Merge pull request #773 from festim-dev/fix-warning

Fix warnings + remove warnings in test

.github/workflows/ci.yml

@@ -13,15 +13,14 @@ jobs:
       uses: conda-incubator/setup-miniconda@v2
       with:
         activate-environment: myenv
-        mamba-version: "*"
+        # mamba-version: "*"
         channels: conda-forge, defaults
 
     - name: Create Conda environment
       shell: bash -l {0}
       run: |
         # conda upgrade --strict-channel-priority -c conda-forge --all
-        conda install -c conda-forge 'conda-libmamba-solver<23.9'
-        mamba install -c conda-forge fenics
+        conda install -c conda-forge fenics numpy=1.24 python=3.10
 
     - name: Install dependencies
       shell: bash -l {0}

docs/source/userguide/export_post_processing.rst

@@ -189,7 +189,7 @@ The data can be accessed in three different ways:
 
     print(flux_surf_3.t)
     print(flux_surf_3.data)
-    print(my_derived_quantities.derived_quantities[2].data)
+    print(my_derived_quantities[2].data)
 
 - export and read from a .csv file:
 

festim/generic_simulation.py

@@ -326,7 +326,7 @@ def initialise(self):
 
         for export in self.exports:
             if isinstance(export, festim.DerivedQuantities):
-                for q in export.derived_quantities:
+                for q in export:
                     if not isinstance(q, tuple(allowed_quantities[self.mesh.type])):
                         warnings.warn(
                             f"{type(q)} may not work as intended for {self.mesh.type} meshes"

test/simulation/test_postprocessing_integration.py

@@ -174,6 +174,7 @@ def test_fluxes(self, my_sim):
         assert np.isclose(data[1][3], -1 * grad_T * lambda_x_0)
         assert np.isclose(data[1][4], -1 * grad_T * lambda_x_1 * -1)
 
+    @pytest.mark.filterwarnings("ignore:in 1D")
     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
@@ -215,6 +216,7 @@ def test_performance_xdmf_export_every_N_iterations(self, my_sim, tmpdir):
                 for t_expected, t in zip(expected_times, times):
                     assert t_expected == pytest.approx(float(t))
 
+    @pytest.mark.filterwarnings("ignore:in 1D")
     def test_xdmf_export_only_last_timestep(self, my_sim, tmpdir):
         """Runs run_post_processing with mode="last":
         - when the time is not the final time and checks that nothing has been

test/unit/test_exports/test_derived_quantities/test_surface_quantity.py

@@ -1,4 +1,3 @@
-from nis import match
 import festim as F
 import pytest
 

test/unit/test_exports/test_derived_quantities/test_volume_quantity.py

@@ -1,4 +1,3 @@
-from nis import match
 import festim as F
 import pytest
 

test/unit/test_exports/test_trap_density_xdmf_export.py

@@ -3,6 +3,7 @@
 import sympy as sp
 from pathlib import Path
 import numpy as np
+import pytest
 
 
 def test_trap_density_xdmf_export_intergration_with_simultion(tmpdir):
@@ -96,6 +97,7 @@ def test_trap_density_xdmf_export_write(tmpdir):
     assert error_L2 < 1e-10
 
 
+@pytest.mark.filterwarnings("ignore:in 1D")
 def test_trap_density_xdmf_export_traps_materials_mixed(tmpdir):
     """Integration test for TrapDensityXDMF.write() with a trap material given
     as a string. Creates a festim simulation and exports the trap density as an

test/unit/test_exports/test_xdmf_export.py

@@ -10,7 +10,7 @@ def folder(tmpdir):
 
 
 def test_define_file_upon_construction(folder):
-    mesh = f.UnitIntervalMesh(10)
+    mesh = f.UnitSquareMesh(8, 8)
     filename = "{}/my_filename.xdmf".format(folder)
     my_xdmf = XDMFExport("solute", label="solute_label", filename=filename)
 
@@ -30,7 +30,7 @@ def test_default_filename():
 
 
 class TestDefineFile:
-    mesh = f.UnitIntervalMesh(10)
+    mesh = f.UnitSquareMesh(8, 8)
     my_xdmf = XDMFExport("solute", "my_label", filename="my_filename.xdmf")
 
     def test_file_exists(self, folder):
@@ -44,7 +44,7 @@ def test_file_exists(self, folder):
 
 
 class TestWrite:
-    mesh = f.UnitIntervalMesh(10)
+    mesh = f.UnitSquareMesh(8, 8)
     V = f.FunctionSpace(mesh, "P", 1)
     u = f.Function(V)
     label_to_function = {"solute": u}