compile creates missing directories (#119)

* compile function creates missing directories
Genentech · Mar 17, 2023 · edd83f3 · edd83f3
1 parent f894d68
commit edd83f3
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Showing 9 changed files with 70 additions and 15 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -16,6 +16,7 @@ export(SurvivalModel)
 export(SurvivalWeibullPH)
 export(as_stan_data)
 export(as_vcov)
+export(compileStanModel)
 export(link_gsf_abstract)
 export(link_gsf_dsld)
 export(link_gsf_ttg)
@@ -36,6 +37,7 @@ export(sld)
 exportMethods(as.StanModule)
 exportMethods(as.character)
 exportMethods(as.list)
+exportMethods(compileStanModel)
 exportMethods(getInits)
 exportMethods(merge)
 exportMethods(show)

diff --git a/R/generics.R b/R/generics.R
@@ -1,5 +1,7 @@
 
-
+# "missing" = no argument provided
+# "NULL" = explicit NULL
+setClassUnion("empty", c("missing", "NULL"))
 
 setGeneric(
     name = "merge",
@@ -16,6 +18,7 @@ setGeneric(
     def = function(x, file_path) standardGeneric("write_stan")
 )
 
+#' @export
 setGeneric(
     name = "compileStanModel",
     def = function(object, exe_file) standardGeneric("compileStanModel")

diff --git a/R/joint_model.R b/R/joint_model.R
@@ -69,19 +69,14 @@ setMethod(
 setMethod(
     f = "compileStanModel",
     signature = "JointModel",
-    definition = function(object, exe_file = NULL) {
-        if (is.null(exe_file)) {
-            exe_file = file.path(tempdir(), "model")
-        }
-        x <- cmdstanr::cmdstan_model(
-            stan_file = cmdstanr::write_stan_file(as.character(object)),
-            exe_file = exe_file
-        )
+    definition = function(object, exe_file) {
+        x <- compileStanModel(object@stan, exe_file)
         invisible(x)
     }
 )
 
 
+
 setMethod(
     f = "sampleStanModel",
     signature = "JointModel",

diff --git a/R/stan_module.R b/R/stan_module.R
@@ -131,6 +131,34 @@ setMethod(
 )
 
 
+#' @export
+setMethod(
+    f = "compileStanModel",
+    signature = signature(object = "StanModule", exe_file = "character"),
+    definition = function(object, exe_file) {
+        if (!dir.exists(dirname(exe_file))) {
+            dir.create(dirname(exe_file), recursive = TRUE)
+        }
+        x <- cmdstanr::cmdstan_model(
+            stan_file = cmdstanr::write_stan_file(as.character(object)),
+            exe_file = exe_file
+        )
+        invisible(x)
+    }
+)
+
+
+#' @export
+setMethod(
+    f = "compileStanModel",
+    signature = signature(object = "StanModule", exe_file = "empty"),
+    definition = function(object, exe_file) {
+        exe_file <- file.path(tempdir(), "model")
+        invisible(compileStanModel(object, exe_file))
+    }
+)
+
+
 
 
 

diff --git a/misc/example_of_use.R b/misc/example_of_use.R
@@ -109,7 +109,6 @@ stan_data <- as_stan_data(dat_os, dat_lm, ~ cov_cat + cov_cont)
 
 ## Sample from JointModel
 
-dir.create(path = file.path("local"), showWarnings = FALSE)
 mp <- sampleStanModel(
     jm,
     data = stan_data,

diff --git a/misc/tests/gsf-no-link.R b/misc/tests/gsf-no-link.R
@@ -123,7 +123,6 @@ stan_data$Times
 
 ## Sample from JointModel
 
-dir.create(path = file.path("local"), showWarnings = FALSE)
 mp <- sampleStanModel(
     jm,
     data = stan_data,

diff --git a/misc/tests/gsf-with-link.R b/misc/tests/gsf-with-link.R
@@ -118,7 +118,6 @@ stan_data$Times
 
 ## Sample from JointModel
 
-dir.create(path = file.path("local"), showWarnings = FALSE)
 mp <- sampleStanModel(
     jm,
     data = stan_data,

diff --git a/misc/tests/lm-with-link.R b/misc/tests/lm-with-link.R
@@ -41,9 +41,8 @@ jlist <- simulate_joint_data(
         phi = 0.1, 
         .debug = TRUE
     ),
-    os_fun = sim_os_weibull(
+    os_fun = sim_os_exponential(
         lambda = 0.00333,  # 1/300
-        gamma = 0.97
     )
 )
 
@@ -61,7 +60,6 @@ stan_data <- as_stan_data(dat_os, dat_lm, ~ cov_cat + cov_cont)
 
 
 ## Sample from JointModel
-dir.create(path = file.path("local"), showWarnings = FALSE)
 mp <- sampleStanModel(
     jm,
     data = stan_data,

diff --git a/test/test-compile.R b/test/test-compile.R
@@ -0,0 +1,32 @@
+
+model <- "
+data {
+    int n;
+    array[n] real x;
+}
+
+parameters {
+    real mu;
+    real sigma;
+}
+
+model {
+    target += normal_lpdf(x | mu, sigma);
+}
+"
+
+
+test_that("compileStanModel doesn't error if the directory doesn't exist", {
+
+
+
+    smod <- StanModule(model)
+    fpath <- file.path(tempdir(), "abcd", "efg", "model")
+    z <- compileStanModel(smod, fpath)
+
+    expect_true(file.exists(fpath))
+})
+
+
+
+