[DOC] Update documentation with the latest additions

Author: Leguark

docs/source/_images/gp-model-in-le.png

@@ -20,7 +20,7 @@
 
 # %%
 # We import a model from an existing folder, representing a subduction
-# zone with onlap relationships.
+# zone with onlap relationships. 
 
 data_path = os.path.abspath('../../')
 

examples/examples/geometries/i09_fold.py

@@ -11,7 +11,7 @@
 from gempy import generate_example_model
 from gempy.core.data.enumerators import ExampleModel
 
-# sphinx_gallery_thumbnail_number = 2
+# sphinx_gallery_thumbnail_number = -1
 
 # %%
 # Loading an example geomodel
@@ -78,4 +78,4 @@
 # Now we can use `this link <https://liquidearth.app.link/gempy-promo>`_ to visualize the model in Liquid Earth.
 
 # %%
-# .. image:: /_static/gp-model-in-le.png
+# .. image:: /_static/gp_model_in_le.png

examples/tutorials/ch1_fundamentals/ch1_4_onlap_relations.py

@@ -0,0 +1,4 @@
+Other tutorials
+---------------
+
+Compilation of tutorials that do not fit in the above categories.

examples/tutorials/ch1_fundamentals/ch1_7_3d_visualization.py

@@ -0,0 +1,116 @@
+"""
+Modeling step by step
+^^^^^^^^^^^^^^^^^^^^^
+
+This tutorial demonstrates step-by-step geological modeling using the `gempy` and `gempy_viewer` libraries. We will start by importing the necessary packages, loading input data, creating a geological model, and then visualizing the results.
+"""
+
+# %%
+# Import minimal requirements
+# We need to import the `gempy` library for geological modeling and `gempy_viewer` for visualization.
+import gempy as gp
+import gempy_viewer as gpv
+
+# %%
+# Define the path to input data
+# Here, we provide two ways to define the path to the input data: using a URL or a local path.
+# Uncomment the first two lines if you want to use the online data source.
+
+# data_path = 'https://raw.githubusercontent.com/cgre-aachen/gempy_data/master/'
+# path_to_data = data_path + "/data/input_data/jan_models/"
+
+# For this tutorial, we will use the local path:
+data_path = '../../'
+path_to_data = data_path + "/data/input_data/jan_models/"
+
+# %%
+# Create a GeoModel instance
+# We create a GeoModel instance with a specified project name and extent. 
+# The ImporterHelper class is used to specify the paths to the orientation and surface points data.
+
+geo_model = gp.create_geomodel(
+    project_name='tutorial_model',
+    extent=[0, 2500, 0, 1000, 0, 1110],
+    refinement=6,
+    importer_helper=gp.data.ImporterHelper(
+        path_to_orientations=path_to_data + "tutorial_model_orientations.csv",
+        path_to_surface_points=path_to_data + "tutorial_model_surface_points.csv"
+    )
+)
+
+# %%
+# Displaying simple data cross section
+# We use the `gempy_viewer` to visualize the initial cross-section of our geological model.
+gpv.plot_2d(geo_model)
+
+# %%
+# Map geological series to surfaces
+# Here, we map the geological series to specific surfaces. This step is crucial for defining the stratigraphic relationships in our model.
+gp.map_stack_to_surfaces(
+    gempy_model=geo_model,
+    mapping_object={
+            "Strat_Series1": ('rock3'),
+            "Strat_Series2": ('rock2', 'rock1'),
+    }
+)
+
+# %%
+# Update transformation and interpolation options
+# We update the model with anisotropy settings and specify various interpolation options to refine the model's accuracy.
+
+geo_model.update_transform(auto_anisotropy=gp.data.GlobalAnisotropy.CUBE)
+
+interpolation_options: gp.data.InterpolationOptions = geo_model.interpolation_options
+
+interpolation_options.mesh_extraction = True
+interpolation_options.evaluation_options.compute_scalar_gradient = True
+
+interpolation_options.kernel_options.range = 1
+interpolation_options.evaluation_options.number_octree_levels_surface = 6
+interpolation_options.evaluation_options.curvature_threshold = 0.6
+
+# %%
+# Compute the geological model
+# We use the specified backend (in this case, PyTorch) to compute the model.
+gp.compute_model(
+    gempy_model=geo_model,
+    engine_config=gp.data.GemPyEngineConfig(backend=gp.data.AvailableBackends.PYTORCH)
+)
+
+# %%
+# Visualize the model: 2D cross-section without scalar field
+# After computing the model, we visualize it again in 2D without the scalar field.
+gpv.plot_2d(geo_model, show_scalar=False, series_n=1)
+
+# %% md
+# Visualize the model: 2D cross-section with scalar field
+# In this cell, we visualize the 2D cross-section with the scalar field enabled.
+# %%
+gpv.plot_2d(geo_model, show_scalar=True, series_n=1)
+
+# %%
+# Visualize the model in 3D
+# Finally, we create a 3D visualization of the geological model without lithological coloring and image.
+gpv.plot_3d(geo_model, show_lith=False, image=False)
+# sphinx_gallery_thumbnail_number = -1
+
+# %%
+# ### Coming up next
+# Additional: Manually adding data (optional)
+# Here is an example of how you can manually add surface points to the model. Uncomment and modify the code as needed.
+
+'''
+gp.add_surface_points(
+    geo_model=geo_model,
+    x=[458, 612],
+    y=[0, 0],
+    z=[-107, -14],
+    elements_names=['surface1', 'surface1']
+)
+'''
+
+# %%
+# Displaying data cross section (optional)
+# You can re-plot the 2D cross-section if needed.
+# gpv.plot_2d(geo_model)
+# %%