Make code 0.6 compatible (#128)

* running v0.6 conversion code proposed by @ovainola in #108.
* change travis so that build is done using 0.6
* documentation is build from 0.6
* fix most of deprecation warnings
* fix test to pass 0.6

.travis.yml

@@ -2,7 +2,7 @@ language: julia
 os:
   - linux
 julia:
-  - 0.5
+  - 0.6
 notifications:
   email: false
   webhooks:

docs/deploy.jl

@@ -7,4 +7,4 @@ using JuliaFEM
 deploydocs(
     deps = Deps.pip("mkdocs", "python-markdown-math"),
     repo = "github.com/JuliaFEM/JuliaFEM.jl.git",
-    julia = "0.5")
+    julia = "0.6")

src/abaqus.jl

@@ -9,12 +9,12 @@ using JuliaFEM.Postprocess
 
 ### Model definitions for ABAQUS data model
 
-abstract AbstractMaterial
-abstract AbstractMaterialProperty
-abstract AbstractProperty
-abstract AbstractStep
-abstract AbstractBoundaryCondition
-abstract AbstractOutputRequest
+abstract type AbstractMaterial end
+abstract type AbstractMaterialProperty end
+abstract type AbstractProperty end
+abstract type AbstractStep end
+abstract type AbstractBoundaryCondition end
+abstract type AbstractOutputRequest end
 
 type Model
     path :: AbstractString
@@ -261,12 +261,12 @@ end
 @register_abaqus_keyword("CLOAD")
 @register_abaqus_keyword("DLOAD")
 @register_abaqus_keyword("DSLOAD")
-typealias BOUNDARY_CONDITIONS Union{BOUNDARY, CLOAD, DLOAD, DSLOAD}
+const BOUNDARY_CONDITIONS = Union{BOUNDARY,CLOAD,DLOAD,DSLOAD}
 
 @register_abaqus_keyword("NODE PRINT")
 @register_abaqus_keyword("EL PRINT")
 @register_abaqus_keyword("SECTION PRINT")
-typealias OUTPUT_REQUESTS Union{NODE_PRINT, EL_PRINT, SECTION_PRINT}
+const OUTPUT_REQUESTS = Union{NODE_PRINT,EL_PRINT,SECTION_PRINT}
 
 ## Properties
 

src/elements.jl

@@ -1,7 +1,7 @@
 # This file is a part of JuliaFEM.
 # License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
 
-abstract AbstractElement
+abstract type AbstractElement end
 
 type Element{E<:AbstractElement}
     id :: Int

src/fields.jl

@@ -1,31 +1,31 @@
 # This file is a part of JuliaFEM.
 # License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
 
-abstract AbstractField
+abstract type AbstractField end
 
-abstract Discrete <: AbstractField
-abstract Continuous <: AbstractField
-abstract Constant <: AbstractField
-abstract Variable <: AbstractField
-abstract TimeVariant <: AbstractField
-abstract TimeInvariant <: AbstractField
+abstract type Discrete<:AbstractField end
+abstract type Continuous<:AbstractField end
+abstract type Constant<:AbstractField end
+abstract type Variable<:AbstractField end
+abstract type TimeVariant<:AbstractField end
+abstract type TimeInvariant<:AbstractField end
 
 type Field{A<:Union{Discrete,Continuous}, B<:Union{Constant,Variable}, C<:Union{TimeVariant,TimeInvariant}}
     data
 end
 
-typealias FieldSet Dict{String, Field}
+const FieldSet = Dict{String,Field}
 
 ### Different field combinations and other typealiases
 
-typealias DCTI Field{Discrete,   Constant, TimeInvariant}
-typealias DVTI Field{Discrete,   Variable, TimeInvariant}
-typealias DCTV Field{Discrete,   Constant, TimeVariant}
-typealias DVTV Field{Discrete,   Variable, TimeVariant}
-typealias CCTI Field{Continuous, Constant, TimeInvariant}
-typealias CVTI Field{Continuous, Variable, TimeInvariant} # can be used to interpolate in spatial dimension
-typealias CCTV Field{Continuous, Constant, TimeVariant} # can be used to interpolate in time
-typealias CVTV Field{Continuous, Variable, TimeVariant}
+const DCTI = Field{Discrete,Constant,TimeInvariant}
+const DVTI = Field{Discrete,Variable,TimeInvariant}
+const DCTV = Field{Discrete,Constant,TimeVariant}
+const DVTV = Field{Discrete,Variable,TimeVariant}
+const CCTI = Field{Continuous,Constant,TimeInvariant}
+const CVTI = Field{Continuous,Variable,TimeInvariant} # can be used to interpolate in spatial dimension
+const CCTV = Field{Continuous,Constant,TimeVariant} # can be used to interpolate in time
+const CVTV = Field{Continuous,Variable,TimeVariant}
 
 # Discrete fields
 
@@ -199,7 +199,7 @@ end
 """ Take dot product of DVTI field and vector T. Vector length must match to the
 field length and this can be used mainly for interpolation purposes, i.e., u = ∑ Nᵢuᵢ.
 """
-function *(T::Vector, f::DVTI)
+function *(T::Union{Vector, RowVector}, f::DVTI)
     @assert length(T) <= length(f)
     return sum([T[i]*f[i] for i=1:length(T)])
 end

src/integrate.jl

@@ -62,9 +62,9 @@ function get_integration_points(element::Poi1)
     [ (1.0, [] ) ]
 end
 
-typealias CartesianLineElement Union{Seg2, Seg3, NSeg}
-typealias CartesianSurfaceElement Union{Quad4, Quad8, Quad9, NSurf}
-typealias CartesianVolumeElement Union{Hex8, Hex20, Hex27, NSolid}
+const CartesianLineElement = Union{Seg2,Seg3,NSeg}
+const CartesianSurfaceElement = Union{Quad4,Quad8,Quad9,NSurf}
+const CartesianVolumeElement = Union{Hex8,Hex20,Hex27,NSolid}
 
 function get_integration_points(element::CartesianLineElement, order::Int64)
     w, xi = get_integration_points(order)
@@ -86,7 +86,7 @@ end
 # http://math2.uncc.edu/~shaodeng/TEACHING/math5172/Lectures/Lect_15.PDF
 # http://libmesh.github.io/doxygen/quadrature__gauss__2D_8C_source.html
 
-typealias TriangularElement Union{Tri3, Tri6, Tri7}
+const TriangularElement = Union{Tri3,Tri6,Tri7}
 
 function get_integration_points(element::TriangularElement, ::Type{Val{1}})
     weights = [0.5]
@@ -203,7 +203,7 @@ end
 
 ### 3d elements
 
-typealias TetrahedralElement Union{Tet4, Tet10}
+const TetrahedralElement = Union{Tet4,Tet10}
 
 function get_integration_points(element::TetrahedralElement, ::Type{Val{1}})
     weights = 1.0/6.0*[1.0]
@@ -273,7 +273,7 @@ end
 
 # http://www.colorado.edu/engineering/CAS/courses.d/AFEM.d/AFEM.Ch12.d/AFEM.Ch12.pdf
 
-typealias PyramidalElement Union{Pyr5,}
+const PyramidalElement = Union{Pyr5,}
 
 function get_integration_points(element::PyramidalElement, ::Type{Val{2}})
     g1 =  0.5842373946721771876874344
@@ -292,7 +292,7 @@ function get_integration_points(element::PyramidalElement, ::Type{Val{2}})
     return zip(weights, points)
 end
 
-typealias PrismaticElement Union{Wedge6, Wedge15}
+const PrismaticElement = Union{Wedge6,Wedge15}
 
 function get_integration_points(element::PrismaticElement, ::Type{Val{2}})
     weights = 1/6*[1.0, 1.0, 1.0, 1.0, 1.0, 1.0]
@@ -436,9 +436,9 @@ end
 ### default number of integration points for each element
 ### 2 for linear elements, 3 for quadratic
 
-typealias LinearElement Union{Seg2, Tri3, Quad4, Tet4, Pyr5, Wedge6, Hex8}
+const LinearElement = Union{Seg2, Tri3, Quad4, Tet4, Pyr5, Wedge6, Hex8}
 
-typealias QuadraticElement Union{Seg3, Tri6, Tri7, Tet10, Quad8, Quad9, Wedge15, Hex20, Hex27}
+const QuadraticElement = Union{Seg3,Tri6,Tri7,Tet10,Quad8,Quad9,Wedge15,Hex20,Hex27}
 
 function get_integration_order(element::LinearElement)
     return 2

src/problems.jl

@@ -1,10 +1,10 @@
 # This file is a part of JuliaFEM.
 # License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
 
-abstract AbstractProblem
-abstract FieldProblem <: AbstractProblem
-abstract BoundaryProblem <: AbstractProblem
-abstract MixedProblem <: AbstractProblem
+abstract type AbstractProblem end
+abstract type FieldProblem<:AbstractProblem end
+abstract type BoundaryProblem<:AbstractProblem end
+abstract type MixedProblem<:AbstractProblem end
 
 """
 General linearized problem to solve

src/problems_contact.jl

@@ -72,4 +72,4 @@ function assemble!(problem::Problem{Contact}, time::Real)
     problem.properties.iteration += 1
 end
 
-typealias ContactElements2D Union{Seg2}
+const ContactElements2D = Union{Seg2}

src/problems_contact_2d.jl

@@ -41,7 +41,7 @@ function create_contact_segmentation(problem::Problem{Contact}, slave_element::E
         # 3.1 calculate segmentation
         xi1a = project_from_master_to_slave(slave_element, x2[1], time)
         xi1b = project_from_master_to_slave(slave_element, x2[2], time)
-        xi1 = clamp([xi1a; xi1b], -1.0, 1.0)
+        xi1 = clamp.([xi1a; xi1b], -1.0, 1.0)
         l = 1/2*abs(xi1[2]-xi1[1])
         if isapprox(l, 0.0)
             continue # no contribution in this master element

src/problems_contact_2d_autodiff.jl

@@ -36,8 +36,8 @@ function project_from_master_to_slave{E<:MortarElements2D}(
     dxi1 = 0.0
     for i=1:max_iterations
         dxi1 = -R(xi1)/dR(xi1)
-        dxi1 = clamp(dxi1, -0.3, 0.3)
-        xi1_next = clamp(xi1 + dxi1, -1.0, 1.0)
+        dxi1 = clamp.(dxi1, -0.3, 0.3)
+        xi1_next = clamp.(xi1 + dxi1, -1.0, 1.0)
         if norm(xi1_next - xi1) < tol
             return xi1_next
         end
@@ -176,7 +176,7 @@ function assemble!(problem::Problem{Contact}, time::Float64,
                 # calculate segmentation: we care only about endpoints
                 xi1a = project_from_master_to_slave(slave_element, x1, n1, x2[1])
                 xi1b = project_from_master_to_slave(slave_element, x1, n1, x2[2])
-                xi1 = clamp([xi1a; xi1b], -1.0, 1.0)
+                xi1 = clamp.([xi1a; xi1b], -1.0, 1.0)
                 l = 1/2*abs(xi1[2]-xi1[1])
                 isapprox(l, 0.0) && continue # no contribution in this master element
 
@@ -211,7 +211,7 @@ function assemble!(problem::Problem{Contact}, time::Float64,
                 # calculate segmentation: we care only about endpoints
                 xi1a = project_from_master_to_slave(slave_element, x1, n1, x2[1])
                 xi1b = project_from_master_to_slave(slave_element, x1, n1, x2[2])
-                xi1 = clamp([xi1a; xi1b], -1.0, 1.0)
+                xi1 = clamp.([xi1a; xi1b], -1.0, 1.0)
                 l = 1/2*abs(xi1[2]-xi1[1])
                 isapprox(l, 0.0) && continue # no contribution in this master element
 

src/problems_contact_3d.jl

@@ -1,7 +1,7 @@
 # This file is a part of JuliaFEM.
 # License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
 
-typealias ContactElements3D Union{Tri3, Tri6, Quad4, Quad8, Quad9}
+const ContactElements3D = Union{Tri3,Tri6,Quad4,Quad8,Quad9}
 
 function create_orthogonal_basis(n)
     I = eye(3)

src/problems_elasticity.jl

@@ -66,15 +66,15 @@ function assemble!(assembly::Assembly, problem::Problem{Elasticity}, element::El
     add!(assembly.f, gdofs, f)
 end
 
-typealias Elasticity2DSurfaceElements Union{Poi1, Seg2, Seg3}
-typealias Elasticity2DVolumeElements Union{Tri3, Tri6, Quad4, Quad8, Quad9}
-typealias Elasticity3DSurfaceElements Union{Poi1, Tri3, Tri6, Quad4, Quad8, Quad9}
-typealias Elasticity3DVolumeElements Union{Tet4, Pyr5, Wedge6, Wedge15, Hex8, Tet10, Hex20, Hex27}
+const Elasticity2DSurfaceElements = Union{Poi1,Seg2,Seg3}
+const Elasticity2DVolumeElements = Union{Tri3,Tri6,Quad4,Quad8,Quad9}
+const Elasticity3DSurfaceElements = Union{Poi1,Tri3,Tri6,Quad4,Quad8,Quad9}
+const Elasticity3DVolumeElements = Union{Tet4, Pyr5, Wedge6, Wedge15, Hex8, Tet10, Hex20, Hex27}
 
 function initialize_internal_params!(params, ip, type_) #::Type{Val{:type_2d}})
     param_keys = keys(params)
     all_keys = ip.fields.keys
-    ip_fields = filter(x->isdefined(all_keys, x), collect(1:length(all_keys)))
+    ip_fields = filter(x->isassigned(all_keys, x), collect(1:length(all_keys)))
 
     if !("params_initialized" in ip_fields)
         for key in param_keys
@@ -96,7 +96,7 @@ end
 
 function get_keys(element)
     all_keys = element.fields.keys
-    idx = filter(x->isdefined(all_keys, x), collect(1:length(all_keys)))
+    idx = filter(x->isassigned(all_keys, x), collect(1:length(all_keys)))
     map(x -> all_keys[x], idx)
 end
 

src/problems_heat.jl

@@ -67,8 +67,8 @@ function assemble!{E}(assembly::Assembly, problem::Problem{Heat}, element::Eleme
     info("Unknown element type $E for 3d heat problem!")
 end
 
-typealias Heat3DVolumeElements Union{Tet4, Tet10, Pyr5, Hex8, Hex20, Hex27}
-typealias Heat3DSurfaceElements Union{Tri3, Tri6, Quad4, Quad8, Quad9}
+const Heat3DVolumeElements = Union{Tet4, Tet10, Pyr5, Hex8, Hex20, Hex27}
+const Heat3DSurfaceElements = Union{Tri3,Tri6,Quad4,Quad8,Quad9}
 
 function assemble!{E<:Heat3DVolumeElements}(assembly::Assembly, problem::Problem{Heat}, element::Element{E}, time, ::Type{Val{Symbol("3D")}})
     gdofs = get_gdofs(problem, element)
@@ -179,8 +179,8 @@ function assemble!{E}(assembly::Assembly, problem::Problem{Heat}, element::Eleme
     info("Unknown element type $E for 2d heat problem!")
 end
 
-typealias Heat2DVolumeElements Union{Tri3, Tri6, Quad4}
-typealias Heat2DSurfaceElements Union{Seg2, Seg3}
+const Heat2DVolumeElements = Union{Tri3,Tri6,Quad4}
+const Heat2DSurfaceElements = Union{Seg2,Seg3}
 
 function assemble!{E<:Heat2DVolumeElements}(assembly::Assembly, problem::Problem{Heat}, element::Element{E}, time, ::Type{Val{Symbol("2D")}})
     gdofs = get_gdofs(problem, element)

src/problems_mortar_2d.jl

@@ -1,7 +1,7 @@
 # This file is a part of JuliaFEM.
 # License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
 
-typealias MortarElements2D Union{Seg2, Seg3}
+const MortarElements2D = Union{Seg2,Seg3}
 
 function newton(f, df, x; tol=1.0e-6, max_iterations=10)
     for i=1:max_iterations
@@ -137,7 +137,7 @@ function assemble!(problem::Problem{Mortar}, time::Float64, ::Type{Val{1}}, ::Ty
             # 3.1 calculate segmentation
             xi1a = project_from_master_to_slave(slave_element, X2[1], time)
             xi1b = project_from_master_to_slave(slave_element, X2[2], time)
-            xi1 = clamp([xi1a; xi1b], -1.0, 1.0)
+            xi1 = clamp.([xi1a; xi1b], -1.0, 1.0)
             l = 1/2*abs(xi1[2]-xi1[1])
             isapprox(l, 0.0) && continue # no contribution in this master element
 

src/problems_mortar_2d_autodiff.jl

@@ -144,7 +144,7 @@ function assemble!(problem::Problem{Mortar}, time::Float64, ::Type{Val{1}}, ::Ty
                 xi1b = project_from_master_to_slave(slave_element, x1, n1, x2[2], time)
 #               xi1a = project_from_master_to_slave(slave_element, X2[1], time)
 #               xi1b = project_from_master_to_slave(slave_element, X2[2], time)
-                xi1 = clamp([xi1a; xi1b], -1.0, 1.0)
+                xi1 = clamp.([xi1a; xi1b], -1.0, 1.0)
                 l = 1/2*abs(xi1[2]-xi1[1])
                 isapprox(l, 0.0) && continue # no contribution in this master element
 

src/problems_mortar_3d.jl

@@ -1,7 +1,7 @@
 # This file is a part of JuliaFEM.
 # License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
 
-typealias MortarElements3D Union{Tri3, Tri6, Quad4}
+const MortarElements3D = Union{Tri3,Tri6,Quad4}
 
 function project_vertex_to_auxiliary_plane(p::Vector, x0::Vector, n0::Vector)
     return p - dot(p-x0, n0)*n0

src/solvers.jl

@@ -1,7 +1,7 @@
 # This file is a part of JuliaFEM.
 # License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
 
-abstract AbstractSolver
+abstract type AbstractSolver end
 
 type Solver{S<:AbstractSolver}
     name :: AbstractString       # some descriptive name for problem

src/sparse.jl

@@ -10,7 +10,7 @@ type SparseMatrixCOO{T<:Real}
     V :: Vector{T}
 end
 
-typealias SparseVectorCOO SparseMatrixCOO
+const SparseVectorCOO = SparseMatrixCOO
 
 function SparseMatrixCOO()
     return SparseMatrixCOO{Float64}([], [], [])
@@ -39,8 +39,20 @@ Parameters
 tol
     used to drop near zero values less than tol.
 """
-function sparse(A::SparseMatrixCOO, args...; tol=1.0e-12)
-    B = sparse(A.I, A.J, A.V, args...)
+function sparse(A::SparseMatrixCOO; tol=1.0e-12)
+    B = sparse(A.I, A.J, A.V)
+    SparseArrays.droptol!(B, tol)
+    return B
+end
+
+function sparse(A::SparseMatrixCOO, n::Int, m::Int; tol=1.0e-12)
+    B = sparse(A.I, A.J, A.V, n, m)
+    SparseArrays.droptol!(B, tol)
+    return B
+end
+
+function sparse(A::SparseMatrixCOO, n::Int, m::Int, f::Function; tol=1.0e-12)
+    B = sparse(A.I, A.J, A.V, n, m, f)
     SparseArrays.droptol!(B, tol)
     return B
 end

src/types.jl

@@ -1,9 +1,9 @@
 # This file is a part of JuliaFEM.
 # License is MIT: see https://github.com/JuliaFEM/JuliaFEM.jl/blob/master/LICENSE.md
 
-typealias Node Vector{Float64}
+const Node = Vector{Float64}
 
-abstract AbstractPoint
+abstract type AbstractPoint end
 
 type Point{P<:AbstractPoint}
     id :: Int
@@ -52,7 +52,7 @@ end
 type IntegrationPoint <: AbstractPoint
 end
 
-typealias IP Point{IntegrationPoint}
+const IP = Point{IntegrationPoint}
 
 function IP(id, weight, coords)
     return IP(id, weight, coords, Dict(), IntegrationPoint())

test/test_fields.jl

@@ -19,7 +19,7 @@ using JuliaFEM.Testing
     @test isapprox(f, 1.0)
     @test 2*f == 2.0 # multiply by constant
     @test f(1.0) == 1.0 # time interpolation
-    @test isapprox([2.0]''*f, 2.0) # wanted behavior?
+    @test isapprox(reshape([2.0],1,1)*f, 2.0) # wanted behavior?
 end
 
 @testset "discrete, variable, time invariant field" begin

test/test_solvers.jl

@@ -59,7 +59,7 @@ end
     push!(s, p)
     get_field_assembly(s)
     @test s.ndofs == 0
-    add!(p.assembly.K, [4], [4], [4.0]'')
+    add!(p.assembly.K, [4], [4], reshape([4.0],1,1))
     get_field_assembly(s)
     @test s.ndofs == 4
 end
@@ -70,8 +70,8 @@ end
     p1 = Problem(Dirichlet, "bc1", 2, "displacement")
     p2 = Problem(Dirichlet, "bc2", 2, "displacement")
     # third dofs constrained 
-    add!(p1.assembly.C2, [3], [3], [1.0]'')
-    add!(p2.assembly.C2, [3], [4], [1.0]'')
+    add!(p1.assembly.C2, [3], [3], reshape([1.0],1,1))
+    add!(p2.assembly.C2, [3], [4], reshape([1.0],1,1))
     s.ndofs = 4
     push!(s, p1, p2)
     @test_throws ErrorException get_boundary_assembly(s)