Update README to reflect current tooling and best practices - #1
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- Fix DOI badge to use {github_id} placeholder instead of hardcoded ID
- Drop stale commented-out black/isort badges; add a ruff badge to
match the actual pre-commit configuration
- Fix typos and shouty caps; switch code fences to triple-backticks
- Replace insecure jupyter command (auth disabled, bound to all
interfaces) with the safe default
- Note GNU vs macOS sed -i portability for the rename one-liner
- Bump example python version from 3.10 to 3.12
- Tighten and de-duplicate the Documentation, Tests, and Linting
sections; rename Linting -> Linting and Formatting since ruff
handles both
- Note that mypy is not wired into pre-commit
- Link the citation-file-format docs from the Citation section
Workflow (.github/workflows/python-app.yml): - Bump actions/checkout v2 -> v4 and actions/setup-python v2 -> v5 - Bump example python from 3.10 to 3.12, enable pip cache - Drop unused flake8 install - Collapse the duplicate plain pytest run; the coverage run already exercises the same tests Pre-commit (.pre-commit-config.yaml): - Bump pre-commit-hooks v4.3.0 -> v5.0.0 - Remove duplicate check-yaml entry - Drop unmaintained pydocstyle hook (covered by ruff's pydocstyle rules) - Drop blacken-docs pinned to black==20.8b1 (ruff-format handles docstring code blocks) - Drop pygrep-hooks python-use-type-annotations (also covered by ruff) - Bump yamllint v1.28.0 -> v1.35.1
- Replace `from my_package import *` placeholder in tests/test_example.py with a plain `import my_package` (with a noqa for the unused-import rule, since this is a template stub) - Apply ruff-format and trailing-whitespace / end-of-file fixes across docs/conf.py, my_package/__init__.py, pyproject.toml, and the tests package, so a fresh `pre-commit run --all-files` is green
The license file was previously deleted, but pyproject.toml's
`license = {file = "LICENSE.md"}` and a link in docs/index.rst still
referenced it. Restore the file as a clearly-marked placeholder so the
package builds and the docs link resolves, while making it obvious that
the user must replace it with a real license before publishing.
Also add a step to the README setup checklist directing the user to
swap in their chosen license and update pyproject.toml.
Three lightweight additions to keep a forked template healthy without demanding active maintenance: - .github/dependabot.yml: weekly PRs for outdated GitHub Actions and pip dependencies (limit 5 open PRs each). - .github/workflows/pre-commit.yml: runs `pre-commit run --all-files` on push and PR to main so lint/format are enforced in CI, not only locally. - .github/workflows/codeql.yml: GitHub's CodeQL static analysis on push, PR, and a weekly Monday schedule, surfacing findings in the Security tab. Document all three in a new CI/CD section of the README.
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match the actual pre-commit configuration
interfaces) with the safe default
sections; rename Linting -> Linting and Formatting since ruff
handles both