Thanks for considering a contribution to pepVet.
pepVet is an R package for proteolytic digest evaluation in proteomics workflows. The project values small, reviewable changes, explicit tests, and documentation that states scope and limitations clearly.
Before you open an issue or pull request
- Search existing issues and pull requests first.
- Use the issue templates when they fit.
- For security-sensitive reports, contact eneskemalergin@gmail.com privately instead of opening a public issue.
Development setup
pepVet depends on Bioconductor packages and uses standard R package tooling. See the README installation section, then install the dev tools:
install.packages(c("devtools", "roxygen2", "testthat", "pkgdown", "lintr"))Clone the repository and load it locally:
devtools::load_all()What to include in a pull request
- A focused change with a clear reason for the change.
- Tests for behavior changes when the code path is testable.
- Documentation updates when the public API, scoring interpretation, or workflow guidance changes.
- Regenerated roxygen output when function signatures or docs change.
Recommended local checks
Run the narrowest relevant checks first, then the broader package checks before opening a PR.
devtools::document()
devtools::test()
devtools::check(document = FALSE, manual = FALSE)
pkgdown::build_site()R CMD check may emit a warning if the external qpdf binary is missing. That is an environment issue, not a package-code failure.
Style expectations
- Keep changes minimal and scoped to the problem.
- Preserve existing naming and table schemas unless the change requires an API update.
- Document scientific limitations directly when adding heuristics or annotations.
- Avoid speculative claims in README, roxygen, or vignettes.
Review notes
- Explain user-visible behavior changes in the pull request description.
- Call out any fixture updates, snapshot updates, or changes to pinned values.
- If a workflow or scoring assumption changes, state whether it is literature-backed, heuristic, or an expert prior.
Community standards
By participating in this project, you agree to follow CODE_OF_CONDUCT.md.