docs: 📝 updating docs for pydata, actually committing changes

Loop3D · May 4, 2022 · be33a6f · be33a6f
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diff --git a/LoopStructural/__init__.py b/LoopStructural/__init__.py
@@ -6,6 +6,7 @@
 
 import logging
 from logging.config import dictConfig
+__all__ = ['GeologicalModel']
 import tempfile
 from pathlib import Path
 from .version import __version__

diff --git a/LoopStructural/interpolators/__init__.py b/LoopStructural/interpolators/__init__.py
@@ -2,6 +2,13 @@
 Interpolators and interpolation supports
 
 """
+__all__ = ['InterpolatorType','GeologicalInterpolator','DiscreteInterpolator','FiniteDifferenceInterpolator','PiecewiseLinearInterpolator','DiscreteFoldInterpolator','SurfeRBFInterpolator','P1Interpolator','P2Interpolator','TetMesh',
+    'StructuredGrid',
+    'UnStructuredTetMesh',
+    'P1Unstructured2d',
+    'P2Unstructured2d',
+    'StructuredGrid2D',
+    'P2UnstructuredTetMesh',]
 from enum import IntEnum
 
 from LoopStructural.utils import getLogger

diff --git a/LoopStructural/modelling/__init__.py b/LoopStructural/modelling/__init__.py
@@ -2,6 +2,7 @@
 Geological modelling classes and functions
 
 """
+__all__ = ['GeologicalModel', 'ProcessInputData', 'LavaVuModelViewer', 'Map2LoopProcessor','LoopProjectfileProcessor','StructuralFrame','FaultSegment']
 from LoopStructural.utils import getLogger
 from LoopStructural.utils import LoopImportError
 

diff --git a/LoopStructural/modelling/core/geological_model.py b/LoopStructural/modelling/core/geological_model.py
@@ -272,12 +272,6 @@ def from_map2loop_directory(
         model = GeologicalModel.from_processor(processor)
         return model, processor
 
-        # from LoopStructural.utils import build_model, process_map2loop
-        # logger.info('LoopStructural model initialised from m2l directory: {}'.format(m2l_directory))
-        # m2lflags = kwargs.pop('m2lflags',{})
-        # m2l_data = process_map2loop(m2l_directory,m2lflags)
-        # return build_model(m2l_data,**kwargs), m2l_data
-
     @classmethod
     def from_processor(cls, processor):
         logger.info("Creating model from processor")

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -39,7 +39,7 @@
 napoleon_numpy_docstring = True #False  # Force consistency, leave only Google
 napoleon_use_rtype = False  # More legible
 autosummary_imported_members = True
-
+autosummary_ignore_module_all = False
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
@@ -65,13 +65,31 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
 
-
+html_theme_options = {
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/loop3d/LoopStructural",
+            "icon": "fab fa-github-square",
+        },
+        {
+            "name": "Twitter",
+            "url": "https://twitter.com/loop3d",
+            "icon": "fab fa-twitter-square",
+        },
+    ],
+#     "navbar_start": ["navbar-logo", "navbar-version"],
+#     "use_edit_page_button": True,
+    "external_links": [
+        {"name": "Loop3d", "url": "https://www.loop3d.org"},
+    ],
+}
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'pydata_sphinx_theme'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
@@ -0,0 +1,12 @@
+Getting Started
+===============
+
+.. toctree::
+   :caption: Getting Started
+
+   installation
+   background
+   auto_examples/index
+   contributors_guide
+   about
+   CHANGELOG
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -28,36 +28,15 @@ and a wrapper for the generalised radial basis functions provided by Surfe :cite
 .. toctree::
    :hidden:
 
-   self
-
-
-.. toctree::
-   :caption: Getting Started
-   :hidden:
-
-   installation
-   background
+   getting_started
    auto_examples/index
-   contributors_guide
-   about
-   CHANGELOG
-
-.. toctree::
-   :caption: User Guide:
-   :hidden:
+   user_guide/index
 
-   user_guide/input_data
-   user_guide/geological_model
-   user_guide/interpolation_options
-   user_guide/fold_modelling
-   user_guide/fault_modelling
-   user_guide/visualisation
-
-.. toctree::
+
+   .. toctree::
    :caption: LoopStructural API
    :hidden:
 
-
 .. autosummary::
    :caption: API
    :toctree: _autosummary
@@ -67,13 +46,3 @@ and a wrapper for the generalised radial basis functions provided by Surfe :cite
    LoopStructural
 
 
-.. .. toctree::
-   :caption: Loop
-
-
-..   map2loop
-   geophysics
-   uncertainty
-
-.. bibliography:: references.bib
-   :style:
diff --git a/docs/source/user_guide/index.rst b/docs/source/user_guide/index.rst
@@ -1 +1,12 @@
+User Guide
+===========
 
+.. toctree::
+   :caption: User Guide
+
+   input_data
+   geological_model
+   interpolation_options
+   fold_modelling
+   fault_modelling
+   visualisation
diff --git a/examples/3_fault/plot_fault_network.py b/examples/3_fault/plot_fault_network.py
@@ -1,47 +1,46 @@
 """
-============================================
-Modelling a fault network in LoopStructural
-
-============================================
+3b. Modelling a fault network in LoopStructural
+===============================================
 Uses GeologicalModel, ProcessInputData and LavaVuModelViewer from LoopStructural library. Also using geopandas to read a shapefile, pandas, matplotlib and numpy."""
 
 import LoopStructural
 LoopStructural.__version__
+
 from LoopStructural import GeologicalModel
 from LoopStructural.modelling import ProcessInputData
 from LoopStructural.visualisation import LavaVuModelViewer
 import geopandas
 import pandas as pd
 import matplotlib.pyplot as plt
 import numpy as np
-# ~~~~~~~~~~~~~~~
+
+##############################
 # Read shapefile
-
-# ~~~~~~~~~~~~~~~
-# 
-# Read the shapefile and create a point for each node of the line 
-# 
-# | **fault_name** | **X** | **Y** | **Z**| 
-# | --------------- |-----| ------| -------|
-#  | ... | . | . | .
+# ~~~~~~~~~~~~~~
+# # Read the shapefile and create a point for each node of the line # # | **fault_name** | **X** | **Y** | **Z**| # | --------------- |-----| ------| -------|#  | ... | . | . | .
+
 fault_trace = geopandas.read_file('fault_trace.shp')
+
 faults = []
 for i in range(len(fault_trace)):
     for x,y in  zip(fault_trace.loc[i,:].geometry.xy[0],fault_trace.loc[i,:].geometry.xy[1]):
         faults.append([fault_trace.loc[i,'fault_name'], x,y,np.random.random()*.4]) # better results if points aren't from a single plane
 df = pd.DataFrame(faults,columns=['fault_name','X','Y','Z'])
+
 fig, ax = plt.subplots()
 ax.scatter(df['X'],df['Y'])
 ax.axis('square')
+
 scale = np.min([df['X'].max()-df['X'].min(),df['Y'].max()-df['Y'].min()])
 df['X']/=scale
 df['Y']/=scale
 
-# ~~~~~~~~~~~~~~~~~
+
+##############################
 # Orientation data
-
-# ~~~~~~~~~~~~~~~~~
+# ~~~~~~~~~~~~~~~~
 # We can generate vertical dip data at the centre of the fault.
+
 ori = []
 for f in df['fault_name'].unique():
     centre = df.loc[df['fault_name']==f,['X','Y','Z']].mean().to_numpy().tolist()
@@ -51,69 +50,59 @@
     ori.append([f,*centre,*norm])#.extend(centre.extend(norm.tolist())))
 # fault_orientations = pd.DataFrame([[
 ori = pd.DataFrame(ori,columns=['fault_name','X','Y','Z','gx','gy','gz'])
-# ~~~~~~~~~~~~~
+
+##############################
 # Model extent
-
-# ~~~~~~~~~~~~~
-# 
-# Calculate the bounding box for the model using the extent of the shapefiles. We make the Z coordinate 10% of the maximum x/y length.
+# ~~~~~~~~~~~~
+# # Calculate the bounding box for the model using the extent of the shapefiles. We make the Z coordinate 10% of the maximum x/y length.
+
 z = np.max([df['X'].max(),df['Y'].max()])- np.min([df['X'].min(),df['Y'].min()])
 z*=.2
 origin = [df['X'].min()-z,df['Y'].min()-z,-z]
 maximum = [df['X'].max()+z,df['Y'].max()+z,z]
-# ~~~~~~~~~~~~~~~~~~~~
+
+##############################
 # Setting up the data
-
-# ~~~~~~~~~~~~~~~~~~~~
-# The `ProcessInputData` class is used to convert common geological map components to the datastructures required by LoopStructural.
-# 
-# To build a fault network we need to provide:
-# * fault locations - a table of x,y,z, and the fault name
-# * fault orientations - a table recording the orientation observations of the fault, e.g. strike, dip or normal vector and x,y,z, fault_name
-# * origin - the origin of the model bounding box
-# * maximum - the maximum extend of the model bounding box
-# * fault_edges - list of intersection relationships between faults e.g. [('fault1','fault2')] indicates that there is a intersection between fault1 and fault2
-# * fault_edge_properties - list of properties for the fault edges - this can be the type of intersection e.g. 'splay' or 'abut' or just the angle between the faults
-# * fault_properties (*optional*)  - a pandas dataframe with any kwargs for the interpolator where the index is the fault name 
-# 
-# Below is an example of setting the number of interpolation elements for each fault
-# ```Python
-# fault_properties = pd.DataFrame([['fault_1',1e4],
-#                                  ['fault_2',1e4]],
-#                                 columns=['fault_name','nelements']).set_index('fault_name')
-# ```
-# ~~~~~~~~~~~~~~~~~~~~~~~
+# ~~~~~~~~~~~~~~~~~~~
+# The `ProcessInputData` class is used to convert common geological map components to the datastructures required by LoopStructural.# # To build a fault network we need to provide:# * fault locations - a table of x,y,z, and the fault name# * fault orientations - a table recording the orientation observations of the fault, e.g. strike, dip or normal vector and x,y,z, fault_name# * origin - the origin of the model bounding box# * maximum - the maximum extend of the model bounding box# * fault_edges - list of intersection relationships between faults e.g. [('fault1','fault2')] indicates that there is a intersection between fault1 and fault2# * fault_edge_properties - list of properties for the fault edges - this can be the type of intersection e.g. 'splay' or 'abut' or just the angle between the faults# * fault_properties (*optional*)  - a pandas dataframe with any kwargs for the interpolator where the index is the fault name # # Below is an example of setting the number of interpolation elements for each fault# ```Python# fault_properties = pd.DataFrame([['fault_1',1e4],#                                  ['fault_2',1e4]],#                                 columns=['fault_name','nelements']).set_index('fault_name')# ```
+
+##############################
 # Modelling splay faults
-
-# ~~~~~~~~~~~~~~~~~~~~~~~
+# ~~~~~~~~~~~~~~~~~~~~~~
 # A splay fault relationship is defined for any fault where the angle between the faults is less than $30^\circ$. In this example we specify the angle between the faults as $10^\circ$.
+
 processor = ProcessInputData(fault_orientations=ori, 
                              fault_locations=df,
                              origin=origin,
                              maximum=maximum,
                              fault_edges=[('fault_2','fault_1')],
                              fault_edge_properties=[{'angle':10}],
                             )
+
 model = GeologicalModel.from_processor(processor)
 model.update()
+
 view = LavaVuModelViewer(model)
 for f in model.faults:
     view.add_isosurface(f,slices=[0])#
 view.rotation = [-50.92916488647461, -30.319700241088867, -20.521053314208984]
 view.display()
-# ~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+##############################
 # Modelling abutting faults
-
-# ~~~~~~~~~~~~~~~~~~~~~~~~~~
+# ~~~~~~~~~~~~~~~~~~~~~~~~~
 # In this exampe we will use the same faults but specify the angle between the faults as $40^\circ$ which will change the fault relationship to be abutting rather than splay. 
+
 processor = ProcessInputData(fault_orientations=ori, 
                              fault_locations=df,
                              origin=origin,
                              maximum=maximum,
                              fault_edges=[('fault_2','fault_1')],
                              fault_edge_properties=[{'angle':40}],
                             )
+
 model = GeologicalModel.from_processor(processor)
+
 view = LavaVuModelViewer(model)
 for f in model.faults:
     view.add_isosurface(f,slices=[0])#