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turbogenius-build-test.yml
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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