CI #115
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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-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/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=900" | |
pytest $PYTEST_ARGS | |