Various fixes to improve running of pytest suite (#327)

* test_sed_slide.py: this was previously a run-alone python script, but
since pytest tries to import every python file starting with test_ it
means this test was always being run even when trying to run a single actual pytest test. Now turned into an actual test
* test_examples: this test runs all python files (except those excluded)
found in the examples/ directories. However the id was set to just the
basename of these python files, and since there are multiple files with
the same name in different subdirectories of examples/, you end up with
multiple tests with the exact same name, meaning you can't easily work
out which one has actually failed from the actions logs and also you
can't run them individiually. Now just using the full path as the id.
Note that the -k argument for pytest does not like forward slashes. If
you want to run a specific test example however you can run something
like:

pytest -k"tohoku_inversion and inverse_problem.py" test/examples/

you want to run a specific single test using -k
* test_bath_smoothing renamed to bath_smoothin_test, again so it doesn't
  accidentily get picked up if you forget to tell pytest to only look in test/

Fixes after master merge

examples/columbia_plume/test_bathy_smoothing.py → examples/columbia_plume/bath_smoothing_test.py

@@ -3,6 +3,7 @@
 ===============================
 """
 from thetis import *
+from firedrake.output.vtk_output import VTKFile
 from bathymetry import get_bathymetry, smooth_bathymetry, smooth_bathymetry_at_bnd
 comm = COMM_WORLD
 

test/examples/test_examples.py

@@ -24,7 +24,7 @@
     'columbia_plume/plot_elevation_ts.py',
     'columbia_plume/plot_salt_profile.py',
     'columbia_plume/roms_forcing.py',
-    'columbia_plume/test_bathy_smoothing.py',
+    'columbia_plume/bath_smoothing_test.py',
     'columbia_plume/tidal_forcing.py',
     'columbia_plume/timeseries_forcing.py',
     'dome/diagnostics.py',
@@ -62,8 +62,7 @@
 all_examples = [f for f in all_examples if f not in exclude_files]
 
 
-@pytest.fixture(params=all_examples,
-                ids=lambda x: os.path.basename(x))
+@pytest.fixture(params=all_examples)
 def example_file(request):
     return os.path.abspath(request.param)
 

test/sediment/test_sed_slide.py

@@ -1,88 +1,88 @@
-"""
-Unphysical Slope Test case
-=======================
-
-Tests the sediment slide mechanism in the Exner equation, by starting with an
-unphysical slope and reducing the slope angle over time
-
-"""
-
 from thetis import *
 
-# define mesh
-mesh2d = RectangleMesh(20, 10, 4, 2)
-x, y = SpatialCoordinate(mesh2d)
-
-vectorP1_2d = VectorFunctionSpace(mesh2d, 'DG', 1)
-V = FunctionSpace(mesh2d, 'CG', 1)
-
-# define initial bathymetry
-bathymetry_2d = Function(V, name='Bathymetry')
-z_init = conditional(x < 2, 0, conditional(x <= 4, 0.5*x-1, 0))
-bathymetry_2d.interpolate(z_init)
-
-# define initial conditions
-uv_init = Function(vectorP1_2d).interpolate(as_vector((Constant(0.46), Constant(0.0))))
-elev_init = Constant(4)
-
-# set up solver
-solver_obj = solver2d.FlowSolver2d(mesh2d, bathymetry_2d)
-options = solver_obj.options
-options.simulation_export_time = 1
-options.simulation_end_time = 20
-options.no_exports = True
-
-options.horizontal_viscosity = Constant(1e-6)
-
-# for the test, only using bedload with sediment slide mechanism
-options.sediment_model_options.solve_suspended_sediment = False
-options.sediment_model_options.use_bedload = True
-options.sediment_model_options.use_slope_mag_correction = False
-options.sediment_model_options.use_angle_correction = False
-options.sediment_model_options.use_sediment_slide = True
-options.sediment_model_options.solve_exner = True
-options.sediment_model_options.average_sediment_size = Constant(2.6e-4)
-options.sediment_model_options.bed_reference_height = Constant(0.0002)
-# average meshgrid stepsize
-options.sediment_model_options.sed_slide_length_scale = Constant(0.2)
-# maximum angle of repose which the slope should have (this is the target angle)
-options.sediment_model_options.max_angle = Constant(22)
-options.sediment_model_options.morphological_acceleration_factor = Constant(20)
-options.sediment_model_options.use_advective_velocity_correction = False
-# using nikuradse friction
-options.nikuradse_bed_roughness = Constant(3*options.sediment_model_options.average_sediment_size)
-
-# crank-nicolson used to integrate in time system of ODEs resulting from application of galerkin FEM
-options.set_timestepper_type('CrankNicolson', implicitness_theta=1.0)
-options.timestep = 0.1
-
-# set boundary conditions
-left_bnd_id = 1
-right_bnd_id = 2
-
-swe_bnd = {}
-uv_vector = as_vector((0.46, 0.0))
-swe_bnd[left_bnd_id] = {'uv': uv_vector}
-swe_bnd[right_bnd_id] = {'elev': Constant(4)}
-solver_obj.bnd_functions['shallow_water'] = swe_bnd
-
-# set initial conditions
-solver_obj.assign_initial_conditions(uv=uv_init, elev=elev_init)
-
-beta = Function(V)
-max_beta_list = []
-
-
-def update_forcing(t_new):
-    # record maximum slope angle and check it is decreasing
-    beta.interpolate(solver_obj.sediment_model.betaangle)
-    max_beta_list.append(max(beta.dat.data[:])*180/pi)
-
-    if len(max_beta_list) > 30:
-        assert max_beta_list[-1] < max_beta_list[-10], 'Sediment slide mechanism is not causing\
-                                                         the angle to decrease'
-
-
-solver_obj.iterate(update_forcings=update_forcing)
-
-assert numpy.round(max_beta_list[-1], 1) == 24.6, 'Sediment slide mechanism has changed'
+
+def test_sediment_slide():
+    """
+    Unphysical Slope Test case
+    =======================
+
+    Tests the sediment slide mechanism in the Exner equation, by starting with an
+    unphysical slope and reducing the slope angle over time
+
+    """
+
+    # define mesh
+    mesh2d = RectangleMesh(20, 10, 4, 2)
+    x, y = SpatialCoordinate(mesh2d)
+
+    vectorP1_2d = VectorFunctionSpace(mesh2d, 'DG', 1)
+    V = FunctionSpace(mesh2d, 'CG', 1)
+
+    # define initial bathymetry
+    bathymetry_2d = Function(V, name='Bathymetry')
+    z_init = conditional(x < 2, 0, conditional(x <= 4, 0.5*x-1, 0))
+    bathymetry_2d.interpolate(z_init)
+
+    # define initial conditions
+    uv_init = Function(vectorP1_2d).interpolate(as_vector((Constant(0.46), Constant(0.0))))
+    elev_init = Constant(4)
+
+    # set up solver
+    solver_obj = solver2d.FlowSolver2d(mesh2d, bathymetry_2d)
+    options = solver_obj.options
+    options.simulation_export_time = 1
+    options.simulation_end_time = 20
+    options.no_exports = True
+
+    options.horizontal_viscosity = Constant(1e-6)
+
+    # for the test, only using bedload with sediment slide mechanism
+    options.sediment_model_options.solve_suspended_sediment = False
+    options.sediment_model_options.use_bedload = True
+    options.sediment_model_options.use_slope_mag_correction = False
+    options.sediment_model_options.use_angle_correction = False
+    options.sediment_model_options.use_sediment_slide = True
+    options.sediment_model_options.solve_exner = True
+    options.sediment_model_options.average_sediment_size = Constant(2.6e-4)
+    options.sediment_model_options.bed_reference_height = Constant(0.0002)
+    # average meshgrid stepsize
+    options.sediment_model_options.sed_slide_length_scale = Constant(0.2)
+    # maximum angle of repose which the slope should have (this is the target angle)
+    options.sediment_model_options.max_angle = Constant(22)
+    options.sediment_model_options.morphological_acceleration_factor = Constant(20)
+    options.sediment_model_options.use_advective_velocity_correction = False
+    # using nikuradse friction
+    options.nikuradse_bed_roughness = Constant(3*options.sediment_model_options.average_sediment_size)
+
+    # crank-nicolson used to integrate in time system of ODEs resulting from application of galerkin FEM
+    options.set_timestepper_type('CrankNicolson', implicitness_theta=1.0)
+    options.timestep = 0.1
+
+    # set boundary conditions
+    left_bnd_id = 1
+    right_bnd_id = 2
+
+    swe_bnd = {}
+    uv_vector = as_vector((0.46, 0.0))
+    swe_bnd[left_bnd_id] = {'uv': uv_vector}
+    swe_bnd[right_bnd_id] = {'elev': Constant(4)}
+    solver_obj.bnd_functions['shallow_water'] = swe_bnd
+
+    # set initial conditions
+    solver_obj.assign_initial_conditions(uv=uv_init, elev=elev_init)
+
+    beta = Function(V)
+    max_beta_list = []
+
+    def update_forcing(t_new):
+        # record maximum slope angle and check it is decreasing
+        beta.interpolate(solver_obj.sediment_model.betaangle)
+        max_beta_list.append(max(beta.dat.data[:])*180/pi)
+
+        if len(max_beta_list) > 30:
+            assert max_beta_list[-1] < max_beta_list[-10], 'Sediment slide mechanism is not causing\
+                                                             the angle to decrease'
+
+    solver_obj.iterate(update_forcings=update_forcing)
+
+    assert numpy.round(max_beta_list[-1], 1) == 24.6, 'Sediment slide mechanism has changed'