fix: Sphinx 9 support (#260)

* fix: sphinx 9 support

* example data

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* oops

* Render notebooks

* bump versions

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: flying-sheep <291575+flying-sheep@users.noreply.github.com>

Author: flying-sheep

.github/workflows/execute-nbs.yaml

@@ -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 }}
@@ -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
@@ -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

.gitignore

@@ -4,7 +4,9 @@
 buck-out/
 
 # Compiled files
-.venv/
+/.venv/
+/.pixi/*
+/pixi.*
 __pycache__/
 .ipynb_checkpoints/
 .*cache/

docs/conf.py

@@ -56,7 +56,6 @@
     "sphinx_issues",
     "sphinxcontrib.bibtex",
     "sphinx_autodoc_typehints",
-    "sphinx_tabs.tabs",
     "sphinx.ext.mathjax",
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinxext.opengraph",

docs/notebooks/anndata_getting_started.ipynb

@@ -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"
      ]

docs/notebooks/basic-scrna-tutorial.ipynb

@@ -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",
 ]