FIX: define dev dependencies as dependency groups (#535)

* BREAK: remove `all` optional depdency * BREAK: remove `phasespace` optional depdency group * BREAK: remove `tensorflow` optional depdency group * BREAK: remove `viz` optional dependency group * DX: move `nbmake` to `dev` dependencies * DX: run `pyright` in `tox -e sty` job * DX: set `PYTHONHASHSEED` in `direnv` environment * FIX: remove `pre-commit-uv` and `tox` from environment * FIX: update links to TRs * MAINT: address Ruff issues * MAINT: update lock files
ComPWA · Oct 29, 2024 · 010faa3 · 010faa3
1 parent a25c6cf
commit 010faa3
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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/.envrc b/.envrc
@@ -1,2 +1,4 @@
 uv sync --all-extras --quiet
 source .venv/bin/activate
+
+export PYTHONHASHSEED=0
diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
@@ -20,21 +20,24 @@ on:
 jobs:
   benchmark:
     name: Performance regression
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v4
-      - uses: ComPWA/actions/pip-install@v1
+      - uses: actions/setup-python@v5
         with:
-          editable: "yes"
-          extras: test,all
-          python-version: "3.9"
-          specific-packages: ${{ inputs.specific-pip-packages }}
+          python-version: "3.12"
+      - uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
       - name: Run pytest-benchmark
         run: |
-          pytest \
-            -k benchmark \
-            --benchmark-json output.json \
-            --durations=0
+          uv run \
+            --group test \
+            --no-dev \
+            pytest \
+              -k benchmark \
+              --benchmark-json output.json \
+              --durations=0
         working-directory: benchmarks
       - name: Store result
         if: github.event_name == 'push'

diff --git a/.github/workflows/ci.yml b/.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
@@ -37,9 +37,8 @@ jobs:
       python-version: "3.10"
       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:
-      additional-extras: all
       coverage-target: tensorwaves
       macos-python-version: "3.9"
       specific-pip-packages: ${{ inputs.specific-pip-packages }}
@@ -48,6 +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: "3.10"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -14,13 +14,13 @@ 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:
-          - --ci-test-extras=all
           - --dev-python-version=3.10
           - --doc-apt-packages=graphviz
+          - --environment-variables=PYTHONHASHSEED=0
           - --repo-name=tensorwaves
           - --repo-title=TensorWaves
           - --update-lock-files=monthly
@@ -62,7 +62,7 @@ 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: 0.4.28
     hooks:
       - id: uv-lock
diff --git a/.readthedocs.yml b/.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
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -15,12 +15,30 @@ cd tensorwaves
 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
+```
diff --git a/docs/amplitude-analysis.ipynb b/docs/amplitude-analysis.ipynb
@@ -345,7 +345,7 @@
    "source": [
     "::::{margin}\n",
     ":::{tip}\n",
-    "{doc}`TR-018<compwa-report:018>` explains some of the mechanisms behind the phase space generator as well as how to do {ref}`importance sampling<compwa-report:018:Intensity distribution>`.\n",
+    "{doc}`TR-018<compwa-report:018/index>` explains some of the mechanisms behind the phase space generator as well as how to do {ref}`importance sampling<compwa-report:018/index:Intensity distribution>`.\n",
     ":::\n",
     "::::\n",
     "\n",

diff --git a/docs/install.md b/docs/install.md
@@ -155,6 +155,7 @@ python3 -m pip install "tensorwaves[jax,pwa] @ git+https://github.com/ComPWA/ten
 
 :::{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!
diff --git a/docs/usage.ipynb b/docs/usage.ipynb
@@ -318,7 +318,7 @@
     "            symbol = sp.Dummy(name)\n",
     "            latex = sp.latex(symbol)\n",
     "            values.append(f\"{latex}={value:.2g}\")\n",
-    "        return f'${\",\".join(values)}$'"
+    "        return f\"${','.join(values)}$\""
    ]
   },
   {

diff --git a/pyproject.toml b/pyproject.toml
@@ -49,26 +49,46 @@ name = "tensorwaves"
 requires-python = ">=3.9"
 
 [project.optional-dependencies]
-all = [
-    "tensorwaves[jax]",
-    "tensorwaves[numba]",
-    "tensorwaves[pwa]",
-    "tensorwaves[scipy]",
-    "tensorwaves[tensorflow]",
-    "tensorwaves[viz]",
+jax = [
+    "jax",
+    "jaxlib",
+]
+numba = ["numba"]
+phsp = [
+    "phasespace[tf] >=1.7.0",
+    "tensorwaves[tf]",
 ]
+pwa = [
+    "ampform[viz]>=0.12.0",
+    "tensorwaves[phsp]",
+]
+scipy = ["scipy >=1"]
+tf = [
+    "numpy~=1.0",
+    "tensorflow >=2.4",
+]
+
+[project.readme]
+content-type = "text/markdown"
+file = "README.md"
+
+[project.urls]
+Changelog = "https://github.com/ComPWA/tensorwaves/releases"
+Documentation = "https://tensorwaves.rtfd.io"
+Source = "https://github.com/ComPWA/tensorwaves"
+Tracker = "https://github.com/ComPWA/tensorwaves/issues"
+
+[dependency-groups]
 dev = [
+    "nbmake",
+    "ruff",
     "sphinx-autobuild",
-    "tensorwaves[all]",
-    "tensorwaves[doc]",
-    "tensorwaves[jupyter]",
-    "tensorwaves[sty]",
-    "tensorwaves[test]",
-    "tox",
+    {include-group = "doc"},
+    {include-group = "jupyter"},
+    {include-group = "style"},
+    {include-group = "test"},
 ]
 doc = [
-    "jupyter",
-    "matplotlib",
     "myst-nb",
     "sphinx",
     "sphinx-api-relink",
@@ -80,98 +100,52 @@ doc = [
     "sphinx-thebe",
     "sphinx-togglebutton",
     "sphobjinv",
-    "tensorwaves[notebooks]",
-]
-jax = [
-    "jax",
-    "jaxlib",
-    "tensorwaves[all]",
+    {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]",
-    "tensorwaves[doc]",
+    {include-group = "doc"},
 ]
 notebooks = [
     "black",
     "ipympl",
+    "matplotlib",
     "pandas",
     "tensorwaves[jax,pwa]",
 ]
-numba = [
-    "numba",
-]
-phasespace = [
-    "tensorwaves[phsp]",
-]
-phsp = [
-    "phasespace[tf] >=1.7.0",
-    "tensorwaves[tensorflow]",
-]
-pwa = [
-    "ampform >=0.12.0", # https://github.com/ComPWA/ampform/pull/177
-    "tensorwaves[phsp]",
-]
-scipy = [
-    "scipy >=1",
-]
-sty = [
-    "mypy >=0.570", # attrs support
-    "pre-commit-uv",
-    "ruff",
-    "tensorwaves[types]",
-]
-tensorflow = [
-    "tensorwaves[tf]",
+style = [
+    "mypy",
+    {include-group = "types"},
 ]
 test = [
-    "ampform >=0.13", # https://github.com/ComPWA/ampform/issues/208
-    "nbmake",
-    "pyarrow", # https://github.com/pandas-dev/pandas/issues/54466
+    "ampform >=0.13",
+    "pyarrow",
     "pytest-benchmark",
     "pytest-cov",
     "pytest-xdist",
-    "tensorflow !=2.17.0", # https://github.com/ComPWA/tensorwaves/actions/runs/10274147572/job/28430227465?pr=530
-    "tensorwaves[test-types]",
+    "tensorwaves[jax,numba,pwa]",
+    {include-group = "test-types"},
 ]
 test-types = [
     "ipython", # test _repr_pretty_
     "pytest",
     "pytest-mock",
 ]
-tf = [
-    "numpy<2",
-    "tensorflow !=2.15.0.post1", # https://github.com/ComPWA/tensorwaves/actions/runs/7147814088/job/19467965144?pr=509
-    "tensorflow >=2.4", # tensorflow.experimental.numpy
-]
 types = [
     "sphinx-api-relink",
-    "tensorwaves[jax]",
-    "tensorwaves[pwa]",
-    "tensorwaves[test-types]",
+    "tensorwaves[jax,pwa]",
     "types-PyYAML",
     "types-requests",
     "types-tensorflow",
     "types-tqdm",
+    {include-group = "test-types"},
 ]
-viz = [
-    "graphviz",
-]
-
-[project.readme]
-content-type = "text/markdown"
-file = "README.md"
-
-[project.urls]
-Changelog = "https://github.com/ComPWA/tensorwaves/releases"
-Documentation = "https://tensorwaves.rtfd.io"
-Source = "https://github.com/ComPWA/tensorwaves"
-Tracker = "https://github.com/ComPWA/tensorwaves/issues"
 
 [tool.setuptools]
 include-package-data = false
@@ -267,6 +241,8 @@ reportUnusedFunction = true
 reportUnusedImport = true
 reportUnusedVariable = true
 typeCheckingMode = "strict"
+venv = ".venv"
+venvPath = "."
 
 [tool.pytest.ini_options]
 addopts = ["--color=yes"]
@@ -609,6 +585,4 @@ allowlist_externals =
 commands =
     pre-commit run --all-files {posargs}
 description = Perform all linting, formatting, and spelling checks
-setenv =
-    SKIP = pyright
 """