From c1453f3e6bc5a42e50e73c62e5a6a5b4c960792e Mon Sep 17 00:00:00 2001 From: Ekin-Kahraman Date: Sun, 5 Apr 2026 16:24:52 +0100 Subject: [PATCH 1/2] docs: add inline example plot to sc.pl.highly_variable_genes --- src/scanpy/plotting/_preprocessing.py | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/src/scanpy/plotting/_preprocessing.py b/src/scanpy/plotting/_preprocessing.py index 8369b2ca58..db4c2afe45 100644 --- a/src/scanpy/plotting/_preprocessing.py +++ b/src/scanpy/plotting/_preprocessing.py @@ -41,6 +41,27 @@ def highly_variable_genes( # noqa: PLR0912 A string is appended to the default filename. Infer the filetype if ending on {{`'.pdf'`, `'.png'`, `'.svg'`}}. + Examples + -------- + Compute and plot highly variable genes from raw PBMC data. + + .. plot:: + :context: close-figs + + import scanpy as sc + adata = sc.datasets.pbmc3k() + sc.pp.normalize_total(adata, target_sum=1e4) + sc.pp.log1p(adata) + sc.pp.highly_variable_genes(adata, min_mean=0.0125, max_mean=3, min_disp=0.5) + sc.pl.highly_variable_genes(adata) + + Plot on logarithmic axes. + + .. plot:: + :context: close-figs + + sc.pl.highly_variable_genes(adata, log=True) + """ if isinstance(adata_or_result, AnnData): result = adata_or_result.var From ad8904b696f27b6ad7277801034b498d4f816f21 Mon Sep 17 00:00:00 2001 From: Phil Schaf Date: Tue, 7 Apr 2026 13:43:34 +0200 Subject: [PATCH 2/2] docs too --- .github/workflows/check-pr.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check-pr.yml b/.github/workflows/check-pr.yml index f898a6ba57..a556b964ab 100644 --- a/.github/workflows/check-pr.yml +++ b/.github/workflows/check-pr.yml @@ -51,7 +51,7 @@ jobs: name: Check for release notes runs-on: ubuntu-latest needs: check-milestone - if: github.event.pull_request.user.login != 'pre-commit-ci[bot]' && needs.check-milestone.outputs.no-relnotes-reason == '' && !contains(fromJSON('["style","refactor","test","build","ci"]'), needs.check-milestone.outputs.type) + if: github.event.pull_request.user.login != 'pre-commit-ci[bot]' && needs.check-milestone.outputs.no-relnotes-reason == '' && !contains(fromJSON('["style","refactor","test","build","docs","ci"]'), needs.check-milestone.outputs.type) steps: - uses: actions/checkout@v6 with: { filter: 'blob:none', fetch-depth: 0 }