Scientific Python - Repo Review¶

Validate-PyProject¶

[ ] VPP001: Validate pyproject.toml

Invalid pyproject.toml! Error: tool.uv.exclude-newer cannot be validated by any definition:

General¶

Detected build backend: hatchling.build
Detected license(s): MIT License
Python requires: >=3.11
[x] PY001: Has a pyproject.toml
[x] PY002: Has a README.(md|rst) file
[x] PY003: Has a LICENSE* file
[x] PY004: Has docs folder
[x] PY005: Has tests folder
[x] PY006: Has pre-commit config
[ ] PY007: Supports an easy task runner (nox, tox, pixi, etc.)

Projects must have a noxfile.py, tox.ini, or tool.hatch.envs/tool.spin/tool.tox in pyproject.toml to encourage new contributors.

Response: currently we support make, in the future we might move to/add support for nox

PyProject¶

[x] PP002: Has a proper build-system table
[x] PP003: Does not list wheel as a build-dep
[x] PP004: Does not upper cap Python requires
[x] PP005: Using SPDX project.license should not use deprecated trove classifiers [skipped]
[x] PP006: The dev dependency group should be defined
[ ] PP301: Has pytest in pyproject

Must have a [tool.pytest] (pytest 9+) or [tool.pytest.ini_options] (pytest 6+) configuration section in pyproject.toml. If you must have it in ini format, ignore this check. pytest.toml and .pytest.toml files (pytest 9+) are also supported.

[ ] PP302: Sets a minimum pytest to at least 6 or 9 [skipped]
[ ] PP303: Sets the test paths [skipped]
[ ] PP304: Sets the log level in pytest [skipped]
[ ] PP305: Specifies strict xfail [skipped]
[ ] PP306: Specifies strict config [skipped]
[ ] PP307: Specifies strict markers [skipped]
[ ] PP308: Specifies useful pytest summary [skipped]
[ ] PP309: Filter warnings specified [skipped]

GitHub Actions¶

[x] GH100: Has GitHub Actions config
[x] GH101: Has nice names
[ ] GH102: Auto-cancel on repeated PRs

At least one workflow should auto-cancel.

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

[x] GH103: At least one workflow with manual dispatch trigger
[x] GH104: Use unique names for upload-artifact
[ ] GH200: Maintained by Dependabot

All projects should have a .github/dependabot.yml file to support at least GitHub Actions regular updates. Something like this:

version: 2
updates:
# Maintain dependencies for GitHub Actions
    - package-ecosystem: "github-actions"
    directory: "/"
    schedule:
        interval: "weekly"

[x] GH210: Maintains the GitHub action versions with Dependabot [skipped]
[x] GH211: Do not pin core actions as major versions [skipped]
[x] GH212:: Require GHA update grouping [skipped]

Pre-commit¶

[x] PC100: Has pre-commit-hooks
[x] PC110: Uses black or ruff-format
[x] PC111: Uses blacken-docs [skipped]
[ ] PC140: Uses a type checker

Must have https://github.com/pre-commit/mirrors-mypy in .pre-commit-config.yaml

Response: we use basedpyright, which has been added to the pre-commit file

[ ] PC160: Uses a spell checker

Must have one of https://github.com/codespell-project/codespell, https://github.com/crate-ci/typos in .pre-commit-config.yaml

Response: common spellcheckers have low signal-to-noise ratio, and should not be run for every commit. Instead, we use this infrequently for code and constantly for documentation

[ ] PC170: Uses PyGrep hooks (only needed if rST present)

Must have https://github.com/pre-commit/pygrep-hooks in .pre-commit-config.yaml

Response: no rST is present, and other hooks are covered by ruff/basedpyright

[x] PC180: Uses a markdown formatter
[x] PC190: Uses Ruff
[x] PC191: Ruff show fixes if fixes enabled
[x] PC192: Ruff uses ruff-check instead of ruff (legacy)
[ ] PC901: Custom pre-commit CI update message

Should have something like this in .pre-commit-config.yaml:

ci:
  autoupdate_commit_msg: "chore(deps): update pre-commit hooks"

[ ] PC902: Custom pre-commit CI autofix message

Should have something like this in .pre-commit-config.yaml:

ci:
  autofix_commit_msg: "style: pre-commit fixes"

[ ] PC903: Specified pre-commit CI schedule

Should set some schedule: weekly (default), monthly, or quarterly.

ci:
  autoupdate_schedule: "monthly"

MyPy¶

Omitted, we use basedpyright

Ruff¶

[x] RF001: Has Ruff config
[x] RF002: Target version must be set
[x] RF003: src directory doesn't need to be specified anymore (0.6+)
[x] RF101: Bugbear must be selected
[x] RF102: isort must be selected
[x] RF103: pyupgrade must be selected
[x] RF201: Avoid using deprecated config settings
[x] RF202: Use (new) lint config section