Skip to content

chore: 🤖 sync copilot instructions - 2026-07-03 #75

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ccbr-bot wants to merge 2 commits into
base: main
Choose a base branch
from
Open

chore: 🤖 sync copilot instructions - 2026-07-03 #75

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
0bbaf7c
chore: 🤖 sync copilot instructions - 2026-07-03
github-actions[bot] Jul 3, 2026
b99d78d
ci: 🤖 auto-format
ccbr-bot[bot] Jul 3, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 15 additions & 3 deletions .github/copilot-instructions.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,9 @@

## CI & enforcement suggestions (automatable)

1. **PR template**: include optional AI-assistance disclosure fields (model used, high-level prompt intent, manual review confirmation).
1. **Pull Request template**: include optional AI-assistance disclosure fields (model used, high-level prompt intent, manual review confirmation).
2. **Pre-merge check (GitHub Action)**: verify `.github/copilot-instructions.md` is present in the repository and that new pipeline files include a `# CRAFT:` header.
3. **Lint jobs**: `ruff` for Python, `shellcheck` for shell, `lintr` for R, and `nf-core lint` or Snakemake lint checks where applicable.
3. **Lint jobs**: `ruff` for Python, `shellcheck` for shell, `lintr` for R, and `nf-core lint` for Snakemake, or Snakemake lint checks where applicable.
4. **Secrets scan**: run `TruffleHog` or `Gitleaks` on PRs to detect accidental credentials.
5. **AI usage label**: if AI usage is declared, an Action should add `generated-by-AI` label (create this label if it does not exist); the PR body should end with the italicized Markdown line: _Generated using AI_, and any associated commit messages should end with the plain footer line: `Generated using AI`.

Expand Down Expand Up @@ -108,7 +108,7 @@ Rules:

## Pull Requests

When opening a pull request, use the repository's pull request template (usually it is `.github/PULL_REQUEST_TEMPLATE.md`).
When opening a pull request, agents and authors must use the repository's pull request template (`.github/PULL_REQUEST_TEMPLATE.md`).
Different repos have different PR templates depending on their needs.
Ensure that the pull request follows the repository's PR template and includes all required information.
Do not allow the developer to proceed with opening a PR if it does not fill out all sections of the template.
Expand Down Expand Up @@ -138,6 +138,18 @@ Example:
- Fix bug in `detect_absolute_paths()` to ignore comments. (#123, @username)
```

## Release Process

To cut a new release in a repo, first use the draft-release workflow
(`.github/workflows/draft-release.yml`) to draft the release.
Then the human developer must review the draft release and ensure it meets
quality standards, then publish the release.
AI agents must not publish a release, it can only be done by human developers.
When the release is published, the post-release workflow (`.github/workflows/post-release.yml`)
will run automatically and open a new Pull Request.
The human developer must then review the PR, and approve & merge it if the PR
meets quality standards.

## Onboarding checklist for new developers

- [ ] Read `.github/CONTRIBUTING.md` and `.github/copilot-instructions.md`.
Expand Down
70 changes: 0 additions & 70 deletions CITATION.cff
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Loading