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Make git-lfs available at cloning time ?

Open blinard-BIOINFO opened this issue 4 months ago • 2 comments

If I'm not mistaken, when running mulled-tests, there seems to be no way to retrieve github test files that are stored via git-lfs. E.g. files that after cloning appear as empty because not stored on github, but linked to their lfs storage. If the package git-lfs is installed on the system, those are cloned too. If a basal git installation is available, these files are cloned as empty files (actually just a few bytes, the link to the storage.

Note that for github, when creating a release archive, this files are by default not inserted in the archive. Only workaround would be to have some CI releasing a custom archive where everything is present.

Potential workaround: Make sure git-lfs is available when bioconda-utils clones something. I know cloning is discouraged and archive are preferred, but they will not contain test files stored in this way without substantial work.

To reproduce:

  • repo: https://github.com/phylo42/IPK/
  • it contains some test files in tests/data
  • it is not cloned by bioconda-utils, right now I use wget to retrieve the raw test files. See recipe ipk (PR in the process of review).

blinard-BIOINFO avatar Feb 23 '24 10:02 blinard-BIOINFO