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Merged
dfkapraun merged 13 commits into from
Jan 21, 2026
Merged

tmp directory model compilation #51

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31e6f42
Initial commit for writing temp model fix
tjzurlin Dec 8, 2025
3cbfcab
Use winslash in normalizePath to remove need to grep for windows-spec…
tjzurlin Jan 17, 2026
b029df5
Define source file on which the hash is determined. The original file…
tjzurlin Jan 17, 2026
25da93a
Fix temp directory bug to ensure source file is hashed before model c…
tjzurlin Jan 18, 2026
3bd6047
Don't show warning for creating test directory for running tests in s…
tjzurlin Jan 18, 2026
ad77be5
Run styler
tjzurlin Jan 18, 2026
82ac7ab
Hash the original source file into the right location during the init…
tjzurlin Jan 18, 2026
66e5f48
run styler
tjzurlin Jan 18, 2026
f21d82a
Rebuild package documentation and fix notes following check. 1. Inclu…
tjzurlin Jan 18, 2026
718d07e
Update man/Model-class.Rd
tjzurlin Jan 18, 2026
58b3ce9
Update R/MCSim_model.R
tjzurlin Jan 18, 2026
7cd350f
Document package after fixing typo
tjzurlin Jan 18, 2026
ff41d03
Remove unused file.copied variable when copying source file to model …
tjzurlin Jan 21, 2026
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1 change: 1 addition & 0 deletions .Rbuildignore
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Expand Up @@ -3,6 +3,7 @@
^\.covrignore$
^\.github$
^.*\.Rproj$
^paper$
^\_pkgdown.yml$
.clang-format
README.md
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Expand Up @@ -15,11 +15,11 @@ Imports:
methods,
tools
URL: https://CRAN.R-project.org/package=MCSimMod, https://github.com/USEPA/MCSimMod
License: GPL-3
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
RoxygenNote: 7.3.3
Suggests:
knitr,
rmarkdown,
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34 changes: 27 additions & 7 deletions R/MCSim_model.R
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Expand Up @@ -33,9 +33,10 @@ Model <- setRefClass("Model",
#' @field paths List of character strings that are names of files associated with the model.
#' @field writeTemp Boolean specifying whether to write model files to a temporary directory. If value is TRUE, model files will be written to a temporary directory; if value is FALSE, model files will be written to the same directory that contains the model specification file.
#' @field verboseOutput Boolean specifying whether to write translator messages to standard output. If value is TRUE, messages will be written to standard output; if value is FALSE, messages will be written to files in a temporary directory.
#' @field recompiled Boolean specifying if the model has been recompiled due to change in source file
mName = "character", mString = "character", initParms = "function",
initStates = "function", Outputs = "ANY", parms = "numeric", Y0 = "numeric",
paths = "list", writeTemp = "logical", verboseOutput = "logical"
paths = "list", writeTemp = "logical", verboseOutput = "logical", recompiled = "logical"
),
methods = list(
initialize = function(...) {
Expand All @@ -53,20 +54,25 @@ Model <- setRefClass("Model",
}
file <- tempfile(pattern = "mcsimmod_", fileext = ".model")
writeLines(mString, file)
source_file <- normalizePath(file, winslash = "/")
file <- source_file
} else {
if (writeTemp == TRUE) {
source_file <- normalizePath(paste0(mName, ".model"))
source_file <- normalizePath(paste0(mName, ".model"), winslash = "/")
temp_directory <- tempdir()
file <- file.path(temp_directory, basename(source_file))
file_copied <- file.copy(from = source_file, to = file)
file.copy(from = source_file, to = file)
file <- normalizePath(file, winslash = "/")
} else {
file <- normalizePath(paste0(mName, ".model"))
source_file <- normalizePath(paste0(mName, ".model"), winslash = "/")
file <- source_file
}
}
mList <- .fixPath(file)
sList <- .fixPath(source_file)
mName <<- mList$mName
mPath <- mList$mPath

sPath <- sList$mPath

paths <<- list(
dll_name = paste0(mName, "_model"),
Expand All @@ -75,17 +81,26 @@ Model <- setRefClass("Model",
dll_file = file.path(mPath, paste0(mName, "_model", .Platform$dynlib.ext)),
inits_file = file.path(mPath, paste0(mName, "_model_inits.R")),
model_file = file.path(mPath, paste0(mName, ".model")),
source_file = file.path(sPath, paste0(mName, ".model")),
hash_file = file.path(mPath, paste0(mName, "_model.md5"))
)

# Calculate and save initial hash during initialization
# This allows loadModel to immediately check if source has changed
if (!file.exists(paths$hash_file)) {
initial_hash <- as.character(tools::md5sum(paths$source_file))
write(initial_hash, file = paths$hash_file)
}
},
loadModel = function(force = FALSE) {
"Translate (if necessary) the model specification text to C, compile (if necessary) the resulting C file to create a dynamic link library (DLL) file (on Windows) or a shared object (SO) file (on Unix), and then load all essential information about the Model object into memory (for use in the current R session)."
hash_exists <- file.exists(paths$hash_file)
if (hash_exists) {
hash_has_changed <- .fileHasChanged(paths$model_file, paths$hash_file)
hash_has_changed <- .fileHasChanged(paths$source_file, paths$hash_file)
} else {
hash_has_changed <- TRUE
}
recompiled <<- FALSE

# Conditions for compiling a model:
# 1. The DLL (on Windows) or SO (on Unix) associated with the model
Expand All @@ -98,7 +113,12 @@ Model <- setRefClass("Model",
# specification file has been changed since the last translation and
# compiling.
if (!file.exists(paths$dll_file) | (force) | (!hash_exists) | (hash_exists & hash_has_changed)) {
compileModel(paths$model_file, paths$c_file, paths$dll_name, paths$dll_file, hash_file = paths$hash_file, verbose_output = verboseOutput)
# When using writeTemp=TRUE, ensure the model file is updated from source before compilation
if (writeTemp & (paths$source_file != paths$model_file)) {
file.copy(from = paths$source_file, to = paths$model_file, overwrite = TRUE)
}
compileModel(paths$model_file, paths$c_file, paths$dll_name, paths$dll_file, source_file = paths$source_file, hash_file = paths$hash_file, verbose_output = verboseOutput)
recompiled <<- TRUE
}

# Load the compiled model (DLL).
Expand Down
13 changes: 7 additions & 6 deletions R/compileModel.R
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Expand Up @@ -8,13 +8,14 @@
#' @param c_file Name of a C source code file to be created by compiling the MCSim model specification file.
#' @param dll_name Name of a DLL or SO file without the extension (".dll" or ".so").
#' @param dll_file Name of the same DLL or SO file with the appropriate extension (".dll" or ".so").
#' @param hash_file Name of a file containing a hash key for determining if `model_file` has changed since the previous translation and compilation.
#' @param source_file Name of the original source file to use for hash calculation. Defaults to \code{model_file} for backward compatibility. When \code{writeTemp=TRUE} in \code{createModel()}, this should be set to the original source file path to ensure hash tracking works correctly when the source file is separate from the compiled model file.
#' @param hash_file Name of a file containing a hash key for determining if `source_file` has changed since the previous translation and compilation.
#' @param verbose_output Boolean specifying whether to write translator messages to standard output. If value is TRUE, messages will be written to standard output; if value is FALSE, messages will be written to files in a temporary directory.
#' @returns No return value. Creates files and saves them in locations specified by function arguments.
#' @import tools
#' @useDynLib MCSimMod, .registration=TRUE
#' @export
compileModel <- function(model_file, c_file, dll_name, dll_file, hash_file = NULL, verbose_output = FALSE) {
compileModel <- function(model_file, c_file, dll_name, dll_file, source_file = model_file, hash_file = NULL, verbose_output = FALSE) {
# Unload DLL if it has been loaded.
mList <- .fixPath(model_file)
model_name <- mList$mName
Expand Down Expand Up @@ -120,7 +121,7 @@ compileModel <- function(model_file, c_file, dll_name, dll_file, hash_file = NUL
"event",
"root"
)
for (idx in seq(length(item_to_replace))) {
for (idx in seq_along(item_to_replace)) {
lines <- gsub(
paste0("\\b", item_to_replace[idx], "\\b"),
paste0(item_to_replace[idx], "_", model_name),
Expand Down Expand Up @@ -151,7 +152,7 @@ compileModel <- function(model_file, c_file, dll_name, dll_file, hash_file = NUL
"initStates",
"initState"
)
for (idx in seq(length(item_to_replace))) {
for (idx in seq_along(item_to_replace)) {
lines <- gsub(
paste0("\\b", item_to_replace[idx], "\\b"),
paste0(item_to_replace[idx], "_", model_name),
Expand Down Expand Up @@ -181,10 +182,10 @@ compileModel <- function(model_file, c_file, dll_name, dll_file, hash_file = NUL
normalizePath(out_file), ".\n"
)

# If hash file name was provided, create a hash (md5 sum) for the model file
# If hash file name was provided, create a hash (md5 sum) for the source file
# and print a message about its location.
if (!is.null(hash_file)) {
file_hash <- as.character(md5sum(model_file))
file_hash <- as.character(tools::md5sum(source_file))
write(file_hash, file = hash_file)
message(
"Hash created and saved in the file ", normalizePath(hash_file),
Expand Down
6 changes: 3 additions & 3 deletions R/fileHasChanged.R
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@@ -1,11 +1,11 @@
#-----------------
# compareHash
#----------------
# Private function to determine if the .model file has changed
# Private function to determine if the source .model file has changed

.fileHasChanged <- function(model_file, hash_file) {
.fileHasChanged <- function(source_file, hash_file) {
# Calculate hash for current model file
current_hash <- as.character(md5sum(model_file))
current_hash <- tools::md5sum(source_file)

# Read saved hash
saved_hash <- readLines(hash_file, n = 1)
Expand Down
3 changes: 0 additions & 3 deletions R/fixPath.R
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Expand Up @@ -7,9 +7,6 @@
.fixPath <- function(file) {
new.mName <- strsplit(basename(file), "[.]")[[1]][1]
new.mPath <- dirname(file)
if (.Platform$OS.type == "windows") {
new.mPath <- gsub("\\\\", "/", utils::shortPathName(new.mPath))
}

has_space <- grepl(" ", new.mPath)
if (has_space == T) {
Expand Down
2 changes: 2 additions & 0 deletions man/Model-class.Rd
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5 changes: 4 additions & 1 deletion man/compileModel.Rd
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47 changes: 47 additions & 0 deletions tests/testthat/test-compareHash.R
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Expand Up @@ -22,3 +22,50 @@ testthat::test_that("test_compareHash", {

model$cleanup()
})

testthat::test_that("test_tmp_compileModel", {
# Test writeTemp=TRUE functionality with proper source/compilation file separation
# Create a proper source file in a permanent location (not temp)
source_dir <- file.path(tempdir(), "sourceDir")
dir.create(source_dir, showWarnings = FALSE)
mName <- file.path(source_dir, "test_model")
mString <- readLines(file.path(testthat::test_path(), "data", "exponential.model"))
writeLines(mString, paste0(mName, ".model"))

# Verify source file exists
testthat::expect_true(file.exists(paste0(mName, ".model")))

# Create model with writeTemp=TRUE - this should use the source file
# and create compilation files in temp directory
model <- createModel(mName, writeTemp = TRUE)

# Verify paths are properly separated
testthat::expect_true(model$paths$source_file != model$paths$model_file)
testthat::expect_true(file.exists(model$paths$source_file))
testthat::expect_true(file.exists(model$paths$model_file))

# First load - should compile
model$loadModel()
testthat::expect_true(file.exists(model$paths$hash_file)) # Check if hash was created
testthat::expect_true(model$recompiled) # Should be TRUE on first compile

# Second load - should NOT recompile (no changes)
model$loadModel()
testthat::expect_false(.fileHasChanged(model$paths$source_file, model$paths$hash_file))
testthat::expect_false(model$recompiled) # Should be FALSE, no recompile needed

# Edit source file (what users actually edit)
write("# File is edited", file = model$paths$source_file, append = TRUE, sep = "\n")
testthat::expect_true(.fileHasChanged(model$paths$source_file, model$paths$hash_file))

# Third load after edit - should recompile
model$loadModel()
testthat::expect_true(model$recompiled) # Should be TRUE, source changed

# Fourth load - should NOT recompile (our bug fix test!)
model$loadModel()
testthat::expect_false(.fileHasChanged(model$paths$source_file, model$paths$hash_file))
testthat::expect_false(model$recompiled) # Should be FALSE, hash should now match

model$cleanup()
})
2 changes: 1 addition & 1 deletion tests/testthat/test-sim.R
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Expand Up @@ -45,7 +45,7 @@ testthat::test_that("Model$absoluteModel", {
# Use absolute path of temp directory,
# Test to make sure changing the file returns a changed path

dir.create(file.path(tempdir(), "testDir"))
dir.create(file.path(tempdir(), "testDir"), showWarnings = FALSE)
mName <- tempfile(pattern = "mcsimmod_", tmpdir = file.path(tempdir(), "testDir"))
mString <- readLines(file.path(testthat::test_path(), "data", "exponential.model"))
writeLines(mString, paste0(mName, ".model"))
Expand Down