Mask for pca

[chelseabright96]

mask parameter added to pca method in _pca.py test_pca_mask added to test_pca.py Deprecation warning on use_highly_variable parameter added to test_deprecations.py

[codecov[bot]]

Codecov Report

Merging #2272 (7839a73) into master (05dcf68) will increase coverage by 0.12%. The diff coverage is 89.65%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2272      +/-   ##
==========================================
+ Coverage   73.12%   73.25%   +0.12%     
==========================================
  Files         111      111              
  Lines       12127    12200      +73     
==========================================
+ Hits         8868     8937      +69     
- Misses       3259     3263       +4     

Files	Coverage Δ
scanpy/experimental/pp/_normalization.py	95.12% <100.00%> (+1.29%)	:arrow_up:
scanpy/get/__init__.py	100.00% <100.00%> (ø)
scanpy/preprocessing/_docs.py	100.00% <100.00%> (ø)
scanpy/preprocessing/_utils.py	46.87% <100.00%> (+1.71%)	:arrow_up:
scanpy/tools/_rank_genes_groups.py	94.35% <100.00%> (+0.13%)	:arrow_up:
scanpy/tools/_umap.py	71.64% <ø> (ø)
scanpy/tools/_utils.py	71.95% <ø> (ø)
scanpy/_utils/__init__.py	65.24% <50.00%> (-0.09%)	:arrow_down:
scanpy/get/get.py	92.63% <94.44%> (+0.18%)	:arrow_up:
scanpy/preprocessing/_simple.py	82.89% <94.73%> (+0.67%)	:arrow_up:
... and 3 more

... and 1 file with indirect coverage changes

[flying-sheep]

Possible TODO:

• normalize_pearson_residuals_pca

@ivirshup I reverted the change in a6290ee9e0d1baf0e3483118aa552b6f6dcf02c0 where you changed

-X_pca = np.zeros((X.shape[0], n_comps), X.dtype)
+X_pca = np.zeros((adata_comp.shape[0], n_comps), adata.X.dtype)

the commit message is “Fix up pca tests”, but that change doesn’t seem to impact tests and it takes properties from several different object without reasoning.