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openpipelines-bio / openpipeline

https://openpipelines.bio
MIT License
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Large refactor #79

Closed rcannood closed 1 year ago

DriesSchaumont commented 1 year ago

filter_with_scrublet and filter_with_counts are failing with:

Traceback (most recent call last):
  File "/viash_automount/tmp//viash-run-filter_with_counts-AziVyk", line 108, in test_filtering_a_little
    self.assertListEqual(list(mu_out.mod['rna'].var['feature_type'].cat.categories), ["Gene Expression"],
  File "/usr/local/lib/python3.8/site-packages/pandas/core/frame.py", line 3505, in __getitem__
    indexer = self.columns.get_loc(key)
  File "/usr/local/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3631, in get_loc
    raise KeyError(key) from err
KeyError: 'feature_type'
rcannood commented 1 year ago

filter_with_scrublet and filter_with_counts are failing with:

Traceback (most recent call last):
  File "/viash_automount/tmp//viash-run-filter_with_counts-AziVyk", line 108, in test_filtering_a_little
    self.assertListEqual(list(mu_out.mod['rna'].var['feature_type'].cat.categories), ["Gene Expression"],
  File "/usr/local/lib/python3.8/site-packages/pandas/core/frame.py", line 3505, in __getitem__
    indexer = self.columns.get_loc(key)
  File "/usr/local/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3631, in get_loc
    raise KeyError(key) from err
KeyError: 'feature_type'

This was due to the test resources not yet having been updated on S3, should be fixed now.

rcannood commented 1 year ago

Merging even though cellranger is hanging