AlexsLemonade / AlexsLemonade/training-modules
Potentially update GSEA notebook gmt file handling
- Dominant language
- HTML
- Stars
- 77
- Forks
- 35
- Avg merge
- 1d 13h
- Merged PRs (30d)
- 4
Description
The step to read in the GMT file in this notebook from a URL has been failing in GHA, even though this link is accessible and this code runs locally: https://github.com/AlexsLemonade/training-modules/actions/runs/25459583659/job/74821716126
If it turns out Broad is somehow now blocking this request from a GHA, we might want to get the file into a data/references directory first separately and have the notebook read from there. That said, we aren't going to be teaching this material for a little while, so we can also comment these notebooks out from running in GHA temporarily.
Contributor guide
Research direction
Start by inspecting the failing GitHub Actions job and the GSEA notebook step that reads the GMT file from its URL. Determine whether the URL request fails only in GitHub Actions; done means the workflow handles the GMT data reliably, either from a repository reference location or by temporarily excluding the affected notebooks from the workflow.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- github-actions, jupyter-notebook
- Domain
- bioinformatics, ci-cd
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 55/100