Merge pull request #286 from cgre-aachen/dev_gemgis3

GemGIS Pre-Release 1.0.12 and 1.1

Author: AlexanderJuestel

.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

README.md

@@ -1,6 +1,6 @@
 <p align="center"><img src="https://raw.githubusercontent.com/cgre-aachen/gemgis/main/docs/getting_started/images/Modern1.png" width="600">
 
-> Spatial data and information processing for geomodeling
+> Spatial data and information processing for geomodeling and subsurface data
 
 
 [![PyPI](https://img.shields.io/badge/python-3-blue.svg)](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.
 
 <p align="center"><img src="https://raw.githubusercontent.com/cgre-aachen/gemgis/main/joss/images/fig1.png" width="800">
 
@@ -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).
 <a name="contributing"></a>
 ## 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
 <a name="ref"></a>
 ## 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

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"]