Merge branch 'festim-dev:main' into CustomSolver

test/h_transport_problem/test_initialisation.py

@@ -2,9 +2,18 @@
 import pytest
 import fenics
 from pathlib import Path
+import os
 
 
 def test_initialisation_from_xdmf(tmpdir):
+    """
+    Test that initialise_solutions interpolates correctly
+    from an XDMF-file
+
+    Args:
+        tmpdir (os.PathLike): path to the pytest temporary folder
+    """
+
     mesh = fenics.UnitSquareMesh(5, 5)
     V = fenics.VectorFunctionSpace(mesh, "P", 1, 2)
     u = fenics.Function(V)
@@ -19,7 +28,6 @@ def test_initialisation_from_xdmf(tmpdir):
     d = tmpdir.mkdir("Initial solutions")
     file1 = d.join("u_1out.xdmf")
     file2 = d.join("u_2out.xdmf")
-    print(Path(file1))
     with fenics.XDMFFile(str(Path(file1))) as f:
         f.write_checkpoint(
             u.sub(0), "1", 2, fenics.XDMFFile.Encoding.HDF5, append=False

test/h_transport_problem/test_solving.py

@@ -14,7 +14,9 @@ def test_default_dt_min_value():
 
     t = 0
     dt = festim.Stepsize(
-        initial_value=0.5, stepsize_change_ratio=1.1, t_stop=430, stepsize_stop_max=0.5
+        initial_value=0.5,
+        stepsize_change_ratio=1.1,
+        max_stepsize=None if t < 430 else 0.5,
     )
 
     my_settings = festim.Settings(
@@ -32,7 +34,8 @@ def test_default_dt_min_value():
     my_problem.F = f.dot(f.grad(my_problem.u), f.grad(my_problem.v)) * f.dx
 
     du = f.TrialFunction(my_problem.u.function_space())
-    my_problem.J = f.derivative(my_problem.F, my_problem.u, du)  # Define the Jacobian
+    # Define the Jacobian
+    my_problem.J = f.derivative(my_problem.F, my_problem.u, du)
     # run & test
     my_problem.update(t, dt)
 

test/simulation/test_construction.py

@@ -2,85 +2,66 @@
 import pytest
 
 
-def test_setting_traps():
-    """Checks traps can be set with the expected types (F.Trap, list, or F.Traps)"""
+class TestSettingTrapsMaterialsExprots:
     my_sim = F.Simulation()
-    my_mat = F.Material(1, 1, 0)
-    trap1 = F.Trap(1, 1, 1, 1, [my_mat], density=1)
-    trap2 = F.Trap(2, 2, 2, 2, [my_mat], density=1)
-
-    combinations = [trap1, [trap1], [trap1, trap2], F.Traps([trap1, trap2])]
-
-    for combination in combinations:
-        my_sim.traps = combination
+    mat1 = F.Material(1, 1, 1)
+    mat2 = F.Material(2, 2, 2)
+    trap1 = F.Trap(1, 1, 1, 1, [mat1], density=1)
+    trap2 = F.Trap(2, 2, 2, 2, [mat1], density=1)
+    export1 = F.XDMFExport("solute")
+    export2 = F.XDMFExport("solute")
+    wrong_types = ["coucou", True]
 
+    @pytest.mark.parametrize(
+        "trap", [trap1, [trap1], [trap1, trap2], F.Traps([trap1, trap2])]
+    )
+    def test_setting_traps(self, trap):
+        """Checks traps can be set with the expected types (F.Trap, list, or F.Traps)"""
 
-def test_setting_traps_wrong_type():
-    """Checks an error is raised when traps is set with the wrong type"""
-    my_sim = F.Simulation()
+        self.my_sim.traps = trap
 
-    combinations = ["coucou", True]
+    @pytest.mark.parametrize("trap", wrong_types)
+    def test_setting_traps_wrong_type(self, trap):
+        """Checks an error is raised when traps is set with the wrong type"""
 
-    for combination in combinations:
         with pytest.raises(
             TypeError,
             match="Accepted types for traps are list, festim.Traps or festim.Trap",
         ):
-            my_sim.traps = combination
-
-
-def test_setting_materials():
-    """Checks materials can be set with the expected types (F.Material, list, or F.Materials)"""
-    my_sim = F.Simulation()
-    mat1 = F.Material(1, 1, 1)
-    mat2 = F.Material(2, 2, 2)
+            self.my_sim.traps = trap
 
-    combinations = [mat1, [mat1], [mat1, mat2], F.Materials([mat1, mat2])]
+    @pytest.mark.parametrize(
+        "mat", [mat1, [mat1], [mat1, mat2], F.Materials([mat1, mat2])]
+    )
+    def test_setting_materials(self, mat):
+        """Checks materials can be set with the expected types (F.Material, list, or F.Materials)"""
 
-    for combination in combinations:
-        my_sim.materials = combination
+        self.my_sim.materials = mat
 
+    @pytest.mark.parametrize("mat", wrong_types)
+    def test_setting_materials_wrong_type(self, mat):
+        """Checks an error is raised when materials is set with the wrong type"""
 
-def test_setting_materials_wrong_type():
-    """Checks an error is raised when materials is set with the wrong type"""
-    my_sim = F.Simulation()
-
-    combinations = ["coucou", True]
-
-    for combination in combinations:
         with pytest.raises(
             TypeError,
             match="accepted types for materials are list, festim.Material or festim.Materials",
         ):
-            my_sim.materials = combination
+            self.my_sim.materials = mat
 
+    @pytest.mark.parametrize(
+        "exp", [export1, [export1], [export1, export2], F.Exports([export1, export2])]
+    )
+    def test_setting_exports(self, exp):
+        """Checks exports can be set with the expected types (F.Material, list, or F.Exports)"""
 
-def test_setting_exports():
-    """Checks exports can be set with the expected types (F.Material, list, or F.Exports)"""
-    my_sim = F.Simulation()
-    export1 = F.XDMFExport("solute")
-    export2 = F.XDMFExport("solute")
-
-    combinations = [
-        export1,
-        [export1],
-        [export1, export2],
-        F.Exports([export1, export2]),
-    ]
-
-    for trap_combination in combinations:
-        my_sim.exports = trap_combination
-
-
-def test_setting_exports_wrong_type():
-    """Checks an error is raised when exports is set with the wrong type"""
-    my_sim = F.Simulation()
+        self.my_sim.exports = exp
 
-    combinations = ["coucou", True]
+    @pytest.mark.parametrize("exp", wrong_types)
+    def test_setting_exports_wrong_type(self, exp):
+        """Checks an error is raised when exports is set with the wrong type"""
 
-    for trap_combination in combinations:
         with pytest.raises(
             TypeError,
             match="accepted types for exports are list, festim.Export or festim.Exports",
         ):
-            my_sim.exports = trap_combination
+            self.my_sim.exports = exp

test/simulation/test_initialise.py

@@ -79,6 +79,9 @@ def test_TXTExport_times_added_to_milestones(tmpdir):
     """Creates a Simulation object and checks that, if no dt.milestones
      are given and TXTExport.times are given, TXTExport.times are
     are added to dt.milestones by .initialise()
+
+    Args:
+        tmpdir (os.PathLike): path to the pytest temporary folder
     """
     # tmpdir
     d = tmpdir.mkdir("test_folder")
@@ -120,8 +123,13 @@ def test_TXTExport_times_added_to_milestones(tmpdir):
 )
 @pytest.mark.parametrize("sys", ["cylindrical", "spherical"])
 def test_cartesian_and_surface_flux_warning(quantity, sys):
-    """Creates a Simulation object and checks that, if either a cylindrical
+    """
+    Creates a Simulation object and checks that, if either a cylindrical
     or spherical meshes are given with a SurfaceFlux, a warning is raised.
+
+    Args:
+        quantity (festim.DerivedQuantity): a festim.DerivedQuantity object
+        sys (str): type of the coordinate system
     """
     # build
     my_model = F.Simulation()

test/simulation/test_meshing.py

@@ -6,6 +6,9 @@
 def test_define_markers(tmpdir):
     """Checks that markers can be defined from XDMF files and that the mesh
     functions have the correct values.
+
+    Args:
+        tmpdir (os.PathLike): path to the pytest temporary folder
     """
     # build
     mesh = fenics.UnitSquareMesh(16, 16)

test/simulation/test_postprocessing_integration.py

@@ -9,6 +9,7 @@
 class TestPostProcessing:
     @pytest.fixture
     def my_sim(self):
+        """A pytest fixture defining the festim.Simulation object"""
         my_sim = festim.Simulation({})
         my_sim.t = 0
         my_sim.mesh = festim.MeshFromRefinements(10, 1)
@@ -42,6 +43,13 @@ def my_sim(self):
         return my_sim
 
     def test_derived_quantities_size(self, my_sim):
+        """
+        Checks that the length of data produced by F.DerivedQuantities
+        equals to the number of post-processing calls
+
+        Args:
+            my_sim (festim.Simulation): the simulation object
+        """
         derived_quantities = festim.DerivedQuantities(
             [
                 festim.SurfaceFlux("solute", 1),
@@ -64,6 +72,12 @@ def test_derived_quantities_size(self, my_sim):
         assert my_sim.exports[0].data[i][0] == t
 
     def test_pure_diffusion(self, my_sim):
+        """
+        Checks that run_post_processing() assigns data correctly
+
+        Args:
+            my_sim (festim.Simulation): the simulation object
+        """
         my_sim.materials = festim.Materials(
             [
                 festim.Material(1, D_0=1, E_D=1, borders=[0, 0.5]),
@@ -164,6 +178,10 @@ def test_performance_xdmf_export_every_N_iterations(self, my_sim, tmpdir):
         """Runs run_post_processing several times with different export.mode
         values and checks that the xdmf
         files have the correct timesteps
+
+        Args:
+            my_sim (festim.Simulation): a festim.Simulation object
+            tmpdir (os.PathLike): path to the pytest temporary folder
         """
         # build
         d = tmpdir.mkdir("test_folder")
@@ -205,8 +223,8 @@ def test_xdmf_export_only_last_timestep(self, my_sim, tmpdir):
         correct timesteps
 
         Args:
-            my_sim (_type_): _description_
-            tmpdir (_type_): _description_
+            my_sim (festim.Simulation): the simulation object
+            tmpdir (os.PathLike): path to the pytest temporary folder
         """
         d = tmpdir.mkdir("test_folder")
 

test/system/test_chemical_potential.py

@@ -7,8 +7,16 @@
 
 
 def compute_error(exact, computed, t, norm):
-    exact_sol = fenics.Expression(sp.printing.ccode(exact), degree=4, t=t)
+    """
+    An auxiliary method to compute the error
 
+    Args:
+        exact (sympy.Expr): exact solution
+        computed (fenics.Function): computed solution
+        t (float): simulation time
+        norm (str): type of norm (maximum absolute error or L2 norm)
+    """
+    exact_sol = fenics.Expression(sp.printing.ccode(exact), degree=4, t=t)
     if norm == "error_max":
         mesh = computed.function_space().mesh()
         vertex_values_u = computed.compute_vertex_values(mesh)
@@ -24,6 +32,9 @@ def test_run_MMS_chemical_pot(tmpdir):
     """
     Test function run() with conservation of chemical potential henry
     (1 material)
+
+    Args:
+        tmpdir (os.PathLike): path to the pytest temporary folder
     """
     d = tmpdir.mkdir("Solution_Test")
     u = 1 + sp.sin(2 * fenics.pi * festim.x) * festim.t + festim.t

test/system/test_misc.py

@@ -4,7 +4,13 @@
 import os
 
 
-def test_convective_flux():
+def test_convective_flux(tmpdir):
+    """
+    Tests that convective boundary condition works correctly
+
+    Args:
+        tmpdir (os.PathLike): path to the pytest temporary folder
+    """
     sim = F.Simulation()
 
     sim.mesh = F.MeshFromVertices(np.linspace(0, 1, num=50))
@@ -19,7 +25,13 @@ def test_convective_flux():
 
     sim.materials = F.Materials([F.Material(1, D_0=1, E_D=0, thermal_cond=2)])
 
-    sim.exports = F.Exports([F.XDMFExport("T", checkpoint=False)])
+    sim.exports = F.Exports(
+        [
+            F.XDMFExport(
+                "T", checkpoint=False, filename="{}/temperature.xdmf".format(tmpdir)
+            )
+        ]
+    )
 
     sim.settings = F.Settings(1e-10, 1e-10, transient=False)
 
@@ -186,6 +198,9 @@ def test_txt_export_desired_times(tmp_path, final_time, stepsize, export_times):
 def test_txt_export_all_times(tmp_path):
     """
     Tests that TXTExport can be exported at all timesteps
+
+    Args:
+        tmp_path (os.PathLike): path to a temporary folder
     """
     my_model = F.Simulation()
 
@@ -214,6 +229,9 @@ def test_txt_export_all_times(tmp_path):
 def test_txt_export_steady_state(tmp_path):
     """
     Tests that TXTExport can be exported in steady state
+
+    Args:
+        tmp_path (os.PathLike): path to a temporary folder
     """
     my_model = F.Simulation()