Fix url for PDB sequence metadata download in PDBManager
#818
Workflow file for this run
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name: minimal_install | |
on: | |
push: | |
paths-ignore: | |
- "README.md" | |
- "docs/**" | |
pull_request: | |
paths-ignore: | |
- "README.md" | |
- "docs/*" | |
- "CHANGELOG.md" | |
- "CONTRIBUTORS.md" | |
- "CONTRIBUTING.md" | |
- "imgs/" | |
jobs: | |
build_cpu: | |
runs-on: ubuntu-latest | |
# https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell | |
defaults: | |
run: | |
shell: bash -l {0} | |
strategy: | |
matrix: | |
python-version: [3.8, 3.9, 3.11] | |
steps: | |
- name: Checkout repository | |
uses: actions/checkout@v3 | |
# See: https://github.com/marketplace/actions/setup-miniconda | |
- name: Setup miniconda | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
auto-update-conda: true | |
miniforge-variant: Mambaforge | |
conda-channels: conda-forge | |
python-version: ${{ matrix.python-version }} | |
use-mamba: true | |
- name: Install Graphein | |
run: pip install -e . | |
- name: Install Extras | |
run: pip install -r .requirements/extras.in | |
- name: Install Dev Dependencies | |
run: pip install -r .requirements/dev.in | |
- name: Run unit tests and generate coverage report | |
run: pytest . --ignore-glob="tests/protein/tensor" --ignore="tests/ml/test_conversion.py" --ignore="tests/ml/test_torch_geometric_dataset.py" | |
- name: Test notebook execution | |
run: pytest --nbval-lax notebooks/ --current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/higher_order_graphs.ipynb" --ignore-glob="notebooks/protein_graph_analytics.ipynb" --ignore-glob="notebooks/subgraphing_tutorial.ipynb" --ignore-glob="notebooks/splitting_a_dataset.ipynb" --ignore-glob="notebooks/protein_tensors.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb" --ignore-glob="notebooks/foldcomp.ipynb" --ignore-glob="notebooks/creating_datasets_from_the_pdb.ipynb" |