Rel 7.2.0

StanJulia · Feb 6, 2023 · 96a2ff8 · 96a2ff8
1 parent 140a134
commit 96a2ff8
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Showing 8 changed files with 25 additions and 36 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -28,7 +28,7 @@ jobs:
       matrix:
         version:
           - '1.8'
-          - '1.9-beta3'
+          #- '1.9-beta3'
           - 'nightly'
         os:
           - ubuntu-latest

diff --git a/ext/BridgeStanExt.jl b/ext/BridgeStanExt.jl
@@ -4,15 +4,14 @@ using StanSample, DocStringExtensions
 
 StanSample.EXTENSIONS_SUPPORTED ? (using BridgeStan) : (using ..BridgeStan)
 
-import StanSample: create_smb
+#import StanSample: create_smb
 
-const BS = BridgeStan
 const BRIDGESTAN_PATH = get_bridgestan_path()
 println(BRIDGESTAN_PATH)
-BS.set_bridgestan_path!(BRIDGESTAN_PATH)
-export BS, BRIDGESTAN_HOME, StanModel
-
+BridgeStan.set_bridgestan_path!(BRIDGESTAN_PATH)
+export StanModel
 
+#=
 """
 
 Create a BridgeStan shared object.
@@ -37,10 +36,10 @@ if either the shared object or data file is missing.
 
 Exported
 """
-function StanSample.create_smb(sm::SampleModel, 
-        data_file=joinpath(sm.tmpdir, sm.name*"_data_1.json");
+function StanSample.create_smb(sm::SampleModel; 
         stanc_args=["--warn-pedantic --O1"],
         make_args=["CXX=clang++", "STAN_THREADS=true"],
+        data_file=joinpath(sm.tmpdir, sm.name*"_data_1.json"),
         seed = 204,
         chain_id = 0
     )
@@ -67,5 +66,6 @@ function StanSample.create_smb(sm::SampleModel,
 
     smb
 end
+=#
 
 end
diff --git a/ext/MonteCarloMeasurementsExt.jl b/ext/MonteCarloMeasurementsExt.jl
@@ -22,18 +22,4 @@ function StanSample.convert_a3d(a3d_array, cnames, ::Val{:particles};
 
 end
 
-#=
-function StanSample.particles(df::DataFrame)
-
-  d = OrderedDict{Symbol, typeof(Particles(size(df, 1), Normal(0.0, 1.0)))}()
-
-  for var in Symbol.(names(df))
-    d[var] = Particles(df[:, var])
-  end
-
-  (;d...)
-
-end
-=#
-
 end
diff --git a/src/stanmodel/extension_functions.jl b/src/stanmodel/extension_functions.jl
@@ -2,14 +2,12 @@
 # Functions to be flashed out using extensions.
 
 function inferencedata() end
-function create_smb() end
-function particles() end
+#function create_smb() end
 function matrix() end
 function convert_a3d() end
 
 export
     inferencedata,
-    create_smb,
-    particles,
+    #create_smb,
     matrix,
     convert_a3d
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -13,14 +13,12 @@ if haskey(ENV, "CMDSTAN") || haskey(ENV, "JULIA_CMDSTAN_HOME")
     include(joinpath(TestDir, "test_bernoulli/test_bernoulli_keyedarray_01.jl"))
 
     if success(rc)
-
-      sdf = read_summary(sm, :dataframe)
+      sdf = read_summary(sm)
       sdf |> display
 
       @test sdf[sdf.parameters .== :theta, :mean][1] ≈ 0.33 rtol=0.05
 
-      (samples, parameters) = read_samples(sm, :array;
-        return_parameters=true)
+      (samples, parameters) = read_samples(sm, :array; return_parameters=true)
       @test size(samples) == (1000, 1, 6)
       @test length(parameters) == 1
 
@@ -58,7 +56,7 @@ if haskey(ENV, "CMDSTAN") || haskey(ENV, "JULIA_CMDSTAN_HOME")
 
   end
 
-  if Int(VERSION.minor) > 8 
+  #if Int(VERSION.minor) > 8 
 
     test_bridgestan = [
       "test_bridgestan/test_bridgestan.jl",
@@ -73,7 +71,7 @@ if haskey(ENV, "CMDSTAN") || haskey(ENV, "JULIA_CMDSTAN_HOME")
       println()
     end
 
-  end
+  #end
 
   println()
   test_inferencedata = [

diff --git a/test/test_bernoulli/test_bernoulli_array_01.jl b/test/test_bernoulli/test_bernoulli_array_01.jl
@@ -1,6 +1,6 @@
 ######### StanSample Bernoulli example  ###########
 
-using StanSample
+using AxisKeys, StanSample
 
 bernoulli_model = "
 data {
@@ -24,7 +24,7 @@ rc = stan_sample(sm; data);
 if success(rc)
   (samples, cnames) = read_samples(sm, :array; return_parameters=true)
 
-  ka = read_samples(sm)
+  ka = read_samples(sm, :keyedarray)
   ka |> display
   println()
 

diff --git a/test/test_bernoulli/test_bernoulli_keyedarray_01.jl b/test/test_bernoulli/test_bernoulli_keyedarray_01.jl
@@ -1,6 +1,6 @@
 ######### StanSample Bernoulli example  ###########
 
-using StanSample
+using AxisKeys, StanSample
 
 bernoulli_model = "
 data {

diff --git a/test/test_bridgestan/test_bridgestan.jl b/test/test_bridgestan/test_bridgestan.jl
@@ -28,7 +28,14 @@ if success(rc)
     post = read_samples(sm, :dataframe)
 end
 
-smb = create_smb(sm, joinpath(sm.tmpdir, "$(sm.name)_data_1.json"))
+smb = BridgeStan.StanModel(;
+    stan_file = sm.output_base * ".stan",
+    stanc_args = ["--warn-pedantic --O1"],
+    make_args = ["CXX=clang++", "STAN_THREADS=true"],
+    data=sm.output_base * "_data_1.json",
+    seed = 204,
+    chain_id = 0
+)
 
 println("This model's name is $(BridgeStan.name(smb)).")
 println("It has $(BridgeStan.param_num(smb)) parameters.")