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Specify pandas version 1.5.3 in setup.py #49

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merged 1 commit into from
Jun 14, 2023

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amilworks
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@amilworks amilworks commented Jun 13, 2023

Reason for PR

Fresh installs of the codebase causes failure at append usage. For instance,

  File "/cvapipe_analysis/cvapipe_analysis/steps/load_data/load_data_tools.py", line 123, in get_interphase_test_set
    df_test = df_test.append(df_struct.sample(n=n, random_state=666, replace=False))
  File "/opt/conda/envs/cvapipe/lib/python3.8/site-packages/pandas/core/generic.py", line 5989, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'append'

Pandas version 2.0 and above has deprecated append. Eventually we will need to convert the syntax and modify parts of the code to work with concat.

Proposed Fix

We define the specific version used in the original development of the codebase pandas==1.5.3 in the setup.py.

Tests

The updated code has been tested with the steps outlined in the README. All steps ran successfully.

@vianamp vianamp merged commit 3e5e3cd into AllenCell:master Jun 14, 2023
@pgarrison pgarrison mentioned this pull request Mar 28, 2024
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2 participants