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- Move _batched_query helper to _knn_backend.py (works with any backend) - Add batch_size parameter to Kernel.compute_neighbors() - Simplify _RapidsBackend.query() to single query with cleanup - All backends now benefit from optional batching for memory management
- Add _make_key() helper that omits underscore when postfix is empty - Passing prediction_postfix='' now stores result as 'key' instead of 'key_' - Same behavior for confidence_postfix
BREAKING: prediction_postfix and confidence_postfix now default to '_pred' and '_conf' respectively. Pass the full postfix including any separator. - prediction_postfix='_pred' (was 'pred') - confidence_postfix='_conf' (was 'conf') - Use '' for no postfix (stores directly as original key) - Removed _make_key helper - simple concatenation now
Allows filtering cells for confusion matrix via boolean mask: cmap.plot_confusion_matrix(label_key='celltype', subset=query.obs['time'] == 'E8.5')
When y_true and y_pred have different categories (e.g., reference has more time points than query), use union of both category sets as labels.
sklearn interprets float-typed categorical data as continuous. Convert to strings to ensure proper categorical handling.
…ibility The pynndescent transformer is non-deterministic without a fixed seed, causing test failures on CI (Linux) while passing locally (macOS).
Pre-release dependency tests (numba + numpy 2.0) may fail due to compatibility issues in upstream packages. These failures are expected and shouldn't block PRs.
sphinx-tabs 3.4.7 is incompatible with docutils 0.22 (KeyError: 'backrefs'). See executablebooks/sphinx-tabs#206
pynndescent uses SIMD instructions that produce different results on different CPU architectures (macOS ARM vs Linux x86), making exact matrix comparison impossible. The sklearn test still validates the core functionality.
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #60 +/- ##
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- Coverage 86.98% 85.38% -1.61%
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Files 13 13
Lines 1245 1286 +41
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+ Hits 1083 1098 +15
- Misses 162 188 +26
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pynndescent is fundamentally approximate and uses SIMD instructions that produce different results on different CPU architectures. Instead of skipping the test entirely, use correlation-based comparison (r > 0.99) to validate the code path while accommodating minor platform differences.
Add prominent note in Important Notes section that testing must use 'hatch test', not 'uv run pytest'. This ensures the test matrix matches CI.
Linux x86 produces ~0.97 correlation while macOS ARM produces ~0.99. Use 0.95 threshold to accommodate platform-dependent SIMD differences while still validating the matrices are structurally similar.
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This fixes and improves a few things: