Changelog

Changelog#

0.6.0 (2026-10-06)#

Features#

  • add compartments and gocc vocabs to grassp (89a80ca)

  • add fingerprint for compartments vocab (3352d4e)

  • gene set reader function (cb6ce27)

  • tutorial and test for reading with alphapepttools (a461cb1)

Bug Fixes#

  • bugfix in tagm-map function (503cae3)

  • read pRolocdata objects with a nested fData data.frame (aa4b019)

  • silence pylint on the intentional bad call in test_gene_sets (9946cc3)

  • update ccompass tutorial with new api (2e6072c)

0.5.1 (2026-09-22)#

Bug Fixes#

  • release please gets the right tag (2b93df8)

0.5.0 (2026-09-22)#

⚠ BREAKING CHANGES#

  • gr.tl.knn_f1_score is now gr.tl.annotation_f1_score, gr.tl.knn_confusion_matrix is now gr.tl.annotation_confusion_matrix, gr.pl.knn_violin is now gr.pl.annotation_violin and gr.pl.knn_marker_df is now gr.pl.annotation_marker_df. pred_col is required on the two tl functions; pass the annotation you want scored, e.g. pred_col=”competitive_diffusion”.

  • read_prolocdata now returns NaN where it previously returned the string “unknown”. Any code that filtered on == “unknown” needs .isna(), and marker counts will change. Pass unknown_to_nan=False to restore the old output.

Features#

  • embeddings with nice labels (#26) (30d754f)

  • pRoloc interoperability — exchange objects as plain h5ad (#31) (63d1463)

  • rename competitive_propagation to competitive_diffusion (c374ffb)

  • warn when competitive_propagation iterates without clamped markers (308217a)

Bug Fixes#

Code Refactoring#

0.4.0 (2026-08-10)#

⚠ BREAKING CHANGES#

  • ds.subcellular_annotations is removed; use pp.add_markers(adata, species=”hsap”) instead.

Features#

0.3.0 (2026-06-05)#

Features#

  • include goterms for human, yeast and mouse (708f65a)

  • option for only merging when improved enrichment (f36d0f3)

Bug Fixes#

  • make sure gene names are str (6a6f97d)

0.2.0 (2026-05-09)#

Features#

  • add custom goterm set for the 3 supported species (21d4d89)

  • add custom goterm set for the 3 supported species (89c9963)

0.1.0 (2026-05-08)#

Features#

  • add bonferroni corrected pval (c412702)

  • add changelog to docs and readme (9e04579)

  • add cluster merging algorithm (7bc2517)

  • add column selection to sensible markers (158b374)

  • add consolidated goterms (d059078)

  • add filter to cluster enrichment (3d87f33)

  • add marker pruning function (a544a97)

  • embedding plots with numericcal alpha (2168e6b)

  • external markers with gene names and sensible colors (c3c763c)

  • knn_annotation has label propagation (a3ab7ff)

Bug Fixes#

0.0.4 (2026-02-09)#

Bug Fixes#

0.0.3 (2026-02-09)#

Bug Fixes#

0.0.3 (2026-02-09)#

Features#

  • add documentation for new grassp functions (bd215f7)

  • add enhanced knn annotation (280fec1)

  • add function to remove cRAP proteins (32bf4a6)

  • add knn-scoring and plotting (e9dccb9)

  • add marker_profiles function (51cfe6b)

  • add neighbors wrapper with layer argument (31d8d2d)

  • add plotting function for markers (2edaab6)

  • add Release Please + PyPI publishing workflow (#17) (327408b)

  • add replicate cv function (0612e6f)

  • add_external_validation_markers function (2867f22)

Bug Fixes#

  • add neighbors and knn_score to init (f26eddc)

  • consistent compartment colors for knn_annotation (287920b)

  • make colors less similar (359762e)

  • preprocessing intregration tests (d82bbba)

  • read prolocdata bug (46c0c56)

  • undo accidental indent (b4a6ba5)

  • update gitignore (3699467)

  • xticklabels centered and refactor (d23f6e0)