Refactor contrast parsing to support either "comparison + blocking_factors" or "formula + make_contrasts_str"

[atrigila]

validatefomcomponents always required a required comparison (variable, reference, target) even when a formula and make_contrasts_str were supplied. This was because the internal TSV structure expected variable, reference, and target column.

The changes introduced here aim to:

1. Remove automatic blocking inference from formula
2. The YAML contrast must specify blocking_factors if needed; otherwise blocking is NA.
3. variable, reference, and target are validated only when comparison is provided, not when formula is used.
4. Add a test case for YAML with testthat.

[pinin4fjords]

Maybe it would be simpler to initialise the frame and then set the values? Also think we can be a little less verbose.

# Parse YAML contrasts into a data frame
contrasts <- do.call(rbind, lapply(contrasts_yaml$contrasts, function(x) {
  stopifnot(!is.null(x$id))  # Require that each contrast has an 'id'

  # --- Start with a data frame with all fields set to NA ---
  row <- data.frame(
    id = x$id,
    variable = NA, reference = NA, target = NA,
    blocking = NA,
    formula = NA,
    make_contrasts_str = NA,
    stringsAsFactors = FALSE
  )

  if (!is.null(x$comparison)) {
    # --- 'comparison'-based contrast ---
    if (!is.null(x$formula) || !is.null(x$make_contrasts_str)) {
      stop(sprintf("Contrast id '%s' with 'comparison' must not have 'formula' or 'make_contrasts_str'.", x$id))
    }

    fields <- setNames(rep(NA, 3), c("variable", "reference", "target"))
    fields[names(fields)[seq_along(x$comparison)]] <- x$comparison

    if (any(is.na(fields)) || any(fields == "")) {
      stop(sprintf("Contrast id '%s' must provide non-empty 'variable', 'reference', and 'target' fields.", x$id))
    }

    row$variable <- fields["variable"]
    row$reference <- fields["reference"]
    row$target <- fields["target"]

    if (!is.null(x$blocking_factors)) {
      row$blocking <- paste(x$blocking_factors, collapse = ";")
    }

  } else if (!is.null(x$formula)) {
    # --- 'formula'-based contrast ---
    if (is.null(x$make_contrasts_str) || !is.null(x$blocking_factors)) {
      stop(sprintf("Contrast id '%s' with 'formula' must have 'make_contrasts_str' and no 'blocking_factors'.", x$id))
    }

    row$formula <- x$formula
    row$make_contrasts_str <- x$make_contrasts_str

  } else {
    stop(sprintf("Contrast id '%s' must provide either 'comparison' or 'formula' + 'make_contrasts_str'.", x$id))
  }

  row
}))

[pinin4fjords]

This is still draft. Good to go?

[atrigila]

Yes, thank you!

[pinin4fjords]

bioconda/bioconda-recipes#55859