From 1c52aa44eb737066b064cfcf478e15d85d858728 Mon Sep 17 00:00:00 2001
From: Michael Catanzaro <catanzaromj@pm.me>
Date: Sat, 6 Jul 2024 08:19:35 -0400
Subject: [PATCH] Switch python-igraph to igraph (#260)

---
 README.md            | 22 +++++++++++-----------
 kmapper/plotlyviz.py |  6 ++----
 setup.py             |  4 ++--
 3 files changed, 15 insertions(+), 17 deletions(-)

diff --git a/README.md b/README.md
index ee466b50..65922f68 100644
--- a/README.md
+++ b/README.md
@@ -9,34 +9,32 @@
 
 > Nature uses as little as possible of anything. - Johannes Kepler
 
-This is a Python implementation of the TDA Mapper algorithm  for visualization of high-dimensional data. For complete documentation, see [https://kepler-mapper.scikit-tda.org](https://kepler-mapper.scikit-tda.org).
+This is a Python implementation of the TDA Mapper algorithm for visualization of high-dimensional data. For complete documentation, see [https://kepler-mapper.scikit-tda.org](https://kepler-mapper.scikit-tda.org).
 
 KeplerMapper employs approaches based on the Mapper algorithm (Singh et al.) as first described in the paper "Topological Methods for the Analysis of High Dimensional Data Sets and 3D Object Recognition".
 
 KeplerMapper can make use of Scikit-Learn API compatible cluster and scaling algorithms.
 
-
 ## Install
 
 ### Dependencies
 
 KeplerMapper requires:
 
-  - Python (>= 3.6)
-  - NumPy
-  - Scikit-learn
+- Python (>= 3.6)
+- NumPy
+- Scikit-learn
 
 Using the plotly visualizations requires a few extra libraries:
 
-  - Python-Igraph
-  - Plotly
-  - Ipywidgets
+- igraph
+- Plotly
+- Ipywidgets
 
 Additionally, running some of the examples requires:
 
-  - matplotlib
-  - umap-learn
-
+- matplotlib
+- umap-learn
 
 ### Installation
 
@@ -47,6 +45,7 @@ pip install kmapper
 ```
 
 To install from source:
+
 ```
 git clone https://github.com/MLWave/kepler-mapper
 cd kepler-mapper
@@ -58,6 +57,7 @@ pip install -e .
 KeplerMapper adopts the scikit-learn API as much as possible, so it should feel very familiar to anyone who has used these libraries.
 
 ### Python code
+
 ```python
 # Import the class
 import kmapper as km
diff --git a/kmapper/plotlyviz.py b/kmapper/plotlyviz.py
index 46531a32..6add0f0a 100644
--- a/kmapper/plotlyviz.py
+++ b/kmapper/plotlyviz.py
@@ -24,9 +24,9 @@
     import plotly.io as pio
 except ImportError:
     print(
-        """To use the plotly visualization tools, you must have the packages python-igraph, plotly, and ipywidgets installed in your environment."""
+        """To use the plotly visualization tools, you must have the packages igraph, plotly, and ipywidgets installed in your environment."""
         """ It looks like at least one of these is missing.  Please install again with"""
-        """\n\n\t`pip install python-igraph plotly ipywidgets`\n\nand try again"""
+        """\n\n\t`pip install igraph plotly ipywidgets`\n\nand try again"""
     )
     raise
 
@@ -226,7 +226,6 @@ def scomplex_to_graph(
     colorscale,
     node_color_function="mean",
 ):
-
     color_values = np.array(color_values)
 
     json_dict = {"nodes": [], "links": []}
@@ -712,7 +711,6 @@ def _get_plotly_data(E, coords):
 
 
 def _text_mapper_summary(mapper_summary):
-
     d = mapper_summary["custom_meta"]
     text = "<br><b>Projection: </b>" + d["projection"]
     text += (
diff --git a/setup.py b/setup.py
index 423a7de7..0d57a2ed 100644
--- a/setup.py
+++ b/setup.py
@@ -33,7 +33,7 @@
             "pytest",  # ~=6.2.5",
             "networkx",  # ~=2.5.1",
             "matplotlib",  # ~=3.3.4",
-            "python-igraph",  # ~=0.9.6",
+            "igraph",
             "plotly",  # ~=5.3.1",
             "ipywidgets",  # ~=7.6.5",
         ],
@@ -45,7 +45,7 @@
             # for building docs for plotlyviz stuff
             "networkx",  # ~=2.5.1",
             "matplotlib",  # ~=3.3.4",
-            "python-igraph",  # ~=0.9.6",
+            "igraph",
             "plotly",  # ~=5.3.1",
             "ipykernel",
             "ipywidgets",  # ~=7.6.5",