11 Pull requests merged by 4 people

• Grammar fixes in sc.tl docstrings

  #3438 merged Jan 15, 2025

• (chore): Update to Ruff 0.9 and add EM lints

  #3437 merged Jan 13, 2025

• (chore): Fix flaky doublet test

  #3436 merged Jan 13, 2025

• (chore) upper bound zarr version in tests to <3

  #3432 merged Jan 10, 2025

• Formatting

  #3414 merged Jan 10, 2025

• Metadata updates

  #3413 merged Jan 9, 2025

• Fix wilcoxon for >10M cells

  #3426 merged Jan 9, 2025

• Mention towncrier in contribution docs

  #3427 merged Jan 9, 2025

• Doc fixes for 1.11

  #3415 merged Jan 9, 2025

• Fix Markdown syntax for preprocessing docs page

  #3418 merged Jan 9, 2025

• [pre-commit.ci] pre-commit autoupdate

  #3404 merged Jan 9, 2025

2 Pull requests opened by 1 person

• Implement missing plot functionality for `pl.rank_genes_groups`

  #3428 opened Jan 9, 2025

• Replace spmatrix with _CSMatrix as appropriate

  #3431 opened Jan 10, 2025

11 Issues closed by 1 person

• Integration Testing CI Test Failure on python 3.10

  #3434 closed Jan 13, 2025

• Is it possible to only label some marker genes that are interested in the `sc.pl.rank_genes_groups_heatmap`?

  #3433 closed Jan 13, 2025

• >>> sc.tl.umap(adata_T) Segmentation fault

  #3435 closed Jan 13, 2025

• Integration Testing CI Test Failure on python 3.12

  #3430 closed Jan 10, 2025

• The results of sc.tl.dpt is too bad

  #2015 closed Jan 9, 2025

• Integration Testing CI Test Failure on python 3.10

  #3425 closed Jan 9, 2025

• why sc.pl.spatial gives a wrong image?

  #3424 closed Jan 9, 2025

• add support for Visium HD Spatial Gene Expression data

  #2973 closed Jan 9, 2025

• How to do `Slingshot` trajectory inference using anndata and `scanpy`?

  #3419 closed Jan 9, 2025

• Rank genes groups wilcoxon test fails for more than 10 million cells

  #3377 closed Jan 9, 2025

• Fix “preprocessing” docs page

  #3360 closed Jan 9, 2025

1 Issue opened by 1 person

• UMAP redesign

  #3429 opened Jan 9, 2025

13 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• DensMAP support

  #2946 commented on Jan 15, 2025 • 1 new comment

• Rank_genes_groups -> does not return Axes

  #3205 commented on Jan 9, 2025 • 0 new comments

• add `mask_obs`/`mask_var` arguments where appropriate

  #2234 commented on Jan 9, 2025 • 0 new comments

• Compute UMAP from pre-existing distance matrix

  #2157 commented on Jan 9, 2025 • 0 new comments

• `sc.pl.stacked_violin`, Is it also possible to add tiny y-axis scale bars to the stacked_violin(`swap_axes = True`)?

  #2092 commented on Jan 9, 2025 • 0 new comments

• Leiden clustering returns different results for Scanpy `1.10.4` and `1.9.3`

  #3422 commented on Jan 9, 2025 • 0 new comments

• UMAP implementation in igraph

  #3408 commented on Jan 9, 2025 • 0 new comments

• Support for `scipy.csr_array`/`scipy.csc_array`

  #3423 commented on Jan 10, 2025 • 0 new comments

• Remove `sc.external`

  #2717 commented on Jan 13, 2025 • 0 new comments

• Loophole with using scaled adata for sc.tl.score_genes_cell_cycle

  #3030 commented on Jan 13, 2025 • 0 new comments

• Multithreading for scanpy.tl.rank_genes_group?

  #2390 commented on Jan 14, 2025 • 0 new comments

• Fix rank_genes_groups_violin’s gene_symbols

  #2554 commented on Jan 13, 2025 • 0 new comments

• (feat): `elem_mul` 64 bit upcast option

  #3392 commented on Jan 14, 2025 • 0 new comments