CI fixes #201
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - "master" | |
| workflow_dispatch: | |
| pull_request: | |
| branches: | |
| - "master" | |
| - "dev" | |
| schedule: | |
| # Run a cron job once daily, weekdays only | |
| - cron: "0 3 1,15 * *" | |
| jobs: | |
| test: | |
| name: Pytest | |
| runs-on: ${{ matrix.cfg.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| cfg: | |
| #- os: ubuntu-latest | |
| # python-version: "3.8" | |
| - os: ubuntu-latest | |
| python-version: "3.9" | |
| #- os: macos-latest | |
| # python-version: "3.9" | |
| #- os: windows-latest | |
| # python-version: "3.9" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # More info on options: https://github.com/conda-incubator/setup-miniconda | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.cfg.python-version }} | |
| miniforge-version: latest | |
| environment-file: environment.yml | |
| channels: conda-forge,defaults | |
| activate-environment: kinfraglib | |
| #auto-update-conda: false | |
| #auto-activate-base: false | |
| #show-channel-urls: true | |
| - name: Additional info about the build | |
| shell: bash | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - name: Environment Information | |
| shell: bash -l {0} | |
| run: | | |
| conda info --all | |
| conda list | |
| #- name: Download external data | |
| # shell: bash -l {0} | |
| # run: | | |
| # echo "Download combinatorial library from zenodo..." | |
| # wget -q -O data/combinatorial_library/combinatorial_library.tar.bz2 https://zenodo.org/record/10843763/files/combinatorial_library.tar.bz2?download=1 | |
| # ls -l data/combinatorial_library/ | |
| # echo "Decompress selected files..." | |
| # tar -xvf data/combinatorial_library/combinatorial_library.tar.bz2 combinatorial_library_deduplicated.json chembl_standardized_inchi.csv | |
| # mv combinatorial_library_deduplicated.json data/combinatorial_library/ | |
| # mv chembl_standardized_inchi.csv data/combinatorial_library/ | |
| # ls -l data/combinatorial_library/ | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| PYTEST_ARGS="--nbval-lax --nbval-current-env --nbval-cell-timeout=360" | |
| PYTEST_IGNORE="--ignore=notebooks/custom_kinfraglib/2_3_custom_filters_paper.ipynb --ignore=notebooks/kinfraglib --ignore=notebooks/custom_kinfraglib/1_1_custom_filters_unwanted_substructures.ipynb --ignore=notebooks/custom_kinfraglib/1_2_custom_filters_drug_likeness.ipynb --ignore=notebooks/custom_kinfraglib/1_3_custom_filters_synthesizability.ipynb --ignore=notebooks/custom_kinfraglib/1_4_custom_filters_pairwise_retrosynthesizability.ipynb --ignore=notebooks/custom_kinfraglib/2_1_custom_filters_pipeline.ipynb" | |
| pytest $PYTEST_ARGS $PYTEST_IGNORE |