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Fix argument deprecation #404

Merged
merged 9 commits into from
Mar 31, 2024
Merged

Fix argument deprecation #404

merged 9 commits into from
Mar 31, 2024

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mumichae
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@mumichae mumichae commented Mar 31, 2024

After scanpy 1.9.6, the deprecated_arg_names function was replaced with renamed_args.

This PR uses the renamed_args instead (and is backwards compatible).

Closes #401
Closes #403

@mumichae mumichae self-assigned this Mar 31, 2024
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codecov bot commented Mar 31, 2024

Codecov Report

Attention: Patch coverage is 43.90244% with 23 lines in your changes are missing coverage. Please review.

Project coverage is 52.81%. Comparing base (ed3e284) to head (75a4309).
Report is 1 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #404      +/-   ##
==========================================
- Coverage   53.29%   52.81%   -0.48%     
==========================================
  Files          22       22              
  Lines        1852     1882      +30     
==========================================
+ Hits          987      994       +7     
- Misses        865      888      +23     
Flag Coverage Δ
unittests 52.81% <43.90%> (-0.48%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Coverage Δ
scib/metrics/pcr.py 81.15% <100.00%> (ø)
scib/utils.py 63.63% <0.00%> (ø)
scib/metrics/ari.py 87.09% <66.66%> (-5.50%) ⬇️
scib/metrics/highly_variable_genes.py 89.74% <60.00%> (-4.71%) ⬇️
scib/metrics/nmi.py 29.72% <71.42%> (+2.19%) ⬆️
scib/metrics/silhouette.py 83.72% <66.66%> (-1.28%) ⬇️
scib/_package_tools.py 46.66% <6.66%> (-40.00%) ⬇️

... and 1 file with indirect coverage changes

@mumichae mumichae merged commit c17e221 into main Mar 31, 2024
11 checks passed
@mumichae mumichae deleted the work_with_scanpy0.10 branch March 31, 2024 17:58
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scib import failure with scanpy 1.10.0
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