Release 2.0 -- merge pull request #139 from n-claes/develop

Releasing Legolas 2.0

.github/workflows/docs_develop.yml

@@ -0,0 +1,46 @@
+name: docs
+
+on:
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ develop ]
+
+jobs:
+  develop:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        # Fix version for now, 3.4 throws an error (see #101)
+        pip install markdown==3.3.7
+        pip install ford==6.1.13 graphviz
+        sudo apt-get install graphviz
+        pip install -U sphinx
+        pip install numpydoc sphinx-rtd-theme lazy-object-proxy==1.4 sphinx-autoapi
+
+    - name: Generate documentation
+      run: |
+        cd docs
+        python generate_docs.py develop
+
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      # only deploy if the branch is develop
+      if: ${{ contains(github.ref, 'refs/heads/develop') }}
+      with:
+          deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
+          external_repository: n-claes/legolas.science-dev
+          publish_branch: main
+          publish_dir: ./docs
+          cname: dev.legolas.science
+          enable_jekyll: true
+          full_commit_message: 'dev: deploy n-claes/legolas@${{ github.sha }}'

.github/workflows/docs_stable.yml

@@ -0,0 +1,46 @@
+name: docs
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  stable:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        # Fix version for now, 3.4 throws an error (see #101)
+        pip install markdown==3.3.7
+        pip install ford==6.1.13 graphviz
+        sudo apt-get install graphviz
+        pip install -U sphinx
+        pip install numpydoc sphinx-rtd-theme lazy-object-proxy==1.4 sphinx-autoapi
+
+    - name: Generate documentation
+      run: |
+        cd docs
+        python generate_docs.py stable
+
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      # only deploy if the branch is master
+      if: ${{ contains(github.ref, 'refs/heads/master') }}
+      with:
+          deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY_STABLE }}
+          external_repository: n-claes/legolas.science-stable
+          publish_branch: main
+          publish_dir: ./docs
+          cname: legolas.science
+          enable_jekyll: true
+          full_commit_message: 'stable: deploy n-claes/legolas@${{ github.sha }}'

.github/workflows/pylbo.yml

@@ -7,8 +7,8 @@ on:
     branches: [master, develop]
 
 env:
-  CC: /usr/bin/gcc-9
-  FC: /usr/bin/gfortran-9
+  CC: /usr/bin/gcc-10
+  FC: /usr/bin/gfortran-10
   LEGOLASDIR: /home/runner/work/legolas/legolas
 
 jobs:
@@ -17,10 +17,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Install dependencies
         run: |
@@ -45,28 +45,26 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.9
 
     - name: Install python dependencies
       run: |
         python -m pip install --upgrade pip
         pip install pytest pytest-cov
+        sudo apt-get update
+        sudo apt-get install ffmpeg
         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
         sudo apt-get install lcov
-        gfortran-9 --version
+        gfortran-10 --version
         cmake --version
 
     - name: Compile Legolas

.github/workflows/regression.yml

@@ -0,0 +1,116 @@
+name: legolas
+
+on:
+  push:
+    branches: [master, develop]
+  pull_request:
+    branches: [master, develop]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        name: [regression]
+        os: [ubuntu-latest]
+        compiler: [gfortran-11]
+        coverage: [true]
+
+    env:
+      FC: ${{ matrix.compiler }}
+      LEGOLASDIR: /home/runner/work/legolas/legolas
+      ARPACK_ROOT: /home/runner/work/legolas/legolas/tests/arpack-ng
+
+    name: ${{ matrix.name }}
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.9
+
+    - name: Install cmake
+      uses: jwlawson/actions-setup-cmake@v1.13.0
+      with:
+        cmake-version: "3.24.x"
+
+    - name: Install Legolas dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install ${{ matrix.compiler }}
+        sudo apt-get install libblas-dev
+        sudo apt-get install liblapack-dev
+        sudo apt-get install lcov
+        ${FC} --version
+        cmake --version
+        gcov --version
+
+    - 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 ARPACK
+      id: arpack-cache
+      uses: actions/cache@v1
+      with:
+        path: tests/arpack-ng/
+        key: ${{ runner.os }}-arpackv3
+
+    - name: Build ARPACK
+      if: steps.arpack-cache.outputs.cache-hit != 'true'
+      run: |
+        cd tests
+        git clone https://github.com/opencollab/arpack-ng.git
+        cd arpack-ng
+        mkdir build
+        mkdir installed
+        cd build
+        cmake -DEXAMPLES=OFF -DMPI=OFF -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=../installed ..
+        make -j 2
+        sudo make -j 2 install
+
+    - name: Compile Legolas
+      run: |
+        mkdir build
+        cd build
+        if [[ "${{ matrix.coverage }}" ]]; then
+          cmake -DCoverage=ON ..
+        else
+          cmake -DDebug=ON ..
+        fi
+        make -j 2
+
+    - name: Run tests
+      run: |
+        cd $LEGOLASDIR/tests/regression_tests
+        pytest
+
+    - name: Generate coverage report
+      if: ${{ matrix.coverage }}
+      run: |
+        mkdir coverage
+        cd coverage
+        lcov --capture --directory $LEGOLASDIR/build \
+            --output-file ${{ matrix.name }}.info \
+            --gcov-tool /usr/bin/gcov-11
+        # 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/test_results
+
+    - name: Upload coverage report
+      uses: codecov/codecov-action@v1
+      if: ${{ matrix.coverage }}
+      with:
+        files: ./coverage/${{ matrix.name }}.info
+        flags: legolas