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updates to pass tests w newer program versions (pandas, black, etc) #101

Merged
merged 12 commits into from
May 23, 2024
Merged

updates to pass tests w newer program versions (pandas, black, etc) #101

merged 12 commits into from
May 23, 2024

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@jbloom jbloom commented May 23, 2024

Fixed
+++++

  • Pass formatting with new black version
  • Pass tests with new pandas version.
  • Fixed simple_mut_consensus for newer versions of pandas when goruping by just one variable.

Changed
+++++++

  • Change code linting to ruff rather than flake8.
  • Test with GitHub Actions rather than Travis CI.
  • Remove mybinder examples.
  • Test on Python 3.11 rather than 3.9.
  • Don't allow pysam version 0.22.1 as it was causing some type of OPENSSL import error.
  • Test with minimap2 version 2.22

@jbloom jbloom merged commit 972f005 into master May 23, 2024
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@jbloom jbloom deleted the pass-tests branch May 23, 2024 18:36
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