ENH: add actions to filter MAGs

[misialq]

Closes #160.

Some artifacts useful for testing can be found here.

[codecov]

Codecov Report

Attention: Patch coverage is 96.98795% with 5 lines in your changes are missing coverage. Please review.

Project coverage is 97.78%. Comparing base (06a920b) to head (5df5b4e).
Report is 3 commits behind head on main.

❗ Current head 5df5b4e differs from pull request most recent head 8c43fcb

Please upload reports for the commit 8c43fcb to get more accurate results.

Files	Patch %	Lines
q2_moshpit/filtering/filter_mags.py	93.44%	4 Missing ⚠️
q2_moshpit/filtering/tests/test_filter.py	98.91%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #169      +/-   ##
==========================================
- Coverage   97.82%   97.78%   -0.04%     
==========================================
  Files          64       67       +3     
  Lines        3534     3700     +166     
==========================================
+ Hits         3457     3618     +161     
- Misses         77       82       +5     

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[VinzentRisch]

Hi @misialq
I ran it with the provided data with no problems.
I have one suggestion. If I understand correctly the metadata is not optional and has to be provided for the filter actions. If the metadata is not given in the command, the error message is NoneType' object has no attribute 'get_ids, what is not very informative. I would add a check that raises an error if metadata is None, with an informative error message.
Apart from that all looks good! :)

[misialq]

Hey @VinzentRisch, thanks, good catch! Actually, it does not make much sense for the metadata to be optional - otherwise, there's nothing to filter on... I just turned it into a required argument - hope that addresses your comment ;)

[VinzentRisch]

Ah yeah that makes sense.
Now I'm thinking that where should also be mandatory.
I saw that if where is None then an artifact is returned with all the original Mags.
But this does not have any application right? It just copies the artifact. So i dont think that where should be allowed to be None.

[misialq]

No, it should not be mandatory. You can also provide a metadata file which contains the IDs you want to filter on - there is no need to provide the "where" condition in such a case (you may already have a metadata table which is pre-filtered). This is explained in the help description of metadata and where parameters.

[VinzentRisch]

Ah okay that makes sense.

[VinzentRisch]

Looks good :)