chore: Migrate to dependency groups (#304)

* chore: Migrate to dependency groups

Also refine the mypy checking configuration and fix a few typing issues

* bump ci python setup

* copilot LIED

* Bump cibuildwheel to 3.3

We need CPython 3.14.0 final because of stdlib bug that triggers
pydantic issue pydantic/pydantic#12527
Available in v3.2.1 but might as well go up one more

* Add dependencies for tutorial notebook

Author: nsmith-

.github/workflows/ci.yml

@@ -43,12 +43,12 @@ jobs:
         fetch-depth: 0
         fetch-tags: true
 
-    - uses: actions/setup-python@v3
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install package
-      run: python -m pip install .[test]
+      run: python -m pip install . --group test
 
     - name: Test package
       run: python -m pytest -ra
@@ -77,7 +77,7 @@ jobs:
 
       - name: Install package
         shell: bash -l {0}
-        run: python -m pip install .[test]
+        run: python -m pip install . --group test
 
       - name: Test package
         shell: bash -l {0}

.github/workflows/docs.yml

@@ -19,13 +19,13 @@ jobs:
 
     - uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: 3.12
 
     - name: Install pandoc
       uses: r-lib/actions/setup-pandoc@v2
 
     - name: Install package
-      run: python -m pip install .[docs]
+      run: python -m pip install . --group docs
 
     - name: Build documentation
       run: |

.github/workflows/wheels.yml

@@ -48,7 +48,7 @@ jobs:
         fetch-tags: true
         fetch-depth: 0
 
-    - uses: pypa/cibuildwheel@v3.1
+    - uses: pypa/cibuildwheel@v3.3
       env:
         CIBW_ARCHS: ${{ matrix.arch }}
         MACOSX_DEPLOYMENT_TARGET: 11.0

.gitignore

@@ -145,3 +145,5 @@ _skbuild
 src/correctionlib/cmake
 src/correctionlib/include
 include/correctionlib_version.h
+
+.vscode

.pre-commit-config.yaml

@@ -40,5 +40,5 @@ repos:
   rev: v1.17.1
   hooks:
   - id: mypy
-    files: src
-    additional_dependencies: [types-setuptools, uhi, pydantic, numpy]
+    pass_filenames: false # to allow mypy to respect pyproject.toml config
+    additional_dependencies: [uhi, pydantic, numpy]

CONTRIBUTING.md

@@ -13,9 +13,20 @@ You can set up a development environment by running:
 ```bash
 python3 -m venv .env
 source .env/bin/activate
-pip install -e .[dev,test]
+pip install -e . --group dev
 ```
 
+Alternatively, you can use `uv`:
+
+```bash
+uv sync --no-editable
+source .venv/bin/activate
+```
+
+The `--no-editable` flag is needed to avoid installing the package in editable mode,
+as the paths to the library and include files are not correctly set up for editable installs,
+preventing C++ compilation.
+
 # Post setup
 
 You should prepare pre-commit, which will help you by checking that commits

binder/correctionlib_tutorial.ipynb

@@ -44,20 +44,22 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
+convert = [
+  "pandas",
+  "uproot >=4.0.4",
+  "requests",
+  "scipy",
+]
+
+[dependency-groups]
 test = [
-  "pytest >=4.6",
+  "pandas",
+  "uproot >=4.0.4",
+  "requests",
   "scipy",
+  "pytest >=4.6",
   "awkward >=2.2.2",
   "dask-awkward >=2024.1.1",
-  "dask <2025.4.0",
-]
-dev = [
-  "pytest >=4.6",
-  "pre-commit",
-  "mypy",
-  "uhi",
-  "awkward >=2",
-  "dask-awkward",
 ]
 docs = [
   "recommonmark >=0.5.0",
@@ -67,16 +69,31 @@ docs = [
   "sphinx-jsonschema",
   "myst-parser",
   "nbsphinx",
+  # to match binder/requirements.txt
+  "awkward",
+  "hist[plot]",
+  "matplotlib",
+  "ipykernel",
 ]
-convert = [
-  "pandas",
-  "uproot >=4.0.4",
-  "requests",
-  "scipy",
+dev = [
+  {include-group = "test"},
+  {include-group = "docs"},
+  "pre-commit",
+  "mypy",
+  "uhi",
 ]
 
 [tool.mypy]
 python_version = "3.9"
+files = ["src"]
+
+[[tool.mypy.overrides]]
+module = ["awkward.*", "uproot.*"]
+follow_untyped_imports = true
+
+[[tool.mypy.overrides]]
+module = ["cppyy.*", "scipy.*"]
+ignore_missing_imports = true
 
 [project.scripts]
 correction = "correctionlib.cli:main"
@@ -96,8 +113,8 @@ BUILD_DEMO = "OFF"
 write_to = "src/correctionlib/version.py"
 
 [tool.cibuildwheel]
-skip = ["pp*-*", "cp313t-*", "cp314t-*"]
-test-extras = "test"
+skip = ["cp314t-*"]
+test-groups = ["test"]
 test-command = "python -m pytest {package}/tests"
 test-skip = ["*-musllinux_*", "cp3{10,11,12}-win32"]
 

pyproject.toml

@@ -3,14 +3,17 @@
 import json
 from collections.abc import Iterator, Mapping
 from numbers import Integral
-from typing import Any, Callable, Union
+from typing import TYPE_CHECKING, Any, Callable, Union
 
 import numpy
 from packaging import version
 
 import correctionlib._core
 import correctionlib.version
 
+if TYPE_CHECKING:
+    import awkward
+
 _min_version_ak = version.parse("2.0.0")
 _min_version_dak = version.parse("2024.1.1")
 
@@ -98,7 +101,7 @@ def _call_as_numpy(
 
 def _wrap_awkward(
     func: Callable[..., Any],
-    *args: Union["numpy.ndarray[Any, Any]", str, int, float],
+    *args: Union["awkward.Array", "numpy.ndarray[Any, Any]", str, int, float],
 ) -> Any:
     from functools import partial