Updates to bounds, TODO

Examples/Bernoulli/bernoulli.jl

@@ -21,7 +21,7 @@ observed_data = Dict("N" => 10, "y" => [0, 1, 0, 1, 0, 0, 0, 0, 0, 1])
 
 # Default for tmpdir is to create a new tmpdir location
 # To prevent recompilation of a Stan progam, choose a fixed location,
-tmpdir=joinpath(@__DIR__, "tmp")
+tmpdir=mktempdir()
 
 sm = SampleModel("bernoulli", bernoullimodel,
   method=StanSample.Sample(save_warmup=true, num_warmup=1000, 
@@ -50,9 +50,9 @@ if !isnothing(sample_file)
   if isdefined(Main, :StatsPlots)
     cd(@__DIR__) do
       p1 = plot(chns)
-      savefig(p1, "traceplot.pdf")
+      savefig(p1, joinpath(tmpdir, "traceplot.pdf"))
       p2 = pooleddensity(chns)
-      savefig(p2, "pooleddensity.pdf")
+      savefig(p2, joinpath(tmpdir, "pooleddensity.pdf"))
     end
   end
 

Manifest.toml

@@ -51,29 +51,23 @@ git-tree-sha1 = "5b08ed6036d9d3f0ee6369410b830f8873d4024c"
 uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
 version = "0.5.8"
 
-[[CSTParser]]
-deps = ["Tokenize"]
-git-tree-sha1 = "99dda94f5af21a4565dc2b97edf6a95485f116c3"
-uuid = "00ebfdb7-1f24-5e51-bd34-a7502290713f"
-version = "1.0.0"
-
 [[CSV]]
-deps = ["CategoricalArrays", "DataFrames", "Dates", "FilePathsBase", "LazyArrays", "Mmap", "Parsers", "PooledArrays", "Profile", "Tables", "Unicode", "WeakRefStrings"]
-git-tree-sha1 = "0c3201d16c65a1453be158189d48df7c357eb7fb"
+deps = ["CategoricalArrays", "DataFrames", "Dates", "FilePathsBase", "LazyArrays", "Mmap", "Parsers", "PooledArrays", "Tables", "Unicode", "WeakRefStrings"]
+git-tree-sha1 = "b5a828cf2774e20b6e5ba8d0e0f31ddffafb37d8"
 uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-version = "0.5.14"
+version = "0.5.18"
 
 [[Calculus]]
-deps = ["Compat"]
-git-tree-sha1 = "bd8bbd105ba583a42385bd6dc4a20dad8ab3dc11"
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad"
 uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
-version = "0.5.0"
+version = "0.5.1"
 
 [[CategoricalArrays]]
 deps = ["Compat", "DataAPI", "Future", "JSON", "Missings", "Printf", "Reexport", "Unicode"]
-git-tree-sha1 = "45101c4d0df3946acb6e9bfcfd3a8c32abbd421b"
+git-tree-sha1 = "4d85a015093760ff23b20f3e25fa195b4cb76794"
 uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597"
-version = "0.7.1"
+version = "0.7.3"
 
 [[Clustering]]
 deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "SparseArrays", "Statistics", "StatsBase"]
@@ -130,9 +124,9 @@ version = "0.19.4"
 
 [[DataStructures]]
 deps = ["InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "1fe8fad5fc84686dcbc674aa255bc867a64f8132"
+git-tree-sha1 = "a1b652fb77ae8ca7ea328fa7ba5aa151036e5c10"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.17.5"
+version = "0.17.6"
 
 [[DataValueInterfaces]]
 git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
@@ -155,9 +149,9 @@ uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 
 [[DiffEqDiffTools]]
 deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"]
-git-tree-sha1 = "21b855cb29ec4594f9651e0e9bdc0cdcfdcd52c1"
+git-tree-sha1 = "81edfb3a8b55154772bb6080b5db40868e1778ed"
 uuid = "01453d9d-ee7c-5054-8395-0335cb756afa"
-version = "1.3.0"
+version = "1.4.0"
 
 [[DiffResults]]
 deps = ["Compat", "StaticArrays"]
@@ -183,9 +177,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[Distributions]]
 deps = ["LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "838a37797ac24c1b4c3353d46ec87ea6598f2308"
+git-tree-sha1 = "ce189b71fac635d6ec9582dc0f208887db25e6d3"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.21.7"
+version = "0.21.8"
 
 [[DocStringExtensions]]
 deps = ["LibGit2", "Markdown", "Pkg", "Test"]
@@ -194,10 +188,10 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 version = "0.8.1"
 
 [[Documenter]]
-deps = ["Base64", "DocStringExtensions", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
-git-tree-sha1 = "d45c163c7a3ae293c15361acc52882c0f853f97c"
+deps = ["Base64", "Dates", "DocStringExtensions", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
+git-tree-sha1 = "0e52069b5970cb27234153f578227947565152c5"
 uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-version = "0.23.4"
+version = "0.24.0"
 
 [[ElasticArrays]]
 git-tree-sha1 = "5b5b7cb8cba44bcf337b8af0a1f3e57c89468660"
@@ -218,9 +212,9 @@ version = "1.1.0"
 
 [[FilePathsBase]]
 deps = ["Dates", "LinearAlgebra", "Printf", "Test", "UUIDs"]
-git-tree-sha1 = "2ee1d999c462425e2f848524f732ed51bc1ab63a"
+git-tree-sha1 = "2cd6e2e7965934f72cb80251f760228e2264bab3"
 uuid = "48062228-2e41-5def-b9a4-89aafe57970f"
-version = "0.6.2"
+version = "0.7.0"
 
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays"]
@@ -278,9 +272,9 @@ uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f"
 version = "1.0.0"
 
 [[IterTools]]
-git-tree-sha1 = "2ebe60d7343962966d1779a74a760f13217a6901"
+git-tree-sha1 = "05110a2ab1fc5f932622ffea2a003221f4782c18"
 uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
-version = "1.2.0"
+version = "1.3.0"
 
 [[IteratorInterfaceExtensions]]
 git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
@@ -301,11 +295,12 @@ version = "0.5.1"
 
 [[LazyArrays]]
 deps = ["FillArrays", "LinearAlgebra", "MacroTools", "StaticArrays"]
-git-tree-sha1 = "01ec151cd0418fb05294b0230471765e0a65adb1"
+git-tree-sha1 = "262c129448cad8b073315244eb54b31932123619"
 uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02"
-version = "0.12.3"
+version = "0.13.1"
 
 [[LibGit2]]
+deps = ["Printf"]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 
 [[Libdl]]
@@ -331,10 +326,10 @@ uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
 version = "0.3.15"
 
 [[MacroTools]]
-deps = ["CSTParser", "Compat", "DataStructures", "Test", "Tokenize"]
-git-tree-sha1 = "d6e9dedb8c92c3465575442da456aec15a89ff76"
+deps = ["Compat", "DataStructures", "Test"]
+git-tree-sha1 = "82921f0e3bde6aebb8e524efc20f4042373c0c06"
 uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
-version = "0.5.1"
+version = "0.5.2"
 
 [[Markdown]]
 deps = ["Base64"]
@@ -362,15 +357,14 @@ uuid = "d41bc354-129a-5804-8e4c-c37616107c6c"
 version = "7.5.0"
 
 [[NaNMath]]
-deps = ["Compat"]
-git-tree-sha1 = "ce3b85e484a5d4c71dd5316215069311135fa9f2"
+git-tree-sha1 = "928b8ca9b2791081dc71a51c55347c27c618760f"
 uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
-version = "0.3.2"
+version = "0.3.3"
 
 [[NamedTupleTools]]
-git-tree-sha1 = "1e410fd6c969e21ad647417d9ab9dff80f26f8ce"
+git-tree-sha1 = "522bcc70c965f156bb2757741a66510799d4d243"
 uuid = "d9ec5142-1e00-5aa0-9d6a-321866360f50"
-version = "0.11.0"
+version = "0.12.0"
 
 [[NearestNeighbors]]
 deps = ["Distances", "LinearAlgebra", "Mmap", "StaticArrays", "Test"]
@@ -415,12 +409,12 @@ version = "0.12.0"
 
 [[Parsers]]
 deps = ["Dates", "Test"]
-git-tree-sha1 = "c56ecb484f286639f161e712b8311f5ab77e8d32"
+git-tree-sha1 = "0139ba59ce9bc680e2925aec5b7db79065d60556"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "0.3.8"
+version = "0.3.10"
 
 [[Pkg]]
-deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [[PlotThemes]]
@@ -431,9 +425,9 @@ version = "0.4.0"
 
 [[PlotUtils]]
 deps = ["Colors", "Dates", "Printf", "Random", "Reexport"]
-git-tree-sha1 = "259a8d3399ea7ba23553aa91eafdf0640f5199f1"
+git-tree-sha1 = "7622cbde3200a9876a14ba85d66f25d7f4e7a6ca"
 uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043"
-version = "0.6.0"
+version = "0.6.1"
 
 [[Plots]]
 deps = ["Base64", "Contour", "Dates", "FFMPEG", "FixedPointNumbers", "GR", "GeometryTypes", "JSON", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "Reexport", "Requires", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"]
@@ -456,10 +450,6 @@ version = "0.2.3"
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
-[[Profile]]
-deps = ["Printf"]
-uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79"
-
 [[QuadGK]]
 deps = ["DataStructures", "LinearAlgebra"]
 git-tree-sha1 = "1af46bf083b9630a5b27d4fd94f496c5fca642a8"
@@ -546,7 +536,7 @@ version = "0.8.0"
 
 [[StanBase]]
 deps = ["CSV", "DataFrames", "DelimitedFiles", "Distributed", "DocStringExtensions", "MCMCChains", "NamedTupleTools", "Parameters", "Random", "Reexport", "StanDump", "StanRun", "StanSamples", "Unicode"]
-git-tree-sha1 = "d8cae1d8d3645075ae8599e1872d08644431e0e8"
+path = "/Users/rob/.julia/dev/StanBase"
 uuid = "d0ee94f6-a23d-54aa-bbe9-7f572d6da7f5"
 version = "1.0.0"
 
@@ -594,9 +584,9 @@ version = "1.0.0"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "1085ffbf5fd48fdba64ef8e902ca429c4e1212d3"
+git-tree-sha1 = "5a3bcb6233adabde68ebc97be66e95dcb787424c"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "0.11.1"
+version = "0.12.1"
 
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
@@ -640,11 +630,6 @@ version = "0.2.11"
 deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
-[[Tokenize]]
-git-tree-sha1 = "dfcdbbfb2d0370716c815cbd6f8a364efb6f42cf"
-uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624"
-version = "0.5.6"
-
 [[URIParser]]
 deps = ["Test", "Unicode"]
 git-tree-sha1 = "6ddf8244220dfda2f17539fa8c9de20d6c575b69"

TODO.md

@@ -2,9 +2,13 @@ Still to look into:
 
 1. Ability display Stan's summary when calling `stan_summary` and/or `read_summary`.
 2. Create an option to (re-)create Stan's summary with a selection of the available chains.
-3. Check if start=... works properly to align sample numbers when saving warmup samples.
 4. Check if the updates in sdewaele's PR need to be applied here as well.
-5. Check if there are additional cases where inside the REPL fails while package testing works, e.g. read_samples(stanmodel).
+
+Provisionally ok:
+
+3. Check if start=... works properly to align sample numbers when saving warmup samples - seems ok.
+5. Check if there are additional cases where inside the REPL fails while package testing works, e.g. read_samples(stanmodel) - seems ok.
 6. Make sure no files are ever created in the `package` dir.
-7. Any conflicts with running CmdStan.jl and Stan.jl in a single julia instantiation.
-8. 
+instantiation - seems ok.
+7. Any conflicts with running CmdStan.jl and Stan.jl in a single julia 
+8. Inclusion of findall() for Julia < v1.3 - seems ok.