ENH: expand predict-genes-prodigal to take SampleData[Contigs] as input

[VinzentRisch]

closes #235

Expands predict-genes-prodigal to take SampleData[Contigs] as input.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.29%. Comparing base (b6d068a) to head (cbaf022).
Report is 16 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #236      +/-   ##
==========================================
- Coverage   95.60%   95.29%   -0.32%     
==========================================
  Files          34       34              
  Lines        1956     1997      +41     
  Branches      226      238      +12     
==========================================
+ Hits         1870     1903      +33     
- Misses         48       51       +3     
- Partials       38       43       +5     

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[misialq]

LGTM overall, just a small comment below. Let's wait for @pmomocabr to test it out before merging ⏳

In the meantime, could you please investigate what happened in the CI tests?

[misialq]

Also, could you please review the parameter/input/output descriptions in the plugin_setup.py? It seems like some of those require updating too 🙏

[VinzentRisch]

So I had a look at the CI failure. It only happens in the macos build but locally the tests run fine.
There is an assertation that os.remove is called once a specific path.

The first call is the correct one:
call('/var/folders/db/x5_t5x655c9_rftmy0wp2t2w0000gn/T/qiime2/runner/processes/26598-1738857143.653269@runner/tmp/q2-OutPath-51u5bu3m/taxdmp.zip'),

The the 4 calls after that look like this:
call(PosixPath('/var/folders/db/x5_t5x655c9_rftmy0wp2t2w0000gn/T/qiime2/runner/processes/26598-1738857143.653269@runner/a565edc1-0bf4-4357-80db-90bef9e8ec63.935881698569870148')),

So it looks like MacOS CI automatically deletes temporary files and is calling os.remove to do so.

To solve this I will change the assertion to: mock_os_rm.assert_any_call(zip_path)

What I dont understand is why is it only now a problem.

[misialq]

LGTM! 🔥