Update template to v0.6.0

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "d4bdfc5ec4c5029aebf7c0cba65609e20358144d",
-  "checkout": null,
+  "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
+  "checkout": "v0.6.0",
   "context": {
     "cookiecutter": {
       "project_name": "cellmapper",
@@ -36,7 +36,7 @@
         "trim_blocks": true
       },
       "_template": "https://github.com/scverse/cookiecutter-scverse",
-      "_commit": "d4bdfc5ec4c5029aebf7c0cba65609e20358144d"
+      "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
     }
   },
   "directory": null

.github/workflows/test.yaml

@@ -78,11 +78,15 @@ jobs:
           MPLBACKEND: agg
           PLATFORM: ${{ matrix.os }}
           DISPLAY: :42
-        run: uvx hatch run ${{ matrix.env.name }}:run-cov
+        run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
       - name: generate coverage report
-        run: uvx hatch run ${{ matrix.env.name }}:coverage xml
+        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
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 

.gitignore

@@ -14,6 +14,7 @@ __pycache__/
 # Tests and coverage
 /data/
 /node_modules/
+/.coverage*
 
 # docs
 /docs/generated/

.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: v2.2.6
     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: v2.11.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.10
+    rev: v0.14.1
     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$'

.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: "3.11"
-sphinx:
-  configuration: docs/conf.py
-  # disable this for more lenient docs builds
-  fail_on_warning: false
-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

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": {

docs/contributing.md

@@ -1,44 +1,137 @@
 # 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,
 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:
+
+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 cellmapper
 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
 
@@ -188,7 +294,7 @@ 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
@@ -200,6 +306,16 @@ 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

pyproject.toml

@@ -19,6 +19,7 @@ classifiers = [
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
 ]
 dynamic = [ "version" ]
 dependencies = [
@@ -46,7 +47,7 @@ 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",
@@ -55,9 +56,10 @@ optional-dependencies.doc = [
   "sphinxext-opengraph",
 ]
 optional-dependencies.test = [
-  "coverage",
+  "coverage>=7.10",
   "faiss-cpu",
   "pytest",
+  "pytest-cov",     # For VS Code's coverage functionality
   "squidpy>=1.6",
 ]
 optional-dependencies.tutorials = [
@@ -100,7 +102,7 @@ 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",
@@ -158,6 +160,7 @@ addopts = [
 
 [tool.coverage.run]
 source = [ "cellmapper" ]
+patch = [ "subprocess" ]
 omit = [
   "**/test_*.py",
 ]