cannot upgrade to python 3.8 because of t_coffee (in the dependency chain of bioperl)

[0xaf1f]

I'm not sure whether t_coffee can be rebuilt for python 3.8+, but my environment is stuck at python 3.7 and I need prokka (the thing needing bioperl) to co-exist with some python code I'm using.

Encountered problems while solving:
  - package t_coffee-11.0.8-py37hea885bf_8 requires python >=3.7,<3.8.0a0, but none of the providers can be installed

[0xaf1f]

related to #29069 and #20459

[matthdsm]

same issue here

[svm-zhang]

I have the same t_coffee problem. The installation was successful using the command below. However, the python shipped along with it was 3.7.12.

mamba create -n test ensembl-vep=105.0

If I tried to update the python to >= 3.9 to work with my other scripts, I saw the exact same error message.

It baffles me and is of course beyond my knowledge about why a perl package requires a very specific python version requirement. I tried to look for t_coffee installation documentation and was not able to find anything that relates to this requirement.

Could someone please help fix this problem or suggest some potential solution that I could try? Much appreciated.

[0xaf1f]

I spent too much time trying to shave this yak at one point and I was at least able to get a good picture of the situation before I ran out of time to do something about it. So gather 'round for story time:

There is t_coffee (Underscore) and t-coffee (Hyphen). Underscore came first, but both are currently on the build blacklist. When packaging Underscore, @ostrokach added a fancy python wrapper to the program executable specifically for the conda package, which is where this python <=3.7 dependency comes in. perl-bio-tools-run-alignment-tcoffee depends on Underscore, so this is how perl and python became intertwined and all these conflicts arose.

I think Hyphen was meant to replace Underscore based on the post-link message in Hyphen:

echo "** WARNING: This T-Coffee recipe is still under development **"
echo ""
echo "It does not contain all required packages to use all T-Coffee modes."
echo "We suggest to use the Bioconda 't_coffee' recipe instead or download it"
echo "from the web site http://www.tcoffee.org"
echo ""

So anyway, we're still stuck with Underscore and its unnecessary dependency on python.

The proper course of action to clean up the situation from what I can tell is to:

• remove Hyphen from the blacklist so that its build doesn't get skipped when you go on to step 2.
• update and finalize the packaging for Hyphen
• change perl-bio-tools-run-alignment-tcoffee so that it depends on Hyphen rather than Underscore. This will break the connection between bioperl and python 3.7.
• celebrate the newfound ability to co-install bioperl and modern versions of python

And then at some point Underscore should be deleted or somehow marked obsolete.

[0xaf1f]

Also related: #10614

[svm-zhang]

@0xaf1f thank you very much for the explanation. Now it all makes sense to me. I will follow the other ticket and hopefully this can get resolved and everybody celebrates!

[0xaf1f]

This has now been fixed!

remove Hyphen from the blacklist so that its build doesn't get skipped when you go on to step 2.

done in a78d91b

update and finalize the packaging for Hyphen

done in #38347

change perl-bio-tools-run-alignment-tcoffee so that it depends on Hyphen rather than Underscore. This will break the connection between bioperl and python 3.7.

done in #38199

celebrate the newfound ability to co-install bioperl and modern versions of python

🎉

There is still a lingering connection between bioperl and python in that t-coffee depends on viennarna, but at least the latter is a declared python package and gets rebuilt when new python packages are introduced. viennarna is only needed by r-coffee, so maybe that could be split out of the t-coffee package at some point.

[amizeranschi]

@0xaf1f many thanks for your help in solving this, once and for all!