Using RecursiveArrayTools (#8)

resolving #5 #7 #9

Author: nantonel

.gitignore

@@ -9,7 +9,9 @@
 *.bbl
 *.blg
 *.log
+*.DS_Store
 
 
 docs/build/
 docs/site/
+docs/Manifest.toml

.travis.yml

@@ -4,8 +4,8 @@ os:
   - linux
   - osx
 julia:
-  - 0.7
   - 1.0
+  - 1.1
   - nightly
 matrix:
   allow_failures:
@@ -17,5 +17,14 @@ notifications:
 after_success:
   - julia -e 'using Pkg; cd(Pkg.dir("AbstractOperators")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(process_folder())'
   - julia -e 'using Pkg; cd(Pkg.dir("AbstractOperators")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
-  - julia -e 'using Pkg; Pkg.add("Documenter")'
-  - julia -e 'using Pkg; cd(Pkg.dir("AbstractOperators")); include(joinpath("docs", "make.jl"))'
+
+jobs:
+  include:
+    - stage: "Documentation"
+      julia: 1.1
+      os: linux
+      script:
+        - julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd()));
+                                               Pkg.instantiate()'
+        - julia --project=docs/ docs/make.jl
+      after_success: skip

README.md

@@ -73,17 +73,19 @@ julia> H = [A B]
 
 In this case `H` has a domain of dimensions `size(H,2) = ((3, 4), (3, 4))` and type `domainType(H) = (Float64, Complex{Float64})`.
 
-When an `AbstractOperators` have multiple domains, this must be multiplied using a `Tuple`s of `AbstractArray`s with corresponding `size(H,2)` and `domainType(H)`, for example: 
+When an `AbstractOperators` have multiple domains, this must be multiplied using an `ArrayPartition` (see [RecursiveArrayTools](https://github.com/JuliaDiffEq/RecursiveArrayTools.jl/]) with corresponding size and domain, for example: 
 
 ```julia
-julia> H*(x, complex(x))
+julia> using RecursiveArrayTools
+
+julia> H*ArrayPartition(x, complex(x))
 3×4 Array{Complex{Float64},2}:
  -16.3603+0.0im      52.4946-8.69342im  -129.014+0.0im      44.6712+8.69342im
   -22.051+23.8135im  16.5309-10.9601im  -22.5719+39.5599im  13.8174+3.81678im
  -5.81874-23.8135im  9.70679-3.81678im  -2.21552-39.5599im  11.5502+10.9601im
 ```
 
-Similarly, when an `AbstractOperators` have multiple codomains, this will return a `Tuple` of `AbstractArray`s with corresponding `size(H,1)` and `codomainType(H)`, for example: 
+Similarly, when an `AbstractOperators` have multiple codomains, this will return an `ArrayPartition`, for example: 
 ```julia
 julia> V = VCAT(Eye(3,3),FiniteDiff((3,3)))
 [I;δx]  ℝ^(3, 3) -> ℝ^(3, 3)  ℝ^(2, 3)

REQUIRE

@@ -1,4 +1,5 @@
-julia 0.7
-AbstractFFTs v0.3.2
-FFTW 0.2.4
-DSP 0.5.1
+julia 1.0
+AbstractFFTs v0.3
+FFTW 0.2
+DSP 0.5
+RecursiveArrayTools 0.18

appveyor.yml

@@ -1,7 +1,7 @@
 environment:
   matrix:
-  - julia_version: 0.7
-  - julia_version: 1
+  - julia_version: 1.0
+  - julia_version: 1.1
   - julia_version: nightly
 
 platform:
@@ -10,7 +10,6 @@ platform:
 
 matrix:
   allow_failures:
-  - julia_version: 1
   - julia_version: nightly
 
 branches:

docs/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

docs/make.jl

@@ -2,10 +2,10 @@ using Documenter, AbstractOperators
 
 makedocs(
   modules = [AbstractOperators],
-  format = :html,
+  format = Documenter.HTML(),
   sitename = "AbstractOperators.jl",
   authors = "Niccolò Antonello and Lorenzo Stella",
-  pages = Any[
+  pages = [
   "Home"               => "index.md",
   "Abstract Operators" => "operators.md",
   "Calculus rules"     => "calculus.md",
@@ -15,9 +15,5 @@ makedocs(
 
 deploydocs(
   repo   = "github.com/kul-forbes/AbstractOperators.jl.git",
-  julia  = "0.6",
-  osname = "linux",
   target = "build",
-  deps = nothing,
-  make = nothing,
 )

docs/src/index.md

@@ -1,5 +1,12 @@
 # AbstractOperators.jl
 
+[![Build Status](https://travis-ci.org/kul-forbes/AbstractOperators.jl.svg?branch=master)](https://travis-ci.org/kul-forbes/AbstractOperators.jl)
+[![Build status](https://ci.appveyor.com/api/projects/status/lfrmkg2s1awyxtk8/branch/master?svg=true)](https://ci.appveyor.com/project/nantonel/abstractoperators-jl/branch/master)
+[![codecov](https://codecov.io/gh/kul-forbes/AbstractOperators.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/kul-forbes/AbstractOperators.jl)
+
+[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://kul-forbes.github.io/AbstractOperators.jl/stable)
+[![](https://img.shields.io/badge/docs-latest-blue.svg)](https://kul-forbes.github.io/AbstractOperators.jl/latest)
+
 ## Description
 
 Abstract operators extend the syntax typically used for matrices to linear mappings of arbitrary dimensions and nonlinear functions. Unlike matrices however, abstract operators apply the mappings with specific efficient algorithms that minimize memory requirements. 
@@ -66,17 +73,19 @@ julia> H = [A B]
 
 In this case `H` has a domain of dimensions `size(H,2) = ((3, 4), (3, 4))` and type `domainType(H) = (Float64, Complex{Float64})`.
 
-When an `AbstractOperators` have multiple domains, this must be multiplied using a `Tuple`s of `AbstractArray`s with corresponding `size(H,2)` and `domainType(H)`, for example: 
+When an `AbstractOperators` have multiple domains, this must be multiplied using an `ArrayPartition` (see [RecursiveArrayTools](https://github.com/JuliaDiffEq/RecursiveArrayTools.jl/]) with corresponding size and domain, for example: 
 
 ```julia
-julia> H*(x, complex(x))
+julia> using RecursiveArrayTools
+
+julia> H*ArrayPartition(x, complex(x))
 3×4 Array{Complex{Float64},2}:
  -16.3603+0.0im      52.4946-8.69342im  -129.014+0.0im      44.6712+8.69342im
   -22.051+23.8135im  16.5309-10.9601im  -22.5719+39.5599im  13.8174+3.81678im
  -5.81874-23.8135im  9.70679-3.81678im  -2.21552-39.5599im  11.5502+10.9601im
 ```
 
-Similarly, when an `AbstractOperators` have multiple codomains, this will return a `Tuple` of `AbstractArray`s with corresponding `size(H,1)` and `codomainType(H)`, for example: 
+Similarly, when an `AbstractOperators` have multiple codomains, this will return an `ArrayPartition`, for example: 
 ```julia
 julia> V = VCAT(Eye(3,3),FiniteDiff((3,3)))
 [I;δx]  ℝ^(3, 3) -> ℝ^(3, 3)  ℝ^(2, 3)

src/AbstractOperators.jl

@@ -2,12 +2,10 @@ __precompile__()
 
 module AbstractOperators
 
-using LinearAlgebra, AbstractFFTs, DSP, FFTW
+using LinearAlgebra, AbstractFFTs, DSP, FFTW, RecursiveArrayTools
 
-# Block stuff
-include("utilities/block.jl")
-using AbstractOperators.BlockArrays
 
+const RealOrComplex{R} = Union{R, Complex{R}}
 abstract type AbstractOperator end
 
 abstract type LinearOperator    <: AbstractOperator end
@@ -18,11 +16,11 @@ import LinearAlgebra: mul!
 export LinearOperator,
        NonLinearOperator,
        AbstractOperator
+export mul!
 
 # Predicates and properties
 
 include("properties.jl")
-
 include("calculus/AdjointOperator.jl")
 
 ## Linear operators

src/calculus/DCAT.jl

@@ -16,7 +16,7 @@ DCAT  ℝ^10  ℝ^10  ℝ^(4, 4) -> ℝ^10  ℝ^10  ℝ^(3, 4)
 To evaluate `DCAT` operators multiply them with a `Tuple` of `AbstractArray` of the correct domain size and type. The output will consist as well of a `Tuple` with the codomain type and size of the `DCAT`.
 
 ```julia
-julia> D*(ones(2),ones(2),ones(3))
+julia> D*ArrayPartition(ones(2),ones(2),ones(3))
 ([2.0, 2.0], Complex{Float64}[3.0+0.0im, 0.0+0.0im, 0.0+0.0im])
 
 ```
@@ -62,9 +62,12 @@ function DCAT(A::Vararg{AbstractOperator})
 end
 
 # Mappings
-@generated function mul!(y, H::DCAT{N,L,P1,P2}, b) where {N,L,P1,P2} 
+@generated function mul!(yy::ArrayPartition, 
+                         H::DCAT{N,L,P1,P2}, 
+                         bb::ArrayPartition) where {N,L,P1,P2} 
 
-	ex = :()
+  # extract stuff
+	ex = :(y = yy.x; b = bb.x )
 
 	for i = 1:N
 
@@ -76,7 +79,7 @@ end
 		# stacked operator 
 		# build mul!(( y[H.idxC[i][1]], y[H.idxC[i][2]] ...  ), H.A[i], b)
         yy =  [ :(y[H.idxC[$i][$ii]]) for ii in eachindex(fieldnames(fieldtype(P2,i)))]
-        yy = :( tuple( $(yy...) ) )
+        yy = :( ArrayPartition( $(yy...) ) )
 		end
 
 		if fieldtype(P1,i) <: Int 
@@ -87,7 +90,7 @@ end
 		# stacked operator 
 		# build mul!(H.buf, H.A[i],( b[H.idxD[i][1]], b[H.idxD[i][2]] ...  ))
         bb = [ :(b[H.idxD[$i][$ii]]) for ii in eachindex(fieldnames(fieldtype(P1,i))) ]
-        bb = :( tuple( $(bb...) ) )
+        bb = :( ArrayPartition( $(bb...) ) )
 		end
 
 		ex = :($ex; mul!($yy,H.A[$i],$bb))
@@ -98,9 +101,12 @@ end
 
 end
 
-@generated function mul!(y, A::AdjointOperator{DCAT{N,L,P1,P2}}, b) where {N,L,P1,P2} 
+@generated function mul!(yy::ArrayPartition, 
+                         A::AdjointOperator{DCAT{N,L,P1,P2}},
+                         bb::ArrayPartition) where {N,L,P1,P2} 
 
-	ex = :(H = A.A)
+  # extract stuff
+	ex = :(H = A.A; y = yy.x; b = bb.x )
 
 	for i = 1:N
 
@@ -112,7 +118,7 @@ end
 		# stacked operator 
 		# build mul!(( y[H.idxD[i][1]], y[H.idxD[i][2]] ...  ), H.A[i]', b)
         yy = [ :(y[H.idxD[$i][$ii]]) for ii in eachindex(fieldnames(fieldtype(P1,i)))]
-        yy = :( tuple( $(yy...) ))
+        yy = :( ArrayPartition( $(yy...) ))
 		end
 
 		if fieldtype(P2,i) <: Int 
@@ -123,7 +129,7 @@ end
 		# stacked operator 
 		# build mul!(H.buf, H.A[i]',( b[H.idxC[i][1]], b[H.idxC[i][2]] ...  ))
         bb = [ :(b[H.idxC[$i][$ii]]) for ii in eachindex(fieldnames(fieldtype(P2,i)))]
-        bb = :( tuple( $(bb...) ) )
+        bb = :( ArrayPartition( $(bb...) ) )
 		end
 
 		ex = :($ex; mul!($yy,H.A[$i]',$bb))
@@ -196,7 +202,7 @@ remove_displacement(D::DCAT) = DCAT(remove_displacement.(D.A), D.idxD, D.idxC)
 
 # special cases
 # Eye constructor
-Eye(x::A) where {N, A <: NTuple{N,AbstractArray}} = DCAT(Eye.(x)...)
+Eye(x::ArrayPartition) = DCAT(Eye.(x.x)...)
 diag(L::DCAT{N,NTuple{N,E}}) where {N, E <: Eye} = 1.
 diag_AAc(L::DCAT{N,NTuple{N,E}}) where {N, E <: Eye} = 1.
 diag_AcA(L::DCAT{N,NTuple{N,E}}) where {N, E <: Eye} = 1.