MAINT: update lock files (#302)

* DOC: update instructions about `tool.tox.env` * DX: always run `pytest` with `nbmake` * DX: convert Tox config to native TOML * DX: run Pyright over correct environment * FIX: downgrade `pygments` and `sphinx-codeautolink` * FIX: ignore Mathworks in linkecheck * FIX: remove `uv --locked` flag from RTD config * MAINT: remove all mentions of `PYTHONHASHSEED` * MAINT: sort cSpell config Co-authored-by: GitHub <[email protected]>
ComPWA · Jan 13, 2025 · c11417b · c11417b
1 parent ac8b316
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diff --git a/.binder/postBuild b/.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
diff --git a/.cspell.json b/.cspell.json
@@ -1,5 +1,4 @@
 {
-  "version": "0.2",
   "allowCompoundWords": false,
   "enableFiletypes": [
     "git-commit",
@@ -31,47 +30,15 @@
     ".pre-commit-config.yaml",
     ".prettierignore",
     ".readthedocs.yml",
+    ".taplo.toml",
     ".vscode/*",
     "CITATION.cff",
     "docs/adr/*/*",
     "docs/conf.py",
     "pyproject.toml"
   ],
-  "language": "en-US",
-  "words": [
-    "AmpForm",
-    "Blatt",
-    "Breit",
-    "Chromodynamics",
-    "Colab",
-    "ComPWA",
-    "Curvenote",
-    "docstrings",
-    "helicity",
-    "lambdify",
-    "Mathematica",
-    "Miniconda",
-    "Numba",
-    "NumPy",
-    "parametrizations",
-    "PyPA",
-    "PyPI",
-    "pytest",
-    "QRules",
-    "Reana",
-    "Scikit",
-    "SciPy",
-    "SymPy",
-    "TensorWaves",
-    "Theano",
-    "TPUs",
-    "unbinned",
-    "Weisskopf",
-    "Zenodo"
-  ],
   "ignoreWords": [
     "MAINT",
-    "PYTHONHASHSEED",
     "codemirror",
     "commitlint",
     "cxxcode",
@@ -113,5 +80,39 @@
     "toprettyxml",
     "unsrt",
     "venv"
+  ],
+  "language": "en-US",
+  "useGitignore": true,
+  "version": "0.2",
+  "words": [
+    "AmpForm",
+    "Blatt",
+    "Breit",
+    "Chromodynamics",
+    "Colab",
+    "ComPWA",
+    "Curvenote",
+    "docstrings",
+    "helicity",
+    "lambdify",
+    "Mathematica",
+    "Miniconda",
+    "Numba",
+    "NumPy",
+    "parametrizations",
+    "PyPA",
+    "PyPI",
+    "pytest",
+    "QRules",
+    "Reana",
+    "Scikit",
+    "SciPy",
+    "SymPy",
+    "TensorWaves",
+    "Theano",
+    "TPUs",
+    "unbinned",
+    "Weisskopf",
+    "Zenodo"
   ]
 }
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -5,9 +5,6 @@ concurrency:
   cancel-in-progress: |-
     ${{ github.ref != format('refs/heads/{0}', github.event.repository.default_branch) }}
 
-env:
-  PYTHONHASHSEED: "0"
-
 on:
   push:
     branches:
@@ -28,7 +25,7 @@ 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
@@ -40,4 +37,4 @@ 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
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -13,7 +13,7 @@ repos:
       - id: check-useless-excludes
 
   - repo: https://github.com/ComPWA/policy
-    rev: 0.5.0
+    rev: 0.5.15
     hooks:
       - id: check-dev-files
         args:
@@ -28,7 +28,7 @@ repos:
       - id: remove-empty-tags
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
         args:
@@ -56,7 +56,7 @@ repos:
             metadata.vscode
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.9.1
     hooks:
       - id: ruff
         args: [--fix]
@@ -90,7 +90,7 @@ repos:
           )$
 
   - repo: https://github.com/ComPWA/prettier-pre-commit
-    rev: v3.3.3
+    rev: v3.4.2
     hooks:
       - id: prettier
 
@@ -100,13 +100,13 @@ repos:
       - id: taplo-format
 
   - repo: https://github.com/pappasam/toml-sort
-    rev: v0.23.1
+    rev: v0.24.2
     hooks:
       - id: toml-sort
         args: [--in-place]
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.29.4
+    rev: 0.31.0
     hooks:
       - id: check-jsonschema
         name: Check CITATION.cff
@@ -119,7 +119,7 @@ repos:
         pass_filenames: false
 
   - repo: https://github.com/streetsidesoftware/cspell-cli
-    rev: v8.15.2
+    rev: v8.17.0
     hooks:
       - id: cspell
 
@@ -145,11 +145,11 @@ repos:
           )$
 
   - repo: https://github.com/ComPWA/pyright-pre-commit
-    rev: v1.1.385
+    rev: v1.1.391
     hooks:
       - id: pyright
 
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.4.25
+    rev: 0.5.18
     hooks:
       - id: uv-lock
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -11,7 +11,13 @@ build:
       pixi global install graphviz uv
     - |-
       export UV_LINK_MODE=copy
-      uv run --extra doc --locked --with tox \
+      uv run \
+        --group doc \
+        --no-dev \
+        --with tox \
         tox -e doc
       mkdir -p $READTHEDOCS_OUTPUT
       mv docs/_build/html $READTHEDOCS_OUTPUT
+
+sphinx:
+  configuration: docs/conf.py
diff --git a/.taplo.toml b/.taplo.toml
@@ -10,3 +10,10 @@ compact_inline_tables = true
 indent_string = "    "
 reorder_arrays = true
 reorder_keys = true
+
+[[rule]]
+include = ["**/pyproject.toml"]
+keys = ["tool.tox"]
+
+[rule.formatting]
+reorder_arrays = false
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -11,6 +11,7 @@
     "mhutchie.git-graph",
     "ms-python.python",
     "ms-python.vscode-pylance",
+    "ms-toolsai.jupyter",
     "ms-toolsai.vscode-jupyter-cell-tags",
     "ms-vscode.live-server",
     "ms-vsliveshare.vsliveshare",
@@ -32,6 +33,7 @@
     "ms-python.isort",
     "ms-python.mypy-type-checker",
     "ms-python.pylint",
+    "ms-toolsai.vscode-jupyter-slideshow",
     "travisillig.vscode-json-stable-stringify",
     "tyriar.sort-lines"
   ]

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -12,15 +12,33 @@ git clone https://github.com/ComPWA/compwa.github.io
 cd compwa.github.io
 ```
 
-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).
+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/layout/#the-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
+```
diff --git a/docs/adr/002/composition.ipynb b/docs/adr/002/composition.ipynb
@@ -190,7 +190,7 @@
     ") -> DynamicsExpression:\n",
     "    edge_ids = determine_attached_final_state(graph, edge_id)\n",
     "    final_state_ids = map(str, edge_ids)\n",
-    "    mass = sp.Symbol(f\"m_{{{\"+\".join(final_state_ids)}}}\")\n",
+    "    mass = sp.Symbol(f\"m_{{{'+'.join(final_state_ids)}}}\")\n",
     "    particle, _ = graph.get_edge_props(edge_id)\n",
     "    mass0 = sp.Symbol(f\"m_{{{particle.latex}}}\")\n",
     "    gamma0 = sp.Symbol(Rf\"\\Gamma_{{{particle.latex}}}\")\n",
@@ -212,7 +212,7 @@
     ") -> DynamicsExpression:\n",
     "    edge_ids = determine_attached_final_state(graph, edge_id)\n",
     "    final_state_ids = map(str, edge_ids)\n",
-    "    mass = sp.Symbol(f\"m_{{{\"+\".join(final_state_ids)}}}\")\n",
+    "    mass = sp.Symbol(f\"m_{{{'+'.join(final_state_ids)}}}\")\n",
     "    particle, _ = graph.get_edge_props(edge_id)\n",
     "    mass0 = sp.Symbol(f\"m_{{{particle.latex}}}\")\n",
     "    gamma0 = sp.Symbol(Rf\"\\Gamma_{{{particle.latex}}}\")\n",

diff --git a/docs/adr/002/expr.ipynb b/docs/adr/002/expr.ipynb
@@ -162,7 +162,7 @@
     "    ) -> RelativisticBreitWigner:\n",
     "        edge_ids = determine_attached_final_state(graph, edge_id)\n",
     "        final_state_ids = map(str, edge_ids)\n",
-    "        mass = sp.Symbol(f\"m_{{{\"+\".join(final_state_ids)}}}\")\n",
+    "        mass = sp.Symbol(f\"m_{{{'+'.join(final_state_ids)}}}\")\n",
     "        particle, _ = graph.get_edge_props(edge_id)\n",
     "        mass0 = sp.Symbol(f\"m_{{{particle.latex}}}\")\n",
     "        gamma0 = sp.Symbol(Rf\"\\Gamma_{{{particle.latex}}}\")\n",
@@ -247,7 +247,7 @@
     "    ) -> RelativisticBreitWignerWithFF:\n",
     "        edge_ids = determine_attached_final_state(graph, edge_id)\n",
     "        final_state_ids = map(str, edge_ids)\n",
-    "        mass = sp.Symbol(f\"m_{{{\"+\".join(final_state_ids)}}}\")\n",
+    "        mass = sp.Symbol(f\"m_{{{'+'.join(final_state_ids)}}}\")\n",
     "        particle, _ = graph.get_edge_props(edge_id)\n",
     "        mass0 = sp.Symbol(f\"m_{{{particle.latex}}}\")\n",
     "        gamma0 = sp.Symbol(Rf\"\\Gamma_{{{particle.latex}}}\")\n",
@@ -459,7 +459,7 @@
     "    ) -> RelativisticBreitWigner:\n",
     "        edge_ids = determine_attached_final_state(graph, edge_id)\n",
     "        final_state_ids = map(str, edge_ids)\n",
-    "        mass = sp.Symbol(f\"m_{{{\"+\".join(final_state_ids)}}}\")\n",
+    "        mass = sp.Symbol(f\"m_{{{'+'.join(final_state_ids)}}}\")\n",
     "        particle, _ = graph.get_edge_props(edge_id)\n",
     "        mass0 = sp.Symbol(Rf\"\\mu_{{{particle.latex}}}\")\n",
     "        gamma0 = sp.Symbol(Rf\"\\sigma_{{{particle.latex}}}\")\n",

diff --git a/docs/adr/002/function.ipynb b/docs/adr/002/function.ipynb
@@ -111,7 +111,7 @@
     "    ) -> \"RelativisticBreitWigner\":\n",
     "        edge_ids = determine_attached_final_state(graph, edge_id)\n",
     "        final_state_ids = map(str, edge_ids)\n",
-    "        mass = sp.Symbol(f\"m_{{{\"+\".join(final_state_ids)}}}\")\n",
+    "        mass = sp.Symbol(f\"m_{{{'+'.join(final_state_ids)}}}\")\n",
     "        particle, _ = graph.get_edge_props(edge_id)\n",
     "        mass0 = sp.Symbol(f\"m_{{{particle.latex}}}\")\n",
     "        gamma0 = sp.Symbol(Rf\"\\Gamma_{{{particle.latex}}}\")\n",
@@ -159,7 +159,7 @@
     "    ) -> \"RelativisticBreitWignerWithFF\":\n",
     "        edge_ids = determine_attached_final_state(graph, edge_id)\n",
     "        final_state_ids = map(str, edge_ids)\n",
-    "        mass = sp.Symbol(f\"m_{{{\"+\".join(final_state_ids)}}}\")\n",
+    "        mass = sp.Symbol(f\"m_{{{'+'.join(final_state_ids)}}}\")\n",
     "        particle, _ = graph.get_edge_props(edge_id)\n",
     "        mass0 = sp.Symbol(f\"m_{{{particle.latex}}}\")\n",
     "        gamma0 = sp.Symbol(Rf\"\\Gamma_{{{particle.latex}}}\")\n",

diff --git a/docs/conf.py b/docs/conf.py
@@ -129,14 +129,14 @@
 html_title = "Common Partial Wave Analysis Project"
 intersphinx_mapping = {
     "ampform": ("https://ampform.readthedocs.io/stable", None),
-    "attrs": (f"https://www.attrs.org/en/{pin("attrs")}", None),
+    "attrs": (f"https://www.attrs.org/en/{pin('attrs')}", None),
     "expertsystem": ("https://expertsystem.readthedocs.io/stable", None),
     "graphviz": ("https://graphviz.readthedocs.io/en/stable", None),
-    "IPython": (f"https://ipython.readthedocs.io/en/{pin("IPython")}", None),
+    "IPython": (f"https://ipython.readthedocs.io/en/{pin('IPython')}", None),
     "jax": ("https://jax.readthedocs.io/en/latest", None),
-    "matplotlib": (f"https://matplotlib.org/{pin("matplotlib")}", None),
-    "numba": (f"https://numba.readthedocs.io/en/{pin("numba")}", None),
-    "numpy": (f"https://numpy.org/doc/{pin_minor("numpy")}", None),
+    "matplotlib": (f"https://matplotlib.org/{pin('matplotlib')}", None),
+    "numba": (f"https://numba.readthedocs.io/en/{pin('numba')}", None),
+    "numpy": (f"https://numpy.org/doc/{pin_minor('numpy')}", None),
     "pwa": ("https://pwa.readthedocs.io", None),
     "python": ("https://docs.python.org/3", None),
     "qrules": ("https://qrules.readthedocs.io/stable", None),
@@ -147,7 +147,6 @@
 }
 linkcheck_anchors = False
 linkcheck_ignore = [
-    "https://github.com/search",
     "http://127.0.0.1:8000",
     "https://atom.io",  # often instable
     "https://doi.org/10.1002/andp.19955070504",  # 403 for onlinelibrary.wiley.com
@@ -156,6 +155,7 @@
     "https://doi.org/10.7566/JPSCP.26.022002",  # 403 for journals.jps.jp
     "https://downloads.hindawi.com",  # 403
     "https://github.com/organizations/ComPWA/settings/repository-defaults",  # private
+    "https://github.com/search",
     "https://ieeexplore.ieee.org/document/6312940",  # 401
     "https://indico.ific.uv.es/event/6803",  # SSL error
     "https://journals.aps.org",
@@ -167,6 +167,7 @@
     "https://via.placeholder.com",  # irregular timeout
     "https://www.andiamo.co.uk/resources/iso-language-codes",  # 443, but works
     "https://www.bookfinder.com",
+    "https://www.mathworks.com/products/matlab.html",
     r"https://github.com/ComPWA/RUB-EP1-AG/.*",  # private
     r"https://github.com/orgs/ComPWA/projects/\d+",  # private
 ]