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Move geneformer test dependency back to requirements-dev.txt #1236

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Jul 11, 2024
Merged

Move geneformer test dependency back to requirements-dev.txt #1236

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4 changes: 0 additions & 4 deletions .github/workflows/py-unittests.yml
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Expand Up @@ -44,10 +44,6 @@ jobs:
pip install --use-pep517 accumulation-tree # Geneformer dependency needs --use-pep517 for Cython
GIT_CLONE_PROTECTION_ACTIVE=false pip install -r ./api/python/cellxgene_census/scripts/requirements-dev.txt
pip install -e './api/python/cellxgene_census/[experimental]'
- name: Install Geneformer (python >=3.10 only)
# Geneformer version should match that specified in api/python/cellxgene_census/src/cellxgene_census/experimental/ml/huggingface/geneformer_tokenizer.py
run: pip install git+https://huggingface.co/ctheodoris/Geneformer@57f02a4
if: matrix.python-version != '3.8' && matrix.python-version != '3.9'
- name: Report Dependency Versions
run: pip list
- name: Test with pytest (API, main tests)
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1 change: 1 addition & 0 deletions api/python/cellxgene_census/scripts/requirements-dev.txt
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Expand Up @@ -5,5 +5,6 @@ twine
coverage
nbqa
transformers[torch]
git+https://huggingface.co/ctheodoris/Geneformer@471eefc; python_version>='3.10'
owlready2
proxy.py
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