Reformat remaining documentation and setup

Author: ragibson

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
 
     steps:
       - uses: actions/checkout@v3

README.md

@@ -17,6 +17,7 @@ https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-022-20142-6/Media
 ).
 
 ## Installation
+
 This project is on [PyPI](https://pypi.org/project/modularitypruning/) and can
 be installed with
 
@@ -31,6 +32,7 @@ Alternatively, you can install it from this repository directly:
     python3 setup.py install
 
 <a name = "Basic Usage"></a>
+
 ## Basic Usage
 
 This package interfaces directly with python-igraph. A simple example of its

figure_generation_runtimes.md

@@ -2,24 +2,24 @@
 
 On a machine with
 
- - CPU: i7-9700K (8 cores, stock, up to 4.9 GHz)
- - RAM: 16 GB DDR4 3200 MHz
+- CPU: i7-9700K (8 cores, stock, up to 4.9 GHz)
+- RAM: 16 GB DDR4 3200 MHz
 
 the figure generation runtimes that exceed ~5 seconds are as follows.
 
-| Figures | Runtime | Saves Progress/Results? |
-|---------|---------|-----------------|
-| [karate_club_gamma_estimates](experiments/karate_club_gamma_estimates/karate_club_gamma_estimates.py) | ~50 s | No
-| [karate_club_estimates_per_community](experiments/karate_club_gamma_estimates/karate_club_estimates_per_community.py) | ~40 s | No
-| [plot_champ_example](experiments/example_figures/plot_champ_example.py) | ~10 s | No
-| [modularity_nonmonotonic_K](experiments/modularity_nonmonotonic_K/modularity_nonmonotonic_K.py) | ~1 m | No
-| [karate_club_test](experiments/karate_club_test/karate_club_test.py) | ~5 m | No
-| [plot_gamma_max_derivatives](experiments/plot_duality_details/plot_gamma_max_derivatives.py) | ~5 m | No
-| [easy_regime_generation](experiments/pamfil_synthetic_networks/easy_regime_generation.py) | ~55 m | Yes
-| [hard_regime_generation](experiments/pamfil_synthetic_networks/hard_regime_generation.py) | ~60 m | Yes
-| [lazega_figures](experiments/lazega_law_firm/lazega_figures.py) | ~25 m | Yes
-| [SNAP_boxplot](experiments/social_networks/SNAP_boxplot.py) | ~55 m | Yes
-| [bistable_SBM_test_constant_probs](experiments/bistable_SBM/bistable_SBM_test_constant_probs.py) | ~2 d | Yes
-| [lfr_benchmark_test](experiments/lfr_benchmark_test/lfr_benchmark_test.py) | ~3.0 h | Yes
-| [hierarchical_SBM_test](experiments/hierarchical_SBM_test/hierarchical_SBM_test.py) | ~1.5 h | Yes
-| [runtime_comparison_with_louvain](experiments/miscellaneous_tests/runetime_comparison_with_louvain.py) | ~25 m | Yes
+| Figures                                                                                                               | Runtime | Saves Progress/Results? |
+|-----------------------------------------------------------------------------------------------------------------------|---------|-------------------------|
+| [karate_club_gamma_estimates](experiments/karate_club_gamma_estimates/karate_club_gamma_estimates.py)                 | ~50 s   | No                      |
+| [karate_club_estimates_per_community](experiments/karate_club_gamma_estimates/karate_club_estimates_per_community.py) | ~40 s   | No                      |
+| [plot_champ_example](experiments/example_figures/plot_champ_example.py)                                               | ~10 s   | No                      |
+| [modularity_nonmonotonic_K](experiments/modularity_nonmonotonic_K/modularity_nonmonotonic_K.py)                       | ~1 m    | No                      |
+| [karate_club_test](experiments/karate_club_test/karate_club_test.py)                                                  | ~5 m    | No                      |
+| [plot_gamma_max_derivatives](experiments/plot_duality_details/plot_gamma_max_derivatives.py)                          | ~5 m    | No                      |
+| [easy_regime_generation](experiments/pamfil_synthetic_networks/easy_regime_generation.py)                             | ~55 m   | Yes                     |
+| [hard_regime_generation](experiments/pamfil_synthetic_networks/hard_regime_generation.py)                             | ~60 m   | Yes                     |
+| [lazega_figures](experiments/lazega_law_firm/lazega_figures.py)                                                       | ~25 m   | Yes                     |
+| [SNAP_boxplot](experiments/social_networks/SNAP_boxplot.py)                                                           | ~55 m   | Yes                     |
+| [bistable_SBM_test_constant_probs](experiments/bistable_SBM/bistable_SBM_test_constant_probs.py)                      | ~2 d    | Yes                     |
+| [lfr_benchmark_test](experiments/lfr_benchmark_test/lfr_benchmark_test.py)                                            | ~3.0 h  | Yes                     |
+| [hierarchical_SBM_test](experiments/hierarchical_SBM_test/hierarchical_SBM_test.py)                                   | ~1.5 h  | Yes                     |
+| [runtime_comparison_with_louvain](experiments/miscellaneous_tests/runetime_comparison_with_louvain.py)                | ~25 m   | Yes                     |

setup.py

@@ -1,6 +1,7 @@
-from setuptools import setup
 import os
 
+from setuptools import setup
+
 here = os.path.abspath(os.path.dirname(__file__))
 
 # Get the long description from the README file