Notebooks #70
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| name: Notebooks | |
| on: | |
| workflow_run: | |
| workflows: ["CI Pipeline"] | |
| types: | |
| - completed | |
| jobs: | |
| notebooks: | |
| runs-on: self-hosted | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: setup python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11.8 | |
| - name: Install dependencies | |
| run: | | |
| pip install -r requirements-dev.txt | |
| - name: Reduce datasets to speedup checks | |
| run: | | |
| sed -i 's/train\[:65%\]/train\[:5%\]/g' ./examples/notebooks/Cell-Type-Annotation.ipynb | |
| sed -i 's/train\[70%:\]/train\[5%:7%\]/g' ./examples/notebooks/Cell-Type-Annotation.ipynb | |
| sed -i 's/get_anndata_from_hf_dataset(ds\[\\"train\\"\])/get_anndata_from_hf_dataset(ds\[\\"train\\"\])[:10]/g' ./examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb | |
| sed -i 's/get_anndata_from_hf_dataset(ds\[\\"test\\"\])/get_anndata_from_hf_dataset(ds\[\\"test\\"\])[:2]/g' ./examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb | |
| sed -i 's/list(np.array(train_dataset.obs\[\\"LVL1\\"].tolist()))/list(np.array(train_dataset.obs\[\\"LVL1\\"].tolist()))[:10]/g' ./examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb | |
| sed -i 's/list(np.array(test_dataset.obs\[\\"LVL1\\"].tolist()))/list(np.array(test_dataset.obs\[\\"LVL1\\"].tolist()))[:2]/g' ./examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb | |
| - name: Run Notebooks | |
| run: | | |
| pytest --durations=0 --nbmake ./examples/notebooks/*.ipynb |