Addresses review comments

Author: StephenNneji

tests/test_inputs.py

@@ -410,14 +410,6 @@ def standard_layers_controls():
     controls.pUnitGamma = 0.2
     controls.boundHandling = BoundHandling.Reflect
     controls.adaptPCR = True
-    # controls.checks.fitParam = [1, 0, 0, 0]
-    # controls.checks.fitBackgroundParam = [0]
-    # controls.checks.fitQzshift = []
-    # controls.checks.fitScalefactor = [0]
-    # controls.checks.fitBulkIn = [0]
-    # controls.checks.fitBulkOut = [0]
-    # controls.checks.fitResolutionParam = [0]
-    # controls.checks.fitDomainRatio = []
 
     return controls
 
@@ -456,14 +448,6 @@ def custom_xy_controls():
     controls.pUnitGamma = 0.2
     controls.boundHandling = BoundHandling.Reflect
     controls.adaptPCR = True
-    # controls.checks.fitParam = [1, 0, 0, 0]
-    # controls.checks.fitBackgroundParam = [0]
-    # controls.checks.fitQzshift = []
-    # controls.checks.fitScalefactor = [0]
-    # controls.checks.fitBulkIn = [0]
-    # controls.checks.fitBulkOut = [0]
-    # controls.checks.fitResolutionParam = [0]
-    # controls.checks.fitDomainRatio = []
 
     return controls
 
@@ -706,48 +690,6 @@ def check_problem_equal(actual_problem, expected_problem) -> None:
     ] == ["NaN" if np.isnan(el) else el for el in expected_problem.contrastCustomFiles]
 
 
-# def check_cells_equal(actual_cells, expected_cells) -> None:
-#     """Compare two instances of the "cells" object for equality."""
-#     assert actual_cells.f1 == expected_cells.f1
-
-#     # Need to test equality of the numpy arrays separately
-#     for a, b in zip(actual_cells.f2, expected_cells.f2):
-#         assert (a == b).all()
-
-#     # f6 may contain "NaN" values, so consider separately
-#     assert actual_cells.f6 == expected_cells.f6 or [
-#         "NaN" if np.isnan(el) else el for entry in actual_cells.f6 for el in entry
-#     ] == ["NaN" if np.isnan(el) else el for entry in expected_cells.f6 for el in entry]
-
-#     mocked_matlab_future = mock.MagicMock()
-#     mocked_engine = mock.MagicMock()
-#     mocked_matlab_future.result.return_value = mocked_engine
-#     with (
-#         mock.patch.object(
-#             RATapi.wrappers.MatlabWrapper,
-#             "loader",
-#             mocked_matlab_future,
-#         ),
-#         mock.patch.object(RATapi.rat_core, "DylibEngine", mock.MagicMock()),
-#         mock.patch.object(
-#             RATapi.inputs,
-#             "get_python_handle",
-#             mock.MagicMock(return_value=dummy_function),
-#         ),
-#         mock.patch.object(
-#             RATapi.wrappers.MatlabWrapper,
-#             "getHandle",
-#             mock.MagicMock(return_value=dummy_function),
-#         ),
-#         mock.patch.object(RATapi.wrappers.DylibWrapper, "getHandle", mock.MagicMock(return_value=dummy_function)),
-#     ):
-#         assert list(actual_cells.f14) == expected_cells.f14
-
-#     for index in chain(range(3, 6), range(7, 14), range(15, 21)):
-#         field = f"f{index}"
-#         assert getattr(actual_cells, field) == getattr(expected_cells, field)
-
-
 def check_controls_equal(actual_controls, expected_controls) -> None:
     """Compare two instances of the "controls" object used as input for the compiled RAT code for equality."""
     controls_fields = [