Fix main for Python > 11 (#1039)

# Description
Please include a summary of the changes.

Relates to <issue>

# Checklist
- [ ] My code uses type hinting for function and method arguments and return values.
- [ ] I have created tests which cover my code.
- [ ] The test code either 1. demonstrates at least one valuable use case (e.g. integration tests) 
or 2. verifies that outputs are as expected for given inputs (e.g. unit tests).
- [ ] New tests pass locally with my changes.

Author: Leguark

gempy/API/examples_generator.py

@@ -180,7 +180,7 @@ def _generate_anticline_model(compute_model: bool) -> gp.data.GeoModel:
         )
     )
 
-    # Map geological series to surfaces
+    # Map geological series to surfaces 
     gp.map_stack_to_surfaces(
         gempy_model=geo_data,
         mapping_object={"Strat_Series": ('rock2', 'rock1')}

gempy/core/data/grid.py

@@ -27,8 +27,8 @@ class GridTypes(enum.Flag):
 
     # ? What should we do with the extent?
 
-    values: Annotated[np.ndarray, Field(exclude=True)] = np.empty((0, 3))
-    length: Annotated[np.ndarray, Field(exclude=True)] = np.empty(0)
+    values: Annotated[np.ndarray, Field(exclude=True)] = dataclasses.field(default_factory=lambda: np.empty((0, 3)))
+    length: Annotated[np.ndarray, Field(exclude=True)] = dataclasses.field(default_factory=lambda: np.empty(0))
 
     _octree_grid: Optional[RegularGrid] = None
     _dense_grid: Optional[RegularGrid] = None

gempy/core/data/grid_modules/regular_grid.py

@@ -16,10 +16,10 @@ class RegularGrid:
     Class with the methods and properties to manage 3D regular grids where the model will be interpolated.
 
     """
-    resolution: Annotated[np.ndarray, numpy_array_short_validator] = np.ones((0, 3), dtype='int64')
-    extent: Annotated[np.ndarray, numpy_array_short_validator] = np.zeros(6, dtype='float64')  #: this is the ORTHOGONAL extent. If the grid is rotated, the extent will be different
-    values: Annotated[np.ndarray, Field(exclude=True)] = np.zeros((0, 3))
-    mask_topo: Annotated[np.ndarray, Field(exclude=True)] = np.zeros((0, 3), dtype=bool)
+    resolution: Annotated[np.ndarray, numpy_array_short_validator] = dataclasses.field(default_factory=lambda: np.ones((0, 3), dtype='int64'))
+    extent: Annotated[np.ndarray, numpy_array_short_validator] = dataclasses.field(default_factory=lambda: np.zeros(6, dtype='float64'))  #: this is the ORTHOGONAL extent. If the grid is rotated, the extent will be different
+    values: Annotated[np.ndarray, Field(exclude=True)] = dataclasses.field(default_factory=lambda: np.zeros((0, 3)))
+    mask_topo: Annotated[np.ndarray, Field(exclude=True)] = dataclasses.field(default_factory=lambda: np.zeros((0, 3), dtype=bool))
     _transform: Transform | None = None  #: If a transform exists, it will be applied to the grid
 
     def __init__(self, extent: np.ndarray, resolution: np.ndarray, transform: Optional[Transform] = None):

gempy/core/data/grid_modules/topography.py

@@ -27,9 +27,9 @@ class Topography:
     source: Optional[str] = None
 
     # Fields managed internally
-    values: short_array_type = field(init=False, default=np.zeros((0, 3)))
+    values: short_array_type = field(init=False, default_factory=lambda: np.zeros((0, 3)))
     resolution: Tuple[int, int] = Field(init=True, default=(0, 0))
-    raster_shape: Tuple[int, ...] = field(init=False, default=())
+    raster_shape: Tuple[int, ...] = field(init=False, default_factory=tuple)
     _mask_topo: Optional[np.ndarray] = field(init=False, default=None, repr=False)
     _x: Optional[np.ndarray] = field(init=False, default=None, repr=False)
     _y: Optional[np.ndarray] = field(init=False, default=None, repr=False)

test/test_api/test_initialization_and_compute_api.py

@@ -9,10 +9,7 @@
 
 def test_api_create_data():
     geo_data = _create_data()
-    
     pprint(geo_data)
-    
-    return geo_data
 
 
 def _create_data():

test/test_api/test_model_construction_granular.py

@@ -23,46 +23,51 @@
 """
 
 def test_read_input_points():
+    _, _ = _read_data()
+
+
+def _read_data() -> tuple[SurfacePointsTable, OrientationsTable]:
     data_path = 'https://raw.githubusercontent.com/cgre-aachen/gempy_data/master/'
     surface_points_file = pooch.retrieve(
         url=data_path + "data/input_data/jan_models/model1_surface_points.csv",
         known_hash="6f1a39ed77e87a4057f03629c946b1876b87e24409cadfe0e1cf7ab1488f69e4"
     )
-
     orientations_file = pooch.retrieve(
         url=data_path + "data/input_data/jan_models/model1_orientations.csv",
         known_hash="04c307ae23f70252fe54144a2fb95ca7d96584a2d497ea539ed32dfd23e7cd5d"
     )
-
     print(pooch.file_hash(surface_points_file))
     print(pooch.file_hash(orientations_file))
-
     surface_points: SurfacePointsTable = read_surface_points(
         path=surface_points_file,
     )
-
     orientations: OrientationsTable = read_orientations(
         path=orientations_file
     )
-
     return surface_points, orientations
 
 
-def test_create_grid() -> gp.data.Grid:
+def test_create_grid():
+    _generate_grid()
+
+
+def _generate_grid():
     grid: gp.data.Grid = gp.data.Grid(
         extent=[0, 1000, 0, 1000, 0, 500],
         resolution=[50, 5, 50]
     )
-
     return grid
 
 
-def test_create_structural_frame() -> StructuralFrame:
+def test_create_structural_frame():
     # * Structural elements
-    surface_points, orientations = test_read_input_points()
+    _create_structural_frame()
+
+
+def _create_structural_frame():
+    surface_points, orientations = _read_data()
     surface_points_groups = surface_points.get_surface_points_by_id_groups()
     orientations_groups = orientations.get_orientations_by_id_groups()
-
     structural_elements = []
     color_gen = ColorsGenerator()
     for i in range(len(surface_points_groups)):
@@ -75,52 +80,52 @@ def test_create_structural_frame() -> StructuralFrame:
         )
 
         structural_elements.append(structural_element)
-
     # * Structural groups definitions
     default_formation: Stack = Stack(
         name="default_formation",
         elements=structural_elements,
         structural_relation=gp.data.StackRelationType.ERODE
     )
-
     # ? Should I move this to the constructor?
     structural_frame: StructuralFrame = StructuralFrame(
         structural_groups=[default_formation],
         color_gen=color_gen
     )
-
     return structural_frame
 
 
-def test_create_interpolation_options() -> InterpolationOptions:
+def test_create_interpolation_options():
+    interpolation_options = _generate_interpolation_options()
+
+
+def _generate_interpolation_options():
     range_ = 1000.0
     interpolation_options: InterpolationOptions = InterpolationOptions.from_args(
         range=range_,
         c_o=(range_ ** 2) / 14 / 3,
     )
-
     return interpolation_options
 
 
-def test_create_geomodel() -> GeoModel:
+def _create_geomodel() -> GeoModel:
     geo_model: GeoModel = GeoModel.from_args(
         name="horizontal",
-        structural_frame=test_create_structural_frame(),
-        grid=test_create_grid(),
-        interpolation_options=test_create_interpolation_options()
+        structural_frame=_create_structural_frame(),
+        grid=_generate_grid(),
+        interpolation_options=_generate_interpolation_options()
     )
 
     return geo_model
 
 
 def test_structural_frame_surface_points():
-    structural_frame: StructuralFrame = test_create_structural_frame()
+    structural_frame: StructuralFrame = _create_structural_frame()
     print(structural_frame.surface_points_copy)
     pass
 
 
-def test_interpolate_numpy() -> GeoModel:
-    geo_model: GeoModel = test_create_geomodel()
+def _interpolate_numpy() -> GeoModel:
+    geo_model: GeoModel = _create_geomodel()
 
     solutions: gempy_engine.core.data.solutions.Solutions = gempy_engine.compute_model(
         interpolation_input=geo_model.interpolation_input_copy,
@@ -147,11 +152,11 @@ def test_interpolate_numpy() -> GeoModel:
 
 
 def test_interpolate_aesara():
-    geo_model: GeoModel = test_create_geomodel()
+    geo_model: GeoModel = _create_geomodel()
 
 
 def test_plot_input():
-    geo_model: GeoModel = test_create_geomodel()
+    geo_model: GeoModel = _create_geomodel()
     gp_viewer: gempy_viewer = require_gempy_viewer()
     # TODO: Add all the plot data in a plot options class
 
@@ -164,7 +169,7 @@ def test_plot_input():
 
 
 def test_plot_results():
-    solved_geo_model: GeoModel = test_interpolate_numpy()
+    solved_geo_model: GeoModel = _interpolate_numpy()
     gp_viewer: gempy_viewer = require_gempy_viewer()
 
     gp_viewer.plot_2d(