Update scvi 1x#88
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Replaces scvi-tools 0.20.3 with >=1.4 (Lightning 2.x), dropping use_gpu in favour of accelerator/devices, adapting to the new _initialize_model / _get_loaded_data / SaveCheckpoint / parse_device_args APIs. Moves GroupDataSplitter to sample-level splitting via external_indexing so that every validation bag is complete, and fixes a floating-point undercount that produced zero-length validation sets. Also fixes a single-layer regressor shape bug (class_input_dim vs z_dim), a .squeeze() dim for the 1-sample edge case, numpy-2 dtype identity check, and pandas-2 groupby observed=True. Switches the package manager to uv (pyproject.toml + uv.lock), bumps requires-python to >=3.12, and adds pytest smoke tests (tests/test_mil.py) plus tutorial-parity scripts (tests/scripts/). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Replace mamba/conda env setup with uv, bump Python requirement to 3.12, and update contributing guide to use uv sync / uv run pytest. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- CI and ReadTheDocs: bump Python 3.10 → 3.12/3.13 to match requires-python - test.yaml: replace 3.10 matrix entry with 3.13; keep 3.12 + pre-release entries - build.yaml + .readthedocs.yaml: 3.10 → 3.12, ubuntu-20.04 → 22.04 - CHANGELOG.md: add Unreleased section for scvi-tools 1.x migration; fix misformatted "## Fixed" → "### Fixed" in 0.3.2 section - docs/api.md: add nn (MLP, Aggregator) and utils (get_sample_representations, score_top_cells, setup_ordinal_regression, plt_plot_losses) sections - mil_classification.ipynb: fix pandas 2.x incompatibilities (.cat.unique() → .unique(), groupby observed=True) before re-running Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Classification: 96/91/93% accuracy across 3 splits (early stopping fired at epochs ~60, ~60, ~55). Regression: R² of -0.26, -0.12, +0.41. Also fixed two pandas 2.x incompatibilities in mil_classification.ipynb: .cat.unique() → .unique(), groupby(observed=True). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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This was referenced Jun 7, 2026
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