Merge branch 'develop' into adaptivity-switch

.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
 

.markdown-link-check-config.json

@@ -1,3 +1,8 @@
 {
-  "aliveStatusCodes": [429, 200]
-}
+  "aliveStatusCodes": [429, 200],
+  "ignorePatterns": [
+    {
+      "pattern": "*.html"
+    }
+  ]
+}

.pre-commit-config.yaml

@@ -12,8 +12,10 @@ repos:
   rev: 22.12.0
   hooks:
     - id: black
-# isort for python imports
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+- repo: https://github.com/precice/precice-pre-commit-hooks
+  rev: 'v3.3'
   hooks:
-    - id: isort
+  - id: format-precice-config
+    files: "^.*/precice-config.xml"
+  - id: check-image-prefix
+    args: [ --prefix=docs-tooling-micro-manager- ]

docs/README.md

@@ -9,7 +9,7 @@ summary: A tool to manage many micro simulations and couple them to a macro simu
 
 The Micro Manager manages many simulations on a micro scale and couples them to one simulation on a macro scale. For the coupling itself, it heavily relies on the coupling library [preCICE](https://precice.org/index.html).
 
-![Micro Manager strategy schematic](images/tooling-micro-manager-manager-solution.png)
+![Micro Manager strategy schematic](images/docs-tooling-micro-manager-manager-solution.png)
 
 ## What can it do?
 

examples/cpp-dummy/.gitignore

@@ -8,4 +8,4 @@ precice-run/
 __pycache__
 
 # Compiled files
-*.so
+*.so

examples/cpp-dummy/run_micro_manager.py

@@ -2,11 +2,14 @@
 Script to run the Micro Manager
 """
 
-from micro_manager import MicroManager
 from argparse import ArgumentParser
 
+from micro_manager import MicroManager
+
 parser = ArgumentParser()
-parser.add_argument("--config", required=True, help="Path to the micro manager configuration file")
+parser.add_argument(
+    "--config", required=True, help="Path to the micro manager configuration file"
+)
 args = parser.parse_args()
 
 manager = MicroManager(args.config)

examples/macro_dummy.py

@@ -33,19 +33,27 @@ def main():
     vertex_ids = interface.set_mesh_vertices(read_mesh_name, coords)
 
     write_scalar_data = np.zeros(nv)
-    write_vector_data = np.zeros((nv, interface.get_data_dimensions(write_mesh_name, "macro-vector-data")))
+    write_vector_data = np.zeros(
+        (nv, interface.get_data_dimensions(write_mesh_name, "macro-vector-data"))
+    )
 
     for i in range(nv):
         write_scalar_data[i] = i
-        for d in range(interface.get_data_dimensions(write_mesh_name, "macro-vector-data")):
+        for d in range(
+            interface.get_data_dimensions(write_mesh_name, "macro-vector-data")
+        ):
             write_vector_data[i, d] = i
 
     if interface.requires_initial_data():
         for name, dim in write_data_names.items():
             if dim == 0:
-                interface.write_data(write_mesh_name, name, vertex_ids, write_scalar_data)
+                interface.write_data(
+                    write_mesh_name, name, vertex_ids, write_scalar_data
+                )
             elif dim == 1:
-                interface.write_data(write_mesh_name, name, vertex_ids, write_vector_data)
+                interface.write_data(
+                    write_mesh_name, name, vertex_ids, write_vector_data
+                )
 
     # initialize preCICE
     interface.initialize()
@@ -61,13 +69,19 @@ def main():
 
         for name, dim in read_data_names.items():
             if dim == 0:
-                read_scalar_data = interface.read_data(read_mesh_name, name, vertex_ids, 1)
+                read_scalar_data = interface.read_data(
+                    read_mesh_name, name, vertex_ids, 1
+                )
             elif dim == 1:
-                read_vector_data = interface.read_data(read_mesh_name, name, vertex_ids, 1)
+                read_vector_data = interface.read_data(
+                    read_mesh_name, name, vertex_ids, 1
+                )
 
         write_scalar_data[:] = read_scalar_data[:]
         for i in range(nv):
-            for d in range(interface.get_data_dimensions(read_mesh_name, "micro-vector-data")):
+            for d in range(
+                interface.get_data_dimensions(read_mesh_name, "micro-vector-data")
+            ):
                 write_vector_data[i, d] = read_vector_data[i, d]
                 if t > 1:  # to trigger adaptivity after some time
                     # ensure that the data is different from the previous time step
@@ -76,9 +90,13 @@ def main():
 
         for name, dim in write_data_names.items():
             if dim == 0:
-                interface.write_data(write_mesh_name, name, vertex_ids, write_scalar_data)
+                interface.write_data(
+                    write_mesh_name, name, vertex_ids, write_scalar_data
+                )
             elif dim == 1:
-                interface.write_data(write_mesh_name, name, vertex_ids, write_vector_data)
+                interface.write_data(
+                    write_mesh_name, name, vertex_ids, write_vector_data
+                )
 
         # do the coupling
         interface.advance(dt)
@@ -96,5 +114,5 @@ def main():
     interface.finalize()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

examples/precice-config-adaptivity.xml

@@ -5,7 +5,7 @@
     <log>
 	<sink type="stream" output="stdout"  filter= "%Severity% > debug" enabled="true" />
     </log>
-  
+
     <data:scalar name="macro-scalar-data"/>
     <data:vector name="macro-vector-data"/>
     <data:scalar name="micro-scalar-data"/>