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global epistasis models give different results with pandas 2.2 #128

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jbloom opened this issue Jan 27, 2024 · 2 comments
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global epistasis models give different results with pandas 2.2 #128

jbloom opened this issue Jan 27, 2024 · 2 comments

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@jbloom
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jbloom commented Jan 27, 2024

@jgallowa07, this seems like potentially a significant bug. When I run the global epistasis models in the dms-vep-pipeline-3/test_example, I get substantially different results depending on whether I use pandas 2.1 or pandas 2.2 (I also have pyarrow installed). The pandas 2.1 results are consistent with earlier versions, but the pandas 2.2 are much different.

Note that I cannot rule out that this caused by a bug in pandas 2.2.0 which is a recent release, but I wanted to flag it here.
@jbloom jbloom mentioned this issue Jan 27, 2024
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jbloom added a commit to dms-vep/dms-vep-pipeline-3 that referenced this issue Jan 28, 2024
@jbloom
update environment (#98)
f54eb3a 
- Update environment:
  - update `polyclonal` to 6.10 (addresses [this issue](#96))
  - update `neutcurve` to 1.1.2
  - update `altair` to 5.2.0
  - update `biopython` to 1.83
  - update `pandas` to 2.1 and add `pyarrow`. Did not update to `pandas` 2.2 due to [this issue](matsengrp/multidms#128).
  - update to `seaborn` 0.13
  - update to `snakemake` 8.3. **Note that this means the recommended usage now changes from `--use-conda` to `--software-deployment-method conda`.**
- sort rows in prob escape values for consistent output, may very slightly change some of the fit antibody-escape values
@jgallowa07 jgallowa07 mentioned this issue Jan 30, 2024
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@jgallowa07
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Good catch @jbloom. Indeed, when I updated to pandas==2.2.0 the unit tests fail. I've added a patch over at #129 That explains things in more detail.

However, this patch is for multidms>=3.1, and I understand that the dms-vep-pipeline is still reliant on an older version of multidms==0.2.1 until dms-vep/dms-vep-pipeline-3#91 gets finished and merged.

Hopefully I will get that PR ready for review this week, but if you need a patch for this issue now I could always branch off of 0.2.1 to patch this specific bug and you could point to that to install directly from github.

@jbloom
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jbloom commented Jan 30, 2024

Great, and thanks for the explanation of the bug. For now I have pinned pandas=2.1 for the pipeline so this should work fine until the new multidms is merged into the pipeline.

@jbloom jbloom mentioned this issue Apr 23, 2024
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