Fixes for constructor docstrings (#347)

* docstring fixes for constructors

* fixed docs

* minor fix for docs

* Update Project.toml

---------

Co-authored-by: Hong Ge <[email protected]>

Author: torfjelde

Project.toml

@@ -1,6 +1,6 @@
 name = "AdvancedHMC"
 uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-version = "0.5.3"
+version = "0.5.4"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"

README.md

@@ -212,22 +212,23 @@ In the previous examples, we built the sampler by manually specifying the integr
 Moreover, there's some flexibility in how these samplers can be initialized. 
 For example, a user can initialize a NUTS (HMC and HMCDA) sampler with their own metrics and integrators. 
 This can be done as follows:
-  ```julia
-  nuts = NUTS(δ, metric = :diagonal) #metric = DiagEuclideanMetric(D) (Default!)
-  nuts = NUTS(δ, metric = :unit)     #metric = UnitEuclideanMetric(D)
-  nuts = NUTS(δ, metric = :dense)    #metric = DenseEuclideanMetric(D)
-  # Provide your own AbstractMetric
-  metric = DiagEuclideanMetric(10)
-  nuts = NUTS(δ, metric = metric) 
-
-  nuts = NUTS(δ, integrator = :leapfrog)         #integrator = Leapfrog(ϵ) (Default!)
-  nuts = NUTS(δ, integrator = :jitteredleapfrog) #integrator = JitteredLeapfrog(ϵ, 0.1ϵ)
-  nuts = NUTS(δ, integrator = :temperedleapfrog) #integrator = TemperedLeapfrog(ϵ, 1.0)
-
-  # Provide your own AbstractIntegrator
-  integrator = JitteredLeapfrog(0.1, 0.2)
-  nuts = NUTS(δ, integrator = integrator) 
-  ```
+
+```julia
+nuts = NUTS(δ, metric = :diagonal) #metric = DiagEuclideanMetric(D) (Default!)
+nuts = NUTS(δ, metric = :unit)     #metric = UnitEuclideanMetric(D)
+nuts = NUTS(δ, metric = :dense)    #metric = DenseEuclideanMetric(D)
+# Provide your own AbstractMetric
+metric = DiagEuclideanMetric(10)
+nuts = NUTS(δ, metric = metric)
+
+nuts = NUTS(δ, integrator = :leapfrog)         #integrator = Leapfrog(ϵ) (Default!)
+nuts = NUTS(δ, integrator = :jitteredleapfrog) #integrator = JitteredLeapfrog(ϵ, 0.1ϵ)
+nuts = NUTS(δ, integrator = :temperedleapfrog) #integrator = TemperedLeapfrog(ϵ, 1.0)
+
+# Provide your own AbstractIntegrator
+integrator = JitteredLeapfrog(0.1, 0.2)
+nuts = NUTS(δ, integrator = integrator) 
+```
 
 ### GPU Sampling with CUDA
 

src/constructors.jl

@@ -67,19 +67,13 @@ sampler_eltype(sampler::HMCSampler) = eltype(sampler.metric)
 ### NUTS ###
 ############
 """
-    NUTS(δ::Real; max_depth::Int=10, Δ_max::Real=1000, init_ϵ::Real=0, integrator = :leapfrog, metric = :diagonal)
+    NUTS(δ::Real; max_depth::Int=10, Δ_max::Real=1000, integrator = :leapfrog, metric = :diagonal)
 
 No-U-Turn Sampler (NUTS) sampler.
 
 # Fields
 
 $(FIELDS)
-
-# Usage:
-
-```julia
-NUTS(δ=0.65)  # Use target accept ratio 0.65.
-```
 """
 struct NUTS{T<:Real,I<:Union{Symbol,AbstractIntegrator},M<:Union{Symbol,AbstractMetric}} <:
        AbstractHMCSampler
@@ -113,12 +107,6 @@ Hamiltonian Monte Carlo sampler with static trajectory.
 # Fields
 
 $(FIELDS)
-
-# Usage:
-
-```julia
-HMC(10, integrator = Leapfrog(0.05), metric = :diagonal)
-```
 """
 struct HMC{I<:Union{Symbol,AbstractIntegrator},M<:Union{Symbol,AbstractMetric}} <:
        AbstractHMCSampler
@@ -140,19 +128,15 @@ sampler_eltype(sampler::HMC) = determine_sampler_eltype(sampler.metric, sampler.
 ### HMCDA ###
 #############
 """
-    HMCDA(δ::Real, λ::Real; ϵ::Real=0, integrator = :leapfrog, metric = :diagonal)
+    HMCDA(δ::Real, λ::Real, integrator = :leapfrog, metric = :diagonal)
 
 Hamiltonian Monte Carlo sampler with Dual Averaging algorithm.
 
 # Fields
 
 $(FIELDS)
 
-# Usage:
-
-```julia
-HMCDA(δ=0.65, λ=0.3)
-```
+# Notes
 
 For more information, please view the following paper ([arXiv link](https://arxiv.org/abs/1111.4246)):