Make shape handling consistent across package for #509#512
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Make shape handling consistent across package for #509#512
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Added an index filtering step to FeatureConcatenator. Previously, if different featurizers dropped different molecules, the raw arrays were still concatenated, resulting in shape mismatches or mismatched rows. The features are now strictly masked to the common indices prior to concatenation.
This overhaul replaces slow, high-dependency integration tests with true unit tests utilizing pytest-mock and synthetic data fixtures. Key changes include swapping tautological file-writing mocks for internal state assertions, enforcing strict disjoint set validation for chemical splitters, and implementing rigorous mathematical validation for uncertainty quantification and evaluation metrics. These updates significantly improve execution speed and cross-platform stability by replacing fragile floating-point equality with robust approximate comparisons and isolating testing boundaries for featurizers, inference orchestration, and CLI logic.
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…un execution-only
…utput-dir semantics
…nd output-dir fallback
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- Strip out unmaintained concrete stub classes. - Use mocker.create_autospec(..., instance=True) to satisfy Pydantic validations. - Centralize mock state injection in the build_workflow helper.
Remove tautological mocking of the model, featurizer, metadata, and data spec in test_inference.py. Replace with real instantiated FingerprintFeaturizer, DummyRegressorModel, CommitteeRegressor, Metadata, and DataSpec objects so that SMILES physically flow through the featurization and prediction pipeline. Only the file I/O boundary (load_anvil_model_and_metadata) remains patched. Assertions now verify mathematically derived values: single model PRED=1.0 (training mean), ensemble PRED=2.0/STD=1.0, and UCB=4.0 (mean + beta*std = 2.0 + 2.0*1.0).
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updates: - [github.com/PyCQA/isort: 8.0.0 → 8.0.1](PyCQA/isort@8.0.0...8.0.1) - [github.com/astral-sh/ruff-pre-commit: v0.15.2 → v0.15.4](astral-sh/ruff-pre-commit@v0.15.2...v0.15.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Add ensure_2d() to eval/utils.py and replace the four inline (N,) → (N, 1) coercion blocks in RegressionMetrics/RegressionPlots and UncertaintyMetrics/UncertaintyPlots with calls to the shared helper. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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See #509