clean up remaining generated test outputs

Author: jcschaff

tests/_internal/simdata/test_vtk.py

@@ -1,4 +1,5 @@
 import os
+import tempfile
 from pathlib import Path
 
 import pytest
@@ -23,53 +24,54 @@
 
 @pytest.mark.skipif(IN_GITHUB_ACTIONS, reason="Test doesn't work in Github Actions.")
 def test_vtk(solver_output_path: Path, solver_output_simid_jobid: tuple[int, int], zarr_path: Path) -> None:
-    sim_id, job_id = solver_output_simid_jobid
-    result = Result(solver_output_dir=solver_output_path, sim_id=sim_id, job_id=job_id, zarr_dir=zarr_path)
-    mesh: CartesianMesh = result.mesh
-    domain_names: list[str] = mesh.get_volume_domain_names()
-    assert domain_names == ["Nucleus", "cytosol", "ec"]
-    channel_names = [c.label for c in result.channel_data]
-    assert channel_names == ["region_mask", "t", "x", "y", "z", "C_cyt", "Ran_cyt", "RanC_cyt", "RanC_nuc", "J_r0"]
-    times: list[float] = result.time_points
-    assert times == [0.0, 0.25, 0.5, 0.75, 1.0]
+    with tempfile.TemporaryDirectory() as tmpdirname, Path(tmpdirname) as tmp_dir:
+        sim_id, job_id = solver_output_simid_jobid
+        result = Result(solver_output_dir=solver_output_path, sim_id=sim_id, job_id=job_id, zarr_dir=tmp_dir)
+        mesh: CartesianMesh = result.mesh
+        domain_names: list[str] = mesh.get_volume_domain_names()
+        assert domain_names == ["Nucleus", "cytosol", "ec"]
+        channel_names = [c.label for c in result.channel_data]
+        assert channel_names == ["region_mask", "t", "x", "y", "z", "C_cyt", "Ran_cyt", "RanC_cyt", "RanC_nuc", "J_r0"]
+        times: list[float] = result.time_points
+        assert times == [0.0, 0.25, 0.5, 0.75, 1.0]
 
-    domain_name = domain_names[0]
+        domain_name = domain_names[0]
 
-    vis_mesh: VisMesh = from_mesh_data(cartesian_mesh=mesh, domain_name=domain_name, b_volume=True)
+        vis_mesh: VisMesh = from_mesh_data(cartesian_mesh=mesh, domain_name=domain_name, b_volume=True)
 
-    assert vis_mesh.visVoxels is not None
-    finite_volume_indices: list[FiniteVolumeIndex] = [
-        vox.finiteVolumeIndex for vox in vis_mesh.visVoxels if vox.finiteVolumeIndex is not None
-    ]
-    finite_volume_index_data: FiniteVolumeIndexData = FiniteVolumeIndexData(
-        domainName=domain_name, finiteVolumeIndices=finite_volume_indices
-    )
-    empty_mesh_file: Path = Path(f"empty_mesh_{domain_name}.vtu")
-    index_file: Path = Path(f"index_file_{domain_name}.json")
-    assert empty_mesh_file.name == "empty_mesh_Nucleus.vtu"
-    assert index_file.name == "index_file_Nucleus.json"
-    write_finite_volume_index_data(
-        finite_volume_index_file=index_file, finite_volume_index_data=finite_volume_index_data
-    )
+        assert vis_mesh.visVoxels is not None
+        finite_volume_indices: list[FiniteVolumeIndex] = [
+            vox.finiteVolumeIndex for vox in vis_mesh.visVoxels if vox.finiteVolumeIndex is not None
+        ]
+        finite_volume_index_data: FiniteVolumeIndexData = FiniteVolumeIndexData(
+            domainName=domain_name, finiteVolumeIndices=finite_volume_indices
+        )
+        empty_mesh_file = tmp_dir / f"empty_mesh_{domain_name}.vtu"
+        index_file = tmp_dir / f"index_file_{domain_name}.json"
+        assert empty_mesh_file.name == "empty_mesh_Nucleus.vtu"
+        assert index_file.name == "index_file_Nucleus.json"
+        write_finite_volume_index_data(
+            finite_volume_index_file=index_file, finite_volume_index_data=finite_volume_index_data
+        )
 
-    write_finite_volume_smoothed_vtk_grid_and_index_data(
-        vis_mesh=vis_mesh, domain_name=domain_name, vtu_file=empty_mesh_file, index_file=index_file
-    )
+        write_finite_volume_smoothed_vtk_grid_and_index_data(
+            vis_mesh=vis_mesh, domain_name=domain_name, vtu_file=empty_mesh_file, index_file=index_file
+        )
 
-    var_name = "Nucleus::RanC_nuc"
-    simple_var_name = var_name.split("::")[-1]
-    time: float = times[0]
-    data_array: NDArray1D = result.pde_dataset.get_data(var_name, time)
-    new_mesh_file: Path = Path(f"mesh_{domain_name}_{simple_var_name}_{time}.vtu")
-    assert new_mesh_file.name == "mesh_Nucleus_RanC_nuc_0.0.vtu"
-    write_data_array_to_new_vtk_file(
-        empty_mesh_file=empty_mesh_file, var_name=var_name, data=data_array, new_mesh_file=new_mesh_file
-    )
+        var_name = "Nucleus::RanC_nuc"
+        simple_var_name = var_name.split("::")[-1]
+        time: float = times[0]
+        data_array: NDArray1D = result.pde_dataset.get_data(var_name, time)
+        new_mesh_file = tmp_dir / f"mesh_{domain_name}_{simple_var_name}_{time}.vtu"
+        assert new_mesh_file.name == "mesh_Nucleus_RanC_nuc_0.0.vtu"
+        write_data_array_to_new_vtk_file(
+            empty_mesh_file=empty_mesh_file, var_name=var_name, data=data_array, new_mesh_file=new_mesh_file
+        )
 
-    # plot with pyvista
-    pyvista_mesh = pyvista.read(str(new_mesh_file))
-    # pyvista_mesh.plot()
-    plotter = pyvista.Plotter(off_screen=True)
-    plotter.add_mesh(pyvista_mesh)
-    plotter.screenshot(f"mesh_{domain_name}_{simple_var_name}_{time}.png")
-    plotter.close()
+        # plot with pyvista
+        pyvista_mesh = pyvista.read(str(new_mesh_file))
+        # pyvista_mesh.plot()
+        plotter = pyvista.Plotter(off_screen=True)
+        plotter.add_mesh(pyvista_mesh)
+        plotter.screenshot(tmp_dir / f"mesh_{domain_name}_{simple_var_name}_{time}.png")
+        plotter.close()

tests/sim_results/test_result.py

@@ -1,5 +1,6 @@
 # test result class
 import os
+import tempfile
 from pathlib import Path
 
 import numpy as np
@@ -13,21 +14,22 @@
 
 @pytest.mark.skipif(IN_GITHUB_ACTIONS, reason="Test doesn't work in Github Actions.")
 def test_plot_slice_2D(solver_output_path: Path, solver_output_simid_jobid: tuple[int, int], zarr_path: Path) -> None:
-    sim_id, job_id = solver_output_simid_jobid
-    result = Result(solver_output_dir=solver_output_path, sim_id=sim_id, job_id=job_id, zarr_dir=zarr_path)
-
-    expected_labels = ["region_mask", "t", "x", "y", "z", "C_cyt", "Ran_cyt", "RanC_cyt", "RanC_nuc", "J_r0"]
-    assert [channel.label for channel in result.channel_data] == expected_labels
-
-    concentrations: NDArray2D = result.concentrations
-    expected_concentrations = [
-        [0.00000000e00, 1.66853643e-07, 5.37844509e-07, 1.01317108e-06, 1.53753808e-06],
-        [0.00000000e00, 1.66853643e-07, 5.37844509e-07, 1.01317108e-06, 1.53753808e-06],
-        [0.00000000e00, 1.16874344e-06, 1.74755208e-06, 2.05505998e-06, 2.20346703e-06],
-        [1.07657211e-05, 9.43012400e-06, 8.48032450e-06, 7.69749002e-06, 7.02471598e-06],
-        [0.00000000e00, 1.16776305e-06, 1.73912167e-06, 2.02778643e-06, 2.14461288e-06],
-    ]
-    assert str(concentrations) == str(np.array(object=expected_concentrations, dtype=np.float64))
-    assert result.zarr_dataset.shape == (5, 10, 25, 71, 71)
-
-    result.plotter.plot_slice_2d(channel_name="Ran_cyt", time_index=0, z_index=0)
+    with tempfile.TemporaryDirectory() as dirname, Path(dirname) as tmp_dir:
+        sim_id, job_id = solver_output_simid_jobid
+        result = Result(solver_output_dir=solver_output_path, sim_id=sim_id, job_id=job_id, zarr_dir=tmp_dir)
+
+        expected_labels = ["region_mask", "t", "x", "y", "z", "C_cyt", "Ran_cyt", "RanC_cyt", "RanC_nuc", "J_r0"]
+        assert [channel.label for channel in result.channel_data] == expected_labels
+
+        concentrations: NDArray2D = result.concentrations
+        expected_concentrations = [
+            [0.00000000e00, 1.66853643e-07, 5.37844509e-07, 1.01317108e-06, 1.53753808e-06],
+            [0.00000000e00, 1.66853643e-07, 5.37844509e-07, 1.01317108e-06, 1.53753808e-06],
+            [0.00000000e00, 1.16874344e-06, 1.74755208e-06, 2.05505998e-06, 2.20346703e-06],
+            [1.07657211e-05, 9.43012400e-06, 8.48032450e-06, 7.69749002e-06, 7.02471598e-06],
+            [0.00000000e00, 1.16776305e-06, 1.73912167e-06, 2.02778643e-06, 2.14461288e-06],
+        ]
+        assert str(concentrations) == str(np.array(object=expected_concentrations, dtype=np.float64))
+        assert result.zarr_dataset.shape == (5, 10, 25, 71, 71)
+
+        result.plotter.plot_slice_2d(channel_name="Ran_cyt", time_index=0, z_index=0)

tests/vcml/test_vcml_writer.py

@@ -36,9 +36,9 @@ def test_vcml_writer_1D(vcml_spatial_model_1d_path: Path) -> None:
         assert compartment.dim == new_compartment.dim
 
     # write out the new vcml string to a file so that it can be compared with original vcml file
-    new_vcml_path = vcml_spatial_model_1d_path.with_name("new_vcml.xml")
-    with open(new_vcml_path, "w") as f:
-        f.write(new_vcml_str)
+    # new_vcml_path = vcml_spatial_model_1d_path.with_name("new_vcml.xml")
+    # with open(new_vcml_path, "w") as f:
+    #     f.write(new_vcml_str)
 
     assert biomodel == new_biomodel
 
@@ -76,9 +76,9 @@ def test_vcml_writer_3D(vcml_spatial_small_3d_path: Path) -> None:
         assert compartment.dim == new_compartment.dim
 
     # write out the new vcml string to a file so that it can be compared with original vcml file
-    new_vcml_path = vcml_spatial_small_3d_path.with_name("new_vcml_3d.xml")
-    with open(new_vcml_path, "w") as f:
-        f.write(new_vcml_str)
+    # new_vcml_path = vcml_spatial_small_3d_path.with_name("new_vcml_3d.xml")
+    # with open(new_vcml_path, "w") as f:
+    #     f.write(new_vcml_str)
 
     assert biomodel == new_biomodel
 
@@ -116,8 +116,8 @@ def test_vcml_writer_bunny_3D(vcml_spatial_bunny_3d_path: Path) -> None:
         assert compartment.dim == new_compartment.dim
 
     # write out the new vcml string to a file so that it can be compared with original vcml file
-    new_vcml_path = vcml_spatial_bunny_3d_path.with_name("new_vcml_3d.xml")
-    with open(new_vcml_path, "w") as f:
-        f.write(new_vcml_str)
+    # new_vcml_path = vcml_spatial_bunny_3d_path.with_name("new_vcml_3d.xml")
+    # with open(new_vcml_path, "w") as f:
+    #     f.write(new_vcml_str)
 
     assert biomodel == new_biomodel