Merge updates in main into release #376
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| name: CI Pipeline | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| - release | |
| jobs: | |
| tests: | |
| 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 | |
| pip install . | |
| # First download before tests as they make use of the downloaded files | |
| - name: Download all files | |
| run: | | |
| python ci/download_all.py | |
| - name: Execute unittests | |
| run: | | |
| pytest --cov-report=html:html_cov --cov-branch --cov-report term --cov=helical ci/ | |
| - name: Upload coverage report | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-report | |
| path: html_cov/ | |
| # Does not seem to work but would be nice to have | |
| # - name: Pytest coverage comment | |
| # uses: MishaKav/pytest-coverage-comment@main | |
| # with: | |
| # pytest-coverage-path: ./pytest-coverage.txt | |
| # junitxml-path: ./pytest.xml | |
| - name: Execute Geneformer v1 | |
| run: | | |
| python examples/run_models/run_geneformer.py ++model_name="gf-12L-30M-i2048" | |
| - name: Execute Geneformer v2 | |
| run: | | |
| python examples/run_models/run_geneformer.py ++model_name="gf-12L-95M-i4096" | |
| - name: Execute scGPT | |
| run: | | |
| python examples/run_models/run_scgpt.py | |
| - name: Execute UCE | |
| run: | | |
| python examples/run_models/run_uce.py | |
| - name: Execute Hyena | |
| run: | | |
| python examples/run_models/run_hyena_dna.py | |
| - name: Execute benchmarking | |
| run: | | |
| pip install scanorama | |
| python examples/run_benchmark.py | |
| notebooks: | |
| needs: tests | |
| 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\[\\"train\\"\])[:100]/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\[\\"test\\"\])[:10]/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()))[:100]/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()))[:10]/g' ./examples/notebooks/Cell-Type-Classification-Fine-Tuning.ipynb | |
| - name: Run Notebooks | |
| run: | | |
| pytest --durations=0 --nbmake ./examples/notebooks/*.ipynb |