add plate compression and validation notebook, helper module, and unit tests

[AmandaBirmingham]

This PR:

1. adds a new sample_validation_and_plate_compression.ipynb notebook and associated unit tests
   • This centralizes the first step of most notebook workflows
   • It also addresses a longstanding request from the wet lab for a notebook they can use to validate that all the samples they have received have Qiita information without having to start prepping them first, since it can be run with an empty compression layout
2. creates a new metapool/notebook_utils.py module that houses some helper functions used in notebooks and adds unit tests
   • NOTE that this PR doesn't remove the in-line definitions of those same functions in the matrix tube notebook. That's coming, but not yet.
3. extends the notebook unit test helper functionality to allow it to handle input files that are expected to be nested under the test's temporary directory
   • This supports the case where autogenerated outputs from one notebook are chained into inputs of another
   • This functionality isn't in use in by anything in this PR; it is to support the next refactor ;)

[Copilot]

Pull request overview

Adds a new “plate compression and validation” notebook plus shared helper utilities and tests to support running/validating notebook-driven workflows and comparing their generated outputs against committed fixtures.

Changes:

• Added plate_compression_and_validation.ipynb and a corresponding notebook execution test.
• Introduced metapool/notebook_utils.py (and unit tests) to share notebook helper functions.
• Added new expected output fixtures for the notebook (plate_df + expt_info).

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
notebooks/plate_compression_and_validation.ipynb	New notebook implementing compression + controls + validation and writing outputs.
notebooks/tests/test_plate_compression_and_validation.py	Executes the new notebook via the shared test harness and verifies expected outputs.
notebooks/tests/notebook_test_helpers.py	Extends notebook test harness to better support auto-constructed paths and directory creation.
metapool/notebook_utils.py	New shared helpers for notebooks (attribute extraction + delimiter inference).
metapool/tests/test_notebook_utils.py	Unit tests for the new notebook utility helpers.
notebooks/test_output/QC/ShotgunMetag_plate_df_compvalid.txt	Fixture output for plate dataframe produced by the new notebook.
notebooks/test_output/QC/ShotgunMetag_expt_info.yml	Fixture output for experiment metadata produced by the new notebook.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[coveralls]

Pull Request Test Coverage Report for Build 21840935318

Details

• 222 of 237 (93.67%) changed or added relevant lines in 7 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.2%) to 92.934%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
metapool/tests/test_notebook_utils.py	69	70	98.57%
notebooks/tests/test_sample_validation_and_plate_compression.py	20	21	95.24%
metapool/metapool.py	37	39	94.87%
notebooks/tests/notebook_test_helpers.py	47	58	81.03%

Totals
Change from base Build 21409204059:	0.2%
Covered Lines:	6997
Relevant Lines:	7529

---

💛 - Coveralls

[Copilot]

Copilot encountered an error and was unable to review this pull request. You can try again by re-requesting a review.

[Copilot]

Pull request overview

Copilot reviewed 8 out of 9 changed files in this pull request and generated 3 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[antgonza]

Looks good, thank you @AmandaBirmingham - just a few questions.

[antgonza]

Are these values OK to add to a repo?

[AmandaBirmingham]

Fair; as test values, these aren't exactly naughty but they also aren't exactly nice. I can't clean these values out of the whole repo, but I can stop propagating them into new test files like these.

[antgonza]

Wonder if the double underscore is needed or would it be fine to only have one?

[AmandaBirmingham]

I used the double underscore to try to differentiate this even more from "real" variable names that anyone might put into a notebook (since those are essentially unconstrained and might be anything).

[antgonza]

FWIW, as it's show in this list, in the past we used TestProjA or TestProjB and fake study ids to minimize overlap with values in qiita.

[AmandaBirmingham]

TestProjB is used here too, for one of the studies. Sadly, the two Celeste studies are completely entwined with our test data; I can change the names by which they are called in the notebook (which I have done), but to change their study ids would require modifying quite lot of known-good files. I don't think I can take that on yet ;)