snakemake: 9.1.10 -> 9.3.0

[r-ryantm]

Automatic update generated by nixpkgs-update tools. This update was made based on information from passthru.updateScript.

meta.description for snakemake is: Python-based execution environment for make-like workflows

meta.homepage for snakemake is: https://snakemake.github.io

meta.changelog for snakemake is: https://github.com/snakemake/snakemake/blob/v9.3.0/CHANGELOG.md

Updates performed

• Ran passthru.UpdateScript

To inspect upstream changes

Impact

Checks done

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• built on NixOS
• The tests defined in passthru.tests, if any, passed
• found 9.3.0 with grep in /nix/store/p1pbg4kk5hzfx1b9s18lpk7zl73qr1kh-snakemake-9.3.0
• found 9.3.0 in filename of file in /nix/store/p1pbg4kk5hzfx1b9s18lpk7zl73qr1kh-snakemake-9.3.0

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Rebuild report (if merged into master) (click to expand)

8 total rebuild path(s)

8 package rebuild(s)

First fifty rebuilds by attrpath

python312Packages.snakemake
python312Packages.snakemake-storage-plugin-s3
python312Packages.snakemake-storage-plugin-xrootd
python313Packages.snakemake
python313Packages.snakemake-storage-plugin-s3
python313Packages.snakemake-storage-plugin-xrootd
snakemake

Instructions to test this update (click to expand)

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Either download from the cache:

nix-store -r /nix/store/p1pbg4kk5hzfx1b9s18lpk7zl73qr1kh-snakemake-9.3.0 \
  --option binary-caches 'https://cache.nixos.org/ https://nixpkgs-update-cache.nix-community.org/' \
  --option trusted-public-keys '
  nixpkgs-update-cache.nix-community.org-1:U8d6wiQecHUPJFSqHN9GSSmNkmdiFW7GW7WNAnHW0SM=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The nixpkgs-update cache is only trusted for this store-path realization.)
For the cached download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.

Or, build yourself:

nix-build -A snakemake https://github.com/r-ryantm/nixpkgs/archive/4ba9631cbc6d3de0e2e2dc6d613954f7cff7e2d3.tar.gz

Or:

nix build github:r-ryantm/nixpkgs/4ba9631cbc6d3de0e2e2dc6d613954f7cff7e2d3#snakemake

After you've downloaded or built it, look at the files and if there are any, run the binaries:

ls -la /nix/store/p1pbg4kk5hzfx1b9s18lpk7zl73qr1kh-snakemake-9.3.0
ls -la /nix/store/p1pbg4kk5hzfx1b9s18lpk7zl73qr1kh-snakemake-9.3.0/bin

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Pre-merge build results

We have automatically built all packages that will get rebuilt due to
this change.

This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review

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x86_64-linux

✅ 12 packages built:

• snakemake (python312Packages.snakemake)
• python312Packages.snakemake-storage-plugin-s3
• python312Packages.snakemake-storage-plugin-s3.dist
• python312Packages.snakemake-storage-plugin-xrootd
• python312Packages.snakemake-storage-plugin-xrootd.dist
• snakemake.dist (python312Packages.snakemake.dist)
• python313Packages.snakemake
• python313Packages.snakemake-storage-plugin-s3
• python313Packages.snakemake-storage-plugin-s3.dist
• python313Packages.snakemake-storage-plugin-xrootd
• python313Packages.snakemake-storage-plugin-xrootd.dist
• python313Packages.snakemake.dist

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Maintainer pings

cc @Helkafen @renatoGarcia @veprbl for testing.

Tip

As a maintainer, if your package is located under pkgs/by-name/*, you can comment @NixOS/nixpkgs-merge-bot merge to automatically merge this update using the nixpkgs-merge-bot.

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