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Merged
novica merged 1 commit into from
Oct 20, 2026
Merged

feat: use cli for messages, warnings and errors #64

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1 change: 1 addition & 0 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ Imports:
graphics,
lhs,
patchwork,
rlang,
stats,
utils
Suggests:
Expand Down
113 changes: 69 additions & 44 deletions R/SmallFuncs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -34,9 +34,10 @@ randParams <- function(boundsDT, rPoints, FAIL = TRUE) {
}

if (attempt >= 100 && FAIL) {
stop(
"Latin Hypercube Sampling could not produce the required distinct parameter sets. \nTry decreasing gsPoints or initPoints."
)
cli::cli_abort(c(
"Latin Hypercube Sampling could not produce the required distinct parameter sets.",
i = "Try decreasing {.arg gsPoints} or {.arg initPoints}."
))
}

attempt <- attempt + 1
Expand Down Expand Up @@ -88,7 +89,7 @@ zeroOneScale <- function(vec) {
# If the scoring function returned the same results
# this results in the function a vector of 1s.
if (r == 0) {
stop("Results from FUN have 0 variance, cannot build GP.")
cli::cli_abort("Results from {.fn FUN} have 0 variance, cannot build GP.")
}

vec <- (vec - min(vec)) / r
Expand Down Expand Up @@ -122,17 +123,15 @@ saveSoFar <- function(optObj, verbose) {
{
suppressWarnings(saveRDS(optObj, file = optObj$saveFile))
if (verbose > 0) {
cat(
" 4) Saving Intermediary Results to: \n ",
optObj$saveFile,
"\n"
)
cli::cli_inform(c(
" " = "4) Saved intermediary results to {.file {optObj$saveFile}}."
))
}
},
error = function(e) {
if (verbose > 0) {
cat(cli::col_red(
" 4) Failed to save intermediary results. Please check file path.\n"
cli::cli_inform(c(
x = "4) Failed to save intermediary results. Please check file path."
))
}
}
Expand Down Expand Up @@ -176,63 +175,86 @@ checkParameters <- function(
errorHandling,
plotProgress,
parallel,
verbose
verbose,
call = rlang::caller_env()
) {
if (iters.n < iters.k) {
stop(
"iters.n cannot be less than iters.k. See ?bayesOpt for parameter definitions."
cli::cli_abort(
c(
"{.arg iters.n} cannot be less than {.arg iters.k}.",
i = "See {.help [?bayesOpt](ParBayesianOptimization::bayesOpt)} for parameter definitions."
),
call = call
)
}
if (iters.n %% 1 != 0 || iters.k %% 1 != 0) {
stop("iters.n and iters.k must be integers.")
cli::cli_abort(
"{.arg iters.n} and {.arg iters.k} must be integers.",
call = call
)
}
if (
!is.character(acq) ||
length(acq) != 1 ||
!acq %in% c("ucb", "ei", "eips", "poi")
) {
stop(
"Acquisition function not recognized. ",
"acq must be one of \"ucb\", \"ei\", \"eips\" or \"poi\"."
cli::cli_abort(
c(
"Acquisition function not recognized.",
i = "{.arg acq} must be one of {.or {.val {c('ucb', 'ei', 'eips', 'poi')}}}."
),
call = call
)
}
if (parallel && (getDoParWorkers() == 1)) {
stop("parallel is set to TRUE but no back end is registered.\n")
cli::cli_abort(
"{.arg parallel} is set to TRUE but no back end is registered.",
call = call
)
}
if (!parallel && getDoParWorkers() > 1 && verbose > 0) {
message(
"parallel back end is registered, but parallel is set to false. Process will not be run in parallel."
cli::cli_inform(
"A parallel back end is registered, but {.arg parallel} is FALSE. Process will not be run in parallel."
)
}
if (!all(names(otherHalting) %in% c("timeLimit", "minUtility"))) {
stop(
"otherHalting element not recognized. Must be one of timeLimit and minUtility."
cli::cli_abort(
c(
"{.arg otherHalting} element not recognized.",
i = "Must be one of {.val timeLimit} and {.val minUtility}."
),
call = call
)
}
if (!inherits(x = bounds, what = "list")) {
stop(
"bounds must be a list of parameter bounds with the same arguments as FUN."
cli::cli_abort(
"{.arg bounds} must be a list of parameter bounds with the same arguments as {.fn FUN}.",
call = call
)
}
if (any(lengths(bounds) != 2)) {
stop("Not all elements in bounds are length 2.")
cli::cli_abort(
"Not all elements in {.arg bounds} are length 2.",
call = call
)
}
if (acqThresh > 1 || acqThresh < 0) {
stop("acqThresh must be in [0,1]")
cli::cli_abort("{.arg acqThresh} must be in [0,1].", call = call)
}
if (!is.logical(plotProgress)) {
stop("plotProgress must be logical")
cli::cli_abort("{.arg plotProgress} must be logical.", call = call)
}
if (!errorHandling %in% c("stop", "continue") && !is.numeric(errorHandling)) {
stop(
"errorHandling is malformed: Must be one of 'stop', 'continue', or an integer."
cli::cli_abort(
"{.arg errorHandling} is malformed: Must be one of {.val stop}, {.val continue}, or an integer.",
call = call
)
}
}

# Arguments in ... are passed to DiceKriging::km(). Catch misspelled or
# unsupported names before FUN runs, instead of when the GP is fitted.
checkKmArgs <- function(...) {
checkKmArgs <- function(..., call = rlang::caller_env()) {
argNames <- names(list(...))
if (is.null(argNames) && ...length() > 0) {
argNames <- rep("", ...length())
Expand All @@ -249,19 +271,22 @@ checkKmArgs <- function(...) {
!is.na(pmatch(argNames, kmArgs, duplicates.ok = TRUE)) &
argNames != ""
if (any(collides)) {
stop(
"Arguments in ... match a DiceKriging::km() argument that is already ",
"supplied or set by updateGP() (design, response, control): ",
paste(argNames[collides], collapse = ", ")
cli::cli_abort(
c(
"Arguments in {.arg ...} match a {.fn DiceKriging::km} argument that is already supplied or set by {.fn updateGP} (design, response, control): {argNames[collides]}."
),
call = call
)
}
bad <- argNames[unmatched]
if (length(bad) > 0) {
bad[bad == ""] <- "<unnamed>"
stop(
"Arguments in ... are passed to DiceKriging::km(), which does not accept: ",
paste(bad, collapse = ", "),
". Check for misspelled arguments."
cli::cli_abort(
c(
"Arguments in {.arg ...} are passed to {.fn DiceKriging::km}, which does not accept: {bad}.",
i = "Check for misspelled arguments."
),
call = call
)
}
}
Expand All @@ -282,10 +307,6 @@ formatOtherHalting <- function(otherHalting) {
return(otherHalting)
}

# When the process stops early it will print this color.
# Built on each call so it uses the colours of the current terminal.
returnEarly <- function(...) cli::make_ansi_style("#FF6200")(...)

# Constructor for stopEarlyMsg class.
makeStopEarlyMessage <- function(msg) {
class(msg) <- "stopEarlyMsg"
Expand All @@ -294,9 +315,13 @@ makeStopEarlyMessage <- function(msg) {

# Multiple places the process can stop early. This just prints the message.
printStopStatus <- function(optObj, verbose) {
if (verbose > 0) cat(returnEarly("\n", optObj$stopStatus, "\n"))
if (verbose > 0) cli::cli_inform(c("!" = "{unclass(optObj$stopStatus)}"))
}

# Printed lines of a table. Messages built from them keep the table layout,
# which cli formatting would collapse.
tableLines <- function(tbl, ...) capture.output(print(tbl, ...))

# Combining function for foreach. Allows the return of message without scores.
rbindFE <- function(...) rbind(..., fill = TRUE)

Expand Down
87 changes: 39 additions & 48 deletions R/addIterations.R
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ addIterations <- function(
) {
startT <- Sys.time()
if (!inherits(x = optObj, what = "bayesOpt")) {
stop("optObj must be of class bayesOpt")
cli::cli_abort("{.arg optObj} must be of class {.cls bayesOpt}.")
}

# Check the parameters
Expand Down Expand Up @@ -119,13 +119,8 @@ addIterations <- function(
scoreSummary$inBounds <- as.logical(apply(inBounds, 1, prod))
if (!all(scoreSummary$inBounds)) {
nOut <- sum(!scoreSummary$inBounds)
warning(
cli::format_inline(
"Bounds have been tightened. {nOut} parameter set{?s} in ",
"scoreSummary {?is/are} outside the new bounds and will be ignored ",
"this round."
),
call. = FALSE
cli::cli_warn(
"Bounds have been tightened. {nOut} parameter set{?s} in scoreSummary {?is/are} outside the new bounds and will be ignored this round."
)
}
# updateGP() fits only on rows flagged inBounds, so store the new flags and
Expand All @@ -135,10 +130,10 @@ addIterations <- function(
optObj$GauProList$gpUpToDate <- FALSE
}
if (sum(scoreSummary$inBounds & is.na(scoreSummary$errorMessage)) <= 2) {
stop(
"Not enough samples in scoreSummary to perform optimizations. ",
"At least 3 error-free samples within bounds are needed."
)
cli::cli_abort(c(
"Not enough samples in scoreSummary to perform optimizations.",
i = "At least 3 error-free samples within bounds are needed."
))
}

# Output from FUN is sunk into a temporary file.
Expand All @@ -159,15 +154,15 @@ addIterations <- function(
Epoch <- Epoch + 1

if (verbose > 0) {
cat("\nStarting Epoch", Epoch, "\n")
cli::cli_inform("Starting Epoch {Epoch}")
}

# How many runs to make this session
runNew <- pmin(iters.t - nrow(scoreSummary), iters.k)

# Fit GP
if (verbose > 0) {
cat(" 1) Fitting Gaussian Process...\n")
cli::cli_inform(c(" " = "1) Fitting Gaussian Process..."))
}
optObj <- updateGP(optObj, bounds = bounds, verbose = 0, ...)

Expand All @@ -180,9 +175,6 @@ addIterations <- function(
}

# Find local optimums of the acquisition function
if (verbose > 0) {
cat(" 2) Running local optimum search...")
}
tm <- system.time({
LocalOptims <- getLocalOptimums(
optObj,
Expand All @@ -192,7 +184,7 @@ addIterations <- function(
)
})[[3]]
if (verbose > 0) {
cat(" ", tm, "seconds\n")
cli::cli_inform(c(" " = "2) Ran local optimum search: {tm} seconds."))
}

# Should we continue?
Expand Down Expand Up @@ -240,15 +232,6 @@ addIterations <- function(

# Try to run the scoring function. If not all (but at least 1) new runs fail,
# then foreach cannot call rbind correctly, and an error is thrown.
if (verbose > 0) {
cat(
" 3) Running FUN",
nrow(nextPars),
"times in",
Workers,
"thread(s)..."
)
}
sink(file = sinkFile)
tm <- system.time({
NewResults <- foreach(
Expand Down Expand Up @@ -321,35 +304,43 @@ addIterations <- function(
)

if (verbose > 0) {
cat(" ", tm, "seconds\n")
cli::cli_inform(c(
" " = "3) Ran {.fn FUN} {nrow(nextPars)} time{?s} in {Workers} thread{?s}: {tm} seconds."
))
}

# Print updates on parameter-score search
if (verbose > 1) {
cat("\nResults from most recent parameter scoring:\n")
print(NewResults, row.names = FALSE)
# Plain message() keeps the table layout.
message(paste(
c(
"Results from most recent parameter scoring:",
tableLines(NewResults, row.names = FALSE)
),
collapse = "\n"
))

if (max(NewResults$Score) > max(scoreSummary$Score)) {
cat("\nNew best parameter set found:\n")
print(
NewResults[
which.max(get("Score")),
c(boundsDT$N, "Score"),
with = FALSE
],
row.names = FALSE
)
bestHeading <- "New best parameter set found:"
bestFrom <- NewResults
} else {
cat("\nMaximum score was not raised this round. Best score is still:\n")
print(
scoreSummary[
which.max(get("Score")),
c(boundsDT$N, "Score"),
with = FALSE
],
row.names = FALSE
)
bestHeading <- "Maximum score was not raised this round. Best score is still:"
bestFrom <- scoreSummary
}
message(paste(
c(
bestHeading,
tableLines(
bestFrom[
which.max(get("Score")),
c(boundsDT$N, "Score"),
with = FALSE
],
row.names = FALSE
)
),
collapse = "\n"
))
}

# Keep track of performance.
Expand Down
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