From e499e9b053e3719f348013f52e41b5faf6ff41c0 Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Tue, 30 Sep 2025 06:32:27 +0000
Subject: [PATCH 1/3] 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 b648b4a..f8b8336 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": "FlowSOM",
@@ -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 c22bb14..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 FlowSOM
 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 a3a1b9f..6bfbf67 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://FlowSOM.readthedocs.io/"
@@ -65,12 +66,29 @@ 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
@@ -121,6 +139,7 @@ addopts = [
 
 [tool.coverage.run]
 source = [ "FlowSOM" ]
+patch = [ "subprocess" ]
 omit = [
   "**/test_*.py",
 ]

From f63386aafbf7dbefeda84df9aaab720bf79b28c8 Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Wed, 24 Dec 2025 10:00:52 +0000
Subject: [PATCH 2/3] Automated template update to v0.7.0

---
 .cruft.json                                |  6 +--
 .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                             | 46 +++++++++++-----------
 11 files changed, 64 insertions(+), 73 deletions(-)

diff --git a/.cruft.json b/.cruft.json
index f8b8336..af57888 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
-  "checkout": "v0.6.0",
+  "commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95",
+  "checkout": "v0.7.0",
   "context": {
     "cookiecutter": {
       "project_name": "FlowSOM",
@@ -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 c1048c6..3ba5aea 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 FlowSOM
-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 0c1ebfa..59a43d7 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 5d4eb71..ca4245e 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("FlowSOM")
-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": "artuurC",
-    "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 6bfbf67..4a5704f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,58 +14,58 @@ maintainers = [
 authors = [
   { name = "Artuur Couckuyt" },
 ]
-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://FlowSOM.readthedocs.io/"
+urls.Homepage = "https://github.com/artuurC/FlowSOM"
+urls.Source = "https://github.com/artuurC/FlowSOM"
+
+[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://FlowSOM.readthedocs.io/"
-urls.Homepage = "https://github.com/artuurC/FlowSOM"
-urls.Source = "https://github.com/artuurC/FlowSOM"
 
 [tool.hatch.build.targets.wheel]
 packages = [ "src/FlowSOM" ]
 
 [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}"
@@ -73,15 +73,15 @@ 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",
@@ -130,9 +130,9 @@ 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
 ]

From c331b71d3ccd5bf57a62c5414d76cae10c5008c8 Mon Sep 17 00:00:00 2001
From: scverse-bot <108668866+scverse-bot@users.noreply.github.com>
Date: Fri, 17 Jul 2026 07:23:48 +0000
Subject: [PATCH 3/3] Automated template update to v0.8.0

---
 .cruft.json                                | 17 ++--
 .github/ISSUE_TEMPLATE/bug_report.yml      |  2 +-
 .github/ISSUE_TEMPLATE/feature_request.yml |  2 +-
 .github/dependabot.yml                     | 12 +++
 .github/workflows/build.yaml               |  8 +-
 .github/workflows/release.yaml             | 12 ++-
 .github/workflows/test.yaml                | 24 ++++--
 .pre-commit-config.yaml                    | 12 ++-
 .readthedocs.yaml                          |  4 +-
 docs/_templates/autosummary/class.rst      | 61 --------------
 docs/conf.py                               | 13 +--
 docs/contributing.md                       | 97 +++++++++++++---------
 docs/extensions/typed_returns.py           | 32 -------
 pyproject.toml                             | 69 +++++++--------
 14 files changed, 158 insertions(+), 207 deletions(-)
 create mode 100644 .github/dependabot.yml
 delete mode 100644 docs/_templates/autosummary/class.rst
 delete mode 100644 docs/extensions/typed_returns.py

diff --git a/.cruft.json b/.cruft.json
index af57888..0599807 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,7 +1,7 @@
 {
-  "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95",
-  "checkout": "v0.7.0",
+  "template": "/tmp/tmpvf8ta0q7",
+  "commit": "6518dfa1abde7379ea7255daf0ce09c23f2b4c94",
+  "checkout": "v0.8.0",
   "context": {
     "cookiecutter": {
       "project_name": "FlowSOM",
@@ -13,6 +13,7 @@
       "github_repo": "FlowSOM",
       "license": "GNU General Public License Version 3",
       "ide_integration": true,
+      "issue_categorization": "",
       "_copy_without_render": [
         ".github/workflows/build.yaml",
         ".github/workflows/test.yaml",
@@ -35,9 +36,11 @@
         "lstrip_blocks": true,
         "trim_blocks": true
       },
-      "_template": "https://github.com/scverse/cookiecutter-scverse",
-      "_commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95"
-    }
+      "_template": "/tmp/tmpvf8ta0q7",
+      "_commit": "4d6aa34fd5be7523ca3bd49fbd81a882dde01d1f"
+    },
+    "_commit": "6518dfa1abde7379ea7255daf0ce09c23f2b4c94",
+    "_template": "https://github.com/scverse/cookiecutter-scverse"
   },
   "directory": null
-}
+}
\ No newline at end of file
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 6104b9e..cc32eda 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
-type: Bug
+labels: bug
 body:
   - type: markdown
     attributes:
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
index 3ba5aea..c1048c6 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 FlowSOM
-type: Enhancement
+labels: enhancement
 body:
   - type: textarea
     id: description
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 0000000..914ad69
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,12 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    cooldown:
+      default-days: 7
+    groups:
+      actions-deps:
+        patterns:
+          - "*"
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index c6ecc2f..6cca7d4 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -10,16 +10,20 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+permissions:
+  contents: read
+
 jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           filter: blob:none
           fetch-depth: 0
+          persist-credentials: false
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
       - name: Build package
         run: uv build
       - name: Check package
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index 59a43d7..cbb43d7 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -5,6 +5,8 @@ on:
     types: [published]
 
 # Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+permissions: {}
+
 jobs:
   release:
     name: Upload release to PyPI
@@ -13,15 +15,19 @@ jobs:
       name: pypi
       url: https://pypi.org/p/FlowSOM
     permissions:
+      contents: read
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           filter: blob:none
           fetch-depth: 0
+          persist-credentials: false
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        with:
+          enable-cache: false
       - name: Build package
         run: uv build
       - name: Publish package distributions to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 6bf473b..0075425 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -12,6 +12,9 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+permissions:
+  contents: read
+
 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
@@ -19,16 +22,17 @@ jobs:
   # 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
+    runs-on: ubuntu-slim
     outputs:
       envs: ${{ steps.get-envs.outputs.envs }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           filter: blob:none
           fetch-depth: 0
+          persist-credentials: false
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
       - name: Get test environments
         id: get-envs
         run: |
@@ -48,6 +52,7 @@ jobs:
     needs: get-environments
     permissions:
        id-token: write  # for codecov OIDC
+       contents: read
 
     strategy:
       fail-fast: false
@@ -60,16 +65,19 @@ jobs:
     continue-on-error: ${{ contains(matrix.env.name, 'pre') }}  # make "all-green" pass even if pre-release job fails
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           filter: blob:none
           fetch-depth: 0
+          persist-credentials: false
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           python-version: ${{ matrix.env.python }}
       - name: create hatch environment
         run: uvx hatch env create ${{ matrix.env.name }}
+      - name: list all all installed package versions
+        run: uvx hatch run ${{ matrix.env.name }}:uv pip list
       - name: run tests using hatch
         env:
           MPLBACKEND: agg
@@ -78,12 +86,12 @@ jobs:
         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
+          # See https://coverage.readthedocs.io/page/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@v5
+        uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
         with:
           fail_ci_if_error: true
           use_oidc: true
@@ -98,6 +106,6 @@ jobs:
       - test
     runs-on: ubuntu-latest
     steps:
-        - uses: re-actors/alls-green@release/v1
+        - uses: re-actors/alls-green@05ac9388f0aebcb5727afa17fcccfecd6f8ec5fe # v1.2.2
           with:
             jobs: ${{ toJSON(needs) }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 27d8a95..3a84322 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,16 +7,16 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.3.10
+    rev: v2.5.3
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.11.1
+    rev: v2.25.3
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.10
+    rev: v0.15.21
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]
@@ -36,3 +36,9 @@ repos:
       # Check that there are no merge conflicts (could be generated by template sync)
       - id: check-merge-conflict
         args: [--assume-in-merge]
+
+  - repo: https://github.com/zizmorcore/zizmor-pre-commit
+    rev: v1.24.1
+    hooks:
+      - id: zizmor
+        args: [--no-progress, --fix]
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 6c28477..67eb948 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,9 +1,9 @@
-# https://docs.readthedocs.io/en/stable/config-file/v2.html
+# https://docs.readthedocs.io/page/config-file/v2.html
 version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.13"
+    python: "3.14"
     nodejs: latest
   jobs:
     create_environment:
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
deleted file mode 100644
index 7b4a0cf..0000000
--- a/docs/_templates/autosummary/class.rst
+++ /dev/null
@@ -1,61 +0,0 @@
-{{ 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/conf.py b/docs/conf.py
index ca4245e..88c4f8b 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -2,7 +2,7 @@
 
 # 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
+# https://www.sphinx-doc.org/page/usage/configuration.html
 
 # -- Path setup --------------------------------------------------------------
 import shutil
@@ -59,9 +59,10 @@
     "sphinxcontrib.bibtex",
     "sphinxcontrib.katex",
     "sphinx_autodoc_typehints",
-    "sphinx_tabs.tabs",
+    "sphinx_design",
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinxext.opengraph",
+    "scverse_misc.sphinx_ext",
     *[p.stem for p in (HERE / "extensions").glob("*.py")],
 ]
 
@@ -87,6 +88,7 @@
 nb_execution_mode = "off"
 nb_merge_streams = True
 typehints_defaults = "braces"
+always_use_bars_union = True  # use `|` instead of `Union` in types even when building with Python ≤3.14
 
 source_suffix = {
     ".rst": "restructuredtext",
@@ -95,10 +97,9 @@
 }
 
 intersphinx_mapping = {
-    # 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),
+    "python": ("https://docs.python.org/3", None),
+    "anndata": ("https://anndata.scverse.org/en/stable/", None),
+    "scanpy": ("https://scanpy.scverse.org/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
 }
 
diff --git a/docs/contributing.md b/docs/contributing.md
index b172fd1..33afd7d 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -9,7 +9,7 @@ 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
+[scanpy developer guide]: https://scanpy.scverse.org/page/dev/
 
 :::{tip} The *hatch* project manager
 
@@ -33,8 +33,9 @@ it is still possible to use different tools to manage dependencies, such as `uv`
 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
+:::::{tab-set}
+::::{tab-item} Hatch
+:sync: hatch
 
 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
@@ -45,11 +46,21 @@ hatch test  # defined in the table [tool.hatch.envs.hatch-test] in pyproject.tom
 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.
+### VS Code
 
+If you are using VS code, install the [hatch-code][] extension.
+Additionally, make sure that the `vscode-python-environments` extension is installed (should be by default)
+and `"python.useEnvironmentsExtension": true` is activated in your `settings.json`.
+
+Next, open the "Python Environment Managers" sidebar.
+You can do so by opening the command palette (Ctrl+Shift+P) and searching for `Python: Focus on Environment Managers View`.
+It will show a collapsible list where you can expand "Hatch"
+and activate an environment by clicking on the checkmark next to it.
+As the main development environment, we recommend to use `hatch-test` with the latest supported Python version.
+
+### Other IDEs
+
+For other IDEs, you’ll have to point the editor at the paths to the virtual environments manually.
 To get a list of all environments for your projects, run
 
 ```bash
@@ -62,7 +73,7 @@ This will list “Standalone” environments and a table of “Matrix” environ
 +------------+---------+--------------------------+----------+---------------------------------+-------------+
 | Name       | Type    | Envs                     | Features | Dependencies                    | Scripts     |
 +------------+---------+--------------------------+----------+---------------------------------+-------------+
-| hatch-test | virtual | hatch-test.py3.11-stable | dev      | coverage-enable-subprocess==1.0 | cov-combine |
+| hatch-test | virtual | hatch-test.py3.12-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     |
@@ -73,6 +84,7 @@ 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.
+As the main development environment, we recommend to use `hatch-test` with the latest supported Python version.
 In this example, it would be `hatch-test.py3.14-stable`.
 
 Next, create the environment with
@@ -87,14 +99,13 @@ Then, obtain the path to the environment using
 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`.
-Choose `Enter Interpreter Path` and paste the path to the virtual environment from above.
+and manually point it to the python binary.
 
-In this future, this may become easier through a hatch vscode extension.
 
 ::::
 
-::::{group-tab} uv
+::::{tab-item} uv
+:sync: 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,
@@ -103,7 +114,7 @@ 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
+To initialize a virtual environment in the `.venv` directory of your project, simply run
 
 ```bash
 uv sync --all-extras
@@ -113,7 +124,8 @@ The `.venv` directory is typically automatically discovered by IDEs such as VS C
 
 ::::
 
-::::{group-tab} Pip
+::::{tab-item} Pip
+:sync: pip
 
 Pip is nowadays mostly superseded by environment manager such as [hatch][].
 However, for the sake of completeness, and since it’s ubiquitously available,
@@ -131,24 +143,26 @@ The `.venv` directory is typically automatically discovered by IDEs such as VS C
 :::::
 
 [hatch environments]: https://hatch.pypa.io/latest/tutorials/environment/basic-usage/
+[hatch-code]: https://marketplace.visualstudio.com/items?itemName=PyPA.hatch
 [uv]: https://docs.astral.sh/uv/
 
 ## 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.
+This package uses [pre-commit][]-style hooks to enforce consistent code-styles.
+We recommend running them with [prek][], a fast, drop-in replacement for `pre-commit` that reads the same `.pre-commit-config.yaml`.
+On every commit, the checks will either automatically fix issues with the code, or raise an error message.
 
-To enable pre-commit locally, simply run
+To enable the checks locally, install [prek][] (e.g. with `uv tool install prek`) and run
 
 ```bash
-pre-commit install
+prek install
 ```
 
 in the root of the repository.
-Pre-commit will automatically download all dependencies when it is run for the first time.
+prek 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 the checks 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
 
@@ -157,12 +171,13 @@ 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.
+While the [pre-commit.ci][] is useful, we strongly encourage installing and running the checks locally first to understand their 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/
+[prek]: https://prek.j178.dev/
 [pre-commit.ci]: https://pre-commit.ci/
 [ruff-editors]: https://docs.astral.sh/ruff/integrations/
 [biome-editors]: https://biomejs.dev/guides/integrate-in-editor/
@@ -175,17 +190,14 @@ 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
-```
+If you set up your virtual environments as described in [installing dev dependencies](#installing-dev-dependencies),
+test cases should be automatically discovered by your IDE.
 
 Alternatively, you can run all tests from the command line by executing
 
-:::::{tabs}
-::::{group-tab} Hatch
+:::::{tab-set}
+::::{tab-item} Hatch
+:sync: hatch
 
 ```bash
 hatch test  # test with the highest supported Python version
@@ -195,7 +207,8 @@ hatch test --all  # test with all supported Python versions
 
 ::::
 
-::::{group-tab} uv
+::::{tab-item} uv
+:sync: uv
 
 ```bash
 uv run pytest
@@ -203,7 +216,8 @@ uv run pytest
 
 ::::
 
-::::{group-tab} Pip
+::::{tab-item} Pip
+:sync: pip
 
 ```bash
 source .venv/bin/activate
@@ -268,11 +282,11 @@ This project uses [sphinx][] with the following features:
 
 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]: https://www.sphinx-doc.org/
+[myst]: https://myst-parser.readthedocs.io/page/intro.html
+[myst-nb]: https://myst-nb.readthedocs.io/
+[numpydoc-napoleon]: https://www.sphinx-doc.org/page/usage/extensions/napoleon.html
+[numpydoc]: https://numpydoc.readthedocs.io/page/format.html
 [sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
 
 ### Tutorials with myst-nb and jupyter notebooks
@@ -297,8 +311,9 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu
 
 ### Building the docs locally
 
-:::::{tabs}
-::::{group-tab} Hatch
+:::::{tab-set}
+::::{tab-item} Hatch
+:sync: hatch
 
 ```bash
 hatch run docs:build
@@ -307,7 +322,8 @@ hatch run docs:open
 
 ::::
 
-::::{group-tab} uv
+::::{tab-item} uv
+:sync: uv
 
 ```bash
 cd docs
@@ -317,7 +333,8 @@ uv run sphinx-build -M html . _build -W
 
 ::::
 
-::::{group-tab} Pip
+::::{tab-item} Pip
+:sync: pip
 
 ```bash
 source .venv/bin/activate
diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
deleted file mode 100644
index 0fbffef..0000000
--- a/docs/extensions/typed_returns.py
+++ /dev/null
@@ -1,32 +0,0 @@
-# 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
index 4a5704f..50e8ad2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,10 +14,9 @@ maintainers = [
 authors = [
   { name = "Artuur Couckuyt" },
 ]
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 classifiers = [
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",
@@ -34,7 +33,7 @@ urls.Source = "https://github.com/artuurC/FlowSOM"
 
 [dependency-groups]
 dev = [
-  "pre-commit",
+  "prek",
   "twine>=4.0.2",
 ]
 test = [
@@ -47,56 +46,43 @@ doc = [
   "ipython",
   "myst-nb>=1.1",
   "pandas",
+  "scverse-misc[sphinx]>=0.1.2",
   "sphinx>=8.1",
   "sphinx-autodoc-typehints",
   "sphinx-book-theme>=1",
   "sphinx-copybutton",
-  "sphinx-tabs",
+  "sphinx-design",
   "sphinxcontrib-bibtex>=1",
   "sphinxcontrib-katex",
   "sphinxext-opengraph",
 ]
 
-[tool.hatch.build.targets.wheel]
-packages = [ "src/FlowSOM" ]
-
-[tool.hatch.envs.default]
-installer = "uv"
-dependency-groups = [ "dev" ]
-
-[tool.hatch.envs.docs]
-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}"
-
-# Test the lowest and highest supported Python versions with normal deps
-[[tool.hatch.envs.hatch-test.matrix]]
-deps = [ "stable" ]
-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 = [ "3.14" ]
-
-[tool.hatch.envs.hatch-test]
-dependency-groups = [ "dev", "test" ]
-
-[tool.hatch.envs.hatch-test.overrides]
+[tool.hatch]
+build.targets.wheel.packages = [ "src/FlowSOM" ]
+envs.default.installer = "uv"
+envs.default.dependency-groups = [ "dev" ]
+envs.docs.scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
+envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
+envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
+envs.docs.dependency-groups = [ "doc" ]
+envs.hatch-test.matrix = [
+  # Test the lowest and highest supported Python versions with normal deps
+  { deps = [ "stable" ], python = [ "3.12", "3.14" ] },
+  # Test the newest supported Python version also with pre-release deps
+  { deps = [ "pre" ], python = [ "3.14" ] },
+]
 # 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" ] },
+envs.hatch-test.overrides.matrix.deps.env-vars = [
+  { value = "allow", key = "UV_PRERELEASE", if = [ "pre" ] },
 ]
+envs.hatch-test.dependency-groups = [ "dev", "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
@@ -131,21 +117,22 @@ lint.per-file-ignores."tests/*" = [ "D" ]
 lint.pydocstyle.convention = "numpy"
 
 [tool.pytest]
-strict = true
-testpaths = [ "tests" ]
 addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
+strict = true
+testpaths = [ "tests" ]
 
-[tool.coverage.run]
-source = [ "FlowSOM" ]
-patch = [ "subprocess" ]
-omit = [
+[tool.coverage]
+run.omit = [
   "**/test_*.py",
 ]
+run.patch = [ "subprocess" ]
+run.source = [ "FlowSOM" ]
 
 [tool.cruft]
 skip = [
+  ".git",
   "tests",
   "src/**/__init__.py",
   "src/**/basic.py",