add autoformatter

.JuliaFormatter.toml

@@ -0,0 +1,29 @@
+always_use_return = false
+annotate_untyped_fields_with_any = true
+conditional_to_if = false
+import_to_using = false
+join_lines_based_on_source = true
+normalize_line_endings = "unix"
+pipe_to_function_call = false
+remove_extra_newlines = true
+short_to_long_function_def = false
+long_to_short_function_def = false
+whitespace_in_kwargs = true
+whitespace_ops_in_indices = true
+whitespace_typedefs = true
+indent = 4
+margin = 92
+format_docstrings = false
+align_struct_field = false
+align_assignment = false
+align_conditional = false
+align_pair_arrow = false
+align_matrix = false
+trailing_comma = false
+trailing_zero = true
+indent_submodule = false
+separate_kwargs_with_semicolon = false
+surround_whereop_typeparameters = true
+variable_call_indent = []
+yas_style_nesting = false
+disallow_single_arg_nesting = true

.github/workflows/Format-PR.yml

@@ -0,0 +1,8 @@
+name: Format Suggestions
+on:
+  pull_request:
+jobs:
+  code-style:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: julia-actions/julia-format@v2

.github/workflows/Format.yml

@@ -0,0 +1,43 @@
+name: Formatter
+on:
+  schedule:
+    - cron: '0 0 * * *'
+  push:
+    branches:
+      - 'master'
+    tags: ['*']
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: x64
+          show-versioninfo: true
+      - uses: julia-actions/cache@v1
+      - name: Install JuliaFormatter and format
+        shell: julia --color=yes {0}
+        run: |
+          using Pkg
+          Pkg.add("JuliaFormatter")
+          using JuliaFormatter
+          format(".")
+
+      # https://github.com/marketplace/actions/create-pull-request
+      # https://github.com/peter-evans/create-pull-request#reference-example
+      - name: Create Pull Request
+        id: cpr
+        uses: peter-evans/create-pull-request@v6
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: Format .jl files
+          title: 'Automatic JuliaFormatter.jl run'
+          branch: auto-juliaformatter-pr
+          delete-branch: true
+          labels: formatting, automated pr, no changelog
+      - name: Check outputs
+        run: |
+          echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}"
+          echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}"

Project.toml

@@ -17,17 +17,17 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 ThreadsX = "ac1d9e8a-700a-412c-b207-f0111f4b6c0d"
 
 [compat]
-AbstractMCMC = "0.5, 1.0.0, 2.0, 3.0, 4.0"
+AbstractMCMC = "4.0,5.0"
 ConcreteStructs = "0.2.0"
 Distributions = "0.22, 0.23, 0.24, 0.25"
 MCMCChains = "4.0, 5.0, 6.0"
 Parameters = "0.12"
 ProgressMeter = "1.2"
 SafeTestsets = "0.0.1, 0.1"
-SequentialSamplingModels = "0.1.0"
+SequentialSamplingModels = "0.8.0"
 StatsBase = "0.32,0.33, 0.34"
 ThreadsX = "0.1.0"
-Turing = "0.20,0.21,0.22.0,0.23.0,0.24.0,0.25.0,0.26.0"
+Turing = "0.26.0 - 0.29.0"
 julia = "1"
 
 [extras]

test/lognormal_race_tests.jl

@@ -1,34 +1,33 @@
-using DifferentialEvolutionMCMC, Test, Random, Turing, Parameters, Distributions
+using DifferentialEvolutionMCMC, Test, Random, Parameters, Distributions
 using SequentialSamplingModels, LinearAlgebra
+using Turing 
 Random.seed!(9918)
 
-dist = LNR(μ=[-2.,-2.,-3.,-3], σ=1.0, ϕ=.5)
+dist = LNR(ν=[-2.,-2.,-3.,-3], σ=fill(1.0, 4), τ=.5)
 data = rand(dist, 100)
 
-function loglike(data, μ, σ, ϕ)
-    dist = LNR(μ, σ, ϕ)
-    return sum(logpdf.(dist, data))
+function loglike(data, ν, τ)
+    dist = LNR(;ν, τ)
+    return sum(logpdf(dist, data))
 end
 
-function prior_loglike(μ, σ, ϕ)
+function prior_loglike(ν, τ)
     LL = 0.0
-    LL += sum(logpdf.(Normal(0, 3), μ))
-    LL += logpdf(truncated(Cauchy(0, 1), 0.0, Inf), σ)
-    LL += logpdf(Uniform(0., min_rt), ϕ)
+    LL += sum(logpdf.(Normal(0, 3), ν))
+    LL += logpdf(Uniform(0., min_rt), τ)
 end
 
 function sample_prior()
     LL = 0.0
-    μ = rand(Normal(0, 3), 4)
-    σ = rand(truncated(Cauchy(0, 1), 0.0, Inf))
-    ϕ = rand(Uniform(0, min_rt))
-    return as_union([μ,σ,ϕ])
+    ν = rand(Normal(0, 3), 4)
+    τ = rand(Uniform(0, min_rt))
+    return as_union([ν, τ])
 end
 
 min_rt = minimum(x -> x[2], data)
 
-bounds = ((-Inf,0.),(1e-10,Inf),(0.,min_rt))
-names = (:μ,:σ,:ϕ)
+bounds = ((-Inf,Inf),(0.,min_rt))
+names = (:ν, :τ)
 
 model = DEModel(; 
     sample_prior, 
@@ -53,17 +52,16 @@ loglikelihood(d::LNR, data::Vector{<:Tuple}) = sum(logpdf.(d, data))
 
 @model model1(data) = begin
     min_rt = minimum(x -> x[2], data)
-    μ ~ MvNormal(zeros(4), I * 3^2)
-    σ ~ truncated(Cauchy(0, 1), 0.0, Inf)
-    ϕ ~ Uniform(0.0, min_rt)
-    data ~ LNR(μ=μ, σ=σ, ϕ=ϕ)
+    ν ~ MvNormal(zeros(4), I * 3^2)
+    τ ~ Uniform(0.0, min_rt)
+    data ~ LNR(;ν, τ)
 end
 
 Random.seed!(68541)
 chn = sample(model1(data), NUTS(1500, .85), 4000)
 μ_nuts = describe(chn)[1][:,:mean]
 σ_nuts = describe(chn)[1][:,:std]
 
-@test all(isapprox.(rhat, fill(1.0, 6), atol=.05))
+@test all(isapprox.(rhat, fill(1.0, 5), atol=.05))
 @test all(isapprox.(μ_nuts, μ_de, rtol=.05))
 @test all(isapprox.(σ_nuts, σ_de, rtol=.05))