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fix: upgrade python-based docker containers to use versions with PYTHONPATH unset #176

Merged
merged 7 commits into from
Nov 26, 2024
Merged

fix: upgrade python-based docker containers to use versions with PYTHONPATH unset #176

merged 7 commits into from
Nov 26, 2024

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kelly-sovacool
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@kelly-sovacool kelly-sovacool commented Nov 26, 2024 •
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Changes

  • Upgrade python-based docker containers to use versions with PYTHONPATH unset.
  • Fix get_flowcell_lanes.py to work with python 3.11 for rule fc_lane.
  • Fix bug during re-run where a function was not imported from ccbr_tools.

Issues

resolves #174

PR Checklist

(Strikethrough any points that are not applicable.)

  • This comment contains a description of changes with justifications, with any relevant issues linked.
  • [ ] Update docs if there are any API changes.
  • Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

@kopardev kopardev added the RENEE RepoName label Nov 26, 2024
@kelly-sovacool kelly-sovacool changed the title Python paths Upgrade python-based docker containers to use versions with PYTHONPATH unset Nov 26, 2024
@kelly-sovacool kelly-sovacool marked this pull request as ready for review November 26, 2024 21:14
@kelly-sovacool kelly-sovacool added the bug Something isn't working label Nov 26, 2024
@kelly-sovacool kelly-sovacool changed the title Upgrade python-based docker containers to use versions with PYTHONPATH unset fix: upgrade python-based docker containers to use versions with PYTHONPATH unset Nov 26, 2024
samarth8392
samarth8392 approved these changes Nov 26, 2024
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A full test run on RENEE test dataset finished successfully.
Slurm Job_id=41749271 Name=pl:renee Ended, Run time 01:15:09, COMPLETED, ExitCode 0

@samarth8392 samarth8392 merged commit 7fe656a into main Nov 26, 2024
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@samarth8392 samarth8392 deleted the python-paths branch November 26, 2024 22:30
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@samarth8392 samarth8392 samarth8392 approved these changes

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upgrade all python dockers
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@kelly-sovacool @samarth8392 @kopardev