From dac7a5eb581688cddff40b075e2eb408058f83e4 Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Wed, 2 Apr 2025 18:24:17 +0000
Subject: [PATCH 1/3] Automated template update to v0.5.0

---
 .cruft.json                           |  22 ++-
 .editorconfig                         |   5 +-
 .github/ISSUE_TEMPLATE/bug_report.yml | 123 ++++++++-------
 .github/workflows/build.yaml          |  24 +--
 .github/workflows/release.yaml        |  15 +-
 .github/workflows/test.yaml           |  50 +++---
 .gitignore                            |  11 +-
 .pre-commit-config.yaml               |  30 ++--
 .vscode/extensions.json               |  18 +++
 .vscode/launch.json                   |  33 ++++
 .vscode/settings.json                 |  18 +++
 biome.jsonc                           |  16 ++
 docs/_templates/autosummary/class.rst |   8 +-
 docs/conf.py                          |   4 +-
 docs/contributing.md                  | 194 ++++++++++++++---------
 docs/extensions/typed_returns.py      |   2 +-
 pyproject.toml                        | 217 +++++++++++++-------------
 17 files changed, 463 insertions(+), 327 deletions(-)
 create mode 100644 .vscode/extensions.json
 create mode 100644 .vscode/launch.json
 create mode 100644 .vscode/settings.json
 create mode 100644 biome.jsonc

diff --git a/.cruft.json b/.cruft.json
index c0a4eb5..e2f5e2a 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "aa877587e59c855e2464d09ed7678af00999191a",
-  "checkout": null,
+  "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
+  "checkout": "v0.5.0",
   "context": {
     "cookiecutter": {
       "project_name": "nichepca",
@@ -10,19 +10,33 @@
       "author_full_name": "Darius P. Schaub",
       "author_email": "schaub.darius@gmail.com",
       "github_user": "imsb-uke",
-      "project_repo": "https://github.com/imsb-uke/nichepca",
+      "github_repo": "nichepca",
       "license": "MIT 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"
+      "_template": "https://github.com/scverse/cookiecutter-scverse",
+      "_commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
     }
   },
   "directory": null
diff --git a/.editorconfig b/.editorconfig
index 050f911..66678e3 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -8,10 +8,7 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
-[*.{yml,yaml}]
-indent_size = 2
-
-[.cruft.json]
+[{*.{yml,yaml,toml},.cruft.json}]
 indent_size = 2
 
 [Makefile]
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index a5a20e6..3ca1ccb 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -23,67 +23,72 @@ body:
   - type: textarea
     id: versions
     attributes:
-      label: Version information
+      label: Versions
       description: |
-        Please paste below the output of
+        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_info
-        session_info.show(html=False, dependencies=True)
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
         ```
+      render: python
       placeholder: |
-        -----
-        anndata             0.8.0rc2.dev27+ge524389
-        session_info        1.0.0
-        -----
-        asttokens           NA
-        awkward             1.8.0
-        backcall            0.2.0
-        cython_runtime      NA
-        dateutil            2.8.2
-        debugpy             1.6.0
-        decorator           5.1.1
-        entrypoints         0.4
-        executing           0.8.3
-        h5py                3.7.0
-        ipykernel           6.15.0
-        jedi                0.18.1
-        mpl_toolkits        NA
-        natsort             8.1.0
-        numpy               1.22.4
-        packaging           21.3
-        pandas              1.4.2
-        parso               0.8.3
-        pexpect             4.8.0
-        pickleshare         0.7.5
-        pkg_resources       NA
-        prompt_toolkit      3.0.29
-        psutil              5.9.1
-        ptyprocess          0.7.0
-        pure_eval           0.2.2
-        pydev_ipython       NA
-        pydevconsole        NA
-        pydevd              2.8.0
-        pydevd_file_utils   NA
-        pydevd_plugins      NA
-        pydevd_tracing      NA
-        pygments            2.12.0
-        pytz                2022.1
-        scipy               1.8.1
-        setuptools          62.5.0
-        setuptools_scm      NA
-        six                 1.16.0
-        stack_data          0.3.0
-        tornado             6.1
-        traitlets           5.3.0
-        wcwidth             0.2.5
-        zmq                 23.1.0
-        -----
-        IPython             8.4.0
-        jupyter_client      7.3.4
-        jupyter_core        4.10.0
-        -----
-        Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
-        Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
-        -----
-        Session information updated at 2022-07-07 17:55
+        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/workflows/build.yaml b/.github/workflows/build.yaml
index 265a95e..83e01a1 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -10,20 +10,24 @@ 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@v3
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: "3.10"
-          cache: "pip"
-          cache-dependency-path: "**/pyproject.toml"
-      - name: Install build dependencies
-        run: python -m pip install --upgrade pip wheel twine build
+          cache-dependency-glob: pyproject.toml
       - name: Build package
-        run: python -m build
+        run: uv build
       - name: Check package
-        run: twine check --strict dist/*.whl
+        run: uvx twine check --strict dist/*.whl
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index d0c1c01..f4107a1 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -4,6 +4,11 @@ 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:
@@ -19,11 +24,11 @@ jobs:
         with:
           filter: blob:none
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: "3.x"
-          cache: "pip"
-      - run: pip install build
-      - run: python -m build
+          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
index f37314f..d5cfb2a 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -12,12 +12,14 @@ 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 }}
-    defaults:
-      run:
-        shell: bash -e {0} # -e to fail on error
 
     strategy:
       fail-fast: false
@@ -25,12 +27,12 @@ jobs:
         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
+          - 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 }}
 
@@ -39,29 +41,19 @@ jobs:
       PYTHON: ${{ matrix.python }}
 
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
         with:
-          python-version: ${{ matrix.python }}
-          cache: "pip"
-          cache-dependency-path: "**/pyproject.toml"
-
-      - name: Install test dependencies
-        run: |
-          python -m pip install --upgrade pip wheel
-      - name: Install dependencies
-        run: |
-          pip install ${{ matrix.pip-flags }} ".[dev,test]"
-      - name: Test
+          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: |
-          coverage run -m pytest -v --color=yes
-      - name: Report coverage
-        run: |
-          coverage report
+        run: uvx hatch test --cover --python ${{ matrix.python }}
       - name: Upload coverage
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
diff --git a/.gitignore b/.gitignore
index eeec7e2..31e10b3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,24 +6,15 @@ buck-out/
 # Compiled files
 .venv/
 __pycache__/
-.mypy_cache/
-.ruff_cache/
+.*cache/
 
 # Distribution / packaging
-/build/
 /dist/
-/*.egg-info/
 
 # Tests and coverage
-/.pytest_cache/
-/.cache/
 /data/
 /node_modules/
 
 # docs
 /docs/generated/
 /docs/_build/
-
-# IDEs
-/.idea/
-/.vscode/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 945b14a..0fcce11 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,27 +2,21 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-  # - repo: https://github.com/pre-commit/mirrors-prettier
-  #   rev: v4.0.0-alpha.8
-  #   hooks:
-  #     - id: prettier
-
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.2
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v1.9.4
     hooks:
-      - id: black
-      - id: black-jupyter
-        # It is recommended to specify the latest version of Python
-        # supported by your project here, or alternatively use
-        # pre-commit's default_language_version, see
-        # https://pre-commit.com/#top_level-default_language_version
-        language_version: python3.11
+      - 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: v0.4.10
+    rev: v0.11.2
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
@@ -30,7 +24,7 @@ repos:
       - id: ruff-format
         types_or: [python, pyi, jupyter]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
new file mode 100644
index 0000000..caaeb4f
--- /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 0000000..36d1874
--- /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 0000000..e034b91
--- /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 0000000..2175c16
--- /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/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
index e4665df..7b4a0cf 100644
--- a/docs/_templates/autosummary/class.rst
+++ b/docs/_templates/autosummary/class.rst
@@ -9,11 +9,11 @@
 {% block attributes %}
 {% if attributes %}
 Attributes table
-~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~
 
 .. autosummary::
 {% for item in attributes %}
-    ~{{ fullname }}.{{ item }}
+    ~{{ name }}.{{ item }}
 {%- endfor %}
 {% endif %}
 {% endblock %}
@@ -26,7 +26,7 @@ Methods table
 .. autosummary::
 {% for item in methods %}
     {%- if item != '__init__' %}
-    ~{{ fullname }}.{{ item }}
+    ~{{ name }}.{{ item }}
     {%- endif -%}
 {%- endfor %}
 {% endif %}
@@ -35,7 +35,7 @@ Methods table
 {% block attributes_documentation %}
 {% if attributes %}
 Attributes
-~~~~~~~~~~~
+~~~~~~~~~~
 
 {% for item in attributes %}
 
diff --git a/docs/conf.py b/docs/conf.py
index 9a787b5..913ba7b 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -37,7 +37,7 @@
 html_context = {
     "display_github": True,  # Integrate GitHub
     "github_user": "imsb-uke",
-    "github_repo": "https://github.com/imsb-uke/nichepca",
+    "github_repo": project_name,
     "github_version": "main",
     "conf_py_path": "/docs/",
 }
@@ -55,6 +55,7 @@
     "sphinx.ext.napoleon",
     "sphinxcontrib.bibtex",
     "sphinx_autodoc_typehints",
+    "sphinx_tabs.tabs",
     "sphinx.ext.mathjax",
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinxext.opengraph",
@@ -93,6 +94,7 @@
 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),
 }
 
diff --git a/docs/contributing.md b/docs/contributing.md
index 50b967b..69e04ff 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -1,22 +1,45 @@
 # 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 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][].
+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_ and _build
-the documentation_. It's easy to install them using `pip`:
+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 nichepca
+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.
@@ -28,10 +51,11 @@ To enable pre-commit locally, simply run
 pre-commit install
 ```
 
-in the root of the repository. Pre-commit will automatically download all dependencies when it is run for the first time.
+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.
+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
 
@@ -42,71 +66,108 @@ 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 [prettier][prettier-editors].
+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/
-[prettier-editors]: https://prettier.io/docs/en/editors.html
+[biome-editors]: https://biomejs.dev/guides/integrate-in-editor/
+
+(writing-tests)=
 
 ## Writing tests
 
-```{note}
-Remember to first install the package with `pip install -e '.[dev,test]'`
+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
 ```
 
-This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added
-to the package.
+::::
 
-Most IDEs integrate with pytest and provide a GUI to run tests. Alternatively, you can run all tests from the
-command line by executing
+::::{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.
-
-[scanpy-test-docs]: https://scanpy.readthedocs.io/en/latest/dev/testing.html#writing-tests
+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
+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.
+> 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.
+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:
+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/)
 
--   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.
 
-See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
-on how to write documentation.
+[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
 
@@ -114,47 +175,40 @@ The documentation is set-up to render jupyter notebooks stored in the `docs/note
 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](https://github.com/scverse/cookiecutter-scverse/issues/40) in the `cookiecutter-scverse`
-repository.
+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`
+- 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
-open _build/html/index.html
+(xdg-)open _build/html/index.html
 ```
 
-<!-- Links -->
-
-[scanpy developer guide]: https://scanpy.readthedocs.io/en/latest/dev/index.html
-[cookiecutter-scverse-instance]: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html
-[github quickstart guide]: https://docs.github.com/en/get-started/quickstart/create-a-repo?tool=webui
-[codecov]: https://about.codecov.io/sign-up/
-[codecov docs]: https://docs.codecov.com/docs
-[codecov bot]: https://docs.codecov.com/docs/team-bot
-[codecov app]: https://github.com/apps/codecov
-[pre-commit.ci]: https://pre-commit.ci/
-[readthedocs.org]: https://readthedocs.org/
-[myst-nb]: https://myst-nb.readthedocs.io/en/latest/
-[jupytext]: https://jupytext.readthedocs.io/en/latest/
-[pre-commit]: https://pre-commit.com/
-[anndata]: https://github.com/scverse/anndata
-[mudata]: https://github.com/scverse/mudata
-[pytest]: https://docs.pytest.org/
-[semver]: https://semver.org/
-[sphinx]: https://www.sphinx-doc.org/en/master/
-[myst]: https://myst-parser.readthedocs.io/en/latest/intro.html
-[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
-[pypi]: https://pypi.org/
-[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository
+::::
+:::::
diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
index 1135204..0fbffef 100644
--- a/docs/extensions/typed_returns.py
+++ b/docs/extensions/typed_returns.py
@@ -12,7 +12,7 @@
 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"]}`)'
+            yield f"-{m['param']} (:class:`~{m['type']}`)"
         else:
             yield line
 
diff --git a/pyproject.toml b/pyproject.toml
index 15c1458..1deecbd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,142 +1,135 @@
 [build-system]
 build-backend = "hatchling.build"
-requires = ["hatchling"]
+requires = [ "hatchling" ]
 
 [project]
 name = "nichepca"
 version = "0.0.1"
 description = "Package for PCA-based spatial domain identification in single-cell spatial transcriptomics data"
 readme = "README.md"
-requires-python = ">=3.10"
-license = {file = "LICENSE"}
+license = { file = "LICENSE" }
+maintainers = [
+  { name = "Darius P. Schaub", email = "schaub.darius@gmail.com" },
+]
 authors = [
-    {name = "Darius P. Schaub"},
+  { name = "Darius P. Schaub" },
 ]
-maintainers = [
-    {name = "Darius P. Schaub", email = "schaub.darius@gmail.com"},
+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",
 ]
-urls.Documentation = "https://nichepca.readthedocs.io/"
-urls.Source = "https://github.com/imsb-uke/nichepca"
-urls.Home-page = "https://github.com/imsb-uke/nichepca"
 dependencies = [
-    "scanpy >=1.9.8",
-    "numpy >= 1.23.4, < 2.0.0",
-    "torch_geometric >= 2.4.0",
-    "torch >= 2.1.2",
-    "scipy >= 1.11.4",
-    "scikit-learn >= 1.3.0",
-    "tqdm >= 4.65.0",
-    "harmonypy >= 0.0.9",
-    "leidenalg >= 0.10.2",
-    # for debug logging (referenced from the issue template)
-    "session-info",
+  "anndata",
+  # for debug logging (referenced from the issue template)
+  "session-info2",
 ]
-
-[project.optional-dependencies]
-dev = [
-    "pre-commit",
-    "twine>=4.0.2",
-    "black",
+optional-dependencies.dev = [
+  "pre-commit",
+  "twine>=4.0.2",
 ]
-doc = [
-    "docutils>=0.8,!=0.18.*,!=0.19.*",
-    "sphinx>=4",
-    "sphinx-book-theme>=1.0.0",
-    "myst-nb>=1.1.0",
-    "sphinxcontrib-bibtex>=1.0.0",
-    "setuptools",  # Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
-    "sphinx-autodoc-typehints",
-    "sphinxext-opengraph",
-    # For notebooks
-    "ipykernel",
-    "ipython",
-    "sphinx-copybutton",
-    "pandas",
+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",
 ]
-test = [
-    "pytest",
-    "coverage",
+optional-dependencies.test = [
+  "coverage",
+  "pytest",
 ]
+# https://docs.pypi.org/project_metadata/#project-urls
+urls.Documentation = "https://nichepca.readthedocs.io/"
+urls.Homepage = "https://github.com/imsb-uke/nichepca"
+urls.Source = "https://github.com/imsb-uke/nichepca"
 
-[tool.coverage.run]
-source = ["nichepca"]
-omit = [
-    "**/test_*.py",
-]
+[tool.hatch.envs.default]
+installer = "uv"
+features = [ "dev" ]
 
-[tool.pytest.ini_options]
-testpaths = ["tests"]
-xfail_strict = true
-addopts = [
-    "--import-mode=importlib",  # allow using test files with same name
-]
+[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 = 88
-src = ["src"]
-extend-include = ["*.ipynb"]
+line-length = 120
+src = [ "src" ]
+extend-include = [ "*.ipynb" ]
 
-[tool.ruff.format]
-docstring-code-format = true
+format.docstring-code-format = true
 
-[tool.ruff.lint]
-select = [
-    "F",  # Errors detected by Pyflakes
-    "E",  # Error detected by Pycodestyle
-    "W",  # Warning detected by Pycodestyle
-    "I",  # isort
-    "D",  # pydocstyle
-    "B",  # flake8-bugbear
-    "TID",  # flake8-tidy-imports
-    "C4",  # flake8-comprehensions
-    "BLE",  # flake8-blind-except
-    "UP",  # pyupgrade
-    "RUF100",  # Report unused noqa directives
+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
 ]
-ignore = [
-    # line too long -> we accept long comment lines; formatter gets rid of long code lines
-    "E501",
-    # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
-    "E731",
-    # allow I, O, l as variable names -> I is the identity matrix
-    "E741",
-    # Missing docstring in public package
-    "D104",
-    # Missing docstring in public module
-    "D100",
-    # Missing docstring in __init__
-    "D107",
-    # Errors from function calls in argument defaults. These are fine when the result is immutable.
-    "B008",
-    # __magic__ methods are often self-explanatory, allow missing docstrings
-    "D105",
-    # first line should end with a period [Bug: doesn't work with single-line docstrings]
-    "D400",
-    # First line should be in imperative mood; try rephrasing
-    "D401",
-    ## Disable one in each pair of mutually incompatible rules
-    # We don’t want a blank line before a class docstring
-    "D203",
-    # We want docstrings to start immediately after the opening triple quote
-    "D213",
+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.ruff.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.ruff.lint.per-file-ignores]
-"docs/*" = ["I"]
-"tests/*" = ["D"]
-"*/__init__.py" = ["F401"]
+[tool.coverage.run]
+source = [ "nichepca" ]
+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",
+  "tests",
+  "src/**/__init__.py",
+  "src/**/basic.py",
+  "docs/api.md",
+  "docs/changelog.md",
+  "docs/references.bib",
+  "docs/references.md",
+  "docs/notebooks/example.ipynb",
 ]

From 3ad7364634bce4c5dc9e05ee2011bc9608c46f8b Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Tue, 30 Sep 2025 06:28:33 +0000
Subject: [PATCH 2/3] 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 e2f5e2a..93093aa 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": "nichepca",
@@ -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 d5cfb2a..0bd76e8 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 31e10b3..bd24e4e 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 0fcce11..b9de3fe 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 69897c3..c3f3f96 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 $READTHEDOCS_OUTPUT
diff --git a/biome.jsonc b/biome.jsonc
index 2175c16..9f8f220 100644
--- a/biome.jsonc
+++ b/biome.jsonc
@@ -1,9 +1,10 @@
 {
-    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "$schema": "https://biomejs.dev/schemas/2.2.0/schema.json",
+    "vcs": { "enabled": true, "clientKind": "git", "useIgnoreFile": true },
     "formatter": { "useEditorconfig": true },
     "overrides": [
         {
-            "include": ["./.vscode/*.json", "**/*.jsonc"],
+            "includes": ["./.vscode/*.json", "**/*.jsonc"],
             "json": {
                 "formatter": { "trailingCommas": "all" },
                 "parser": {
diff --git a/docs/Makefile b/docs/Makefile
deleted file mode 100644
index d4bb2cb..0000000
--- a/docs/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
-BUILDDIR      = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(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 69e04ff..699d942 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 nichepca
 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 1deecbd..0e74a13 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://nichepca.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 = [ "nichepca" ]
+patch = [ "subprocess" ]
 omit = [
   "**/test_*.py",
 ]

From 64f0404d17e8ead921e911c2e0c6dd484ce7efe4 Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Wed, 24 Dec 2025 09:55:53 +0000
Subject: [PATCH 3/3] Automated template update to v0.7.0

---
 .cruft.json                                |  8 ++--
 .github/ISSUE_TEMPLATE/bug_report.yml      |  5 +--
 .github/ISSUE_TEMPLATE/feature_request.yml |  2 +-
 .github/workflows/build.yaml               | 11 +----
 .github/workflows/release.yaml             | 11 +----
 .github/workflows/test.yaml                | 20 ++++-----
 .pre-commit-config.yaml                    |  6 +--
 .readthedocs.yaml                          |  3 +-
 docs/conf.py                               | 15 ++++---
 docs/contributing.md                       | 12 +++---
 pyproject.toml                             | 48 +++++++++++-----------
 11 files changed, 66 insertions(+), 75 deletions(-)

diff --git a/.cruft.json b/.cruft.json
index 93093aa..0653dee 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,12 +1,12 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
-  "checkout": "v0.6.0",
+  "commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95",
+  "checkout": "v0.7.0",
   "context": {
     "cookiecutter": {
       "project_name": "nichepca",
       "package_name": "nichepca",
-      "project_description": "Package for PCA-based spatial domain identification in single-cell spatial transcriptomics data",
+      "project_description": "Package for PCA-based spatial domain identification in single-cell spatial transcriptomics data.",
       "author_full_name": "Darius P. Schaub",
       "author_email": "schaub.darius@gmail.com",
       "github_user": "imsb-uke",
@@ -36,7 +36,7 @@
         "trim_blocks": true
       },
       "_template": "https://github.com/scverse/cookiecutter-scverse",
-      "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
+      "_commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95"
     }
   },
   "directory": null
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 3ca1ccb..6104b9e 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -1,6 +1,6 @@
 name: Bug report
 description: Report something that is broken or incorrect
-labels: bug
+type: Bug
 body:
   - type: markdown
     attributes:
@@ -9,8 +9,7 @@ body:
         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.
+          * Replicate problems on public datasets or share data subsets when full sharing isn't possible.
 
   - type: textarea
     id: report
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
index 822d8f3..9732c7d 100644
--- a/.github/ISSUE_TEMPLATE/feature_request.yml
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,6 +1,6 @@
 name: Feature request
 description: Propose a new feature for nichepca
-labels: enhancement
+type: Enhancement
 body:
   - type: textarea
     id: description
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index 83e01a1..c6ecc2f 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -10,23 +10,16 @@ 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
+      - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
-        with:
-          cache-dependency-glob: pyproject.toml
+        uses: astral-sh/setup-uv@v7
       - name: Build package
         run: uv build
       - name: Check package
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index f4107a1..e8da5f8 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -4,11 +4,6 @@ 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:
@@ -20,14 +15,12 @@ jobs:
     permissions:
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
-        with:
-          cache-dependency-glob: pyproject.toml
+        uses: astral-sh/setup-uv@v7
       - name: Build package
         run: uv build
       - name: Publish package distributions to PyPI
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 0bd76e8..6bf473b 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -12,11 +12,6 @@ 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:
   # 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
@@ -28,12 +23,12 @@ jobs:
     outputs:
       envs: ${{ steps.get-envs.outputs.envs }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
       - name: Get test environments
         id: get-envs
         run: |
@@ -51,6 +46,8 @@ jobs:
   # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
   test:
     needs: get-environments
+    permissions:
+       id-token: write  # for codecov OIDC
 
     strategy:
       fail-fast: false
@@ -60,17 +57,17 @@ jobs:
 
     name: ${{ matrix.env.label }}
     runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ contains(matrix.env.name, 'pre') }}  # make "all-green" pass even if pre-release job fails
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         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
@@ -87,6 +84,9 @@ jobs:
           uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
       - name: Upload coverage
         uses: codecov/codecov-action@v5
+        with:
+          fail_ci_if_error: true
+          use_oidc: true
 
   # 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.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b9de3fe..27d8a95 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,16 +7,16 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.2.4
+    rev: v2.3.10
     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: v2.6.0
+    rev: v2.11.1
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.13.2
+    rev: v0.14.10
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index c3f3f96..6c28477 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -3,7 +3,8 @@ version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.12"
+    python: "3.13"
+    nodejs: latest
   jobs:
     create_environment:
       - asdf plugin add uv
diff --git a/docs/conf.py b/docs/conf.py
index 913ba7b..ca531ff 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -5,11 +5,14 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 # -- Path setup --------------------------------------------------------------
+import shutil
 import sys
 from datetime import datetime
 from importlib.metadata import metadata
 from pathlib import Path
 
+from sphinxcontrib import katex
+
 HERE = Path(__file__).parent
 sys.path.insert(0, str(HERE / "extensions"))
 
@@ -19,7 +22,7 @@
 # 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("nichepca")
-project_name = info["Name"]
+project = info["Name"]
 author = info["Author"]
 copyright = f"{datetime.now():%Y}, {author}."
 version = info["Version"]
@@ -37,7 +40,7 @@
 html_context = {
     "display_github": True,  # Integrate GitHub
     "github_user": "imsb-uke",
-    "github_repo": project_name,
+    "github_repo": project,
     "github_version": "main",
     "conf_py_path": "/docs/",
 }
@@ -54,9 +57,9 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
     "sphinxcontrib.bibtex",
+    "sphinxcontrib.katex",
     "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")],
@@ -92,7 +95,8 @@
 }
 
 intersphinx_mapping = {
-    "python": ("https://docs.python.org/3", None),
+    # TODO: replace `3.13` with `3` once ReadTheDocs supports building with Python 3.14
+    "python": ("https://docs.python.org/3.13", None),
     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
     "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
@@ -113,7 +117,7 @@
 html_static_path = ["_static"]
 html_css_files = ["css/custom.css"]
 
-html_title = project_name
+html_title = project
 
 html_theme_options = {
     "repository_url": repository_url,
@@ -123,6 +127,7 @@
 }
 
 pygments_style = "default"
+katex_prerender = shutil.which(katex.NODEJS_BINARY) is not None
 
 nitpick_ignore = [
     # If building the documentation fails because of a missing link that is outside your control,
diff --git a/docs/contributing.md b/docs/contributing.md
index 699d942..b172fd1 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -62,9 +62,9 @@ This will list “Standalone” environments and a table of “Matrix” environ
 +------------+---------+--------------------------+----------+---------------------------------+-------------+
 | 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         |
+| hatch-test | virtual | hatch-test.py3.11-stable | dev      | coverage-enable-subprocess==1.0 | cov-combine |
+|            |         | hatch-test.py3.14-stable | test     | coverage[toml]~=7.4             | cov-report  |
+|            |         | hatch-test.py3.14-pre    |          | pytest-mock~=3.12               | run         |
 |            |         |                          |          | pytest-randomly~=3.15           | run-cov     |
 |            |         |                          |          | pytest-rerunfailures~=14.0      |             |
 |            |         |                          |          | pytest-xdist[psutil]~=3.5       |             |
@@ -73,18 +73,18 @@ This will list “Standalone” environments and a table of “Matrix” environ
 ```
 
 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`.
+In this example, it would be `hatch-test.py3.14-stable`.
 
 Next, create the environment with
 
 ```bash
-hatch env create hatch-test.py3.13-stable
+hatch env create hatch-test.py3.14-stable
 ```
 
 Then, obtain the path to the environment using
 
 ```bash
-hatch env find hatch-test.py3.13-stable
+hatch env find hatch-test.py3.14-stable
 ```
 
 In case you are using VScode, now open the command palette (Ctrl+Shift+P) and search for `Python: Select Interpreter`.
diff --git a/pyproject.toml b/pyproject.toml
index 0e74a13..31027af 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ requires = [ "hatchling" ]
 [project]
 name = "nichepca"
 version = "0.0.1"
-description = "Package for PCA-based spatial domain identification in single-cell spatial transcriptomics data"
+description = "Package for PCA-based spatial domain identification in single-cell spatial transcriptomics data."
 readme = "README.md"
 license = { file = "LICENSE" }
 maintainers = [
@@ -14,55 +14,55 @@ maintainers = [
 authors = [
   { name = "Darius P. Schaub" },
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 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",
+  "Programming Language :: Python :: 3.14",
 ]
 dependencies = [
   "anndata",
   # for debug logging (referenced from the issue template)
   "session-info2",
 ]
-optional-dependencies.dev = [
+# https://docs.pypi.org/project_metadata/#project-urls
+urls.Documentation = "https://nichepca.readthedocs.io/"
+urls.Homepage = "https://github.com/imsb-uke/nichepca"
+urls.Source = "https://github.com/imsb-uke/nichepca"
+
+[dependency-groups]
+dev = [
   "pre-commit",
   "twine>=4.0.2",
 ]
-optional-dependencies.doc = [
-  "docutils>=0.8,!=0.18.*,!=0.19.*",
+test = [
+  "coverage>=7.10",
+  "pytest",
+  "pytest-cov",     # For VS Code’s coverage functionality
+]
+doc = [
   "ipykernel",
   "ipython",
   "myst-nb>=1.1",
   "pandas",
-  # Until pybtex >0.24.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
-  "setuptools",
   "sphinx>=8.1",
   "sphinx-autodoc-typehints",
   "sphinx-book-theme>=1",
   "sphinx-copybutton",
   "sphinx-tabs",
   "sphinxcontrib-bibtex>=1",
+  "sphinxcontrib-katex",
   "sphinxext-opengraph",
 ]
-optional-dependencies.test = [
-  "coverage>=7.10",
-  "pytest",
-  "pytest-cov",     # For VS Code’s coverage functionality
-]
-# https://docs.pypi.org/project_metadata/#project-urls
-urls.Documentation = "https://nichepca.readthedocs.io/"
-urls.Homepage = "https://github.com/imsb-uke/nichepca"
-urls.Source = "https://github.com/imsb-uke/nichepca"
 
 [tool.hatch.envs.default]
 installer = "uv"
-features = [ "dev" ]
+dependency-groups = [ "dev" ]
 
 [tool.hatch.envs.docs]
-features = [ "doc" ]
+dependency-groups = [ "doc" ]
 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}"
@@ -70,15 +70,15 @@ 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" ]
+python = [ "3.11", "3.14" ]
 
 # Test the newest supported Python version also with pre-release deps
 [[tool.hatch.envs.hatch-test.matrix]]
 deps = [ "pre" ]
-python = [ "3.13" ]
+python = [ "3.14" ]
 
 [tool.hatch.envs.hatch-test]
-features = [ "dev", "test" ]
+dependency-groups = [ "dev", "test" ]
 
 [tool.hatch.envs.hatch-test.overrides]
 # If the matrix variable `deps` is set to "pre",
@@ -127,9 +127,9 @@ lint.per-file-ignores."docs/*" = [ "I" ]
 lint.per-file-ignores."tests/*" = [ "D" ]
 lint.pydocstyle.convention = "numpy"
 
-[tool.pytest.ini_options]
+[tool.pytest]
+strict = true
 testpaths = [ "tests" ]
-xfail_strict = true
 addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]