Merge pull request #57 from precice/micro-manager-v0.3.0

Release v0.3.0

.github/workflows/check-links.yml

@@ -0,0 +1,14 @@
+name: Check links (manual)
+on: workflow_dispatch
+jobs:
+  check_links:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+      - 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'

.github/workflows/check-markdown.yml

@@ -0,0 +1,13 @@
+name: Lint docs
+on: [push, pull_request]
+jobs:
+  check_md:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+      - name: Lint markdown files (markdownlint)
+        uses: articulate/actions-markdownlint@v1
+        with:
+          config: .markdownlint.json
+          files: '.'

.github/workflows/check-pep8.yml

@@ -2,7 +2,8 @@ name: autopep8
 on:
   push:
     branches:
-      - "*"
+      - main
+      - develop
   pull_request:
     branches:
       - "*"

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

@@ -0,0 +1,105 @@
+name: Test adaptivity
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - "*"
+jobs:  
+  integration_test:
+    name: Run integration test
+    runs-on: ubuntu-latest
+    container: precice/precice
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          path: micro-manager
+
+      - 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
+
+      - name: Install Micro Manager
+        working-directory: micro-manager
+        run: pip3 install --user .
+
+      - name: Run integration test with local adaptivity
+        timeout-minutes: 3
+        working-directory: micro-manager/tests/integration/test_unit_cube
+        run: python3 unit_cube.py & python3 run_micro_manager.py --config micro-manager-config-local-adaptivity.json
+
+      - name: Run integration test serially with global adaptivity
+        timeout-minutes: 3
+        working-directory: micro-manager/tests/integration/test_unit_cube
+        run: python3 unit_cube.py & python3 run_micro_manager.py --config micro-manager-config-global-adaptivity.json
+
+  unit_tests_serial:
+    name: Run unit tests (serial variants)
+    runs-on: ubuntu-latest
+    container: precice/precice
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+        with:
+          path: micro-manager
+
+      - 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
+
+      - name: Install Micro Manager
+        working-directory: micro-manager
+        run: pip3 install --user .
+
+      - name: Run unit tests
+        working-directory: micro-manager/tests/unit
+        run: python3 -m unittest test_adaptivity_serial.py
+
+  unit_tests_parallel:
+    name: Run unit tests (parallel variants)
+    runs-on: ubuntu-latest
+    container: precice/precice
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+        with:
+          path: micro-manager
+
+      - name: Install sudo for MPI
+        working-directory: micro-manager
+        run: |
+          apt-get -qq update
+          apt-get -qq install sudo
+
+      - name: Use mpi4py
+        uses: mpi4py/setup-mpi@v1
+
+      - name: Add user precice
+        run: useradd -m -s /bin/bash precice
+
+      - 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
+          su -c "python -m pip install --upgrade pip" precice
+          su -c "pip install setuptools wheel twine" precice
+
+      - name: Install Micro Manager
+        working-directory: micro-manager
+        run: su -c "pip3 install --user ." precice
+
+      - name: Run unit tests
+        working-directory: micro-manager/tests/unit
+        run: su -c "mpiexec -n 2 python3 -m unittest test_adaptivity_parallel.py" precice

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

@@ -0,0 +1,83 @@
+name: Test domain decomposition
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - "*"
+jobs:  
+  integration_test:
+    name: Run integration tests
+    runs-on: ubuntu-latest
+    container: precice/precice
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          path: micro-manager
+
+      - name: Install sudo for MPI
+        working-directory: micro-manager
+        run: |
+          apt-get -qq update
+          apt-get -qq install sudo
+
+      - name: Use mpi4py
+        uses: mpi4py/setup-mpi@v1
+
+      - name: Add user precice
+        run: useradd -m -s /bin/bash precice
+
+      - name: Install Dependencies
+        working-directory: micro-manager
+        run: |
+          apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config
+          su -c "python -m pip install --upgrade pip" precice
+          su -c "pip install setuptools wheel twine" precice
+
+      - name: Install micro-manager
+        working-directory: micro-manager
+        run: su -c "pip3 install --user ." precice
+
+      - name: Run integration test (variant 1)
+        timeout-minutes: 3
+        working-directory: micro-manager/tests/integration
+        run: |
+          chown -R precice test_unit_cube/
+          cd test_unit_cube/
+          su -c "mpiexec -n 2 python3 run_micro_manager.py --config micro-manager-config-parallel-1.json & python3 unit_cube.py" precice
+      
+      - name: Run integration test (variant 2)
+        timeout-minutes: 3
+        working-directory: micro-manager/tests/integration
+        run: |
+          cd test_unit_cube/
+          su -c "mpiexec -n 6 --oversubscribe python3 run_micro_manager.py --config micro-manager-config-parallel-2.json & python3 unit_cube.py" precice
+
+  unit_tests:
+    name: Run unit tests
+    runs-on: ubuntu-latest
+    container: precice/precice
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+        with:
+          path: micro-manager
+
+      - 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
+
+      - name: Install Micro Manager
+        working-directory: micro-manager
+        run: pip3 install --user .
+
+      - name: Run unit tests
+        working-directory: micro-manager/tests/unit
+        run: python3 -m unittest test_domain_decomposition.py

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

@@ -1,30 +1,58 @@
-name: Run macro-micro dummy case
+name: Run macro-micro dummy
 on:
   push:
     branches:
-      - "*"
+      - main
+      - develop
   pull_request:
     branches:
       - "*"
 jobs:  
-  run_macro_micro_dummy:
-    name: Run macro-micro dummy
+  run_dummy:
+    name: Run dummy
     runs-on: ubuntu-latest
     container: precice/precice
     steps:
+
       - name: Checkout Repository
-        uses: actions/checkout@v2      
+        uses: actions/checkout@v3
+        with:
+          path: micro-manager
+
       - 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
+          apt-get -qq install sudo
           python -m pip install --upgrade pip
           pip install setuptools wheel twine
-      - name: Install pyprecice
-        run: pip3 install --user pyprecice
+
       - name: Install micro-manager
+        working-directory: micro-manager
         run: pip3 install --user .
-      - name: Run macro-micro dummy
+
+      - 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
+
+      - 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
+
+      - name: Run c++ macro-micro dummy
+        timeout-minutes: 3
+        working-directory: micro-manager/examples
         run: |
-          cd examples/macro-micro-dummy/
-          python3 macro_dummy.py & python3 run_micro_manager.py
+          cd cpp-dummy/
+          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
+
+      - 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

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

@@ -0,0 +1,29 @@
+name: Run unit tests
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - "*"
+jobs:
+  unit-tests:
+    runs-on: ubuntu-latest
+    container: precice/precice
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          path: micro-manager
+
+      - name: Install Micro Manager and uninstall pyprecice
+        working-directory: micro-manager
+        run: |
+          apt-get -qq update
+          apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config
+          python3 -m pip install --user .
+          python3 -m pip uninstall -y pyprecice
+
+      - name: Run unit tests
+        working-directory: micro-manager/tests/unit
+        run: python3 -m unittest test_micro_manager.py

.github/workflows/update-website.yml

@@ -0,0 +1,22 @@
+name: Update website
+on:
+  push:
+    branches:
+      - 'develop'
+    paths:
+      - 'docs/**'
+jobs:
+  trigger:
+    runs-on: ubuntu-latest
+    env:
+      WORKFLOW_FILENAME: update-submodules.yml
+    steps:
+    - name: Trigger workflow
+      run: |
+        curl \
+        --request POST \
+        --url https://api.github.com/repos/precice/precice.github.io/actions/workflows/$WORKFLOW_FILENAME/dispatches \
+        --header "authorization: token ${{ secrets.WORKFLOW_DISPATCH_TOKEN }}" \
+        --header "Accept: application/vnd.github.v3+json" \
+        --data '{"ref":"master"}' \
+        --fail

.gitignore

@@ -4,7 +4,14 @@ __pycache__
 
 # Building artifacts
 build
+micro_manager_precice.egg-info/
 micro_manager.egg-info/
 
 # Packaging artifacts
 dist
+
+# vscode
+.vscode
+
+# Tests output
+*.log

.markdown-link-check-config.json

@@ -0,0 +1,3 @@
+{
+  "aliveStatusCodes": [429, 200]
+}

.markdownlint.json

@@ -0,0 +1,5 @@
+{
+    "MD013": false,
+    "MD033": false,
+    "MD034": false
+}

CHANGELOG.md

@@ -2,9 +2,18 @@
 
 ## latest
 
+## v0.3.0
+
+- Add global variant to adaptivity (still experimental) https://github.com/precice/micro-manager/pull/42
+- Add norm-based (L1 and L2) support for functions in similarity distance calculation with absolute and relative variants https://github.com/precice/micro-manager/pull/40
+- New domain decomposition strategy based on user input of number of processors along each axis https://github.com/precice/micro-manager/pull/41
+- Add pickling support for C++ solver dummy https://github.com/precice/micro-manager/pull/30
+- Add C++ solver dummy to show how a C++ micro simulation can be controlled by the Micro Manager https://github.com/precice/micro-manager/pull/22
+- Add local adaptivity https://github.com/precice/micro-manager/pull/21
+
 ## v0.2.1
 
-- Fixing the broken action workflow `run-macro-micro-dummy` 
+- Fixing the broken action workflow `run-macro-micro-dummy`
 
 ## v0.2.0