update for Julia 1.0

Author: ChrisRackauckas

.gitignore

@@ -1,3 +1,4 @@
 *.jl.cov
 *.jl.*.cov
 *.jl.mem
+Manifest.toml

.travis.yml

@@ -4,8 +4,8 @@ os:
   - linux
   - osx
 julia:
-  - 0.6
-  - nightly
+  - 1
+  - 1.3
 notifications:
   email: false
 git:

Project.toml

@@ -4,6 +4,7 @@ uuid = "1aa9af3a-2424-508f-bb7e-0626de155470"
 [deps]
 Bridge = "2d3116d5-4b8f-5680-861c-71f149790274"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 

REQUIRE

@@ -1,16 +1,17 @@
 environment:
   matrix:
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x86/0.6/julia-0.6-latest-win32.exe"
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
-  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x86/julia-latest-win32.exe"
-  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
-
-## uncomment the following lines to allow failures on nightly julia
-## (tests will run but not make your overall status red)
-#matrix:
-#  allow_failures:
-#  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x86/julia-latest-win32.exe"
-#  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
+  - julia_version: 1.0
+  - julia_version: 1
+
+platform:
+  - x86 # 32-bit
+  - x64 # 64-bit
+
+# # Uncomment the following lines to allow failures on nightly julia
+# # (tests will run but not make your overall status red)
+# matrix:
+#   allow_failures:
+#   - julia_version: nightly
 
 branches:
   only:
@@ -24,24 +25,18 @@ notifications:
     on_build_status_changed: false
 
 install:
-  - ps: "[System.Net.ServicePointManager]::SecurityProtocol = [System.Net.SecurityProtocolType]::Tls12"
-# If there's a newer build queued for the same PR, cancel this one
-  - ps: if ($env:APPVEYOR_PULL_REQUEST_NUMBER -and $env:APPVEYOR_BUILD_NUMBER -ne ((Invoke-RestMethod `
-        https://ci.appveyor.com/api/projects/$env:APPVEYOR_ACCOUNT_NAME/$env:APPVEYOR_PROJECT_SLUG/history?recordsNumber=50).builds | `
-        Where-Object pullRequestId -eq $env:APPVEYOR_PULL_REQUEST_NUMBER)[0].buildNumber) { `
-        throw "There are newer queued builds for this pull request, failing early." }
-# Download most recent Julia Windows binary
-  - ps: (new-object net.webclient).DownloadFile(
-        $env:JULIA_URL,
-        "C:\projects\julia-binary.exe")
-# Run installer silently, output to C:\projects\julia
-  - C:\projects\julia-binary.exe /S /D=C:\projects\julia
+  - ps: iex ((new-object net.webclient).DownloadString("https://raw.githubusercontent.com/JuliaCI/Appveyor.jl/version-1/bin/install.ps1"))
 
 build_script:
-# Need to convert from shallow to complete for Pkg.clone to work
-  - IF EXIST .git\shallow (git fetch --unshallow)
-  - C:\projects\julia\bin\julia -e "versioninfo();
-      Pkg.clone(pwd(), \"DiffEqBridge\"); Pkg.build(\"DiffEqBridge\")"
+  - echo "%JL_BUILD_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_BUILD_SCRIPT%"
 
 test_script:
-  - C:\projects\julia\bin\julia -e "Pkg.test(\"DiffEqBridge\")"
+  - echo "%JL_TEST_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_TEST_SCRIPT%"
+
+# # Uncomment to support code coverage upload. Should only be enabled for packages
+# # which would have coverage gaps without running on Windows
+# on_success:
+#   - echo "%JL_CODECOV_SCRIPT%"
+#   - C:\julia\bin\julia -e "%JL_CODECOV_SCRIPT%"

appveyor.yml

@@ -1,11 +1,9 @@
-__precompile__(true)
-
 module BridgeDiffEq
 
 using Reexport
 @reexport using DiffEqBase
 
-using StaticArrays
+using StaticArrays, LinearAlgebra
 import Bridge
 
 import DiffEqBase: solve
@@ -19,12 +17,13 @@ const warnkeywords =
      :calck, :progress, :tstops, :saveat, :dense)
 
 function __init__()
-    const global warnlist = Set(warnkeywords)
+    global warnlist = Set(warnkeywords)
 end
 
 include("algorithms.jl")
 include("solve.jl")
 
-export BridgeAlgorithm, BridgeEuler, BridgeHeun, BridgeSRK, BridgeR3, BridgeBS3
+export BridgeAlgorithm, BridgeEuler, BridgeHeun, BridgeSRK, BridgeR3, BridgeBS3,
+       BridgeMdb
 
 end # module

src/BridgeDiffEq.jl

@@ -1,6 +1,7 @@
-abstract type BridgeAlgorithm <: DEAlgorithm end
+abstract type BridgeAlgorithm <: DiffEqBase.DEAlgorithm end
 struct BridgeEuler <: BridgeAlgorithm end
 struct BridgeHeun <: BridgeAlgorithm end
+struct BridgeMdb <: BridgeAlgorithm end
 struct BridgeSRK <: BridgeAlgorithm end
 struct BridgeR3 <: BridgeAlgorithm end
 struct BridgeBS3 <: BridgeAlgorithm end

src/algorithms.jl

@@ -1,12 +1,12 @@
-function solve{uType,tType,isinplace,AlgType<:BridgeAlgorithm}(
-    prob::Union{AbstractODEProblem{uType,tType,isinplace},
-                AbstractSDEProblem{uType,tType,isinplace}},
+function solve(
+    prob::Union{DiffEqBase.AbstractODEProblem{uType,tType,isinplace},
+                DiffEqBase.AbstractSDEProblem{uType,tType,isinplace}},
     alg::AlgType,
     timeseries=[],ts=[],ks=[];
     verbose=true,
     dt = nothing,
     timeseries_errors=true,
-    callback=nothing,kwargs...)
+    callback=nothing,kwargs...) where {uType,tType,isinplace,AlgType<:BridgeAlgorithm}
 
     if dt == nothing
         error("dt required for fixed timestep methods.")
@@ -17,7 +17,7 @@ function solve{uType,tType,isinplace,AlgType<:BridgeAlgorithm}(
         warned && warn_compat()
     end
 
-    if prob.callback != nothing || callback != nothing
+    if callback != nothing || :callback in keys(prob.kwargs)
         error("Bridge is not compatible with callbacks.")
     end
 
@@ -26,12 +26,12 @@ function solve{uType,tType,isinplace,AlgType<:BridgeAlgorithm}(
 
     if isinplace
         f = (t,u) -> (du = similar(u); prob.f(du,u,p,t); Diagonal(du))
-        if typeof(prob) <: AbstractSDEProblem
+        if typeof(prob) <: DiffEqBase.AbstractSDEProblem
             g = (t,u) -> (du = similar(u); prob.g(du,u,p,t,u); Diagonal(du))
         end
     else
         f = (t,u) -> prob.f(u,p,t)
-        if typeof(prob) <: AbstractSDEProblem
+        if typeof(prob) <: DiffEqBase.AbstractSDEProblem
             if typeof(u0) <: Number
                 g = (t,u) -> prob.g(u,p,t)
             else
@@ -41,7 +41,7 @@ function solve{uType,tType,isinplace,AlgType<:BridgeAlgorithm}(
     end
 
     t = prob.tspan[1]:dt:prob.tspan[2]
-    if typeof(prob) <: AbstractSDEProblem
+    if typeof(prob) <: DiffEqBase.AbstractSDEProblem
         W = Bridge.samplepath(t, zero(u0))
         samp = Bridge.sample(t, Bridge.Wiener{typeof(u0)}())
         if typeof(alg) <: BridgeEuler
@@ -54,7 +54,7 @@ function solve{uType,tType,isinplace,AlgType<:BridgeAlgorithm}(
             error("BridgeSRK is not compatible with non Number types")
         end
     else # ODE
-        samp = Bridge.SamplePath(t,Vector{typeof(u0)}(length(t)))
+        samp = Bridge.SamplePath(t,Vector{typeof(u0)}(undef,length(t)))
         W = nothing
         if typeof(alg) <: BridgeR3
             u = Bridge.solve!(Bridge.R3(),samp,u0,f)
@@ -63,7 +63,7 @@ function solve{uType,tType,isinplace,AlgType<:BridgeAlgorithm}(
         end
     end
 
-    build_solution(prob,  alg, u.tt, u.yy,
+    DiffEqBase.build_solution(prob,  alg, u.tt, u.yy,
                    W = W,
                    timeseries_errors = timeseries_errors,
                    retcode = :Success)

src/solve.jl

@@ -1,5 +1,5 @@
 using BridgeDiffEq, StaticArrays
-using Base.Test
+using Test
 
 α=1
 β=1
@@ -19,7 +19,6 @@ sol = solve(prob,BridgeHeun(),dt=dt)
 sol = solve(prob,BridgeSRK(),dt=dt)
 
 
-
 u0 = @SVector [2.0,3.0]
 prob = ODEProblem(f,u0,(0.0,1.0))
 sol = solve(prob,BridgeR3(),dt=dt)