FIX: define dev dependencies as dependency groups (#108)

* BREAK: convert package dependencies to notebook dependencies
* DX: define `tox -e nb` job
* DX: move `sphinx-autobuild` to `dev dependencies
* FIX: remove `pre-commit-uv` and `tox` from environment
* FIX: remove duplicate `taplo` pre-commit hook
* FIX: set `passenv` in jobs that have a different `base`
* MAINT: apply Ruff fixes
* MAINT: move `pre-commit` `--all-files` flag
* MAINT: update lock files

.binder/postBuild

@@ -3,9 +3,12 @@ set -ex
 curl -LsSf https://astral.sh/uv/install.sh | sh
 source $HOME/.cargo/env
 uv export \
-  --extra jupyter \
+  --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

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ 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:
@@ -51,7 +51,7 @@ 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]
@@ -81,11 +81,6 @@ repos:
     hooks:
       - id: taplo-format
 
-  - repo: https://github.com/ComPWA/taplo-pre-commit
-    rev: v0.9.3
-    hooks:
-      - id: taplo-format
-
   - repo: https://github.com/pappasam/toml-sort
     rev: v0.23.1
     hooks:
@@ -105,6 +100,6 @@ repos:
           )$
 
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.4.24
+    rev: 0.4.27
     hooks:
       - id: uv-lock

.readthedocs.yml

@@ -10,7 +10,11 @@ build:
       pixi global install 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

docs/eta-pi-p/automated.ipynb

@@ -537,7 +537,7 @@
     "    color_id = 0\n",
     "    for recoil_id, ax in enumerate(axes):\n",
     "        decay_products = sorted({0, 1, 2} - {recoil_id})\n",
-    "        key = f\"m_{\"\".join(str(i) for i in decay_products)}\"\n",
+    "        key = f\"m_{''.join(str(i) for i in decay_products)}\"\n",
     "        bin_values, bin_edges = jax.numpy.histogram(\n",
     "            phsp[key].real,\n",
     "            bins=120,\n",

docs/lambda-k-pi/ampform.ipynb

@@ -705,7 +705,7 @@
     "    color_id = 0\n",
     "    for recoil_id, ax in enumerate(axes):\n",
     "        decay_products = sorted({0, 1, 2} - {recoil_id})\n",
-    "        key = f\"m_{\"\".join(str(i) for i in decay_products)}\"\n",
+    "        key = f\"m_{''.join(str(i) for i in decay_products)}\"\n",
     "        bin_values, bin_edges = jax.numpy.histogram(\n",
     "            phsp[key].real,\n",
     "            bins=120,\n",

pyproject.toml

@@ -4,62 +4,50 @@ requires = ["setuptools"]
 
 [project]
 authors = [{name = "Vitor Shen"}]
-dependencies = [
-    "ampform",
-    "ampform-dpd",
-    "graphviz",
-    "ipympl",
-    "ipywidgets",
-    "jax",
-    "jaxlib",
-    "matplotlib",
-    "myst-nb",
-    "numpy",
-    "pandas",
-    "phasespace",
-    "pre-commit-uv",
-    "python-lsp-ruff",
-    "python-lsp-server",
-    "qrules",
-    "ruff",
-    "sphinx-autobuild",
-    "sphinx-book-theme",
-    "sphinx-comments",
-    "sphinx-copybutton",
-    "sympy",
-    "tensorflow",
-    "tensorwaves",
-]
 license = {file = "LICENSE"}
 name = "gluex-nstar"
 readme = "README.md"
 requires-python = ">=3.12"
 version = "0.1.0"
 
-[project.optional-dependencies]
+[dependency-groups]
 dev = [
-    "gluex-nstar[doc]",
-    "gluex-nstar[jupyter]",
-    "gluex-nstar[sty]",
-    "pre-commit-uv",
-    "tox",
+    "ruff",
+    "sphinx-autobuild",
+    {include-group = "doc"},
+    {include-group = "jupyter"},
+    {include-group = "test"},
 ]
 doc = [
-    "sphinx-autobuild",
+    "myst-nb",
     "sphinx-book-theme",
     "sphinx-comments",
     "sphinx-copybutton",
+    {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]",
+    {include-group = "notebooks"},
+]
+notebooks = [
+    "ampform",
+    "ampform-dpd",
+    "ipympl",
+    "ipywidgets",
+    "matplotlib",
+    "qrules[viz]",
+    "tensorwaves[jax,pwa]",
+]
+test = [
+    "nbmake",
+    {include-group = "notebooks"},
 ]
-sty = ["ruff"]
 
 [tool.ruff]
 extend-include = ["*.ipynb"]
@@ -192,13 +180,15 @@ setenv =
 [testenv:docnb]
 base = doc
 description = {[testenv:doc]description} with cached notebook execution
+passenv = *
 setenv =
     {[testenv:doc]setenv}
     EXECUTE_NB = yes
 
 [testenv:docnb-force]
 base = doc
 description = {[testenv:doc]description} with notebook execution (no cache)
+passenv = *
 setenv =
     {[testenv:doc]setenv}
     FORCE_EXECUTE_NB = yes
@@ -238,6 +228,7 @@ setenv =
 [testenv:docnblive]
 base = doclive
 description = {[testenv:doclive]description} with cached notebook execution
+passenv = *
 setenv =
     {[testenv:doclive]setenv}
     EXECUTE_NB = yes
@@ -254,10 +245,17 @@ description = Check external links in the documentation (requires internet conne
 setenv =
     {[testenv:doclive]setenv}
 
+[testenv:nb]
+allowlist_externals =
+    pytest
+commands =
+    pytest --nbmake {posargs:docs}
+description = Run all notebooks with pytest
+
 [testenv:sty]
 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
 """