Add lint CI workflow and clean up package lints - #1117
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Adds .github/workflows/lint.yaml running lintr::lint_package() with LINTR_ERROR_ON_LINT=true on pushes to main and pull requests. The lint gate covers package code in R/; tests, inst, vignettes, and generated files are excluded for now. High-violation style linters are disabled in .lintr with counts so they can be ratcheted down later. Fixes applied across R/: trailing whitespace, compound semicolons split into statements, spaces inside/before parentheses, T/F expanded to TRUE/FALSE, = and -> assignments converted to <-, and targeted nolint tags for deliberate names (ggplot2 conventions, C-name mirrors, checkmate-style .var.name arguments) and known-complex functions. Also fixes a real bug found by the linter: attr(rxUiGet.thetaUpper, "desc") used -> instead of <-, so the desc attribute was never set and a stray thetaUpper variable was created in the namespace. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Summary
.github/workflows/lint.yaml: runslintr::lint_package()on pushes tomainand on pull requests, failing the job on any lint (LINTR_ERROR_ON_LINT=true). Matches the setup style ofR-CMD-check.yaml(installs the package plus the nlmixr2 GitHub dependencies soobject_usage-style linters could be enabled later).lintr::lint_package()).Lint configuration (
.lintr)The package had ~11,000 lints, most of which cannot be mechanically fixed (3,548 are object names that would require renaming exported API). Following the existing precedent in
.lintrof disabling high-count linters with their violation counts:R/;tests/,inst/,vignettes/, and generated files (RcppExports.R,rxrandomui.R,parseFuns.R,rxSyntaxFunctions.R,rxode2_md5.R,dfIni.R) are excluded for now.return_linter(533; codebase style is explicitreturn()),indentation(292),commented_code(147),line_length(112),object_usage(NSE/symengine false positives),brace(78)..var.name,..lhsenv-protocol names), snake_case S3 methods for other packages' generics (as_tibble.rxEt), and initial-caps names (ggproto objects,RxODE, math notation like.J).cyclocomp(160)andobject_length(45)caps with targeted# nolinttags on the handful of existing outliers.Fixes applied (
R/, 44 files)All position-driven from lintr output (never blind regex over strings), each file parse-verified before writing:
a; bstatements onto separate linesT/FtoTRUE/FALSE=and right-assign (->) statements to<-Bug fix found by the linter
attr(rxUiGet.thetaUpper, "desc") -> "thetaUpper"(note->) assigned the attribute's value (NULL) to a straythetaUppervariable instead of setting thedescattribute; every sibling uses<-. Fixed and noted inNEWS.md.Testing
lintr::lint_package(): 0 lintsdevtools::test(filter='basic'): 49 pass / 0 fail / 0 warn🤖 Generated with Claude Code