diff --git a/.github/workflows/py-unittests.yml b/.github/workflows/py-unittests.yml index 88ecce036..404902c38 100644 --- a/.github/workflows/py-unittests.yml +++ b/.github/workflows/py-unittests.yml @@ -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) diff --git a/api/python/cellxgene_census/scripts/requirements-dev.txt b/api/python/cellxgene_census/scripts/requirements-dev.txt index 7fab730ad..7b6200587 100644 --- a/api/python/cellxgene_census/scripts/requirements-dev.txt +++ b/api/python/cellxgene_census/scripts/requirements-dev.txt @@ -5,5 +5,6 @@ twine coverage nbqa transformers[torch] +git+https://huggingface.co/ctheodoris/Geneformer@471eefc; python_version>='3.10' owlready2 proxy.py