Filter

[Sakshi-2797]

In this contribution , we have introduced a new flow for filtering in the form of a function 'filter' in the already existing filtering implementation by combining 'filter cells' , 'filter genes', 'normtotal_log1p' and 'highly_variabe_gene(use_fastpp) for overall faster preprocessing. This new flow also introduces changes in log1p in the form of a new function 'normtotal_log1p' ,combining normalisation and log1p functionalities together. It also introduced a new flavour 'use_fastpp' in already existing 'highly_variable_gene' function for faster preprocessing. The filter function gives an overall speedup of approx ~2x from the normal preprocessing flow.

[codecov[bot]]

Codecov Report

Merging #2455 (16b72ff) into master (d08518f) will decrease coverage by 1.17%. The diff coverage is 8.67%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2455      +/-   ##
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- Coverage   72.12%   70.95%   -1.17%     
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  Files         104      104              
  Lines       11688    11907     +219     
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+ Hits         8430     8449      +19     
- Misses       3258     3458     +200     

Files Changed	Coverage Δ
scanpy/preprocessing/_simple.py	61.68% <6.01%> (-18.42%)	:arrow_down:
scanpy/preprocessing/_highly_variable_genes.py	73.56% <10.44%> (-21.80%)	:arrow_down:
scanpy/preprocessing/_normalization.py	74.03% <21.05%> (-11.85%)	:arrow_down: