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Fix issue where nemo1 to nemo2 conversion tests (esm2 and geneformer) only work when run by themselves. #226

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jstjohn opened this issue Oct 1, 2024 · 1 comment

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@jstjohn
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jstjohn commented Oct 1, 2024

To replicate remove the pytest.mark.skip on:

  • sub-packages/bionemo-esm2/tests/bionemo/esm2/model/test_model.py::test_nemo1_checkpoint_conversion
  • sub-packages/bionemo-geneformer/tests/bionemo/geneformer/test_model.py::test_nemo1_checkpoint_conversion

For ESM2:

This works:

sub-packages/bionemo-esm2/tests/bionemo/esm2/model/test_model.py::test_nemo1_checkpoint_conversion

This works:

sub-packages/bionemo-esm2/tests/bionemo/esm2/model/test_model.py

This fails:

py.test sub-packages/bionemo-esm2/tests/bionemo/esm2/model/finetune/test_finetune.py  sub-packages/bionemo-esm2/tests/bionemo/esm2/model/test_model.py

For Geneformer:

This works:

sub-packages/bionemo-geneformer/tests/bionemo/geneformer/test_model.py::test_nemo1_checkpoint_conversion

Move the test_nemo1_checkpoint_conversion to after the test_geneformer_nemo1_v_nemo2_inference_golden_values function and re-run to get the failure.

@ghstrider
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Hi,
If no one is working on this issue. I would like to support on this issue.

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