CI #102
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: "3.7" | |
| - os: ubuntu-latest | |
| python-version: "3.8" | |
| - os: ubuntu-latest | |
| python-version: "3.11" | |
| #- os: macos-latest | |
| # python-version: "3.10" | |
| #- os: windows-latest | |
| # python-version: "3.6" | |
| 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 }} | |
| #mamba-version: "*" | |
| miniforge-variant: Mambaforge | |
| 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/3956580/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 --current-env --nbval-cell-timeout=900" | |
| pytest $PYTEST_ARGS | |