use the run command of conda / mamba / micromamba and support pixi

[keewis]

Change Summary

This adds the --environment-manager and --environment-manager-path cli options, as well as replacing the activate step with the run subcommand.

No tests, yet.

Related issue number

• closes use the run command of conda / mamba / micromamba #257, closes execute command before entering conda environment #248

Checklist

• Unit tests for the changes exist
• Tests pass on CI
• Documentation reflects the changes where applicable

[keewis]

this should be ready, but we could in theory also add support for uv (which should be pretty close to pixi, but with slightly different options for run)

cc @andersy005

[andersy005]

thank you so much for putting this together, @keewis! It looks solid

[andersy005]

this should be ready, but we could in theory also add support for uv (which should be pretty close to pixi, but with slightly different options for run)

if you don't have time/capacity to work on uv support, let's leave it for another PR in the future

[keewis]

looking at it again, uv appears to be a bit different in that you manually include dependency groups or optional dependencies instead of choosing an environment. Possibly we can come up with a way to encode this in the environment string, like

<path>:extras=extra1,extra2:groups=group1,group2,-default  # `-default` means exclude the default group
<path>:extras=+,-extra1:groups=-group3  # `+` means all extras

or add a way to pass options to uv, but I do think that this is complex enough that it should be a different PR.

(also, I don't know uv well enough to really know what I'm proposing)

[keewis]

or maybe the default group (dev) is enough for now, in which case this should be simple enough to implement