Merge pull request #70 from n-claes/tests/improved_testing

Improved CI, code coverage and test extensions

.github/workflows/legolas.yml

@@ -0,0 +1,146 @@
+name: legolas
+
+on:
+  push:
+    branches: [master, develop]
+  pull_request:
+    branches: [master, develop]
+
+env:
+  CC: /usr/bin/gcc-9
+  FC: /usr/bin/gfortran-9
+  PFUNIT_DIR: /home/runner/work/legolas/legolas/tests/pFUnit/build/installed
+  LEGOLASDIR: /home/runner/work/legolas/legolas
+  ARPACK_ROOT: /home/runner/work/legolas/legolas/tests/arpack-ng
+
+jobs:
+  test:
+    name: "${{ matrix.name }}"
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: unit-tests
+            coverage: true
+          - name: regression
+            coverage: true
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        sudo add-apt-repository ppa:ubuntu-toolchain-r/test
+        sudo apt update
+        sudo apt-get install gfortran-9
+        sudo apt-get -y install cmake
+        sudo apt-get install libblas-dev
+        sudo apt-get install liblapack-dev
+        sudo apt-get install lcov
+        gfortran-9 --version
+        cmake --version
+        which gcov
+        which gcov-9
+
+    - name: Install Python dependencies & Pylbo
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest numpy matplotlib f90nml tqdm psutil pytest-mpl
+        cd post_processing
+        python setup.py develop
+
+    - name: Cache pFUnit
+      id: pfunit-cache
+      uses: actions/cache@v1
+      with:
+        path: tests/pFUnit/
+        key: ${{ runner.os }}-pfunitv1
+
+    - name: Build pFUnit
+      if: steps.pfunit-cache.outputs.cache-hit != 'true'
+      run: |
+        cd tests/
+        git clone https://github.com/Goddard-Fortran-Ecosystem/pFUnit.git
+        cd pFUnit
+        mkdir build
+        cd build
+        cmake .. -DSKIP_MPI=YES -DSKIP_OPENMP=YES -DSKIP_FHAMCREST=YES
+        make -j 2 tests
+        make -j 2 install
+
+    - name: Cache ARPACK
+      id: arpack-cache
+      uses: actions/cache@v1
+      with:
+        path: tests/arpack-ng/
+        key: ${{ runner.os }}-arpackv2
+
+    - name: Build ARPACK
+      if: steps.arpack-cache.outputs.cache-hit != 'true'
+      run: |
+        cd tests
+        git clone https://github.com/opencollab/arpack-ng.git
+        cd arpack-ng
+        mkdir build
+        mkdir installed
+        cd build
+        cmake -DEXAMPLES=OFF -DMPI=OFF -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=../installed ..
+        make -j 2
+        sudo make -j 2 install
+
+    - name: Compile Legolas
+      run: |
+        mkdir build
+        cd build
+        if [[ "${{ matrix.coverage }}" ]]; then
+          cmake -DCoverage=ON ..
+        else
+          cmake ..
+        fi
+        make -j 2
+
+    - name: Run tests
+      run: |
+        # depending on unit or regression tests we use different coverage options
+        if [[ "${{ matrix.name }}" == "unit-tests" ]]; then
+          cd $LEGOLASDIR/tests/unit_tests
+          mkdir build
+          cd build
+          cmake -DCoverage=ON ..
+          make -j 2
+          cd ..
+          ./test_legolas
+        elif [[ "${{ matrix.name }}" == "regression" ]]; then
+          cd $LEGOLASDIR/tests/regression_tests
+          pytest -v regression.py test*
+        fi
+        if [[ "${{ matrix.coverage }}" ]]; then
+          # generate coverage report
+          cd $LEGOLASDIR
+          mkdir coverage
+          cd coverage
+          lcov --capture --directory $LEGOLASDIR/build \
+             --output-file ${{ matrix.name }}.info \
+             --gcov-tool /usr/bin/gcov-9
+        fi
+        # filter out coverage files
+        find $LEGOLASDIR/build -name '*.gc*' -delete
+
+    - name: Archive failed logs
+      uses: actions/upload-artifact@v2
+      if: failure()
+      with:
+        name: failed_logs
+        path: tests/regression_tests/image_comparisons
+
+    - name: Upload coverage report
+      uses: codecov/codecov-action@v1
+      if: ${{ matrix.coverage }}
+      with:
+        files: ./coverage/${{ matrix.name }}.info

.github/workflows/pylbo_core.yml → .github/workflows/pylbo.yml

@@ -1,4 +1,4 @@
-name: pylbo-core
+name: pylbo
 
 on:
   push:
@@ -53,32 +53,11 @@ jobs:
     - name: Install python dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest numpy matplotlib f90nml tqdm psutil pytest-mpl pytest-timeout
+        pip install pytest pytest-cov
         cd post_processing
         python setup.py develop
 
-    - name: Install Legolas dependencies
-      run: |
-        sudo add-apt-repository ppa:ubuntu-toolchain-r/test
-        sudo apt update
-        sudo apt-get install gfortran-9
-        sudo apt-get -y install cmake
-        sudo apt-get install libblas-dev
-        sudo apt-get install liblapack-dev
-        gfortran-9 --version
-        cmake --version
-
-    - name: Compile Legolas
-      run: sh setup_tools/buildlegolas.sh
-
     - name: Test Pylbo core
       run: |
         cd tests/pylbo_tests
-        pytest --mpl --mpl-results-path=results --verbose
-
-    - name: Archive failed logs
-      uses: actions/upload-artifact@v1
-      if: failure()
-      with:
-        name: failed_logs
-        path: tests/pylbo_tests/results
+        pytest -v

post_processing/pylbo/automation/defaults.py

@@ -12,6 +12,7 @@
         ("sigma_1", (int, np.integer, float)),
         ("sigma_2", (int, np.integer, float)),
         ("force_r0", bool),
+        ("coaxial", bool),
     ],
     "equilibriumlist": [
         ("equilibrium_type", str),

post_processing/pylbo/testing.py

@@ -0,0 +1,12 @@
+import pickle
+
+
+def pickle_dataseries_to_file(series, filepath):
+    with open(filepath, "wb") as ostream:
+        pickle.dump(series, ostream, pickle.HIGHEST_PROTOCOL)
+
+
+def load_pickled_dataseries(filepath):
+    with open(filepath, "rb") as istream:
+        series = pickle.load(istream)
+    return series