Notebook unittests for metag (matrix tube) notebook

[AmandaBirmingham]

• modify matrix_tube notebook to support unit tests
• add unit tests for standard and absquant workflows
• update test files to reflect change in add_controls output from previous PR

[coveralls]

Pull Request Test Coverage Report for Build 20790643300

Details

• 20 of 21 (95.24%) changed or added relevant lines in 1 file are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.1%) to 92.748%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
notebooks/tests/test_matrix_tube_pipeline_seqcount_norm.py	20	21	95.24%

Totals
Change from base Build 20783776123:	0.1%
Covered Lines:	6574
Relevant Lines:	7088

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💛 - Coveralls

[antgonza]

Last file has a lot of commented out lines, is that expected? If yes, why not remove them ?

[antgonza]

Are these comments expected?

[antgonza]

Same here?

[AmandaBirmingham]

@antgonza Ah, a very fair question! In this case, the commented-out lines are not really surplus to requirements, but are a requirement of the way the notebook unit testing works. Basically, the unit test injects settings for all the inputs (all at once) into the first cell of the notebook when the test is run. In order for this to work, obviously, the notebook has to NOT re-set those inputs in any later cells, which is why, as you noticed, every input cell in the notebook is commented out. Those cells/lines can't be deleted, however, because they are what the users modify to provide the real inputs when they are running the notebook in production (rather than for unit tests). They can uncomment an entire jupyter cell with two shortcuts (ctrl+A then ctrl+/)--and the wet lab already know this trick :)-- so it is easy for them to do. (By the way, this is also why some of the lines, like the second one you noted above, have # # at the beginning--it is so that when the users uncomment the entire cell, those lines still stay commented :) You will see this same pattern in all the notebooks going forward.