diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index b39e1ad3..3c308e68 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -19,6 +19,9 @@ formats:
# Optionally set the version of Python and requirements required to build your docs
python:
version: 3.8
+ install:
+ - method: pip
+ path: .
conda:
environment: environment_dev.yml
\ No newline at end of file
diff --git a/README.md b/README.md
index 6a3f8ad6..c2b1af06 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
-> Spatial data and information processing for geomodeling
+> Spatial data and information processing for geomodeling and subsurface data
[](https://www.python.org/downloads/)
@@ -17,11 +17,11 @@
## Overview
-We attempt to simplify the access to open-source spatial data processing for geological modeling with the development of **GemGIS, a Python-based open-source library**.
+We attempt to simplify the access to open-source spatial data processing for geological modeling and for subsurface data (wells, seismic, etc.) with the development of **GemGIS, a Python-based open-source library**.
GemGIS wraps and extends the functionality of packages known to the geo-community such as [GeoPandas](https://geopandas.org/), [rasterio](https://rasterio.readthedocs.io/en/latest/#), [OWSLib](https://geopython.github.io/OWSLib/), [Shapely](https://shapely.readthedocs.io/en/latest/manual.html), [PyVista](https://docs.pyvista.org/), [Pandas](https://pandas.pydata.org/), [NumPy](https://numpy.org/) and the geomodeling package [GemPy](https://docs.gempy.org/).
-The aim of GemGIS, as indicated by the name, is to become a bridge between conventional geoinformation systems (GIS) such as ArcGIS and QGIS, and geomodeling tools such as GemPy, allowing simpler and more automated workflows from one environment to the other. This also includes making it simpler to visualize the results obtained from GemGIS and GemPy with PyVista or Blender.
+The aim of GemGIS, as indicated by the name, is to become a bridge between conventional geoinformation systems (GIS) such as ArcGIS and QGIS, and geomodeling tools such as GemPy, allowing simpler and more automated workflows from one environment to the other. This also includes making it simpler to visualize the results obtained from GemGIS and GemPy with PyVista or Blender. Further, subsurface data processing workflows are implemented for integrated data analyses.
@@ -31,7 +31,7 @@ The aim of GemGIS, as indicated by the name, is to become a bridge between conve
[Find the documentation of GemGIS here](https://gemgis.readthedocs.io/en/latest/index.html). It includes introductions to the main libraries used and to introductory topics like "What is vector data?" or "What is raster data?".
In addition, [tutorial notebooks](https://gemgis.readthedocs.io/en/latest/getting_started/tutorial/index.html) provide an overview of the different features of GemGIS. The notebooks can also be downloaded directly from [here](https://rwth-aachen.sciebo.de/s/AfXRsZywYDbUF34/download?path=%2F&files=tutorials01_53.zip).
-Furthermore, many [example models](https://gemgis.readthedocs.io/en/latest/getting_started/example/index.html) showcase a variety of geological structures that can be modeled with GemGIS and GemPy.
+Furthermore, many [example models](https://gemgis.readthedocs.io/en/latest/getting_started/example/index.html) showcase a variety of geological structures that can be modeled with GemGIS and GemPy. The [API Reference](https://gemgis.readthedocs.io/en/latest/getting_started/api.html#) provides an overview of the implemented functions in GemGIS and how to use them.
@@ -44,6 +44,7 @@ It is recommended to use GemGIS with **python">=3.10"** in a separated environme
Check out the [Installation Page](https://gemgis.readthedocs.io/en/latest/getting_started/installation.html) for more detailed instructions.
+If you are an open-source software developer, please install **GemGIS** and its dependencies, also for building the documentation, using the [development YML file](https://github.com/cgre-aachen/gemgis/blob/main/environment_dev.yml).
## Contribution Guidelines
The Contribution Guidelines for GemGIS can be found here: [Contribution Guidelines](https://github.com/cgre-aachen/gemgis/blob/main/CONTRIBUTING.md)
@@ -54,6 +55,8 @@ We welcome issue reports, questions, ideas for new features and pull-requests to
## References
+* Jüstel et al., (2023). From Maps to Models - Tutorials for structural geological modeling using GemPy and GemGIS. Journal of Open Source Education, 6(66), 185, https://doi.org/10.21105/jose.00185
+* Jüstel et al., (2022). GemGIS - Spatial Data Processing for Geomodeling. Journal of Open Source Software, 7(73), 3709, https://doi.org/10.21105/joss.03709
* Jüstel, A., Endlein Correira, A., Wellmann, F. and Pischke, M.: GemGIS – GemPy Geographic: Open-Source Spatial Data Processing for Geological Modeling. EGU General Assembly 2021, https://doi.org/10.5194/egusphere-egu21-4613, 2021
* Jüstel, A.: 3D Probabilistic Modeling and Data Analysis of the Aachen-Weisweiler Area: Implications for Deep Geothermal Energy Exploration, unpublished Master Thesis at RWTH Aachen University, 2020
* de la Varga, M., Schaaf, A., and Wellmann, F.: GemPy 1.0: open-source stochastic geological modeling and inversion, Geosci. Model Dev., 12, 1-32, https://doi.org/10.5194/gmd-12-1-2019, 2019
diff --git a/docs/conf.py b/docs/conf.py
index 7a1466ca..c763ca23 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -9,13 +9,6 @@
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-import os
-import sys
-sys.path.insert(0, os.path.abspath(".."))
-
-# import sphinx_rtd_theme
-
# -- Project information -----------------------------------------------------
@@ -24,12 +17,17 @@
author = 'Alexander Juestel'
# The full version, including alpha/beta/rc tags
-release = '1.0.11'
+release = '1.0.12'
version = release
# -- GemGIS configuration ---------------------------------------------------
-#sys.path.append('../../gemgis')
-
+import os
+import sys
+sys.path.insert(0, os.path.abspath(".."))
+sys.path.insert(0, os.path.abspath('../..'))
+sys.path.insert(0, os.path.abspath("gemgis/"))
+sys.path.insert(0, os.path.abspath("../gemgis/"))
+sys.path.insert(0, os.path.abspath("../../gemgis/"))
# -- General configuration ---------------------------------------------------
@@ -39,14 +37,12 @@
extensions = [
'nbsphinx',
'sphinx_book_theme',
- #'sphinx.ext.autodoc',
+ 'sphinx.ext.autodoc',
'sphinx.ext.napoleon',
'sphinx.ext.doctest',
- #'sphinx.ext.autosummary',
+ 'sphinx.ext.autosummary',
'sphinx_markdown_tables',
- # 'notfound.extension',
'sphinx_copybutton',
- #'sphinx_gallery.gen_gallery',
'sphinx.ext.extlinks',
'sphinx.ext.coverage',
'sphinx.ext.mathjax',
@@ -75,12 +71,10 @@
html_logo = "getting_started/images/Modern1.png"
html_favicon = "https://raw.githubusercontent.com/cgre-aachen/gemgis/main/docs/getting_started/images/favicon.ico"
-#html_theme_options = {
-# "repository_url": "https://github.com/cgre-aachen/gemgis",
-# "use_repository_button": True,
-# "use_issues_button": True,
-# "use_edit_page_button": True,
-#}
+html_theme_options = {
+ "navbar_end": ["navbar-icon-links.html", "search-field.html"],
+
+}
nbsphinx_execute = 'never'
@@ -90,3 +84,5 @@
]
copybutton_prompt_text = ">>> "
+
+#autodoc_mock_imports = ["gemgis"]
diff --git a/docs/getting_started/api.rst b/docs/getting_started/api.rst
new file mode 100644
index 00000000..1daf72d8
--- /dev/null
+++ b/docs/getting_started/api.rst
@@ -0,0 +1,440 @@
+.. _api_ref:
+
+GemGIS API Reference
+=====================
+
+The API reference provides an overview of all functions and methods implemented in GemGIS.
+
+Vector
+______
+
+The following sections provide an overview of the methods implemented in the GemGIS Vector module.
+
+Extracting Coordinates from GeoDataFrames
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are used to extract X and Y coordinates or X, Y, and Z coordinates from GeoDataFrames or Shapely Base Geometries for further usage.
+
+.. autosummary::
+ :toctree: reference/vector_api
+
+ gemgis.vector.extract_xy
+
+ gemgis.vector.extract_xy_linestring
+ gemgis.vector.extract_xy_linestrings
+ gemgis.vector.extract_xy_points
+ gemgis.vector.extract_xyz
+ gemgis.vector.extract_xyz_array
+ gemgis.vector.extract_xyz_rasterio
+ gemgis.vector.extract_xyz_points
+ gemgis.vector.extract_xyz_linestrings
+ gemgis.vector.extract_xyz_polygons
+
+
+Extracting Coordinates and Intersections from GeoDataFrames/Shapely Polygons
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are used to extract coordinates and intersections from GeoDataFrames containing Shapely Polygons
+or from single Shapely Polygons or multiple Shapely Polygons.
+
+
+.. autosummary::
+ :toctree: reference/vector_api
+
+ gemgis.vector.extract_xy_from_polygon_intersections
+ gemgis.vector.intersection_polygon_polygon
+ gemgis.vector.intersections_polygon_polygons
+ gemgis.vector.intersections_polygons_polygons
+
+
+Calculating and extracting coordinates from cross sections
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are used to calculate and extract coordinates from cross sections where data was stored as Shape
+Files and is now loaded as GeoDataFrames.
+
+.. autosummary::
+ :toctree: reference/vector_api
+
+ gemgis.vector.extract_interfaces_coordinates_from_cross_section
+ gemgis.vector.extract_xyz_from_cross_sections
+ gemgis.vector.calculate_coordinates_for_point_on_cross_section
+ gemgis.vector.calculate_coordinates_for_linestring_on_cross_sections
+ gemgis.vector.calculate_coordinates_for_linestrings_on_cross_sections
+ gemgis.vector.extract_interfaces_coordinates_from_cross_section
+
+Calculating and extracting angles from cross sections and maps
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are used to calculate and extract angles from cross sections.
+
+.. autosummary::
+ :toctree: reference/vector_api
+
+ gemgis.vector.calculate_angle
+ gemgis.vector.calculate_azimuth
+ gemgis.vector.calculate_strike_direction_straight_linestring
+ gemgis.vector.calculate_strike_direction_bent_linestring
+ gemgis.vector.calculate_dipping_angle_linestring
+ gemgis.vector.calculate_dipping_angles_linestrings
+ gemgis.vector.calculate_orientation_from_bent_cross_section
+ gemgis.vector.calculate_orientation_from_cross_section
+ gemgis.vector.calculate_orientations_from_cross_section
+ gemgis.vector.extract_orientations_from_cross_sections
+ gemgis.vector.extract_orientations_from_map
+ gemgis.vector.calculate_orientations_from_strike_lines
+ gemgis.vector.calculate_orientation_for_three_point_problem
+
+
+Exploding Geometries
+~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are used to explode geometries for further usage in GemGIS
+
+.. autosummary::
+ :toctree: reference/vector_api
+
+ gemgis.vector.explode_linestring
+ gemgis.vector.explode_linestring_to_elements
+ gemgis.vector.explode_multilinestring
+ gemgis.vector.explode_multilinestrings
+ gemgis.vector.explode_polygon
+ gemgis.vector.explode_polygons
+ gemgis.vector.explode_geometry_collection
+ gemgis.vector.explode_geometry_collections
+
+Removing Points within Buffers
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are used to remove Points within Buffers. This can be used to remove interface points in the
+vicinity of faults.
+
+.. autosummary::
+ :toctree: reference/vector_api
+
+ gemgis.vector.remove_object_within_buffer
+ gemgis.vector.remove_objects_within_buffer
+ gemgis.vector.remove_interfaces_within_fault_buffers
+
+
+Vector Methods for Raster Data
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are used to work with raster data
+
+.. autosummary::
+ :toctree: reference/vector_api
+
+ gemgis.vector.interpolate_raster
+
+
+
+Working with GPX Data
+~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are used to work with GPX data
+
+.. autosummary::
+ :toctree: reference/vector_api
+
+ gemgis.vector.load_gpx
+ gemgis.vector.load_gpx_as_dict
+ gemgis.vector.load_gpx_as_geometry
+
+
+Miscellaneous vector data methods
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are further vector data methods used in GemGIS
+
+.. autosummary::
+ :toctree: reference/vector_api
+
+ gemgis.vector.calculate_distance_linestrings
+ gemgis.vector.calculate_midpoint_linestring
+ gemgis.vector.calculate_midpoints_linestrings
+ gemgis.vector.clip_by_bbox
+ gemgis.vector.clip_by_polygon
+ gemgis.vector.create_bbox
+ gemgis.vector.create_buffer
+ gemgis.vector.create_unified_buffer
+ gemgis.vector.create_linestring_from_points
+ gemgis.vector.create_linestring_from_xyz_points
+ gemgis.vector.create_linestring_gdf
+ gemgis.vector.create_linestrings_from_contours
+ gemgis.vector.create_linestrings_from_xyz_points
+ gemgis.vector.create_polygons_from_faces
+ gemgis.vector.unify_linestrings
+ gemgis.vector.unify_polygons
+
+
+Special Methods
+~~~~~~~~~~~~~~~~
+
+The following methods are special methods used in GemGIS
+
+.. autosummary::
+ :toctree: reference/vector_api
+
+ gemgis.vector.set_dtype
+ gemgis.vector.sort_by_stratigraphy
+ gemgis.vector.subtract_geom_objects
+ gemgis.vector.create_hexagon
+ gemgis.vector.create_hexagon_grid
+ gemgis.vector.create_voronoi_polygons
+
+Raster
+______
+
+The following sections provide an overview of the methods implemented in the GemGIS Raster module.
+
+Raster Calculations
+~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are used to perform calculations on rasters
+
+.. autosummary::
+ :toctree: reference/raster_api
+
+ gemgis.raster.calculate_aspect
+ gemgis.raster.calculate_difference
+ gemgis.raster.calculate_hillshades
+ gemgis.raster.calculate_slope
+
+
+Sampling from a Raster
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are used to sample values from a raster
+
+.. autosummary::
+ :toctree: reference/raster_api
+
+ gemgis.raster.sample_from_array
+ gemgis.raster.sample_from_rasterio
+ gemgis.raster.sample_interfaces
+ gemgis.raster.sample_orientations
+ gemgis.raster.sample_randomly
+
+Reading different raster formats
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are used to read different raster formats into Python
+
+.. autosummary::
+ :toctree: reference/raster_api
+
+ gemgis.raster.read_asc
+ gemgis.raster.read_msh
+ gemgis.raster.read_ts
+ gemgis.raster.read_zmap
+
+Miscellaneous raster data methods
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are further raster data methods used in GemGIS
+
+.. autosummary::
+ :toctree: reference/raster_api
+
+ gemgis.raster.clip_by_bbox
+ gemgis.raster.clip_by_polygon
+ gemgis.raster.create_filepaths
+ gemgis.raster.extract_contour_lines_from_raster
+ gemgis.raster.merge_tiles
+ gemgis.raster.reproject_raster
+ gemgis.raster.resize_by_array
+ gemgis.raster.resize_raster
+ gemgis.raster.save_as_tiff
+
+
+Visualization
+______________
+
+The following sections provide an overview of the methods implemented in the GemGIS Visualization module.
+
+
+Creating PolyData and Grid Data from GeoDataFrames, Rasters, and GemPy Models
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are used to create PolyData from various input data formats.
+
+.. autosummary::
+ :toctree: reference/visualization_api
+
+ gemgis.visualization.create_depth_map
+ gemgis.visualization.create_depth_maps_from_gempy
+ gemgis.visualization.create_thickness_maps
+ gemgis.visualization.create_temperature_map
+ gemgis.visualization.create_delaunay_mesh_from_gdf
+ gemgis.visualization.create_dem_3d
+ gemgis.visualization.create_lines_3d_linestrings
+ gemgis.visualization.create_lines_3d_polydata
+ gemgis.visualization.create_mesh_from_cross_section
+ gemgis.visualization.create_meshes_from_cross_sections
+ gemgis.visualization.create_meshes_hypocenters
+ gemgis.visualization.create_points_3d
+ gemgis.visualization.create_polydata_from_dxf
+ gemgis.visualization.create_polydata_from_msh
+ gemgis.visualization.create_polydata_from_ts
+ gemgis.visualization.create_structured_grid_from_asc
+ gemgis.visualization.create_structured_grid_from_zmap
+
+
+
+Working with Boreholes
+~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are used to work with boreholes in GemGIS.
+
+.. autosummary::
+ :toctree: reference/visualization_api
+
+ gemgis.visualization.add_row_to_boreholes
+ gemgis.visualization.create_borehole_labels
+ gemgis.visualization.create_borehole_tube
+ gemgis.visualization.create_borehole_tubes
+ gemgis.visualization.create_boreholes_3d
+ gemgis.visualization.create_lines_from_points
+ gemgis.visualization.create_deviated_borehole_df
+ gemgis.visualization.create_deviated_boreholes_3d
+ gemgis.visualization.group_borehole_dataframe
+ gemgis.visualization.resample_between_well_deviation_points
+ gemgis.visualization.show_well_log_along_well
+
+Miscellaneous visualization methods
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are further visualization methods used in GemGIS.
+
+.. autosummary::
+ :toctree: reference/visualization_api
+
+ gemgis.visualization.calculate_vector
+ gemgis.visualization.clip_seismic_data
+ gemgis.visualization.convert_to_rgb
+ gemgis.visualization.drape_array_over_dem
+ gemgis.visualization.get_batlow_cmap
+ gemgis.visualization.get_color_lot
+ gemgis.visualization.get_mesh_geological_map
+ gemgis.visualization.get_petrel_cmap
+ gemgis.visualization.get_points_along_spline
+ gemgis.visualization.get_seismic_cmap
+ gemgis.visualization.plane_through_hypocenters
+ gemgis.visualization.plot_data
+ gemgis.visualization.plot_orientations
+ gemgis.visualization.polyline_from_points
+ gemgis.visualization.read_raster
+ gemgis.visualization.seismic_to_array
+ gemgis.visualization.seismic_to_mesh
+
+Utils
+______________
+
+The following sections provide an overview of the methods implemented in the GemGIS Utils module.
+
+Miscellaneous utils methods
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following methods are further visualization methods used in GemGIS.
+
+.. autosummary::
+ :toctree: reference/utils_api
+
+ gemgis.utils.assign_properties
+ gemgis.utils.build_style_dict
+ gemgis.utils.parse_categorized_qml
+ gemgis.utils.load_surface_colors
+ gemgis.utils.create_surface_color_dict
+ gemgis.utils.calculate_lines
+ gemgis.utils.calculate_number_of_isopoints
+ gemgis.utils.convert_location_dict_to_gdf
+ gemgis.utils.convert_to_gempy_df
+ gemgis.utils.convert_to_petrel_points_with_attributes
+ gemgis.utils.create_polygon_from_location
+ gemgis.utils.create_virtual_profile
+ gemgis.utils.create_zmap_grid
+ gemgis.utils.extract_zmap_data
+ gemgis.utils.get_location_coordinate
+ gemgis.utils.get_locations
+ gemgis.utils.get_nearest_neighbor
+ gemgis.utils.getfeatures
+ gemgis.utils.interpolate_strike_lines
+ gemgis.utils.ray_trace_multiple_surfaces
+ gemgis.utils.ray_trace_one_surface
+ gemgis.utils.read_csv_as_gdf
+ gemgis.utils.save_zmap_grid
+ gemgis.utils.set_extent
+ gemgis.utils.set_resolution
+ gemgis.utils.show_number_of_data_points
+ gemgis.utils.to_section_dict
+ gemgis.utils.transform_location_coordinate
+
+Web
+______________
+
+The following sections provide an overview of the methods implemented in the GemGIS Web module.
+
+.. autosummary::
+ :toctree: reference/web_api
+
+ gemgis.web.create_request
+ gemgis.web.load_as_array
+ gemgis.web.load_as_file
+ gemgis.web.load_as_files
+ gemgis.web.load_as_gpd
+ gemgis.web.load_as_map
+ gemgis.web.load_wcs
+ gemgis.web.load_wfs
+ gemgis.web.load_wms
+
+Miscellaneous
+______________
+
+The following sections provide an overview of the methods implemented in the GemGIS Misc module.
+
+.. autosummary::
+ :toctree: reference/misc_api
+
+ gemgis.misc.get_meta_data
+ gemgis.misc.get_meta_data_df
+ gemgis.misc.get_stratigraphic_data
+ gemgis.misc.get_stratigraphic_data_df
+ gemgis.misc.load_formations
+ gemgis.misc.load_pdf
+ gemgis.misc.load_symbols
+
+
+Postprocessing
+______________
+
+The following section provides an overview of the methods implemented in the GemGIS postprocessing module.
+
+.. autosummary::
+ :toctree: reference/postprocessing_api
+
+ gemgis.postprocessing.calculate_dip_and_azimuth_from_mesh
+ gemgis.postprocessing.create_attributes
+ gemgis.postprocessing.create_subelement
+ gemgis.postprocessing.create_symbol
+ gemgis.postprocessing.crop_block_to_topography
+ gemgis.postprocessing.extract_borehole
+ gemgis.postprocessing.extract_lithologies
+ gemgis.postprocessing.extract_orientations_from_mesh
+ gemgis.postprocessing.save_model
+ gemgis.postprocessing.save_qgis_qml_file
+ gemgis.postprocessing.clip_fault_of_gempy_model
+ gemgis.postprocessing.create_plane_from_interface_and_orientation_dfs
+ gemgis.postprocessing.translate_clipping_plane
+
+
+Download GemGIS Data
+_____________________
+
+The following section provides an overview of the methods implemented in the GemGIS module that downloads the tutorial data.
+
+.. autosummary::
+ :toctree: reference/download_gemgis_data_api
+
+ gemgis.download_gemgis_data.create_pooch
+ gemgis.download_gemgis_data.download_tutorial_data
\ No newline at end of file
diff --git a/docs/getting_started/images/tutorial67_cover.png b/docs/getting_started/images/tutorial67_cover.png
new file mode 100644
index 00000000..129652c6
Binary files /dev/null and b/docs/getting_started/images/tutorial67_cover.png differ
diff --git a/docs/getting_started/images/tutorial68_cover.png b/docs/getting_started/images/tutorial68_cover.png
new file mode 100644
index 00000000..d227d17e
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diff --git a/docs/getting_started/index.rst b/docs/getting_started/index.rst
index ba3af77e..12c0955e 100644
--- a/docs/getting_started/index.rst
+++ b/docs/getting_started/index.rst
@@ -18,3 +18,6 @@ Index
whatiswhat/index
tutorial/index
example/index
+
+ api
+ reference/index
diff --git a/docs/getting_started/tutorial/12_visualizing_cross_sections_in_pyvista.ipynb b/docs/getting_started/tutorial/12_visualizing_cross_sections_in_pyvista.ipynb
index b19e82f2..220d71cf 100644
--- a/docs/getting_started/tutorial/12_visualizing_cross_sections_in_pyvista.ipynb
+++ b/docs/getting_started/tutorial/12_visualizing_cross_sections_in_pyvista.ipynb
@@ -706,7 +706,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.10.0"
+ "version": "3.8.5"
},
"varInspector": {
"cols": {
diff --git a/docs/getting_started/tutorial/38_interactive_plotting_with_bokeh_in gemgis.ipynb b/docs/getting_started/tutorial/38_interactive_plotting_with_bokeh_in gemgis.ipynb
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--- a/docs/getting_started/tutorial/38_interactive_plotting_with_bokeh_in gemgis.ipynb
+++ /dev/null
@@ -1,1980 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# 38 Interactive plotting with Bokeh in GemGIS\n",
- "\n",
- "The ``bokeh`` package allows it to create interactive plots of the available geo data. \n"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Set File Paths and download Tutorial Data\n",
- "\n",
- "If you downloaded the latest `GemGIS` version from the Github repository, append the path so that the package can be imported successfully. Otherwise, it is recommended to install `GemGIS` via `pip install gemgis` and import `GemGIS` using `import gemgis as gg`. In addition, the file path to the folder where the data is being stored is set. The tutorial data is downloaded using Pooch (https://www.fatiando.org/pooch/latest/index.html) and stored in the specified folder. Use `pip install pooch` if Pooch is not installed on your system yet."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 1,
- "metadata": {
- "ExecuteTime": {
- "end_time": "2021-03-17T12:01:03.074704Z",
- "start_time": "2021-03-17T12:01:00.812181Z"
- }
- },
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "WARNING (theano.configdefaults): g++ not available, if using conda: `conda install m2w64-toolchain`\n",
- "C:\\Users\\ale93371\\Anaconda3\\envs\\test_gempy\\lib\\site-packages\\theano\\configdefaults.py:560: UserWarning: DeprecationWarning: there is no c++ compiler.This is deprecated and with Theano 0.11 a c++ compiler will be mandatory\n",
- " warnings.warn(\"DeprecationWarning: there is no c++ compiler.\"\n",
- "WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.\n",
- "WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.\n"
- ]
- }
- ],
- "source": [
- "import gemgis as gg\n",
- "\n",
- "file_path ='../../../../gemgis_data/data/38_interactive_plotting_with_bokeh_in gemgis/'"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 3,
- "metadata": {
- "ExecuteTime": {
- "end_time": "2021-03-17T12:01:32.205446Z",
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- },
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "Downloading file '38_interactive_plotting_with_bokeh_in gemgis.zip' from 'https://rwth-aachen.sciebo.de/s/AfXRsZywYDbUF34/download?path=%2F38_interactive_plotting_with_bokeh_in gemgis.zip' to 'C:\\Users\\ale93371\\Documents\\gemgis_data\\data\\38_interactive_plotting_with_bokeh_in gemgis'.\n"
- ]
- }
- ],
- "source": [
- "gg.download_gemgis_data.download_tutorial_data(filename=\"38_interactive_plotting_with_bokeh_in gemgis.zip\", dirpath=file_path)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Loading Libraries"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 2,
- "metadata": {
- "ExecuteTime": {
- "end_time": "2020-12-26T22:13:10.845566Z",
- "start_time": "2020-12-26T22:13:05.319280Z"
- }
- },
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "WARNING (theano.configdefaults): g++ not available, if using conda: `conda install m2w64-toolchain`\n",
- "C:\\Users\\ale93371\\Anaconda3\\envs\\test_gempy\\lib\\site-packages\\theano\\configdefaults.py:560: UserWarning: DeprecationWarning: there is no c++ compiler.This is deprecated and with Theano 0.11 a c++ compiler will be mandatory\n",
- " warnings.warn(\"DeprecationWarning: there is no c++ compiler.\"\n",
- "WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.\n",
- "WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.\n"
- ]
- }
- ],
- "source": [
- "import geopandas as gpd\n",
- "import rasterio"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Importing Bokeh \n",
- "\n",
- "Bokeh is being imported and the output of the plots is set to be in the notebooks."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 3,
- "metadata": {
- "ExecuteTime": {
- "end_time": "2020-12-26T22:13:11.574415Z",
- "start_time": "2020-12-26T22:13:10.848563Z"
- }
- },
- "outputs": [
- {
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Loading BokehJS ...\n",
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\\n\"+\n",
- " \"
\\n\"+\n",
- " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
- " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
- " \"
\\n\"+\n",
- " \"
\\n\"+\n",
- " \"- re-rerun `output_notebook()` to attempt to load from CDN again, or
\\n\"+\n",
- " \"- use INLINE resources instead, as so:
\\n\"+\n",
- " \"
\\n\"+\n",
- " \"
\\n\"+\n",
- " \"from bokeh.resources import INLINE\\n\"+\n",
- " \"output_notebook(resources=INLINE)\\n\"+\n",
- " \"\\n\"+\n",
- " \"
\\n\"+\n \"
\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"
\\n\"+\n \"
\\n\"+\n \"- re-rerun `output_notebook()` to attempt to load from CDN again, or
\\n\"+\n \"- use INLINE resources instead, as so:
\\n\"+\n \"
\\n\"+\n \"
\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
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