MAINT: move partitioning and collating actions to q2-types

[VinzentRisch]

solves #172
blocked by qiime2/q2-types#334

• Removed partitioning and collating actions that have been moved to q2-types.
• Removed actions partition_feature_data_mags, collate_feature_data_mags, collate_annotations, collate_orthologs, partition_orthologs, partition_sample_data_mags, collate_sample_data_mags, _validate_mag_ids and _validate_num_partitions from q2-moshpit.
• Removed partition module.
• Moved collate_busco_results to file partition.py in busco module.
• Added test for collate_busco_results.
• Changed all instances where these actions are used in q2-moshpit to be imported from q2-types.

[misialq]

Hey @VinzentRisch, could you please update this PR to:

• modify it in the context of ENH: Migrated partition and collating actions from q2-moshpit to q2-types qiime2/q2-types#334, if needed
• resolve the merge conflicts

I'd like to review this PR together with the other one in q2-types 😄 Also, after you do that the CI should be working fine again 🚀

[github-actions]

This PR/issue depends on:

• ENH: Migrated partition and collating actions from q2-moshpit to q2-types qiime2/q2-types#334

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.23%. Comparing base (2562a9a) to head (8f5cc81).
Report is 3 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #175      +/-   ##
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- Coverage   98.56%   98.23%   -0.33%     
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  Files          85      142      +57     
  Lines        4872     9286    +4414     
  Branches        0      386     +386     
==========================================
+ Hits         4802     9122    +4320     
- Misses         70      116      +46     
- Partials        0       48      +48     

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[misialq]

Hey @VinzentRisch, seems like the tests still are failing after merging the PR in q2-types. Could you please investigate?

[misialq]

Hey @VinzentRisch, still failing?

[VinzentRisch]

@misialq sorry I got sidetracked with amrfinderplus.
So I forgot to add the files to the package data and i thought that was the bug but there is still this error:
FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/q2-moshpit/q2-moshpit/test-env/lib/python3.9/site-packages/q2_moshpit/busco/tests/data/busco_results/sample1/busco_results.tsv'

even though the file is pushed and in the package data. Do you know what the problem could be?

[VinzentRisch]

Good Morning @misialq
Now there is a conflict. I added your suggestion and there it already pops up. Also after the merge its still there.
Could not solve for environment specs The following package could not be installed └─ q2-moshpit 2024.10.0.dev0+37.g600da44** is not installable because it requires ├─ python_abi 3.10.* *_cp310, which can be installed; └─ qiime2 2024.10.* , which requires └─ python_abi 3.9.* *_cp39, which conflicts with any installable versions previously reported.

[misialq]

Hey @VinzentRisch, this is due to the last PR we merged which updated Python to 3.10... I'm guessing this will get resolved soon so maybe we can keep this PR open for now and re-run the CI when everything is expected to work again.

Hey @lizgehret, do you think you can give us an estimate when that would be the case (approximately)? Thanks!

[lizgehret]

Hey @misialq, this should be fixed by EOD, sorry about the delay! I'll re-run these jobs once metagenome is all squared away 🙂

[misialq]

No worries, no rush @lizgehret and thanks a lot!

[lizgehret]

Okay @misialq, metagenome is g2g! Just re-ran the actions on this PR, so you should get a solved env this time around. Let me know if you run into anything else that's weird!

[misialq]

Great work @VinzentRisch, thanks! 🚀