Merge remote-tracking branch 'origin/main'

Author: javoha

WhatsNewGemPy3.md

@@ -43,7 +43,7 @@ To ensure compatibility with our new octree approach, we have implemented dual c
 
 **7. Initial Steps in LiquidEarth Integration**
 
-We have begun integrating GemPy with the LiquidEarth app to significantly extend GemPy's applicability in practical scenarios, enhancing workflow integration and data visualization capabilities. LiquidEarth, developed by the same main developers as GemPy, is a commercial, cloud-based software solution. It empowers experts to visualize, edit, and communicate geological data and models in intuitive 3D, facilitating real-time collaboration across multiple devices, independent of location.
+We have begun integrating GemPy with the [LiquidEarth app](https://www.terranigma-solutions.com/liquid-earth-one) to significantly extend GemPy's applicability in practical scenarios, enhancing workflow integration and data visualization capabilities. LiquidEarth, developed by the same main developers as GemPy, is a commercial, cloud-based software solution. It empowers experts to visualize, edit, and communicate geological data and models in intuitive 3D, facilitating real-time collaboration across multiple devices, independent of location.
 
 This integration aims to leverage LiquidEarth's commercial platform, which utilizes emerging technologies to provide novel environments for working with 3D geoscience data and focuses on ease of use and on offering a low entry barrier. Simultaneously, GemPy will continue to serve as a completely free and open-source tool, offering a flexible, reliable, and transparent solution for 3D geological modeling. Together, this direct integration between GemPy and LiquidEarth is designed to maximize the strengths of both systems: enhancing the visual representation of 3D geoscience projects, connecting them to the broader open-source geoscience ecosystem, and enhancing the utility of GemPy for companies and industry applications.
 
@@ -55,4 +55,4 @@ GemPy v3 introduces numerous other smaller changes and feature prototypes. These
 
 **In Conclusion**
 
-With the release of v3, we are reinforcing the role of GemPy as a key contributing piece within the larger open-source geoscience ecosystem. This update not only improves core functionalities but also introduces important integrations and enhancements that make it more robust and pave the way for future developments. Dedicated to advancing GemPy as a valuable tool for both academic research and industry applications, our team values your ongoing support and feedback. We invite you to explore the new features and join us in shaping the future of open-source geosciences. Looking forward to the results and innovative applications you achieve with this new version of GemPy!
+With the release of v3, we are reinforcing the role of GemPy as a key contributing piece within the larger open-source geoscience ecosystem. This update not only improves core functionalities but also introduces important integrations and enhancements that make it more robust and pave the way for future developments. Dedicated to advancing GemPy as a valuable tool for both academic research and industry applications, our team values your ongoing support and feedback. We invite you to explore the new features and join us in shaping the future of open-source geosciences. Looking forward to the results and innovative applications you achieve with this new version of GemPy!

docs/developers_notes/dev_log/log_2024-06-25.md

@@ -0,0 +1,17 @@
+## Goals
+
+- [ ] 1. Fixing 2024.2.0 for whatever version of python that is not working
+
+
+## TODO:
+
+- [x] Analyze error:
+    - [x] Set up environment 3.11
+- [x] Fixing the lines of code
+- [x] Test the code 
+- [ ] Release hot fix
+
+## Extra points:
+- [ ] Setting up github actions
+  - [ ] Categories for the tests like I did in subsurface
+  - [ ] Run tests in python 3.10, 3.11 and 3.12

docs/developers_notes/dev_log/log_2024-06.md

@@ -6,6 +6,16 @@
 - [ ] Run something with octrees again
 - [ ] **We do need settings presets**
 
+
+## Release Notes:
+- (Beta) Pivot grids 
+- Analysis tools: 
+  - Eigenvalues and condition numbers
+  - Transformed data plots
+  - Octree refinement evaluation
+- Improved octree testing
+- LiquidEarth integration
+- Chunking for large grids
 
 ## Notes:
 ### Optimizing interpolation June 2024

docs/source/api_reference.rst

@@ -15,6 +15,31 @@ GemPy API
     compute_model
     create_geomodel
     map_stack_to_surfaces
+    structural_elements_from_borehole_set
+    set_section_grid
+    set_active_grid
+    set_topography_from_random
+    set_topography_from_file
+    set_topography_from_subsurface_structured_grid
+    set_topography_from_arrays
+    set_custom_grid
+    set_centered_grid
+    generate_example_model
+    set_fault_relation
+    set_is_fault
+    set_is_finite_fault
+    add_surface_points
+    add_orientations
+    delete_surface_points
+    delete_orientations
+    create_orientations_from_surface_points_coords
+    modify_surface_points
+    modify_orientations
+    add_structural_group
+    remove_structural_group_by_index
+    remove_structural_group_by_name
+    remove_element_by_name
+    calculate_gravity_gradient
 
 
 Plot
@@ -48,8 +73,12 @@ Modeling Classes
     OrientationsTable
     InterpolationOptions
     Grid
+    Topography
     Solutions
     RawArraysSolution
+    FaultsData
+    GeophysicsInput
+    Transform
 
 Helper Classes
 --------------
@@ -59,6 +88,8 @@ Helper Classes
     :template: class.rst
 
     ImporterHelper
+    GemPyEngineConfig
+    ColorsGenerator
 
 Enumerators
 -----------
@@ -68,3 +99,6 @@ Enumerators
     :template: class.rst
 
     StackRelationType
+    GlobalAnisotropy
+    AvailableBackends
+    FaultsRelationSpecialCase

docs/source/conf.py

@@ -22,11 +22,16 @@
 import sys
 import warnings
 
-import sphinx_gallery
+import pyvista
 from sphinx_gallery.sorting import FileNameSortKey
+
 import gempy
-import pyvista
-import numpy as np
+
+# External examples:
+sys.path.insert(0, os.path.abspath('.'))
+import make_external_gallery
+
+make_external_gallery.make_example_gallery()
 
 # region PyVista Configuration
 pyvista.set_error_output_file('errors.txt')
@@ -61,6 +66,10 @@
         'sphinx.ext.githubpages',
         'sphinx.ext.napoleon',
         'sphinx_gallery.gen_gallery',
+        "pyvista.ext.plot_directive",
+        "sphinx_design",
+        'sphinx_automodapi.automodapi',
+        'sphinx_automodapi.smart_resolver',
 ]
 
 if run_intersphinx := False:  # Example configuration for intersphinx: refer to the Python standard library.

docs/source/external/_do_not_delete.txt

@@ -42,6 +42,12 @@ Contents:
    tutorials/index
    examples/index
 
+.. toctree::
+    :maxdepth: 2
+    :caption: External examples
+    
+    external/external_examples
+
 .. toctree::
    :maxdepth: 2
    :caption: API Reference

docs/source/index.rst

@@ -0,0 +1,115 @@
+"""
+Modified after https://github.com/pyvista/pyvista/blob/ab70c26edbcfb107286c827bd4914562056219fb/docs/make_external_gallery.py
+
+A helper script to generate the external 2-examples gallery.
+"""
+import os
+from io import StringIO
+
+
+def format_icon(title, description, link, image):
+    body = r"""
+   .. grid-item-card:: {}
+      :link: {}
+      :text-align: center
+      :class-title: pyvista-card-title
+
+      .. image:: {}
+"""
+    content = body.format(title, link, image)
+    return content
+
+
+class Example():
+    def __init__(self, title, description, link, image):
+        self.title = title
+        self.description = description
+        self.link = link
+        self.image = image
+
+    def format(self):
+        return format_icon(self.title, self.description, self.link, self.image)
+
+
+###############################################################################
+
+articles = dict(
+    _1=Example(
+        title="Vector Model 1: Construction",
+        description="Build a basic structural model",
+        link="https://vector-raw-materials.github.io/vector-geology/examples/02_structural_modeling/01_model_1_gempy_step_by_step.html#sphx-glr-examples-02-structural-modeling-01-model-1-gempy-step-by-step-py",
+        image="https://vector-raw-materials.github.io/vector-geology/_images/sphx_glr_01_model_1_gempy_step_by_step_001.png",
+    ),
+    _2=Example(
+        title="Vector Model 1: Forward Gravity",
+        description="Get the gravity response of the model",
+        link="https://vector-raw-materials.github.io/vector-geology/examples/03_forward_engines/02_model_1_gempy_fw_gravity.html#sphx-glr-examples-03-forward-engines-02-model-1-gempy-fw-gravity-py",
+        image="https://vector-raw-materials.github.io/vector-geology/_images/sphx_glr_02_model_1_gempy_fw_gravity_003.png",
+    ),
+    _3=Example(
+        title="Spremberg: Importing Boreholes",
+        description="Import data from well csv files",
+        link="https://vector-raw-materials.github.io/vector-geology/examples/02_structural_modeling/03_model_spremberg_import.html#sphx-glr-examples-02-structural-modeling-03-model-spremberg-import-py",
+        image="https://vector-raw-materials.github.io/vector-geology/_images/sphx_glr_03_model_spremberg_import_003.png",
+    ),
+    _4=Example(
+        title="Spremberg: Constructing the Model",
+        description="Build a structural model from borehole data",
+        link="https://vector-raw-materials.github.io/vector-geology/examples/02_structural_modeling/04_model_spremberg_building.html#sphx-glr-examples-02-structural-modeling-04-model-spremberg-building-py",
+        image="https://vector-raw-materials.github.io/vector-geology/_images/sphx_glr_04_model_spremberg_building_008.png",
+    ),
+)
+
+
+###############################################################################
+
+def make_example_gallery():
+    """Make the example gallery."""
+    path = "./external/external_examples.rst"
+
+    with StringIO() as new_fid:
+        new_fid.write(
+            """
+.. _external_examples:
+
+External Examples
+==================
+
+Vector Examples
+---------------
+These are examples from the Vector project.
+
+.. grid:: 3
+   :gutter: 1
+
+"""
+        )
+        # Reverse to put the latest items at the top
+        for example in list(articles.values())[::-1]:
+            new_fid.write(example.format())
+
+        new_fid.write(
+            """
+
+.. raw:: html
+
+    <div class="sphx-glr-clear"></div>
+
+
+"""
+        )
+        new_fid.seek(0)
+        new_text = new_fid.read()
+
+    # check if it's necessary to overwrite the table
+    existing = ""
+    if os.path.exists(path):
+        with open(path) as existing_fid:
+            existing = existing_fid.read()
+
+    # write if different or does not exist
+    if new_text != existing:
+        with open(path, "w", encoding="utf-8") as fid:
+            fid.write(new_text)
+
+    return