add bioservices

[hadim]

Checklist

• Title of this PR is meaningful: e.g. "Adding my_nifty_package", not "updated meta.yaml".
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[conda-forge-linter]

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/bioservices) and found some lint.

Here's what I've got...

For recipes/bioservices:

• noarch: python recipes are required to have a lower bound on the python version. Typically this means putting python >=3.6 in both host and run but you should check upstream for the package's Python compatibility.

For recipes/bioservices:

• Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.
• License is not an SPDX identifier (or a custom LicenseRef) nor an SPDX license expression.

Documentation on acceptable licenses can be found here.

[conda-forge-linter]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/bioservices) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipes/bioservices:

• Recipe with the same name exists in bioconda: please discuss with @conda-forge/bioconda-recipes.

[hadim]

Ping @conda-forge/bioconda-recipes about this package. Are you ok adding it to conda-forge?

[hadim]

@conda-forge/staged-recipes please review

[jakirkham]

LGTM. Had one question above

[jakirkham]

Just noticed they also mention BSD-3-Clause despite including GPL 3. Asking about that here ( cokelaer/bioservices#187 )

[hadim]

Just noticed they also mention BSD-3-Clause despite including GPL 3. Asking about that here ( cokelaer/bioservices#187 )

Thanks for doing that.

[hadim]

Is that ok to merge here and fix the license once that has been clarified? Or is it a blocker in your opinion @jakirkham ?

[jakirkham]

I've tried to poke that issue. It feels a little messy atm since there is a wide gap between GPL-3 and BSD-3. I think just getting an answer from the author would help

[jakirkham]

cc @conda-forge/bioconda-recipes (as it looks like the same recipe may be in Bioconda)

[hadim]

The licensing seems to have been clarified. Is that ok to merge @jakirkham or do we need specific approval from bioconda folks?

[jakirkham]

We need feedback from Bioconda since they already package this

[mbargull]

Hi @hadim and @jakirkham, sorry for the late reply.
The license should be GPL-3.0-only since the source does not seem to have the "or any later version" phrase in it (apart from the GPL text itself which just describes on how to apply it).
What is the intend on moving this over from Bioconda?

Cheers,
Marcel
(I'm going AFK for today, but will get back to you in the following days.)

[hadim]

@mbargull the main motivation for moving it on conda-forge is to rely only on the conda-forge channel to build our stack. As adding more channels tends to the complexity the graph of deps solving step with conda/mamba.

[bgruening]

@hadim thats ok. Just make sure you remove the recipe from the bioconda side.

[hadim]

Is that ok to merge here?

@bgruening once merged here I can remove the recipe from bioconda. Is there is a specific procedure to follow?

[mbargull]

Sorry for the delay.

As adding more channels tends to the complexity the graph of deps solving step with conda/mamba.

Understandable, both implementations have different deficiencies with this, indeed.

@bgruening once merged here I can remove the recipe from bioconda. Is there is a specific procedure to follow?

Yes, please open a PR on bioconda-recipes to remove the recipe with a reference to this PR; much appreciated!

[hadim]

Thank you. See the PR bioconda/bioconda-recipes#28010

[cokelaer]

@hadim @bgruening
I'm the main author of bioservices and I am not sure I understood the rational in moving bioservices from bioconda to conda-forge. BioServices is indeed a software that is dedicated to bioinformatics and biological web services access and I have the feeling it would be more visible in bioconda rather than conda-forge ? For end-users, it should be equivalent of course but I ust want to make sure that it makes sense before updating the documentation. thanks

[hadim]

@cokelaer I think the main motivation is to reduce the number of conda channels in a custom conda environment. Having a lower number of channels reduces the dep graph solver computational time and in consequence reduces the conda env creation in CI, local machines, docker images, production, etc.

Since (if I am not mistaken), bioconda is relying on conda-forge as you said it should not change anything to the main user.

As for the visibility I understand having it in conda-forge makes it less visible but maybe this is not the most important channel of communication?

I apologize if you feel strongly against the move.

[cokelaer]

@hadim thanks for the quick reply and explanations. If it does not change anything for the user, I believe this move is for the best. thanks for your work. best