fix for Julia 1.x

Author: tknopp

.travis.yml

@@ -2,25 +2,24 @@
 language: julia
 os:
   - linux
-sudo: required
 julia:
-  - release
-#  - nightly
-
+  - 1.1
 notifications:
   email: false
-# uncomment the following lines to override the default test script
-script:
-#  - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
-  - LD_PRELOAD=${HOME}/.julia/v0.6/Conda/deps/usr/lib/libz.so julia -e 'Pkg.clone(pwd()); Pkg.build("OpenMPIData"); Pkg.test("OpenMPIData"; coverage=true)'
-before_install:
-  - julia -e 'Pkg.update()'
-  #- test "x$TRAVIS_OS_NAME" = xosx -o "x$PYTHON" = xConda-python || (sudo apt-get -qq update && sudo apt-get install -y $PYTHON)
-  # Work around (part 1/2) matplotlib backend error leading to "matplotlib.pyplot could not be found by pyimport": can't just set env PYTHON="".
-  - julia -e 'ENV["PYTHON"]=""; Pkg.add("Conda"); using Conda; Conda.update(); Conda.add("matplotlib"); Pkg.add("PyCall"); Pkg.build("PyCall"); Pkg.add("PyPlot");'
+branches:
+  only: master
+
+## uncomment following lines to deploy documentation
+jobs:
+   include:
+     - stage: Documentation
+       julia: 1.1
+       os: linux
+       script:
+         - julia --project=docs -e 'using Pkg; Pkg.instantiate(); Pkg.add(PackageSpec(path=pwd()))'
+         - julia --project=docs docs/make.jl
+       after_success: skip
+
 after_success:
-  # push coverage results to Coveralls
-  #- export LD_LIBRARY_PATH=$HOME/.julia/v0.6/Conda/deps/usr/lib julia -e 'cd(Pkg.dir("OpenMPIData")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
-  # push coverage results to Codecov
-  #- export LD_LIBRARY_PATH=$HOME/.julia/v0.6/Conda/deps/usr/lib julia -e 'cd(Pkg.dir("OpenMPIData")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
-  - LD_PRELOAD=${HOME}/.julia/v0.6/Conda/deps/usr/lib/libz.so julia -e 'cd(Pkg.dir("OpenMPIData")); ENV["DOCUMENTER_DEBUG"] = "true"; include(joinpath("docs", "make.jl"))'
+  - julia --project=test/coverage -e 'using Pkg; Pkg.instantiate()'
+  - julia --project=test/coverage test/coverage/coverage.jl

REQUIRE

@@ -1,5 +1,8 @@
 julia 1.0
 Documenter
-#Requests
+Reexport
 PyPlot
 HDF5
+MPIFiles
+RegularizedLeastSquares
+HTTP

docs/Project.toml

@@ -0,0 +1,10 @@
+[deps]
+MPIFiles = "371237a9-e6c1-5201-9adb-3d8cfa78fa9f"
+RegularizedLeastSquares = "1e9c538a-f78c-5de5-8ffb-0b6dbe892d23"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+LinearOperators = "5c8ed15e-5a4c-59e4-a42b-c7e8811fb125"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
+Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
+OpenMPIData = "46e8875b-c064-59da-a3bf-c1683cc8c07a"

docs/make.jl

@@ -16,10 +16,8 @@ makedocs(
         "Datasets" => "datasets.md",
         "Reconstruction"=> "reconstructions.md"
     ],
+    html_prettyurls = false, #!("local" in ARGS)
 )
 
 deploydocs(repo   = "github.com/MagneticParticleImaging/OpenMPIData.jl.git",
-           julia  = "release",
-           target = "build",
-           deps   = nothing,
-           make   = nothing)
+           target = "build")

src/OpenMPIData.jl

@@ -1,15 +1,11 @@
 module OpenMPIData
 
 using Reexport
-if !isdir(Pkg.dir("MPIFiles"))
-  println("Installing MPIFiles...")
-  Pkg.clone("https://github.com/MagneticParticleImaging/MPIFiles.jl.git")
-end
 @reexport using MPIFiles
-@reexport using PyPlot
+#@reexport using PyPlot
 
 include("download.jl")
 include("reconstruction.jl")
-include("visualization.jl")
+#include("visualization.jl")
 
 end # module

src/download.jl

@@ -1,4 +1,4 @@
-using Requests
+using Pkg, HTTP
 
 export downloadOpenMPIData, downloadCalibrationDataHighRes, downloadCalibrationDataLowRes,
        download2DData, download3DData
@@ -27,8 +27,11 @@ function download1DData()
            "data/measurements/concentrationPhantom/1.mdf"]
 
   for file in files
-    stream = get("http://media.tuhh.de/ibi/openMPIData/"*file)
-    save(stream, Pkg.dir("OpenMPIData",file))
+    HTTP.open("GET", "http://media.tuhh.de/ibi/openMPIData/"*file) do http
+      open(Pkg.dir("OpenMPIData",file), "w") do file
+        write(file, http)
+      end
+    end
   end
 end
 function download2DData()
@@ -39,8 +42,11 @@ function download2DData()
            "data/measurements/concentrationPhantom/2.mdf"]
 
   for file in files
-    stream = get("http://media.tuhh.de/ibi/openMPIData/"*file)
-    save(stream, Pkg.dir("OpenMPIData",file))
+    HTTP.open("GET", "http://media.tuhh.de/ibi/openMPIData/"*file) do http
+      open(Pkg.dir("OpenMPIData",file), "w") do file
+        write(file, http)
+      end
+    end
   end
 end
 
@@ -51,8 +57,11 @@ function download3DData()
            "data/measurements/concentrationPhantom/3.mdf"]
 
   for file in files
-    stream = get("http://media.tuhh.de/ibi/openMPIData/"*file)
-    save(stream, Pkg.dir("OpenMPIData",file))
+    HTTP.open("GET", "http://media.tuhh.de/ibi/openMPIData/"*file) do http
+      open(Pkg.dir("OpenMPIData",file), "w") do file
+        write(file, http)
+      end
+    end
   end
 end
 
@@ -64,8 +73,11 @@ function downloadCalibrationDataLowRes()
            "data/calibrations/3.mdf",]
 
   for file in files
-    stream = get("http://media.tuhh.de/ibi/openMPIData/"*file)
-    save(stream, Pkg.dir("OpenMPIData",file))
+    HTTP.open("GET", "http://media.tuhh.de/ibi/openMPIData/"*file) do http
+      open(Pkg.dir("OpenMPIData",file), "w") do file
+        write(file, http)
+      end
+    end
   end
 end
 
@@ -77,7 +89,10 @@ function downloadCalibrationDataHighRes()
            "data/calibrations/6.mdf",]
 
   for file in files
-    stream = get("http://media.tuhh.de/ibi/openMPIData/"*file)
-    save(stream, Pkg.dir("OpenMPIData",file))
+    HTTP.open("GET", "http://media.tuhh.de/ibi/openMPIData/"*file) do http
+      open(Pkg.dir("OpenMPIData",file), "w") do file
+        write(file, http)
+      end
+    end
   end
 end

src/reconstruction.jl

@@ -54,7 +54,7 @@ argminₓ(‖Ax-b‖² + λ‖b‖²).
 * `enforceReal::Bool`: Enable projection of solution on real plane during iteration
 * `enforcePositive::Bool`: Enable projection of solution onto positive halfplane during iteration
 """ ->
-function kaczmarzReg{T}(A::AbstractMatrix{T}, b::Vector{T}, iterations, lambd, shuff, enforceReal, enforcePositive )
+function kaczmarzReg(A::AbstractMatrix{T}, b::Vector{T}, iterations, lambd, shuff, enforceReal, enforcePositive ) where T
   M = size(A,2)
   N = size(A,1)
 

test/runtests.jl

@@ -1,5 +1,5 @@
 using OpenMPIData
-using Base.Test
+using Test
 
 # write your own tests here
 @test 1 == 1