updated WF modules #37
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| # This workflow will build and test TurboGenius. | |
| name: TurboGenius build, and test (GNU) | |
| on: | |
| push: | |
| branches: [ "main", "devel" ] | |
| pull_request: | |
| branches: [ "main", "devel" ] | |
| jobs: | |
| gnu-test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Install gfortran and gcc | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install gfortran | |
| - name: Install OpenBLAS and LAPACK | |
| run: sudo apt-get install libopenblas-dev liblapack-dev | |
| - name: Install CMake | |
| run: sudo apt-get install cmake | |
| - name: Install and Setup Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: 3.8 | |
| - name: Install python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install numpy scipy pandas | |
| - name: Checkout the TurboRVB repository | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: sissaschool/turborvb | |
| ref: devel | |
| path: turborvb | |
| - name: Build TurboRVB with cmake serial version | |
| working-directory: turborvb | |
| run: | | |
| cmake -S. -Bbuild -DEXT_PARALLEL=OFF -DEXT_OPT=OFF -DCMAKE_C_COMPILER=gcc -DCMAKE_Fortran_COMPILER=gfortran | |
| cmake --build build -j 2 | |
| - name: Test TurboRVB with ctest serial version | |
| working-directory: turborvb | |
| run: | | |
| ctest --test-dir build --output-on-failure -j 2 | |
| - name: Copy the compiled binaries and set env. | |
| working-directory: turborvb | |
| run: | | |
| cp $GITHUB_WORKSPACE/turborvb/build/*.x $GITHUB_WORKSPACE/turborvb/bin/ | |
| echo "export PATH=$GITHUB_WORKSPACE/turborvb/bin:\$PATH" >> $GITHUB_ENV | |
| cat "$GITHUB_ENV" | |
| - name: Checkout the TurboGenius repository | |
| uses: actions/checkout@v3 | |
| with: | |
| path: turbogenius | |
| - name: Install TurboGenius | |
| working-directory: turbogenius | |
| run: | | |
| python -m pip install flake8 pytest | |
| python -m pip install . | |
| - name: Lint TurboGenius with flake8 | |
| working-directory: turbogenius | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test TurboGenius with pytest | |
| working-directory: turbogenius | |
| run: | | |
| export TURBORVB_ROOT=$GITHUB_WORKSPACE/turborvb | |
| pytest |