From 33cad3a8db12647dca3aa09bbeb3588c5d282e82 Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Wed, 21 May 2025 18:27:23 +0100
Subject: [PATCH 01/15] Add three of the DPPL models from
 https://arxiv.org/pdf/2002.02702

---
 .github/workflows/generate_website.yml |  1 +
 Project.toml                           |  3 +++
 main.jl                                |  3 +++
 models/dppl_gauss_unknown.jl           | 12 ++++++++++++
 models/dppl_high_dim_gauss.jl          |  5 +++++
 models/dppl_naive_bayes.jl             | 27 ++++++++++++++++++++++++++
 6 files changed, 51 insertions(+)
 create mode 100644 models/dppl_gauss_unknown.jl
 create mode 100644 models/dppl_high_dim_gauss.jl
 create mode 100644 models/dppl_naive_bayes.jl

diff --git a/.github/workflows/generate_website.yml b/.github/workflows/generate_website.yml
index 2218856..420bf1f 100644
--- a/.github/workflows/generate_website.yml
+++ b/.github/workflows/generate_website.yml
@@ -88,6 +88,7 @@ jobs:
         env:
           ADTYPE_KEYS: ${{ needs.setup-keys.outputs.adtype_keys }}
           ADTESTS_MODELS_TO_LOAD: ${{ matrix.model }}
+          DATADEPS_ALWAYS_ACCEPT: "true"
 
       - name: Output matrix values
         id: output-matrix
diff --git a/Project.toml b/Project.toml
index af96777..00f9471 100644
--- a/Project.toml
+++ b/Project.toml
@@ -3,13 +3,16 @@ ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 Chairmarks = "0ca39b1e-fe0b-4e98-acfc-b1656634c4de"
 DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+DistributionsAD = "ced4e74d-a319-5a8a-b0ac-84af2272839c"
 DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
 Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
 FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c"
+MLDatasets = "eb30cadb-4394-5ae3-aed4-317e484a6458"
 Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
+MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
diff --git a/main.jl b/main.jl
index 7faffc9..61ebdd9 100644
--- a/main.jl
+++ b/main.jl
@@ -100,6 +100,9 @@ end
 @include_model "demo_dot_assume_observe_submodel"
 @include_model "dot_assume"
 @include_model "dot_observe"
+@include_model "dppl_gauss_unknown.jl"
+@include_model "dppl_high_dim_gauss.jl"
+@include_model "dppl_naive_bayes.jl"
 @include_model "dynamic_constraint"
 @include_model "multiple_constraints_same_var"
 @include_model "multithreaded"
diff --git a/models/dppl_gauss_unknown.jl b/models/dppl_gauss_unknown.jl
new file mode 100644
index 0000000..a79a212
--- /dev/null
+++ b/models/dppl_gauss_unknown.jl
@@ -0,0 +1,12 @@
+n = 10_000
+s = abs(rand()) + 0.5
+y = randn() .+ s * randn(n)
+
+@model function dppl_gauss_unknown(y)
+    N = length(y)
+    m ~ Normal(0, 1)
+    s ~ truncated(Cauchy(0, 5); lower=0)
+    y ~ filldist(Normal(m, s), N)
+end
+
+@register dppl_gauss_unknown(y)
diff --git a/models/dppl_high_dim_gauss.jl b/models/dppl_high_dim_gauss.jl
new file mode 100644
index 0000000..2275b6a
--- /dev/null
+++ b/models/dppl_high_dim_gauss.jl
@@ -0,0 +1,5 @@
+@model function dppl_high_dim_gauss(D)
+    m ~ filldist(Normal(0, 1), D)
+end
+
+@register dppl_high_dim_gauss(10_000)
diff --git a/models/dppl_naive_bayes.jl b/models/dppl_naive_bayes.jl
new file mode 100644
index 0000000..3ed7f4f
--- /dev/null
+++ b/models/dppl_naive_bayes.jl
@@ -0,0 +1,27 @@
+using MLDatasets: MNIST
+using MultivariateStats: fit, PCA, transform
+
+# Load MNIST images and labels
+features = MNIST(split=:train).features
+nrows, ncols, nimages = size(features)
+image_raw = Float64.(reshape(features, (nrows * ncols, nimages)))
+labels = MNIST(split=:train).targets .+ 1
+C = 10 # Number of labels
+
+# Preprocess the images by reducing dimensionality
+D = 40
+pca = fit(PCA, image_raw; maxoutdim=D)
+image = transform(pca, image_raw)
+
+# Take only the first 1000 images and vectorise
+N = 1000
+image_subset = image[:, 1:N]'
+image_vec = vec(image_subset[:, :])
+labels = labels[1:N]
+
+@model dppl_naive_bayes(image_vec, labels, C, D) = begin
+    m ~ filldist(Normal(0, 10), C, D)
+    image_vec ~ MvNormal(vec(m[labels, :]), I)
+end
+
+@register dppl_naive_bayes(image_vec, labels, C, D)

From 6af413e6b31b18cbefca1efb591aaf4f1a70763b Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Wed, 21 May 2025 18:41:04 +0100
Subject: [PATCH 02/15] Add datadeps envvar

---
 .github/workflows/generate_website.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/generate_website.yml b/.github/workflows/generate_website.yml
index 420bf1f..f9fda06 100644
--- a/.github/workflows/generate_website.yml
+++ b/.github/workflows/generate_website.yml
@@ -53,6 +53,8 @@ jobs:
       - name: Setup keys
         id: keys
         run: uv run ad.py setup
+        env:
+          DATADEPS_ALWAYS_ACCEPT: "true"
 
   run-models:
     runs-on: ubuntu-latest

From 86bb6a9513bdb80c5218e40d11751a8389b51e86 Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Thu, 19 Jun 2025 23:08:46 +0100
Subject: [PATCH 03/15] add three more models

---
 Project.toml                       |  2 ++
 main.jl                            |  5 ++++-
 models/dppl_hier_poisson.jl        | 27 +++++++++++++++++++++++++++
 models/dppl_logistic_regression.jl | 21 +++++++++++++++++++++
 models/dppl_sto_volatility.jl      |  5 +++++
 5 files changed, 59 insertions(+), 1 deletion(-)
 create mode 100644 models/dppl_hier_poisson.jl
 create mode 100644 models/dppl_logistic_regression.jl
 create mode 100644 models/dppl_sto_volatility.jl

diff --git a/Project.toml b/Project.toml
index 00f9471..0783a3a 100644
--- a/Project.toml
+++ b/Project.toml
@@ -8,6 +8,7 @@ DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
 Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
 FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c"
 MLDatasets = "eb30cadb-4394-5ae3-aed4-317e484a6458"
@@ -16,6 +17,7 @@ MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
 Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
diff --git a/main.jl b/main.jl
index 61ebdd9..92bd483 100644
--- a/main.jl
+++ b/main.jl
@@ -102,7 +102,10 @@ end
 @include_model "dot_observe"
 @include_model "dppl_gauss_unknown.jl"
 @include_model "dppl_high_dim_gauss.jl"
-@include_model "dppl_naive_bayes.jl"
+# Disabled because of https://github.com/TuringLang/ADTests/issues/24
+# @include_model "dppl_naive_bayes"
+@include_model "dppl_logistic_regression"
+@include_model "dppl_hier_poisson"
 @include_model "dynamic_constraint"
 @include_model "multiple_constraints_same_var"
 @include_model "multithreaded"
diff --git a/models/dppl_hier_poisson.jl b/models/dppl_hier_poisson.jl
new file mode 100644
index 0000000..aa1c591
--- /dev/null
+++ b/models/dppl_hier_poisson.jl
@@ -0,0 +1,27 @@
+using LazyArrays
+using Turing: LogPoisson
+
+nd, ns = 5, 10
+a0, a1, a0_sig = 1.0, 0.5, 0.3
+n = nd * ns
+# simulate group level parameters
+a0s = rand(Normal(0, a0_sig), ns)
+logpop = rand(Normal(9, 1.5), ns)
+λ = exp.(a0 .+ a0s + (a1 * logpop))
+# and individual data
+y = mapreduce(λi -> rand(Poisson(λi), nd), vcat, λ)
+x = repeat(logpop, inner=nd)
+idx = repeat(collect(1:ns), inner=nd)
+
+lazyarray(f, x) = LazyArray(Base.broadcasted(f, x))
+
+@model dppl_hier_poisson(y, x, idx, ns) = begin
+    a0 ~ Normal(0, 10)
+    a1 ~ Normal(0, 1)
+    a0_sig ~ truncated(Cauchy(0, 1); lower=0)
+    a0s ~ filldist(Normal(0, a0_sig), ns)
+    alpha = a0 .+ a0s[idx] .+ a1 * x
+    y ~ arraydist(lazyarray(LogPoisson, alpha))
+end
+
+@register dppl_hier_poisson(y, x, idx, ns)
diff --git a/models/dppl_logistic_regression.jl b/models/dppl_logistic_regression.jl
new file mode 100644
index 0000000..0a3ada9
--- /dev/null
+++ b/models/dppl_logistic_regression.jl
@@ -0,0 +1,21 @@
+using StatsFuns: logistic
+using LazyArrays
+
+d, n = 100, 10_000
+X = randn(d, n)
+w = randn(d)
+y = Int.(logistic.(X' * w) .> 0.5)
+
+function safelogistic(x::T) where {T}
+    logistic(x) * (1 - 2 * eps(T)) + eps(T)
+end
+
+lazyarray(f, x) = LazyArray(Base.broadcasted(f, x))
+
+@model dppl_logistic_regression(Xt, y) = begin
+    N, D = size(Xt)
+    w ~ filldist(Normal(), D)
+    y ~ arraydist(lazyarray(x -> Bernoulli(safelogistic(x)), Xt * w))
+end
+
+@register dppl_logistic_regression(X', y)
diff --git a/models/dppl_sto_volatility.jl b/models/dppl_sto_volatility.jl
new file mode 100644
index 0000000..a849767
--- /dev/null
+++ b/models/dppl_sto_volatility.jl
@@ -0,0 +1,5 @@
+using Downloads, CSV
+
+URL =
+http_response = Downloads.download(url)
+file = CSV.File(http_response)

From c9318903d38b655d32fbb57a37fc524756eb6371 Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Fri, 20 Jun 2025 00:11:49 +0100
Subject: [PATCH 04/15] Add the last two DPPL models

---
 main.jl                     |  7 +++--
 models/dppl_hier_poisson.jl |  2 +-
 models/dppl_hmm_semisup.jl  | 59 +++++++++++++++++++++++++++++++++++++
 models/dppl_lda.jl          | 34 +++++++++++++++++++++
 4 files changed, 99 insertions(+), 3 deletions(-)
 create mode 100644 models/dppl_hmm_semisup.jl
 create mode 100644 models/dppl_lda.jl

diff --git a/main.jl b/main.jl
index 92bd483..97d9407 100644
--- a/main.jl
+++ b/main.jl
@@ -101,11 +101,14 @@ end
 @include_model "dot_assume"
 @include_model "dot_observe"
 @include_model "dppl_gauss_unknown.jl"
+@include_model "dppl_hier_poisson"
 @include_model "dppl_high_dim_gauss.jl"
+@include_model "dppl_hmm_semisup"
+@include_model "dppl_lda"
+@include_model "dppl_logistic_regression"
 # Disabled because of https://github.com/TuringLang/ADTests/issues/24
 # @include_model "dppl_naive_bayes"
-@include_model "dppl_logistic_regression"
-@include_model "dppl_hier_poisson"
+@include_model "dppl_sto_volatility"
 @include_model "dynamic_constraint"
 @include_model "multiple_constraints_same_var"
 @include_model "multithreaded"
diff --git a/models/dppl_hier_poisson.jl b/models/dppl_hier_poisson.jl
index aa1c591..f432839 100644
--- a/models/dppl_hier_poisson.jl
+++ b/models/dppl_hier_poisson.jl
@@ -15,7 +15,7 @@ idx = repeat(collect(1:ns), inner=nd)
 
 lazyarray(f, x) = LazyArray(Base.broadcasted(f, x))
 
-@model dppl_hier_poisson(y, x, idx, ns) = begin
+@model function dppl_hier_poisson(y, x, idx, ns)
     a0 ~ Normal(0, 10)
     a1 ~ Normal(0, 1)
     a0_sig ~ truncated(Cauchy(0, 1); lower=0)
diff --git a/models/dppl_hmm_semisup.jl b/models/dppl_hmm_semisup.jl
new file mode 100644
index 0000000..de23a75
--- /dev/null
+++ b/models/dppl_hmm_semisup.jl
@@ -0,0 +1,59 @@
+using StatsFuns: logsumexp
+
+# Set up hyperparameters
+K, v, T, T_unsup = 5, 20, 100, 200
+alpha = fill(1.0, K)
+beta = fill(0.1, v)
+theta = rand(Dirichlet(alpha), K)
+phi = rand(Dirichlet(beta), K)
+
+# Simulate data (supervised)
+w = Vector{Int}(undef, T)
+z = Vector{Int}(undef, T)
+z[1] = rand(1:K)
+w[1] = rand(Categorical(phi[:, z[1]]))
+for t in 2:T
+    z[t] = rand(Categorical(theta[:, z[t - 1]]))
+    w[t] = rand(Categorical(phi[:, z[t]]))
+end
+
+# Unsupervised
+u = Vector{Int}(undef, T_unsup)
+y = Vector{Int}(undef, T_unsup)
+y[1] = rand(1:K)
+u[1] = rand(Categorical(phi[:, y[1]]))
+for t in 2:T_unsup
+    y[t] = rand(Categorical(theta[:, y[t - 1]]))
+    u[t] = rand(Categorical(phi[:, y[t]]))
+end
+
+@model function dppl_hmm_semisup(K, T, T_unsup, w, z, u, alpha, beta)
+    theta ~ filldist(Dirichlet(alpha), K)
+    phi ~ filldist(Dirichlet(beta), K)
+    for t in 1:T
+        w[t] ~ Categorical(phi[:, z[t]]);
+    end
+    for t in 2:T
+        z[t] ~ Categorical(theta[:, z[t - 1]]);
+    end
+
+    TF = eltype(theta)
+    acc = similar(alpha, TF, K)
+    gamma = similar(alpha, TF, K)
+    temp_gamma = similar(alpha, TF, K)
+    for k in 1:K
+        gamma[k] = log(phi[u[1],k])
+    end
+    for t in 2:T_unsup
+        for k in 1:K
+            for j in 1:K
+                acc[j] = gamma[j] + log(theta[k, j]) + log(phi[u[t], k])
+            end
+            temp_gamma[k] = logsumexp(acc)
+        end
+        gamma .= temp_gamma
+    end
+    DynamicPPL.@addlogprob! logsumexp(gamma)
+end
+
+@register dppl_hmm_semisup(K, T, T_unsup, w, z, u, alpha, beta)
diff --git a/models/dppl_lda.jl b/models/dppl_lda.jl
new file mode 100644
index 0000000..a28ff6f
--- /dev/null
+++ b/models/dppl_lda.jl
@@ -0,0 +1,34 @@
+v = 100      # words
+k = 5        # topics
+m = 10       # number of docs
+alpha = ones(k)
+beta = ones(v)
+
+phi = rand(Dirichlet(beta), k)
+theta = rand(Dirichlet(alpha), m)
+doc_lengths = rand(Poisson(1_000), m)
+n = sum(doc_lengths)
+
+w_lda = Vector{Int}(undef, n)
+doc_lda = Vector{Int}(undef, n)
+for i in 1:m
+    # Because all the models exist in the same scope, we need
+    # to add some variable suffixes to avoid local/global 
+    # scope warnings. This is quite ugly and should be solved
+    # properly, using e.g. modules or functions.
+    local idx_lda = sum(doc_lengths[1:i-1]) # starting index for inner loop
+    for j in 1:doc_lengths[i]
+        z_lda = rand(Categorical(theta[:, i]))
+        w_lda[idx_lda + j] = rand(Categorical(phi[:, z_lda]))
+        doc_lda[idx_lda + j] = i
+    end
+end
+
+@model function dppl_lda(k, m, w, doc, alpha, beta)
+    theta ~ filldist(Dirichlet(alpha), m)
+    phi ~ filldist(Dirichlet(beta), k)
+    log_phi_dot_theta = log.(phi * theta)
+    DynamicPPL.@addlogprob! sum(log_phi_dot_theta[CartesianIndex.(w, doc)])
+end
+
+@register dppl_lda(k, m, w_lda, doc_lda, alpha, beta)

From 46f46857acddcd56d3907a9e25f0f56611f6e1ba Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Fri, 20 Jun 2025 00:19:15 +0100
Subject: [PATCH 05/15] fix function names

---
 models/dppl_logistic_regression.jl |  2 +-
 models/dppl_naive_bayes.jl         |  2 +-
 models/dppl_sto_volatility.jl      | 24 +++++++++++++++++++++---
 3 files changed, 23 insertions(+), 5 deletions(-)

diff --git a/models/dppl_logistic_regression.jl b/models/dppl_logistic_regression.jl
index 0a3ada9..e09f606 100644
--- a/models/dppl_logistic_regression.jl
+++ b/models/dppl_logistic_regression.jl
@@ -12,7 +12,7 @@ end
 
 lazyarray(f, x) = LazyArray(Base.broadcasted(f, x))
 
-@model dppl_logistic_regression(Xt, y) = begin
+@model function dppl_logistic_regression(Xt, y)
     N, D = size(Xt)
     w ~ filldist(Normal(), D)
     y ~ arraydist(lazyarray(x -> Bernoulli(safelogistic(x)), Xt * w))
diff --git a/models/dppl_naive_bayes.jl b/models/dppl_naive_bayes.jl
index 3ed7f4f..5b23add 100644
--- a/models/dppl_naive_bayes.jl
+++ b/models/dppl_naive_bayes.jl
@@ -19,7 +19,7 @@ image_subset = image[:, 1:N]'
 image_vec = vec(image_subset[:, :])
 labels = labels[1:N]
 
-@model dppl_naive_bayes(image_vec, labels, C, D) = begin
+@model function dppl_naive_bayes(image_vec, labels, C, D)
     m ~ filldist(Normal(0, 10), C, D)
     image_vec ~ MvNormal(vec(m[labels, :]), I)
 end
diff --git a/models/dppl_sto_volatility.jl b/models/dppl_sto_volatility.jl
index a849767..26a318c 100644
--- a/models/dppl_sto_volatility.jl
+++ b/models/dppl_sto_volatility.jl
@@ -1,5 +1,23 @@
 using Downloads, CSV
 
-URL =
-http_response = Downloads.download(url)
-file = CSV.File(http_response)
+path = "$(@__DIR__)/../data/dppl_sto_volatility.csv"
+data, _ = readdlm(path, ',', header=true)
+to_num(x) = x isa Number ? x : 0.1
+y = map(to_num, data[1:500, 2])
+
+@model function dppl_sto_volatility(y, ::Type{Tv}=Vector{Float64}) where {Tv}
+    T = length(y)
+    μ ~ Cauchy(0, 10)
+    ϕ ~ Uniform(-1, 1)
+    σ ~ truncated(Cauchy(0, 5); lower=0)
+
+    h = Tv(undef, T)
+    h[1] ~ Normal(μ, σ / sqrt(1 - ϕ^2))
+    y[1] ~ Normal(0, exp(h[1] / 2))
+    for t in 2:T
+        h[t] ~ Normal(μ + ϕ * (h[t-1] - μ), σ)
+        y[t] ~ Normal(0, exp(h[t] / 2))
+    end
+end
+
+@register dppl_sto_volatility(y)

From c41459d99e818b46673637b83891f5e5d0586cc4 Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Fri, 20 Jun 2025 00:21:44 +0100
Subject: [PATCH 06/15] fix refresh website workflow for PRs

---
 .github/workflows/refresh_website.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/refresh_website.yml b/.github/workflows/refresh_website.yml
index 4465450..6fce188 100644
--- a/.github/workflows/refresh_website.yml
+++ b/.github/workflows/refresh_website.yml
@@ -32,9 +32,9 @@ jobs:
 
       - name: Download results to web/src/data
         run: |
-          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/adtests.json
-          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/manifest.json
-          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/model_definitions.json
+          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${{ github.event_name == 'pull_request' && '/pr' || '' }}adtests.json
+          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${{ github.event_name == 'pull_request' && '/pr' || '' }}manifest.json
+          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${{ github.event_name == 'pull_request' && '/pr' || '' }}model_definition.json
         working-directory: web/src/data
 
       # This isn't needed to build the website, it's just there so that the

From 131071169f062d6157f04f2095073b6c31788db4 Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Fri, 20 Jun 2025 00:22:37 +0100
Subject: [PATCH 07/15] actually fix it

---
 .github/workflows/refresh_website.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/refresh_website.yml b/.github/workflows/refresh_website.yml
index 6fce188..cf73fa2 100644
--- a/.github/workflows/refresh_website.yml
+++ b/.github/workflows/refresh_website.yml
@@ -32,9 +32,9 @@ jobs:
 
       - name: Download results to web/src/data
         run: |
-          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${{ github.event_name == 'pull_request' && '/pr' || '' }}adtests.json
-          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${{ github.event_name == 'pull_request' && '/pr' || '' }}manifest.json
-          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${{ github.event_name == 'pull_request' && '/pr' || '' }}model_definition.json
+          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${{ github.event_name == 'pull_request' && 'pr/' || '' }}adtests.json
+          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${{ github.event_name == 'pull_request' && 'pr/' || '' }}manifest.json
+          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${{ github.event_name == 'pull_request' && 'pr/' || '' }}model_definition.json
         working-directory: web/src/data
 
       # This isn't needed to build the website, it's just there so that the

From 0d7db2ee9063ae4e2456af96e27b06de7a1b0f89 Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Fri, 20 Jun 2025 00:23:53 +0100
Subject: [PATCH 08/15] i lied

---
 .github/workflows/refresh_website.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/refresh_website.yml b/.github/workflows/refresh_website.yml
index cf73fa2..d849733 100644
--- a/.github/workflows/refresh_website.yml
+++ b/.github/workflows/refresh_website.yml
@@ -34,7 +34,7 @@ jobs:
         run: |
           curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${{ github.event_name == 'pull_request' && 'pr/' || '' }}adtests.json
           curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${{ github.event_name == 'pull_request' && 'pr/' || '' }}manifest.json
-          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${{ github.event_name == 'pull_request' && 'pr/' || '' }}model_definition.json
+          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${{ github.event_name == 'pull_request' && 'pr/' || '' }}model_definitions.json
         working-directory: web/src/data
 
       # This isn't needed to build the website, it's just there so that the

From e3d97e79da0bc234e8dc005f9240d41fb80f6bc8 Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Fri, 20 Jun 2025 00:27:15 +0100
Subject: [PATCH 09/15] cancel old workflows

---
 .github/workflows/generate_website.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/generate_website.yml b/.github/workflows/generate_website.yml
index f9fda06..86807f8 100644
--- a/.github/workflows/generate_website.yml
+++ b/.github/workflows/generate_website.yml
@@ -23,6 +23,11 @@ permissions:
   actions: write
   contents: write
 
+# Cancel existing tests on the same PR if a new commit is added to a pull request
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+
 jobs:
   setup-keys:
     runs-on: ubuntu-latest

From c1b0cee016570c01357d97ca0ee350941f808824 Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Sun, 29 Jun 2025 17:57:09 +0100
Subject: [PATCH 10/15] use `model = ` instead of `@register`

---
 models/dppl_gauss_unknown.jl       | 2 +-
 models/dppl_hier_poisson.jl        | 2 +-
 models/dppl_high_dim_gauss.jl      | 2 +-
 models/dppl_hmm_semisup.jl         | 2 +-
 models/dppl_lda.jl                 | 2 +-
 models/dppl_logistic_regression.jl | 2 +-
 models/dppl_naive_bayes.jl         | 2 +-
 models/dppl_sto_volatility.jl      | 2 +-
 8 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/models/dppl_gauss_unknown.jl b/models/dppl_gauss_unknown.jl
index a79a212..b70bacd 100644
--- a/models/dppl_gauss_unknown.jl
+++ b/models/dppl_gauss_unknown.jl
@@ -9,4 +9,4 @@ y = randn() .+ s * randn(n)
     y ~ filldist(Normal(m, s), N)
 end
 
-@register dppl_gauss_unknown(y)
+model = dppl_gauss_unknown(y)
diff --git a/models/dppl_hier_poisson.jl b/models/dppl_hier_poisson.jl
index f432839..6850353 100644
--- a/models/dppl_hier_poisson.jl
+++ b/models/dppl_hier_poisson.jl
@@ -24,4 +24,4 @@ lazyarray(f, x) = LazyArray(Base.broadcasted(f, x))
     y ~ arraydist(lazyarray(LogPoisson, alpha))
 end
 
-@register dppl_hier_poisson(y, x, idx, ns)
+model = dppl_hier_poisson(y, x, idx, ns)
diff --git a/models/dppl_high_dim_gauss.jl b/models/dppl_high_dim_gauss.jl
index 2275b6a..58d09ef 100644
--- a/models/dppl_high_dim_gauss.jl
+++ b/models/dppl_high_dim_gauss.jl
@@ -2,4 +2,4 @@
     m ~ filldist(Normal(0, 1), D)
 end
 
-@register dppl_high_dim_gauss(10_000)
+model = dppl_high_dim_gauss(10_000)
diff --git a/models/dppl_hmm_semisup.jl b/models/dppl_hmm_semisup.jl
index de23a75..8c8fd8a 100644
--- a/models/dppl_hmm_semisup.jl
+++ b/models/dppl_hmm_semisup.jl
@@ -56,4 +56,4 @@ end
     DynamicPPL.@addlogprob! logsumexp(gamma)
 end
 
-@register dppl_hmm_semisup(K, T, T_unsup, w, z, u, alpha, beta)
+model = dppl_hmm_semisup(K, T, T_unsup, w, z, u, alpha, beta)
diff --git a/models/dppl_lda.jl b/models/dppl_lda.jl
index a28ff6f..43f8bd8 100644
--- a/models/dppl_lda.jl
+++ b/models/dppl_lda.jl
@@ -31,4 +31,4 @@ end
     DynamicPPL.@addlogprob! sum(log_phi_dot_theta[CartesianIndex.(w, doc)])
 end
 
-@register dppl_lda(k, m, w_lda, doc_lda, alpha, beta)
+model = dppl_lda(k, m, w_lda, doc_lda, alpha, beta)
diff --git a/models/dppl_logistic_regression.jl b/models/dppl_logistic_regression.jl
index e09f606..3b21928 100644
--- a/models/dppl_logistic_regression.jl
+++ b/models/dppl_logistic_regression.jl
@@ -18,4 +18,4 @@ lazyarray(f, x) = LazyArray(Base.broadcasted(f, x))
     y ~ arraydist(lazyarray(x -> Bernoulli(safelogistic(x)), Xt * w))
 end
 
-@register dppl_logistic_regression(X', y)
+model = dppl_logistic_regression(X', y)
diff --git a/models/dppl_naive_bayes.jl b/models/dppl_naive_bayes.jl
index 5b23add..2bc1cfa 100644
--- a/models/dppl_naive_bayes.jl
+++ b/models/dppl_naive_bayes.jl
@@ -24,4 +24,4 @@ labels = labels[1:N]
     image_vec ~ MvNormal(vec(m[labels, :]), I)
 end
 
-@register dppl_naive_bayes(image_vec, labels, C, D)
+model = dppl_naive_bayes(image_vec, labels, C, D)
diff --git a/models/dppl_sto_volatility.jl b/models/dppl_sto_volatility.jl
index 26a318c..e664773 100644
--- a/models/dppl_sto_volatility.jl
+++ b/models/dppl_sto_volatility.jl
@@ -20,4 +20,4 @@ y = map(to_num, data[1:500, 2])
     end
 end
 
-@register dppl_sto_volatility(y)
+model = dppl_sto_volatility(y)

From 544016d9073dd22116589e18a7b94dc64903439a Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Sun, 29 Jun 2025 18:37:47 +0100
Subject: [PATCH 11/15] fix

---
 main.jl | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/main.jl b/main.jl
index 97d9407..e12c3bd 100644
--- a/main.jl
+++ b/main.jl
@@ -100,14 +100,13 @@ end
 @include_model "demo_dot_assume_observe_submodel"
 @include_model "dot_assume"
 @include_model "dot_observe"
-@include_model "dppl_gauss_unknown.jl"
+@include_model "dppl_gauss_unknown"
 @include_model "dppl_hier_poisson"
-@include_model "dppl_high_dim_gauss.jl"
+@include_model "dppl_high_dim_gauss"
 @include_model "dppl_hmm_semisup"
 @include_model "dppl_lda"
 @include_model "dppl_logistic_regression"
-# Disabled because of https://github.com/TuringLang/ADTests/issues/24
-# @include_model "dppl_naive_bayes"
+@include_model "dppl_naive_bayes"
 @include_model "dppl_sto_volatility"
 @include_model "dynamic_constraint"
 @include_model "multiple_constraints_same_var"

From f9603628607572a998946f8833619106f47437e9 Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Sun, 29 Jun 2025 18:43:40 +0100
Subject: [PATCH 12/15] fixes

---
 models/dppl_hmm_semisup.jl |  2 +-
 models/dppl_lda.jl         | 20 ++++++++------------
 2 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/models/dppl_hmm_semisup.jl b/models/dppl_hmm_semisup.jl
index 8c8fd8a..a165e94 100644
--- a/models/dppl_hmm_semisup.jl
+++ b/models/dppl_hmm_semisup.jl
@@ -53,7 +53,7 @@ end
         end
         gamma .= temp_gamma
     end
-    DynamicPPL.@addlogprob! logsumexp(gamma)
+    @addlogprob! logsumexp(gamma)
 end
 
 model = dppl_hmm_semisup(K, T, T_unsup, w, z, u, alpha, beta)
diff --git a/models/dppl_lda.jl b/models/dppl_lda.jl
index 43f8bd8..b807d38 100644
--- a/models/dppl_lda.jl
+++ b/models/dppl_lda.jl
@@ -9,18 +9,14 @@ theta = rand(Dirichlet(alpha), m)
 doc_lengths = rand(Poisson(1_000), m)
 n = sum(doc_lengths)
 
-w_lda = Vector{Int}(undef, n)
-doc_lda = Vector{Int}(undef, n)
+w = Vector{Int}(undef, n)
+doc = Vector{Int}(undef, n)
 for i in 1:m
-    # Because all the models exist in the same scope, we need
-    # to add some variable suffixes to avoid local/global 
-    # scope warnings. This is quite ugly and should be solved
-    # properly, using e.g. modules or functions.
-    local idx_lda = sum(doc_lengths[1:i-1]) # starting index for inner loop
+    local idx = sum(doc_lengths[1:i-1]) # starting index for inner loop
     for j in 1:doc_lengths[i]
-        z_lda = rand(Categorical(theta[:, i]))
-        w_lda[idx_lda + j] = rand(Categorical(phi[:, z_lda]))
-        doc_lda[idx_lda + j] = i
+        z = rand(Categorical(theta[:, i]))
+        w[idx + j] = rand(Categorical(phi[:, z]))
+        doc[idx + j] = i
     end
 end
 
@@ -28,7 +24,7 @@ end
     theta ~ filldist(Dirichlet(alpha), m)
     phi ~ filldist(Dirichlet(beta), k)
     log_phi_dot_theta = log.(phi * theta)
-    DynamicPPL.@addlogprob! sum(log_phi_dot_theta[CartesianIndex.(w, doc)])
+    @addlogprob! sum(log_phi_dot_theta[CartesianIndex.(w, doc)])
 end
 
-model = dppl_lda(k, m, w_lda, doc_lda, alpha, beta)
+model = dppl_lda(k, m, w, doc, alpha, beta)

From e27139d6e453f57b53ef42de988303afd5125c05 Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Sun, 29 Jun 2025 18:50:20 +0100
Subject: [PATCH 13/15] fix

---
 models/dppl_sto_volatility.jl | 2 --
 1 file changed, 2 deletions(-)

diff --git a/models/dppl_sto_volatility.jl b/models/dppl_sto_volatility.jl
index e664773..27bb213 100644
--- a/models/dppl_sto_volatility.jl
+++ b/models/dppl_sto_volatility.jl
@@ -1,5 +1,3 @@
-using Downloads, CSV
-
 path = "$(@__DIR__)/../data/dppl_sto_volatility.csv"
 data, _ = readdlm(path, ',', header=true)
 to_num(x) = x isa Number ? x : 0.1

From d781d5334ffbe369b76a8ef0d3e762deffb2199e Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Sun, 29 Jun 2025 19:09:12 +0100
Subject: [PATCH 14/15] fixes

---
 Project.toml                  | 1 +
 main.jl                       | 2 +-
 models/dppl_sto_volatility.jl | 2 ++
 3 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index 0783a3a..db204b1 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,6 +1,7 @@
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 Chairmarks = "0ca39b1e-fe0b-4e98-acfc-b1656634c4de"
+DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DistributionsAD = "ced4e74d-a319-5a8a-b0ac-84af2272839c"
diff --git a/main.jl b/main.jl
index e12c3bd..71e9e72 100644
--- a/main.jl
+++ b/main.jl
@@ -17,7 +17,7 @@ ADTYPES = Dict(
     "ForwardDiff" => AutoForwardDiff(),
     "ReverseDiff" => AutoReverseDiff(; compile = false),
     "ReverseDiffCompiled" => AutoReverseDiff(; compile = true),
-    "Mooncake" => AutoMooncake(; config = nothing),
+    "Mooncake" => AutoMooncake(),
     "EnzymeForward" => AutoEnzyme(; mode = set_runtime_activity(Forward, true)),
     "EnzymeReverse" => AutoEnzyme(; mode = set_runtime_activity(Reverse, true)),
     "Zygote" => AutoZygote(),
diff --git a/models/dppl_sto_volatility.jl b/models/dppl_sto_volatility.jl
index 27bb213..381075a 100644
--- a/models/dppl_sto_volatility.jl
+++ b/models/dppl_sto_volatility.jl
@@ -1,3 +1,5 @@
+using DelimitedFiles: readdlm
+
 path = "$(@__DIR__)/../data/dppl_sto_volatility.csv"
 data, _ = readdlm(path, ',', header=true)
 to_num(x) = x isa Number ? x : 0.1

From 07c976f947faead41cc720c8e2b173e89294b284 Mon Sep 17 00:00:00 2001
From: Penelope Yong <penelopeysm@gmail.com>
Date: Sun, 29 Jun 2025 19:31:13 +0100
Subject: [PATCH 15/15] try with unbuffered

---
 .github/workflows/generate_website.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/generate_website.yml b/.github/workflows/generate_website.yml
index 86807f8..f206337 100644
--- a/.github/workflows/generate_website.yml
+++ b/.github/workflows/generate_website.yml
@@ -96,6 +96,7 @@ jobs:
           ADTYPE_KEYS: ${{ needs.setup-keys.outputs.adtype_keys }}
           ADTESTS_MODELS_TO_LOAD: ${{ matrix.model }}
           DATADEPS_ALWAYS_ACCEPT: "true"
+          PYTHONUNBUFFERED: "1"
 
       - name: Output matrix values
         id: output-matrix