Contributing to neuroatlas • neuroatlas

Report bugs or propose changes through GitHub issues. Include a small reproducible example, sessionInfo(), and the atlas/template identifiers. Describe the intended behavior and any download or optional-package requirements.

Work on a branch and submit a pull request against the repository’s default branch. Read AGENTS.md and the instructions for the directories you change. Use two-space indentation, snake_case function names, and synthetic atlas helpers in unit tests. Keep changes scoped and document every exported function with roxygen2, including return values and a short example. Generate documentation with devtools::document(); do not edit NAMESPACE or man/ by hand.

The repository’s .lintr profile checks maintained R code for formatting and correctness. Function names use snake_case, with UpperCamelCase constructors and the existing MNI conversion functions accepted. Established public argument names and mathematical local variables are preserved. The 80-column target excludes string contents so URLs and diagnostic text keep their values. Both supported pipe forms and explicit or implicit returns are accepted. Short single-line guards follow existing package conventions. There is no project rule limiting identifier length or cyclomatic complexity; review complex changes with their tests and numerical evidence. Downloaded libraries, generated websites and frozen qualification snapshots are excluded so their bytes and historical results remain intact. New maintained source is checked under the same profile as existing code.

The project CI lint gate covers package, test and vignette code. Data builders and scientific qualification protocols have their own dependency environments and execution checks. Run Rscript .github/scripts/lint.R to reproduce the CI gate. The OS matrix, generated documentation, package check, website and coverage measurement are required. rOpenSci diagnostics remain visible for review; branch naming and complexity recommendations do not determine the project gate.

Install development dependencies from DESCRIPTION. The reproducible surface engine setup and machine-specific build receipts are described in plans/resume-neuroatlas.md. New runtime dependencies or architectural changes should be discussed in an issue first.

Run these checks before submitting:

devtools::document()
devtools::test(stop_on_failure = TRUE)
devtools::check(manual = TRUE)

Load the package with devtools::load_all() before running an individual testthat::test_file(). Network and slow integration tests must use skip_on_cran() and opt-in fixtures where appropriate. Report warnings, skips and unavailable checks explicitly. Do not count a skipped check as a pass.

Template mappings need exact input identities, immutable checksums, declared direction and data semantics, and independent numerical qualification. Freeze acceptance thresholds before evaluating candidates. Preserve failed evidence; do not widen thresholds to make an existing candidate pass. Interpolation agreement does not establish anatomical accuracy, an inverse, or conservation. Follow the licenses of externally downloaded inputs separately from this package’s code license.

Mote’s Git-tracked .mote/ops/ history is the shared work board. Set a distinct actor, inspect mote board, and claim/reserve the bounded task before editing. Do not run mote init in this repository. Commit and push relevant Mote operations with the code, and release claims/reservations when handing work off.