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WIP: Python-based action#237

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MillironX wants to merge 34 commits into
nf-core:masterfrom
MillironX:feat/python
Draft

WIP: Python-based action#237
MillironX wants to merge 34 commits into
nf-core:masterfrom
MillironX:feat/python

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@MillironX

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This PR is a work-in-progress to allow me to test some ideas in real, live CI before proposing sweeping changes. DO NOT review or merge until the Work-in-progress/draft flag has been removed. The tl;dr is that I think the JavaScript Action is too hard to maintain, but Philip Ewels' proposed Bash Action isn't quite powerful enough, so I am attempting a Python revision. Unfortunately, these kinds of changes really have to be tested in the CI system itself - act is throwing a fit at the current revision.

MillironX added 30 commits May 29, 2026 16:46
GitHub Actions cannot access the `secrets` scope, they instead need to
default to `github.token`.
In the case of a patch release that comes out after an edge release, we
need to sort by release version, and not time. Leverage a single request
to be able to get whichever version is actually the largest.
This was determined not to be the issue, and adds complexity

This reverts commit 071009e.
This is in anticipation of adding more unit testing
MillironX added 4 commits June 2, 2026 14:03
As previous written, this action was not able to work on external
pipelines. This is because the `github.action_path` scope is not
available in a `uses:` block, but otherwise the consuming pipeline
interprets `./` as relative to _its own_ working directory. This is
another scuffed decision on GHA's part, but we have to live with it, and
it actually explains some of the previous scoping issues and why we had
a back-and-forth with requiring `actions/checkout` within this action.
We fix that by moving everything into one YAML soup, and referencing
each Python relative to `github.action_path`. There is also a change in
scope of which directories are actually cached, as we need to ensure
that secrets are not incorporated into the cache.
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