clean up

junipertcy · Nov 22, 2023 · 7768557 · 7768557
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diff --git a/COPYING.LESSER b/COPYING.LESSER
diff --git a/COPYING → LICENSE b/COPYING → LICENSE
diff --git a/README.md b/README.md
@@ -1,9 +1,9 @@
-# Regularized-SpringRank
+# rSpringRank
 
-[![license](https://img.shields.io/badge/license-LGPL-green.svg?style=flat)](https://github.com/junipertcy/Regularized-SpringRank/blob/main/COPYING)
+[![license](https://img.shields.io/badge/license-LGPL-green.svg?style=flat)](https://github.com/junipertcy/rSpringRank/blob/main/LICENSE)
 
 
-**Regularized_SpringRank** implements a collection of regularized, convex models (+solvers) that allow the inference of hierarchical structure in a directed network, which exists due to dominance, social status, or prestige. Specifically, this work leverages the time-varying structure and/or the node metadata present in the data set.
+**rSpringRank** implements a collection of regularized, convex models (+solvers) that allow the inference of hierarchical structure in a directed network, which exists due to dominance, social status, or prestige. Specifically, this work leverages the time-varying structure and/or the node metadata present in the data set.
 
 This is the software repository behind the paper:
 * Tzu-Chi Yen and Stephen Becker, *Regularized methods for efficient ranking in networks*, in preparation.
@@ -14,15 +14,21 @@ This is the software repository behind the paper:
 * For software-related bugs, issues, or suggestions, please use [Issues](https://).
 
 
-First steps
------------
-`Regularized-SpringRank` _will be_ on PyPI. To start, hit this command on the shell:
 
-```sh
-$ pip install regularized-springrank
+Installation
+------------
+**rSpringRank** is available on PyPi:
+```
+pip install rSpringRank
 ```
 
-In your Python console, `Regularized-SpringRank` is invoked using:
+The dependencies needed to use graph-tool-based input are not installed by default. You will need to install:
+* Graph-tool: https://graph-tool.skewed.de/
+
+
+First steps
+-----------
+In your Python console, `rSpringRank` is invoked using:
 
 ```python
 >>> from reg_sr import rSpringRank, PhDExchange
@@ -59,3 +65,8 @@ TODO.
 Acknowledgement
 ---------------
 TODO.
+
+
+License
+-------
+**rSpringRank** is open-source and licensed under the [GNU Lesser General Public License v3.0](https://www.gnu.org/licenses/lgpl-3.0.en.html).
diff --git a/pyproject.toml b/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "rSpringRank"
 authors = [{ name = "Tzu-Chi Yen", email = "tzuchi.yen@colorado.edu" }]
 description = "Regularized methods for efficient ranking in networks"
-requires-python = ">=3.10"
+requires-python = ">=3.9"
 keywords = [
     'network-analysis',
     'convex-optimization',
@@ -23,6 +23,7 @@ classifiers = [
     'Operating System :: POSIX',
     'Operating System :: Unix',
     'Operating System :: MacOS',
+    'Programming Language :: Python :: 3.9',
     'Programming Language :: Python :: 3.10',
     'Programming Language :: Python :: 3.11',
     'Programming Language :: Python :: 3.12',
@@ -33,7 +34,15 @@ classifiers = [
 
 dynamic = ["version"]
 
-dependencies = ["networkx==2.8.8"]
+dependencies = [
+    "networkx==2.8.8",
+    "scipy==1.11.4",
+    "cvxpy==1.4.1",
+    "matplotlib==3.8.2",
+    "numba==0.58.1",
+    "bson==0.5.10",
+    "pymongo==4.6.0"
+]
 
 [project.optional-dependencies]
 dev = ["pytest==7.4.3", "click==8.1.7", "sphinx==7.2.6"]

diff --git a/reg_sr/__init__.py b/reg_sr/__init__.py
@@ -27,8 +27,8 @@
 from .utils import *
 from .experiments import *
 
-__package__ = 'regularized_springrank'
-__title__ = 'regularized_springrank: regularized methods for efficient ranking in networks.'
+__package__ = 'rSpringRank'
+__title__ = 'rSpringRank: Regularized methods for efficient ranking in networks.'
 __description__ = ''
 __copyright__ = 'Copyright (C) 2023 Tzu-Chi Yen'
 __license__ = "LGPL version 3 or above"

diff --git a/reg_sr/experiments.py b/reg_sr/experiments.py
@@ -30,7 +30,7 @@
 import matplotlib.pyplot as plt
 from collections import defaultdict
 from itertools import combinations
-import graph_tool.all as gt
+# import graph_tool.all as gt
 import numpy as np
 from math import comb
 from reg_sr.losses import *

diff --git a/reg_sr/models.py b/reg_sr/models.py
@@ -19,7 +19,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 import reg_sr.losses as losses
 import reg_sr.regularizers as regularizers
-import graph_tool.all as gt
+# import graph_tool.all as gt
 
 import numpy as np
 from numba import jit

diff --git a/reg_sr/utils.py b/reg_sr/utils.py
@@ -1,4 +1,4 @@
-import graph_tool.all as gt
+# import graph_tool.all as gt
 import numpy as np
 from numba import jit
 from scipy.sparse import csr_matrix, csc_matrix, issparse