Update for CppODE

simonbeyer1 · simonbeyer1 · commit c961adb7940c · 2026-01-14T12:21:39.000+01:00
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -38,7 +38,7 @@ Imports:
     reticulate,
     BH
 Remotes:
-    simonbeyer1/CppODE@v1.0.0
+    simonbeyer1/CppODE
 Suggests:
     MASS,
     pander,
diff --git a/NAMESPACE b/NAMESPACE
@@ -288,7 +288,6 @@ import(data.table)
 import(ggplot2)
 import(parallel)
 import(stringr)
-importFrom(CppODE,ensurePythonEnv)
 importFrom(CppODE,funCpp)
 importFrom(abind,abind)
 importFrom(data.table,as.data.table)
diff --git a/R/classes.R b/R/classes.R
@@ -143,14 +143,14 @@ odemodel <- function(f, deriv = TRUE, deriv2 = FALSE, forcings=NULL, events = NU
     if (length(unsupported) > 0) {
       warning(sprintf("The following arguments are not (yet) supported by the solver 'boost::rosenbrock4' and will be ignored: %s", paste(unsupported, collapse = ", ")), call. = FALSE)
     }
-    func <- CppODE::CppODE(f, events = events, fixed = fixed, modelname = modelname, deriv = FALSE, verbose = verbose, ...)
+    func <- CppODE::CppODE(f, events = events, fixed = fixed, modelname = modelname, outdir = getwd(), deriv = FALSE, verbose = verbose, ...)
     extended <- NULL
     extended2 <- NULL
     if (!deriv2 & deriv) {
-      extended <- CppODE::CppODE(f, events = events, fixed = fixed, modelname = paste0(modelname, "_s"), deriv = TRUE, verbose = verbose, ...)
+      extended <- CppODE::CppODE(f, events = events, fixed = fixed, modelname = paste0(modelname, "_s"), outdir = getwd(), deriv = TRUE, verbose = verbose, ...)
     } else if (deriv2 & deriv) {
-      extended <- CppODE::CppODE(f, events = events, fixed = fixed, modelname = paste0(modelname, "_s"), deriv = TRUE, verbose = verbose, ...)
-      extended2 <- CppODE::CppODE(f, events = events, fixed = fixed, modelname = paste0(modelname, "_s2"), deriv = TRUE, deriv2 = TRUE, verbose = verbose, ...)
+      extended <- CppODE::CppODE(f, events = events, fixed = fixed, modelname = paste0(modelname, "_s"), outdir = getwd(), deriv = TRUE, verbose = verbose, ...)
+      extended2 <- CppODE::CppODE(f, events = events, fixed = fixed, modelname = paste0(modelname, "_s2"), outdir = getwd(), deriv = TRUE, deriv2 = TRUE, verbose = verbose, ...)
     }
     out <- list(func = func, extended = extended, extended2 = extended2)
     class(out) <- c("boost", "odemodel")
diff --git a/R/parameters.R b/R/parameters.R
@@ -270,6 +270,7 @@ Pexpl <- function(trafo,
       fixed      = fixed,
       compile    = compile,
       modelname  = modelname,
+      outdir = getwd(),
       verbose    = verbose,
       convenient = FALSE,
       deriv      = deriv,
@@ -817,6 +818,7 @@ Pimpl <- function(x,
       fixed      = fixed,
       compile    = compile,
       modelname  = modelname,
+      outdir = getwd(),
       verbose    = verbose,
       convenient = FALSE,
       deriv      = TRUE,  # Always need Jacobian for nleqslv
diff --git a/R/prediction.R b/R/prediction.R
@@ -732,6 +732,7 @@ Y <- function(g, f = NULL, states = NULL, parameters = NULL, condition = NULL,
     parameters = obsParams,
     compile    = compile,
     modelname  = modelname,
+    outdir = getwd(),
     verbose    = verbose,
     convenient = FALSE,
     warnings   = FALSE,
diff --git a/R/steadyStates.R b/R/steadyStates.R
@@ -30,12 +30,9 @@
 #'   
 #' @export
 #' @importFrom utils write.table
-#' @importFrom CppODE ensurePythonEnv
 #' @example inst/examples/steadystates.R
 steadyStates <- function(model, file=NULL, rates = NULL, forcings = NULL, givenCQs = NULL, neglect=NULL, sparsifyLevel = 2, outputFormat = "R", testSteady = "T", resolve = TRUE) {
   
-  CppODE::ensurePythonEnv(envname = "dMod")
-  
   # Check if model is an equation list
   if (inherits(model, "eqnlist")) {
     if(is.null(file)) file <- "reactions_for_Alyssa"
