Fix pandas CopyWarning - Githubissues

CVUA-RRW / FooDMe

A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.

https://cvua-rrw.github.io/FooDMe

BSD 3-Clause "New" or "Revised" License

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Fix pandas CopyWarning #35

Closed gregdenay closed 2 years ago

gregdenay commented 2 years ago

Fix pandas CopyWarning #31 Replaced dataframe selection with direct reference by selecion with the .loc[] operator in concatenate_uniq() in workflow/rules/common.smk

Checklist

[x] Title of this PR is meaningful
[x] Comprehensive description of the changes
[x] Link eventual issues
[x] Test modifications
[x] If there are new parameters: update foodme.py
[x] If there are new parameters: update config template
[x] Update README if nescessary
[x] Add modifications to changelog.md

gregdenay commented 2 years ago

New problem in newer pandas version:

FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.

Need to fix before merge!

Warning comes for the rule filter_blast

gregdenay commented 2 years ago

Replaced

df.append(new_rows)

pd.concat([df, new_rows])