Add API docs

TuringLang · Sep 27, 2024 · 2efffe2 · 2efffe2
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diff --git a/docs/Project.toml b/docs/Project.toml
@@ -0,0 +1,6 @@
+[deps]
+Bijectors = "76274a88-744f-5084-9051-94815aaf08c4"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656"
+Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
diff --git a/docs/README.md b/docs/README.md
diff --git a/docs/make.jl b/docs/make.jl
@@ -0,0 +1,37 @@
+using Documenter
+using Turing
+# Need to import Distributions and Bijectors to generate docs for functions
+# from those packages.
+using Distributions
+using Bijectors
+
+using DocumenterInterLinks
+
+links = InterLinks(
+    "DynamicPPL" => "https://turinglang.org/DynamicPPL.jl/stable/objects.inv",
+    "AbstractPPL" => "https://turinglang.org/AbstractPPL.jl/dev/objects.inv",
+    "ADTypes" => "https://sciml.github.io/ADTypes.jl/stable/objects.inv",
+)
+
+# Doctest setup
+DocMeta.setdocmeta!(Turing, :DocTestSetup, :(using Turing); recursive=true)
+
+makedocs(;
+    sitename="Turing",
+    modules=[Turing, Distributions, Bijectors],
+    pages=[
+        "Home" => "index.md",
+        "API" => "api.md",
+        "Submodule APIs" => [
+            "Inference" => "api/Inference.md",
+            "Optimisation" => "api/Optimisation.md",
+        ]
+    ],
+    checkdocs=:exports,
+    # checkdocs_ignored_modules=[Turing, Distributions, DynamicPPL, AbstractPPL, Bijectors],
+    doctest=false,
+    warnonly=true,
+    plugins=[links],
+)
+
+deploydocs(; repo="github.com/TuringLang/Turing.jl.git", push_preview=true)
diff --git a/docs/src/api.md b/docs/src/api.md
@@ -0,0 +1,168 @@
+# API
+## Module-wide re-exports
+
+Turing.jl directly re-exports the entire public API of the following packages:
+
+ - [Distributions.jl](https://juliastats.org/Distributions.jl)
+ - [MCMCChains.jl](https://turinglang.org/MCMCChains.jl)
+ - [AbstractMCMC.jl](https://turinglang.org/AbstractMCMC.jl)
+ - [Bijectors.jl](https://turinglang.org/Bijectors.jl)
+ - [Libtask.jl](https://github.com/TuringLang/Libtask.jl)
+
+Please see the individual packages for their documentation.
+
+## Individual exports and re-exports
+
+**All** of the following symbols are exported unqualified by Turing, even though the documentation suggests that many of them are qualified.
+That means, for example, you can just write
+
+```julia
+using Turing
+
+@model function my_model(...)
+
+sample(my_model(), Prior(), 100)
+```
+
+instead of
+
+```julia
+sample(model, Turing.Inference.Prior(), 100)
+```
+
+even though [`Prior()`](@ref) is actually defined in the `Turing.Inference` module.
+
+### Modelling
+
+| Exported symbol | Documentation                     | Description                                  |
+| ---             | ---                               | ---                                          |
+| `@model`        | [`DynamicPPL.@model`](@extref)    | Define a probabilistic model                 |
+| `@varname`      | [`AbstractPPL.@varname`](@extref) | Generate a `VarName` from a Julia expression |
+| `@submodel`     | [`DynamicPPL.@submodel`](@extref) | Define a submodel                            |
+
+### Inference
+
+| Exported symbol | Documentation                                                                                    | Description         |
+| ---             | ---                                                                                              | ---                 |
+| `sample`        | [`StatsBase.sample`](https://turinglang.org/AbstractMCMC.jl/stable/api/#Sampling-a-single-chain) | Sample from a model |
+
+### Samplers
+
+| Exported symbol      | Documentation                                 | Description                                                      |
+| ---                  | ---                                           | ---                                                              |
+| `Prior`              | [`Turing.Inference.Prior`](@ref)              | Sample from the prior distribution                               |
+| `MH`                 | [`Turing.Inference.MH`](@ref)                 | Metropolis–Hastings                                              |
+| `Emcee`              | [`Turing.Inference.Emcee`](@ref)              | Affine-invariant ensemble sampler                                |
+| `ESS`                | [`Turing.Inference.ESS`](@ref)                | Elliptical slice sampling                                        |
+| `Gibbs`              | [`Turing.Inference.Gibbs`](@ref)              | Gibbs sampling                                                   |
+| `GibbsConditional`   | [`Turing.Inference.GibbsConditional`](@ref)   | A "pseudo-sampler" to provide analytical conditionals to `Gibbs` |
+| `HMC`                | [`Turing.Inference.HMC`](@ref)                | Hamiltonian Monte Carlo                                          |
+| `SGLD`               | [`Turing.Inference.SGLD`](@ref)               | Stochastic gradient Langevin dynamics                            |
+| `SGHMC`              | [`Turing.Inference.SGHMC`](@ref)              | Stochastic gradient Hamiltonian Monte Carlo                      |
+| `HMCDA`              | [`Turing.Inference.HMCDA`](@ref)              | Hamiltonian Monte Carlo with dual averaging                      |
+| `NUTS`               | [`Turing.Inference.NUTS`](@ref)               | No-U-Turn Sampler                                                |
+| `PolynomialStepsize` | [`Turing.Inference.PolynomialStepsize`](@ref) | A function to generate a polynomially decaying step size         |
+| `IS`                 | [`Turing.Inference.IS`](@ref)                 | Importance sampling                                              |
+| `SMC`                | [`Turing.Inference.SMC`](@ref)                | Sequential Monte Carlo                                           |
+| `PG`                 | [`Turing.Inference.PG`](@ref)                 | Particle Gibbs                                                   |
+| `CSMC`               | [`Turing.Inference.CSMC`](@ref)               | The same as PG                                                   |
+| `externalsampler`    | [`Turing.Inference.externalsampler`](@ref)    | Wrap an external sampler for use in Turing                       |
+
+### Variational inference
+
+These functions are not (yet) formally documented.
+Please see the [variational inference tutorial](https://turinglang.org/docs/tutorials/09-variational-inference/) for a walkthrough on how to use these.
+
+TODO: Generate docs for AdvancedVI 0.2, update the InterLinks object.inv, and update the table below to include `@extref`.
+
+| Exported symbol | Documentation     | Description                             |
+| ---             | ---               | ---                                     |
+| `vi`            | `AdvancedVI.vi`   | Perform variational inference           |
+| `ADVI`          | `AdvancedVI.ADVI` | Construct an instance of a VI algorithm |
+
+### Automatic differentiation types
+
+These are used to specify the automatic differentiation backend to use.
+
+| Exported symbol   | Documentation                        | Description                               |
+| ---               | ---                                  | ---                                       |
+| `AutoForwardDiff` | [`ADTypes.AutoForwardDiff`](@extref) | ForwardDiff.jl backend                    |
+| `AutoReverseDiff` | [`ADTypes.AutoReverseDiff`](@extref) | ReverseDiff.jl backend                    |
+| `AutoZygote`      | [`ADTypes.AutoZygote`](@extref)      | Zygote.jl backend                         |
+| `AutoTracker`     | [`ADTypes.AutoTracker`](@extref)     | Tracker.jl backend                        |
+| `AutoTapir`       | [`ADTypes.AutoTapir`](@extref)       | Tapir.jl backend, only for ADTypes >= 1.0 |
+
+### Debugging
+
+```@docs
+setprogress!
+```
+
+### Distributions
+
+These distributions are defined in Turing.jl, but not in Distributions.jl.
+
+```@docs
+Flat
+FlatPos
+BinomialLogit
+OrderedLogistic
+LogPoisson
+```
+
+`BernoulliLogit` is part of Distributions.jl since version 0.25.77.
+If you are using an older version of Distributions where this isn't defined, Turing will export the same distribution.
+
+```@docs
+Distributions.BernoulliLogit
+```
+
+### Tools to work with distributions
+
+TODO: DistributionsAD needs docs
+
+| Exported symbol | Documentation                     | Description                                                    |
+| ---             | ---                               | ---                                                            |
+| `filldist`      | `DistributionsAD.filldist`        | Create a product distribution from a distribution and integers |
+| `arraydist`     | `DistributionsAD.arraydist`       | Create a product distribution from an array of distributions   |
+| `NamedDist`     | [`DynamicPPL.NamedDist`](@extref) | A distribution that carries the name of the variable           |
+
+### Predictions
+
+```@docs
+predict
+```
+
+### Re-exports from DynamicPPL / AbstractPPL
+
+| Exported symbol            | Documentation                                                                                                                     | Description                                                     |
+| ---                        | ---                                                                                                                               | ---                                                             |
+| `pointwise_loglikelihoods` | [`DynamicPPL.pointwise_loglikelihoods`](@extref)                                                                                  | Compute log likelihoods for each sample in a chain              |
+| `generated_quantities`     | [`DynamicPPL.generated_quantities`](@extref)                                                                                      | Calculate additional quantities defined in a model              |
+| `logprior`                 | [`DynamicPPL.logprior`](@extref)                                                                                                  | Compute log prior probability                                   |
+| `logjoint`                 | [`DynamicPPL.logjoint`](@extref)                                                                                                  | Compute log joint probability                                   |
+| `LogDensityFunction`       | [`DynamicPPL.LogDensityFunction`](@extref)                                                                                        | Wrap a Turing model to satisfy LogDensityFunctions.jl interface |
+| `condition`                | [`AbstractPPL.condition`](@extref)                                                                                                | Condition a model on data                                       |
+| `decondition`              | [`AbstractPPL.decondition`](@extref)                                                                                              | Remove conditioning on data                                     |
+| `conditioned`              | [`DynamicPPL.conditioned`](@extref)                                                                                               | Return the conditioned values of a model                        |
+| `fix`                      | [`DynamicPPL.fix`](@extref)                                                                                                       | Fix the value of a variable                                     |
+| `unfix`                    | [`DynamicPPL.unfix`](@extref)                                                                                                     | Unfix the value of a variable                                   |
+| `OrderedDict`              | [`OrderedCollections.OrderedDict`](https://juliacollections.github.io/OrderedCollections.jl/dev/ordered_containers/#OrderedDicts) | An ordered dictionary                                           |
+
+### Extra re-exports from Bijectors
+
+Note that Bijectors itself does not export `ordered`.
+
+```@docs
+Bijectors.ordered
+```
+
+### Point estimates
+
+| Exported symbol        | Documentation                                      | Description                                  |
+| ---                    | ---                                                | ---                                          |
+| `maximum_a_posteriori` | [`Turing.Optimisation.maximum_a_posteriori`](@ref) | Find a MAP estimate for a model              |
+| `maximum_likelihood`   | [`Turing.Optimisation.maximum_likelihood`](@ref)   | Find a MLE estimate for a model              |
+| `MAP`                  | [`Turing.Optimisation.MAP`](@ref)                  | Type to use with Optim.jl for MAP estimation |
+| `MLE`                  | [`Turing.Optimisation.MLE`](@ref)                  | Type to use with Optim.jl for MLE estimation |
+
diff --git a/docs/src/api/Inference.md b/docs/src/api/Inference.md
@@ -0,0 +1,6 @@
+# API: `Turing.Inference`
+
+```@autodocs
+Modules = [Turing.Inference]
+Order  = [:type, :function]
+```
diff --git a/docs/src/api/Optimisation.md b/docs/src/api/Optimisation.md
@@ -0,0 +1,6 @@
+# API: `Turing.Optimisation`
+
+```@autodocs
+Modules = [Turing.Optimisation]
+Order  = [:type, :function]
+```
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -0,0 +1,5 @@
+# Turing.jl
+
+This site contains the API documentation for the identifiers exported by Turing.jl.
+
+If you are looking for usage examples and guides, please visit [https://turinglang.org/docs](https://turinglang.org/docs).
diff --git a/docs/src/library/advancedhmc.md b/docs/src/library/advancedhmc.md
diff --git a/docs/src/library/api.md b/docs/src/library/api.md
diff --git a/docs/src/library/bijectors.md b/docs/src/library/bijectors.md
diff --git a/src/Turing.jl b/src/Turing.jl
@@ -100,8 +100,8 @@ export @model,                 # modelling
     vi,                     # variational inference
     ADVI,
     sample,                 # inference
-    @logprob_str,
-    @prob_str,
+    @logprob_str,  # TODO: Remove, see https://github.com/TuringLang/DynamicPPL.jl/issues/356
+    @prob_str,     # TODO: Remove, see https://github.com/TuringLang/DynamicPPL.jl/issues/356
     externalsampler,
     AutoForwardDiff,        # ADTypes
     AutoReverseDiff,

diff --git a/src/mcmc/Inference.jl b/src/mcmc/Inference.jl
@@ -168,7 +168,11 @@ function DynamicPPL.unflatten(vi::TypedVarInfo, θ::NamedTuple)
 end
 DynamicPPL.unflatten(vi::SimpleVarInfo, θ::NamedTuple) = SimpleVarInfo(θ, vi.logp, vi.transformation)
 
-# Algorithm for sampling from the prior
+"""
+    Prior()
+
+Algorithm for sampling from the prior.
+"""
 struct Prior <: InferenceAlgorithm end
 
 function AbstractMCMC.step(

diff --git a/src/mcmc/emcee.jl b/src/mcmc/emcee.jl
@@ -2,6 +2,17 @@
 ### Sampler states
 ###
 
+"""
+    Emcee(n_walkers::Int, stretch_length=2.0)
+
+Affine-invariant ensemble sampling algorithm.
+
+# Reference
+
+Foreman-Mackey, D., Hogg, D. W., Lang, D., & Goodman, J. (2013).
+emcee: The MCMC Hammer. Publications of the Astronomical Society of the
+Pacific, 125 (925), 306. https://doi.org/10.1086/670067
+"""
 struct Emcee{space,E<:AMH.Ensemble} <: InferenceAlgorithm
     ensemble::E
 end

diff --git a/src/mcmc/particle_mcmc.jl b/src/mcmc/particle_mcmc.jl
@@ -220,6 +220,11 @@ function PG(nparticles::Int, space::Tuple)
     return PG(nparticles, AdvancedPS.ResampleWithESSThreshold(), space)
 end
 
+"""
+    CSMC(...)
+
+Equivalent to [`PG`](@ref).
+"""
 const CSMC = PG # type alias of PG as Conditional SMC
 
 struct PGTransition{T,F<:AbstractFloat} <: AbstractTransition