Skip to content

With Cmdstan 2.22+ use JSON by default #110

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jgabry merged 5 commits into from
Feb 17, 2020
Merged

With Cmdstan 2.22+ use JSON by default #110

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
4845369
Revert "Switch back to using Rdata temporarily while issue with 0x0s …
rok-cesnovar Jan 16, 2020
42f34d5
Merge branch 'master' into revert-100-stan_rdump
rok-cesnovar Jan 21, 2020
f2f4843
use json by default only if version of cmdstan is 2.22+
rok-cesnovar Feb 3, 2020
5f8e59a
Merge branch 'master' into revert-100-stan_rdump
rok-cesnovar Feb 10, 2020
856285e
add rstan check before using stan_rdump
rok-cesnovar Feb 17, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,12 +24,12 @@ Imports:
checkmate,
posterior (>= 0.0.1),
processx,
rstan,
R6
Suggests:
jsonlite (>= 1.2.0),
knitr,
rmarkdown,
rstan,
testthat (>= 2.1.0)
VignetteBuilder: knitr
Remotes:
Expand Down
12 changes: 10 additions & 2 deletions R/model.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -664,8 +664,16 @@ process_data <- function(data) {
} else if (is.character(data)) {
path <- absolute_path(data)
} else if (is.list(data) && !is.data.frame(data)) {
path <- tempfile(pattern = "standata-", fileext = ".dat")
rstan::stan_rdump(names(data), file = path, env = list2env(data))
if (cmdstan_version() >= "2.22") {
path <- tempfile(pattern = "standata-", fileext = ".json")
write_stan_json(data = data, file = path)
} else {
path <- tempfile(pattern = "standata-", fileext = ".dat")
if (!requireNamespace("rstan", quietly = TRUE)) {
stop("For CmdStan < 2.22 the rstan package is required for writing data.")
}
rstan::stan_rdump(names(data), file = path, env = list2env(data))
}
} else {
stop("'data' should be a path or a named list.", call. = FALSE)
}
Expand Down
6 changes: 3 additions & 3 deletions tests/testthat/test-fit-shared.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -96,16 +96,16 @@ test_that("saving data file works", {
for (method in all_methods) {
fit <- fits[[method]]
old_path <- fit$data_file()
checkmate::expect_file_exists(old_path, extension = "dat")
checkmate::expect_file_exists(old_path, extension = "json")

expect_message(
path <- fit$save_data_file(tempdir(), basename = NULL,
timestamp = FALSE, random = FALSE),
"Moved data file and set internal path"
)
checkmate::expect_file_exists(path, extension = "dat")
checkmate::expect_file_exists(path, extension = "json")
expect_true(file.size(path) > 0)
expect_equal(basename(path), "logistic.dat")
expect_equal(basename(path), "logistic.json")

expect_false(file.exists(old_path))
expect_equal(fit$data_file(), path)
Expand Down