Trim dependencies

Project.toml

@@ -4,37 +4,23 @@ authors = ["David Lung <[email protected]> and contributors"]
 version = "0.1.0"
 
 [deps]
-BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
-BlackBoxOptim = "a134a8b2-14d6-55f6-9291-3336d3ab0209"
-CMAEvolutionStrategy = "8d3b24bd-414e-49e0-94fb-163cc3a3e411"
-Cthulhu = "f68482b8-f384-11e8-15f7-abe071a5a75f"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 DiffEqFlux = "aae7a2af-3d4f-5e19-a356-7da93b79d9d0"
 DiffEqSensitivity = "41bf760c-e81c-5289-8e54-58b1f1f8abe2"
-DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Evolutionary = "86b6b26d-c046-49b6-aa0b-5f0f74682bd6"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
-GR = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
 GalacticOptim = "a75be94c-b780-496d-a8a9-0878b188d577"
 IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
-Juno = "e5e0dc1b-0480-54bc-9374-aad01c23163d"
 MLDataPattern = "9920b226-0b2a-5f5f-9153-9aa70a013f8b"
 MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 NLopt = "76087f3c-5699-56af-9a33-bf431cd00edd"
-NPZ = "15e1cf62-19b3-5cfa-8e77-841668bca605"
-ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c"
-ODEInterfaceDiffEq = "09606e27-ecf5-54fc-bb29-004bd9f985bf"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-PProf = "e4faabce-9ead-11e9-39d9-4379958e3056"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-ProfileView = "c46f51b8-102a-5cf2-8d2c-8597cb0e0da7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]
 julia = "1"

src/LTC.jl

@@ -3,28 +3,14 @@ module LTC
 using Reexport
 
 using Distributions
-import NPZ: npzread
-export npzread
-using Juno
 using DiffEqBase
 using OrdinaryDiffEq
 using DiffEqSensitivity
-using DiffEqFlux
-using DiffEqFlux: initial_params, paramlength, FastChain, FastDense, sciml_train
 import DiffEqFlux: initial_params, paramlength, FastChain, FastDense, sciml_train
-import DifferentialEquations: PresetTimeCallback, PeriodicCallback
-export sciml_train
 using GalacticOptim
 using ModelingToolkit
-using Zygote
-using Zygote: @adjoint, Numeric, literal_getproperty, accum
-export Zygote
-using Flux: reset!, Zeros, Data.DataLoader
-using Flux: Data.DataLoader
-import Flux: reset!
-export DataLoader
-using IterTools: ncycle
-export ncycle
+using Flux
+using IterTools
 
 
 rand_uniform(TYPE, lb,ub,dims...) = TYPE.(rand(Uniform(lb,ub),dims...))

src/layers.jl

@@ -31,7 +31,7 @@ struct Broadcaster{M,P}
   paramlength::Int
 end
 function Broadcaster(model)
-  p = DiffEqFlux.initial_params(model)
+  p = initial_params(model)
   paramlength = length(p)
   Broadcaster(model,p,paramlength)
 end
@@ -89,7 +89,7 @@ paramlength(m::FluxLayerWrapper) = m.paramlength
 
 reset_state!(m,p) = nothing
 
-function reset_state!(m::Union{Flux.Chain, DiffEqFlux.FastChain}, p)
+function reset_state!(m::Union{Flux.Chain, FastChain}, p)
   start_idx = 1
   for l in m.layers
     pl = paramlength(l)
@@ -111,13 +111,13 @@ function get_bounds(m::Mapper)
   lb, ub
 end
 
-function get_bounds(m::Union{Flux.Chain, DiffEqFlux.FastChain})
+function get_bounds(m::Union{Flux.Chain, FastChain})
   lb = vcat([get_bounds(layer)[1] for layer in m.layers]...)
   ub = vcat([get_bounds(layer)[2] for layer in m.layers]...)
   lb, ub
 end
 
-function get_bounds(m::DiffEqFlux.FastDense)
+function get_bounds(m::FastDense)
   lb = vcat(fill(-10.1, m.out*m.in),
             fill(-10.1, m.out)) |> f32
   ub = vcat(fill(10.1, m.out*m.in),

src/losses.jl

@@ -15,7 +15,7 @@ function loss_seq(p, re, x, y)
   return mean(Flux.Losses.mse.(ŷ,y, agg=mean)), ŷ, y
 end
 
-function loss_seq(p, m::DiffEqFlux.FastChain, x, y)
+function loss_seq(p, m::FastChain, x, y)
   # ŷ = m.(x, [p])
 
   LTC.reset_state!(m, p)

src/mtk_recur.jl

@@ -7,7 +7,7 @@ mutable struct RecurMTK{T,V,S}# <:MTKLayer
   state::S
 end
 function RecurMTK(cell; seq_len=1)
-  p = DiffEqFlux.initial_params(cell)
+  p = initial_params(cell)
   RecurMTK(cell, p, length(p), cell.state0)
 end
 function (m::RecurMTK)(x, p=m.p)