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workflow catalog not being build for past months #29

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m-jahn opened this issue Oct 11, 2024 · 1 comment
Open

workflow catalog not being build for past months #29

m-jahn opened this issue Oct 11, 2024 · 1 comment

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@m-jahn
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m-jahn commented Oct 11, 2024

First of all I like to say that I really love the idea of this catalog.
However, in order to be useful for the community, it needs to build correctly. Looking at the GH Actions runs status of the past months, it seems like the catalog has not been (fully?) built for several months now (generate-catalog action fails).
I can see several issues:

  1. latest issue: mamba-org/provision-with-micromamba@main --> This action is deprecated and no longer maintained. Seems to lead to micromamba not accepting the -p option anymore (?). With this issue the wf fails after a couple of seconds
  2. Request GET /search/repositories?sort=updated&q=snakemake+workflow+in%3Areadme+archived%3Afalse&page=3 failed with 403: Forbidden. This appears after a while and after a couple of dozen repos have been catalogued. It happens repeatedly and after X trys the action stops (too many 403 error responses). Likely some GH server limitation.
  3. several weeks ago the catalog was being build by generate-catalog, but the next action cleanup-catalog failed with this rather strange error:
Run git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
  git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
  git config --local user.name "github-actions[bot]"
  git commit -m "Add changes" -a
  shell: /usr/bin/bash -e {0}
  env:
    MSYS: winsymlinks:nativestrict
    MAMBA_ROOT_PREFIX: /home/runner/micromamba-root
    MAMBA_EXE: /home/runner/micromamba-bin/micromamba
On branch main
Your branch is up to date with 'origin/main'.

nothing to commit, working tree clean
Error: Process completed with exit code 1.

I think the catalog is too good a project to be stalled like this! If we look at the nextflow/nf-core community, they have extremely nicely documented workflows and I think that the catalog could be something like that, but it needs more development.

I would try to fix some of this if I'd have a starting point, but I fear it's troublesome to debug a GH actions workflow in another repo. Are there any recommendations on how to run/debug this locally?

@m-jahn
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m-jahn commented Nov 4, 2024

Any ideas how to fix these issues or enable the SM community to fix them @johanneskoester ?

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