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scpviz

Changelog

Changelog

scpviz

0.6.0 April 14, 2026

Build System

(Deps)

Restructure dependencies with optional extras and bump min Python to 3.10 #33 (12f5dbd…)
Move openpyxl to core and set min versions for [dev] #30 #31 (0024f0d…)

(Setup)

Update setup.py with updated deps (87fe954…)

(V0.6.0)

Update to stable launch, add gseapy analysis and plotting, refactor plotting and utils (d3fbfa7…)

CI

Automate changelog and PyPI release workflows (a773a00…)

Changed

(Plotting)

Plotting module refactor (3da4e61…)

(Utils)

Utils module refactor (b54988f…)

Chores

(Merge)

Merge main into development, resolve conflicts (80c9dc7…)
Merge changes to .gitignore (491ee9a…)
Update changelogs [skip ci] (5391347…)
Update changelogs [skip ci] (37fc44b…)
Update changelogs [skip ci] (5e6b792…)

Documentation

(Links)

Fix wrong/dead links (5d28169…)

(Version bump)

Document optional sc extras and update Python requirement to 3.10 #31 #33 (85d10c8…)

Fixed

(Tests)

Typo in test assertion for test_print_versions_runs() (ffb3b0a…)

Other

(Paper)

Update Paper PDF Draft (f4b1e86…)
Update Paper PDF Draft (6451bae…)

Tests

(Analysis)

Remove xfail from passing tests due to bump in python version (634addd…)

(Import)

Debug test_import_pd_excel #30 (cd4c98c…)
Exclude macos py3.8 due to scikit installation error (7efb218…)

0.5.9 April 08, 2026

Build System

(V0.5.9)

Bump version to 0.5.9 (8599fc8…)

Chores

(Todo)

Refactor todo list w priority and better oganization (e6d3c4b…)
Update changelogs [skip ci] (7a6cced…)
Update changelogs [skip ci] (ba29e77…)
Update changelogs [skip ci] (85a5de7…)
Update changelogs [skip ci] (4eb539a…)
Update changelogs [skip ci] (fa78650…)
Update changelogs [skip ci] (8c0fd83…)
Update changelogs [skip ci] (2b5f382…)
Update changelogs [skip ci] (8f3d47a…)
Update changelogs [skip ci] (017730b…)
Update changelogs [skip ci] (b5a4837…)
Update changelogs [skip ci] (e8b0949…)

Documentation

(Tutorial)

Update single cell tutorial to push deployment again (285510f…)
Docs(citation): add CITATION.cff, closes [JOSS] Add CITATION.cff (f1d7bfe…)
Docs(makefile): add makefile, closes [JOSS] No Makefile/Justfile (198692f…)

Fixed

(Docs)

Update deployment workflow to run only on push to docs on main branch (830bbb3…)
Fixed broken link to function hyperlink, added colab button (7662ea8…)

Other

(Paper)

Update Paper PDF Draft (da1b895…)
Update Paper PDF Draft (01dbb0a…)
Update research impact statement regarding collaborative effort #36 (b3e540a…)
Update Paper PDF Draft (3d2700f…)
Update bib to remove local file paths #28 (1b11b77…)
Update Paper PDF Draft (148081f…)

Style

(Docs)

Fix formatting in single-cell tutorial header (73970d3…)

(Readme)

Update contributing and license (cbb355b…)

0.5.8-alpha March 16, 2026

Build System

(V0.5.8a)

Update to new patch with additional tutorials (42ac903…)

Chores

Update changelogs [skip ci] (787c652…)
Update changelogs [skip ci] (f33ed77…)

Documentation

(Tutorial)

Update single cell and quickstart tutorial (1a04522…)
Update single_cell.ipynb (b5eb1fb…)

0.5.7-alpha January 29, 2026

Added

(Analysis)

Add pimms imputation (3745120…)
Add ssGSEA and declare gseapy dependency (33a3578…)
Add pairwise_correlation function (d5a62b9…)
Add log_transform for preprocessing and update handling of log data on de(), pca() and pairwise_correlation() (e8f9af4…)

(Directlfq)

Make strict/loose flag instead to replicate older behavior (d976225…)

(Editing)

Update export_layer to support multiple labels (25dd299…)

(Enrichment)

Allow category argument for plot_enrichment_svg (297e9f7…)
Add enrichment_functional_pca for STRING on PCA loadings (0099128…)

(Filtering)

Add warning about underscores in class_type throwing error within annotate_found and annotate_significant (51b0664…)

(PAnnData)

Layer provenance registry, log_transform, and show_layer_provenance (5cceb9a…)
Update layer provenance in .analysis functions (c1cca58…)

(Pca_gsea)

Implement gseapy prerank, using multi-library default, FDR counts in verbose (1b6cd7d…)

(Plot_abundance_boxgrid)

Add publication quality abundance plot function (2957b40…)

(Plotting)

Add classes=None support to plot_abundance_boxgrid, also fixed flipped label error by enforcing order from start (27043ea…)
Add shift_legend() convenience function (53a95df…)
Add ax input for plot_abundance_boxgrid, update wrapper in pAnnData (2caf525…)
Add plot_volcano_adata to support transcriptomics plotting, add mark_volcano_by_significance for more flexibility with marks (e859a97…)
Add flexible plotting options to plot_pca and plot_umap (dc36d29…)
Add text adjustments to plot_volcano (4580a12…)
Text adjustments to mark_volcano and mark_volcano_significance (2c8219a…)
Add weighted option to plot_venn (4e516a4…)
Update plot_abundance_boxgrid to more flexible plotting style, bug fixes (4276636…)
Update plot_abundance_boxgrid and add tests (2c1b0cd…)
Add PCA-GSEA plots and pAnnData wrappers (44d82f2…)
Add plot_pairwise_correlation (86483c3…)
Add accession and gene columns to plot_cv() returned df (ac850b9…)

(Utils)

Add parse_filename_index to help with formatting imports (eb9da97…)
Add de_adata to support transcriptomics DE (e0cdb74…)
Add condition flag for parse_filename_index to parse subset of samples, added tests for condition (09ce308…)
Additional fixes to de_adata() (0a09fda…)

Build System

(.gitignore)

Add parquet file (eecb64d…)

(Docs)

Enforce version type on mkdocstrings since new build broke render (36b3734…)
Fix versions of mkdocstrings (feec11a…)

(V0.5.3a)

Update readme and dependencies (4abf8c2…)

(V0.5.6a)

Update dependencies and bump to updated readme link (4239e51…)

(V0.5.7a)

Update to new patch with plotting overhaul (9bfed9e…)
Update to new patch with plotting overhaul (c0a92bf…)

CI

(Codecov)

Update patch pass to 80% (809e06a…)
Patch pass to 70% (c19c842…)

(Docs)

Update to local editable copy of scpviz for docs serve (f069efa…)

(Package)

Modify readme to show status matrix (5202a0e…)
Split ci tests into individual workflows (59dd2c9…)
Update with codecov token (24f61bf…)
Fix secrets passthrough to reusable workflow (70fd891…)

(Pytest)

Update to test on macos and windows as well (66afe02…)

Changed

(Directlfq)

Default to strict (876a237…)

(Enrichment)

Moved get_string_mappings() to utils to for ease of use for user, refactored enrichment mixin (b8cfc76…)

(Git LFS)

Remove large tutorial parquet from LFS; keep small test parquet (5c46f16…)
Remove LFS flag from pytest workflow (b8b98c4…)
Move large parquet file to release and update download links in docs (dafcc43…)
Move small test parquet from LFS to local (c0170bf…)

(Joss)

Update to new joss paper format (46e5048…)
Added state of field section (18d4a4b…)

(Plotting)

Add _add_continuous_colorbar helper function, clean plot_pca and plot_umap code (60c724a…)
Update pca and umap to pass kwargs to scatter plot (fffa5e1…)
Enable label_x for box=True in plot_abundance_boxgrid (d789d43…)
Refactor volcano adata (0b2079d…)
Update docstrings, update references to old uniprot naming (64af394…)
Reorganize imports (56d478b…)
Overhaul plot_umap and plot_pca to use common _plot_embedding_scatter, revamp ellipse handling (026ef71…)
Return ax on plot_venn to match other plot functions, change test (5722d3c…)
Cleanup, move single use functions into helper functions (643061c…)
Refactor both biplots for protein and pathway vectors to accept n_vectors per pc, fix bug on ylim/xlim, allow cmap coloring (3112be7…)

(Setup)

Add GLOBAL_DEBUG flag to suppress runtime warnings for user but allow at pytest logging (ad48d06…)

Chores

(Codecov)

Set success flag for ci (0f1f2bc…)

(Gitignore)

Extend .gitignore for save tar folders etc (a89b398…)

(Plot_abundance)

Default to raw abundance with y-log scale (92beb20…)

(Readme)

Update CI badge link in README.md (8ef019a…)

(Todo)

Refactor todo list w priority and better oganization (cf4d03c…)
Update changelogs [skip ci] (9b4fecb…)
Update changelogs [skip ci] (0a63f6b…)
Update changelogs [skip ci] (525bdb9…)
Update changelogs [skip ci] (6c89f44…)
Expose version, align print_versions, ignore logo asset (e750e24…)
Update changelogs [skip ci] (fe0eb7b…)
Update changelogs [skip ci] (48a0c89…)
Update changelogs [skip ci] (2bc44af…)
Update changelogs [skip ci] (a9ebeff…)
Update changelogs [skip ci] (d9e026b…)
Update changelogs [skip ci] (f3bb302…)

Documentation

(Plotting)

Update examples for various plotting functions (cc43b62…)

(Quickstart)

Update quickstart to include new plotting functions (d4f1d48…)

(Refactor)

Overhaul documentation layout for API pAnnData reference (df24ead…)

(Tutorial)

Add wget downloads to importing ipynb (f9d34fa…)

(Tutorials)

Complete importing tutorial (3534a19…)
General updates to site style, formatting for mixins (d0a1bca…)

(Upload)

Upload test_input.csv (94ca178…)

(Utils)

Synchronize docs layout for utilies and plotting modules (d83cb71…)

Fixed

(Analysis)

Suppress warnings about nanmean (3b2f505…)

(Directlfq)

Handle bug with multi proteins associated with same peptide in output file producing NaNs output (e.g. 'P03995;P03995-2') (ef8a915…)
Move expansion to peptide level data so normalization algorithm maps to correct protein (f676b44…)

(Docs)

Fix link to importing tutorial (541b849…)

(Get_abundance)

Bug fix on get_abundance throwing error when passing in string instead of list (9b70b75…)

(Io)

Bug fix on _import_proteomeDiscoverer() where peptide has no matching protein (248e03d…)

(Mkdocstrings)

Downgrade to v0.30.1 for now while we figure out handler error (7d7ba8c…)

(Plot_umap)

Fix force to propagate through umap, neighbors and pca (9092ebb…)

(Plotting)

Bug fix for plot_abundance_boxgrid when xtick only exists for one class (4e267fd…)
Default plot_abundnace_boxgrid to dodge=False when classes is None (6290754…)
Fix GLOBAL_DEBUG flag to be updated at start of test_utils.py (4c84318…)
Allow n_comps or n_components (as per error message) to be passed to pca_params in plot_pca (0005636…)
Fix return on plot_venn to pass test (6d1709c…)
Update plot_venn to override alpha if provided (32afcbe…)

(Summary)

Check and remove_unused_categories after filter, mostly for PD data (925e72d…)

(Test_provenance_chain_depth_after_chain)

Add update to current_X_layer in editing.py (ae7d7de…)

(Tests)

Typos on errortype and assertion match (f0b9674…)
Correct GLOBAL_DEBUG import in pytest_configure (4d7a271…)

(Umap)

Fix force=True not propagating down to neighbors() and pca() (d75f1ed…)

(Utils)

Add warning/hint about source of length mismatch error in format_class_filter (664bfdf…)
Fix for py3.8 compatibility (8163c5c…)
Force string typecast on join for get_classlist() (474f97b…)

Other

(Paper)

Update Paper PDF Draft (4644379…)
Update Paper PDF Draft (ebe6943…)
Update Paper PDF Draft (c371cd7…)
Update Paper PDF Draft (d65ce10…)

Style

(Analysis)

Remove extra blank lines (1897136…)
Fix typo in pca_gsea() printed results key (f28f201…)

(Docs)

Change root_heading to true, remove others section (bb68f1d…)
Add tabs back to website for better navigation (45ba11f…)
Fix griffe errors for plot.py (c3cf62d…)
Fix griffe errors for pAnnData.py (f7dd584…)

(Editing)

Edit mixin docstring to include export_layer (b3d2cba…)

(Enrichment)

Add categories to docstring of plot_enrichment_svg (06858b2…)
Add catch for no enrichment result (85c0399…)

(Filter_prot_found)

Add new line after rs message (7a4146b…)
Reorder automatic annotation message (9147fea…)

(Filtering)

Refactor the print statements from filter_prot_found to match filter_prot_significant, fix style for filter_prot valid genes and unique profile (1660e0b…)

(Plotting)

More verbose error message for errors in resolve_plot_colors (1f2dc63…)

(Readme)

Update badges (f773576…)

(Rs)

Show rs filter message after instead of before printouts (2d1803f…)

(Utils)

Fix formatting on example for get_string_mappings (7f38f7c…)

Tests

(Add files)

Add files for tests (5718f9e…)

(Analysis)

Add mark xfail for failure due to potential package version mismatch (a7c808a…)
Cover ssGSEA storage, gene column, and duplicate collapse (e1e8d04…)

(Boxgrid)

Fix boxgrid assertion error (c8c204f…)

(De_adata)

Refactor raise error to earlier in check for method (41ba612…)

(Directlfq)

Add tests for strict flag and no pep situation (cd05079…)

(Editing)

Add tests for layer provenance (2b13eac…)

(Enrichment)

Add test for helper _scalarize_taxon() within get_string_mappings (485b830…)
Cover enrichment_functional_pca PC tails and key suffix (8ca4855…)

(Filter_prot_found)

Add test for automated annotation with simple group (451ce0a…)

(Import)

Add test for pep xlsx import (6d67ccb…)

(Impute)

Add test for use_zeros_as_nan flag (32fa2bd…)

(PAnnData_plot)

Refactor base plot tests into test_pAnnData_plot file, centralize where to test pdata plotting functions (3c4c264…)

(Pimms)

Add tests for pimm imputation (d3a1832…)
Add skip for pimms-learn dependency issue (6485e2e…)

(Plotting)

Add tests for plot_abundance_boxgrid (a42eb76…)
Add test for abundance_boxgrid classes = None case (121a9f5…)
Add test for abundance_boxgrid when show_n is true and parameterize box (e8aaf3b…)
Add test for plot_umap with classes as None (6bbbe6c…)
Add tests for shift_legend() (ed80cd9…)
Add mark xfail for known plt version error, add test for violin (c6a3854…)
Add test for plot_volcano_adata with no data (6791ad6…)
Update test names for plot_abundance_boxgrid (21933a5…)
Cover PCA-GSEA plots, protein loading vectors, and pAnnData wrappers (297e698…)

(Umap)

Update larger perturbation on force_neighbors to pass test on py3.11 (more stable umap) (571149f…)
Remove assertion on neighbour due to different stabilities across python versions (60badf5…)

(Utils)

Add tests to exception and error for parse_filename_index (2446b41…)
Add test for parse_filename_index (ae713de…)
Add tests for get_string_mappings() (a31e3cd…)

0.5.2-alpha November 16, 2025

Added

(Io)

Add delimiter support for parsing imports (b1a23eb…)

Build System

(Dependencies)

Add directlfq (c6dd2c3…)

CI

(Changelog)

Add two minute sleep timer to prevent clash with joss workflow (478bacd…)
Add rebase after sleep (4500b28…)

(Joss)

Update workflow to pull before pushing due to changelog upload (514d580…)
Remove dynamic ref logic to fix wrong head (ee792f4…)
Add local checkout to main for pull (959a605…)

Chores

Update changelogs [skip ci] (20d06bc…)
Update changelogs [skip ci] (9e5bac4…)
Update changelogs [skip ci] (3e16c2e…)
Update changelogs [skip ci] (752f655…)
Update changelogs [skip ci] (3b72040…)
Update changelogs [skip ci] (ddbbfd8…)
Update changelogs [skip ci] (0033c88…)
Update changelogs [skip ci] (5201ba9…)
Update changelogs [skip ci] (366a05d…)
Update changelogs [skip ci] (d35654a…)
Update changelogs [skip ci] (1450a6d…)
Update changelogs [skip ci] (14c452a…)
Update changelogs [skip ci] (f920f5b…)
Update changelogs [skip ci] (b73cbc1…)
Update changelogs [skip ci] (2ee80b8…)
Update changelogs [skip ci] (73f898a…)

Fixed

(Ci)

Parquets were updated to lfs, add lfs request to pytest checks (391bb8b…)
Add lfs update to python-package.yml (13f335f…)
Trigger pytest workflow (1a44b79…)

(Lfs)

Fix LFS tracking for DIANN parquet fixture (9417883…)

Other

(Paper)

Update with comments from coauthors (c916be0…)
Update Paper PDF Draft (a637997…)
Update references (0b80c03…)
Update Paper PDF Draft (74ab75a…)
Final updates to paper.md (20b500c…)
Update acknowledgements (0eb8e8b…)
Update references (6cb919d…)
Update Paper PDF Draft (4d41ca6…)
Update Paper PDF Draft (7bf727d…)

Tests

(Io)

Add python check to mapping function to account for function deprecation in pandas (8b6b130…)

0.5.1-alpha November 10, 2025

Added

(Filtering)

Add exclude_file_list argument (2f592f1…)

(Plot_cv)

Add palette flag (f92100b…)

Build System

Bump scpviz to v0.5.0-alpha (1942e28…)

CI

(Changelog)

Update .git-cliff.toml (85f2304…)

(Joss)

Rename joss commit message to match conventional commit style (83c4935…)
Update test CI to run only on changes to /src or /tests (06b3dc6…)

Chores

(Assets)

Move assets out of src (917be4c…)

(Git lfs)

Update .gitattributes for lfs upload of parquet files (ccf0e04…)

(Todo)

Update todo list (388fdf3…)
Update changelogs [skip ci] (8e09ce2…)
Update changelogs [skip ci] (dfff921…)
Update changelogs [skip ci] (6e3f746…)
Update changelogs [skip ci] (8a99267…)
Update changelogs [skip ci] (d6d3633…)
Update changelogs [skip ci] (f0cbb17…)
Update changelogs [skip ci] (00d4bf8…)
Update changelogs [skip ci] (f849dd9…)
Update changelogs [skip ci] (aa84d7c…)
Update changelogs [skip ci] (11a3754…)
Update changelogs [skip ci] (b7f7e72…)

Documentation

(Assets)

Upload logo and test assets (e1ee49b…)

(Filtering)

Finished filtering tutorial, update docstrings (9a3f6a5…)

(Package rename)

Rename all links in docs (cfc8344…)
Update mkdocs.yml (838fa33…)

(Quickstart)

Update tutorial files (422ae4f…)
Upload diann_report.parquet, using git lfs (32501ee…)
Update download links (22c60d9…)

(Quicstart)

Add colab link for user ease of use (8fbf44c…)

(Readme)

Update readme (b8637fb…)
Update broken links and logo (8d7b64a…)

(Setup)

Update mkdocs.yml, add dev and js for navigation (6427731…)

(Tutorial)

Update quickstart, some tutorials in works (91e10bf…)
Update tutorial home page (f1a0cb9…)

(Tutorials)

Add pending notice (23b7d0c…)
Update readme to proper image (7b82bea…)
Remove conda installation from readme, update gitignore (0e5e5ac…)
Update joss paper.md (11151fc…)

Fixed

(Io)

Implement handler for diann files when using suggest_obs_columns (93cfac5…)
Push python version fix for .map() (49be220…)

Other

(Paper)

Update Paper PDF Draft (2fe3401…)
Update paper.md and bib (f587cb5…)
Update Paper PDF Draft (8c63425…)

Performance

(Io)

Initialize rs as sparse, memory improvement from 6+ GB usage to ~60MB (da721b6…)

Style

(Cv)

Default to false verbose on cv resolve_class_filter (ee346ca…)

(Filtering)

Fix print statements to be more verbose (2fdeae3…)
Updated print statements to include exclude_file_list (3efd2c6…)
Add print for cleanup with no empty prots (b71aab6…)
Fix typo in print statement of annotate_significant_prot (9445f0a…)

(Readme)

Update version on docs badge (ad74fa6…)

0.4.1-alpha November 04, 2025

Added

(Base)

Add compare_current_to_raw and get_X_raw_aligned functionality (043251b…)

(Filtering)

Add valid_genes, unique_profiles to filter_prot and cleanup (nans) to filter_sample (e251c8a…)
Add handling of duplicate gene name in filter_prot (01d750e…)

(Import)

Add cleanup after import (b290ec8…)
Add support for pd3.2 import (592a814…)

(Plot)

Add plot_abundnace wrapper from pdata (8e2a01c…)

Build System

Update pyproject.toml (18af439…)
Update pyproject.toml and workflow bug (19f4c7a…)
Fix changelog yml tag fetch error (5b20d69…)

CI

(Changelog)

Upload changelog.md (2be787e…)

(Pytest.ini)

Add test "slow" marker (8280133…)

Chores

(Changelog)

Changelog sync to docs (84e991d…)
Final updates (6b94c5b…)
Edit changelog workflow (0ec6ab5…)

(Docs)

Update deploy workflow to use committed changelog (9fa1705…)
Fix github workflow bugs (1ef2b00…)
Fix workflow yml (cc2544f…)
Fix changelog yml workflow (cb956b1…)
Fix changelog toml format (7c5dcc8…)
Fix attempt for workflow (506109b…)
Update full changelog [skip ci] (b8b5634…)
Update changelogs [skip ci] (c3a8704…)
Update changelogs [skip ci] (2356fff…)
Update changelogs [skip ci] (9910211…)
Update changelogs [skip ci] (b5d04c7…)
Update changelogs [skip ci] (7e5d8b6…)
Update changelogs [skip ci] (a688e34…)
Update changelogs [skip ci] (265982c…)
Update changelogs [skip ci] (ca558ad…)

(Workflow)

Build and deploy runs after changelog is finished (97491c3…)

Documentation

(Coc)

Add contributor covenant code of conduct (72fd27e…)

(Contributing)

Update contributing.md file (4002003…)
Update markdown files (d72e6fa…)

Fixed

(Base)

Anndata automatically aligns X_raw, removed function and tests (ce82a52…)

(Export)

Handle export of .X (a3028bd…)

(Filtering)

Fix bug on import with non-matching obs/summary after nan protein cleanup (f61c0b5…)

(Import)

Renaming scheme for pd prot var (9bcbf44…)

(Plotting)

Fix bug for volcano_df handling of "not comparable" (1d3d87b…)

Other

(Identifier)

Fix indentation on update_identifiers tip (90b7bec…)

(Package name)

Rename scviz to scpviz (9bc6347…)

Style

(Changelog)

Edit markdown formatting for docs changelog (ff92df7…)
Update parsers to match conventional commit format (a870d32…)

(De)

Add comment on metaboanalyst median normalization (42c0260…)

(Summary)

Edit table of usage scenarios for update_summary to be clearer (ffd2a37…)

Tests

(Filtering,import)

Add tests for duplicate gene handling, import pd32 (4cf1b86…)

(Test files)

Add test for pd3.2 import with prot and pep, upload pd3.2 mock files (3c96c45…)

0.4.0-alpha October 28, 2025

Changed

Chores

Add git-cliff config and changelog workflows (0159d05…)

0.3.0-alpha October 08, 2025

Added

Changed

Documentation

Include changelog in docs (9d7dbc0…)

Fixed

Other

Tests