Rel 4.0.0 - Switch to JSON3

Project.toml

@@ -1,7 +1,7 @@
 name = "StanOptimize"
 uuid = "fbd8da12-e93d-5a64-9231-612a0707ab99"
 authors = ["Rob J Goedman <[email protected]>"]
-version = "3.3.0"
+version = "4.0.0"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -20,13 +20,13 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unicode = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [compat]
-CSV = "0.9, 0.10"
-DataFrames = "1.0"
+CSV = "0.10"
+DataFrames = "1.3"
 DocStringExtensions = "0.8"
 Documenter = "0.27"
 Parameters = "0.12"
 Reexport = "1.2"
-StanBase = "3.2"
+StanBase = "4.0"
 StanDump = "0.2"
 julia = "1"
 

examples/Bernoulli/bernoulli.jl

@@ -17,10 +17,11 @@ model {
 ";
 
 data = Dict("N" => 10, "y" => [0, 1, 0, 1, 0, 0, 0, 0, 0, 1])
+init = (theta = .5,)
 tmpdir = joinpath(@__DIR__, "tmp")
 
 stanmodel = OptimizeModel("bernoulli",  bernoulli_model, tmpdir);
-rc = stan_optimize(stanmodel; data);
+rc = stan_optimize(stanmodel; data, init);
 
 if success(rc)
   optim1, cnames = read_optimize(stanmodel)

src/StanOptimize.jl

@@ -16,7 +16,7 @@ using DocStringExtensions: FIELDS, SIGNATURES, TYPEDEF
 
 import StanBase: update_model_file, par, handle_keywords!
 import StanBase: executable_path, ensure_executable, stan_compile
-import StanBase: update_R_files
+import StanBase: update_R_files, update_json_files
 import StanBase: data_file_path, init_file_path, sample_file_path
 import StanBase: generated_quantities_file_path, log_file_path
 import StanBase: diagnostic_file_path, setup_diagnostics

src/stanrun/stan_run.jl

@@ -10,6 +10,7 @@ Optimize a StanJulia OptimizationModel <: CmdStanModel
 ### Dispatch arguments
 ```julia
 * `m:: OptimizeModel`             # CmdStanModel subtype
+* `use_json=true`                 # Use JSON3 for data and init files
 ```
 
 ### Keyword arguments
@@ -51,7 +52,7 @@ See extended help for other keyword arguments ( `??stan_optimize` ).
 * `save_iterations=0`                  # Stream iterations to output
 ```
 """
-function stan_run(m::T; kwargs...) where {T <: CmdStanModels}
+function stan_run(m::T, use_json=true; kwargs...) where {T <: CmdStanModels}
 
     handle_keywords!(m, kwargs)
 
@@ -61,10 +62,17 @@ function stan_run(m::T; kwargs...) where {T <: CmdStanModels}
         isfile(sfile) && rm(sfile)
     end
 
-    :init in keys(kwargs) && update_R_files(m, kwargs[:init],
-        m.num_chains, "init")
-    :data in keys(kwargs) && update_R_files(m, kwargs[:data],
-        m.num_chains, "data")
+    if use_json
+        :init in keys(kwargs) && update_json_files(m, kwargs[:init],
+            m.num_chains, "init")
+        :data in keys(kwargs) && update_json_files(m, kwargs[:data],
+            m.num_chains, "data")
+    else
+        :init in keys(kwargs) && update_R_files(m, kwargs[:init],
+            m.num_chains, "init")
+        :data in keys(kwargs) && update_R_files(m, kwargs[:data],
+            m.num_chains, "data")
+    end
 
     m.cmds = [stan_cmds(m, id; kwargs...) for id in 1:m.num_chains]