Skip to content

Latest commit

 

History

History
146 lines (90 loc) · 5.35 KB

workflows.md

File metadata and controls

146 lines (90 loc) · 5.35 KB
Raw

What these workflows do?

audit.yaml

This workflow scans dependencies of your package for vulnerabilities using oysteR. Dependencies can be retrieved either from DESCRIPTION file or from renv.lock file.

bioccheck.yaml

This workflow implements Bioconductor-specific R package checks with BiocCheck.

build-check-install.yaml

This workflow includes the following activities:

  1. Build an R package.
  2. Run R CMD check.
  3. Publish unit test summary.
  4. Catch any notes, warnings etc. in the R CMD check output.
  5. Install the package.

gitleaks.yaml

This workflow runs gitleaks on the repo to discover any secrets that might have been hardcoded.

Additionally, it runs presidio-cli to find any personally identifiable information (PII) within the git repo.

grammar.yaml

This workflow uses write-good to check changed files with names matching a pattern for English sentences that could be corrected. Then, it adds annotations to the pull request so that problematic grammar can be reviewed.

licenses.yaml

This workflow generates a license report of R package's dependencies for continuous compliance.

links.yaml

This workflow checks whether URLs embedded in code and documentation are valid. This workflow uses lychee to detect broken links. Occasionally, this check will detect false positives of strings that look like URLs. To remedy, please add this false positive to the .lycheeignore file.

linter.yaml

This workflow lints the codebase using super-linter.

pkgdown.yaml

Documentation for the R package is generated via this workflow. This workflow uses the pkgdown framework to generate documentation in HTML, and the HTML pages are then deployed to the gh-pages branch.

Moreover, an additional Versions dropdown is generated via the GitHub Action, so that the end user can view multiple versions of the documentation for the package.

release.yaml

This workflow creates a GitHub release from a git tag and generates changelog based on NEWS.md file.

roxygen.yaml

This workflow uses roxygen to generate .Rd files in man/ directory. It also checks if manuals are up-to-date with roxygen comments in the code.

spelling.yaml

Spellchecks are performed by this workflow, and the spelling R package is used to detect spelling mistakes. In the inst/WORDLIST file, you can add words and/or acronyms that you want the spell check to ignore.

style.yaml

Code style is enforced via the styler R package. The workflow can be configured to commit files that had styling problems automatically, after remediating the problems.

test-coverage.yaml

This workflow examines the test coverage of given R package with covr. Following that, coverage report is added to the PR. Additional feature is the ability to compare code coverage between branches, so the PR can be declined if the coverage would decrease following the merge.

The second part of the workflow runs utilizes covtracer to:

  • prepare traceability matrix
  • identify untested behavior
  • verify directly tested functions

validation.yaml

This workflow generates and publishes validation report.

version-bump.yaml

This workflow increases R package version in NEWS.md and DESCRIPTION files and commits this change to the repository.

version.yaml

This workflow checks if NEWS.md and DESCRPTION files have the same R package version.