GemGIS 1.2 and PyOpenSci Submission - Issue Tracker

README.md

@@ -1,6 +1,7 @@
+# GemGIS - Spatial data and information processing for geomodeling and subsurface data
+
 <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 and subsurface data
 
 
 [![PyPI](https://img.shields.io/badge/python-3-blue.svg)](https://www.python.org/downloads/)
@@ -40,9 +41,9 @@ Furthermore, many [example models](https://gemgis.readthedocs.io/en/latest/getti
 
 <a name="installation"></a>
 ## Installation
-It is recommended to use GemGIS with **python">=3.10"** in a separated environment. The main packages and its dependencies can be installed via the conda-forge channel. GemGIS is then available through PyPi or Conda. 
-1) `conda install -c conda-forge geopandas">=0.13.2" rasterio">=1.3.8"`
-2) `conda install -c conda-forge pyvista">=0.42.1"`
+It is recommended to use GemGIS with **python">=3.11"** in a separated environment. The main packages and its dependencies can be installed via the conda-forge channel. GemGIS is then available through PyPi or Conda. 
+1) `conda install -c conda-forge geopandas">=1.0.1" rasterio">=1.4.3"`
+2) `conda install -c conda-forge pyvista">=0.44.2"`
 3) `pip install gemgis` / `conda install -c conda-forge gemgis`
 
 Check out the [Installation Page](https://gemgis.readthedocs.io/en/latest/getting_started/installation.html) for more detailed instructions. 
@@ -55,13 +56,35 @@ The Contribution Guidelines for GemGIS can be found here: [Contribution Guidelin
 We welcome issue reports, questions, ideas for new features and pull-requests to fix issues or even add new features to the software. Once a pull-request is opened, we will guide through the review process. 
 
 
+<a name="citation"></a>
+## Citation
+
+If you use GemGIS for any published work, please cite it using the reference below:
+
+Jüstel, A., Endlein Correira, A., Pischke, M., de la Varga, M., Wellmann, F.: GemGIS - Spatial Data Processing for Geomodeling. Journal of Open Source Software, 7(73), 3709, https://doi.org/10.21105/joss.03709, 2022.
+
+```
+@article{Jüstel2022, 
+doi = {10.21105/joss.03709}, 
+url = {https://doi.org/10.21105/joss.03709}, 
+year = {2022}, 
+publisher = {The Open Journal}, 
+volume = {7}, 
+number = {73}, 
+pages = {3709}, 
+author = {Alexander Jüstel and Arthur Endlein Correira and Marius Pischke and Miguel de la Varga and Florian Wellmann}, 
+title = {GemGIS - Spatial Data Processing for Geomodeling}, 
+journal = {Journal of Open Source Software}
+}
+```
+
 <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
-* Powell, D.: Interpretation of Geological Structures Through Maps: An Introductory Practical Manual, Longman, pp. 192, 1992
-* Bennison, G.M.: An Introduction to Geological Structures and Maps, Hodder Education Publication, pp. 78, 1990
+* Jüstel, A. et al.: 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, 2023.
+* Jüstel, A. et al.: GemGIS - Spatial Data Processing for Geomodeling. Journal of Open Source Software, 7(73), 3709, https://doi.org/10.21105/joss.03709, 2022.
+* 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.
+* Powell, D.: Interpretation of Geological Structures Through Maps: An Introductory Practical Manual, Longman, pp. 192, 1992.
+* Bennison, G.M.: An Introduction to Geological Structures and Maps, Hodder Education Publication, pp. 78, 1990.

docs/getting_started/api.rst

@@ -42,9 +42,9 @@ or from single Shapely Polygons or multiple Shapely Polygons.
    :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
+   gemgis.vector.intersect_polygon_polygon
+   gemgis.vector.intersect_polygon_polygons
+   gemgis.vector.intersect_polygons_polygons
 
 
 Calculating and extracting coordinates from cross sections

environment.yml

@@ -1,13 +1,19 @@
-# Requirements as of October 2023
+# Requirements as of December 2024
 name: gemgis_env
 channels:
   - conda-forge
 dependencies: 
-  - python>=3.10
-  # geopandas will also install numpy, pandas, shapely, fiona, and pyproj
-  - geopandas>=0.14.0
+  - python>=3.11
+  # geopandas will also install numpy, pandas, shapely, pyogrio, and pyproj
+  - geopandas>=1.0.1
+  - shapely>=2.0.6
+  - pandas>=2.2.3
+  - numpy>=2.1.3
+  - affine>=2.4.0
+  - pyproj>=3.7.0
   # rasterio will also install affine
-  - rasterio>=1.3.8
+  - rasterio>=1.4.3
   # pyvista also install pooch and matplotlib
-  - pyvista>=0.42.2
+  - pyvista>=0.44.2
+  - matplotlib>=3.9.3
   - gemgis>=1.1

environment_dev.yml

@@ -2,13 +2,19 @@ name: gemgis_dev_env
 channels:
   - conda-forge
 dependencies:
-  - python>=3.10
-  # geopandas will also install numpy, pandas, shapely, fiona, and pyproj
-  - geopandas>=0.14.0
+  - python>=3.11
+  # geopandas will also install numpy, pandas, shapely, pyogrio, and pyproj
+  - geopandas>=1.0.1
+  - shapely>=2.0.6
+  - pandas>=2.2.3
+  - numpy>=2.1.3
+  - affine>=2.4.0
+  - pyproj>=3.7.0
   # rasterio will also install affine
-  #- rasterio>=1.3.8 will be installed through rioxarray
+  - rasterio>=1.4.3
   # pyvista also install pooch and matplotlib
-  #- pyvista>=0.42.2 will be installed through pvgeo
+  - pyvista>=0.44.2
+  - matplotlib>=3.9.3
   - gemgis>=1.1
   - rioxarray
   - scipy

gemgis/download_gemgis_data.py

@@ -23,11 +23,8 @@
 import zipfile
 
 
-def create_pooch(storage_url: str,
-                 files: List[str],
-                 target: str):
-    """
-    Create pooch class to fetch files from a website.
+def create_pooch(storage_url: str, files: List[str], target: str):
+    """Create pooch class to fetch files from a website.
 
     Parameters
     __________
@@ -46,58 +43,62 @@ def create_pooch(storage_url: str,
     See also
     ________
         download_tutorial_data: Download the GemGIS data for each tutorial.
+
     """
     try:
         import pooch
     except ModuleNotFoundError:
         raise ModuleNotFoundError(
-            'Pooch package is not installed. Use pip install pooch to install the latest version')
+            "Pooch package is not installed. Use pip install pooch to install the latest version"
+        )
 
     # Create new pooch
-    pc = pooch.create(base_url=storage_url,
-                      path=target,
-                      registry={i: None for i in files})
+    pc = pooch.create(
+        base_url=storage_url, path=target, registry={i: None for i in files}
+    )
 
     return pc
 
 
-def download_tutorial_data(filename: str,
-                           dirpath: str = '',
-                           storage_url: str = 'https://rwth-aachen.sciebo.de/s/AfXRsZywYDbUF34/download?path=%2F'):
-    """
-    Download the GemGIS data for each tutorial.
+def download_tutorial_data(
+    filename: str,
+    dirpath: str = "",
+    storage_url: str = "https://rwth-aachen.sciebo.de/s/AfXRsZywYDbUF34/download?path=%2F",
+):
+    """Download the GemGIS data for each tutorial.
 
     Parameters
     __________
         filename : str
             File name to be downloaded by pooch, e.g. ``filename='file.zip'``.
+
         dirpath : str, default: ``''``
             Path to the directory where the data is being stored, default to the directory where the notebook is
             located, e.g. ``dirpath='Documents/gemgis/'``.
+
         storage_url : str, default 'https://rwth-aachen.sciebo.de/s/AfXRsZywYDbUF34/download?path=%2F'
             URL to the GemGIS data storage, default is the RWTH Aachen University Sciebo Cloud Storage.
 
     See also
     ________
         create_pooch : Create pooch class to fetch files from a website.
+
     """
     try:
-        import pooch
         from pooch import HTTPDownloader
+
         download = HTTPDownloader(progressbar=False)
     except ModuleNotFoundError:
         raise ModuleNotFoundError(
-            'Pooch package is not installed. Use pip install pooch to install the latest version')
+            "Pooch package is not installed. Use pip install pooch to install the latest version"
+        )
 
     # Creating pooch object
-    pooch_data = create_pooch(storage_url=storage_url,
-                              files=[filename],
-                              target=dirpath)
+    pooch_data = create_pooch(storage_url=storage_url, files=[filename], target=dirpath)
 
     # Downloading data to the defined folder
-    pooch_data.fetch(fname=filename,
-                     downloader=download)
+    pooch_data.fetch(fname=filename, downloader=download)
 
     # Opening zip file and unzip in specified directory
-    with zipfile.ZipFile(dirpath + filename, 'r') as zip_ref:
+    with zipfile.ZipFile(dirpath + filename, "r") as zip_ref:
         zip_ref.extractall(dirpath)