fixed tests, needed updated list of channels to include region_mask, etc

Author: jcschaff

tests/data_model/test_result.py

@@ -16,7 +16,7 @@ def test_plot_slice_2D(solver_output_path: Path, solver_output_simid_jobid: tupl
     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 = ["C_cyt", "Ran_cyt", "RanC_cyt", "RanC_nuc", "J_r0"]
+    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

tests/data_model/test_simulations.py

@@ -44,8 +44,30 @@ def test_sbml_model_parse_1d(sbml_spatial_model_1d_path: Path) -> None:
 
     channels_orig = results_orig.channel_data
     channels_changed = results_changed.channel_data
-    assert [ch.label for ch in channels_orig] == ["s0", "s1", "J_r0", "s0_init_umol_l_1", "s1_init_umol_l_1"]
-    assert [ch.label for ch in channels_changed] == ["s0", "s1", "J_r0", "s0_init_umol_l_1", "s1_init_umol_l_1"]
+    assert [ch.label for ch in channels_orig] == [
+        "region_mask",
+        "t",
+        "x",
+        "y",
+        "z",
+        "s0",
+        "s1",
+        "J_r0",
+        "s0_init_umol_l_1",
+        "s1_init_umol_l_1",
+    ]
+    assert [ch.label for ch in channels_changed] == [
+        "region_mask",
+        "t",
+        "x",
+        "y",
+        "z",
+        "s0",
+        "s1",
+        "J_r0",
+        "s0_init_umol_l_1",
+        "s1_init_umol_l_1",
+    ]
     assert np.allclose(
         results_orig.concentrations[0, 0::10],
         np.array(
@@ -131,6 +153,11 @@ def test_sbml_model_parse_3d(sbml_spatial_model_3d_path: Path) -> None:
     channels_orig = results_orig.channel_data
     channels_changed = results_changed.channel_data
     assert [channel.label for channel in channels_orig] == [
+        "region_mask",
+        "t",
+        "x",
+        "y",
+        "z",
         "s0",
         "s1",
         "s3",
@@ -140,6 +167,11 @@ def test_sbml_model_parse_3d(sbml_spatial_model_3d_path: Path) -> None:
         "s3_init_umol_l_1",
     ]
     assert [channel.label for channel in channels_changed] == [
+        "region_mask",
+        "t",
+        "x",
+        "y",
+        "z",
         "s0",
         "s1",
         "s3",
@@ -201,8 +233,30 @@ def test_vcml_model_parse_3d(vcml_spatial_model_1d_path: Path) -> None:
 
     channels_orig = results_orig.channel_data
     channels_changed = results_changed.channel_data
-    assert [channel.label for channel in channels_orig] == ["s0", "s1", "J_r0", "s0_init_uM", "s1_init_uM"]
-    assert [channel.label for channel in channels_changed] == ["s0", "s1", "J_r0", "s0_init_uM", "s1_init_uM"]
+    assert [channel.label for channel in channels_orig] == [
+        "region_mask",
+        "t",
+        "x",
+        "y",
+        "z",
+        "s0",
+        "s1",
+        "J_r0",
+        "s0_init_uM",
+        "s1_init_uM",
+    ]
+    assert [channel.label for channel in channels_changed] == [
+        "region_mask",
+        "t",
+        "x",
+        "y",
+        "z",
+        "s0",
+        "s1",
+        "J_r0",
+        "s0_init_uM",
+        "s1_init_uM",
+    ]
     assert np.allclose(
         results_orig.concentrations[0, 0::10],
         np.array(

tests/simdata/test_vtk.py

@@ -29,7 +29,7 @@ def test_vtk(solver_output_path: Path, solver_output_simid_jobid: tuple[int, int
     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 == ["C_cyt", "Ran_cyt", "RanC_cyt", "RanC_nuc", "J_r0"]
+    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]