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KwanLab / Autometa

Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
https://autometa.readthedocs.io
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:art::snake: Update deprecated pandas method invocation #279

Closed evanroyrees closed 2 years ago

evanroyrees commented 2 years ago

Update bedtools column summation to prevent emit of FutureWarning:

/home/evan/miniconda3/envs/autometa/lib/python3.9/site-packages/autometa/common/external/bedtools.py:107: FutureWarning: Indexing with multiple keys (implicitly converted to a tuple of keys) will be deprecated, use a list instead.
  dff = df.groupby(contig)[depth_product, bases].sum()

Now explicitly passes list, e.g.

dff = df.groupby(contig)[["depth_product", "bases"]].sum()

PR checklist

github-actions[bot] commented 2 years ago

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 7fca841

+| ✅  62 tests passed       |+
#| ❔  34 tests were ignored |#
!| ❗   9 tests had warnings |!
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codecov[bot] commented 2 years ago

Codecov Report

Merging #279 (7fca841) into dev (86b9550) will not change coverage. The diff coverage is 100.00%.

@@           Coverage Diff           @@
##              dev     #279   +/-   ##
=======================================
  Coverage   27.40%   27.40%           
=======================================
  Files          48       48           
  Lines        5469     5469           
=======================================
  Hits         1499     1499           
  Misses       3970     3970
Flag Coverage Δ
unittests 27.40% <100.00%> (ø)

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Impacted Files Coverage Δ
autometa/common/external/bedtools.py 58.49% <100.00%> (ø)

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