Reorganize gempy_probability package structure and update imports (#4)

# Reorganize code structure to follow Terranigma architecture

This PR reorganizes the codebase to follow the Terranigma default structure by:

- Creating a modular directory structure with `api`, `core`, `modules`, and `plugins` folders
- Moving plotting utilities to `modules/plot/` directory
- Moving field-related code to `modules/fields/`
- Relocating deprecated code to a new `obsolete/` directory
- Moving specialized tools to the `plugins/` directory
- Updating import paths in all example files to reflect the new structure

These changes maintain functionality while providing a more organized and maintainable codebase.

Author: Leguark

examples/WIP/3.2_WIP_gravity_inversion.py

@@ -17,7 +17,6 @@
 # Auxiliary libraries
 import numpy as np
 import matplotlib.pyplot as plt
-import matplotlib.image as mpimg
 import pandas as pd
 # %% md
 # Packages for inversion
@@ -213,7 +212,7 @@ def pyro_model(y_obs_list, interpolation_input):
 # %%
 # Create density plots for posterior and prior distributions
 # These plots provide insights into the parameter distributions and their changes.
-from gempy_probability.plot_posterior import default_red, default_blue
+from gempy_probability.modules.plot.plot_posterior import default_red, default_blue
 az.plot_density(
     data=[data, data.prior],
     shade=.9,

examples/tutorials/1-first_example_of_inference/1-bayesian_basics/1.1_Intro_to_Bayesian_Inference.py

@@ -11,7 +11,7 @@
 import pyro
 import torch
 
-from gempy_probability.plot_posterior import PlotPosterior
+from gempy_probability.modules.plot.plot_posterior import PlotPosterior
 from _aux_func import infer_model
 
 az.style.use("arviz-doc")

examples/tutorials/1-first_example_of_inference/1-bayesian_basics/1.2_Intro_to_Bayesian_Inference.py

@@ -19,7 +19,7 @@
 import torch
 from matplotlib.ticker import StrMethodFormatter
 
-from gempy_probability.plot_posterior import PlotPosterior
+from gempy_probability.modules.plot.plot_posterior import PlotPosterior
 from _aux_func import infer_model
 az.style.use("arviz-doc")
 

examples/tutorials/1-first_example_of_inference/1-bayesian_basics/1.3_Intro_to_Bayesian_Inference.py

@@ -10,7 +10,7 @@
 import pyro
 import torch
 
-from gempy_probability.plot_posterior import PlotPosterior
+from gempy_probability.modules.plot.plot_posterior import PlotPosterior
 
 from _aux_func import infer_model
 

examples/tutorials/1-first_example_of_inference/1-bayesian_basics/1.4_Intro_to_Bayesian_Inference.py

@@ -11,7 +11,7 @@
 import torch
 from matplotlib.ticker import StrMethodFormatter
 
-from gempy_probability.plot_posterior import PlotPosterior
+from gempy_probability.modules.plot.plot_posterior import PlotPosterior
 
 from _aux_func import infer_model
 

examples/tutorials/2-basic_geology/1-thickness_problem.py

@@ -41,7 +41,7 @@
 import torch
 from pyro.infer import MCMC, NUTS, Predictive
 from pyro.infer.inspect import get_dependencies
-from gempy_probability.plot_posterior import PlotPosterior, default_red, default_blue
+from gempy_probability.modules.plot.plot_posterior import PlotPosterior, default_red, default_blue
 import arviz as az
 
 az.style.use("arviz-doc")

examples/tutorials/2-basic_geology/2-thickness_problem_gempy.py

@@ -22,7 +22,7 @@
 import arviz as az
 
 from gempy_engine.core.data.interpolation_input import InterpolationInput
-from gempy_probability.plot_posterior import default_red, default_blue
+from gempy_probability.modules.plot.plot_posterior import default_red, default_blue
 
 # sphinx_gallery_thumbnail_number = -1