R/conditions.R

In bioLeak: Leakage-Safe Modeling and Auditing for Genomic and Clinical Data

# Structured condition constructors for bioLeak ---------------------------------
#
# These use base-R condition construction (no rlang dependency).
# Users can catch specific error categories via:
#   tryCatch(..., bioLeak_input_error = function(e) ...)

#' @keywords internal
.bio_stop <- function(message, class = NULL, ..., call = NULL) {
  cond <- structure(
    class = c(class, "bioLeak_error", "error", "condition"),
    list(message = message, call = call, ...)
  )
  stop(cond)
}

#' @keywords internal
.bio_warn <- function(message, class = NULL, ..., call = NULL) {
  cond <- structure(
    class = c(class, "bioLeak_warning", "warning", "condition"),
    list(message = message, call = call, ...)
  )
  warning(cond)
}

#' @keywords internal
.bio_is_strict <- function() {
  isTRUE(getOption("bioLeak.strict", FALSE))
}

#' @keywords internal
.bio_strict_checks <- function(context = "bioLeak", seed = NULL,
                               nested = FALSE, mode = NA_character_) {
  if (!.bio_is_strict()) return(invisible(NULL))

  if (is.null(seed) || is.na(seed)) {
    .bio_warn(
      sprintf("%s [strict]: No explicit seed provided. Set 'seed' for reproducibility.", context),
      "bioLeak_validation_warning"
    )
  }

  if (isTRUE(nested) && identical(mode, "combined")) {
    .bio_warn(
      sprintf("%s [strict]: nested=TRUE with mode='combined' may produce empty inner folds.", context),
      "bioLeak_validation_warning"
    )
  }

  invisible(NULL)
}

# Condition class taxonomy:
#
# Errors:
#   bioLeak_input_error      — Bad argument type/value/missing
#   bioLeak_column_error     — Missing or invalid metadata column
#   bioLeak_split_error      — Split generation failures
#   bioLeak_overlap_error    — Overlap invariant violations
#   bioLeak_fit_error        — Model fitting failures
#   bioLeak_audit_error      — Audit-specific failures
#   bioLeak_dependency_error — Missing optional package
#
# Warnings:
#   bioLeak_validation_warning — Recipe/workflow leakage guardrail
#   bioLeak_fold_warning       — Fold-level issues
#   bioLeak_fallback_warning   — Fallback behavior triggered