kammerje / spaceKLIP

Pipeline for reducing JWST high-contrast imaging data. Published in Kammerer et al. 2022 and Carter et al. 2022.
https://ui.adsabs.harvard.edu/abs/2022SPIE12180E..3NK/abstract
MIT License
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spaceKLIP CI testing broken by some git clone hook thing #177

Closed mperrin closed 3 weeks ago

mperrin commented 1 month ago

All CI tests for spaceKLIP are apparently failing, due to error when cloning pyKLIP. Like this:

Collecting pyklip@ git+https://bitbucket.org/pyKLIP/pyklip.git@jwst (from -r requirements.txt (line 12))
  Cloning https://bitbucket.org/pyKLIP/pyklip.git (to revision jwst) to /tmp/pip-install-
  Running command git clone --filter=blob:none --quiet https://bitbucket.org/pyKLIP/pyklip.git /tmp/pip-install-
  warning: filtering not recognized by server, ignoring
  warning: filtering not recognized by server, ignoring
  fatal: active `post-checkout` hook found during `git clone`:
        /tmp/pip-install-cp5at_9t/pyklip_b58c0333991a47c882d2193ee7dbb39d/.git/hooks/post-checkout
  For security reasons, this is disallowed by default.
  If this is intentional and the hook should actually be run, please
  run the command again with `GIT_CLONE_PROTECTION_ACTIVE=false`
  warning: Clone succeeded, but checkout failed.
  You can inspect what was checked out with 'git status'
  and retry with 'git restore --source=HEAD :/'

  error: subprocess-exited-with-error

Paging @semaphoreP in case you might understand this better than I do?

mperrin commented 1 month ago

oh, it's related to an upstream bug and security fix in git itself, apparently.

https://github.com/git-lfs/git-lfs/issues/5749

mperrin commented 1 month ago

I guess we workaround by setting GIT_CLONE_PROTECTION_ACTIVE=false in the CI setup

semaphoreP commented 1 month ago

welp... hopefully that gets fixed shortly. hopefully in the future we can use the pip version of pyklip once all these changes get merged.

AarynnCarter commented 4 weeks ago

CI tests are working now, I think this has been resolved?

mperrin commented 3 weeks ago

Yes confirmed, this was fixed upstream last week or so.