Feature/json io

[flohorovicic]

Description

This PR introduces JSON input/output functionality to GemPy, allowing users to save and load geological models in JSON format. This new feature provides:

1. Initial implementation of JSON serialization and deserialization for GemPy models
2. Complete support for all essential model components:
   • Surface points and orientations
   • Series and structural relationships
   • Fault relations
   • Grid settings
   • Interpolation options
   • Model metadata
   • Element colors and styling

The JSON format offers several advantages:

• Human-readable and editable model representation
• Language-agnostic data format for interoperability
• Structured validation of model data
• Easy version control and model sharing

The implementation includes:

• JsonIO class with save_model_to_json and load_model_from_json methods
• Schema validation for JSON data
• Sensible defaults for optional parameters
• Comprehensive error handling

Key improvements in latest commits:

• Colors are now correctly preserved when loading models from JSON
• Structural relationships (ERODE, ONLAP) are properly handled
• Fault relations matrix is correctly saved and restored
• Metadata (creation_date, last_modification_date) is properly managed
• Default values are provided for optional parameters
• Comprehensive error handling for invalid data structures

Relates to #1003

Checklist

• My code uses type hinting for function and method arguments and return values.
  • Added type hints in JsonIO class methods (load_model_from_json, save_model_to_json)
  • All helper methods include proper type annotations
• I have created tests which cover my code.
  • Added 19 comprehensive tests in test_json_io.py
  • Tests cover both success and failure cases
  • Edge cases are properly tested
• The test code either:
  1. demonstrates at least one valuable use case (e.g. integration tests)
     • test_multiple_series_relationships demonstrates real-world usage with multiple series
     • test_combination_model shows complex model with faults and unconformities
     • test_fault_relationships verifies fault relation handling
  2. verifies that outputs are as expected for given inputs (e.g. unit tests)
     • Unit tests for surface points loading/saving
     • Unit tests for orientations handling
     • Unit tests for metadata preservation
     • Unit tests for color preservation
• New tests pass locally with my changes.
  • All 19 tests pass successfully
  • Only expected warnings are present (deprecation notices and known basement color warning)

[javoha]

Hi,
looks good to me and tests pass. Just two notes (I also pushed them as TODOs)

1. In 04_combination_model.py you wrote code for saving the model after computation - the resulting file is exactly the same as the one before. So this is not implemted yet - question would be if we want to do that before merging.
2. As far as I can tell in the current version the last modification date ist nor actually updated. There is an example for getting the current date in 02_horizontal_stratigraphic.py but I am not sure if that is the final version.

Cheers,
Jan

[flohorovicic]

Thanks a lot for the checks and the comments, @javoha!

1. Good point - is left from a check I had done before. But it would make sense to include it, again - the functionality itself is now included in a test.
2. True, but not required - this was mostly to show how it can be set. Maybe more something to describe in a bit more detail in an example.

Anyway, I'd say both are rather minor aspects, can be adjusted after the merge :-)

[javoha]

Looks good. I think this feature should be part of the core gempy functionality. In the future we should include the possibility to store results. Thanks @flohorovicic!

[Leguark]

gempy/init.py:10: in
from .core import data
gempy/core/data/init.py:1: in
from .geo_model import GeoModel
gempy/core/data/geo_model.py:20: in
from .grid import Grid
gempy/core/data/grid.py:11: in
from .grid_modules import RegularGrid, CustomGrid, Sections
gempy/core/data/grid_modules/init.py:2: in
from .topography import Topography
gempy/core/data/grid_modules/topography.py:7: in
from ....modules.grids.create_topography import _LoadDEMArtificial
gempy/modules/init.py:5: in
from . import json_io
gempy/modules/json_io/init.py:6: in
from .json_operations import JsonIO
gempy/modules/json_io/json_operations.py:11: in
from .schema import SurfacePoint, Orientation, GemPyModelJson, IdNameMapping
gempy/modules/json_io/schema.py:6: in
from typing import TypedDict, List, Dict, Any, Optional, Union, Sequence, NotRequired
E ImportError: cannot import name 'NotRequired' from 'typing' (/usr/lib/python3.10/typing.py)

[flohorovicic]

(Previous fail seems to be related to CI running Python 3.10 - now included an option that should work for 3.10 and >+ 3.11)