chore: use dependency-groups (#973)

Signed-off-by: Henry Schreiner <[email protected]>

Author: henryiii

.github/CONTRIBUTING.md

@@ -57,10 +57,11 @@ package is in a virtual environment. This is how you would set one up with
 Python's built-in venv:
 
 ```bash
-python3 -m venv .env
-source ./.env/bin/activate
-pip install -U pip
-pip install -ve .[all]
+python3 -m venv .venv
+source ./.venv/bin/activate
+pip install dependency-groups
+pip-install-dependency-groups dev
+pip install -ve.
 ```
 
 <details><summary>Optional: External Jupyter kernel (click to expand)</summary>
@@ -109,7 +110,8 @@ Here is the recommendation for a CMake install:
 ```bash
 python3 -m venv env_cmake
 source ./env_cmake/bin/activate
-pip install -r dev-requirements.txt
+pip install dependency-groups
+pip-install-dependency-groups dev
 cmake -S . -B build-debug \
     -GNinja \
     -DCMAKE_INSTALL_PREFIX=$(python -c "import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False,standard_lib=False))")
@@ -285,7 +287,8 @@ This requires LLVM 9+, and is based on [this post](https://aras-p.info/blog/2019
 brew install llvm         # macOS way to get clang-9
 python3 -m venv .env_core # general environment (no install will be made)
 . .env_core/bin/activate
-pip install -r dev-requirements.txt
+pip install dependency-groups
+pip-install-dependency-groups dev
 CXX="/usr/local/opt/llvm/bin/clang++" cmake -S . -B build-llvm \
     -DCMAKE_CXX_FLAGS="-ftime-trace" \
     -DPYTHON_EXECUTABLE=$(which python)

.github/workflows/examples.yml

@@ -6,6 +6,7 @@ on:
     paths:
       - "examples/*.py"
       - "notebooks/*.ipynb"
+      - ".github/workflows/examples.yml"
   push:
     branches:
       - master
@@ -21,13 +22,10 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.9"
-      - name: Pre-install NumPy
-        run: python -m pip install -r dev-requirements.txt nbconvert ipykernel
-      - name: Install kernel
-        run: python -m ipykernel install --user --name boost-hist
-      - name: Build
-        run: python -m pip install .[examples]
+      - uses: astral-sh/setup-uv@v4
+      - name: Build and install kernel
+        run: uv run --group examples -m ipykernel install --user --name boost-hist
       - name: Examples
-        run: for f in examples/*.py; do python "$f"; done
+        run: for f in examples/*.py; do uv run "$f"; done
       - name: Notebooks
-        run: jupyter nbconvert --execute --ExecutePreprocessor.timeout=90 --inplace notebooks/*.ipynb
+        run: uv run jupyter nbconvert --execute --ExecutePreprocessor.timeout=90 --inplace notebooks/*.ipynb

.github/workflows/tests.yml

@@ -78,13 +78,18 @@ jobs:
 
       - uses: rui314/setup-mold@v1
 
-      - uses: yezz123/setup-uv@v4
+      - uses: astral-sh/setup-uv@v4
 
       - uses: hendrikmuhs/[email protected]
         with:
           key: ${{ matrix.python-version }}
           create-symlink: true
 
+      - name: Make requirements.txt
+        run: |
+          uv pip install --system dependency-groups
+          dependency-groups dev > dev-requirements.txt
+
       - name: Install python tools
         run: uv pip install --system -r dev-requirements.txt pytest-github-actions-annotate-failures
         env:

.github/workflows/weekly.yml

@@ -21,10 +21,13 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Build and install wheel
-        run: pip install -v .[test]
+        run: |
+          pip install dependency-groups
+          pip-install-dependency-groups test
+          pip install -v .
 
       - name: Test
         run: python -m pytest

.pre-commit-config.yaml

@@ -21,7 +21,6 @@ repos:
       - id: debug-statements
       - id: end-of-file-fixer
       - id: mixed-line-ending
-      - id: requirements-txt-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/cheshirekow/cmake-format-precommit
@@ -54,7 +53,7 @@ repos:
     rev: v2.3.0
     hooks:
       - id: codespell
-        args: ["-L", "hist,nd,circularly,ba", "-w"]
+        args: ["-L", "hist,nd,circularly,ba,fo", "-w"]
         exclude: ^(notebooks/xarray.ipynb|notebooks/BoostHistogramHandsOn.ipynb|.*\.svg)$
 
   - repo: local

.readthedocs.yml

@@ -6,20 +6,14 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: "ubuntu-22.04"
   tools:
-    python: "3"
-
-# Build documentation in the docs/ directory with Sphinx
-sphinx:
-  configuration: docs/conf.py
-
-# Include PDF and ePub
-formats: all
-
-python:
-  install:
-    - requirements: docs/requirements.txt
+    python: "3.12"
+  commands:
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv run --only-group docs sphinx-build -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
 
 submodules:
   exclude: all

dev-requirements.txt

@@ -8,6 +8,7 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import contextlib
+import importlib.metadata
 import shutil
 import sys
 from pathlib import Path
@@ -31,11 +32,8 @@
 copyright = "2020, Henry Schreiner, Hans Dembinski"
 author = "Henry Schreiner, Hans Dembinski"
 
-# It is better to use pkg_resources, but we can't build on RtD
-from pkg_resources import DistributionNotFound, get_distribution
-
-with contextlib.suppress(DistributionNotFound):
-    version = get_distribution("boost_histogram").version
+with contextlib.suppress(ModuleNotFoundError):
+    version = importlib.metadata.version("boost_histogram")
     # passed if no version (latest/git hash)
 
 

docs/conf.py

@@ -394,7 +394,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

docs/requirements.txt

@@ -137,7 +137,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

notebooks/PerformanceComparison.ipynb

@@ -198,7 +198,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

notebooks/SimpleExample.ipynb

@@ -2,44 +2,55 @@
 
 import argparse
 from pathlib import Path
+from typing import Any
 
 import nox
 
-nox.needs_version = ">=2024.3.2"
+nox.needs_version = ">=2024.4.15"
 nox.options.default_venv_backend = "uv|virtualenv"
-nox.options.sessions = ["lint", "tests"]
 
 
-@nox.session
+def _get_group(name: str, groups: dict[str, Any]) -> list[str]:
+    group = groups[name]
+    return [d if isinstance(d, str) else _get_group(d, groups) for d in group]
+
+
+def dependency_groups(pyproject: dict[str, Any], *names: str) -> list[str]:
+    groups = pyproject["dependency-groups"]
+    return [item for name in names for item in _get_group(name, groups)]
+
+
 def tests(session: nox.Session) -> None:
     """
     Run the unit and regular tests.
     """
-
-    session.install(".[test]")
+    pyproject = nox.project.load_toml("pyproject.toml")
+    session.install(".", *dependency_groups(pyproject, "test"))
     session.run("pytest", *session.posargs)
 
 
-@nox.session
+@nox.session(default=False)
 def hist(session: nox.Session) -> None:
     """
     Run Hist's test suite
     """
+    pyproject = nox.project.load_toml("pyproject.toml")
     session.install(".")
     tmpdir = session.create_tmp()
     session.chdir(tmpdir)
     session.run("git", "clone", "https://github.com/scikit-hep/hist", external=True)
     session.chdir("hist")
-    session.install(".[test,plot]")
+    session.install(".", *dependency_groups(pyproject, "test", "plot"))
     session.run("pip", "list")
     session.run("pytest", *session.posargs)
 
 
-@nox.session(reuse_venv=True)
+@nox.session(reuse_venv=True, default=False)
 def docs(session: nox.Session) -> None:
     """
     Build the docs. Pass --non-interactive to avoid serving. Pass "-b linkcheck" to check links.
     """
+    pyproject = nox.project.load_toml("pyproject.toml")
 
     parser = argparse.ArgumentParser()
     parser.add_argument(
@@ -49,7 +60,7 @@ def docs(session: nox.Session) -> None:
     serve = args.builder == "html" and session.interactive
 
     extra_installs = ["sphinx-autobuild"] if serve else []
-    session.install("-r", "docs/requirements.txt", *extra_installs)
+    session.install(*dependency_groups(pyproject, "docs"), *extra_installs)
 
     shared_args = (
         "-n",  # nitpicky mode
@@ -67,13 +78,14 @@ def docs(session: nox.Session) -> None:
         session.run("sphinx-build", "--keep-going", *shared_args)
 
 
-@nox.session
+@nox.session(default=False)
 def build_api_docs(session: nox.Session) -> None:
     """
     Build (regenerate) API docs.
     """
+    pyproject = nox.project.load_toml("pyproject.toml")
 
-    session.install(".", "-r", "docs/requirements.txt")
+    session.install(*dependency_groups(pyproject, "docs"))
     session.run(
         "sphinx-apidoc",
         "-o",
@@ -121,10 +133,11 @@ def pylint(session: nox.Session) -> None:
     session.run("pylint", "boost_histogram", *session.posargs)
 
 
-@nox.session
+@nox.session(default=False)
 def make_pickle(session: nox.Session) -> None:
     """
     Make a pickle file for this version
     """
-    session.install(".[dev]")
+    pyproject = nox.project.load_toml("pyproject.toml")
+    session.install(".", *dependency_groups(pyproject, "dev"))
     session.run("python", "tests/pickles/make_pickle.py", *session.posargs)

notebooks/ThreadedFills.ipynb

@@ -50,27 +50,37 @@ dependencies = [
     "numpy",
 ]
 
-[project.optional-dependencies]
+[project.urls]
+"Bug Tracker" = "https://github.com/scikit-hep/boost-histogram/issues"
+Changelog = "https://boost-histogram.readthedocs.io/en/latest/CHANGELOG.html"
+Chat = " https://gitter.im/HSF/PyHEP-histogramming"
+Discussions = "https://github.com/scikit-hep/boost-histogram/discussions"
+Documentation = "https://boost-histogram.readthedocs.io/"
+Homepage = "https://github.com/scikit-hep/boost-histogram"
+
+[dependency-groups]
 dev = [
-    "cloudpickle",
-    "hypothesis>=6.0",
+    { include-group = "test" },
     "ipykernel",
-    "pytest-benchmark",
-    "pytest>=6.0",
+    "nbconvert",
+    "numpy",
+    "setuptools_scm",
     "typer",
 ]
 docs = [
+    "ipython",
     "myst_parser>=0.13",
     "nbsphinx",
+    "numpy",
     "sphinx-book-theme>=0.0.33",
-    "Sphinx>=4.0",
+    "sphinx>=4.0",
     "sphinx_copybutton",
 ]
 examples = [
     "matplotlib",
     "netCDF4",
     "numba",
-    "uproot3",
+    "uproot",
     "xarray",
     "xhistogram",
 ]
@@ -81,14 +91,6 @@ test = [
     "pytest>=6.0",
 ]
 
-[project.urls]
-"Bug Tracker" = "https://github.com/scikit-hep/boost-histogram/issues"
-Changelog = "https://boost-histogram.readthedocs.io/en/latest/CHANGELOG.html"
-Chat = " https://gitter.im/HSF/PyHEP-histogramming"
-Discussions = "https://github.com/scikit-hep/boost-histogram/discussions"
-Documentation = "https://boost-histogram.readthedocs.io/"
-Homepage = "https://github.com/scikit-hep/boost-histogram"
-
 
 [tool.scikit-build]
 minimum-version = "build-system.requires"
@@ -159,7 +161,7 @@ ignore_missing_imports = true
 
 [tool.cibuildwheel]
 build-frontend = "build[uv]"
-test-extras = "test"
+test-groups = ["test"]
 test-command = "pytest --benchmark-disable {project}/tests"
 skip = [
   "pp38-*",