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pepkit / peppy

Project metadata manager for PEPs in Python
https://pep.databio.org/peppy
BSD 2-Clause "Simplified" License
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Pandas frame.append method is deprecated #416

Open matinnuhamunada opened 1 year ago

matinnuhamunada commented 1 year ago

Hi, thanks for the nice tool here :)

When running peppy.Project(project_config_file), I keep getting this warning:

/home/matinnu/miniconda3/envs/snakemake/lib/python3.10/site-packages/peppy/project.py:103: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  df = df.append(ser, ignore_index=True)

This is how the config file looks like:

name: example2
pep_version: 2.0.0
description: "test_project"
sample_table: samples.csv
prokka-db: prokka-db.csv
gtdb-tax: gtdbtk.bac120.summary.tsv
output_dir: "$HOME/test"

This does not throw an error, but might be something to be addressed in the long run?

vreuter commented 1 year ago

@nsheff @Khoroshevskyi it looks like this has been fixed?

khoroshevskyi commented 1 year ago

I am not sure if it was fixed, but also I can't see pandas append function used anywhere. So I it's probably fixed.