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)

[Leguark]

Checks are green here. Very good encapsulated in a module. If it becomes a widely used feature, we will have to create a couple of functions on the API to expose them in gp. but for now we can leave as is since it is well documented.

The only risky aspect I see, is the redundancy in classes. Ideally we will move to have a single definition of "Surface" for example where some of the fields are serializable. Otherwise we can end up having the schema and the core object out of sync. In any case this is something I (or anybody with a lot of time allocated for thinking of this) can do in the future

[Leguark]

Merge activity

• May 1, 7:32 AM EDT: A user started a stack merge that includes this pull request via Graphite.
• May 1, 7:32 AM EDT: Graphite couldn't merge this PR because it failed for an unknown reason (Stack merges are not currently supported for forked repositories. Please create a branch in the target repository in order to merge).