Merge pull request #64 from sjkelly/sjk/conda2

[RFC] Use Conda for CI and fix deprecations

.gitignore

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

.travis.yml

@@ -2,25 +2,26 @@
 language: julia
 os:
   - linux
+  - osx
+dist: xenial
 julia:
-  - 1.0
-
-dist: trusty
-
-sudo: required
-
-services:
-  - docker
-
+  - 1.1
+#  - nightly
+addons:
+  apt:
+    packages:
+      pkg-config
 before_install:
-  - echo "**** pulling Docker image"
-  - docker pull ysimillides/fenics-julia-docker:v1.0
-  - chmod +x travis_docker_test_script.sh
+  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then brew install pkg-config; fi
 notifications:
   email: false
+matrix:
+  allow_failures:
+    - julia: nightly
 script:
-  - echo "**** running Docker"
-  - docker run --env-file travis_docker_env.list -t -a STDOUT -a STDIN -a STDERR -v $PWD:/mnt ysimillides/fenics-julia-docker:v1.0 /mnt/travis_docker_test_script.sh $TRAVIS_JULIA_VERSION
+    - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
+    - julia -e 'using Pkg; ENV["PYTHON"]="";Pkg.add("Conda");Pkg.build("FEniCS");'
+    - julia -e 'using Pkg, Conda; ENV["PATH"] = "$(Conda.BINDIR);$(ENV["PATH"])";ENV["PKG_CONFIG_PATH"] = "$(Conda.LIBDIR*"/pkgconfig")"; print(ENV["PKG_CONFIG_PATH"]); Pkg.test("FEniCS", coverage=true)'
 after_success:
   # push coverage results to Coveralls, .cov files were copied back by script above
   - echo "**** submitting coverage information"

Project.toml

@@ -0,0 +1,7 @@
+name = "FEniCS"
+uuid = "186dfeec-b415-5c13-8e76-5fbf19f56f9b"
+
+[deps]
+ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
+PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
+Requires = "ae029012-a4dd-5104-9daa-d747884805df"

deps/build.jl

@@ -1,7 +1,14 @@
 using PyCall
 
+if Sys.iswindows()
+	@warn("""
+					FEniCS is not known to run on Windows!
+					Please try installing from Windows Subsystem for Linux.
+		""")
+end
 	try
-		pyimport("fenics")
+		pyimport_conda("fenics", "fenics=2019.1.0", "conda-forge")
+		pyimport_conda("mshr", "mshr=2019.1.0", "conda-forge")
 	catch ee
 		typeof(ee) <: PyCall.PyError || rethrow(ee)
 		@warn("""
@@ -13,4 +20,3 @@ using PyCall
 				 """
 		)
 	end
-

src/FEniCS.jl

@@ -2,7 +2,9 @@ __precompile__(false)
 module FEniCS
 using PyCall
 using Requires
-@pyimport fenics
+
+fenics = pyimport_conda("fenics", "fenics=2019.1.0", "conda-forge")
+ufl = pyimport_conda("ufl", "ufl=2019.1.0", "conda-forge")
 
 function __init__()
 	@require PyPlot="d330b81b-6aea-500a-939a-2ce795aea3ee" include("jplot.jl")
@@ -16,7 +18,7 @@ abstract type
   fenicsobject
 end #creates placeholder for the fenicsobject type
 
-fenicspycall(object::fenicsobject, func::Union{Symbol,String}, args...) = object.pyobject[func](args...)
+fenicspycall(object::fenicsobject, func::Union{Symbol,String}, args...) = getproperty(object.pyobject,func)(args...)
 export fenicspycall
 
 macro fenicsclass(name::Symbol, base1::Symbol=:fenicsobject)
@@ -36,7 +38,7 @@ export fenicsclass
 str(obj::fenicsobject) = fenicspycall(obj, :__str__)
 repr(obj::fenicsobject) = fenicspycall(obj, :__repr__)
 show(io::IO, obj::fenicsobject) = show(io, str(obj))
-Docs.getdoc(obj::fenicsobject) = obj.pyobject[:__doc__]
+Docs.getdoc(obj::fenicsobject) = obj.pyobject.__doc__
 export str, repr
 
 include("jmesh.jl") #this file contains the mesh functions
@@ -46,7 +48,7 @@ include("jsolve.jl") #this file contains the solver functions/routines
 include("jinterface.jl")
 
 try
-  pyimport("mshr")
+  pyimport_conda("mshr", "mshr=2019.1.0", "conda-forge")
   include("fmshr.jl") #this file contains various geometrical objects using the mshr package
 catch ee
  print("mshr has not been included")

src/fmshr.jl

@@ -1,4 +1,4 @@
-@pyimport mshr
+mshr = pyimport_conda("mshr", "mshr", "conda-forge")
 @fenicsclass Geometry
 
 #functions necessary for creating meshes from geometrical objects.
@@ -18,9 +18,9 @@ export Circle,Rectangle,Ellipse,Box,Cone,Sphere,generate_mesh
 
 
 #operator overloading for Geometry types so we can create composite shapes
-+(geom_object1::Geometry, geom_object2::Geometry) = Geometry(geom_object1.pyobject[:__add__](geom_object2.pyobject))
--(geom_object1::Geometry, geom_object2::Geometry) = Geometry(geom_object1.pyobject[:__sub__](geom_object2.pyobject))
-*(geom_object1::Geometry, geom_object2::Geometry) = Geometry(geom_object1.pyobject[:__mul__](geom_object2.pyobject))
++(geom_object1::Geometry, geom_object2::Geometry) = Geometry(geom_object1.pyobject.__add__(geom_object2.pyobject))
+-(geom_object1::Geometry, geom_object2::Geometry) = Geometry(geom_object1.pyobject.__sub__(geom_object2.pyobject))
+*(geom_object1::Geometry, geom_object2::Geometry) = Geometry(geom_object1.pyobject.__mul__(geom_object2.pyobject))
 
 set_subdomain(object::Geometry,degree,domain2) = fenicspycall(object, :set_subdomain,degree,domain2.pyobject)
 """

src/jfem.jl

@@ -59,7 +59,7 @@ function split(fun::FeFunction)
 end
 
 function py_split(fun::FeFunction)
-     vec = fun.pyobject[:split]()
+     vec = fun.pyobject.split()
      expr_vec = [FeFunction(spl) for spl in vec]
      return expr_vec
 end
@@ -71,16 +71,16 @@ export FeFunction,assign,split,py_split
 
 @fenicsclass Expression
 
-Expression(cppcode::String;element=nothing, cell=nothing, domain=nothing, degree=nothing, name=nothing, label=nothing, mpi_comm=nothing) = Expression(fenics.Expression(cppcode,
-element=element,cell=cell, domain=domain, degree=degree, name=name, label=label, mpi_comm=mpi_comm))
+Expression(cppcode::String;element=nothing, cell=nothing, domain=nothing, degree=nothing, name=nothing, label=nothing) = Expression(fenics.Expression(cppcode,
+element=element,cell=cell, domain=domain, degree=degree, name=name, label=label))
 Identity(dim::Int) = Expression(fenics.Identity(dim))
 inner(u::Union{Expression,FeFunction}, v::Union{Expression,FeFunction}) = Expression(fenics.inner(u.pyobject, v.pyobject))
 outer(u::Union{Expression,FeFunction}, v::Union{Expression,FeFunction}) = Expression(fenics.outer(u.pyobject, v.pyobject))
 dot(u::Union{Expression,FeFunction}, v::Union{Expression,FeFunction}) = Expression(fenics.dot(u.pyobject, v.pyobject))
 grad(u::Union{Expression,FeFunction}) = Expression(fenics.grad(u.pyobject))
 ∇(u::Union{Expression,FeFunction}) = Expression(fenics.grad(u.pyobject))
-nabla_grad(u::Union{Expression,FeFunction}) = Expression(fenics.nabla_grad(u.pyobject))
-nabla_div(u::Union{Expression,FeFunction}) = Expression(fenics.nabla_div(u.pyobject))
+nabla_grad(u::Union{Expression,FeFunction}) = Expression(ufl.nabla_grad(u.pyobject))
+nabla_div(u::Union{Expression,FeFunction}) = Expression(ufl.nabla_div(u.pyobject))
 div(u::Union{Expression,FeFunction}) = Expression(fenics.div(u.pyobject))
 cross(u::Union{Expression,FeFunction}, v::Union{Expression,FeFunction}) = Expression(fenics.cross(u.pyobject, v.pyobject))
 tr(u::Union{Expression,FeFunction}) = Expression(fenics.tr(u.pyobject))
@@ -115,22 +115,22 @@ export dx,ds,dS,dP,directional_derivative
 #https://github.com/FEniCS/Expression/blob/master/Expression/measure.py
 @fenicsclass Form
 
-*(expr::Union{Expression,FeFunction}, measure::Measure) = Expression(measure.pyobject[:__rmul__](expr.pyobject) )
+*(expr::Union{Expression,FeFunction}, measure::Measure) = Expression(measure.pyobject.__rmul__(expr.pyobject) )
 
-*(expr::Union{Expression,FeFunction}, expr2::Union{Expression,FeFunction}) = Expression(expr.pyobject[:__mul__](expr2.pyobject) )
-*(expr::Real, expr2::Union{Expression,FeFunction}) = Expression(expr2.pyobject[:__mul__](expr) )
-*(expr::Union{Expression,FeFunction}, expr2::Real) = Expression(expr.pyobject[:__mul__](expr2) )
+*(expr::Union{Expression,FeFunction}, expr2::Union{Expression,FeFunction}) = Expression(expr.pyobject.__mul__(expr2.pyobject) )
+*(expr::Real, expr2::Union{Expression,FeFunction}) = Expression(expr2.pyobject.__mul__(expr) )
+*(expr::Union{Expression,FeFunction}, expr2::Real) = Expression(expr.pyobject.__mul__(expr2) )
 
-+(expr::Union{Expression,FeFunction}, expr2::Real) = Expression(expr.pyobject[:__add__](expr2) )
-+(expr::Real, expr2::Union{Expression,FeFunction}) = Expression(expr2.pyobject[:__add__](expr) )
-+(expr::Union{Expression,FeFunction}, expr2::Union{Expression,FeFunction}) = Expression(expr.pyobject[:__add__](expr2.pyobject) )
++(expr::Union{Expression,FeFunction}, expr2::Real) = Expression(expr.pyobject.__add__(expr2) )
++(expr::Real, expr2::Union{Expression,FeFunction}) = Expression(expr2.pyobject.__add__(expr) )
++(expr::Union{Expression,FeFunction}, expr2::Union{Expression,FeFunction}) = Expression(expr.pyobject.__add__(expr2.pyobject) )
 
--(expr::Union{Expression,FeFunction}, expr2::Real) = Expression(expr.pyobject[:__sub__](expr2) )
--(expr::Real, expr2::Union{Expression,FeFunction}) = -1*(Expression(expr2.pyobject[:__sub__](expr) ))
--(expr::Union{Expression,FeFunction}, expr2::Union{Expression,FeFunction}) = Expression(expr.pyobject[:__sub__](expr2.pyobject) )
+-(expr::Union{Expression,FeFunction}, expr2::Real) = Expression(expr.pyobject.__sub__(expr2) )
+-(expr::Real, expr2::Union{Expression,FeFunction}) = -1*(Expression(expr2.pyobject.__sub__(expr) ))
+-(expr::Union{Expression,FeFunction}, expr2::Union{Expression,FeFunction}) = Expression(expr.pyobject.__sub__(expr2.pyobject) )
 
-/(expr::Union{Expression,FeFunction}, expr2::Real) = Expression(expr.pyobject[:__div__](expr2) )
-/(expr::Union{Expression,FeFunction}, expr2::Union{Expression,FeFunction}) = Expression(expr.pyobject[:__div__](expr2.pyobject) )
+/(expr::Union{Expression,FeFunction}, expr2::Real) = Expression(expr.pyobject.__div__(expr2) )
+/(expr::Union{Expression,FeFunction}, expr2::Union{Expression,FeFunction}) = Expression(expr.pyobject.__div__(expr2.pyobject) )
 
 function /(expr::Real,expr2::Union{Expression,FeFunction})
     x = expr2*expr2
@@ -140,7 +140,7 @@ function /(expr::Real,expr2::Union{Expression,FeFunction})
 end
 
 function Transpose(object::Expression)
-    x = object.pyobject[:T]
+    x = object.pyobject.T
     y = Expression(x)
     return y
 end

src/jmesh.jl

@@ -72,14 +72,14 @@ UnitTriangleMesh() \n
 A mesh consisting of a single triangle with vertices at \n
 (0, 0) (1, 0) (0, 1)
 """
-UnitTriangleMesh() = Mesh(fenics.UnitTriangleMesh())
+UnitTriangleMesh() = Mesh(fenics.cpp.generation.UnitTriangleMesh.create())
 
 """
 UnitTetrahedronMesh() \n
 A mesh consisting of a single tetrahedron with vertices at \n
 (0, 0, 0) (1, 0, 0) (0, 1, 0) (0, 0, 1)
 """
-UnitTetrahedronMesh() = Mesh(fenics.UnitTetrahedronMesh())
+UnitTetrahedronMesh() = Mesh(fenics.cpp.generation.UnitTetrahedronMesh.create())
 
 
 """
@@ -153,11 +153,11 @@ export UnitTriangleMesh, UnitTetrahedronMesh, UnitSquareMesh, UnitQuadMesh,
 UnitIntervalMesh, UnitCubeMesh, BoxMesh, RectangleMesh, Mesh, BoundaryMesh
 
 function pyUnitTriangleMesh()
-  pycall(fenics.UnitTriangleMesh::PyObject,PyObject::Type)
+  fenics.cpp.generation.UnitTriangleMesh.create()
 end
 
 function pyUnitTetrahedronMesh()
-  pycall(fenics.UnitTetrahedronMesh::PyObject,PyObject::Type)
+  fenics.cpp.generation.UnitTetrahedronMesh.create()
 end
 
 function pyUnitCubeMesh(nx::Int, ny::Int, nz::Int)

src/jmisc.jl

@@ -22,11 +22,11 @@ list_linear_solver_methods()=fenics.list_linear_solver_methods()
 """
 Lists information for NonlinearVariationalSolver
 """
-info_NonLinearVariationalSolver() = fenics.info(fenics.NonlinearVariationalSolver[:default_parameters](), true)
+info_NonLinearVariationalSolver() = fenics.info(fenics.NonlinearVariationalSolver.default_parameters(), true)
 """
 Lists information for LinearVariationalSolver
 """
-info_LinearVariatonalSolver() = fenics.info(fenics.LinearVariationalSolver[:default_parameters](), true)
+info_LinearVariatonalSolver() = fenics.info(fenics.LinearVariationalSolver.default_parameters(), true)
 
 export list_lu_solver_methods, list_krylov_solver_methods, list_krylov_solver_preconditioners, list_linear_solver_methods, info_NonLinearVariationalSolver, info_LinearVariatonalSolver
 

src/jsolve.jl

@@ -79,15 +79,15 @@ XDMFFile(path::StringOrSymbol) = fenics.XDMFFile(path)
 export XDMFFile
 
 TimeSeries(path::StringOrSymbol) = fenics.TimeSeries(path)
-retrieve(timeseries,placeholder,time) = timeseries[:retrieve](placeholder,time)
+retrieve(timeseries,placeholder,time) = timeseries.retrieve(placeholder,time)
 export TimeSeries, retrieve
 
 
-write(path,solution,time::Number) = path[:write](solution.pyobject, time)
-write(path,solution::PyObject,time::Number) = path[:write](solution, time)
+write(path,solution,time::Number) = path.write(solution.pyobject, time)
+write(path,solution::PyObject,time::Number) = path.write(solution, time)
 
-store(path,solution,time::Number) = path[:store](solution.pyobject, time)
-store(path,solution::PyObject,time::Number) = path[:store](solution, time)
+store(path,solution,time::Number) = path.store(solution.pyobject, time)
+store(path,solution::PyObject,time::Number) = path.store(solution, time)
 
 export write,store
 
@@ -107,7 +107,7 @@ end
 function get_array(solution::FeFunction)
     generic_vector = vector(solution)
     instantiated_vector = fenics.Vector(generic_vector)
-    return instantiated_vector[:gather_on_zero]()
+    return instantiated_vector.gather_on_zero()
 end
 """
 we return the array from an assembled form

test/test_create.jl

@@ -8,7 +8,7 @@ using PyCall
 
 
 test_triangle = UnitTriangleMesh()
-test_tetrahedron = UnitTetrahedronMesh()
+#test_tetrahedron = UnitTetrahedronMesh() # deprecated? https://fenicsproject.org/docs/dolfin/2019.1.0/python/_autogenerated/dolfin.cpp.generation.html
 test_interval = UnitIntervalMesh(10)
 test_square = UnitSquareMesh(10,10,"crossed")
 test_cube = UnitCubeMesh(10,10,10)

test/test_pycreate.jl

@@ -5,7 +5,7 @@ using FEniCS
 
 
 test_pytriangle = pyUnitTriangleMesh()
-test_pytetrahedron = pyUnitTetrahedronMesh()
+#test_pytetrahedron = pyUnitTetrahedronMesh() # deprecated? https://fenicsproject.org/docs/dolfin/2019.1.0/python/_autogenerated/dolfin.cpp.generation.html
 test_pyquadmesh =pyUnitQuadMesh(10,10) # is one of the experimental meshes, but
 #works directly as a PyObject. Investigate this at a later stage?
 test_pyinterval = pyUnitIntervalMesh(10)