Contributing to misha

First-time setup

After cloning, install the repo’s git hooks (one-time, per clone):

tools/install-hooks.sh

This wires up:

  • pre-commit — runs styler on staged R files (matches the CI style pass) and refuses to commit anything under dev/.
  • pre-push — runs pkgbuild::compile_dll() when pushed commits touch src/, and devtools::document() when they touch R/ (aborts the push if the regenerated man/ or NAMESPACE differ from what’s committed).

Branch naming

  • fix/... — bug fixes
  • feat/... — new features
  • refactor/... — code restructuring without behavior change
  • docs/... — documentation only
  • test/... — tests only

Tests

The full test suite is run on the Tanay Lab cluster (some tests require cluster-only data and resources). For external contributions, run the subset relevant to your change locally and rely on CI for the rest.

# run a single test file
testthat::test_file("tests/testthat/test-foo.R")

# run everything available locally, in parallel (some tests will skip
# without cluster-only data)
Sys.setenv(TESTTHAT_PARALLEL = "TRUE")
devtools::test()

GitHub Actions runs R CMD check on every push and PR — treat that as the authoritative signal.

Other dev commands

Compile after C++ changes:

pkgbuild::compile_dll(debug = FALSE)

Regenerate documentation:

devtools::document()