Tests #84
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| workflow_dispatch: | |
| pull_request: | |
| branches-ignore: [] | |
| schedule: | |
| - cron: '0 0 1 * *' | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| python: [3.8, 3.9, '3.10'] | |
| fail-fast: false | |
| steps: | |
| - name: install graphviz | |
| run: | | |
| sudo apt-get install -y graphviz | |
| - name: checkout git repo | |
| uses: actions/checkout@v2 | |
| - name: Set up Python 3.X | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: install apptainer | |
| run: | | |
| sudo add-apt-repository -y ppa:apptainer/ppa | |
| sudo apt update | |
| sudo apt install -y apptainer | |
| singularity version | |
| - name: install package itself | |
| shell: bash -l {0} | |
| run: | | |
| pip install . | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| pip install coveralls pytest-cov pytest pytest-xdist | |
| pip install damona | |
| - name: Activate Damona | |
| run: | | |
| bash | |
| damona # this creates the bash script | |
| echo " source ~/.config/damona/damona.sh" >> ~/.bashrc | |
| - name: Create env, install bcl2fastq | |
| run: | | |
| bash | |
| damona create TEST | |
| damona activate TEST | |
| damona install bcl2fastq | |
| env: | |
| DAMONA_EXE: /usr/share/miniconda/bin/damona | |
| DAMONA_PATH: /home/runner/.config/damona | |
| DAMONA_SINGULARITY_OPTIONS: "" | |
| DAMONA_ENV: /home/runner/.config/damona/envs/TEST | |
| DAMONA_SHELL_INFO: "bash" | |
| - name: install package itself | |
| run: | | |
| pip install . | |
| - name: testing | |
| run: | | |
| damona activate TEST | |
| pytest --cov-report term --cov=sequana_pipelines.demultiplex | |
| env: | |
| DAMONA_EXE: /usr/share/miniconda/bin/damona | |
| DAMONA_PATH: /home/runner/.config/damona | |
| DAMONA_SINGULARITY_OPTIONS: "" | |
| DAMONA_ENV: /home/runner/.config/damona/envs/TEST | |
| DAMONA_SHELL_INFO: "bash" | |
| - name: coveralls | |
| run: | | |
| echo $COVERALLS_REPO_TOKEN | |
| coveralls --service=github | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} |