chore: use dependency groups (#550)

Signed-off-by: Henry Schreiner <henryfs@princeton.edu>

Author: henryiii

.github/workflows/ci.yml

@@ -54,7 +54,7 @@ jobs:
     - uses: astral-sh/setup-uv@v7
 
     - name: Install package
-      run: uv pip install --system -e .[test]
+      run: uv pip install --system -e. --group=test
 
     - name: Pytest
       if: runner.os == 'Linux'
@@ -90,7 +90,7 @@ jobs:
       run: sudo apt-get install graphviz
 
     - name: Install package
-      run: uv pip install --system -e .[test]
+      run: uv pip install --system -e. --group=test
 
     - name: Install notebook requirements
       run: uv pip install --system nbconvert jupyter_client ipykernel pydot

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
   rev: "v0.14.14"
   hooks:
     - id: ruff-check
-      args: ["--fix", "--show-fixes"]
+      args: ["--fix"]
     - id: ruff-format
 
 - repo: https://github.com/pre-commit/mirrors-mypy

.readthedocs.yml

@@ -13,13 +13,10 @@ sphinx:
 formats: all
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.11"
-
-python:
-  install:
-  - method: pip
-    path: .
-    extra_requirements:
-    - docs
+    python: "3.14"
+  jobs:
+    install:
+    - pip install --upgrade pip
+    - pip install --group docs

noxfile.py

@@ -16,24 +16,22 @@
 
 @nox.session
 def lint(session):
-    session.install("pre-commit")
-    session.run("pre-commit", "run", "--all-files", *session.posargs)
+    session.install("prek")
+    session.run("prek", "run", "--all-files", *session.posargs)
 
 
 @nox.session
 def pylint(session: nox.Session) -> None:
     """
     Run pylint.
     """
-
-    session.install("pylint")
-    session.install("-e.[dev]")
+    session.install("-e.", "--group=dev", "pylint")
     session.run("pylint", "src", *session.posargs)
 
 
 @nox.session(python=ALL_PYTHONS)
 def tests(session):
-    session.install(".[test]")
+    session.install(".", "--group=test")
     session.run("pytest", *session.posargs)
 
 

pyproject.toml

@@ -52,9 +52,9 @@ dependencies = [
 ]
 dynamic = ["version"]
 
-[project.optional-dependencies]
+[dependency-groups]
 dev = [
-    "pytest>=6",
+    { include-group = "test" }
 ]
 docs = [
     "sphinx-rtd-theme>=0.5.0",
@@ -146,6 +146,9 @@ messages_control.disable = [
     "duplicate-code",
 ]
 
+[tool.ruff]
+show-fixes = true
+
 [tool.ruff.lint]
 extend-select = [
   "B",           # flake8-bugbear