Changelog

Changelog#

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]#

Added#

  • Basic tool, preprocessing and plotting functions

  • Test suite (tests/) covering the public pp, tl, and pl APIs against a synthetic SpatialData fixture (tests/conftest.py), including pytest.mark.xfail/skip markers documenting known spatialdata-0.4.0 incompatibilities and pl/plotting.py legacy-pipeline drift.

Fixed#

  • tl.adaptative_source_score_optimized: AttributeError: 'numpy.ndarray' object has no attribute 'tocsr' when sdata["table"].X is a dense array — now converts via csr_matrix(...) instead of calling .tocsr().

  • pl.global_distribution_from_source: fixed the default cluster_key ("kmeans_from_distribution" → "kmeans_distribution") to match the column actually written by tl.cluster_distribution_from_source and used by pl.distributions_by_cluster.

  • pp.filter_urna/pp.aggregate_urna: fixed dask/spatialdata compatibility issues — boolean-indexing the transcripts points dataframe no longer drops required .attrs, and an unnecessary .compute() that broke on newer dask is removed.

  • tl.calculate_target_cells: fixed gene alignment (reindex instead of a join that broke under pandas 2.3.x with a CategoricalIndex).

  • Added troutpy[spatial-stats] to the test extra so the test suite’s optional dependencies (sainsc, squidpy) are installed in CI.

  • docs/notebooks/Basic_tutorial.ipynb: fixed cells with stray leading whitespace (caused ruff/pre-commit parse failures), an unused numpy import, and two calls using troutpy.pl.... instead of the notebook’s tp alias.

  • Excluded anndata==0.13.0rc1 (anndata!=0.13.0rc1): this release candidate makes AnnData(X=...) populate adata.layers with a None key, which crashes spatialdata’s TableModel.parse validation (AttributeError: 'NoneType' object has no attribute 'lower') and broke the PRE-RELEASE DEPENDENCIES CI job.

  • Pinned setuptools<81 in the doc extra: setuptools>=81 removed pkg_resources, which xarray_schema (a spatialdata dependency) still imports at module load, crashing import troutpy and, with it, the ReadTheDocs build (sphinx.errors.ExtensionError: ... no module named troutpy.pl).

  • Fixed ~170 nitpicky Sphinx warnings that made the ReadTheDocs build fail under fail_on_warning: true:

    • Added seaborn and squidpy to intersphinx_mapping so their type cross-references resolve.

    • Extended nitpick_ignore for napoleon’s “type, optional”/”… or iterable” parameter descriptions, typing.Union, and runtime-derived qualnames that don’t match their public, intersphinx-mapped names (pandas.core.frame.DataFrame, SpatialData, seaborn.axisgrid.JointGrid, seaborn.matrix.ClusterGrid) or have no hosted inventory (mpl_chord_diagram.chord_diagram, sainsc.LazyKDE*).

    • pl.basic/pl.metric_analysis/pl.scatter/pl.factor_analysis: fixed :func: refs pointing at troutpy.pl.colors.get_palette/ get_colormap to troutpy.pl.get_palette/get_colormap, matching how they’re documented in docs/api/plotting.md.

    • tl.source_cell: removed a :func: cross-reference to the private, undocumented _core_scoring_engine_chunk helper.

[0.1.1]#

Removed#

  • Deprecated functions tl.compute_source_cells, tl.distance_to_source_cell, tl.compute_distant_cells_proportion, tl.compute_source_score, and tl.characterize_cell_like_structures (superseded by tl.adaptative_source_score / tl.adaptative_source_score_optimized).

Changed#

  • Trimmed dependencies to the minimal set required to import troutpy (added a missing numba, dropped unused joblib), and moved sainsc, points2regions, squidpy, mpl-chord-diagram, scikit-image, and drvi to lazily-imported optional extras (spatial-stats, segmentation-free, chord, morphology, factor-analysis; pip install troutpy[all] for everything).

  • docs/api/*.md now reflects the full public API exported by troutpy.pp, troutpy.tl, and troutpy.pl.

Contents