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Add t5common package #29

Merged
merged 15 commits into from
Mar 8, 2025
Merged

Add t5common package #29

merged 15 commits into from
Mar 8, 2025

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ajtritt
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@ajtritt ajtritt commented Feb 26, 2025

Add a package for common operations in the Taskforce5 commons.

  • A class for connecting to and interacting with Jira (Python class t5common.jira.JiraConnector)
  • A framework for polling Jira for new issues, and starting workflows (commands init-db, check-jira, and mark-job)
  • A class for building SLURM sbatch scripts (Python class t5common.job.SlurmJob)

Fixes #15

@ajtritt ajtritt requested review from rly and oruebel February 26, 2025 01:01
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oruebel commented Feb 26, 2025

Should the cron jobs/code for pulling data from CSBID and pushing to Jira go here too? @yonglbl @ajtritt

If yes, this can be a separate issue/pr. Just wanted to check.

oruebel
oruebel previously approved these changes Feb 26, 2025
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ajtritt commented Feb 26, 2025

Should the cron jobs/code for pulling data from CSBID and pushing to Jira go here too? @yonglbl @ajtritt

I think we should put the CSBID-specific code in its own package or subdirectory.

@oruebel oruebel added the t5common Shared code for interacting with jira and nersc label Feb 26, 2025
oruebel
oruebel previously approved these changes Mar 5, 2025
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Looks good. It would be useful to add docstrings for the public functions to make it easier for us to reuse the code when setting up new integrations.

@ajtritt ajtritt merged commit 39f0a13 into main Mar 8, 2025
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@ajtritt ajtritt deleted the enh/wf branch March 8, 2025 00:07
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Script for running polling Jira project and running AlphaFold
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