Update documentation

_sources/contributing.rst.txt

@@ -1,7 +1,7 @@
 Contributing
 ------------
 
-The package ``VisualBayesic`` is a community effort, and contributions of any kind
+The package ``vector-geology`` is a community effort, and contributions of any kind
 (code, documentation, bug reports, examples) are very welcomed; please get in
 touch!
 

_sources/examples/examples/index.rst.txt

@@ -2,8 +2,8 @@
 
 .. _sphx_glr_examples_examples:
 
-Vector Examples
-===============
+Geological Models
+-----------------
 
 Here you will find a selection of examples showing what can you do and how
 you can do it in Vector.

_sources/examples/examples/read_OMF_sites.rst.txt

@@ -172,14 +172,14 @@ Use Subsurface and PyVista to visualize the unstructured data.
  .. code-block:: none
 
 
-    <pyvista.plotting.plotting.Plotter object at 0x7f3754893a60>
+    <pyvista.plotting.plotting.Plotter object at 0x7f5cbc0f39a0>
 
 
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  2.498 seconds)
+   **Total running time of the script:** ( 0 minutes  2.677 seconds)
 
 
 .. _sphx_glr_download_examples_examples_read_OMF_sites.py:

_sources/examples/examples/sg_execution_times.rst.txt

@@ -6,8 +6,8 @@
 
 Computation times
 =================
-**00:02.498** total execution time for **examples_examples** files:
+**00:02.677** total execution time for **examples_examples** files:
 
 +-----------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_examples_read_OMF_sites.py` (``read_OMF_sites.py``) | 00:02.498 | 0.0 MB |
+| :ref:`sphx_glr_examples_examples_read_OMF_sites.py` (``read_OMF_sites.py``) | 00:02.677 | 0.0 MB |
 +-----------------------------------------------------------------------------+-----------+--------+

_sources/examples/index.rst.txt

@@ -1,7 +1,7 @@
 :orphan:
 
-Vector Examples II
-==================
+Contents
+========
 
 Here you will find a selection of examples showing what can you do and how
 you can do it in Vector.
@@ -17,8 +17,8 @@ you can do it in Vector.
 
     </div>
 
-Vector Examples
-===============
+Geological Models
+-----------------
 
 Here you will find a selection of examples showing what can you do and how
 you can do it in Vector.

_sources/index.rst.txt

@@ -1,12 +1,12 @@
 .. _subsurface-manual:
 
 ########################
-subsurface Documentation
+vector-geology Documentation
 ########################
 
 :Release: |version|
 :Date: |today|
-:Source: `github.com/softwareunderground/subsurface <https://github.com/softwareunderground/subsurface>`_
+:Source: `github.com/vector-raw-materials/vector-geology <https://github.com/vector-raw-materials/vector-geology>`_
 
 ----
 
@@ -17,10 +17,10 @@ subsurface Documentation
 
 Requirements
 ------------
+The requirements for the core functionality of the package are:
 
-The **only** requirement for ``subsurface`` is ``xarray`` (which, in turn,
-requires ``pandas`` and ``numpy``).
-
+.. include:: ../../requirements.txt
+   :literal:
 
 Optional requirements
 ---------------------

contributing.html

@@ -5,7 +5,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Contributing &#8212; Visual Bayesic 0.1.dev16+g525c9e2 documentation</title>
+    <title>Contributing &#8212; Vector Geology 0.1.dev16+g525c9e2 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b849a4e9" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=039e1c02" />
     <link rel="stylesheet" type="text/css" href="_static/style.css?v=f2a985cd" />
@@ -39,7 +39,7 @@
 
   <section id="contributing">
 <h1>Contributing<a class="headerlink" href="#contributing" title="Permalink to this heading">¶</a></h1>
-<p>The package <code class="docutils literal notranslate"><span class="pre">VisualBayesic</span></code> is a community effort, and contributions of any kind
+<p>The package <code class="docutils literal notranslate"><span class="pre">vector-geology</span></code> is a community effort, and contributions of any kind
 (code, documentation, bug reports, examples) are very welcomed; please get in
 touch!</p>
 <div class="admonition-todo admonition" id="id1">
@@ -56,9 +56,9 @@ <h1>Contributing<a class="headerlink" href="#contributing" title="Permalink to t
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
             <p class="logo"><a href="index.html">
-              <img class="logo" src="_static/subsurface.png" alt="Logo"/>
+              <img class="logo" src="_static/vector-logo.png" alt="Logo"/>
             </a></p>
-<h1 class="logo"><a href="index.html">Visual Bayesic</a></h1>
+<h1 class="logo"><a href="index.html">Vector Geology</a></h1>
 
 
 
@@ -76,8 +76,7 @@ <h3>Navigation</h3>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Galleries</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="examples/index.html">Vector Examples II</a></li>
-<li class="toctree-l1"><a class="reference internal" href="examples/index.html#vector-examples">Vector Examples</a></li>
+<li class="toctree-l1"><a class="reference internal" href="examples/index.html">Contents</a></li>
 <li class="toctree-l1"><a class="reference internal" href="external/external_examples.html">External Examples</a></li>
 </ul>
 
@@ -97,7 +96,7 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2023-2023, Miguel de la Varga and Maximilian Hallenberger.
+      &copy;2023-2023, Vector Geology Team.
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 7.1.1</a>

docs/build/html/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: fc2c3683f946fbb7f38bc837f719f7aa
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_downloads/4369ad747c2f34721fbe1dde6c7ad931/read_OMF_sites.py

@@ -0,0 +1,73 @@
+"""
+Reading COLLINSTOWN OMF project
+================================
+
+This tutorial demonstrates how to read an OMF project file in COLLINSTOWN.
+
+"""
+
+# %%
+# Required Libraries:
+# ~~~~~~~~~~~~~~~~~~~
+#
+# Import the required libraries. 
+
+import omfvista
+import pyvista
+import subsurface
+from subsurface import TriSurf
+from subsurface.visualization import to_pyvista_mesh, pv_plot
+from subsurface.writer import base_structs_to_binary_file
+from dotenv import dotenv_values
+
+# %%
+# Load OMF Project:
+# ~~~~~~~~~~~~~~~~~
+#
+# Load the OMF project using a fixture.
+
+def load_omf():
+    config = dotenv_values()
+    path = config.get('PATH_TO_COLLINSTOWN')
+    omf = omfvista.load_project(path)
+    return omf
+
+omf = load_omf()
+
+# %%
+# Read OMF with PyVista:
+# ~~~~~~~~~~~~~~~~~~~~~~
+#
+# Visualize the OMF project with PyVista.
+
+omf.plot(multi_colors=True, show_edges=True, notebook=False)
+
+# %%
+# Convert OMF to Unstructured Single Block:
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+# Convert the loaded OMF project into an unstructured single block for further analysis.
+
+block_name = omf.get_block_name(4)
+polydata_obj: pyvista.PolyData = omf[block_name]
+unstruct_pyvista: pyvista.UnstructuredGrid = polydata_obj.cast_to_unstructured_grid()
+cells_pyvista = unstruct_pyvista.cells.reshape(-1, 4)[:, 1:]
+
+unstruct: subsurface.UnstructuredData = subsurface.UnstructuredData.from_array(
+    vertex=unstruct_pyvista.points,
+    cells=cells_pyvista,
+)
+
+if False:  # Replace with condition for exporting to Liquid Earth
+    base_structs_to_binary_file("leapfrog1", unstruct)
+
+# %%
+# Visualize Unstructured Data:
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+# Use Subsurface and PyVista to visualize the unstructured data.
+
+ts = TriSurf(mesh=unstruct)
+s = to_pyvista_mesh(ts)
+pv_plot([s], image_2d=False)
+

docs/build/html/_downloads/edd47a65ee199bebd83ea6e0a7f6412e/read_OMF_sites.ipynb

@@ -0,0 +1,133 @@
+{
+  "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "%matplotlib inline\nfrom pyvista import set_plot_theme\nset_plot_theme('document')"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "\n# Reading COLLINSTOWN OMF project\n\nThis tutorial demonstrates how to read an OMF project file in COLLINSTOWN.\n"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Required Libraries:\n\nImport the required libraries. \n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "import omfvista\nimport pyvista\nimport subsurface\nfrom subsurface import TriSurf\nfrom subsurface.visualization import to_pyvista_mesh, pv_plot\nfrom subsurface.writer import base_structs_to_binary_file\nfrom dotenv import dotenv_values"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Load OMF Project:\n\nLoad the OMF project using a fixture.\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "def load_omf():\n    config = dotenv_values()\n    path = config.get('PATH_TO_COLLINSTOWN')\n    omf = omfvista.load_project(path)\n    return omf\n\nomf = load_omf()"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Read OMF with PyVista:\n\nVisualize the OMF project with PyVista.\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "omf.plot(multi_colors=True, show_edges=True, notebook=False)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Convert OMF to Unstructured Single Block:\n\nConvert the loaded OMF project into an unstructured single block for further analysis.\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "block_name = omf.get_block_name(4)\npolydata_obj: pyvista.PolyData = omf[block_name]\nunstruct_pyvista: pyvista.UnstructuredGrid = polydata_obj.cast_to_unstructured_grid()\ncells_pyvista = unstruct_pyvista.cells.reshape(-1, 4)[:, 1:]\n\nunstruct: subsurface.UnstructuredData = subsurface.UnstructuredData.from_array(\n    vertex=unstruct_pyvista.points,\n    cells=cells_pyvista,\n)\n\nif False:  # Replace with condition for exporting to Liquid Earth\n    base_structs_to_binary_file(\"leapfrog1\", unstruct)"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Visualize Unstructured Data:\n\nUse Subsurface and PyVista to visualize the unstructured data.\n\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "ts = TriSurf(mesh=unstruct)\ns = to_pyvista_mesh(ts)\npv_plot([s], image_2d=False)"
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "codemirror_mode": {
+        "name": "ipython",
+        "version": 3
+      },
+      "file_extension": ".py",
+      "mimetype": "text/x-python",
+      "name": "python",
+      "nbconvert_exporter": "python",
+      "pygments_lexer": "ipython3",
+      "version": "3.10.12"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 0
+}

docs/build/html/_sources/contributing.rst.txt

@@ -0,0 +1,10 @@
+Contributing
+------------
+
+The package ``vector-geology`` is a community effort, and contributions of any kind
+(code, documentation, bug reports, examples) are very welcomed; please get in
+touch!
+
+.. todo::
+
+    Write!