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fix: Sphinx 9 support #260

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Merged
grst merged 7 commits into from
Jan 30, 2026
+272 −189
Merged

fix: Sphinx 9 support #260

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1cf8215
fix: sphinx 9 support
flying-sheep Jan 20, 2026
854cb09
example data
flying-sheep Jan 29, 2026
252b89e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 29, 2026
690e472
Merge branch 'main' into sphinx-9
flying-sheep Jan 29, 2026
c593340
oops
flying-sheep Jan 29, 2026
64e1526
Render notebooks
flying-sheep Jan 29, 2026
7cf1bd0
bump versions
flying-sheep Jan 29, 2026
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12 changes: 6 additions & 6 deletions .github/workflows/execute-nbs.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,8 @@ on:
- "environment.yml"

defaults:
run:
shell: bash -el {0}
run: # add -l to GitHub’s defaults to make conda work
shell: bash -leo pipefail {0}

concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
Expand All @@ -21,22 +21,22 @@ jobs:
permissions:
contents: write # Allow GH actions to push changes to repo
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v6
with:
repository: ${{ github.event.pull_request.head.repo.full_name }}
ref: ${{ github.head_ref }}
filter: blob:none
fetch-depth: 0
- name: Cache conda
uses: actions/cache@v4
uses: actions/cache@v5
env:
# Increase this value to reset cache if env file has not changed
CACHE_NUMBER: 0
with:
path: ~/conda_pkgs_dir
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
- name: Cache notebooks
uses: actions/cache@v4
uses: actions/cache@v5
env:
# Increase this value to reset cache if env file has not changed
CACHE_NUMBER: 0
Expand Down Expand Up @@ -83,6 +83,6 @@ jobs:
jcache notebook merge $f $f
done

- uses: stefanzweifel/git-auto-commit-action@v5
- uses: stefanzweifel/git-auto-commit-action@v7
with:
commit_message: Render notebooks
4 changes: 3 additions & 1 deletion .gitignore
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Expand Up @@ -4,7 +4,9 @@
buck-out/

# Compiled files
.venv/
/.venv/
/.pixi/*
/pixi.*
__pycache__/
.ipynb_checkpoints/
.*cache/
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1 change: 0 additions & 1 deletion docs/conf.py
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Expand Up @@ -56,7 +56,6 @@
"sphinx_issues",
"sphinxcontrib.bibtex",
"sphinx_autodoc_typehints",
"sphinx_tabs.tabs",
"sphinx.ext.mathjax",
"IPython.sphinxext.ipython_console_highlighting",
"sphinxext.opengraph",
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17 changes: 8 additions & 9 deletions docs/notebooks/anndata_getting_started.ipynb
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188 changes: 87 additions & 101 deletions docs/notebooks/basic-scrna-tutorial.ipynb
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174 changes: 131 additions & 43 deletions docs/notebooks/scverse_data_backed.ipynb
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50 changes: 27 additions & 23 deletions docs/notebooks/tutorial_axes_anndata_mudata.ipynb
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12 changes: 9 additions & 3 deletions docs/notebooks/tutorial_concatenation_anndata_mudata.ipynb
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Expand Up @@ -119,10 +119,16 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1798: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
" utils.warn_names_duplicates(\"var\")\n",
"/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1798: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
"/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1813: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
" utils.warn_names_duplicates(\"var\")\n",
"/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1813: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
" utils.warn_names_duplicates(\"var\")\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/mudata/_core/mudata.py:947: UserWarning: var_names are not unique. To make them unique, call `.var_names_make_unique`.\n",
" warnings.warn(\n"
]
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3 changes: 1 addition & 2 deletions pyproject.toml
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Expand Up @@ -23,12 +23,11 @@ optional-dependencies.docs = [
"ipykernel",
"ipython",
"myst-nb>=1.1",
"sphinx>=7",
"sphinx>=9",
"sphinx-autodoc-typehints",
"sphinx-book-theme>=1.1",
"sphinx-copybutton",
"sphinx-issues>=5.0.1",
"sphinx-tabs",
"sphinxcontrib-bibtex>=1",
"sphinxext-opengraph",
]
Expand Down
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