a few changes

efmanu · Sep 13, 2021 · d411f55 · d411f55
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commit d411f55
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Showing 5 changed files with 61 additions and 29 deletions.
diff --git a/Manifest.toml b/Manifest.toml
@@ -132,6 +132,12 @@ git-tree-sha1 = "ed720e2622820bf584d4ad90e6fcb93d95170b44"
 uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"
 version = "0.1.3"
 
+[[CSV]]
+deps = ["Dates", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode"]
+git-tree-sha1 = "b83aa3f513be680454437a0eee21001607e5d983"
+uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+version = "0.8.5"
+
 [[ChainRules]]
 deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Random", "Statistics"]
 git-tree-sha1 = "0902fc7f416c8f1e3b1e014786bb65d0c2241a9b"
@@ -269,6 +275,12 @@ git-tree-sha1 = "bec2532f8adb82005476c141ec23e921fc20971b"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
 version = "1.8.0"
 
+[[DataFrames]]
+deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
+git-tree-sha1 = "d785f42445b63fc86caa08bb9a9351008be9b765"
+uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+version = "1.2.2"
+
 [[DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
 git-tree-sha1 = "7d9d316f04214f7efdbb6398d545446e246eff02"
@@ -835,6 +847,12 @@ git-tree-sha1 = "371a19bb801c1b420b29141750f3a34d6c6634b9"
 uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad"
 version = "0.1.0"
 
+[[PooledArrays]]
+deps = ["DataAPI", "Future"]
+git-tree-sha1 = "a193d6ad9c45ada72c14b731a318bedd3c2f00cf"
+uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
+version = "1.3.0"
+
 [[Preferences]]
 deps = ["TOML"]
 git-tree-sha1 = "00cfd92944ca9c760982747e9a1d0d5d86ab1e5a"
@@ -959,6 +977,12 @@ git-tree-sha1 = "9c1a0dea3b442024c54ca6a318e8acf842eab06f"
 uuid = "30f210dd-8aff-4c5f-94ba-8e64358c1161"
 version = "2.2.0"
 
+[[SentinelArrays]]
+deps = ["Dates", "Random"]
+git-tree-sha1 = "54f37736d8934a12a200edea2f9206b03bdf3159"
+uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
+version = "1.3.7"
+
 [[Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 
@@ -1119,7 +1143,7 @@ uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
 version = "0.18.0"
 
 [[TuringDash]]
-deps = ["Dash", "DashBootstrapComponents", "DashCoreComponents", "DashHtmlComponents", "PlotlyJS", "Turing"]
+deps = ["CSV", "Dash", "DashBootstrapComponents", "DashCoreComponents", "DashHtmlComponents", "DataFrames", "PlotlyJS", "Random", "Turing"]
 path = "TuringDash"
 uuid = "ff11d773-741b-488a-a49d-ae0d842bee15"
 version = "0.1.0"

diff --git a/Project.toml b/Project.toml
@@ -1,3 +1,4 @@
 [deps]
+Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 TuringDash = "ff11d773-741b-488a-a49d-ae0d842bee15"
diff --git a/TuringDash/src/TuringDash.jl b/TuringDash/src/TuringDash.jl
@@ -1,6 +1,5 @@
 module TuringDash
 
-
 include("render_funcs.jl")
 include("utils.jl")
 using Dash, DashBootstrapComponents
@@ -31,7 +30,8 @@ function make_app()
     y_graph1 = []
     itr = 0
     df = nothing
-
+    nperiteration = 1
+
     external_stylesheets = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css"
     app = dash(external_stylesheets=[dbc_themes.BOOTSTRAP,external_stylesheets], 
 	    suppress_callback_exceptions=true)
@@ -70,30 +70,32 @@ function make_app()
         if (user_funcs == "") || (funcs_init == "")
             throw(PreventUpdate())
         end
-        
+
         x_graph = []
         y_graph = []
         y_graph1 = []
         itr = 0
-              
+
         for colname in Symbol.(names(df))
             @eval $colname = df.$colname
-        end        
-        #evealuate model
+        end
+        # evealuate model
         eval(Meta.parse(user_funcs))
 
         #evaluate eval_definition
         model = eval(Meta.parse(funcs_init))
 
-        alg = MH()
+        alg = MH(
+            [0.25 0.05;
+             0.05 0.50]
+        )
         rng = Random.GLOBAL_RNG
 
-        nperiteration = 5
         nsamples = 1000
         @async begin
             r = sample(rng, model, alg, nperiteration; chain_type=MCMCChains.Chains, save_state=true, progress=false)
             put!(chn, Array(r)[end,1:2])
-            for i in (nperiteration + 1):nperiteration:nsamples
+            for _ in (nperiteration + 1):nperiteration:nsamples
                 r = Turing.Inference.resume(r, nperiteration, save_state=true, progress=false)
                 put!(chn, Array(r)[end,1:2])
             end
@@ -114,7 +116,7 @@ function make_app()
         global x_graph, y_graph, y_graph1, chn, itr
         if isready(chn)
             val = take!(chn)
-            itr += 5
+            itr += nperiteration
             append!(x_graph, itr)
             append!(y_graph, val[1])
 			append!(y_graph1, val[2])

diff --git a/TuringDash/src/render_funcs.jl b/TuringDash/src/render_funcs.jl
@@ -6,7 +6,7 @@ function render_all()
         dbc_row([
             render_func_init(),
             dbc_col([
-                dbc_button("Sample !", color="success", id="dtu-btn-turing")
+                dbc_button("Sample", color="success", id="dtu-btn-turing")
             ], md =2),            
             render_plots()
         ])
@@ -17,12 +17,12 @@ function render_info()
         dbc_jumbotron([
             html_h1("Dash Turing App", className="dtu-display-3"),
             html_p(
-                "Web app for Bayesian inference using  Dash.jl and Turing.jl ",
+                "Web app for Bayesian inference using Dash.jl and Turing.jl ",
                 className="lead",
             ),
             html_hr(className="my-2"),
             html_p(
-                "User can define Turing model",
+                "User can define a Turing model. The dataset's column names are available as variable names.",
             )
         ])
     ])
@@ -39,18 +39,18 @@ end
 function render_function()
     return dbc_card([
         dbc_cardbody([
-            html_h4("Model specification", className="card-title"),
+            html_h4("Model specification:", className="card-title"),
             html_div([
                 dbc_textarea(
                     id = "dtu-user-funcs",
                     bs_size="lg",
                     className="mb-3",
                     rows  = 6,
                     value="""
-                        @model turingmodel(x, y) = begin
+                        @model regression_model(x, y) = begin
                             a ~ Normal()
                             b ~ Normal()
-                            for i in 1:length(x)
+                            for i in 1:10
                                 y[i] ~ Normal(a + b * x[i], 1.0)
                             end
                         end
@@ -63,13 +63,13 @@ end
 function render_init()
     return dbc_card([
             dbc_cardbody([
-                html_h4("Conditional Model", className="card-title"),
+                html_h4("Conditional model:", className="card-title"),
                 html_div([
                     dbc_input(
                         id = "dtu-user-func-init",
                         bs_size="lg",
                         className="mb-3",
-                        value="turingmodel(x, y)",
+                        value="regression_model(x, y)",
                     )
                 ]),
             ])
@@ -83,7 +83,7 @@ function render_uploader()
                     html_div(
                         id="dtu-def-upload-data",
                         [
-                        html_label("Select a default dataset:")
+                        html_label("Select a dataset:")
                         dcc_dropdown(
                             id="dtu-def-data-drop",
                             options =[
@@ -96,7 +96,7 @@ function render_uploader()
                             )
                         ],
                     ),
-                    html_h3("OR"),
+                    html_h3("or"),
                     dcc_upload(
                         id="dtu-upload-datan",
                         children=html_div([

diff --git a/precompile_funcs.jl b/precompile_funcs.jl
@@ -1,32 +1,36 @@
 module PrecompileFuncs
-    using TuringDash
-    using TuringDash.Turing
-    using TuringDash.Random
-    using TuringDash.CSV, TuringDash.DataFrames
+
+using TuringDash
+using TuringDash.Turing
+using TuringDash.Random
+using TuringDash.CSV, TuringDash.DataFrames
 
 function precompile_turing()
     chn = Base.Channel{Vector{Float64}}(Inf)
     df1 = nothing
     global df1
     df1 = CSV.read(download("https://raw.githubusercontent.com/efmanu/TuringDashApp.jl/master/TuringDash/datasets/data1.csv"), DataFrame)
     model_str1 = """
-    @model turingmodel(x, y) = begin
+    @model regression_model(x, y) = begin
         a ~ Normal()
         b ~ Normal()
-        for i in 1:length(x)
+        for i in 1:10
             y[i] ~ Normal(a + b * x[i], 1.0)
         end
     end
     """
-    model_str2 = "turingmodel(x, y)"
+    model_str2 = "regression_model(x, y)"
     for colname in Symbol.(names(df1))
         @eval $colname = df1.$colname
     end
 
     eval(Meta.parse(model_str1))
     model = eval(Meta.parse(model_str2))
 
-    alg = MH()
+    alg = MH(
+        [0.25 0.05;
+         0.05 0.50]
+    )
     rng = Random.GLOBAL_RNG
 
     nperiteration = 50
@@ -40,4 +44,5 @@ function precompile_turing()
     end
     return "success"
 end
+
 end