From 4845369cdf66cdfded08f38f669a75a40b1000e3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rok=20=C4=8Ce=C5=A1novar?= <rok.cesnovar@fri.uni-lj.si>
Date: Thu, 16 Jan 2020 14:09:31 +0100
Subject: [PATCH 1/3] Revert "Switch back to using Rdata temporarily while
 issue with 0x0s gets resolved for JSON"

---
 DESCRIPTION                      | 2 +-
 R/model.R                        | 4 ++--
 tests/testthat/test-fit-shared.R | 6 +++---
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6299c0823..8092c55ba 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -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: 
diff --git a/R/model.R b/R/model.R
index 9d9f12005..6ba91ab3c 100644
--- a/R/model.R
+++ b/R/model.R
@@ -664,8 +664,8 @@ 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))
+    path <- tempfile(pattern = "standata-", fileext = ".json")
+    write_stan_json(data = data, file = path)
   } else {
     stop("'data' should be a path or a named list.", call. = FALSE)
   }
diff --git a/tests/testthat/test-fit-shared.R b/tests/testthat/test-fit-shared.R
index 8d6ba591e..67c301696 100644
--- a/tests/testthat/test-fit-shared.R
+++ b/tests/testthat/test-fit-shared.R
@@ -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)

From f2f4843ae9b91377a4cc2b876db534e9536afe83 Mon Sep 17 00:00:00 2001
From: rok-cesnovar <rok.cesnovar@fri.uni-lj.si>
Date: Mon, 3 Feb 2020 09:58:50 +0100
Subject: [PATCH 2/3] use json by default only if version of cmdstan is 2.22+

---
 R/model.R | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/R/model.R b/R/model.R
index 6ba91ab3c..e7859a1c6 100644
--- a/R/model.R
+++ b/R/model.R
@@ -664,8 +664,13 @@ 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 = ".json")
-    write_stan_json(data = data, file = path)
+    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")
+      rstan::stan_rdump(names(data), file = path, env = list2env(data))
+    }
   } else {
     stop("'data' should be a path or a named list.", call. = FALSE)
   }

From 856285ebb370ecc37f25584dde805328a79a87e9 Mon Sep 17 00:00:00 2001
From: rok-cesnovar <rok.cesnovar@fri.uni-lj.si>
Date: Mon, 17 Feb 2020 20:06:07 +0100
Subject: [PATCH 3/3] add rstan check before using stan_rdump

---
 R/model.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/model.R b/R/model.R
index e7859a1c6..4f9ca3f36 100644
--- a/R/model.R
+++ b/R/model.R
@@ -669,6 +669,9 @@ process_data <- function(data) {
       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 {