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Add test coverage for UME#169

Merged
ncfrey merged 27 commits intoprescient-design:mainfrom
etherealsunshine:add_test_coverage_ume
Aug 5, 2025
Merged

Add test coverage for UME#169
ncfrey merged 27 commits intoprescient-design:mainfrom
etherealsunshine:add_test_coverage_ume

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@etherealsunshine
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@etherealsunshine etherealsunshine commented Jul 30, 2025 •
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Description

Improves test coverage for the UME model class. Addresses #80

What's added

  • test_malformed_smiles_behavior - Documents how UME handles invalid SMILES strings
  • test_malformed_protein_behavior - Tests UME's robustness with invalid protein sequences

Features

  • Edge case documentation: Tests 11 types of malformed SMILES (unclosed parentheses, invalid characters, empty strings, etc.)
  • Protein sequence validation: Tests 10 types of invalid protein inputs (invalid amino acids, special characters, mixed case, etc.)

Usage

# Run the new robustness tests
pytest tests/lobster/model/test__ume.py::TestUME::test_malformed_smiles_behavior -v
pytest tests/lobster/model/test__ume.py::TestUME::test_malformed_protein_behavior -v

Type of Change

  • Bug fix
  • New feature
  • Documentation update
  • Performance improvement
  • Code refactoring

Testing

  • Tests pass locally
  • Added new tests for new functionality
  • Updated existing tests if needed

Checklist

  • Code follows style guidelines
  • Self-review completed
  • Documentation updated if needed
  • No breaking changes (or clearly documented)

@etherealsunshine
added wrapper for concept names
be17eed
@etherealsunshine
Add unit test for concept_names property
53841f1
@etherealsunshine
added support for PTM Dataset
07f66d2
@etherealsunshine
Add unit test for concept_names property
5a4241d
@etherealsunshine
added tests and integration for ptm datasets
e464051
@etherealsunshine
Fix pooch.retrieve() call - add known_hash=None
b0ea49d
@etherealsunshine
updated column names
a0aa2d5
@etherealsunshine
fixed column names to include token
b86208f
@etherealsunshine
added code to download the PTM Dataset
c744b32
@etherealsunshine
Fix code formatting issues (ruff)
08f1bae
@etherealsunshine
Move PTM test to correct datasets directory and fix column names
f42fe0e
@etherealsunshine
Clean up commit history
815c48d
@etherealsunshine
Merge branch 'main' into add-ptm-dataset
bc7d722
@etherealsunshine
added fixes for code formatting
455ccdf
@etherealsunshine
Remove duplicate concept_names code
6e2f853
@etherealsunshine
added additional extensive tests for sequence and profiling.
cde1f55
@etherealsunshine
Merge remote-tracking branch 'upstream/main' into add_test_coverage_ume
20a7d86
@etherealsunshine
removed extraneous comments
837bd31
@etherealsunshine
changed batch_size to accomodate memory constraints
ce12ae0
@etherealsunshine
fixes regarding batch size
3bcbdee
@etherealsunshine
added rdkit to the list of dependencies
611d389
@etherealsunshine
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etherealsunshine commented Jul 30, 2025

Hi @ncfrey, I've added some tests addressing #80, considering some of the issues were addressed in existing PR's and added RDKit to the list of dependencies since it had probably been missed out. Let me know if this looks good!

ncfrey
ncfrey reviewed Jul 30, 2025
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karinazad
karinazad reviewed Jul 30, 2025
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karinazad
karinazad reviewed Jul 30, 2025
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karinazad
karinazad reviewed Jul 30, 2025
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karinazad commented Jul 30, 2025 •
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I'm actually working on making Nathan's detect_modality the default option in the UME tokenizer if no modality is specified, so these malformed inputs will be a good stress test for that as well

@etherealsunshine
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etherealsunshine commented Aug 1, 2025

let me know if these changes look good!

karinazad
karinazad reviewed Aug 1, 2025
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karinazad
karinazad reviewed Aug 1, 2025
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karinazad
karinazad reviewed Aug 1, 2025
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karinazad
karinazad reviewed Aug 1, 2025
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@etherealsunshine etherealsunshine changed the title Add test coverage for UME, Add test coverage for UME Aug 4, 2025
@etherealsunshine etherealsunshine requested a review from ncfrey August 4, 2025 17:37
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ncfrey commented Aug 5, 2025

@etherealsunshine approved and merged!

@ncfrey ncfrey merged commit 967cd74 into prescient-design:main Aug 5, 2025
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@karinazad karinazad Awaiting requested review from karinazad

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@ncfrey ncfrey ncfrey approved these changes

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@etherealsunshine @karinazad @ncfrey