Merge remote-tracking branch 'origin/main' into py/dppl-models

Author: penelopeysm

.github/workflows/refresh_website.yml

@@ -32,10 +32,12 @@ 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/${{ github.event_name == 'pull_request' && 'pr/' || '' }}model_definitions.json
+          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${PR}adtests.json
+          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${PR}manifest.json
+          curl -O https://raw.githubusercontent.com/TuringLang/ADTests/refs/heads/gh-pages/${PR}model_definitions.json
         working-directory: web/src/data
+        env:
+          PR: ${{ github.event_name == 'pull_request' && 'pr/' || '' }}
 
       # This isn't needed to build the website, it's just there so that the
       # JSON is easily accessible on the gh-pages branch

README.md

@@ -13,11 +13,30 @@ You can modify the list of AD types in `main.jl`.
 ## I want to add more models!
 
 You can modify the list of models by adding a new file inside the `models` directory.
-This file should contain the model definition, and call the `@register` macro to register the model with the `ADTests` package.
-See the existing files in that directory for examples.
-Then, make sure to `include` the new source file in `main.jl`.
 
-To make sure that the definition is included in the final website, you will have to make sure that the filename is the same as the model name (i.e. a model `@model function f()` is in `models/f.jl`).
+Inside this file, you do not need to call `using Turing` or any of the AD backends.
+However, you will have to make sure to import any other packages that your model uses.
+
+This file should have, as the final line, the creation of the Turing model object using `model = model_f(...)`.
+(It is mandatory for the model object to be called `model`.)
+
+Then, inside `main.jl`, call `@include_model category_heading model_name`.
+
+- `category_heading` is a string that is used to determine which table the model appears under on the website.
+- For the automated tests to run properly, `model_name` **must** be consistent between the following:
+  - The name of the model itself i.e. `@model function model_name(...)`
+  - The filename i.e. `models/model_name.jl`
+  - The name of the model in `main.jl` i.e. `@include_model "Category Heading" model_name`
+
+Ideally, `model_name` would be self-explanatory, i.e. it would serve to illustrate exactly one feature and the name would indicate this.
+However, if necessary, you can add explanatory comments inside the model definition file.
+
+You can see the existing files in that directory for examples.
+
+> [!NOTE]
+> This setup does admittedly feel a bit complicated.
+> Unfortunately I could not find a simpler way to get all the components (Julia, Python, web app) to work together in an automated fashion.
+> Hopefully it is a small price to pay for the ability to just add a new model and have it be automatically included on the website.
 
 ## I want to edit the website!
 

ad.py

@@ -83,6 +83,15 @@ def run_ad(args):
     else:
         RUN_JULIA_COMMAND = JULIA_COMMAND
 
+    # Get category
+    try:
+        category = run_and_capture([*RUN_JULIA_COMMAND, "--get-category", model_key])
+    except sp.CalledProcessError as e:
+        print(f"Julia crashed when getting category for {model_key}.")
+        print(f"To reproduce, run: `julia --project=. main.jl --get-category {model_key}`")
+        category = "error"
+    results["__category__"] = category
+
     # Run tests
     for adtype in adtypes:
         print(f"Running {model_key} with {adtype}...")
@@ -127,12 +136,14 @@ def html(_args):
     # [
     #     {"model_name": "model1",
     #      "results": {
+    #          "__category_": "category1",
     #          "AD1": "result1",
     #          "AD2": "result2"
     #      }
     #     },
     #     {"model_name": "model2",
     #      "results": {
+    #          "__category_": "category2",
     #          "AD1": "result3",
     #          "AD2": "result4"
     #      }

main.jl

@@ -1,8 +1,6 @@
-import Test: @test, @testset
 using DynamicPPL: DynamicPPL, VarInfo
 using DynamicPPL.TestUtils.AD: run_ad, ADResult, ADIncorrectException
 using ADTypes
-using Printf: @printf
 
 import FiniteDifferences: central_fdm
 import ForwardDiff
@@ -13,30 +11,26 @@ import Zygote
 
 # AD backends to test.
 ADTYPES = Dict(
-    "FiniteDifferences" => AutoFiniteDifferences(; fdm = central_fdm(5, 1)),
+    "FiniteDifferences" => AutoFiniteDifferences(; fdm=central_fdm(5, 1)),
     "ForwardDiff" => AutoForwardDiff(),
-    "ReverseDiff" => AutoReverseDiff(; compile = false),
-    "ReverseDiffCompiled" => AutoReverseDiff(; compile = true),
-    "Mooncake" => AutoMooncake(),
-    "EnzymeForward" => AutoEnzyme(; mode = set_runtime_activity(Forward, true)),
-    "EnzymeReverse" => AutoEnzyme(; mode = set_runtime_activity(Reverse, true)),
+    "ReverseDiff" => AutoReverseDiff(; compile=false),
+    "ReverseDiffCompiled" => AutoReverseDiff(; compile=true),
+    "Mooncake" => AutoMooncake(; config=nothing),
+    "EnzymeForward" => AutoEnzyme(; mode=set_runtime_activity(Forward, true)),
+    "EnzymeReverse" => AutoEnzyme(; mode=set_runtime_activity(Reverse, true)),
     "Zygote" => AutoZygote(),
 )
 
-# Models to test. The convention is that:
-#    a, b, c, ... are assumed variables
-#    x, y, z, ... are observed variables
-# although it's hardly a big deal.
-MODELS = Dict{String,DynamicPPL.Model}()
-macro register(model)
-    :(MODELS[string($(esc(model)).f)] = $(esc(model)))
+MODELS = Dict{String,Tuple{String,DynamicPPL.Model}}()
+macro register(category, model)
+    :(MODELS[string($(esc(model)).f)] = ($(esc(category)), $(esc(model))))
 end
 
 """
-    include_model(model_name::AbstractString)
+    include_model(category::AbstractString, model_name::AbstractString)
 
 Add the model defined in `models/model_name.jl` to the full list of models
-tested in this script.
+tested in this script. The model is registered under the given `category`.
 
 We want to isolate every model in its own module, so that we avoid e.g.
 variable clashes, and also so that we make imports explicit.
@@ -57,17 +51,17 @@ definition file:
  - Once defined, the model is created using `model = model_name(...)`. The
    `model` on the left-hand side is mandatory.
 """
-macro include_model(model_name::AbstractString)
+macro include_model(category::AbstractString, model_name::AbstractString)
     MODELS_TO_LOAD = get(ENV, "ADTESTS_MODELS_TO_LOAD", "__all__")
     if MODELS_TO_LOAD == "__all__" || model_name in split(MODELS_TO_LOAD, ",")
         # Declare a module containing the model. In principle esc() shouldn't
         # be needed, but see https://github.com/JuliaLang/julia/issues/55677
         Expr(:toplevel, esc(:(
             module $(gensym())
-                using .Main: @register
-                using Turing
-                include("models/" * $(model_name) * ".jl")
-                @register model
+            using .Main: @register
+            using Turing
+            include("models/" * $(model_name) * ".jl")
+            @register $(category) model
             end
         )))
     else
@@ -76,71 +70,78 @@ macro include_model(model_name::AbstractString)
     end
 end
 
-@include_model "assume_beta"
-@include_model "assume_dirichlet"
-@include_model "assume_lkjcholu"
-@include_model "assume_mvnormal"
-@include_model "assume_normal"
-@include_model "assume_submodel"
-@include_model "assume_wishart"
-@include_model "broadcast_macro"
-@include_model "control_flow"
-@include_model "demo_assume_dot_observe"
-@include_model "demo_assume_dot_observe_literal"
-@include_model "demo_assume_index_observe"
-@include_model "demo_assume_matrix_observe_matrix_index"
-@include_model "demo_assume_multivariate_observe"
-@include_model "demo_assume_multivariate_observe_literal"
-@include_model "demo_assume_observe_literal"
-@include_model "demo_assume_submodel_observe_index_literal"
-@include_model "demo_dot_assume_observe"
-@include_model "demo_dot_assume_observe_index"
-@include_model "demo_dot_assume_observe_index_literal"
-@include_model "demo_dot_assume_observe_matrix_index"
-@include_model "demo_dot_assume_observe_submodel"
-@include_model "dot_assume"
-@include_model "dot_observe"
-@include_model "dppl_gauss_unknown"
-@include_model "dppl_hier_poisson"
-@include_model "dppl_high_dim_gauss"
-@include_model "dppl_hmm_semisup"
-@include_model "dppl_lda"
-@include_model "dppl_logistic_regression"
-@include_model "dppl_naive_bayes"
-@include_model "dppl_sto_volatility"
-@include_model "dynamic_constraint"
-@include_model "multiple_constraints_same_var"
-@include_model "multithreaded"
-@include_model "n010"
-@include_model "n050"
-@include_model "n100"
-@include_model "n500"
-@include_model "observe_bernoulli"
-@include_model "observe_categorical"
-@include_model "observe_index"
-@include_model "observe_literal"
-@include_model "observe_multivariate"
-@include_model "observe_submodel"
-@include_model "pdb_eight_schools_centered"
-@include_model "pdb_eight_schools_noncentered"
-@include_model "von_mises"
+# Models to test. The convention is that:
+#    a, b, c, ... are assumed variables
+#    x, y, z, ... are observed variables
+# although it's hardly a big deal.
+@include_model "Base Julia features" "control_flow"
+@include_model "Base Julia features" "multithreaded"
+@include_model "Core Turing syntax" "broadcast_macro"
+@include_model "Core Turing syntax" "dot_assume"
+@include_model "Core Turing syntax" "dot_observe"
+@include_model "Core Turing syntax" "dynamic_constraint"
+@include_model "Core Turing syntax" "multiple_constraints_same_var"
+@include_model "Core Turing syntax" "observe_index"
+@include_model "Core Turing syntax" "observe_literal"
+@include_model "Core Turing syntax" "observe_multivariate"
+@include_model "Core Turing syntax" "observe_submodel"
+@include_model "Distributions" "assume_beta"
+@include_model "Distributions" "assume_dirichlet"
+@include_model "Distributions" "assume_lkjcholu"
+@include_model "Distributions" "assume_mvnormal"
+@include_model "Distributions" "assume_normal"
+@include_model "Distributions" "assume_submodel"
+@include_model "Distributions" "assume_wishart"
+@include_model "Distributions" "observe_bernoulli"
+@include_model "Distributions" "observe_categorical"
+@include_model "Distributions" "observe_von_mises"
+@include_model "DynamicPPL arXiV paper" "dppl_gauss_unknown"
+@include_model "DynamicPPL arXiV paper" "dppl_hier_poisson"
+@include_model "DynamicPPL arXiV paper" "dppl_high_dim_gauss"
+@include_model "DynamicPPL arXiV paper" "dppl_hmm_semisup"
+@include_model "DynamicPPL arXiV paper" "dppl_lda"
+@include_model "DynamicPPL arXiV paper" "dppl_logistic_regression"
+@include_model "DynamicPPL arXiV paper" "dppl_naive_bayes"
+@include_model "DynamicPPL arXiV paper" "dppl_sto_volatility"
+@include_model "DynamicPPL demo models" "demo_assume_dot_observe"
+@include_model "DynamicPPL demo models" "demo_assume_dot_observe_literal"
+@include_model "DynamicPPL demo models" "demo_assume_index_observe"
+@include_model "DynamicPPL demo models" "demo_assume_matrix_observe_matrix_index"
+@include_model "DynamicPPL demo models" "demo_assume_multivariate_observe"
+@include_model "DynamicPPL demo models" "demo_assume_multivariate_observe_literal"
+@include_model "DynamicPPL demo models" "demo_assume_observe_literal"
+@include_model "DynamicPPL demo models" "demo_assume_submodel_observe_index_literal"
+@include_model "DynamicPPL demo models" "demo_dot_assume_observe"
+@include_model "DynamicPPL demo models" "demo_dot_assume_observe_index"
+@include_model "DynamicPPL demo models" "demo_dot_assume_observe_index_literal"
+@include_model "DynamicPPL demo models" "demo_dot_assume_observe_matrix_index"
+@include_model "DynamicPPL demo models" "demo_dot_assume_observe_submodel"
+@include_model "Effect of model size" "n010"
+@include_model "Effect of model size" "n050"
+@include_model "Effect of model size" "n100"
+@include_model "Effect of model size" "n500"
+@include_model "PosteriorDB" "pdb_eight_schools_centered"
+@include_model "PosteriorDB" "pdb_eight_schools_noncentered"
 
 # The entry point to this script itself begins here
 if ARGS == ["--list-model-keys"]
     foreach(println, sort(collect(keys(MODELS))))
 elseif ARGS == ["--list-adtype-keys"]
     foreach(println, sort(collect(keys(ADTYPES))))
+elseif length(ARGS) == 2 && ARGS[1] == "--get-category"
+    println(MODELS[ARGS[2]][1])
 elseif length(ARGS) == 3 && ARGS[1] == "--run"
-    model, adtype = MODELS[ARGS[2]], ADTYPES[ARGS[3]]
+    model_name, adtype_name = ARGS[2], ARGS[3]
+    model, adtype = MODELS[model_name][2], ADTYPES[adtype_name]
 
     try
-        if ARGS[2] == "control_flow"
+        if model_name == "control_flow"
             # https://github.com/TuringLang/ADTests/issues/4
             vi = DynamicPPL.unflatten(VarInfo(model), [0.5, -0.5])
             params = [-0.5, 0.5]
-            result = run_ad(model, adtype; varinfo = vi, params = params, benchmark = true)
+            result = run_ad(model, adtype; varinfo=vi, params=params, benchmark=true)
         else
-            result = run_ad(model, adtype; benchmark = true)
+            result = run_ad(model, adtype; benchmark=true)
         end
         # If reached here - nothing went wrong
         println(result.time_vs_primal)
@@ -170,4 +171,5 @@ else
     println("Usage: julia main.jl --list-model-keys")
     println("       julia main.jl --list-adtype-keys")
     println("       julia main.jl --run <model> <adtype>")
+    println("       julia main.jl --get-category <model>")
 end

models/observe_von_mises.jl

@@ -0,0 +1,6 @@
+@model function observe_von_mises(x)
+    a ~ InverseGamma(2, 3)
+    x ~ VonMises(0, a)
+end
+
+model = observe_von_mises(0.4)

models/von_mises.jl

@@ -2,6 +2,30 @@
     import data from "./data/adtests.json";
     import modelDefinitions from "./data/model_definitions.json";
 
+    // Parse data into nice JS objects.
+    // Obviously, the nested strings are a bit ugly. From outer to inner, they are:
+    // category -> model_name -> adtype -> result
+    let categorisedData = new Map<
+        string,
+        Map<string, Map<string, string | number>>
+    >();
+    for (const [model_name, results] of Object.entries(data)) {
+        let category = results.__category__;
+        delete results.__category__;
+        let resultsMap = new Map<string, string | number>();
+        for (const [adtype, result] of Object.entries(results)) {
+            resultsMap.set(adtype, result);
+        }
+        if (!categorisedData.has(category)) {
+            categorisedData.set(
+                category,
+                new Map<string, Map<string, string | number>>(),
+            );
+        }
+        categorisedData.get(category).set(model_name, resultsMap);
+    }
+    console.log(categorisedData);
+
     import Manifest from "./lib/Manifest.svelte";
     import ResultsTable from "./lib/ResultsTable.svelte";
 </script>
@@ -78,7 +102,10 @@
                 >Download the raw data (JSON)</a
             >
         </p>
-        <ResultsTable {data} {modelDefinitions} />
+        {#each categorisedData.entries() as [category, modelData]}
+            <h3>{category}</h3>
+            <ResultsTable data={modelData} {modelDefinitions} />
+        {/each}
 
         <h2>Manifest</h2>
         <p>The tests above were run with the following package versions:</p>

web/src/App.svelte

@@ -1,5 +1,11 @@
 <script lang="ts">
-    import manifest from "../data/manifest.json";
+    import manifestObj from "../data/manifest.json";
+
+    // convert manifest to a Map
+    let manifest = new Map<string, string | null>();
+    for (const [packageName, version] of Object.entries(manifestObj)) {
+        manifest.set(packageName, version === "" ? null : version);
+    }
 
     import { getSortedEntries } from "./utils";
 </script>

web/src/lib/Manifest.svelte

@@ -5,13 +5,14 @@
     import { getSortedEntries } from "./utils";
 
     interface Props {
-        data: object;
+        // model name -> adtype -> result
+        data: Map<string, Map<string, string | number>>;
         modelDefinitions: object;
     }
     const { data, modelDefinitions }: Props = $props();
 
-    const models = Object.keys(data);
-    const adtypes = Object.keys(data[models[0]]);
+    const models = [...data.keys()];
+    const adtypes = data.get(models[0]).keys();
 
     // Known errors
     const ENZYME_FWD_BLAS = "https://github.com/EnzymeAD/Enzyme.jl/issues/1995";

web/src/lib/ResultsTable.svelte

@@ -1,5 +1,5 @@
-export function getSortedEntries(obj: object) {
-    return Object.entries(obj).sort(([a, _x], [b, _y]) =>
-        a.localeCompare(b),
+export function getSortedEntries(m: Map<string, any>) {
+    return [...m.entries()].sort(([k1, _v1], [k2, _v2]) =>
+        k1.localeCompare(k2),
     );
 }