xukai92

using InteractiveUtils
versioninfo()

using DrWatson
@quickactivate

using Comonicon, Test, BenchmarkTools, ExprOptimization
using ExprOptimization.ProbabilisticExprRules: RuleNode, mindepth_map, ProbabilisticGrammar
using GeneralizedGenerated: mk_function

xukai92

struct TakeUntil{I}
    cond::Function
    xs::I
end

"""
    takeuntil(cond, xs)
An iterator that yields values from the iterator `xs` as long as the
predicate `cond` is true. Unlike `takewhile`, it also take the last 
value for which the predicate `cond` is false.

xukai92

using Random: AbstractRNG, GLOBAL_RNG
using AdvancedHMC: PhasePoint, phasepoint

function AdvancedHMC.refresh(
    rng::Union{AbstractRNG, AbstractVector{<:AbstractRNG}},
    z::PhasePoint{T},
    h::Hamiltonian
) where {T<:CuArray}
    r = CuArray{Float32, 2}(undef, size(h.metric)...)
    CUDA.CURAND.randn!(r)

xukai92

# Modifed from https://github.com/cambridge-mlg/Covid19/blob/master/src/utils.jl#L79
function generated_quantities(m::Turing.Model, c::MCMCChains.Chains)
    # If `c` is multiple chains, we convert them into a single chain
    chain = length(chains(c)) == 1 ? c : MCMCChains.pool_chain(c)
    vi = Turing.DynamicPPL.VarInfo(m)
    return map(1:length(chain)) do i
        Turing.DynamicPPL._setval!(vi, chain[i])
        m(vi)
    end
end

xukai92

using LibGit2
LibGit2.set_ssl_cert_locations("/etc/ssl/certs/ca-certificates.crt")