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DE/DA method refactor #98
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #98 +/- ##
==========================================
- Coverage 93.21% 92.24% -0.97%
==========================================
Files 7 7
Lines 869 929 +60
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+ Hits 810 857 +47
- Misses 59 72 +13
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martinkim0
reviewed
Mar 26, 2024
Comment on lines
+35
to
+99
| @pytest.mark.parametrize( | ||
| "setup_kwargs, de_kwargs", | ||
| [ | ||
| ( | ||
| {"sample_key": "sample", "batch_key": "batch"}, | ||
| [ | ||
| { | ||
| "sample_cov_keys": ["meta1_cat", "meta2", "cont_cov"], | ||
| "store_lfc": True, | ||
| "add_batch_specific_offsets": True, | ||
| }, | ||
| { | ||
| "sample_cov_keys": ["meta1_cat", "meta2", "cont_cov"], | ||
| "store_lfc": True, | ||
| "lambd": 1e-1, | ||
| "add_batch_specific_offsets": True, | ||
| }, | ||
| { | ||
| "sample_cov_keys": ["meta1_cat", "meta2", "cont_cov"], | ||
| "store_lfc": True, | ||
| "filter_inadmissible_samples": True, | ||
| "add_batch_specific_offsets": True, | ||
| }, | ||
| { | ||
| "sample_cov_keys": ["meta1_cat", "meta2", "cont_cov"], | ||
| "store_lfc": True, | ||
| "add_batch_specific_offsets": False, | ||
| }, | ||
| ], | ||
| ), | ||
| ( | ||
| { | ||
| "sample_key": "sample", | ||
| "batch_key": "batch", | ||
| "continuous_covariate_keys": ["cont_cov"], | ||
| }, | ||
| [ | ||
| { | ||
| "sample_cov_keys": ["meta1_cat", "meta2", "cont_cov"], | ||
| "store_lfc": True, | ||
| "add_batch_specific_offsets": False, | ||
| } | ||
| ], | ||
| ), | ||
| ( | ||
| {"sample_key": "sample", "batch_key": "dummy_batch"}, | ||
| [ | ||
| { | ||
| "sample_cov_keys": ["meta1_cat", "meta2", "cont_cov"], | ||
| "store_lfc": True, | ||
| }, | ||
| { | ||
| "sample_cov_keys": ["meta1_cat", "meta2", "cont_cov"], | ||
| "store_lfc": True, | ||
| "lambd": 1e-1, | ||
| }, | ||
| { | ||
| "sample_cov_keys": ["meta1_cat", "meta2", "cont_cov"], | ||
| "store_lfc": True, | ||
| "filter_inadmissible_samples": True, | ||
| }, | ||
| ], | ||
| ), | ||
| ], | ||
| ) |
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This is lowkey kind of hard to parse, is there a way to simplify it?
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ok nvm I see what it's doing now
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yea..it's because its replicating the old behavior, which was not neatly combinatorial way, but I did not want to significantly change what was being tested. We can refactor it again if needed and it will be easier this time with parametrize
martinkim0
reviewed
Mar 26, 2024
PierreBoyeau
approved these changes
Mar 28, 2024
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This PR prepares the DE and DA functions for public use:
perform_multivariate_analysistodifferential_expressiondonortosamplein many placesdifferential_abundancemethod that wraps theget_aggregated_posteriormethod and uses a similar API todifferential_expressiontest_models.pyto use pytest parameterize, and adds tests for DA.Addresses #94 #95