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Pandas 2 Compatibility #193

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merged 3 commits into from
Aug 15, 2023
Merged

Pandas 2 Compatibility #193

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b8d6d38
Updating to be compatible with Pandas2.
emarinier Aug 11, 2023
e9a0c02
Updating GH workflow and changelog.
emarinier Aug 15, 2023
ddbd534
Trying to add Perl dependency.
emarinier Aug 15, 2023
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6 changes: 3 additions & 3 deletions .github/workflows/ci-test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,8 @@ jobs:
fail-fast: False
matrix:
include:
- python-version: "3.7"
other-packages: "mlst 'numpy <1.23.5' 'pandas <2'"
- python-version: "3.9"
other-packages: "mlst numpy pandas"

steps:
- uses: actions/checkout@v2
Expand All @@ -47,7 +47,7 @@ jobs:
conda config --add channels bioconda
conda install -n base conda-libmamba-solver
conda config --set solver libmamba
conda install Cython blast git ${{ matrix.other-packages }} -y
conda install Cython blast git perl-list-moreutils ${{ matrix.other-packages }} -y

- name: Setup python packages
shell: bash -l {0}
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1 change: 1 addition & 0 deletions CHANGELOG.md
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@@ -1,5 +1,6 @@
# Unreleased

* Upgraded to pandas version 2.
* Added CGE-predicted phenotypes to Pointfinder output.
* The resfinder.tsv and pointfinder.tsv outputs now contain a Notes column.
* Updated the help description of the --mlst-scheme parameter to include a more useful link for available schemas.
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4 changes: 2 additions & 2 deletions staramr/subcommand/Search.py
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Expand Up @@ -203,7 +203,7 @@ def _print_dataframes_to_excel(self, outfile_path, summary_dataframe, resfinder_
settings_dataframe.to_excel(writer, 'Settings')
self._resize_columns({'Settings': settings_dataframe}, writer, max_width=75, text_wrap=False)

writer.save()
writer.close()

def _resize_columns(self, sheetname_dataframe, writer, max_width, text_wrap=True):
"""
Expand Down Expand Up @@ -555,7 +555,7 @@ def run(self, args):
logger.info("Writing Excel to [%s]", output_excel)
settings_dataframe = pd.DataFrame.from_dict(settings, orient='index')
settings_dataframe.index.name = 'Key'
settings_dataframe.set_axis(['Value'], axis='columns', inplace=True)
settings_dataframe = settings_dataframe.set_axis(['Value'], axis='columns', copy=False)

self._print_dataframes_to_excel(output_excel,
amr_detection.get_summary_results(),
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