Pixi creates incorrect shims when globally installed package has two executables with the same stem

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Pixi creates incorrect shims when globally installed package has two executables with the same stem #1619

Open jdidion opened 3 months ago

jdidion commented 3 months ago

Checks

[X] I have checked that this issue has not already been reported.
[X] I have confirmed this bug exists on the latest version of pixi, using pixi --version.

Reproducible example

pixi global install -c bioconda samtools

Issue description

The samtools package has a samtools and a samtools.pl binary. The samtools shim created in the global bin folder calls samtools.pl rather than samtools.

Expected behavior

Each executable has it's own shim with the same name.

davised commented 3 months ago

Not a pixi dev, but this is how they handle all binaries for global installs. Suffix gets stripped off and binary gets converted to lowercase.

I suggest not using a global install for samtools to get around this issue.

jdidion commented 3 months ago

@davised thanks for confirming that this is an issue.

I'd really appreciate a Pixi dev explaining why this is the behavior. Was there a motivating use case?

I'd like to propose a better solution: leave any file extensions on a binary in place, and create a link to the binary with extensions stripped off only if there is no conflict with an existing binary. If installing a new binary would conflict with an existing link, warn the user and require them to pass a flag to force overwriting the link.

davised commented 2 months ago

I understand the rationale. If you have a samtools.pl file and try to run it like perl samtools.pl, it will not work. Since the files are actually wrappers rather than say python or perl code, it doesn't make sense to leave the suffix.

I haven't seen the rationale explained anywhere, but it does seem to make sense to me.

allytrope commented 1 month ago

I'm encountering this problem too. samtools does work correctly when used in a project environment instead of globally. So this behavior just needs to be carried over to global way as well.

tdejager commented 1 month ago

Note that we are working on a revamped pixi global, so this consideration might need to be taken into account: https://pixi.sh/latest/design_proposals/pixi_global_manifest/

cc @Hofer-Julian @nichmor