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theislab / scib

Benchmarking analysis of data integration tools
MIT License
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Fix argument deprecation #404

Closed mumichae closed 4 months ago

mumichae commented 4 months ago

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

codecov[bot] commented 4 months ago

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 ```diff @@ 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](https://app.codecov.io/gh/theislab/scib/pull/404/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/theislab/scib/pull/404/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab) | `52.81% <43.90%> (-0.48%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files](https://app.codecov.io/gh/theislab/scib/pull/404?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab) | Coverage Δ | | |---|---|---| | [scib/metrics/pcr.py](https://app.codecov.io/gh/theislab/scib/pull/404?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c2NpYi9tZXRyaWNzL3Bjci5weQ==) | `81.15% <100.00%> (ø)` | | | [scib/utils.py](https://app.codecov.io/gh/theislab/scib/pull/404?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c2NpYi91dGlscy5weQ==) | `63.63% <0.00%> (ø)` | | | [scib/metrics/ari.py](https://app.codecov.io/gh/theislab/scib/pull/404?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c2NpYi9tZXRyaWNzL2FyaS5weQ==) | `87.09% <66.66%> (-5.50%)` | :arrow_down: | | [scib/metrics/highly\_variable\_genes.py](https://app.codecov.io/gh/theislab/scib/pull/404?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c2NpYi9tZXRyaWNzL2hpZ2hseV92YXJpYWJsZV9nZW5lcy5weQ==) | `89.74% <60.00%> (-4.71%)` | :arrow_down: | | [scib/metrics/nmi.py](https://app.codecov.io/gh/theislab/scib/pull/404?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c2NpYi9tZXRyaWNzL25taS5weQ==) | `29.72% <71.42%> (+2.19%)` | :arrow_up: | | [scib/metrics/silhouette.py](https://app.codecov.io/gh/theislab/scib/pull/404?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c2NpYi9tZXRyaWNzL3NpbGhvdWV0dGUucHk=) | `83.72% <66.66%> (-1.28%)` | :arrow_down: | | [scib/\_package\_tools.py](https://app.codecov.io/gh/theislab/scib/pull/404?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c2NpYi9fcGFja2FnZV90b29scy5weQ==) | `46.66% <6.66%> (-40.00%)` | :arrow_down: | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/theislab/scib/pull/404/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab)