Release v0.5.0

.github/pull_request_template.md

@@ -0,0 +1,8 @@
+<!-- Add a short description of your contribution here. Skip this if the title is self-explanatory -->
+
+Checklist:
+
+- [ ] I made sure that the CI passed before I ask for a review.
+- [ ] I added a summary of the changes (compared to the last release) in the `CHANGELOG.md`.
+- [ ] If necessary, I made changes to the documentation and/or added new content.
+- [ ] I will remember to squash-and-merge, providing a useful summary of the changes of this PR.

.github/workflows/pythonpublish.yml

@@ -15,13 +15,15 @@ jobs:
       with:
         python-version: '3.x'
     - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+      uses: BSFishy/pip-action@v1
+      with:
+        packages: |
+          twine
+          build
     - name: Build and publish
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
       run: |
-        python setup.py sdist
+        pyproject-build
         twine upload dist/*

.github/workflows/run-adaptivity-test.yml

@@ -7,14 +7,14 @@ on:
   pull_request:
     branches:
       - "*"
-jobs:  
+jobs:
   adaptivity_integration_tests:
     name: Run adaptivity integration tests
     runs-on: ubuntu-latest
     container: precice/precice:nightly
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: micro-manager
 
@@ -23,34 +23,33 @@ jobs:
         run: |
           apt-get -qq update
           apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config
-          python -m pip install --upgrade pip
-          pip install setuptools wheel
+          pip3 install --upgrade pip
 
       - name: Install Micro Manager
         working-directory: micro-manager
-        run: pip3 install --user .
+        run: pip3 install .
 
       - name: Run integration test with local adaptivity
         timeout-minutes: 3
         working-directory: micro-manager/tests/integration/test_unit_cube
         run: |
-          export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
-          python3 unit_cube.py & python3 run_micro_manager.py --config micro-manager-config-local-adaptivity.json
+          micro-manager-precice micro-manager-config-local-adaptivity.json &
+          python3 unit_cube.py
 
       - name: Run integration test with global adaptivity
         timeout-minutes: 3
         working-directory: micro-manager/tests/integration/test_unit_cube
         run: |
-          export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
-          python3 unit_cube.py & python3 run_micro_manager.py --config micro-manager-config-global-adaptivity.json
+          micro-manager-precice micro-manager-config-global-adaptivity.json &
+          python3 unit_cube.py
 
   adaptivity_unit_tests_serial:
     name: Run adaptivity unit tests in serial
     runs-on: ubuntu-latest
     container: precice/precice:nightly
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: micro-manager
 
@@ -59,8 +58,7 @@ jobs:
         run: |
           apt-get -qq update
           apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config
-          python -m pip install --upgrade pip
-          pip install setuptools wheel
+          pip3 install --upgrade pip
 
       - name: Install Micro Manager
         working-directory: micro-manager
@@ -76,7 +74,7 @@ jobs:
     container: precice/precice:nightly
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: micro-manager
 
@@ -94,8 +92,7 @@ jobs:
         run: |
           apt-get -qq update
           apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config
-          python -m pip install --upgrade pip
-          pip install setuptools wheel twine
+          pip3 install --upgrade pip
 
       - name: Install Micro Manager
         working-directory: micro-manager

.github/workflows/run-checks.yml

@@ -0,0 +1,55 @@
+name: Run checks for markdown, links, and pre-commit
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - "*"
+jobs:
+  check_md:
+    name: Lint markdown files
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Lint markdown files (markdownlint)
+        uses: articulate/actions-markdownlint@v1
+        with:
+          config: .markdownlint.json
+          files: '.'
+
+  check_links:
+    name: Check links in markdown files
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Check links in markdown files (markdown-link-check)
+        uses: gaurav-nelson/github-action-markdown-link-check@v1
+        with:
+          use-quiet-mode: 'yes'
+          use-verbose-mode: 'no'
+          config-file: '.markdown-link-check-config.json'
+
+  precommit:
+    name: pre-commit checks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+          check-latest: true
+      - name: Install pre-commit
+        run: pip install pre-commit
+      - name: Run checks
+        run: pre-commit run -a -v
+      - name: Git status
+        if: always()
+        run: git status
+      - name: Full diff
+        if: always()
+        run: git diff

.github/workflows/run-domain-decomposition-tests.yml

@@ -7,14 +7,14 @@ on:
   pull_request:
     branches:
       - "*"
-jobs:  
+jobs:
   domain_decomposition_integration_tests:
     name: Run domain decomposition integration tests
     runs-on: ubuntu-latest
     container: precice/precice:nightly
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: micro-manager
 
@@ -30,31 +30,35 @@ jobs:
       - name: Install Dependencies
         working-directory: micro-manager
         run: |
+          apt-get -qq update
           apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config
-          python -m pip install --upgrade pip
-          pip install setuptools wheel twine
+          pip3 install --upgrade pip
 
       - name: Install micro-manager
         working-directory: micro-manager
-        run: pip3 install --user .
+        run: pip3 install .
 
-      - name: Run integration test (variant 1)
+      - name: Run integration test (2 processes)
         timeout-minutes: 3
         working-directory: micro-manager/tests/integration/test_unit_cube
-        run: mpiexec -n 2 --allow-run-as-root python3 run_micro_manager.py --config micro-manager-config-parallel-1.json & python3 unit_cube.py
-
-      - name: Run integration test (variant 2)
+        run: |
+          mpiexec -n 2 --allow-run-as-root micro-manager-precice micro-manager-config-parallel-1.json &
+          python3 unit_cube.py
+
+      - name: Run integration test (6 processes)
         timeout-minutes: 3
         working-directory: micro-manager/tests/integration/test_unit_cube
-        run: mpiexec -n 6 --oversubscribe --allow-run-as-root python3 run_micro_manager.py --config micro-manager-config-parallel-2.json & python3 unit_cube.py
+        run: |
+          mpiexec -n 6 --oversubscribe --allow-run-as-root micro-manager-precice micro-manager-config-parallel-2.json &
+          python3 unit_cube.py
 
   domain_decomposition_unit_tests:
     name: Run domain decomposition unit tests
     runs-on: ubuntu-latest
     container: precice/precice:nightly
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: micro-manager
 
@@ -63,8 +67,7 @@ jobs:
         run: |
           apt-get -qq update
           apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config
-          python -m pip install --upgrade pip
-          pip install setuptools wheel
+          pip3 install --upgrade pip
 
       - name: Install Micro Manager
         working-directory: micro-manager

.github/workflows/run-macro-micro-dummy.yml

@@ -7,15 +7,15 @@ on:
   pull_request:
     branches:
       - "*"
-jobs:  
+jobs:
   run_dummy:
     name: Run dummy
     runs-on: ubuntu-latest
     container: precice/precice:nightly
     steps:
 
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: micro-manager
 
@@ -25,22 +25,26 @@ jobs:
           apt-get -qq update
           apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config
           apt-get -qq install sudo
-          python -m pip install --upgrade pip
-          pip install setuptools wheel twine
+          pip3 install --upgrade pip
 
       - name: Install micro-manager
         working-directory: micro-manager
-        run: pip3 install --user .
+        run: |
+          pip3 install .
 
       - name: Run python macro-micro dummy
         timeout-minutes: 3
         working-directory: micro-manager/examples
-        run: python3 python-dummy/run_micro_manager.py --config micro-manager-config.json & python3 macro_dummy.py
+        run: |
+          micro-manager-precice micro-manager-python-config.json &
+          python3 macro_dummy.py
 
       - name: Run adaptive python macro-micro dummy
         timeout-minutes: 3
         working-directory: micro-manager/examples
-        run: python3 python-dummy/run_micro_manager.py --config micro-manager-adaptivity-config.json & python3 macro_dummy.py
+        run: |
+          micro-manager-precice micro-manager-python-adaptivity-config.json &
+          python3 macro_dummy.py
 
       - name: Run c++ macro-micro dummy
         timeout-minutes: 3
@@ -50,9 +54,12 @@ jobs:
           pip install pybind11
           c++ -O3 -Wall -shared -std=c++11 -fPIC $(python3 -m pybind11 --includes) micro_cpp_dummy.cpp -o micro_dummy$(python3-config --extension-suffix)
           cd ../
-          python3 cpp-dummy/run_micro_manager.py --config micro-manager-config.json & python3 macro_dummy.py
+          micro-manager-precice micro-manager-cpp-config.json &
+          python3 macro_dummy.py
 
       - name: Run adaptive c++ macro-micro dummy
         timeout-minutes: 3
         working-directory: micro-manager/examples
-        run: python3 cpp-dummy/run_micro_manager.py --config micro-manager-adaptivity-config.json & python3 macro_dummy.py
+        run: |
+          micro-manager-precice micro-manager-cpp-adaptivity-config.json &
+          python3 macro_dummy.py