FIX: define dev dependencies as dependency groups (#441)

* BREAK: remove `all` optional depdency
* DX: run `pyright` in `tox -e sty` job
* MAINT: update links to TRs
* MAINT: update lock files

.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/benchmark.yml

@@ -41,8 +41,9 @@ jobs:
       - name: Run pytest-benchmark
         run: |
           uv run \
-            --extra all \
-            --extra test \
+            --all-extras \
+            --group test \
+            --no-dev \
             ${{ steps.with.outputs.packages }} \
             pytest \
               -k benchmark \

.github/workflows/ci-qrules-v0.9.yml

@@ -35,6 +35,6 @@ jobs:
       - name: Run pytest with QRules v0.9
         run: |
           uv run \
-            --extra test \
+            --group test \
             --with qrules~=0.9.0 \
             pytest --numprocesses auto

.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: "3.11"
       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: ampform
       macos-python-version: "3.9"
@@ -46,6 +46,6 @@ 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: "3.11"

.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]
@@ -128,7 +128,7 @@ repos:
         pass_filenames: false
 
   - repo: https://github.com/streetsidesoftware/cspell-cli
-    rev: v8.15.1
+    rev: v8.15.2
     hooks:
       - id: cspell
 
@@ -154,11 +154,11 @@ 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: 0.4.27
     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 ampform
 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/_extend_docstrings.py

@@ -509,7 +509,7 @@ def extend_chew_mandelstam_s_wave() -> None:
 
     with :math:`q^2(s)` defined as :eq:`BreakupMomentumSquared`.
 
-    .. seealso:: :doc:`compwa-report:003`
+    .. seealso:: :doc:`compwa-report:003/index`
     """,
     )
 

docs/install.md

@@ -47,6 +47,7 @@ python3 -m pip install git+https://github.com/ComPWA/ampform@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!

docs/usage/dynamics/analytic-continuation.ipynb

@@ -63,7 +63,7 @@
    "source": [
     ":::{note}\n",
     "\n",
-    "Improvements to analytic continuation in AmpForm are currently being developed in {doc}`compwa-report:003` and {doc}`compwa-report:004`.\n",
+    "Improvements to analytic continuation in AmpForm are currently being developed in {doc}`compwa-report:003/index` and {doc}`compwa-report:004/index`.\n",
     "\n",
     ":::"
    ]

docs/usage/dynamics/k-matrix.ipynb

@@ -74,7 +74,7 @@
     "\n",
     ":::{note}\n",
     "\n",
-    "The $\\boldsymbol{K}$-matrix approach was originally worked worked out in {doc}`compwa-report:005`, {doc}`compwa-report:009`, and {doc}`compwa-report:010`. Those reports contained a few mistakes, which have been addressed here.\n",
+    "The $\\boldsymbol{K}$-matrix approach was originally worked worked out in {doc}`compwa-report:005/index`, {doc}`compwa-report:009/index`, and {doc}`compwa-report:010/index`. Those reports contained a few mistakes, which have been addressed here.\n",
     "\n",
     ":::\n",
     "\n",
@@ -331,7 +331,7 @@
     "\\end{eqnarray}\n",
     "$$ (K-hat-and-T-hat)\n",
     "\n",
-    "[^rho-dagger]: An unpublished primer on the $\\boldsymbol{K}$-matrix by Chung {cite}`chungPrimerKmatrixFormalism1995` uses a conjugate transpose of $\\boldsymbol{\\rho}$, e.g. $\\boldsymbol{T} = \\sqrt{\\boldsymbol{\\rho^\\dagger}} \\; \\boldsymbol{\\hat{T}} \\sqrt{\\boldsymbol{\\rho}}$. This should not matter above threshold, where the phase space factor is real, but could have effects below threshold. This is where things become tricky: on the one hand, we need to ensure that $\\boldsymbol{K}$ remains real (unitarity) and on the other, we need to take keep track of which imaginary square root we choose (**Riemann sheet**). The latter is often called the requirement of **analyticity**. This is currently being explored in {doc}`compwa-report:003` and {doc}`compwa-report:004`.\n",
+    "[^rho-dagger]: An unpublished primer on the $\\boldsymbol{K}$-matrix by Chung {cite}`chungPrimerKmatrixFormalism1995` uses a conjugate transpose of $\\boldsymbol{\\rho}$, e.g. $\\boldsymbol{T} = \\sqrt{\\boldsymbol{\\rho^\\dagger}} \\; \\boldsymbol{\\hat{T}} \\sqrt{\\boldsymbol{\\rho}}$. This should not matter above threshold, where the phase space factor is real, but could have effects below threshold. This is where things become tricky: on the one hand, we need to ensure that $\\boldsymbol{K}$ remains real (unitarity) and on the other, we need to take keep track of which imaginary square root we choose (**Riemann sheet**). The latter is often called the requirement of **analyticity**. This is currently being explored in {doc}`compwa-report:003/index` and {doc}`compwa-report:004/index`.\n",
     "\n",
     "With these definitions, we can deduce that:\n",
     "\n",

docs/usage/helicity/spin-alignment.ipynb

@@ -93,7 +93,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "As described in {doc}`compwa-report:015`, the {doc}`'standard' helicity formalism </usage/helicity/formalism>` is not suited for state transitions that have different decay topologies. For this reason, the {class}`.HelicityAmplitudeBuilder` can insert a number of Wigner-$D$ functions into the amplitude model to 'align' the final state spins of underlying {class}`~qrules.topology.Topology` instances in the full decay.\n",
+    "As described in {doc}`compwa-report:015/index`, the {doc}`'standard' helicity formalism </usage/helicity/formalism>` is not suited for state transitions that have different decay topologies. For this reason, the {class}`.HelicityAmplitudeBuilder` can insert a number of Wigner-$D$ functions into the amplitude model to 'align' the final state spins of underlying {class}`~qrules.topology.Topology` instances in the full decay.\n",
     "\n",
     "Imagine we have the following the decay:"
    ]
@@ -388,7 +388,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "For more information about these angles, see {ref}`compwa-report:015:Compute Wigner rotation angles` in {doc}`TR-015 <compwa-report:015>`."
+    "For more information about these angles, see {ref}`compwa-report:015/index:Compute Wigner rotation angles` in {doc}`TR-015 <compwa-report:015/index>`."
    ]
   }
  ],

docs/usage/kinematics.ipynb

@@ -260,7 +260,7 @@
    "metadata": {},
    "source": [
     ":::{margin}\n",
-    "This notebook originates from {doc}`compwa-report:017`.\n",
+    "This notebook originates from {doc}`compwa-report:017/index`.\n",
     ":::\n",
     "\n",
     "Kinematics for a three-body decay $0 \\to 123$ can be fully described by two **Mandelstam variables** $\\sigma_1, \\sigma_2$, because the third variable $\\sigma_3$ can be expressed in terms $\\sigma_1, \\sigma_2$, the mass $m_0$ of the initial state, and the masses $m_1, m_2, m_3$ of the final state. As can be seen, the roles of $\\sigma_1, \\sigma_2, \\sigma_3$ are interchangeable.\n",
@@ -384,7 +384,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "See {doc}`compwa-report:017` for an interactive visualization of the phase space region and an analytic expression for the phase space boundary."
+    "See {doc}`compwa-report:017/index` for an interactive visualization of the phase space region and an analytic expression for the phase space boundary."
    ]
   }
  ],

pyproject.toml

@@ -46,21 +46,29 @@ name = "ampform"
 requires-python = ">=3.9"
 
 [project.optional-dependencies]
-all = [
-    "ampform[scipy]",
-    "ampform[viz]",
-]
+scipy = ["scipy"]
+viz = ["graphviz"]
+
+[project.readme]
+content-type = "text/markdown"
+file = "README.md"
+
+[project.urls]
+Changelog = "https://github.com/ComPWA/ampform/releases"
+Documentation = "https://ampform.rtfd.io"
+Source = "https://github.com/ComPWA/ampform"
+Tracker = "https://github.com/ComPWA/ampform/issues"
+
+[dependency-groups]
 dev = [
-    "ampform[all]",
-    "ampform[doc]",
-    "ampform[jupyter]",
-    "ampform[sty]",
-    "ampform[test]",
+    "ruff",
     "sphinx-autobuild",
-    "tox",
+    {include-group = "doc"},
+    {include-group = "jupyter"},
+    {include-group = "style"},
+    {include-group = "test"},
 ]
 doc = [
-    "ampform[notebooks]",
     "myst-nb",
     "sphinx",
     "sphinx-api-relink >=0.0.4",
@@ -74,18 +82,20 @@ doc = [
     "sphinx-thebe",
     "sphinx-togglebutton",
     "sphinxcontrib-bibtex >=2",
+    {include-group = "notebooks"},
 ]
 jupyter = [
     "jupyterlab",
     "jupyterlab-code-formatter >=3.0.0",
+    "jupyterlab-code-formatter",
     "jupyterlab-git",
     "jupyterlab-lsp",
     "jupyterlab-myst",
     "python-lsp-ruff",
     "python-lsp-server[rope]",
 ]
 notebooks = [
-    "ampform[all]",
+    "ampform[scipy,viz]",
     "black",
     "ipympl",
     "matplotlib <3.9.0", # https://github.com/ComPWA/ampform/issues/279
@@ -94,12 +104,9 @@ notebooks = [
     "numpy",
     "rich",
 ]
-scipy = ["scipy"]
-sty = [
-    "ampform[types]",
+style = [
     "mypy >=0.730",
-    "pre-commit-uv",
-    "ruff",
+    {include-group = "types"},
 ]
 test = [
     "ampform[scipy]",
@@ -120,17 +127,6 @@ types = [
     "pytest-benchmark",
     "sphinx-api-relink >=0.0.3",
 ]
-viz = ["graphviz"]
-
-[project.readme]
-content-type = "text/markdown"
-file = "README.md"
-
-[project.urls]
-Changelog = "https://github.com/ComPWA/ampform/releases"
-Documentation = "https://ampform.rtfd.io"
-Source = "https://github.com/ComPWA/ampform"
-Tracker = "https://github.com/ComPWA/ampform/issues"
 
 [tool.setuptools]
 include-package-data = false
@@ -235,6 +231,8 @@ reportUnusedFunction = true
 reportUnusedImport = true
 reportUnusedVariable = true
 typeCheckingMode = "strict"
+venv = ".venv"
+venvPath = "."
 
 [tool.pytest.ini_options]
 addopts = [
@@ -568,10 +566,8 @@ description = Run all notebooks with pytest
 allowlist_externals =
     pre-commit
 commands =
-    pre-commit run {posargs} --all-files
+    pre-commit run --all-files {posargs}
 description = Perform all linting, formatting, and spelling checks
-setenv =
-    SKIP = pyright
 """
 
 [tool.uv]

src/ampform/dynamics/form_factor.py

@@ -52,7 +52,7 @@ class BlattWeisskopfSquared(sp.Expr):
     :pdg-review:`2021; Resonances; p.9`. We normalize the form factor such that
     :math:`B_L^2(1)=1` and that :math:`B_L^2` is unitless no matter what :math:`z` is.
 
-    .. seealso:: :ref:`usage/dynamics:Form factor`, :doc:`TR-029<compwa-report:029>`,
+    .. seealso:: :ref:`usage/dynamics:Form factor`, :doc:`TR-029<compwa-report:029/index>`,
       and :cite:`chungFormulasAngularMomentumBarrier2015`.
 
     With this, the implementation becomes
@@ -94,7 +94,7 @@ def _formulate_blatt_weisskopf(ell, z) -> sp.Expr:
 class SphericalHankel1(sp.Expr):
     r"""Spherical Hankel function of the first kind for real-valued :math:`z`.
 
-    See :cite:`VonHippel:1972fg`, Equation (A12), and :doc:`TR-029<compwa-report:029>`
+    See :cite:`VonHippel:1972fg`, Equation (A12), and :doc:`TR-029<compwa-report:029/index>`
     for more info. `This page
     <https://mathworld.wolfram.com/SphericalHankelFunctionoftheFirstKind.html>`_
     explains the difference with the *general* Hankel function of the first kind,

src/ampform/dynamics/kmatrix.py

@@ -2,8 +2,8 @@
 
 .. seealso:: :doc:`/usage/dynamics/k-matrix`.
 
-This module is an implementation of :doc:`compwa-report:005`,
-:doc:`compwa-report:009`, and :doc:`compwa-report:010`. It works with classes to
+This module is an implementation of :doc:`compwa-report:005/index`,
+:doc:`compwa-report:009/index`, and :doc:`compwa-report:010/index`. It works with classes to
 keep the code organized and to enable caching of the matrix multiplications, but this
 might change once these dynamics are implemented into the amplitude builder.
 """

src/ampform/sympy/deprecated.py

@@ -31,7 +31,7 @@ class UnevaluatedExpression(sp.Expr):
     1. condense the LaTeX representation of an expression tree by providing a custom
        :meth:`_latex` method.
     2. overwrite its printer methods (see `.NumPyPrintable` and e.g.
-       :doc:`compwa-report:001`).
+       :doc:`compwa-report:001/index`).
 
     The `UnevaluatedExpression` base class makes implementations of its derived classes
     more secure by enforcing the developer to provide implementations for these methods,

src/ampform/sympy/math.py

@@ -26,7 +26,7 @@ class ComplexSqrt(NumPyPrintable):
 
     A special version :func:`~sympy.functions.elementary.miscellaneous.sqrt` that
     renders nicely as LaTeX and and can be used as a handle for lambdify printers. See
-    :doc:`compwa-report:000`, :doc:`compwa-report:001`, and
+    :doc:`compwa-report:000/index`, :doc:`compwa-report:001/index`, and
     :doc:`sympy:modules/printing` for how to implement a custom
     :func:`~sympy.utilities.lambdify.lambdify` printer.
     """