Add continuous integration with Travis-CI (#67)

* Add Travis-CI configuration file

* Remove VTK postprocessing from this package, because python-vtk installation is unreliable

* No longer need to install any extra dependencies

* Remove use of obsoleted firedrake.Expression

* Add continuous integration status button

.travis.yml

@@ -0,0 +1,15 @@
+services:
+  - docker
+
+branches:
+    only:
+        - master
+
+before_install:
+- docker pull firedrakeproject/firedrake
+- docker run -dti -v `pwd`:/home/firedrake/sapphire -w /home/firedrake --name fd firedrakeproject/firedrake
+- docker exec fd ls
+- docker exec fd pip3 install pytest
+
+script:
+- docker exec fd bash -c "source firedrake/bin/activate && python3 -m pytest -v sapphire/tests"

README.md

@@ -5,7 +5,7 @@ is an engine for constructing PDE-based simulations
 discretized in space with mixed finite elements
 and in time with finite differences.
 
-
+![](https://travis-ci.org/geo-fluid-dynamics/sapphire.svg?branch=master)
 [![DOI](https://zenodo.org/badge/157389237.svg)](https://zenodo.org/badge/latestdoi/157389237)
 
 

sapphire/benchmarks/freeze_water_in_cavity.py

@@ -70,10 +70,8 @@ def dirichlet_boundary_conditions(sim):
 
     W = sim.function_space
 
-    dim = sim.mesh.geometric_dimension()
-
     return [fe.DirichletBC(
-        W.sub(1), (0.,)*dim, "on_boundary"),
+        W.sub(1), (0., 0.), "on_boundary"),
         fe.DirichletBC(W.sub(2), sim.hot_wall_temperature, 1),
         fe.DirichletBC(W.sub(2), sim.cold_wall_temperature, 2)]
 
@@ -90,22 +88,22 @@ def initial_values(sim):
 
     sim.prandtl_number = sim.prandtl_number.assign(Pr)
 
-    dim = sim.mesh.geometric_dimension()
+    w = fe.Function(sim.function_space)
+
+    p, u, T = w.split()
+
+    p.assign(0.)
+
+    ihat, jhat = sim.unit_vectors()
 
-    T_c = sim.cold_wall_temperature.__float__()
+    u.assign(0.*ihat + 0.*jhat)
 
-    w = fe.interpolate(
-        fe.Expression(
-            (0.,) + (0.,)*dim + (T_c,),
-            element = sim.element),
-        sim.function_space)
+    T.assign(sim.cold_wall_temperature)
 
     F = heat_driven_cavity_variational_form_residual(
         sim = sim,
         solution = w)*fe.dx(degree = sim.quadrature_degree)
 
-    T_h = sim.hot_wall_temperature.__float__()
-
     problem = fe.NonlinearVariationalProblem(
         F = F,
         u = w,
@@ -158,25 +156,17 @@ def variational_form_residual(sim, solution):
 
 class Simulation(sapphire.simulations.convection_coupled_phasechange.Simulation):
 
-    def __init__(self, *args, spatial_dimensions, meshsize, **kwargs):
+    def __init__(self, *args, meshsize, **kwargs):
 
         self.reference_temperature_range__degC = fe.Constant(10.)
 
         self.hot_wall_temperature = fe.Constant(1.)
 
         self.cold_wall_temperature = fe.Constant(0.)
 
-        if spatial_dimensions == 2:
-
-            Mesh = fe.UnitSquareMesh
-
-        elif spatial_dimensions == 3:
-
-            Mesh = fe.UnitCubeMesh
-
         super().__init__(
             *args,
-            mesh = Mesh(*(meshsize,)*spatial_dimensions),
+            mesh = fe.UnitSquareMesh(meshsize, meshsize),
             variational_form_residual = variational_form_residual,
             initial_values = initial_values,
             dirichlet_boundary_conditions = dirichlet_boundary_conditions,

sapphire/benchmarks/melt_octadecane_in_cavity.py

@@ -4,13 +4,21 @@
 
 def initial_values(sim):
 
-    return fe.interpolate(
-        fe.Expression(
-            (0., 0., 0., sim.cold_wall_temperature.__float__()),
-            element = sim.element),
-        sim.function_space)
-
-
+    w = fe.Function(sim.function_space)
+
+    p, u, T = w.split()
+
+    p.assign(0.)
+
+    ihat, jhat = sim.unit_vectors()
+
+    u.assign(0.*ihat + 0.*jhat)
+
+    T.assign(sim.cold_wall_temperature)
+
+    return w
+
+
 def dirichlet_boundary_conditions(sim):
 
     W = sim.function_space

sapphire/simulation.py

@@ -177,6 +177,10 @@ def assign_parameters(self, parameters):
 
         return self
 
+    def unit_vectors(self):
+
+        return unit_vectors(self.mesh)
+
 
 def unit_vectors(mesh):
 

setup.py

@@ -3,11 +3,6 @@
 
 setuptools.setup(
     name = 'sapphire',
-    version = '0.4.3a0',
+    version = '0.4.4a0',
     packages = setuptools.find_packages(),
-    install_requires = [
-        'matplotlib',
-        'numpy',
-        'scipy',
-        'vtk']
 )

tests/model_validation/test__convection_coupled_phasechange.py

@@ -73,7 +73,7 @@ def test__validate__melt_octadecane__regression():
     assert(abs(sim.liquid_area - expected_liquid_area) < tolerance)
 
 
-def freeze_water(endtime, s, tau, rx, nx, rt, nt, q, dim = 2, outdir = ""):
+def freeze_water(endtime, s, tau, rx, nx, rt, nt, q, outdir = ""):
 
     mu_l__SI = 8.90e-4  # [Pa s]
 
@@ -97,11 +97,9 @@ def freeze_water(endtime, s, tau, rx, nx, rt, nt, q, dim = 2, outdir = ""):
         quadrature_degree = q,
         element_degree = rx - 1,
         time_stencil_size = rt + 1,
-        spatial_dimensions = dim,
         meshsize = nx,
         output_directory_path = str(outdir.join(
             "freeze_water/"
-            + "dim{0}/".format(dim)
             + "s{0}_tau{1}/".format(s, tau)
             + "rx{0}_nx{1}_rt{2}_nt{3}/".format(rx, nx, rt, nt)
             + "q{0}/".format(q))))