FIX: define dev dependencies as dependency groups (#299)

* DX: run `pyright` in `tox -e sty` job
* FIX: remove `pre-commit-uv` and `tox` from environment
* MAINT: address Ruff issues
* MAINT: update lock files

Author: redeboer

.binder/postBuild

@@ -3,10 +3,12 @@ set -ex
 curl -LsSf https://astral.sh/uv/install.sh | sh
 source $HOME/.cargo/env
 uv export \
-  --extra jupyter \
-  --extra notebooks \
+  --group jupyter \
+  --group notebooks \
+  --no-dev \
   > requirements.txt
 uv pip install \
   --requirement requirements.txt \
   --system
+rm requirements.txt
 uv cache clean

.github/workflows/ci.yml

@@ -28,7 +28,7 @@ on:
 
 jobs:
   doc:
-    uses: ComPWA/actions/.github/workflows/ci-docs.yml@v2
+    uses: ComPWA/actions/.github/workflows/ci-docs.yml@v2.1
     permissions:
       pages: write
       id-token: write
@@ -37,7 +37,7 @@ jobs:
       python-version: "3.9"
       specific-pip-packages: ${{ inputs.specific-pip-packages }}
   pytest:
-    uses: ComPWA/actions/.github/workflows/pytest.yml@v2
+    uses: ComPWA/actions/.github/workflows/pytest.yml@v2.1
     with:
       coverage-target: qrules
       macos-python-version: "3.9"
@@ -47,6 +47,6 @@ jobs:
     if: inputs.specific-pip-packages == ''
     secrets:
       token: ${{ secrets.PAT }}
-    uses: ComPWA/actions/.github/workflows/pre-commit.yml@v2
+    uses: ComPWA/actions/.github/workflows/pre-commit.yml@v2.1
     with:
       python-version: "3.9"

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
       - id: check-useless-excludes
 
   - repo: https://github.com/ComPWA/policy
-    rev: 0.5.0
+    rev: 0.5.5
     hooks:
       - id: check-dev-files
         args:
@@ -61,7 +61,7 @@ repos:
             metadata.vscode
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.7.1
     hooks:
       - id: ruff
         args: [--fix]
@@ -123,7 +123,7 @@ repos:
         pass_filenames: false
 
   - repo: https://github.com/streetsidesoftware/cspell-cli
-    rev: v8.15.1
+    rev: v8.15.2
     hooks:
       - id: cspell
 
@@ -149,11 +149,11 @@ repos:
           - python
 
   - repo: https://github.com/ComPWA/pyright-pre-commit
-    rev: v1.1.385
+    rev: v1.1.386
     hooks:
       - id: pyright
 
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.4.24
+    rev: 0.4.28
     hooks:
       - id: uv-lock

.readthedocs.yml

@@ -11,7 +11,11 @@ build:
       pixi global install graphviz uv
     - |-
       export UV_LINK_MODE=copy
-      uv run --extra doc --locked --with tox \
+      uv run \
+        --group doc \
+        --locked \
+        --no-dev \
+        --with tox \
         tox -e doc
       mkdir -p $READTHEDOCS_OUTPUT
       mv docs/_build/html $READTHEDOCS_OUTPUT

CONTRIBUTING.md

@@ -15,12 +15,30 @@ cd qrules
 Now it's simply a matter of creating and activating the [virtual environment](https://docs.astral.sh/uv/pip/environments) with [`uv sync`](https://docs.astral.sh/uv/reference/cli/#uv-sync). The dependencies for the project are 'pinned' in each commit through the [`uv.lock` file](https://docs.astral.sh/uv/concepts/projects/#project-lockfile).
 
 ```shell
-uv sync
+uv sync --all-extras
 source .venv/bin/activate
 ```
 
-Formatting and linting checks are automatically performed when committing changes. This is done with [pre-commit](https://pre-commit.com). To install the hooks in your local repository, run [`pre-commit install`](https://pre-commit.com/#3-install-the-git-hook-scripts) **once**:
+Formatting and linting checks are automatically performed when committing changes. This is done with [pre-commit](https://pre-commit.com). To install the hooks in your local repository, run install `pre-commit` with `uv`:
+
+```shell
+uv tool install pre-commit --with pre-commit-uv --force-reinstall
+```
+
+and [`pre-commit install`](https://pre-commit.com/#3-install-the-git-hook-scripts) **once**:
 
 ```shell
 pre-commit install --install-hooks
 ```
+
+In addition, it may be handy to install `tox`:
+
+```shell
+uv tool install tox --with tox-uv
+```
+
+If the repository provides a Tox configuration under [`pyproject.toml`](./pyproject.toml), you can see which jobs it defines with:
+
+```shell
+tox list
+```

docs/install.md

@@ -47,6 +47,7 @@ python3 -m pip install git+https://github.com/ComPWA/qrules@main
 
 :::{include} ../CONTRIBUTING.md
 :start-after: **[compwa.github.io/develop](https://compwa.github.io/develop)**!
+:end-before: If the repository provides a Tox configuration
 :::
 
 That's all! Have a look at {doc}`/usage` to try out the package. You can also have a look at {doc}`compwa:develop` for tips on how to work with this 'editable' developer setup!

pyproject.toml

@@ -49,21 +49,29 @@ name = "qrules"
 requires-python = ">=3.9"
 
 [project.optional-dependencies]
-all = [
-    "qrules[viz]",
-]
+viz = ["graphviz"]
+
+[project.readme]
+content-type = "text/markdown"
+file = "README.md"
+
+[project.urls]
+Changelog = "https://github.com/ComPWA/qrules/releases"
+Documentation = "https://qrules.rtfd.io"
+Source = "https://github.com/ComPWA/qrules"
+Tracker = "https://github.com/ComPWA/qrules/issues"
+
+[dependency-groups]
 dev = [
-    "qrules[all]",
-    "qrules[doc]",
-    "qrules[jupyter]",
-    "qrules[sty]",
-    "qrules[test]",
+    "ruff",
     "sphinx-autobuild",
-    "tox",
+    {include-group = "doc"},
+    {include-group = "jupyter"},
+    {include-group = "style"},
+    {include-group = "test"},
 ]
 doc = [
     "myst-nb",
-    "qrules[notebooks]",
     "sphinx",
     "sphinx-api-relink",
     "sphinx-book-theme",
@@ -76,56 +84,41 @@ doc = [
     "sphinx-thebe",
     "sphinx-togglebutton",
     "sphinxcontrib-bibtex >=2",
+    {include-group = "notebooks"},
 ]
 jupyter = [
     "ipywidgets",
     "jupyterlab",
-    "jupyterlab-code-formatter >=3.0.0",
+    "jupyterlab-code-formatter",
     "jupyterlab-git",
     "jupyterlab-lsp",
     "jupyterlab-myst",
     "python-lsp-ruff",
     "python-lsp-server[rope]",
+    {include-group = "notebooks"},
 ]
-notebooks = [
-    "qrules[viz]",
-]
-sty = [
+notebooks = ["qrules[viz]"]
+style = [
     "mypy",
-    "pre-commit-uv",
-    "qrules[types]",
-    "ruff",
+    {include-group = "types"},
 ]
 test = [
     "ipython",
     "nbmake",
-    "pydot <2", # problem with pydot.graph_from_dot_data
+    "pydot <2",
     "pytest",
     "pytest-cov",
     "pytest-profiling",
     "pytest-xdist",
 ]
 types = [
     "ipython",
-    "pydot <2", # problem with pydot.graph_from_dot_data
+    "pydot <2",
     "pytest",
     "sphinx-api-relink",
     "types-PyYAML",
     "types-setuptools",
 ]
-viz = [
-    "graphviz",
-]
-
-[project.readme]
-content-type = "text/markdown"
-file = "README.md"
-
-[project.urls]
-Changelog = "https://github.com/ComPWA/qrules/releases"
-Documentation = "https://qrules.rtfd.io"
-Source = "https://github.com/ComPWA/qrules"
-Tracker = "https://github.com/ComPWA/qrules/issues"
 
 [tool.setuptools]
 include-package-data = false
@@ -242,6 +235,8 @@ reportUnusedFunction = true
 reportUnusedImport = true
 reportUnusedVariable = true
 typeCheckingMode = "strict"
+venv = ".venv"
+venvPath = "."
 
 [tool.pytest.ini_options]
 addopts = [
@@ -512,8 +507,6 @@ allowlist_externals =
 commands =
     pre-commit run --all-files {posargs}
 description = Perform all linting, formatting, and spelling checks
-setenv =
-    SKIP = pyright
 
 [testenv:test]
 allowlist_externals =

src/qrules/transition.py

@@ -250,10 +250,11 @@ def __init__(  # noqa: C901, PLR0912, PLR0917
         self.__number_of_threads = NumberOfThreads.get()
         if interaction_type_settings is None:
             interaction_type_settings = {}
-        if formalism not in set(SpinFormalism.__args__):  # type: ignore[attr-defined]
+        spin_formalisms = SpinFormalism.__args__  # type: ignore[attr-defined]
+        if formalism not in set(spin_formalisms):
             msg = (
                 f'Formalism "{formalism}" not implemented. Use one of'
-                f" {', '.join(SpinFormalism.__args__)} instead."  # type: ignore[attr-defined]
+                f" {', '.join(spin_formalisms)} instead."
             )
             raise NotImplementedError(msg)
         self.__formalism = formalism