[BUG] Fix typo in test_topography_II and update Spremberg file paths (#1033)

# Description
This PR fixes a typo in the test function name `test_topography_II` (previously misspelled as `test_topogrphy_II`) and adds model serialization verification to this test. It also updates the environment variable paths in the `TestStratigraphicPile` class to use a base path with `PATH_TO_SPREMBERG` instead of separate environment variables for each file.


# Checklist
- [x] My code uses type hinting for function and method arguments and return values.
- [x] I have created tests which cover my code.
- [x] 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).
- [x] New tests pass locally with my changes.

Author: Leguark

gempy/modules/serialization/save_load.py

@@ -1,7 +1,5 @@
 import re
 
-from typing import Literal
-
 import warnings
 
 from ...core.data import GeoModel
@@ -159,47 +157,3 @@ def _validate_serialization(original_model, model_deserialized):
     assert deserialized___str__ == original_model___str__
 
 
-def verify_model_serialization(model: GeoModel, verify_moment: Literal["before", "after"], file_name: str):
-    """
-    Verifies the serialization and deserialization process of a GeoModel instance
-    by ensuring the serialized JSON and binary data match during either the
-    initial or post-process phase, based on the specified verification moment.
-
-    Args:
-        model: The GeoModel instance to be verified.
-        verify_moment: A literal value specifying whether to verify the model
-            before or after the deserialization process. Accepts "before"
-            or "after" as valid inputs.
-        file_name: The filename to associate with the verification process for
-            logging or output purposes.
-
-    Raises:
-        ValueError: If `verify_moment` is not set to "before" or "after".
-    """
-    model_json = model.model_dump_json(by_alias=True, indent=4)
-
-    # Compress the binary data
-    zlib = require_zlib()
-    compressed_binary = zlib.compress(model.structural_frame.input_tables_binary)
-
-    binary_file = _to_binary(model_json, compressed_binary)
-
-
-    original_model = model
-    original_model.meta.creation_date = "<DATE_IGNORED>"
-
-    from verify_helper import verify_json
-    if verify_moment == "before":
-        verify_json(
-            item=original_model.model_dump_json(by_alias=True, indent=4),
-            name=file_name
-        )
-    elif verify_moment == "after":
-        model_deserialized = _deserialize_binary_file(binary_file)
-        model_deserialized.meta.creation_date = "<DATE_IGNORED>"
-        verify_json(
-            item=model_deserialized.model_dump_json(by_alias=True, indent=4),
-            name=file_name
-        )
-    else:
-        raise ValueError("Invalid model parameter")

test/test_modules/_geophysics_TO_UPDATE/test_gravity.py

@@ -4,7 +4,7 @@
 # Importing auxiliary libraries
 import numpy as np
 
-from gempy.modules.serialization.save_load import verify_model_serialization
+from test.verify_helper import verify_model_serialization
 
 
 def test_gravity():
@@ -59,7 +59,7 @@ def test_gravity():
         structural_frame=frame,
     )
 
-    # gp.compute_model(geo_model)
+    gp.compute_model(geo_model, validate_serialization=False)
 
     import gempy_viewer as gpv
     gpv.plot_2d(geo_model, cell_number=0)

test/test_modules/_geophysics_TO_UPDATE/test_gravity.test_gravity.verify/2-layers.approved.txt

@@ -26,7 +26,7 @@
                             },
                             "_model_transform": null
                         },
-                        "scalar_field_at_interface": null,
+                        "scalar_field_at_interface": 0.09000000000000002,
                         "_id": -1
                     },
                     {
@@ -43,7 +43,7 @@
                             "name_id_map": null,
                             "_model_transform": null
                         },
-                        "scalar_field_at_interface": null,
+                        "scalar_field_at_interface": -0.2483333333333333,
                         "_id": -1
                     }
                 ],
@@ -154,7 +154,7 @@
             "mesh_extraction_masking_options": 3,
             "mesh_extraction_fancy": true,
             "evaluation_chunk_size": 500000,
-            "compute_scalar_gradient": false,
+            "compute_scalar_gradient": true,
             "verbose": false
         },
         "debug": true,

test/test_modules/test_faults/test_finite_faults.py

@@ -4,7 +4,7 @@
 import gempy as gp
 import gempy_viewer as gpv
 from gempy.core.data.enumerators import ExampleModel
-from gempy.modules.serialization.save_load import verify_model_serialization
+from test.verify_helper import verify_model_serialization
 from gempy_viewer.optional_dependencies import require_pyvista
 from test.conftest import TEST_SPEED, TestSpeed
 

test/test_modules/test_grids/test_custom_grid.py

@@ -1,7 +1,7 @@
 import numpy as np
 import pytest
 
-from gempy.modules.serialization.save_load import verify_model_serialization
+from test.verify_helper import verify_model_serialization
 from test.conftest import TEST_SPEED, TestSpeed
 import gempy as gp
 from gempy.core.data.enumerators import ExampleModel

test/test_modules/test_grids/test_grids_sections.py

@@ -4,7 +4,7 @@
 import gempy as gp
 import gempy_viewer as gpv
 from gempy.core.data.enumerators import ExampleModel
-from gempy.modules.serialization.save_load import verify_model_serialization
+from test.verify_helper import verify_model_serialization
 
 from test.conftest import TEST_SPEED, TestSpeed
 
@@ -64,7 +64,7 @@ def test_section_grids():
 
 
 @pytest.mark.skipif(TEST_SPEED.value < TestSpeed.MINUTES.value, reason="Global test speed below this test value.")
-def test_topogrphy_II():
+def test_topography_II():
     geo_model: gp.data.GeoModel = gp.generate_example_model(
         example_model=ExampleModel.TWO_AND_A_HALF_D,
         compute_model=False
@@ -77,7 +77,12 @@ def test_topogrphy_II():
         show_lith=False,
         image=True
     )
-    
+
+    verify_model_serialization(
+        model=geo_model,
+        verify_moment="after",
+        file_name=f"verify/{geo_model.meta.name}"
+    )
     gp.compute_model(geo_model)
 
     gpv.plot_2d(geo_model, show_boundaries=False, section_names=['topography'])

test/test_modules/test_pile/test_stratigraphic_pile.py

@@ -17,15 +17,15 @@
 
 # Check if PATH_TO_SPREMBERG_STRATIGRAPHY is set if not skip the test
 @pytest.mark.skipif(
-    os.getenv("PATH_TO_SPREMBERG_STRATIGRAPHY") is None,
+    os.getenv("PATH_TO_SPREMBERG") is None,
     reason="PATH_TO_SPREMBERG_STRATIGRAPHY is not set"
 )
 
 class TestStratigraphicPile:
     @pytest.fixture(autouse=True)
     def borehole_set(self):
         reader: GenericReaderFilesHelper = GenericReaderFilesHelper(
-            file_or_buffer=os.getenv("PATH_TO_SPREMBERG_STRATIGRAPHY"),
+            file_or_buffer=os.getenv("PATH_TO_SPREMBERG") + "Spremberg_stratigraphy.csv",
             columns_map={
                     'hole_id'   : 'id',
                     'depth_from': 'top',
@@ -36,7 +36,7 @@ def borehole_set(self):
 
         lith: pd.DataFrame = read_lith(reader)
         reader: GenericReaderFilesHelper = GenericReaderFilesHelper(
-            file_or_buffer=os.getenv("PATH_TO_SPREMBERG_SURVEY"),
+            file_or_buffer=os.getenv("PATH_TO_SPREMBERG") + "Spremberg_survey.csv",
             columns_map={
                     'depth'  : 'md',
                     'dip'    : 'dip',
@@ -49,7 +49,7 @@ def borehole_set(self):
         survey.update_survey_with_lith(lith)
 
         reader_collar: GenericReaderFilesHelper = GenericReaderFilesHelper(
-            file_or_buffer=os.getenv("PATH_TO_SPREMBERG_COLLAR"),
+            file_or_buffer=os.getenv("PATH_TO_SPREMBERG") + "Spremberg_collar_updated.csv",
             header=0,
             usecols=[0, 1, 2, 4],
             columns_map={

test/verify_helper.py

@@ -1,3 +1,5 @@
+from typing import Literal
+
 import subprocess
 
 import numpy as np
@@ -8,6 +10,10 @@
 from approvaltests.namer import NamerFactory
 from approvaltests.reporters import GenericDiffReporter, GenericDiffReporterConfig
 
+from gempy.core.data import GeoModel
+from gempy.modules.serialization.save_load import _to_binary, _deserialize_binary_file
+from gempy.optional_dependencies import require_zlib
+
 
 class WSLWindowsDiffReporter(GenericDiffReporter):
     def get_command(self, received, approved):
@@ -94,4 +100,49 @@ def get_default_extension(self) -> str:
 
     def write(self, received, received_path: str) -> None:
         with open(received_path, "w", encoding="utf-8") as f:
-            json.dump(received, f, indent=2, ensure_ascii=False)
+            json.dump(received, f, indent=2, ensure_ascii=False)
+
+
+def verify_model_serialization(model: GeoModel, verify_moment: Literal["before", "after"], file_name: str):
+    """
+    Verifies the serialization and deserialization process of a GeoModel instance
+    by ensuring the serialized JSON and binary data match during either the
+    initial or post-process phase, based on the specified verification moment.
+
+    Args:
+        model: The GeoModel instance to be verified.
+        verify_moment: A literal value specifying whether to verify the model
+            before or after the deserialization process. Accepts "before"
+            or "after" as valid inputs.
+        file_name: The filename to associate with the verification process for
+            logging or output purposes.
+
+    Raises:
+        ValueError: If `verify_moment` is not set to "before" or "after".
+    """
+    model_json = model.model_dump_json(by_alias=True, indent=4)
+
+    # Compress the binary data
+    zlib = require_zlib()
+    compressed_binary = zlib.compress(model.structural_frame.input_tables_binary)
+
+    binary_file = _to_binary(model_json, compressed_binary)
+
+
+    original_model = model
+    original_model.meta.creation_date = "<DATE_IGNORED>"
+
+    if verify_moment == "before":
+        verify_json(
+            item=original_model.model_dump_json(by_alias=True, indent=4),
+            name=file_name
+        )
+    elif verify_moment == "after":
+        model_deserialized = _deserialize_binary_file(binary_file)
+        model_deserialized.meta.creation_date = "<DATE_IGNORED>"
+        verify_json(
+            item=model_deserialized.model_dump_json(by_alias=True, indent=4),
+            name=file_name
+        )
+    else:
+        raise ValueError("Invalid model parameter")