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Support pandas v2 #1671

Merged
merged 4 commits into from
Nov 13, 2024
Merged

Support pandas v2 #1671

merged 4 commits into from
Nov 13, 2024

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corneliusroemer
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@corneliusroemer corneliusroemer commented Nov 10, 2024

Support pandas v2.

Pathogen CI uses whatever pandas version is installed by conda base if augur doesn't have conflicting requirements, which is v1 right now, so I made an ephemeral test PR to exclude v2 to test pathogen CI with v2 and it passed, see #1672

Related issue(s)

Resolves #1471
Part of #1473

Checklist

  • Automated checks pass
  • Check if you need to add a changelog message
  • Check if you need to add tests
  • Check if you need to update docs

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codecov bot commented Nov 10, 2024

Codecov Report

Attention: Patch coverage is 66.66667% with 1 line in your changes missing coverage. Please review.

Project coverage is 72.30%. Comparing base (4b5ad2a) to head (5b4efab).
Report is 1 commits behind head on master.

Files with missing lines Patch % Lines
augur/parse.py 66.66% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1671      +/-   ##
==========================================
+ Coverage   72.29%   72.30%   +0.01%     
==========================================
  Files          79       79              
  Lines        8276     8276              
  Branches     1691     1691              
==========================================
+ Hits         5983     5984       +1     
+ Misses       2008     2007       -1     
  Partials      285      285              

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@victorlin victorlin mentioned this pull request Nov 11, 2024
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@corneliusroemer corneliusroemer changed the title Cornelius' attempt to unblock pandas v2 Support pandas v2 Nov 12, 2024
@corneliusroemer corneliusroemer marked this pull request as ready for review November 12, 2024 13:52
@victorlin victorlin mentioned this pull request Nov 12, 2024
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@victorlin
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I've moved the post-merge checklist to the task list in #1473

@corneliusroemer
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Not merging this yet so we can release what's on master right now (quite a bit), so we can detect pandas changes in a following release.

CHANGES.md Outdated
@@ -4,6 +4,7 @@

### Features

* Support pandas v2. [#1671] (@corneliusroemer and @victorlin)
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Reminder to rebase and update the Changelog so it doesn't get out-of-sync due to the latest release of v26.1.0.

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Or merge via CLI to fix it during the merge as explained in #1620 (comment)

@corneliusroemer corneliusroemer merged commit 3f72c40 into master Nov 13, 2024
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@corneliusroemer corneliusroemer deleted the pandas-v2 branch November 13, 2024 12:37
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4 participants