Add basic integration tests for process_samples #967
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dorien-er
reviewed
Feb 25, 2025
| @@ -0,0 +1,42 @@ | |||
| name: "assert_test_workflow_2_output" | |||
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Should this just be "assert_test_workflow_output", and the folder name as well?
| @@ -7,6 +7,8 @@ info: | |||
| namespace: transform | |||
| - name: remove_modality | |||
| namespace: filter | |||
| - name: assert_test_workflow_2_output | |||
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cf comment below, should this just be 'assert_test_workflow_output'?
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| def test_modalities_present(output_h5mu): | ||
| assert all(k in output_h5mu.obsm.keys() for k in ("rna", "rna")) |
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Do we want to test for all modalities present in the test data, or just rna?
Suggested change
| assert all(k in output_h5mu.obsm.keys() for k in ("rna", "rna")) | |
| assert all(k in output_h5mu.obsm.keys() for k in ("rna", "prot")) |
| ) | ||
| ) | ||
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It would be nice to also test for the generated rna .obs columns, e.g. filter_with_hvg, fraction_mitochondrial
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Changelog
Add basic integration tests for process_samples
Issue ticket number and link
Closes #xxxx (Replace xxxx with the GitHub issue number)Checklist before requesting a review
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Proposed changes are described in the CHANGELOG.md
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