download and build dune modules
-mkdir ~/dune-modules && cd ~/dune-modules
-
-# fetch dependencies & dune-copasi in ~/dune-modules folder
-git clone -b releases/2.7 https://gitlab.dune-project.org/core/dune-common
-git clone -b releases/2.7 https://gitlab.dune-project.org/core/dune-geometry
-git clone -b releases/2.7 https://gitlab.dune-project.org/core/dune-grid
-git clone -b releases/2.7 https://gitlab.dune-project.org/staging/dune-uggrid
-git clone -b releases/2.7 https://gitlab.dune-project.org/core/dune-istl
-git clone -b releases/2.7 https://gitlab.dune-project.org/core/dune-localfunctions
-git clone -b releases/2.7 https://gitlab.dune-project.org/staging/dune-functions
-git clone -b support/dune-copasi --recursive https://gitlab.dune-project.org/copasi/dune-logging
-git clone -b support/dune-copasi https://gitlab.dune-project.org/copasi/dune-typetree
-git clone -b support/dune-copasi https://gitlab.dune-project.org/copasi/dune-pdelab
-git clone -b support/dune-copasi https://gitlab.dune-project.org/copasi/dune-multidomaingrid
-git clone -b master https://gitlab.dune-project.org/copasi/dune-copasi
-
-# configure and build dune modules
-./dune-common/bin/dunecontrol make all
-
-# install dune-copasi (this operation may requiere sudo)
-./dune-common/bin/dunecontrol --only=dune-copasi bexec make install
-
-# if you do not want to install dune-copasi system-wide, you can set
-# the CMAKE_INSTALL_PREFIX to a non restricted folder
-# see https://cmake.org/cmake/help/latest/variable/CMAKE_INSTALL_PREFIX.html
-
-# remove source and build files
-cd .. && rm -r ~/dune-modules
-```
-
-For further info on dune module installation process, please check out
-the [dune-project web page](https://www.dune-project.org/doc/installation/)
-
-## Usage
-
-If you installed `dune-copasi` system-wide, you should be able to call the program
-`dune_copasi_md` from your command line accompained with a configuration file.
-
-```bash
-dune_copasi_md config.ini
-```
-
-### Configuration File
-
-The configuration file follows [INI file format](https://en.wikipedia.org/wiki/INI_file).
-It should contain at least two sections: `grid`, and `model`, whereas a third section
-`logging` is optional.
-
-#### Grid
-
-The grid section is fairly simple as it only contains the path to a [gmsh file](http://gmsh.info/)
-and its initial refinement level:
-
-```ini
-[grid]
-file = my_gmsh_file.msh
-initial_level = 1
-```
-
-The grid should be formed by 2D traingles and squares where each *physical group* can only
-only be formed by one of these type. That is, each *physical group* can have different types of
-geometries, but whithin each *physical group* there cannot be more than one type. The GMSH file
-should be v2 and it should not contain the *physical group* identifiers at the begining of the file
-(this is a bug in the `dune-grid` reader).
-
-#### Model
-
-The model section starts with the definitions of the simulation time interval
-and the polynomal order of the local finite element (currently only supports `0`, `1` and `2`),
-where `0` refers for finite volume and higher for continuous galerking methods. This order refers
-to the domains composed with triangles. Domains compose with squares are always solved with the
-finite volume method.
-
-```ini
-[model]
-begin_time = 0.
-end_time = 10
-time_step = 0.1
-order = 1
-```
-
-The following is the definition of the compartments of the model.
-Each compartment corresponds to a *physical group* in the gmsh jargon.
-Although the gmsh format allows you to name such physical groups,
-we still need to assign them to a `dune-copasi` compartmet and for that
-we use the *physical group* index. Notice that `dune-copasi` uses 0-based
- indices while `gmsh` uses 1-based indices. In other words,
-`<gmsh_physical_group> = <dune_copasi_compartment> + 1`.
-Let's say for example that there is two *physical groups* in our gmsh file
-and we are going to use them as `nucleous` and `cytoplasm` compartments:
-
-```ini
-[model.compartments]
- # nucleous corresponds to the physical group 1 in the gmsh file
-nucleous  = 0
- # cytoplasm corresponds to the physical group 2 in the gmsh file
-cytoplasm = 0
-```
-
-Now, each of these compartments will define its own initial conditions,
-its diffusion-reaction system, and its vtk writter. For that, you have to expand
-the `model` section with the defined compartments, e.g. `model.nucleous` or `model.cytoplasm`.
-The subsection `initial`, `reaction`, `diffusion` and `operator` define the system variables
-and its properties. You can put as many variables as desired as long as they are the same
-in this three subsections. Notice that each variable defines a new diffusion-reaction partial
-differential equation associated with it.
-
-  * The `initial` subsection allow the initialization of each of the variables.
-  * The `diffusion` subsection defines the diffusion coefficient math
-  expression associated with each variable. It may only depend on the grid coordinates `x` and `y`.
-  * The `reaction` subsection defines the reaction part of each equation in the PDE.
-  Since this is the souce of non-linearities, it allows to be dependent on other defined variables
-  within the compartment. This section has to include yet another subsection called `jacobian`.
-  * The `reaction.jacobian` subsection must describe the
-  [jacobian matrix](https://en.wikipedia.org/wiki/Jacobian_matrix_and_determinant)
-  of the `reaction` part. It must follow the syntax of `d<var_i>_d<var_j>`, which
-  reads as the *partial derivate of `<var_i>` with respect to `<var_j>`*.
-  * The `operator` subsection is an experimental feature and we recommend to set all variables to the
-  same index, e.g. 0.
-  * Finally, the subsection `writer` will define the file name for the vtk output.
-
-For example, the following `mode.nucleous` section defines a [Gray-Scott
-model with `F=0.0420` and `k=0.0610`](http://mrob.com/pub/comp/xmorphia/F420/F420-k610.html):
-
-```ini
-[model.nucleous.initial]
-u = 0.5
-v = (x>0) && (x<0.5) && (y>0.) && (y<0.5) ? 1 : 0
-
-[model.nucleous.diffusion]
-u = 2e-5
-v = 2e-5/2
-
-[model.nucleous.reaction]
-u = -u*v^2+0.0420*(1-u)
-v = u*v^2-(0.0420+0.0610)*v
-
-[model.nucleous.reaction.jacobian]
-du_du = -v^2-0.0420
-du_dv = -2*u*v
-dv_du = v^2
-dv_dv = 2*u*v-(0.0420+0.0610)
-
-[model.nucleous.operator]
-u = 0
-v = 0
-
-[model.nucleous.writer]
-file_name = nucleous_output
-```
-The `model.cytoplasm` would have to be defined in similar way. An important aspect when working
-with different compartments is the interface fluxes. In `dune-copasi` thex fluxes are set
-automatically to [dirichlet-dirichlet](https://en.wikipedia.org/wiki/Dirichlet_boundary_condition)
-boundary conditions iff the variable is shared between the two intersecting domains. Further
-improvements will come for interface treatment.
-
-#### Logging
-
-The logging settings are directly forwarded to the `dune-logging` module. Please check
-its doxygen documentation for detailed information. A simple configuration is the following:
-
-```ini
-[logging]
-# possible levels: off, critical, error, waring, notice, info, debug, trace, all
-default.level = trace
-
-[logging.sinks.stdout]
-pattern = [{reldays:0>2}-{reltime:8%T}] [{backend}] {msg}
-```
\ No newline at end of file
+Get started [here](https://dune-copasi.netlify.app/docs/).
--- a/VERSION
+++ b/VERSION
-0.2.0
\ No newline at end of file
+0.3.0
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -7,14 +7,9 @@ clone_folder: C:\msys64\home\appveyor\dune-copasi
 install:
  - set PATH=C:\msys64\usr\bin;%PATH%
  # download muparser, gmp and libtiff as static libraries: install to C:\libs
-  - mkdir temp
-  - cd temp
-  - appveyor DownloadFile "https://github.com/lkeegan/libsbml-static/releases/latest/download/libsbml-static-windows.zip"
-  - 7z x libsbml-static-windows.zip
-  - mkdir C:\libs
-  - mv include C:\libs\.
-  - mv lib C:\libs\.
-  - dir "C:\libs"
+  - appveyor DownloadFile "https://github.com/spatial-model-editor/sme_deps_common/releases/latest/download/sme_deps_common_win64.tgz"
+  - tar xf sme_deps_common_win64.tgz -C /
+  - dir "C:\smelibs"
  - cd C:\msys64\home\appveyor

 before_build:
@@ -23,11 +18,11 @@ before_build:
  - echo CMAKE_FLAGS+=" -DCMAKE_DISABLE_FIND_PACKAGE_QuadMath=TRUE" >> C:\msys64\home\appveyor\dune.txt
  - echo CMAKE_FLAGS+=" -DBUILD_TESTING=OFF -DDUNE_USE_ONLY_STATIC_LIBS=ON " >> C:\msys64\home\appveyor\dune.txt
  - echo CMAKE_FLAGS+=" -DF77=true -DCMAKE_CXX_FLAGS='-Wa,-mbig-obj -static -static-libgcc -static-libstdc++' " >> C:\msys64\home\appveyor\dune.txt
-  - echo CMAKE_FLAGS+=" -DGMPXX_INCLUDE_DIR:PATH=C:/libs/include " >> C:\msys64\home\appveyor\dune.txt
-  - echo CMAKE_FLAGS+=" -DGMPXX_LIB:FILEPATH=C:/libs/lib/libgmpxx.a " >> C:\msys64\home\appveyor\dune.txt
-  - echo CMAKE_FLAGS+=" -DGMP_LIB:FILEPATH=C:/libs/lib/libgmp.a " >> C:\msys64\home\appveyor\dune.txt
-  - echo CMAKE_FLAGS+=" -DCMAKE_PREFIX_PATH=C:/libs " >> C:\msys64\home\appveyor\dune.txt
-  - echo CMAKE_FLAGS+=" -Dfmt_ROOT=C:/libs " >> C:\msys64\home\appveyor\dune.txt
+  - echo CMAKE_FLAGS+=" -DGMPXX_INCLUDE_DIR:PATH=C:/smelibs/include " >> C:\msys64\home\appveyor\dune.txt
+  - echo CMAKE_FLAGS+=" -DGMPXX_LIB:FILEPATH=C:/smelibs/lib/libgmpxx.a " >> C:\msys64\home\appveyor\dune.txt
+  - echo CMAKE_FLAGS+=" -DGMP_LIB:FILEPATH=C:/smelibs/lib/libgmp.a " >> C:\msys64\home\appveyor\dune.txt
+  - echo CMAKE_FLAGS+=" -DCMAKE_PREFIX_PATH=C:/smelibs " >> C:\msys64\home\appveyor\dune.txt
+  - echo CMAKE_FLAGS+=" -Dfmt_ROOT=C:/smelibs " >> C:\msys64\home\appveyor\dune.txt
  - echo MAKE_FLAGS="-j2 VERBOSE=1" >> C:\msys64\home\appveyor\dune.txt
  - type C:\msys64\home\appveyor\dune.txt
  - set DUNE_OPTIONS_FILE=dune.txt

--- a/cmake/modules/DuneCopasiMacros.cmake
+++ b/cmake/modules/DuneCopasiMacros.cmake
@@ -2,3 +2,4 @@

 find_package (muparser REQUIRED)
 find_package (TIFF REQUIRED)
+find_package (Filesystem)
\ No newline at end of file
--- a/cmake/modules/FindFilesystem.cmake
+++ b/cmake/modules/FindFilesystem.cmake
+# https://github.com/vector-of-bool/CMakeCM/blob/master/modules/FindFilesystem.cmake
+# commit 6cb8a6ada09eb40c271d2f83a032e03cd4005fa3
+# Distributed under the OSI-approved BSD 3-Clause License.  See accompanying
+# file Copyright.txt or https://cmake.org/licensing for details.
+
+#[=======================================================================[.rst:
+
+FindFilesystem
+##############
+
+This module supports the C++17 standard library's filesystem utilities. Use the
+:imp-target:`std::filesystem` imported target to
+
+Options
+*******
+
+The ``COMPONENTS`` argument to this module supports the following values:
+
+.. find-component:: Experimental
+    :name: fs.Experimental
+
+    Allows the module to find the "experimental" Filesystem TS version of the
+    Filesystem library. This is the library that should be used with the
+    ``std::experimental::filesystem`` namespace.
+
+.. find-component:: Final
+    :name: fs.Final
+
+    Finds the final C++17 standard version of the filesystem library.
+
+If no components are provided, behaves as if the
+:find-component:`fs.Final` component was specified.
+
+If both :find-component:`fs.Experimental` and :find-component:`fs.Final` are
+provided, first looks for ``Final``, and falls back to ``Experimental`` in case
+of failure. If ``Final`` is found, :imp-target:`std::filesystem` and all
+:ref:`variables <fs.variables>` will refer to the ``Final`` version.
+
+
+Imported Targets
+****************
+
+.. imp-target:: std::filesystem
+
+    The ``std::filesystem`` imported target is defined when any requested
+    version of the C++ filesystem library has been found, whether it is
+    *Experimental* or *Final*.
+
+    If no version of the filesystem library is available, this target will not
+    be defined.
+
+    .. note::
+        This target has ``cxx_std_17`` as an ``INTERFACE``
+        :ref:`compile language standard feature <req-lang-standards>`. Linking
+        to this target will automatically enable C++17 if no later standard
+        version is already required on the linking target.
+
+
+.. _fs.variables:
+
+Variables
+*********
+
+.. variable:: CXX_FILESYSTEM_IS_EXPERIMENTAL
+
+    Set to ``TRUE`` when the :find-component:`fs.Experimental` version of C++
+    filesystem library was found, otherwise ``FALSE``.
+
+.. variable:: CXX_FILESYSTEM_HAVE_FS
+
+    Set to ``TRUE`` when a filesystem header was found.
+
+.. variable:: CXX_FILESYSTEM_HEADER
+
+    Set to either ``filesystem`` or ``experimental/filesystem`` depending on
+    whether :find-component:`fs.Final` or :find-component:`fs.Experimental` was
+    found.
+
+.. variable:: CXX_FILESYSTEM_NAMESPACE
+
+    Set to either ``std::filesystem`` or ``std::experimental::filesystem``
+    depending on whether :find-component:`fs.Final` or
+    :find-component:`fs.Experimental` was found.
+
+
+Examples
+********
+
+Using `find_package(Filesystem)` with no component arguments:
+
+.. code-block:: cmake
+
+    find_package(Filesystem REQUIRED)
+
+    add_executable(my-program main.cpp)
+    target_link_libraries(my-program PRIVATE std::filesystem)
+
+
+#]=======================================================================]
+
+
+if(TARGET std::filesystem)
+    # This module has already been processed. Don't do it again.
+    return()
+endif()
+
+cmake_minimum_required(VERSION 3.10)
+
+include(CMakePushCheckState)
+include(CheckIncludeFileCXX)
+
+# If we're not cross-compiling, try to run test executables.
+# Otherwise, assume that compile + link is a sufficient check.
+if(CMAKE_CROSSCOMPILING)
+    include(CheckCXXSourceCompiles)
+    macro(_cmcm_check_cxx_source code var)
+        check_cxx_source_compiles("${code}" ${var})
+    endmacro()
+else()
+    include(CheckCXXSourceRuns)
+    macro(_cmcm_check_cxx_source code var)
+        check_cxx_source_runs("${code}" ${var})
+    endmacro()
+endif()
+
+cmake_push_check_state()
+
+set(CMAKE_REQUIRED_QUIET ${Filesystem_FIND_QUIETLY})
+
+# All of our tests required C++17 or later
+set(CMAKE_CXX_STANDARD 17)
+
+# Normalize and check the component list we were given
+set(want_components ${Filesystem_FIND_COMPONENTS})
+if(Filesystem_FIND_COMPONENTS STREQUAL "")
+    set(want_components Final)
+endif()
+
+# Warn on any unrecognized components
+set(extra_components ${want_components})
+list(REMOVE_ITEM extra_components Final Experimental)
+foreach(component IN LISTS extra_components)
+    message(WARNING "Extraneous find_package component for Filesystem: ${component}")
+endforeach()
+
+# Detect which of Experimental and Final we should look for
+set(find_experimental TRUE)
+set(find_final TRUE)
+if(NOT "Final" IN_LIST want_components)
+    set(find_final FALSE)
+endif()
+if(NOT "Experimental" IN_LIST want_components)
+    set(find_experimental FALSE)
+endif()
+
+if(find_final)
+    check_include_file_cxx("filesystem" _CXX_FILESYSTEM_HAVE_HEADER)
+    mark_as_advanced(_CXX_FILESYSTEM_HAVE_HEADER)
+    if(_CXX_FILESYSTEM_HAVE_HEADER)
+        # We found the non-experimental header. Don't bother looking for the
+        # experimental one.
+        set(find_experimental FALSE)
+    endif()
+else()
+    set(_CXX_FILESYSTEM_HAVE_HEADER FALSE)
+endif()
+
+if(find_experimental)
+    check_include_file_cxx("experimental/filesystem" _CXX_FILESYSTEM_HAVE_EXPERIMENTAL_HEADER)
+    mark_as_advanced(_CXX_FILESYSTEM_HAVE_EXPERIMENTAL_HEADER)
+else()
+    set(_CXX_FILESYSTEM_HAVE_EXPERIMENTAL_HEADER FALSE)
+endif()
+
+if(_CXX_FILESYSTEM_HAVE_HEADER)
+    set(_have_fs TRUE)
+    set(_fs_header filesystem)
+    set(_fs_namespace std::filesystem)
+    set(_is_experimental FALSE)
+elseif(_CXX_FILESYSTEM_HAVE_EXPERIMENTAL_HEADER)
+    set(_have_fs TRUE)
+    set(_fs_header experimental/filesystem)
+    set(_fs_namespace std::experimental::filesystem)
+    set(_is_experimental TRUE)
+else()
+    set(_have_fs FALSE)
+endif()
+
+set(CXX_FILESYSTEM_HAVE_FS ${_have_fs} CACHE BOOL "TRUE if we have the C++ filesystem headers")
+set(CXX_FILESYSTEM_HEADER ${_fs_header} CACHE STRING "The header that should be included to obtain the filesystem APIs")
+set(CXX_FILESYSTEM_NAMESPACE ${_fs_namespace} CACHE STRING "The C++ namespace that contains the filesystem APIs")
+set(CXX_FILESYSTEM_IS_EXPERIMENTAL ${_is_experimental} CACHE BOOL "TRUE if the C++ filesystem library is the experimental version")
+
+set(_found FALSE)
+
+if(CXX_FILESYSTEM_HAVE_FS)
+    # We have some filesystem library available. Do link checks
+    string(CONFIGURE [[
+        #include <cstdlib>
+        #include <@CXX_FILESYSTEM_HEADER@>
+
+        int main() {
+            auto cwd = @CXX_FILESYSTEM_NAMESPACE@::current_path();
+            printf("%s", cwd.c_str());
+            return EXIT_SUCCESS;
+        }
+    ]] code @ONLY)
+
+    # Check a simple filesystem program without any linker flags
+    _cmcm_check_cxx_source("${code}" CXX_FILESYSTEM_NO_LINK_NEEDED)
+
+    set(can_link ${CXX_FILESYSTEM_NO_LINK_NEEDED})
+
+    if(NOT CXX_FILESYSTEM_NO_LINK_NEEDED)
+        set(prev_libraries ${CMAKE_REQUIRED_LIBRARIES})
+        # Add the libstdc++ flag
+        set(CMAKE_REQUIRED_LIBRARIES ${prev_libraries} -lstdc++fs)
+        _cmcm_check_cxx_source("${code}" CXX_FILESYSTEM_STDCPPFS_NEEDED)
+        set(can_link ${CXX_FILESYSTEM_STDCPPFS_NEEDED})
+        if(NOT CXX_FILESYSTEM_STDCPPFS_NEEDED)
+            # Try the libc++ flag
+            set(CMAKE_REQUIRED_LIBRARIES ${prev_libraries} -lc++fs)
+            _cmcm_check_cxx_source("${code}" CXX_FILESYSTEM_CPPFS_NEEDED)
+            set(can_link ${CXX_FILESYSTEM_CPPFS_NEEDED})
+        endif()
+    endif()
+
+    if(can_link)
+        add_library(std::filesystem INTERFACE IMPORTED)
+        set_property(TARGET std::filesystem APPEND PROPERTY INTERFACE_COMPILE_FEATURES cxx_std_17)
+        set(_found TRUE)
+
+        if(CXX_FILESYSTEM_NO_LINK_NEEDED)
+            # Nothing to add...
+        elseif(CXX_FILESYSTEM_STDCPPFS_NEEDED)
+            set_property(TARGET std::filesystem APPEND PROPERTY INTERFACE_LINK_LIBRARIES -lstdc++fs)
+        elseif(CXX_FILESYSTEM_CPPFS_NEEDED)
+            set_property(TARGET std::filesystem APPEND PROPERTY INTERFACE_LINK_LIBRARIES -lc++fs)
+        endif()
+    endif()
+endif()
+
+cmake_pop_check_state()
+
+set(Filesystem_FOUND ${_found} CACHE BOOL "TRUE if we can run a program using std::filesystem" FORCE)
+
+if(Filesystem_FIND_REQUIRED AND NOT Filesystem_FOUND)
+    message(FATAL_ERROR "Cannot run simple program using std::filesystem")
+endif()
--- a/doc/docusaurus/README.md
+++ b/doc/docusaurus/README.md
+[![Netlify Status](https://api.netlify.com/api/v1/badges/6fc6d371-87df-49b5-8e72-e1873fa5d54b/deploy-status)](https://app.netlify.com/sites/dune-copasi/deploys)
+
+# DuneCopasi Website
+
+This website is built using [Docusaurus 2](https://v2.docusaurus.io/), a modern static website generator.
+
+### Installation
+
+```
+$ yarn
+```
+
+### Local Development
+
+```
+$ yarn start
+```
+
+This command starts a local development server and open up a browser window. Most changes are reflected live without having to restart the server.
+
+### Build
+
+```
+$ yarn build
+```
+
+This command generates static content into the `build` directory and can be served using any static contents hosting service.
+
+### Deployment
+
+This is automatically done by Netlify on every branch of the GitHub mirror. See
+https://app.netlify.com/teams/soilros/builds/.
--- a/doc/docusaurus/babel.config.js
+++ b/doc/docusaurus/babel.config.js
+module.exports = {
+  presets: [require.resolve('@docusaurus/core/lib/babel/preset')],
+};
--- a/doc/docusaurus/blog/2020-08-26-xx.md
+++ b/doc/docusaurus/blog/2020-08-26-xx.md
+---
+id: xx
+title: Xx Xx
+author: Xx Xx
+author_title: Xx Xx
+author_url: https://x.com/
+author_image_url: https://x.com/
+tags: [xx, yy]
+---
--- a/doc/docusaurus/docs/about.md
+++ b/doc/docusaurus/docs/about.md
+---
+id: about
+title: About
+sidebar_label: About
+---
+
+`DuneCopasi` is a library that provides numerical solutions of
+reaction-diffusion systems on single and multiple compartments. We do so by
+providing [C++ classes](api.md) that represent a solution state as well as the
+means to evolve them with respect to time. We also provide **ready-to-use**
+executables able to perform forward simulations. Both classes and executables
+shall be configured using a [Parameter Tree](param_tree.md).