Deprecations are fixed for julia-0.7

Author: Dae Woo Kim

.gitignore

@@ -2,3 +2,4 @@
 *.jl.*.cov
 *.jl.mem
 deps/deps.jl
+Manifest.toml

.travis.yml

@@ -0,0 +1,27 @@
+# Documentation: http://docs.travis-ci.com/user/languages/julia/
+language: julia
+os:
+  - linux
+julia:
+  - 0.7
+  - 1.0
+notifications:
+  email: false
+script:
+  - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
+  - julia -e 'using Pkg, LibGit2;
+              user_regs = joinpath(DEPOT_PATH[1],"registries");
+              mkpath(user_regs);
+              all_registries = Dict("General" => "https://github.com/JuliaRegistries/General.git",
+                            "HolyLabRegistry" => "[email protected]:HolyLab/HolyLabRegistry.git");
+              Base.shred!(LibGit2.CachedCredentials()) do creds
+                for (reg, url) in all_registries
+                  path = joinpath(user_regs, reg);
+                  LibGit2.with(Pkg.GitTools.clone(url, path; header = "registry $reg from $(repr(url))", credentials = creds)) do repo end
+                end
+              end'
+  - julia -e 'using Pkg; Pkg.build(); Pkg.test("RegisterDriver"; coverage=false)'
+after_success:
+# update the documentation
+  - julia -e 'using Pkg; Pkg.add("Documenter")'
+  - julia -e 'using RegisterDriver; cd(dirname(dirname(pathof(RegisterDriver)))); ENV["DOCUMENTER_DEBUG"] = "true"; include(joinpath("docs", "make.jl"))'

Project.toml

@@ -0,0 +1,24 @@
+name = "RegisterDriver"
+uuid = "935ac36e-2656-11e9-1e3b-cbaa636797af"
+authors = ["Tim Holy <[email protected]>"]
+version = "0.1.0"
+
+[deps]
+Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
+Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+Formatting = "59287772-0a20-5a39-b81b-1366585eb4c0"
+HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
+Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
+JLD = "4138dd39-2aa7-5051-a626-17a0bb65d9c8"
+RegisterCore = "67712758-55e7-5c3c-8e85-dda1d7758434"
+RegisterWorkerShell = "978d31ce-2656-11e9-22d6-b5c46a1a3d3e"
+SharedArrays = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+
+[extras]
+Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Compat", "Test", "Pkg"]

src/RegisterDriver.jl

@@ -1,10 +1,10 @@
 module RegisterDriver
 
-using Images, JLD, HDF5, StaticArrays, Formatting
+using Images, JLD, HDF5, StaticArrays, Formatting, SharedArrays, Distributed
 using RegisterCore
 using RegisterWorkerShell
 
-export driver
+export driver, mm_package_loader
 export PreprocessSNF
 
 """
@@ -43,7 +43,7 @@ function driver(outfile::AbstractString, algorithm::Vector, img, mon::Vector)
     nworkers = length(algorithm)
     length(mon) == nworkers || error("Number of monitors must equal number of workers")
     use_workerprocs = nworkers > 1 || workerpid(algorithm[1]) != myid()
-    rralgorithm = Array{RemoteChannel}(nworkers)
+    rralgorithm = Array{RemoteChannel}(undef, nworkers)
     if use_workerprocs
         # Push the algorithm objects to the worker processes. This elminates
         # per-iteration serialization penalties, and ensures that any
@@ -155,15 +155,15 @@ function initialize_jld!(dsets, file, mon, fs, n)
     for (k,v) in mon
         kstr = string(k)
         if isa(v, Number)
-            write(file, kstr, Vector{typeof(v)}(n))
+            write(file, kstr, Vector{typeof(v)}(undef, n))
             dsets[k] = file[kstr]
         elseif isa(v, Array) || isa(v, SharedArray)
             v = nicehdf5(v)
             if eltype(v) <: HDF5.HDF5BitsKind
                 fullsz = (size(v)..., n)
                 dsets[k] = d_create(file.plain, kstr, datatype(eltype(v)), dataspace(fullsz))
             else
-                write(file, kstr, Array{eltype(v)}(size(v)..., n))  # might fail if it's too big, but we tried
+                write(file, kstr, Array{eltype(v)}(undef, size(v)..., n))  # might fail if it's too big, but we tried
             end
             dsets[k] = file[kstr]
         elseif isa(v, ArrayDecl)  # maybe this never happens?
@@ -182,11 +182,11 @@ function initialize_jld!(dsets, file, mon, fs, n)
 end
 
 function nicehdf5(v::Union{Array{T},SharedArray{T}}) where T<:StaticArray
-    nicehdf5(reinterpret(eltype(T), sdata(v), (size(eltype(v))..., size(v)...)))
+    nicehdf5(reshape(reinterpret(eltype(T), vec(sdata(v))), (size(eltype(v))..., size(v)...)))
 end
 
 function nicehdf5(v::Union{Array{T},SharedArray{T}}) where T<:NumDenom
-    nicehdf5(reinterpret(eltype(T), sdata(v), (2, size(v)...)))
+    nicehdf5(reshape(reinterpret(eltype(T), vec(sdata(v))), (2, size(v)...)))
 end
 
 nicehdf5(v::SharedArray) = sdata(v)
@@ -241,11 +241,31 @@ end
 function sqrt_subtract_bias(A, bias)
 #    T = typeof(sqrt(one(promote_type(eltype(A), typeof(bias)))))
     T = Float32
-    out = Array{T}(size(A))
+    out = Array{T}(undef, size(A))
     for I in eachindex(A)
         @inbounds out[I] = sqrt(max(zero(T), convert(T, A[I]) - bias))
     end
     out
 end
 
+mm_package_loader(algorithm::AbstractWorker) = mm_package_loader([algorithm])
+function mm_package_loader(algorithms::Vector)
+    nworkers = length(algorithms)
+    use_workerprocs = nworkers > 1 || workerpid(algorithms[1]) != myid()
+    rrdev = Array{RemoteChannel}(undef, nworkers)
+    if use_workerprocs
+        for i = 1:nworkers
+            dev = algorithms[i].dev
+            rrdev[i] = put!(RemoteChannel(workerpid(algorithms[i])), dev)
+        end
+        @sync for i = 1:nworkers
+            p = workerpid(algorithms[i])
+            @async remotecall_fetch(load_mm_package, p, rrdev[i])
+        end
+    else
+        load_mm_package(algorithms[1].dev)
+    end
+    nothing
+end
+
 end # module

test/WorkerDummy.jl

@@ -1,7 +1,7 @@
 ### Dummy algorithms to test features of `driver`
 module WorkerDummy
 
-using RegisterWorkerShell
+using RegisterWorkerShell, Distributed
 import RegisterWorkerShell: worker
 using Compat
 
@@ -47,10 +47,10 @@ end
 
 function worker(algorithm::Alg2, moving, tindex, mon)
     # Do stuff to set tform
-    tform = range(1, stop=12, length=12)+tindex
+    tform = range(1, stop=12, length=12).+tindex
     monitor!(mon, :tform, tform)
     # Do more computations...
-    monitor!(mon, :u0, zeros(size(algorithm.u0))-tindex)
+    monitor!(mon, :u0, zeros(size(algorithm.u0)).-tindex)
 end
 
 function worker(algorithm::Alg3, moving, tindex, mon)

test/runtests.jl

@@ -1,21 +1,18 @@
-driverprocs = addprocs(2)
-
-# Work around julia #3674
-using Images, JLD, Test
-using BlockRegistration, BlockRegistrationScheduler
+using Test, Distributed, SharedArrays
+using Images, JLD
 using RegisterDriver, RegisterWorkerShell
+
+driverprocs = addprocs(2)
+include("WorkerDummy.jl")
 @sync for p in driverprocs
     @spawnat p eval(quote
-        using Images, JLD, Test
-        using BlockRegistrationScheduler, RegisterDriver, RegisterWorkerShell
+        using Pkg
+        Pkg.activate(".")
+        Pkg.instantiate()
+        include("WorkerDummy.jl")
     end)
 end
-
-include("WorkerDummy.jl")
 using .WorkerDummy
-for p in driverprocs
-    remotecall_fetch(eval, p, :(include("WorkerDummy.jl"); using .WorkerDummy))  # workaround #3674 if this is re-run
-end
 
 workdir = tempname()
 mkdir(workdir)
@@ -39,7 +36,7 @@ fn = joinpath(workdir, "file2.jld")
 driver(fn, alg, img, mon)
 tform = JLD.load(fn, "tform")
 u0    = JLD.load(fn, "u0")
-@test tform[:,4] == collect(range(1, stop=12, length=12)+4)
+@test tform[:,4] == collect(range(1, stop=12, length=12).+4)
 @test u0[:,:,2] == fill(-2,(3,3))
 rm(fn)
 
@@ -59,8 +56,8 @@ rm(fn)
 
 # Multi-process
 nw = length(driverprocs)
-alg = Vector{Any}(nw)
-mon = Vector{Any}(nw)
+alg = Vector{Any}(undef, nw)
+mon = Vector{Any}(undef, nw)
 for i = 1:nw
     alg[i] = Alg2(rand(100,100), Float32, (3,3), pid=driverprocs[i])
     mon[i] = monitor(alg[i], (:tform,:u0,:workerpid))