Pacbio 20251014

[AmandaBirmingham]

No description provided.

[coveralls]

Pull Request Test Coverage Report for Build 19077243312

Details

• 205 of 219 (93.61%) changed or added relevant lines in 13 files are covered.
• 223 unchanged lines in 6 files lost coverage.
• Overall coverage decreased (-2.6%) to 89.813%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
metapool/sample_sheet.py	9	10	90.0%
notebooks/tests/test_amplicon_pre_prep_file_generator.py	9	10	90.0%
notebooks/tests/test_matrix_tube_pipeline_seqcount_norm.py	20	21	95.24%
notebooks/tests/test_metatranscriptomics_matrix_pipeline_seqcount_norm.py	12	13	92.31%
notebooks/tests/notebook_test_helpers.py	54	64	84.38%

Files with Coverage Reduction	New Missed Lines	%
metapool/tests/test_sample_sheet.py	1	99.76%
metapool/tests/diff_dataframes.py	4	0.0%
metapool/scripts/seqpro_mf.py	19	0.0%
metapool/scripts/seqpro.py	31	0.0%
metapool/scripts/tests/test_seqpro_mf.py	55	0.0%
metapool/scripts/tests/test_seqpro.py	113	0.0%

Totals
Change from base Build 18386258335:	-2.6%
Covered Lines:	6489
Relevant Lines:	7225

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💛 - Coveralls

[Copilot]

Pull Request Overview

This PR migrates the test framework from nose to pytest, updates test configuration, and renames test classes for better consistency. The changes include:

• Replacement of nose with pytest and pytest-cov in testing dependencies
• Addition of pytest.ini configuration file with test discovery settings
• Renaming of test classes to follow a more descriptive naming pattern
• Addition of new test files for notebook testing with a helper base class
• Standardization of column name from "sample sheet Sample_ID" to "Sample_ID" across test output files

Reviewed Changes

Copilot reviewed 35 out of 39 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
setup.py	Replaced nose testing framework with pytest; removed test_suite configuration
pytest.ini	New pytest configuration file defining test paths, patterns, and options
notebooks/tests/test_tellseq_D_variable_volume_pooling.py	Renamed test class from TestTellseqD to TestTellseqDNotebook; renamed test method for clarity
notebooks/tests/test_metatranscriptomics_matrix_pipeline_seqcount_norm.py	New test file for metatranscriptomics notebook testing
notebooks/tests/test_matrix_tube_pipeline_seqcount_norm.py	New test file for matrix tube pipeline notebook testing
notebooks/tests/test_amplicon_pre_prep_file_generator.py	New test file for amplicon pre-prep notebook testing
notebooks/tests/notebook_test_helpers.py	New base class providing common test infrastructure for notebook tests
notebooks/test_output files	Updated column header from "sample sheet Sample_ID" to "Sample_ID" for consistency
notebooks/init.py	Empty init file added (standard Python package marker)

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[Copilot]

Hard-coded personal directory path should be removed. This exposes a username and is not portable across different development environments. Consider using a temporary directory or making this configurable.

[Copilot]

Debug flag _SAVE_UNMATCHED_OUTPUTS is set to True with a TODO comment to turn it off before committing. This should be set to False by default to avoid saving debug output in production test runs.

[Copilot]

Comment contains duplicate 'Step 2' which appears to be a typo. Should likely be 'Step 5 output - index picklist' or clarify which step this refers to.