Merge pull request #54 from ysimillides/master

version 1.0 changes

Author: ChrisRackauckas

.travis.yml

@@ -3,8 +3,7 @@ language: julia
 os:
   - linux
 julia:
-  - 0.7
-  - nightly
+  - 1.0
 
 dist: trusty
 
@@ -15,13 +14,13 @@ services:
 
 before_install:
   - echo "**** pulling Docker image"
-  - docker pull ysimillides/fenics-julia-docker:v0.7
+  - docker pull ysimillides/fenics-julia-docker:v1.0
   - chmod +x travis_docker_test_script.sh
 notifications:
   email: false
 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:v0.7 /mnt/travis_docker_test_script.sh $TRAVIS_JULIA_VERSION
+  - 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
 after_success:
   # push coverage results to Coveralls, .cov files were copied back by script above
   - echo "**** submitting coverage information"

REQUIRE

@@ -1,4 +1,4 @@
-julia 0.7-beta2
+julia 1.0
 PyCall
 Requires
 ProgressMeter

src/FEniCS.jl

@@ -1,3 +1,4 @@
+__precompile__(false)
 module FEniCS
 using PyCall
 using Requires

src/jfem.jl

@@ -90,7 +90,7 @@ len(U::Union{Expression,FeFunction}) = length(U.pyobject)
 
 interpolate(solution1::FeFunction,solution2::Expression) = FeFunction(fenicspycall(solution1,:interpolate,solution2.pyobject))
 
-
+Expression(x::FEniCS.Expression) = convert(Expression,x)
 export Expression,Identity,inner,grad, nabla_grad, nabla_div,div, outer,dot,cross, tr, sqrt, sym, len, interpolate
 export ∇
 

test/acoustic.jl

@@ -5,7 +5,7 @@ using PyCall
 c = 5000
 #problem variables, have been scaled down for faster test solution
 dt = 0.00004;
-t = 0;
+global t = 0;
 T = 0.0004;
 
 mesh = RectangleMesh(Point([-2., -2.]),Point([2., 2.]),40,40)
@@ -51,7 +51,7 @@ while t <= T
     solve(A, vector(u), b)
     assign(u0,u1)
     assign(u1,u)
-    t +=dt
+    global t +=dt
     #fenics.plot(u.pyobject,title="Acoustic wave Equation")#,mode="auto")
 
 end

test/acoustic_new_assemble.jl

@@ -6,7 +6,7 @@ using PyCall
 c = 5000
 #problem variables
 dt = 0.000004;
-t = 0;
+global t = 0;
 T = 0.004;
 
 mesh = RectangleMesh(Point([-2., -2.]),Point([2., 2.]),40,40)
@@ -49,7 +49,7 @@ while t <= T
     lvsolve(a,L,u,bcs_dir) #linear variational solver
     assign(u0,u1)
     assign(u1,u)
-    t +=dt
+    global t +=dt
 end
 println("Acoustic problem finished")
 true

test/tutorial3.jl

@@ -23,10 +23,10 @@ F = u*v*dx + dt*dot(grad(u), grad(v))*dx - (u_n + dt*f)*v*dx
 a, L = lhs(F),rhs(F)
 
 u=FeFunction(V)
-t = 0
+global t = 0
 
 for n = 0:(num_steps-1)
-    t=t+dt
+    global t=t+dt
     u_D.pyobject[:t]=t
     lvsolve(a,L,u,bc)
     u_e= interpolate(u_D,V)

test/tutorial4.jl

@@ -34,11 +34,11 @@ a, L = lhs(F), rhs(F)
 
 # Time-stepping
 u=FeFunction(V)
-t = 0
+global t = 0
 #fig = PyPlot.figure()
 for n = 0:(num_steps-1)
     # Update current time
-    t += dt
+    global t += dt
 
     # Compute solution
     lvsolve(a,L,u,bc)

test/tutorial5.jl

@@ -8,7 +8,7 @@ V = FunctionSpace(mesh, "P", 1)
 u_code = "x[0]+2*x[1]+1"
 f_code = "-10*x[0]-20*x[1]-10"
 
-calc(var) = 1+var^2
+calc(var) = 1+var*var
 
 u_D = Expression(u_code, degree=2)
 bc = DirichletBC(V, u_D, "on_boundary")

test/tutorial7.jl

@@ -70,11 +70,11 @@ A3 = assemble(a3)
 [apply(bc,A2) for bc in bcp]
 
 # Time-stepping
-t = 0
+global t = 0
 for n = 0:(num_steps-1)
 
     # Update current time
-    t =t + dt
+    global t += dt
 
     # Step 1: Tentative velocity step
     b1 = assemble(L1)

test/tutorial8.jl

@@ -104,12 +104,12 @@ File("navier_stokes_cylinder/cylinder.xml.gz",mesh)
 
 
 
-t = 0
+global t = 0
 #@showprogress 1 "Solving..." for n=0:num_steps #for native julia progress
 for n =0:(num_steps-1)
 
     # Update current time
-    t += dt
+    global t += dt
 
     # Step 1: Tentative velocity step
     b1 = assemble(L1)

test/tutorial9.jl

@@ -74,11 +74,11 @@ vtkfile_u_2 = File("reaction_system/u_2.pvd")
 vtkfile_u_3 = File("reaction_system/u_3.pvd")
 
 # Time-stepping
-t = 0
+global t = 0
 for n=0:num_steps
 
     # Update current time
-    t += dt
+    global t += dt
 
     # Read velocity from file
     retrieve(timeseries_w,vector(w),t)

travis_docker_test_script.sh

@@ -9,10 +9,10 @@ cd /mnt && if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
 
 # run tests
 #julia -e "Pkg.clone(\"https://github.com/JuliaPy/PyCall.jl\"); ENV[\"PYTHON\"] = \"/usr/bin/python3\"; Pkg.build(\"PyCall\")"
-julia -e "Pkg.clone(\"/mnt/\", \"$PKGNAME\"); Pkg.build(\"$PKGNAME\"); Pkg.test(\"$PKGNAME\"; coverage=true)"
+julia -e "import Pkg; Pkg.clone(\"/mnt/\", \"$PKGNAME\"); Pkg.build(\"$PKGNAME\"); Pkg.test(\"$PKGNAME\"; coverage=true)"
 TEST_EXIT=$?                    # return with this
 
 # save coverage results back to host
-PKGDIR=`julia -e "print(Pkg.dir(\"$PKGNAME\"))"`
+PKGDIR=`julia -e "import Pkg; print(Pkg.dir(\"$PKGNAME\"))"`
 rsync --no-o --no-g --no-perms -mav --include="*/" --include="*.cov" --exclude="*" $PKGDIR/ /mnt/
 exit $TEST_EXIT