Mismatch between pip and conda dependency pins: which is the intended one?

[corneliusroemer]

In this docker-base PR nextstrain/docker-base#145 the build failed because pip seems to think that evofr constrains jaxlib as 0.3.10 <= jaxlib < 0.4.0 and I upgraded jaxlib to 0.4.6 (see for error in build https://github.com/nextstrain/docker-base/actions/runs/4881147643/jobs/8709697128#step:8:2789)

evofr 0.1.18 depends on jaxlib<0.4.0 and >=0.3.10

I was surprised by this, as the conda recipe has different version pins, allowing any minor version

jaxlib >=0.3.10, <1

see https://github.com/bioconda/bioconda-recipes/blob/master/recipes/evofr/meta.yaml#LL27C7-L27C26

You specify the pip dependencies here as

evofr/pyproject.toml

Line 13 in 8009bb6

jaxlib = "^0.3.10"

The caret ^ pins the minor version for major version 0 only (for all major versions >0 it pins only major version), see https://python-poetry.org/docs/dependency-specification/

So either:

• a) you weren't aware of this when writing the pyproject.toml, you actually wanted to pin major version only, or
• b) the translation from pyproject.toml to conda is not 1-to-1

jaxlib isn't the only dependency where this matters, same issue for jax, numpyro and blackjax

Would be good to sort out what is intended and align conda and pip to whatever you want it to be.

[tsibley]

Ah, good catch. This is a mistake in my translation of the Poetry dependency specs to Conda specs. I'll make a fix to the Conda packaging so it matches the Python packaging.

If @marlinfiggins wants to relax the dependency specs (or not), that's up to him and can be handled separately. I think Poetry, like npm, defaults to the "compatible release" operator (^) when adding dependencies.

[tsibley]

@corneliusroemer If you could review bioconda/bioconda-recipes#40779, that'd be appreciated.

[corneliusroemer]

Done! Thanks!