From d2c4404496c566435165c5eec37d6d8e40b5b6ec Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Wed, 2 Apr 2025 18:27:30 +0000
Subject: [PATCH 1/2] Automated template update to v0.5.0

---
 .codecov.yaml                              |  17 ++
 .cruft.json                                |  43 +++++
 .editorconfig                              |  15 ++
 .github/ISSUE_TEMPLATE/bug_report.yml      |  94 +++++++++
 .github/ISSUE_TEMPLATE/config.yml          |   5 +
 .github/ISSUE_TEMPLATE/feature_request.yml |  11 ++
 .github/workflows/build.yaml               |  33 ++++
 .github/workflows/release.yaml             |  34 ++++
 .github/workflows/test.yaml                |  59 ++++++
 .gitignore                                 | 139 ++-----------
 .pre-commit-config.yaml                    |  47 +++++
 .readthedocs.yaml                          |  16 ++
 .vscode/extensions.json                    |  18 ++
 .vscode/launch.json                        |  33 ++++
 .vscode/settings.json                      |  18 ++
 biome.jsonc                                |  16 ++
 docs/Makefile                              |  20 ++
 docs/_static/.gitkeep                      |   0
 docs/_static/css/custom.css                |   4 +
 docs/_templates/.gitkeep                   |   0
 docs/_templates/autosummary/class.rst      |  61 ++++++
 docs/changelog.md                          |   3 +
 docs/conf.py                               | 131 +++++++++++++
 docs/contributing.md                       | 214 +++++++++++++++++++++
 docs/extensions/typed_returns.py           |  32 +++
 pyproject.toml                             | 135 +++++++++++++
 26 files changed, 1074 insertions(+), 124 deletions(-)
 create mode 100644 .codecov.yaml
 create mode 100644 .cruft.json
 create mode 100644 .editorconfig
 create mode 100644 .github/ISSUE_TEMPLATE/bug_report.yml
 create mode 100644 .github/ISSUE_TEMPLATE/config.yml
 create mode 100644 .github/ISSUE_TEMPLATE/feature_request.yml
 create mode 100644 .github/workflows/build.yaml
 create mode 100644 .github/workflows/release.yaml
 create mode 100644 .github/workflows/test.yaml
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 .readthedocs.yaml
 create mode 100644 .vscode/extensions.json
 create mode 100644 .vscode/launch.json
 create mode 100644 .vscode/settings.json
 create mode 100644 biome.jsonc
 create mode 100644 docs/Makefile
 create mode 100644 docs/_static/.gitkeep
 create mode 100644 docs/_static/css/custom.css
 create mode 100644 docs/_templates/.gitkeep
 create mode 100644 docs/_templates/autosummary/class.rst
 create mode 100644 docs/changelog.md
 create mode 100644 docs/conf.py
 create mode 100644 docs/contributing.md
 create mode 100644 docs/extensions/typed_returns.py
 create mode 100644 pyproject.toml

diff --git a/.codecov.yaml b/.codecov.yaml
new file mode 100644
index 000000000..d0c0e2917
--- /dev/null
+++ b/.codecov.yaml
@@ -0,0 +1,17 @@
+# Based on pydata/xarray
+codecov:
+  require_ci_to_pass: no
+
+coverage:
+  status:
+    project:
+      default:
+        # Require 1% coverage, i.e., always succeed
+        target: 1
+    patch: false
+    changes: false
+
+comment:
+  layout: diff, flags, files
+  behavior: once
+  require_base: no
diff --git a/.cruft.json b/.cruft.json
new file mode 100644
index 000000000..1855686b1
--- /dev/null
+++ b/.cruft.json
@@ -0,0 +1,43 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
+  "checkout": "v0.5.0",
+  "context": {
+    "cookiecutter": {
+      "project_name": "squidpy",
+      "package_name": "squidpy",
+      "project_description": "Spatial Single Cell Analysis in Python",
+      "author_full_name": "Giovanni Palla",
+      "author_email": "giovanni.palla@helmholtz-muenchen.de",
+      "github_user": "giovp",
+      "github_repo": "squidpy",
+      "license": "BSD 3-Clause License",
+      "ide_integration": true,
+      "_copy_without_render": [
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_exclude_on_template_update": [
+        "CHANGELOG.md",
+        "LICENSE",
+        "README.md",
+        "docs/api.md",
+        "docs/index.md",
+        "docs/notebooks/example.ipynb",
+        "docs/references.bib",
+        "docs/references.md",
+        "src/**",
+        "tests/**"
+      ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
+      "_template": "https://github.com/scverse/cookiecutter-scverse",
+      "_commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
+    }
+  },
+  "directory": null
+}
diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 000000000..66678e378
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,15 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[{*.{yml,yaml,toml},.cruft.json}]
+indent_size = 2
+
+[Makefile]
+indent_style = tab
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
new file mode 100644
index 000000000..3ca1ccbde
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -0,0 +1,94 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+        detailing how to provide the necessary information for us to reproduce your bug. In brief:
+          * Please provide exact steps how to reproduce the bug in a clean Python environment.
+          * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+          * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
+            available datasets or to share a subset of your data.
+
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: versions
+    attributes:
+      label: Versions
+      description: |
+        Which version of packages.
+
+        Please install `session-info2`, run the following command in a notebook,
+        click the “Copy as Markdown” button, then paste the results into the text box below.
+
+        ```python
+        In[1]: import session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
+
+        ```python
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
+        ```
+      render: python
+      placeholder: |
+        anndata	0.11.3
+        ----	----
+        charset-normalizer	3.4.1
+        coverage	7.7.0
+        psutil	7.0.0
+        dask	2024.7.1
+        jaraco.context	5.3.0
+        numcodecs	0.15.1
+        jaraco.functools	4.0.1
+        Jinja2	3.1.6
+        sphinxcontrib-jsmath	1.0.1
+        sphinxcontrib-htmlhelp	2.1.0
+        toolz	1.0.0
+        session-info2	0.1.2
+        PyYAML	6.0.2
+        llvmlite	0.44.0
+        scipy	1.15.2
+        pandas	2.2.3
+        sphinxcontrib-devhelp	2.0.0
+        h5py	3.13.0
+        tblib	3.0.0
+        setuptools-scm	8.2.0
+        more-itertools	10.3.0
+        msgpack	1.1.0
+        sparse	0.15.5
+        wrapt	1.17.2
+        jaraco.collections	5.1.0
+        numba	0.61.0
+        pyarrow	19.0.1
+        pytz	2025.1
+        MarkupSafe	3.0.2
+        crc32c	2.7.1
+        sphinxcontrib-qthelp	2.0.0
+        sphinxcontrib-serializinghtml	2.0.0
+        zarr	2.18.4
+        asciitree	0.3.3
+        six	1.17.0
+        sphinxcontrib-applehelp	2.0.0
+        numpy	2.1.3
+        cloudpickle	3.1.1
+        sphinxcontrib-bibtex	2.6.3
+        natsort	8.4.0
+        jaraco.text	3.12.1
+        setuptools	76.1.0
+        Deprecated	1.2.18
+        packaging	24.2
+        python-dateutil	2.9.0.post0
+        ----	----
+        Python	3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
+        OS	Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
+        Updated	2025-03-18 15:47
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
new file mode 100644
index 000000000..5b62547f9
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Scverse Community Forum
+    url: https://discourse.scverse.org/
+    about: If you have questions about “How to do X”, please ask them here.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
new file mode 100644
index 000000000..b11e828fe
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for squidpy
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
new file mode 100644
index 000000000..83e01a1ee
--- /dev/null
+++ b/.github/workflows/build.yaml
@@ -0,0 +1,33 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+      - name: Build package
+        run: uv build
+      - name: Check package
+        run: uvx twine check --strict dist/*.whl
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
new file mode 100644
index 000000000..b4bf7da2a
--- /dev/null
+++ b/.github/workflows/release.yaml
@@ -0,0 +1,34 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/squidpy
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+      - name: Build package
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
new file mode 100644
index 000000000..d5cfb2a9c
--- /dev/null
+++ b/.github/workflows/test.yaml
@@ -0,0 +1,59 @@
+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: "3.10"
+          - os: ubuntu-latest
+            python: "3.12"
+          - os: ubuntu-latest
+            python: "3.12"
+            pip-flags: "--pre"
+            name: PRE-RELEASE DEPENDENCIES
+
+    name: ${{ matrix.name }} Python ${{ matrix.python }}
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+      - name: run tests using hatch
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: uvx hatch test --cover --python ${{ matrix.python }}
+      - name: Upload coverage
+        uses: codecov/codecov-action@v4
diff --git a/.gitignore b/.gitignore
index b6e47617d..31e10b3ea 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,129 +1,20 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
+# Temp files
+.DS_Store
+*~
+buck-out/
 
-# C extensions
-*.so
+# Compiled files
+.venv/
+__pycache__/
+.*cache/
 
 # Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
+/dist/
 
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
+# Tests and coverage
+/data/
+/node_modules/
 
-# Pyre type checker
-.pyre/
+# docs
+/docs/generated/
+/docs/_build/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 000000000..0fcce11e2
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,47 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v1.9.4
+    hooks:
+      - id: biome-format
+        exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.5.1
+    hooks:
+      - id: pyproject-fmt
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.2
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
new file mode 100644
index 000000000..69897c3b3
--- /dev/null
+++ b/.readthedocs.yaml
@@ -0,0 +1,16 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
+sphinx:
+  configuration: docs/conf.py
+  # disable this for more lenient docs builds
+  fail_on_warning: true
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
new file mode 100644
index 000000000..caaeb4f73
--- /dev/null
+++ b/.vscode/extensions.json
@@ -0,0 +1,18 @@
+{
+    "recommendations": [
+        // GitHub integration
+        "github.vscode-github-actions",
+        "github.vscode-pull-request-github",
+        // Language support
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-toolsai.jupyter",
+        "tamasfe.even-better-toml",
+        // Dependency management
+        "ninoseki.vscode-mogami",
+        // Linting and formatting
+        "editorconfig.editorconfig",
+        "charliermarsh.ruff",
+        "biomejs.biome",
+    ],
+}
diff --git a/.vscode/launch.json b/.vscode/launch.json
new file mode 100644
index 000000000..36d187461
--- /dev/null
+++ b/.vscode/launch.json
@@ -0,0 +1,33 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Documentation",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": {
+                "PYTEST_ADDOPTS": "--color=yes",
+            },
+            "presentation": {
+                "hidden": true,
+            },
+        },
+    ],
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 000000000..e034b91f7
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,18 @@
+{
+    "[python][json][jsonc]": {
+        "editor.formatOnSave": true,
+    },
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+        "editor.codeActionsOnSave": {
+            "source.fixAll": "always",
+            "source.organizeImports": "always",
+        },
+    },
+    "[json][jsonc]": {
+        "editor.defaultFormatter": "biomejs.biome",
+    },
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestEnabled": true,
+    "python.testing.pytestArgs": ["-vv", "--color=yes"],
+}
diff --git a/biome.jsonc b/biome.jsonc
new file mode 100644
index 000000000..2175c16e6
--- /dev/null
+++ b/biome.jsonc
@@ -0,0 +1,16 @@
+{
+    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "formatter": { "useEditorconfig": true },
+    "overrides": [
+        {
+            "include": ["./.vscode/*.json", "**/*.jsonc"],
+            "json": {
+                "formatter": { "trailingCommas": "all" },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 000000000..d4bb2cbb9
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_static/.gitkeep b/docs/_static/.gitkeep
new file mode 100644
index 000000000..e69de29bb
diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
new file mode 100644
index 000000000..b8c8d47fa
--- /dev/null
+++ b/docs/_static/css/custom.css
@@ -0,0 +1,4 @@
+/* Reduce the font size in data frames - See https://github.com/scverse/cookiecutter-scverse/issues/193 */
+div.cell_output table.dataframe {
+    font-size: 0.8em;
+}
diff --git a/docs/_templates/.gitkeep b/docs/_templates/.gitkeep
new file mode 100644
index 000000000..e69de29bb
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
new file mode 100644
index 000000000..7b4a0cf87
--- /dev/null
+++ b/docs/_templates/autosummary/class.rst
@@ -0,0 +1,61 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. add toctree option to make autodoc generate the pages
+
+.. autoclass:: {{ objname }}
+
+{% block attributes %}
+{% if attributes %}
+Attributes table
+~~~~~~~~~~~~~~~~
+
+.. autosummary::
+{% for item in attributes %}
+    ~{{ name }}.{{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
+
+{% block methods %}
+{% if methods %}
+Methods table
+~~~~~~~~~~~~~
+
+.. autosummary::
+{% for item in methods %}
+    {%- if item != '__init__' %}
+    ~{{ name }}.{{ item }}
+    {%- endif -%}
+{%- endfor %}
+{% endif %}
+{% endblock %}
+
+{% block attributes_documentation %}
+{% if attributes %}
+Attributes
+~~~~~~~~~~
+
+{% for item in attributes %}
+
+.. autoattribute:: {{ [objname, item] | join(".") }}
+{%- endfor %}
+
+{% endif %}
+{% endblock %}
+
+{% block methods_documentation %}
+{% if methods %}
+Methods
+~~~~~~~
+
+{% for item in methods %}
+{%- if item != '__init__' %}
+
+.. automethod:: {{ [objname, item] | join(".") }}
+{%- endif -%}
+{%- endfor %}
+
+{% endif %}
+{% endblock %}
diff --git a/docs/changelog.md b/docs/changelog.md
new file mode 100644
index 000000000..d9e79ba64
--- /dev/null
+++ b/docs/changelog.md
@@ -0,0 +1,3 @@
+```{include} ../CHANGELOG.md
+
+```
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 000000000..3625ea241
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,131 @@
+# Configuration file for the Sphinx documentation builder.
+
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+import sys
+from datetime import datetime
+from importlib.metadata import metadata
+from pathlib import Path
+
+HERE = Path(__file__).parent
+sys.path.insert(0, str(HERE / "extensions"))
+
+
+# -- Project information -----------------------------------------------------
+
+# NOTE: If you installed your project in editable mode, this might be stale.
+#       If this is the case, reinstall it to refresh the metadata
+info = metadata("squidpy")
+project_name = info["Name"]
+author = info["Author"]
+copyright = f"{datetime.now():%Y}, {author}."
+version = info["Version"]
+urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
+repository_url = urls["Source"]
+
+# The full version, including alpha/beta/rc tags
+release = info["Version"]
+
+bibtex_bibfiles = ["references.bib"]
+templates_path = ["_templates"]
+nitpicky = True  # Warn about broken links
+needs_sphinx = "4.0"
+
+html_context = {
+    "display_github": True,  # Integrate GitHub
+    "github_user": "giovp",
+    "github_repo": project_name,
+    "github_version": "main",
+    "conf_py_path": "/docs/",
+}
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings.
+# They can be extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = [
+    "myst_nb",
+    "sphinx_copybutton",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinxcontrib.bibtex",
+    "sphinx_autodoc_typehints",
+    "sphinx_tabs.tabs",
+    "sphinx.ext.mathjax",
+    "IPython.sphinxext.ipython_console_highlighting",
+    "sphinxext.opengraph",
+    *[p.stem for p in (HERE / "extensions").glob("*.py")],
+]
+
+autosummary_generate = True
+autodoc_member_order = "groupwise"
+default_role = "literal"
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_use_rtype = True  # having a separate entry generally helps readability
+napoleon_use_param = True
+myst_heading_anchors = 6  # create anchors for h1-h6
+myst_enable_extensions = [
+    "amsmath",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "html_image",
+    "html_admonition",
+]
+myst_url_schemes = ("http", "https", "mailto")
+nb_output_stderr = "remove"
+nb_execution_mode = "off"
+nb_merge_streams = True
+typehints_defaults = "braces"
+
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".ipynb": "myst-nb",
+    ".myst": "myst-nb",
+}
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
+    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+}
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_book_theme"
+html_static_path = ["_static"]
+html_css_files = ["css/custom.css"]
+
+html_title = project_name
+
+html_theme_options = {
+    "repository_url": repository_url,
+    "use_repository_button": True,
+    "path_to_docs": "docs/",
+    "navigation_with_keys": False,
+}
+
+pygments_style = "default"
+
+nitpick_ignore = [
+    # If building the documentation fails because of a missing link that is outside your control,
+    # you can add an exception to this list.
+    #     ("py:class", "igraph.Graph"),
+]
diff --git a/docs/contributing.md b/docs/contributing.md
new file mode 100644
index 000000000..f6fe73712
--- /dev/null
+++ b/docs/contributing.md
@@ -0,0 +1,214 @@
+# Contributing guide
+
+Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this project, too.
+This document will not reproduce the entire content from there.
+Instead, it aims at summarizing the most important information to get you started on contributing.
+
+We assume that you are already familiar with git and with making pull requests on GitHub.
+If not, please refer to the [scanpy developer guide][].
+
+[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
+
+## Installing dev dependencies
+
+In addition to the packages needed to _use_ this package,
+you need additional python packages to [run tests](#writing-tests) and [build the documentation](#docs-building).
+
+:::::{tabs}
+::::{group-tab} Hatch
+The easiest way is to get familiar with [hatch environments][], with which these tasks are simply:
+
+```bash
+hatch test  # defined in the table [tool.hatch.envs.hatch-test] in pyproject.toml
+hatch run docs:build  # defined in the table [tool.hatch.envs.docs]
+```
+
+::::
+
+::::{group-tab} Pip
+If you prefer managing environments manually, you can use `pip`:
+
+```bash
+cd squidpy
+python3 -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev,test,doc]"
+```
+
+::::
+:::::
+
+[hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+
+## Code-style
+
+This package uses [pre-commit][] to enforce consistent code-styles.
+On every commit, pre-commit checks will either automatically fix issues with the code, or raise an error message.
+
+To enable pre-commit locally, simply run
+
+```bash
+pre-commit install
+```
+
+in the root of the repository.
+Pre-commit will automatically download all dependencies when it is run for the first time.
+
+Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub.
+If you didn't run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
+
+If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
+
+```bash
+git pull --rebase
+```
+
+to integrate the changes into yours.
+While the [pre-commit.ci][] is useful, we strongly encourage installing and running pre-commit locally first to understand its usage.
+
+Finally, most editors have an _autoformat on save_ feature.
+Consider enabling this option for [ruff][ruff-editors] and [biome][biome-editors].
+
+[pre-commit]: https://pre-commit.com/
+[pre-commit.ci]: https://pre-commit.ci/
+[ruff-editors]: https://docs.astral.sh/ruff/integrations/
+[biome-editors]: https://biomejs.dev/guides/integrate-in-editor/
+
+(writing-tests)=
+
+## Writing tests
+
+This package uses [pytest][] for automated testing.
+Please write {doc}`scanpy:dev/testing` for every function added to the package.
+
+Most IDEs integrate with pytest and provide a GUI to run tests.
+Just point yours to one of the environments returned by
+
+```bash
+hatch env create hatch-test  # create test environments for all supported versions
+hatch env find hatch-test  # list all possible test environment paths
+```
+
+Alternatively, you can run all tests from the command line by executing
+
+:::::{tabs}
+::::{group-tab} Hatch
+
+```bash
+hatch test  # test with the highest supported Python version
+# or
+hatch test --all  # test with all supported Python versions
+```
+
+::::
+
+::::{group-tab} Pip
+
+```bash
+source .venv/bin/activate
+pytest
+```
+
+::::
+:::::
+
+in the root of the repository.
+
+[pytest]: https://docs.pytest.org/
+
+### Continuous integration
+
+Continuous integration will automatically run the tests on all pull requests and test
+against the minimum and maximum supported Python version.
+
+Additionally, there's a CI job that tests against pre-releases of all dependencies (if there are any).
+The purpose of this check is to detect incompatibilities of new package versions early on and
+gives you time to fix the issue or reach out to the developers of the dependency before the package is released to a wider audience.
+
+## Publishing a release
+
+### Updating the version number
+
+Before making a release, you need to update the version number in the `pyproject.toml` file.
+Please adhere to [Semantic Versioning][semver], in brief
+
+> Given a version number MAJOR.MINOR.PATCH, increment the:
+>
+> 1. MAJOR version when you make incompatible API changes,
+> 2. MINOR version when you add functionality in a backwards compatible manner, and
+> 3. PATCH version when you make backwards compatible bug fixes.
+>
+> Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
+
+Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
+Specify `vX.X.X` as a tag name and create a release.
+For more information, see [managing GitHub releases][].
+This will automatically create a git tag and trigger a Github workflow that creates a release on [PyPI][].
+
+[semver]: https://semver.org/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository
+[pypi]: https://pypi.org/
+
+## Writing documentation
+
+Please write documentation for new or changed features and use-cases.
+This project uses [sphinx][] with the following features:
+
+- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
+- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
+- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+
+See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own.
+
+[sphinx]: https://www.sphinx-doc.org/en/master/
+[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
+[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
+[numpydoc-napoleon]: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
+[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
+[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
+
+### Tutorials with myst-nb and jupyter notebooks
+
+The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
+Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
+It is your responsibility to update and re-run the notebook whenever necessary.
+
+If you are interested in automatically running notebooks as part of the continuous integration,
+please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
+
+[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
+
+#### Hints
+
+- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`.
+  Only if you do so can sphinx automatically create a link to the external documentation.
+- If building the documentation fails because of a missing link that is outside your control,
+  you can add an entry to the `nitpick_ignore` list in `docs/conf.py`
+
+(docs-building)=
+
+#### Building the docs locally
+
+:::::{tabs}
+::::{group-tab} Hatch
+
+```bash
+hatch run docs:build
+hatch run docs:open
+```
+
+::::
+
+::::{group-tab} Pip
+
+```bash
+source .venv/bin/activate
+cd docs
+make html
+(xdg-)open _build/html/index.html
+```
+
+::::
+:::::
diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
new file mode 100644
index 000000000..0fbffefe3
--- /dev/null
+++ b/docs/extensions/typed_returns.py
@@ -0,0 +1,32 @@
+# code from https://github.com/theislab/scanpy/blob/master/docs/extensions/typed_returns.py
+# with some minor adjustment
+from __future__ import annotations
+
+import re
+from collections.abc import Generator, Iterable
+
+from sphinx.application import Sphinx
+from sphinx.ext.napoleon import NumpyDocstring
+
+
+def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
+    for line in lines:
+        if m := re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line):
+            yield f"-{m['param']} (:class:`~{m['type']}`)"
+        else:
+            yield line
+
+
+def _parse_returns_section(self: NumpyDocstring, section: str) -> list[str]:
+    lines_raw = self._dedent(self._consume_to_next_section())
+    if lines_raw[0] == ":":
+        del lines_raw[0]
+    lines = self._format_block(":returns: ", list(_process_return(lines_raw)))
+    if lines and lines[-1]:
+        lines.append("")
+    return lines
+
+
+def setup(app: Sphinx):
+    """Set app."""
+    NumpyDocstring._parse_returns_section = _parse_returns_section
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 000000000..ba634f06a
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,135 @@
+[build-system]
+build-backend = "hatchling.build"
+requires = [ "hatchling" ]
+
+[project]
+name = "squidpy"
+version = "0.0.1"
+description = "Spatial Single Cell Analysis in Python"
+readme = "README.md"
+license = { file = "LICENSE" }
+maintainers = [
+  { name = "Giovanni Palla", email = "giovanni.palla@helmholtz-muenchen.de" },
+]
+authors = [
+  { name = "Giovanni Palla" },
+]
+requires-python = ">=3.10"
+classifiers = [
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+]
+dependencies = [
+  "anndata",
+  # for debug logging (referenced from the issue template)
+  "session-info2",
+]
+optional-dependencies.dev = [
+  "pre-commit",
+  "twine>=4.0.2",
+]
+optional-dependencies.doc = [
+  "docutils>=0.8,!=0.18.*,!=0.19.*",
+  "ipykernel",
+  "ipython",
+  "myst-nb>=1.1",
+  "pandas",
+  # Until pybtex >0.24.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
+  "setuptools",
+  "sphinx>=4",
+  "sphinx-autodoc-typehints",
+  "sphinx-book-theme>=1",
+  "sphinx-copybutton",
+  "sphinx-tabs",
+  "sphinxcontrib-bibtex>=1",
+  "sphinxext-opengraph",
+]
+optional-dependencies.test = [
+  "coverage",
+  "pytest",
+]
+# https://docs.pypi.org/project_metadata/#project-urls
+urls.Documentation = "https://squidpy.readthedocs.io/"
+urls.Homepage = "https://github.com/giovp/squidpy"
+urls.Source = "https://github.com/giovp/squidpy"
+
+[tool.hatch.envs.default]
+installer = "uv"
+features = [ "dev" ]
+
+[tool.hatch.envs.docs]
+features = [ "doc" ]
+scripts.build = "sphinx-build -M html docs docs/_build {args}"
+scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
+scripts.clean = "git clean -fdX -- {args:docs}"
+
+[tool.hatch.envs.hatch-test]
+features = [ "test" ]
+
+[tool.ruff]
+line-length = 120
+src = [ "src" ]
+extend-include = [ "*.ipynb" ]
+
+format.docstring-code-format = true
+
+lint.select = [
+  "B",      # flake8-bugbear
+  "BLE",    # flake8-blind-except
+  "C4",     # flake8-comprehensions
+  "D",      # pydocstyle
+  "E",      # Error detected by Pycodestyle
+  "F",      # Errors detected by Pyflakes
+  "I",      # isort
+  "RUF100", # Report unused noqa directives
+  "TID",    # flake8-tidy-imports
+  "UP",     # pyupgrade
+  "W",      # Warning detected by Pycodestyle
+]
+lint.ignore = [
+  "B008", # Errors from function calls in argument defaults. These are fine when the result is immutable.
+  "D100", # Missing docstring in public module
+  "D104", # Missing docstring in public package
+  "D105", # __magic__ methods are often self-explanatory, allow missing docstrings
+  "D107", # Missing docstring in __init__
+  # Disable one in each pair of mutually incompatible rules
+  "D203", # We don’t want a blank line before a class docstring
+  "D213", # <> We want docstrings to start immediately after the opening triple quote
+  "D400", # first line should end with a period [Bug: doesn’t work with single-line docstrings]
+  "D401", # First line should be in imperative mood; try rephrasing
+  "E501", # line too long -> we accept long comment lines; formatter gets rid of long code lines
+  "E731", # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
+  "E741", # allow I, O, l as variable names -> I is the identity matrix
+]
+lint.per-file-ignores."*/__init__.py" = [ "F401" ]
+lint.per-file-ignores."docs/*" = [ "I" ]
+lint.per-file-ignores."tests/*" = [ "D" ]
+lint.pydocstyle.convention = "numpy"
+
+[tool.pytest.ini_options]
+testpaths = [ "tests" ]
+xfail_strict = true
+addopts = [
+  "--import-mode=importlib", # allow using test files with same name
+]
+
+[tool.coverage.run]
+source = [ "squidpy" ]
+omit = [
+  "**/test_*.py",
+]
+
+[tool.cruft]
+skip = [
+  "tests",
+  "src/**/__init__.py",
+  "src/**/basic.py",
+  "docs/api.md",
+  "docs/changelog.md",
+  "docs/references.bib",
+  "docs/references.md",
+  "docs/notebooks/example.ipynb",
+]

From 2089b5aa835faffe59b0537e0a4a91134f192cbc Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Tue, 30 Sep 2025 06:34:23 +0000
Subject: [PATCH 2/2] Automated template update to v0.6.0

---
 .cruft.json                 |   6 +-
 .github/workflows/test.yaml |  80 +++++++++++++++-----
 .gitignore                  |   1 +
 .pre-commit-config.yaml     |  19 ++---
 .readthedocs.yaml           |  23 +++---
 biome.jsonc                 |   5 +-
 docs/Makefile               |  20 -----
 docs/contributing.md        | 144 ++++++++++++++++++++++++++++++++----
 pyproject.toml              |  27 ++++++-
 9 files changed, 238 insertions(+), 87 deletions(-)
 delete mode 100644 docs/Makefile

diff --git a/.cruft.json b/.cruft.json
index 1855686b1..744ae8c70 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
-  "checkout": "v0.5.0",
+  "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
+  "checkout": "v0.6.0",
   "context": {
     "cookiecutter": {
       "project_name": "squidpy",
@@ -36,7 +36,7 @@
         "trim_blocks": true
       },
       "_template": "https://github.com/scverse/cookiecutter-scverse",
-      "_commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
+      "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
     }
   },
   "directory": null
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index d5cfb2a9c..0bd76e8cf 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -18,27 +18,48 @@ defaults:
     shell: bash -euo pipefail {0}
 
 jobs:
+  # Get the test environment from hatch as defined in pyproject.toml.
+  # This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
+  # run locally and on continuous integration.
+  # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
+  # more details.
+  get-environments:
+    runs-on: ubuntu-latest
+    outputs:
+      envs: ${{ steps.get-envs.outputs.envs }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: Get test environments
+        id: get-envs
+        run: |
+          ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
+            | map(
+                select(.key | startswith("hatch-test"))
+                | {
+                    name: .key,
+                    label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
+                    python: .value.python
+                  }
+              )')
+          echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+
+  # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
   test:
-    runs-on: ${{ matrix.os }}
+    needs: get-environments
 
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - os: ubuntu-latest
-            python: "3.10"
-          - os: ubuntu-latest
-            python: "3.12"
-          - os: ubuntu-latest
-            python: "3.12"
-            pip-flags: "--pre"
-            name: PRE-RELEASE DEPENDENCIES
-
-    name: ${{ matrix.name }} Python ${{ matrix.python }}
-
-    env:
-      OS: ${{ matrix.os }}
-      PYTHON: ${{ matrix.python }}
+        os: [ubuntu-latest]
+        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+
+    name: ${{ matrix.env.label }}
+    runs-on: ${{ matrix.os }}
 
     steps:
       - uses: actions/checkout@v4
@@ -48,12 +69,35 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v5
         with:
+          python-version: ${{ matrix.env.python }}
           cache-dependency-glob: pyproject.toml
+      - name: create hatch environment
+        run: uvx hatch env create ${{ matrix.env.name }}
       - name: run tests using hatch
         env:
           MPLBACKEND: agg
           PLATFORM: ${{ matrix.os }}
           DISPLAY: :42
-        run: uvx hatch test --cover --python ${{ matrix.python }}
+        run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
+      - name: generate coverage report
+        run: |
+          # See https://coverage.readthedocs.io/en/latest/config.html#run-patch
+          test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
+          uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
+          uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
       - name: Upload coverage
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
+
+  # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
+  # protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
+  check:
+    name: Tests pass in all hatch environments
+    if: always()
+    needs:
+      - get-environments
+      - test
+    runs-on: ubuntu-latest
+    steps:
+        - uses: re-actors/alls-green@release/v1
+          with:
+            jobs: ${{ toJSON(needs) }}
diff --git a/.gitignore b/.gitignore
index 31e10b3ea..bd24e4e00 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,6 +14,7 @@ __pycache__/
 # Tests and coverage
 /data/
 /node_modules/
+/.coverage*
 
 # docs
 /docs/generated/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0fcce11e2..b9de3fe04 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,24 +7,24 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v1.9.4
+    rev: v2.2.4
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.5.1
+    rev: v2.6.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.2
+    rev: v0.13.2
     hooks:
-      - id: ruff
+      - id: ruff-check
         types_or: [python, pyi, jupyter]
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
         types_or: [python, pyi, jupyter]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast
@@ -36,12 +36,3 @@ repos:
       # Check that there are no merge conflicts (could be generated by template sync)
       - id: check-merge-conflict
         args: [--assume-in-merge]
-  - repo: local
-    hooks:
-      - id: forbid-to-commit
-        name: Don't commit rej files
-        entry: |
-          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
-          Fix the merge conflicts manually and remove the .rej files.
-        language: fail
-        files: '.*\.rej$'
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 69897c3b3..c3f3f96fb 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,16 +1,15 @@
 # https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: "3.10"
-sphinx:
-  configuration: docs/conf.py
-  # disable this for more lenient docs builds
-  fail_on_warning: true
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - doc
+    python: "3.12"
+  jobs:
+    create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+    build:
+      html:
+        - uvx hatch run docs:build
+        - mv docs/_build $READTHEDOCS_OUTPUT
diff --git a/biome.jsonc b/biome.jsonc
index 2175c16e6..9f8f2208c 100644
--- a/biome.jsonc
+++ b/biome.jsonc
@@ -1,9 +1,10 @@
 {
-    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "$schema": "https://biomejs.dev/schemas/2.2.0/schema.json",
+    "vcs": { "enabled": true, "clientKind": "git", "useIgnoreFile": true },
     "formatter": { "useEditorconfig": true },
     "overrides": [
         {
-            "include": ["./.vscode/*.json", "**/*.jsonc"],
+            "includes": ["./.vscode/*.json", "**/*.jsonc"],
             "json": {
                 "formatter": { "trailingCommas": "all" },
                 "parser": {
diff --git a/docs/Makefile b/docs/Makefile
deleted file mode 100644
index d4bb2cbb9..000000000
--- a/docs/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
-BUILDDIR      = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/contributing.md b/docs/contributing.md
index f6fe73712..699d94291 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -1,14 +1,33 @@
 # Contributing guide
 
-Scanpy provides extensive [developer documentation][scanpy developer guide], most of which applies to this project, too.
-This document will not reproduce the entire content from there.
-Instead, it aims at summarizing the most important information to get you started on contributing.
-
+This document aims at summarizing the most important information for getting you started on contributing to this project.
 We assume that you are already familiar with git and with making pull requests on GitHub.
-If not, please refer to the [scanpy developer guide][].
 
+For more extensive tutorials, that also cover the absolute basics,
+please refer to other resources such as the [pyopensci tutorials][],
+the [scientific Python tutorials][], or the [scanpy developer guide][].
+
+[pyopensci tutorials]: https://www.pyopensci.org/learn.html
+[scientific Python tutorials]: https://learn.scientific-python.org/development/tutorials/
 [scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
 
+:::{tip} The *hatch* project manager
+
+We highly recommend to familiarize yourself with [`hatch`][hatch].
+Hatch is a Python project manager that
+
+- manages virtual environments, separately for development, testing and building the documentation.
+  Separating the environments is useful to avoid dependency conflicts.
+- allows to run tests locally in different environments (e.g. different python versions)
+- allows to run tasks defined in `pyproject.toml`, e.g. to build documentation.
+
+While the project is setup with `hatch` in mind,
+it is still possible to use different tools to manage dependencies, such as `uv` or `pip`.
+
+:::
+
+[hatch]: https://hatch.pypa.io/latest/
+
 ## Installing dev dependencies
 
 In addition to the packages needed to _use_ this package,
@@ -16,29 +35,103 @@ you need additional python packages to [run tests](#writing-tests) and [build th
 
 :::::{tabs}
 ::::{group-tab} Hatch
-The easiest way is to get familiar with [hatch environments][], with which these tasks are simply:
+
+On the command line, you typically interact with hatch through its command line interface (CLI).
+Running one of the following commands will automatically resolve the environments for testing and
+building the documentation in the background:
 
 ```bash
 hatch test  # defined in the table [tool.hatch.envs.hatch-test] in pyproject.toml
 hatch run docs:build  # defined in the table [tool.hatch.envs.docs]
 ```
 
+When using an IDE such as VS Code,
+you’ll have to point the editor at the paths to the virtual environments manually.
+The environment you typically want to use as your main development environment is the `hatch-test`
+environment with the latest Python version.
+
+To get a list of all environments for your projects, run
+
+```bash
+hatch env show -i
+```
+
+This will list “Standalone” environments and a table of “Matrix” environments like the following:
+
+```
++------------+---------+--------------------------+----------+---------------------------------+-------------+
+| Name       | Type    | Envs                     | Features | Dependencies                    | Scripts     |
++------------+---------+--------------------------+----------+---------------------------------+-------------+
+| hatch-test | virtual | hatch-test.py3.10-stable | dev      | coverage-enable-subprocess==1.0 | cov-combine |
+|            |         | hatch-test.py3.13-stable | test     | coverage[toml]~=7.4             | cov-report  |
+|            |         | hatch-test.py3.13-pre    |          | pytest-mock~=3.12               | run         |
+|            |         |                          |          | pytest-randomly~=3.15           | run-cov     |
+|            |         |                          |          | pytest-rerunfailures~=14.0      |             |
+|            |         |                          |          | pytest-xdist[psutil]~=3.5       |             |
+|            |         |                          |          | pytest~=8.1                     |             |
++------------+---------+--------------------------+----------+---------------------------------+-------------+
+```
+
+From the `Envs` column, select the environment name you want to use for development.
+In this example, it would be `hatch-test.py3.13-stable`.
+
+Next, create the environment with
+
+```bash
+hatch env create hatch-test.py3.13-stable
+```
+
+Then, obtain the path to the environment using
+
+```bash
+hatch env find hatch-test.py3.13-stable
+```
+
+In case you are using VScode, now open the command palette (Ctrl+Shift+P) and search for `Python: Select Interpreter`.
+Choose `Enter Interpreter Path` and paste the path to the virtual environment from above.
+
+In this future, this may become easier through a hatch vscode extension.
+
+::::
+
+::::{group-tab} uv
+
+A popular choice for managing virtual environments is [uv][].
+The main disadvantage compared to hatch is that it supports only a single environment per project at a time,
+which requires you to mix the dependencies for running tests and building docs.
+This can have undesired side-effects,
+such as requiring to install a lower version of a library your project depends on,
+only because an outdated sphinx plugin pins an older version.
+
+To initalize a virtual environment in the `.venv` directory of your project, simply run
+
+```bash
+uv sync --all-extras
+```
+
+The `.venv` directory is typically automatically discovered by IDEs such as VS Code.
+
 ::::
 
 ::::{group-tab} Pip
-If you prefer managing environments manually, you can use `pip`:
+
+Pip is nowadays mostly superseded by environment manager such as [hatch][].
+However, for the sake of completeness, and since it’s ubiquitously available,
+we describe how you can manage environments manually using `pip`:
 
 ```bash
-cd squidpy
 python3 -m venv .venv
 source .venv/bin/activate
 pip install -e ".[dev,test,doc]"
 ```
 
+The `.venv` directory is typically automatically discovered by IDEs such as VS Code.
+
 ::::
 :::::
 
 [hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+[uv]: https://docs.astral.sh/uv/
 
 ## Code-style
 
@@ -55,7 +148,7 @@ in the root of the repository.
 Pre-commit will automatically download all dependencies when it is run for the first time.
 
 Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub.
-If you didn't run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
+If you didn’t run `pre-commit` before pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
 
 If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
 
@@ -102,6 +195,14 @@ hatch test --all  # test with all supported Python versions
 
 ::::
 
+::::{group-tab} uv
+
+```bash
+uv run pytest
+```
+
+::::
+
 ::::{group-tab} Pip
 
 ```bash
@@ -118,12 +219,17 @@ in the root of the repository.
 
 ### Continuous integration
 
-Continuous integration will automatically run the tests on all pull requests and test
+Continuous integration via GitHub actions will automatically run the tests on all pull requests and test
 against the minimum and maximum supported Python version.
 
-Additionally, there's a CI job that tests against pre-releases of all dependencies (if there are any).
+Additionally, there’s a CI job that tests against pre-releases of all dependencies (if there are any).
 The purpose of this check is to detect incompatibilities of new package versions early on and
-gives you time to fix the issue or reach out to the developers of the dependency before the package is released to a wider audience.
+gives you time to fix the issue or reach out to the developers of the dependency before the package
+is released to a wider audience.
+
+The CI job is defined in `.github/workflows/test.yaml`,
+however the single point of truth for CI jobs is the Hatch test matrix defined in `pyproject.toml`.
+This means that local testing via hatch and remote testing on CI tests against the same python versions and uses the same environments.
 
 ## Publishing a release
 
@@ -189,7 +295,7 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu
 
 (docs-building)=
 
-#### Building the docs locally
+### Building the docs locally
 
 :::::{tabs}
 ::::{group-tab} Hatch
@@ -201,12 +307,22 @@ hatch run docs:open
 
 ::::
 
+::::{group-tab} uv
+
+```bash
+cd docs
+uv run sphinx-build -M html . _build -W
+(xdg-)open _build/html/index.html
+```
+
+::::
+
 ::::{group-tab} Pip
 
 ```bash
 source .venv/bin/activate
 cd docs
-make html
+sphinx-build -M html . _build -W
 (xdg-)open _build/html/index.html
 ```
 
diff --git a/pyproject.toml b/pyproject.toml
index ba634f06a..9e8740c51 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,7 @@ optional-dependencies.doc = [
   "pandas",
   # Until pybtex >0.24.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
   "setuptools",
-  "sphinx>=4",
+  "sphinx>=8.1",
   "sphinx-autodoc-typehints",
   "sphinx-book-theme>=1",
   "sphinx-copybutton",
@@ -48,8 +48,9 @@ optional-dependencies.doc = [
   "sphinxext-opengraph",
 ]
 optional-dependencies.test = [
-  "coverage",
+  "coverage>=7.10",
   "pytest",
+  "pytest-cov",     # For VS Code’s coverage functionality
 ]
 # https://docs.pypi.org/project_metadata/#project-urls
 urls.Documentation = "https://squidpy.readthedocs.io/"
@@ -62,12 +63,29 @@ features = [ "dev" ]
 
 [tool.hatch.envs.docs]
 features = [ "doc" ]
-scripts.build = "sphinx-build -M html docs docs/_build {args}"
+scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
 scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
 scripts.clean = "git clean -fdX -- {args:docs}"
 
+# Test the lowest and highest supported Python versions with normal deps
+[[tool.hatch.envs.hatch-test.matrix]]
+deps = [ "stable" ]
+python = [ "3.10", "3.13" ]
+
+# Test the newest supported Python version also with pre-release deps
+[[tool.hatch.envs.hatch-test.matrix]]
+deps = [ "pre" ]
+python = [ "3.13" ]
+
 [tool.hatch.envs.hatch-test]
-features = [ "test" ]
+features = [ "dev", "test" ]
+
+[tool.hatch.envs.hatch-test.overrides]
+# If the matrix variable `deps` is set to "pre",
+# set the environment variable `UV_PRERELEASE` to "allow".
+matrix.deps.env-vars = [
+  { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
+]
 
 [tool.ruff]
 line-length = 120
@@ -118,6 +136,7 @@ addopts = [
 
 [tool.coverage.run]
 source = [ "squidpy" ]
+patch = [ "subprocess" ]
 omit = [
   "**/test_*.py",
 ]