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kaizhang / SnapATAC2

Single-cell epigenomics analysis tools
https://kzhang.org/SnapATAC2/
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Fix failing docker image builds #282

Closed njmei closed 3 months ago

njmei commented 3 months ago

  1. It turns out tests were failing because the github actions/checkout plugin by default does not download git LFS files. This was causing later tests to fail because they were expecting full test files instead of git LFS pointers.

  2. This commit also restores the matrixed snap-atac-flavor options. Each run of the updated workflow will release default as well as a recommend-interactive snapatac2 docker image.

Note: tests in this PR are probably failing because it is still pointing at: kaizhang/SnapATAC2/.github/workflows/docker.yml@main

https://github.com/kaizhang/SnapATAC2/blob/b7854948133e7a1a59badcf53432fc57ef236f98/.github/workflows/test_python.yml#L47-L50

Validation: On my fork, the Test Docker Image portion passes. Note that the login step fails (because I didn't set up docker credentials on my fork): https://github.com/njmei/SnapATAC2/actions/runs/8503169951/job/23288304288

njmei commented 3 months ago

@kaizhang It would probably also be a good idea to prevent external PR requests to accidentally trigger your github actions workflows. It will use up your github actions credits and malicious actors could submit bogus PRs that could hijack the github actions runners to do unsavory things.

I think you can do this by following this guide: https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/enabling-features-for-your-repository/managing-github-actions-settings-for-a-repository#controlling-changes-from-forks-to-workflows-in-public-repositories

Require approval for all outside collaborators. is probably the safest option.

codecov-commenter commented 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 98.23%. Comparing base (b785494) to head (e2bf521).

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #282 +/- ## ======================================= Coverage 98.23% 98.23% ======================================= Files 4 4 Lines 227 227 ======================================= Hits 223 223 Misses 4 4 ```

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