Update GitHub Actions workflow files

.github/workflows/pythonpublish.yml

@@ -9,9 +9,9 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

.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
 
@@ -50,7 +50,7 @@ jobs:
     container: precice/precice:nightly
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: micro-manager
 
@@ -76,7 +76,7 @@ jobs:
     container: precice/precice:nightly
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: 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
 
@@ -42,7 +42,7 @@ jobs:
         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)
         timeout-minutes: 3
         working-directory: micro-manager/tests/integration/test_unit_cube
@@ -54,7 +54,7 @@ jobs:
     container: precice/precice:nightly
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: 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
 

.github/workflows/run-unit-tests.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     container: precice/precice:nightly
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: micro-manager