colomoto / colomoto-docker

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
https://colomoto.github.io/colomoto-docker/
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CasQ is outdated #139

Closed pauleve closed 2 months ago

pauleve commented 6 months ago

Reported by @soli

The conda package of CasQ https://anaconda.org/colomoto/casq is outdated (1.0.3)

The source is in the CasQ repository https://github.com/soli/casq, however it is likely not packaged upon release. We need to either package it externally in colomoto/colomoto-conda repo and find a way to sync with Pypi releases ; or include the casq conda packaging in the casq release workflow.

soli commented 6 months ago

Ha ha, I just opened an issue about that in colomoto-conda ^^ Yes, Aurélien used to publish directly from casq repo I think, but we need to:

Both are fine with me.

EDIT: After a little time reading about it, would publishing CaSQ on conda-forge be a solution? It seems they provide a pretty streamlined way to automatically build conda packages from PyPI published packages: https://www.pyopensci.org/python-package-guide/tutorials/publish-conda-forge.html

pauleve commented 6 months ago

conda-forge sounds a great solution indeed, provided all your dependencies are in it already (which seems the case). I never looked how to do that concretely. Do you want to give it a try? I can also take a look later.

Adding the conda packaging to the release workflow is quite simple (e.g. https://github.com/bnediction/bonesis/blob/master/.github/workflows/release.yml#L37) ; we can provide you a token for pushing to the colomoto channel.

But maybe give a try to conda-forge first? If it works, it could be a great solution for us in general.

soli commented 6 months ago

I'll try conda-forge then. I wonder if this will create a "conflict" with the casq package from colomoto on anaconda.org, but maybe you'll just need to force the "channel" when building the image?

I'll keep you posted on how the conda-forge thing goes anyway.

pauleve commented 6 months ago

Awesome, thanks :-)

No problem with the channel, we can handle that.

soli commented 5 months ago

Ok, it ended up being very slow due to subtle technical issues (so, I'm not sure I'd recommend the conda-forge way… still, when it works, it seems great) but here we have it: https://anaconda.org/conda-forge/casq

pauleve commented 5 months ago

Great! Thanks a lot. It will be in the next release: #144

For the record:

pauleve commented 2 months ago

Released with image 2024-09-01