File size: 3,028 Bytes
efd3676 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 | # Various helpers to make up for the fact that the swig wrapper prevents decent integration with any IDE.
# quickly reloads all of CoRC and the copasi backed for development.
# clears the workspace.
# set ´current_example´ to have it ready for testing.
reset_copasi <- function() {
rm(list = ls(envir = .GlobalEnv) %>% .[!(. %in% c("reset_copasi", "current_example", "ls_corc", "inspect"))], envir = .GlobalEnv)
gc()
if (exists("unloadAllModels")) unloadAllModels()
if (exists("clearCustomKineticFunctions")) clearCustomKineticFunctions()
# It seems that sometimes CoRC is randomly loaded already (knitr?).
# If so, load_all will fail due to a locked import environment
# If import env is locked, unload CoRC
if (isNamespaceLoaded("CoRC")) {
import_env <- parent.env(getNamespace("CoRC"))
stopifnot(environmentName(import_env) == "imports:CoRC")
if (environmentIsLocked(import_env))
unloadNamespace("CoRC")
}
pkgload::load_all(reset = FALSE)
examples <- loadExamples()
# current_example is typically defined in global_env
if (exists("current_example"))
setCurrentModel(examples[[current_example]])
assign("c_datamodel", getCurrentModel(), envir = .GlobalEnv)
}
ls_corc <- function(pattern) {ls(pattern = pattern, name = "package:CoRC", all.names = TRUE)}
# inspect swig functions and objects
# e.g.
# c_datamodel <- CRootContainer_addDatamodel()
# c_datamodel %>% inspect()
# c_datamodel$addModel %>% inspect()
inspect <- function(object) {
if (is.function(object)) {
funtext <- object %>% environment() %>% .$f %>% format()
funinfo <- funtext %>% paste0(collapse = "\n") %>% stringr::str_match(stringr::regex("\\n\\s*(?:ans = )?(\\.Call\\(COPASI\\$`?([^,]+)`?,?.*\\))\\n"))
if (!all(is.na(funinfo))) {
cat(
funinfo[,3] %>% stringr::str_sub(8),
funtext[1] %>% stringr::str_sub(11, -2),
"",
funinfo[,3],
funinfo[,2] %>% stringr::str_replace("\\n\\s*", ""),
sep = "\n"
)
} else {
funinfo <- funtext %>% stringr::str_match("^\\s*f <- ((\\w+)__SWIG\\w*)$") %>% na.omit()
cat(
funinfo[1,3],
"",
paste0(funinfo[,2], collapse = "\n"),
sep = "\n"
)
}
} else {
classes <- is(object)
functions <-
classes %>%
map(safely(getMethod, quiet = TRUE), f = "$") %>%
transpose() %>%
.$result
to_keep <- map_lgl(functions, negate(is_null))
classes <- classes[to_keep]
functions <- functions[to_keep]
functions %>%
map(~ {
funtext <- format(.x)
liststart <- stringr::str_which(funtext, "accessorFuns =")
listend <- stringr::str_which(funtext %>% tail(-liststart + 1L), "\\)$")
listtext <- paste0(funtext[seq(liststart, listend[1] + liststart - 1L)], collapse = "\n")
parse(text = paste0(listtext, "\n", "names(accessorFuns)")) %>% eval()
}) %>%
set_names(classes) %>%
{.[length(.):1L]}
}
}
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