chore: updates from learn-scientific-python

.github/dependabot.yml

@@ -7,4 +7,7 @@ updates:
       interval: "monthly"
     commit-message:
       prefix: "chore"
-      include:
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/workflows/ci.yml

@@ -16,37 +16,24 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
 # Use bash by default in all jobs
 defaults:
   run:
     shell: bash -el {0}
 
 jobs:
-  # run pre-commit which includes many formatting and linting tools
-  pre-commit:
-    name: Format
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.x"
-      - uses: pre-commit/[email protected]
-        with:
-          extra_args: --hook-stage manual --all-files
-      - name: Run PyLint
-        run: pipx run nox -s pylint -- --output-format=github
-
   # Run tests and upload to codecov
   test:
     name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
     runs-on: ${{ matrix.runs-on }}
     if: |
       ${{!startsWith(github.event.head_commit.message, 'docs:') }} ||
       ${{!startsWith(github.event.head_commit.message, 'style:') }}
-    needs: [pre-commit]
     strategy:
       # Otherwise, the workflow would stop if a single job fails. We want to
       # run all of them to catch failures in different combinations.
@@ -55,7 +42,6 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
     env:
-      FORCE_COLOR: 3
       NUMBA_DISABLE_JIT: "1"
     timeout-minutes: 30
     steps:
@@ -98,3 +84,5 @@ jobs:
         uses: codecov/[email protected]
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+

.pre-commit-config.yaml

@@ -27,11 +27,6 @@ exclude: |
   )$
 
 repos:
-  # - repo: https://github.com/psf/black-pre-commit-mirror
-  #   rev: "23.9.1"
-  #   hooks:
-  #     - id: black-jupyter
-
   - repo: https://github.com/adamchainz/blacken-docs
     rev: "1.16.0"
     hooks:
@@ -110,3 +105,16 @@ repos:
         language: pygrep
         entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
         exclude: .pre-commit-config.yaml
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.18"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.29.0"
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+      - id: check-readthedocs

noxfile.py

@@ -22,7 +22,9 @@
 
 DIR = Path(__file__).parent.resolve()
 
+nox.needs_version = ">=2024.3.2"
 nox.options.sessions = ["lint", "pylint", "tests"]
+nox.options.default_venv_backend = "uv|virtualenv"
 
 
 @nox.session
@@ -71,41 +73,31 @@ def tests(session: nox.Session) -> None:
 @nox.session(reuse_venv=True)
 def docs(session: nox.Session) -> None:
     """
-    Build the docs. Pass "--serve" to serve. Pass "-b linkcheck" to check links.
+    Build the docs. Pass --non-interactive to avoid serving. First positional
+    argument is the target directory.
     """
 
     parser = argparse.ArgumentParser()
-    parser.add_argument("--serve", action="store_true", help="Serve after building")
     parser.add_argument(
         "-b", dest="builder", default="html", help="Build target (default: html)"
     )
+    parser.add_argument("output", nargs="?", help="Output directory")
     args, posargs = parser.parse_known_args(session.posargs)
+    serve = args.builder == "html" and session.interactive
 
-    if args.builder != "html" and args.serve:
-        session.error("Must not specify non-HTML builder with --serve")
-
-    extra_installs = ["sphinx-autobuild"] if args.serve else []
-
-    session.install("-e.[docs]", *extra_installs)
-    session.chdir("docs")
-
-    if args.builder == "linkcheck":
-        session.run(
-            "sphinx-build", "-b", "linkcheck", ".", "_build/linkcheck", *posargs
-        )
-        return
+    session.install("-e.[docs]", "sphinx-autobuild")
 
     shared_args = (
         "-n",  # nitpicky mode
         "-T",  # full tracebacks
         f"-b={args.builder}",
-        ".",
-        f"_build/{args.builder}",
+        "docs",
+        args.output or f"docs/_build/{args.builder}",
         *posargs,
     )
 
-    if args.serve:
-        session.run("sphinx-autobuild", *shared_args)
+    if serve:
+        session.run("sphinx-autobuild", "--open-browser", *shared_args)
     else:
         session.run("sphinx-build", "--keep-going", *shared_args)
 
@@ -117,11 +109,10 @@ def build_api_docs(session: nox.Session) -> None:
     """
 
     session.install("sphinx")
-    session.chdir("docs")
     session.run(
         "sphinx-apidoc",
         "-o",
-        "api/",
+        "docs/api/",
         "--module-first",
         "--no-toc",
         "--force",

pyproject.toml

@@ -151,7 +151,6 @@ files = ["src"]
 python_version = "3.9"
 warn_unused_configs = true
 strict = true
-show_error_codes = true
 enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
 warn_unreachable = true
 disallow_untyped_defs = false
@@ -191,7 +190,7 @@ lint.select = [
   "NPY",         # NumPy specific rules
   "PD",          # pandas-vet
 ]
-lint.extend-ignore = [
+lint.ignore = [
   "PLR",    # Design related pylint codes
   "G004",   # Logging with f-strings
   "PD901",  # Bad variable name warning