probcomp · sritchie · May 6, 2024 · Mar 28, 2024 · Apr 10, 2024 · Apr 16, 2024
diff --git a/docs/.gitignore b/docs/.gitignore
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,6 +1,7 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Gen = "ea4f424c-a589-11e8-07c0-fd5c91b9da4a"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 
 [compat]
-Documenter = "0.27"
+Documenter = "1"
diff --git a/docs/README b/docs/README
@@ -0,0 +1,16 @@
+# Website Docs
+- `pages.jl` to find skeleton of website.
+- `make.jl` to build the website index.
+
+# How to add tutorials
+Currently you must write the tutorial directly in the docs rather than a source file (e.g. Quarto). See `getting_started` or `tutorials` for examples.
+
+Code snippets must use the triple backtick with a label to run. The environment carries over so long as the labels match. Example:
+
+```@example tutorial_1
+x = rand()
+```
+
+```@example tutorial_1
+print(x)
+```
diff --git a/docs/build_docs_locally.sh b/docs/build_docs_locally.sh
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,37 +1,19 @@
+# Run: julia --project make.jl
 using Documenter, Gen
 
+include("pages.jl")
 makedocs(
-    sitename = "Gen",
     modules = [Gen],
-    pages = [
-        "Home" => "index.md",
-        "Getting Started" => "getting_started.md",
-        "Tutorials" => "tutorials.md",
-        "Modeling Languages and APIs" => [
-            "Generative Functions" => "ref/gfi.md",
-            "Probability Distributions" => "ref/distributions.md",
-            "Built-in Modeling Language" => "ref/modeling.md",
-            "Generative Function Combinators" => "ref/combinators.md",
-            "Choice Maps" => "ref/choice_maps.md",
-            "Selections" => "ref/selections.md",
-            "Optimizing Trainable Parameters" => "ref/parameter_optimization.md",
-            "Trace Translators" => "ref/trace_translators.md",
-            "Extending Gen" => "ref/extending.md"
-         ],
-        "Standard Inference Library" => [
-            "Importance Sampling" => "ref/importance.md",
-            "MAP Optimization" => "ref/map.md",
-            "Markov chain Monte Carlo" => "ref/mcmc.md",
-            "MAP Optimization" => "ref/map.md",
-            "Particle Filtering" => "ref/pf.md",
-            "Variational Inference" => "ref/vi.md",
-            "Learning Generative Functions" => "ref/learning.md"
-        ],
-        "Internals" => [
-            "Optimizing Trainable Parameters" => "ref/internals/parameter_optimization.md",
-            "Modeling Language Implementation" => "ref/internals/language_implementation.md"
-         ]
-    ]
+    # linkcheck = true,
+    doctest = false,
+    clean = true,
+    warnonly = true,
+    # warnonly = [:missing_docs],
+    format = Documenter.HTML(;
+        assets = String["assets/header.js", "assets/header.css", "assets/theme.css"]
+    ),
+    sitename = "Gen.jl",
+    pages = pages,
 )
 
 deploydocs(

diff --git a/docs/pages.jl b/docs/pages.jl
@@ -0,0 +1,53 @@
+pages = [
+    "Home" => "index.md",
+    "Getting Started" => [
+        "Example 1: Linear Regression" => "getting_started/linear_regression.md",
+        "Example 2: Hidden Markov Models" => "getting_started/hidden_markov_model.md",
+    ],
+    "Tutorials" => [
+        "Basics" => [
+            "tutorials/modeling_in_gen.md",
+            "tutorials/combinators.md",
+            "tutorials/gfi.md",
+            "tutorials/mcmc.md",
+            "tutorials/vi.md"
+        ],
+        "Advanced" => [
+            "tutorials/modeling_in_gen.md",
+            "tutorials/trace_translators.md"
+            # "tutorials/data_driven_proposals.md",
+        ],
+        "Modeling Languages" => [
+            "tutorials/languages/static_dsl.md",
+            "tutorials/languages/extending.md"
+        ],
+    ],
+    "Modeling Languages and APIs" => [
+        "Generative Functions" => "api/gfi.md",
+        "Probability Distributions" => "api/distributions.md",
+        "Built-in Modeling Language" => "api/modeling.md",
+        "Generative Function Combinators" => "api/combinators.md",
+        "Choice Maps" => "api/choice_maps.md",
+        "Selections" => "api/selections.md",
+        "Optimizing Trainable Parameters" => "api/parameter_optimization.md",
+        "Trace Translators" => "api/trace_translators.md",
+     ],
+    "Standard Inference Library" => [
+        "Importance Sampling" => "api/importance.md",
+        "MAP Optimization" => "api/map.md",
+        "Markov chain Monte Carlo" => "api/mcmc.md",
+        "MAP Optimization" => "api/map.md",
+        "Particle Filtering" => "api/pf.md",
+        "Variational Inference" => "api/vi.md",
+        "Learning Generative Functions" => "api/learning.md"
+    ],
+    "Internals" => [
+        "Optimizing Trainable Parameters" => "api/internals/parameter_optimization.md",
+        "Modeling Language Implementation" => "api/internals/language_implementation.md"
+    ],
+    "Miscellanea" => [
+        "Changelog" => "misc/changelog.md",
+        "Contributing" => "misc/contributing.md",
+        "References" => "misc/references.md"
+    ]
+]
diff --git a/docs/src/ref/choice_maps.md → docs/src/api/choice_maps.md b/docs/src/ref/choice_maps.md → docs/src/api/choice_maps.md
diff --git a/docs/src/ref/combinators.md → docs/src/api/combinators.md b/docs/src/ref/combinators.md → docs/src/api/combinators.md
diff --git a/docs/src/ref/distributions.md → docs/src/api/distributions.md b/docs/src/ref/distributions.md → docs/src/api/distributions.md
diff --git a/docs/src/api/gfi.md b/docs/src/api/gfi.md
@@ -0,0 +1,33 @@
+## Generative Functions
+
+```@docs
+GenerativeFunction
+```
+
+add example
+```julia
+@gen function model()
+end
+```
+
+The complete set of methods in the generative function interface (GFI) is:
+```@docs
+simulate
+generate
+update
+regenerate
+get_args
+get_retval
+get_choices
+get_score
+get_gen_fn
+Base.getindex
+project
+propose
+assess
+has_argument_grads
+accepts_output_grad
+accumulate_param_gradients!
+choice_gradients
+get_params
+```
diff --git a/docs/src/ref/importance.md → docs/src/api/importance.md b/docs/src/ref/importance.md → docs/src/api/importance.md
diff --git a/.../ref/internals/language_implementation.md → .../api/internals/language_implementation.md b/.../ref/internals/language_implementation.md → .../api/internals/language_implementation.md
diff --git a/...c/ref/internals/parameter_optimization.md → ...c/api/internals/parameter_optimization.md b/...c/ref/internals/parameter_optimization.md → ...c/api/internals/parameter_optimization.md
diff --git a/docs/src/ref/learning.md → docs/src/api/learning.md b/docs/src/ref/learning.md → docs/src/api/learning.md
diff --git a/docs/src/ref/map.md → docs/src/api/map.md b/docs/src/ref/map.md → docs/src/api/map.md
diff --git a/docs/src/api/mcmc.md b/docs/src/api/mcmc.md
@@ -0,0 +1,13 @@
+# Markov chain Monte Carlo (MCMC)
+```@docs
+metropolis_hastings
+mh
+mala
+hmc
+elliptical_slice
+@pkern
+@kern
+@rkern
+reversal
+involutive_mcmc
+```
diff --git a/docs/src/ref/modeling.md → docs/src/api/modeling.md b/docs/src/ref/modeling.md → docs/src/api/modeling.md
diff --git a/docs/src/ref/parameter_optimization.md → docs/src/api/parameter_optimization.md b/docs/src/ref/parameter_optimization.md → docs/src/api/parameter_optimization.md
diff --git a/docs/src/ref/pf.md → docs/src/api/pf.md b/docs/src/ref/pf.md → docs/src/api/pf.md
diff --git a/docs/src/ref/selections.md → docs/src/api/selections.md b/docs/src/ref/selections.md → docs/src/api/selections.md
diff --git a/docs/src/api/trace_translators.md b/docs/src/api/trace_translators.md
@@ -0,0 +1,15 @@
+## Trace Translators
+
+```@docs
+@transform
+@read
+@write
+@copy
+pair_bijections!
+is_involution!
+inverse
+DeterministicTraceTranslator
+GeneralTraceTranslator
+SimpleExtendingTraceTranslator
+SymmetricTraceTranslator
+```
diff --git a/docs/src/api/vi.md b/docs/src/api/vi.md
@@ -0,0 +1,7 @@
+## Variational inference
+There are two procedures in the inference library for performing black box variational inference.
+Each of these procedures can also train the model using stochastic gradient descent, as in a variational autoencoder.
+```@docs
+black_box_vi!
+black_box_vimco!
+```
diff --git a/docs/src/assets/header.css b/docs/src/assets/header.css
@@ -0,0 +1,138 @@
+
+@media all and (max-width: 560px) {
+    header.navigation {
+        position: fixed !important;
+        left:0;
+        top: 0;
+        width: 100%;
+    }
+
+    header.navigation div.container {
+        margin-left: 0rem;
+    }
+
+    header.navigation div.container nav.navbar {
+        min-height: 1rem !important;
+    }
+
+    header.navigation div.container nav.navbar ul.navbar-nav {
+        min-height: 1rem !important;
+        margin-left: 0.5rem !important;
+    }
+
+    header.navigation div.container nav.navbar ul.navbar-nav li.small-item {
+        visibility: visible !important;
+        display: block !important;
+        margin: 0.5rem;
+    }
+
+    header.navigation div.container nav.navbar ul.navbar-nav li.nav-item {
+        visibility: hidden;
+        display: none;
+    }
+
+    header.navigation div.container nav.navbar ul.navbar-nav li.nav-item a {
+        visibility: hidden;
+        display: none;
+    }
+
+    html:not(.theme--documenter-dark) body #documenter .docs-main {
+        margin-top: 2rem !important;
+    }
+}
+
+@media all and (max-width: 1055px) and (min-width: 561px){
+    header.navigation {
+        position: fixed !important;
+        left:0;
+        top: 0;
+        width: 100%;
+    }
+
+    header.navigation div.container {
+        margin-left: 0rem;
+    }
+
+    header.navigation div.container nav.navbar ul.navbar-nav {
+        width: 80% !important;
+    }
+}
+
+@media all and (min-width: 1056px) {
+    header.navigation {
+        position: fixed !important;
+        left:0;
+        top: 0;
+        width: 100%;
+    }
+
+    header.navigation div.container {
+        margin-left: 18rem;
+    }
+
+}
+
+html.theme--documenter-dark header.navigation {
+    background-color: #1f2424 !important;
+}
+
+html.theme--documenter-dark header.navigation div.container {
+    border-bottom: 1px solid #5e6d6f;
+}
+
+html.theme--documenter-dark header.navigation div.container nav.navbar {
+    background-color: #1f2424 !important;
+}
+
+html.theme--documenter-dark header.navigation div.container nav.navbar ul.navbar-nav li.nav-item a.nav-link {
+    color: white;
+    transition: color 100ms;
+}
+
+html.theme--documenter-dark header.navigation div.container nav.navbar ul.navbar-nav li.nav-item a.nav-link:hover {
+    color: #0aa8a7
+}
+
+html header.navigation {
+    background-color: white !important;
+}
+
+html header.navigation div.container {
+    border-bottom: 1px solid #dbdbdb;
+}
+
+html header.navigation div.container nav.navbar ul.navbar-nav li.nav-item a.nav-link {
+    color: #222;
+    transition: color 100ms;
+}
+
+html header.navigation div.container nav.navbar ul.navbar-nav li.nav-item a.nav-link:hover {
+    color: #0aa8a7
+}
+
+header.navigation {
+    z-index: 3;
+}
+
+header.navigation div.container nav.navbar ul.navbar-nav {
+    margin-left: 4rem;
+    min-height: 3.25rem;
+    width: 70%;
+    display: flex;
+    align-self: auto;
+    flex-direction: row;
+    justify-content: space-around;
+}
+
+header.navigation div.container nav.navbar ul.navbar-nav li.nav-item {
+    align-self: stretch;
+    align-content: space-around;
+    justify-content: center;
+    display: flex;
+    flex-direction: column;
+}
+
+header.navigation div.container nav.navbar ul.navbar-nav li.small-item {
+    visibility: hidden;
+    display: none;
+}