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Fix compatibility issue with pandas >=2 #906

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merged 1 commit into from
Apr 26, 2023

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abretaud
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While testing funannotate compare 1.8.15 in a freshly installed conda env, I got this error:

[Apr 25 03:14 PM]: Summarizing fungal transcription factors
[Apr 25 03:14 PM]: Running GO enrichment for each genome
Traceback (most recent call last):
  File "/_conda/envs/__funannotate@1.8.15/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3652, in get_loc
    return self._engine.get_loc(casted_key)
  File "pandas/_libs/index.pyx", line 147, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 176, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 7080, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 7088, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'GO'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/_conda/envs/__funannotate@1.8.15/bin/funannotate", line 10, in <module>
    sys.exit(main())
  File "/_conda/envs/__funannotate@1.8.15/lib/python3.8/site-packages/funannotate/funannotate.py", line 716, in main
    mod.main(arguments)
  File "/_conda/envs/__funannotate@1.8.15/lib/python3.8/site-packages/funannotate/compare.py", line 986, in main
    + df2["GO"].astype(str)
  File "/_conda/envs/__funannotate@1.8.15/lib/python3.8/site-packages/pandas/core/frame.py", line 3760, in __getitem__
    indexer = self.columns.get_loc(key)
  File "/_conda/envs/__funannotate@1.8.15/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3654, in get_loc
    raise KeyError(key) from err
KeyError: 'GO'

After some debugging, I found out that it comes from a breaking change in pandas2

Change the default argument of regex for Series.str.replace() from True to False. Additionally, a single character pat with regex=True is now treated as a regular expression instead of a string literal. (GH36695, GH24804)

Here's a PR that always set the regex param to True, so it should work whatever pandas version is installed

abretaud added a commit to bioconda/bioconda-recipes that referenced this pull request Apr 26, 2023
@nextgenusfs nextgenusfs merged commit f6063f3 into nextgenusfs:master Apr 26, 2023
nextgenusfs pushed a commit to bioconda/bioconda-recipes that referenced this pull request Apr 26, 2023
* Pin pandas

nextgenusfs/funannotate#906

* Add comment for future update
cokelaer pushed a commit to cokelaer/bioconda-recipes that referenced this pull request Apr 28, 2023
* Pin pandas

nextgenusfs/funannotate#906

* Add comment for future update
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2 participants