Add test kwarg to methods

[scottgigante-immunai]

Prerequisite for #313

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• This submission adds a new feature not listed above

Testing

• This submission was written on a forked copy of SingleCellOpenProblems
• GitHub Actions "Run Benchmark" tests are passing on this base branch of this pull request (include link to passed test: https://github.com/scottgigante-immunai/openproblems/runs/5679148523?check_suite_focus=true)

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• This submission follows the guidelines in our Contributing document
• I have checked to ensure there aren't other open Pull Requests for the same update/change

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• The latest version of master is merged and tested

[LuckyMD]

some questions about changes in explicit parameter passing in function headers.

[LuckyMD]

@danielStrobl if this gets merged, you will need to adapt this convention into the batch removal PR as well. Just a heads up for now.

[codecov-commenter]

Codecov Report

Merging #330 (45b6767) into main (eb7ee58) will decrease coverage by 1.18%.
The diff coverage is 65.82%.

@@            Coverage Diff             @@
##             main     #330      +/-   ##
==========================================
- Coverage   86.36%   85.18%   -1.19%     
==========================================
  Files          77       77              
  Lines        1702     1735      +33     
  Branches      100      107       +7     
==========================================
+ Hits         1470     1478       +8     
- Misses        201      220      +19     
- Partials       31       37       +6     

Flag	Coverage Δ
unittests	85.18% <65.82%> (-1.19%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
openproblems/tasks/denoising/methods/alra.py	0.00% <0.00%> (ø)
.../tasks/multimodal_data_integration/methods/scot.py	0.00% <0.00%> (ø)
.../multimodal_data_integration/methods/procrustes.py	89.47% <50.00%> (-10.53%)	⬇️
...dal_data_integration/methods/harmonic_alignment.py	78.57% <64.28%> (-9.31%)	⬇️
...tasks/regulatory_effect_prediction/methods/beta.py	84.40% <66.66%> (-1.45%)	⬇️
openproblems/tasks/label_projection/methods/mlp.py	85.71% <72.72%> (-14.29%)	⬇️
...ms/tasks/dimensionality_reduction/methods/phate.py	90.00% <77.77%> (-10.00%)	⬇️
openproblems/tasks/denoising/methods/magic.py	100.00% <100.00%> (ø)
...enproblems/tasks/denoising/methods/no_denoising.py	100.00% <100.00%> (ø)
...lems/tasks/dimensionality_reduction/methods/pca.py	100.00% <100.00%> (ø)
... and 8 more

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[LuckyMD]

Don't know anything about this method, but would top_genes not also be a test parameter?

[scottgigante]

Seems reasonable to me.

[LuckyMD]

Didn't know about the n_svd = n_svd or 20 notation. Pretty cool! Only 1 question about the beta function parameter top_genes.