Merge pull request #70 from ai4er-cdt/feature/misc-issues

Misc Issues PR

Author: herbiebradley

PYPI_README.md

@@ -1,24 +1,41 @@
 <p align="center">
-<img src="https://raw.githubusercontent.com/ai4er-cdt/gtc-biodiversity/main/docs/images/geograph_logo.png" alt="GeoGraph" width="300px">
+<img src="https://raw.githubusercontent.com/ai4er-cdt/geograph/main/docs/images/geograph_logo.png" alt="GeoGraph" width="300px">
 </p>
 
-_Created as part of the AI4ER Group Team Challenge 2021 by the Biodiversity Team._
-
-
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ai4er-cdt/gtc-biodiversity/main?urlpath=lab%2Ftree%2Fnotebooks)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ai4er-cdt/geograph/main?urlpath=lab%2Ftree%2Fnotebooks)
 [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 <a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
 [![Documentation Status](https://readthedocs.org/projects/geograph/badge/?version=latest)](https://geograph.readthedocs.io/en/latest/?badge=latest)
 
-See the [Github repository](https://github.com/ai4er-cdt/gtc-biodiversity) for full details.
 
-## 1. Features
+__Table of contents:__
+1. Description
+2. Installation
+3. Requirements
+4. Documentation
+
+## 1. Description
+
+GeoGraph provides a tool for analysing habitat fragmentation and related problems in landscape ecology. GeoGraph builds a geospatially referenced graph from land cover or field survey data and enables graph-based landscape ecology analysis as well as interactive visualizations. Beyond the graph-based features, GeoGraph also enables the computation of common landscape metrics.
+
+## 2. Installation
+
+GeoGraph is available via pip, so you can install it using
+
+```
+pip install geograph
+```
+
+Done, you're ready to go!
+
+You can also visit the [Github repository](https://github.com/ai4er-cdt/geograph).
+
+See the [documentation](https://geograph.readthedocs.io/) for a full getting started guide or check out the [binder](https://mybinder.org/v2/gh/ai4er-cdt/geograph/main?urlpath=lab%2Ftree%2Fnotebooks) for tutorials on how to get started .
 
-GeoGraph provides a full-stack tool for analysing habitat fragmentation, and other related problems. It includes models to predict land cover classes, a method to extract graph structure from the resulting land cover maps and an extensive range of visualisation and analysis tools.
+## 3. Requirements
 
-## 2. Requirements
+GeoGraph is written in Python 3.8 and builds on [NetworkX](https://github.com/NetworkX/NetworkX), [ipyleaflet](https://github.com/jupyter-widgets/ipyleaflet), [geopandas](https://geopandas.org/), [rasterio](https://rasterio.readthedocs.io/en/latest/) and many more packages. See the [requirements directory](./requirements) for a full list of dependencies.
 
-GeoGraph is written in Python 3.8 and builds on [NetworkX](https://github.com/NetworkX/NetworkX), [ipyleaflet](https://github.com/jupyter-widgets/ipyleaflet) and many more packages. See the [requirements directory](https://github.com/ai4er-cdt/gtc-biodiversity/tree/main/requirements) for a full list of dependencies.
-## 3. Documentation
+## 4. Documentation
 
 Our documentation is available at [geograph.readthedocs.io](https://geograph.readthedocs.io/).

README.md

@@ -3,10 +3,11 @@
 </p>
 
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ai4er-cdt/gtc-biodiversity/main?urlpath=lab%2Ftree%2Fnotebooks)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ai4er-cdt/geograph/main?urlpath=lab%2Ftree%2Fnotebooks)
 [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 <a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
 [![Documentation Status](https://readthedocs.org/projects/geograph/badge/?version=latest)](https://geograph.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/geograph.svg)](https://badge.fury.io/py/geograph)
 
 ![GeoGraphViewer demo gif](docs/images/viewer_demo.gif)
 
@@ -39,4 +40,4 @@ GeoGraph is written in Python 3.8 and builds on [NetworkX](https://github.com/Ne
 
 ## 4. Documentation
 
-Our documentation is available at [geograph.readthedocs.io](https://geograph.readthedocs.io/).
+Our documentation is available at [geograph.readthedocs.io](https://geograph.readthedocs.io/).

geograph/binary_graph_operations.py

@@ -15,7 +15,7 @@
 
 
 class NodeMap:
-    """Class to store node mappings between two graphs (the src_graph and trg_graph)"""
+    """Class to store node mappings between two graphs (the src_graph and trg_graph)."""
 
     def __init__(
         self,
@@ -24,7 +24,7 @@ def __init__(
         mapping: Dict[int, List[int]],
     ) -> None:
         """
-        Class to store node mappings between two graphs (`trg_graph` and `src_graph`)
+        Class to store node mappings between two graphs (`trg_graph` and `src_graph`).
 
         This class stores a dictionary of node one-to-many relationships of nodes from
         `src_graph` to `trg_graph`. It also provides support for convenient methods for
@@ -45,36 +45,36 @@ def __init__(
 
     @property
     def src_graph(self) -> geograph.GeoGraph:
-        """Keys in the mapping dict correspond to node indices in the `src_graph`"""
+        """Keys in the mapping dict correspond to node indices in the `src_graph`."""
         return self._src_graph
 
     @property
     def trg_graph(self) -> geograph.GeoGraph:
-        """Values in the mapping dict correspond to node indices in the `trg_graph`"""
+        """Values in the mapping dict correspond to node indices in the `trg_graph`."""
         return self._trg_graph
 
     @property
     def mapping(self) -> Dict[int, List[int]]:
-        """
-        Look-up table connecting node indices from `src_graph` to those of `trg_graph`.
-        """
+        """Look-up table connecting node indices from `src_graph` to `trg_graph`."""
         return self._mapping
 
     def __invert__(self) -> NodeMap:
-        """Compute the inverse NodeMap"""
+        """Compute the inverse NodeMap."""
         return self.invert()
 
-    def __eq__(self, other: NodeMap) -> bool:
-        """Check two NodeMaps for equality"""
+    def __eq__(self, other: object) -> bool:
+        """Check two NodeMaps for equality."""
+        if not isinstance(other, NodeMap):
+            return False
         return (
             self.src_graph == other.src_graph
             and self.trg_graph == other.trg_graph
             and self.mapping == other.mapping
         )
 
     def invert(self) -> NodeMap:
-        """Compute the inverse NodeMap from `trg_graph` to `src_graph`"""
-        inverted_mapping = {index: [] for index in self.trg_graph.df.index}
+        """Compute the inverse NodeMap from `trg_graph` to `src_graph`."""
+        inverted_mapping: Dict = {index: [] for index in self.trg_graph.df.index}
 
         for src_node in self.src_graph.df.index:
             for trg_node in self.mapping[src_node]:
@@ -117,7 +117,7 @@ def identify_graphs(
     graph1: geograph.GeoGraph, graph2: geograph.GeoGraph, mode: str
 ) -> NodeMap:
     """
-    Idenitfy all nodes from `graph1` with nodes from `graph2` based on the given `mode`
+    Idenitfy all nodes from `graph1` with nodes from `graph2` based on the given `mode`.
 
     Args:
         graph1 (GeoGraph): The GeoGraph whose node indicies will form the domain
@@ -143,8 +143,7 @@ def identify_graphs(
 
 def graph_polygon_diff(node_map: NodeMap) -> Tuple[gpd.GeoDataFrame, gpd.GeoDataFrame]:
     """
-    Return the (multi)polygon areas that were added/removed when going
-    from `src_graph` to `trg_graph`.
+    Return the polygons that were added/removed going from `src_graph` to `trg_graph`.
 
     Args:
         node_map (NodeMap): The node map from `src_graph` to `trg_graph`
@@ -193,7 +192,6 @@ def node_polygon_diff(
         Tuple[BaseGeometry, BaseGeometry]: Added part and removed part as shapely
             BaseGeometry objects.
     """
-
     src_polygon: Polygon = node_map.src_graph.df.geometry.loc[src_node_id]
     trg_node_ids: List[int] = node_map.mapping[src_node_id]
 

geograph/constants.py

@@ -1,8 +1,4 @@
-"""
-This file is used to save all project wide constants such as the path of the
-source folder, the project path, etc.
-"""
-
+"""All project wide constants are saved in this module."""
 # Place all your constants here
 import os
 import pathlib