Release v0.9.0

.github/workflows/check-coverage.yml

@@ -0,0 +1,108 @@
+name: Check test coverage
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - "*"
+
+jobs:
+  coverage:
+    name: Run test coverage check
+    runs-on: ubuntu-latest
+    container: precice/precice:nightly
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          path: micro-manager
+
+      - name: Install dependencies
+        run: |
+          apt-get -qq update
+          apt-get -qq install python3-dev python3-venv git pkg-config
+          apt-get -qq install wget build-essential
+
+      - name: Load Cache OpenMPI 5
+        id: ompi-cache-load
+        uses: actions/cache/restore@v5
+        with:
+          path: ~/openmpi
+          key: openmpi-v5-${{ runner.os }}-build
+
+      - name: Build OpenMPI 5
+        if: steps.ompi-cache-load.outputs.cache-hit != 'true'
+        run: |
+          wget https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.gz
+          tar -xzf openmpi-5.0.5.tar.gz
+          cd openmpi-5.0.5
+          mkdir -p ~/openmpi
+          ./configure --prefix=$HOME/openmpi
+          make -j$(nproc)
+          make install
+
+      - name: Save OpenMPI 5 to cache
+        if: steps.ompi-cache-load.outputs.cache-hit != 'true'
+        uses: actions/cache/save@v5
+        with:
+          path: ~/openmpi
+          key: openmpi-v5-${{ runner.os }}-build
+
+      - name: Configure OpenMPI
+        run: |
+          cp -r ~/openmpi/* /usr/local/
+          ldconfig
+          which mpiexec
+          mpiexec --version
+
+      - name: Create a virtual environment and install Micro Manager with coverage
+        timeout-minutes: 6
+        working-directory: micro-manager
+        run: |
+          python3 -m venv .venv
+          . .venv/bin/activate
+          pip install coverage
+          pip install .[sklearn,snapshot]
+          pip uninstall -y pyprecice
+
+      - name: Run serial unit tests with coverage
+        working-directory: micro-manager/tests/unit
+        env:
+          PYTHONPATH: .
+        run: |
+          . ../../.venv/bin/activate
+          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_micro_manager
+          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_micro_simulation_crash_handling
+          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_adaptivity_serial
+          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_domain_decomposition
+          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_interpolation
+          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_hdf5_functionality
+          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_snapshot_computation
+          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_micro_simulation
+
+      - name: Run tasking unit tests with coverage
+        working-directory: micro-manager/tests/unit
+        env:
+          PYTHONPATH: .
+          OMPI_ALLOW_RUN_AS_ROOT: "1"
+          OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: "1"
+        run: |
+          . ../../.venv/bin/activate
+          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_tasking
+
+      - name: Run parallel unit tests with coverage
+        working-directory: micro-manager/tests/unit
+        run: |
+          . ../../.venv/bin/activate
+          mpirun -n 2 --allow-run-as-root -x PYTHONPATH=. python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_adaptivity_parallel
+          mpirun -n 2 --allow-run-as-root -x PYTHONPATH=. python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_load_balancing
+
+      - name: Combine coverage data
+        working-directory: micro-manager/tests/unit
+        run: |
+          . ../../.venv/bin/activate
+          python3 -m coverage combine
+          python3 -m coverage report --format=total | python3 ../../check_coverage.py

.github/workflows/release.yml

@@ -17,7 +17,7 @@ jobs:
       - run: pip install --upgrade build
       - name: Build package
         run: pyproject-build
-      - uses: actions/upload-artifact@v6
+      - uses: actions/upload-artifact@v7
         with:
           name: dist
           path: dist
@@ -33,7 +33,7 @@ jobs:
       id-token: write
     steps:
       - name: Download package
-        uses: actions/download-artifact@v7
+        uses: actions/download-artifact@v8
         with:
           name: dist
           path: dist

.github/workflows/run-adaptivity-tests-parallel.yml

@@ -59,14 +59,20 @@ jobs:
         with:
           path: micro-manager
 
-      - name: Install sudo for MPI
-        working-directory: micro-manager
-        run: |
-          apt-get -qq update
-          apt-get -qq install sudo
+      - name: Load Cache OpenMPI 5
+        id: ompi-cache-load
+        uses: actions/cache/restore@v5
+        with:
+          path: ~/openmpi
+          key: openmpi-v5-${{ runner.os }}-build
+          # If this fails, cache gets built in run-unit-tests
 
-      - name: Use mpi4py
-        uses: mpi4py/setup-mpi@v1
+      - name: Configure OpenMPI
+        run: |
+          cp -r ~/openmpi/* /usr/local/
+          ldconfig
+          which mpiexec
+          mpiexec --version
 
       - name: Install Dependencies
         working-directory: micro-manager
@@ -94,12 +100,12 @@ jobs:
         run: |
           . .venv/bin/activate
           cd tests/unit
-          mpiexec -n 2 --allow-run-as-root python3 -m unittest test_global_adaptivity_lb.py
+          mpiexec -n 2 --allow-run-as-root python3 -m unittest test_load_balancing.py
 
-      - name: Run load balancing tests with 4 ranks
+      - name: Run load balancing unit tests with 4 ranks
         timeout-minutes: 3
         working-directory: micro-manager
         run: |
           . .venv/bin/activate
           cd tests/unit
-          mpiexec -n 4 --allow-run-as-root --oversubscribe python3 -m unittest test_global_adaptivity_lb.py
+          mpiexec -n 4 --oversubscribe --allow-run-as-root python3 -m unittest test_load_balancing.py

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

@@ -20,6 +20,40 @@ jobs:
         run: |
           apt-get -qq update
           apt-get -qq install python3-dev python3-venv git pkg-config
+          apt-get -qq install wget build-essential
+
+      - name: Load Cache OpenMPI 5
+        id: ompi-cache-load
+        uses: actions/cache/restore@v5
+        with:
+          path: ~/openmpi
+          key: openmpi-v5-${{ runner.os }}-build
+
+      - name: Build OpenMPI 5
+        if: steps.ompi-cache-load.outputs.cache-hit != 'true'
+        run: |
+          wget https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.gz
+          tar -xzf openmpi-5.0.5.tar.gz
+          cd openmpi-5.0.5
+          mkdir -p ~/openmpi
+          ./configure --prefix=$HOME/openmpi
+          make -j$(nproc)
+          make install
+
+      - name: Save OpenMPI 5 to cache
+        if: steps.ompi-cache.outputs.cache-hit != 'true'
+        id: ompi-cache-store
+        uses: actions/cache/save@v5
+        with:
+          path: ~/openmpi
+          key: openmpi-v5-${{ runner.os }}-build
+
+      - name: Configure OpenMPI
+        run: |
+          cp -r ~/openmpi/* /usr/local/
+          ldconfig
+          which mpiexec
+          mpiexec --version
 
       - name: Create a virtual environment and install Micro Manager in it
         timeout-minutes: 6
@@ -37,6 +71,16 @@ jobs:
           cd tests/unit
           python3 -m unittest test_micro_manager.py
 
+      - name: Install Micro Manager and run tasking unit test
+        working-directory: micro-manager
+        env:
+          OMPI_ALLOW_RUN_AS_ROOT: "1"
+          OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: "1"
+        run: |
+          . .venv/bin/activate
+          cd tests/unit
+          python3 -m unittest test_tasking.py
+
       - name: Install Micro Manager and run interpolation unit test
         working-directory: micro-manager
         run: |

.github/workflows/test-pip-install.yml

@@ -0,0 +1,51 @@
+name: Test pip installation and dependency check
+
+on:
+  push:
+    branches:
+      - develop
+      - main
+  pull_request:
+    branches:
+      - "*"
+
+jobs:
+  test-pip-install:
+    runs-on: ubuntu-latest
+    container: precice/precice:nightly
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          path: micro-manager
+
+      - name: Install dependencies
+        run: |
+          apt-get -qq update
+          apt-get -qq install python3-dev python3-venv git pkg-config
+
+      - name: Create a virtual environment and install Micro Manager in it
+        working-directory: micro-manager
+        run: |
+          python3 -m venv .venv
+          . .venv/bin/activate
+          pip install .
+
+      - name: Run dependency check with all dependencies present
+        working-directory: micro-manager
+        run: |
+          . .venv/bin/activate
+          micro-manager-precice --test-dependencies
+
+      - name: Run dependency check with pyprecice uninstalled
+        working-directory: micro-manager
+        run: |
+          . .venv/bin/activate
+          pip uninstall -y pyprecice
+          if micro-manager-precice --test-dependencies; then
+            echo "ERROR: dependency check should have failed but passed"
+            exit 1
+          else
+            echo "OK: dependency check correctly reported missing pyprecice"
+          fi

.gitignore

@@ -21,3 +21,4 @@ dist
 precice-profiling/
 precice-run/
 *events.json
+.coverage*

CHANGELOG.md

@@ -1,5 +1,22 @@
 # Micro Manager changelog
 
+## v0.9.0
+
+- Refactored `DomainDecomposer` class and added a new variant of non-uniform decomposition [#243](https://github.com/precice/micro-manager/pull/243)
+- Fixed load balancing configuration `partitioning` parameter setting [#245](https://github.com/precice/micro-manager/pull/245)
+- Fixed comparison of zero values of type float32 and float64 in simulation deactivation [#244](https://github.com/precice/micro-manager/pull/244)
+- Optimized norm calculations and further fixed lazy initialization [#241](https://github.com/precice/micro-manager/pull/241)
+- Fixed lazy initialization for ranks without (active) micro simulations [#238](https://github.com/precice/micro-manager/pull/238)
+- Added coverage testing and simulation interface tests [#225](https://github.com/precice/micro-manager/pull/225)
+- Added `--test-dependencies` CLI flag to check if all required dependencies are correctly installed, with clear error messages listing missing packages and how to fix them [#221](https://github.com/precice/micro-manager/pull/221)
+- Added load balancing based on micro simulation solve timings [#228](https://github.com/precice/micro-manager/pull/228)
+- Fixed invalid value in division warning in L1rel/L2rel adaptivity when data contains zeros [#234](https://github.com/precice/micro-manager/pull/234)
+- Fixed duplicate micro simulations for macro-points on rank boundaries by filtering coordinates already claimed by lower-ranked ranks [#230](https://github.com/precice/micro-manager/pull/230)
+- Exposed `MicroSimulationInterface` as a public abstract base class for user subclassing [#224](https://github.com/precice/micro-manager/pull/224)
+- Added option to use compute instances to reduce memory consumption [#226](https://github.com/precice/micro-manager/pull/226)
+- Added support to run micro simulations in separate processes with workers [#219](https://github.com/precice/micro-manager/pull/219)
+- Added abstraction layers to micro simulations to support more features [#218](https://github.com/precice/micro-manager/pull/218)
+
 ## v0.8.0
 
 - Conformed to naming standard in precice/tutorials [#215](https://github.com/precice/micro-manager/pull/215)

check_coverage.py

@@ -0,0 +1,32 @@
+"""
+Script to check if test coverage is above a predefined threshold.
+Reads total coverage percentage from stdin (output of coverage report --format=total).
+"""
+
+import sys
+
+THRESHOLD = 60  # Minimum required coverage percentage
+
+
+if __name__ == "__main__":
+    try:
+        coverage = int(sys.stdin.read().strip())
+    except ValueError:
+        print("Error: could not parse coverage value from stdin.")
+        sys.exit(1)
+
+    print("Total coverage: {}%".format(coverage))
+    if coverage < THRESHOLD:
+        print(
+            "Coverage {}% is below the required threshold of {}%.".format(
+                coverage, THRESHOLD
+            )
+        )
+        sys.exit(1)
+    else:
+        print(
+            "Coverage {}% meets the required threshold of {}%.".format(
+                coverage, THRESHOLD
+            )
+        )
+        sys.exit(0)