V0.1.1 (#16)

* moved unique edge size function from hypergraph class and fixed bug.

* update version

* Fixed small documentation issue

* fixed numpy dependency

* update long description

CITATION.cff

@@ -11,5 +11,5 @@ cff-version: "1.1.0"
 license: "BSD-3"
 message: "If you use this software, please cite it using these metadata."
 title: XGI
-version: "0.1"
+version: "0.1.1"
 ...

README.md

@@ -40,7 +40,7 @@ To get started, take a look at the [tutorials](/tutorials/) illustrating the lib
 
 ## Documentation
 
-For more documentation, see our [Read The Docs](https://xgi.readthedocs.io/en/latest/) page
+For more documentation, see our [Read The Docs](https://xgi.readthedocs.io/en/latest/) page.
 
 ## Contributing
 Contributions are always welcome. Please report any bugs that you find [here](../../issues). Or, even better, fork the repository on [GitHub](../../) and create a pull request (PR). We welcome all changes, big or small, and we will help you make the PR if you are new to `git` (just ask on the issue and/or see our [contributing guidelines](CONTRIBUTING.md)).
@@ -60,16 +60,18 @@ a citation in your preferred format, and will also integrate well with citation
 Our full code of conduct, and how we enforce it, can be read in [our repository](CODE_OF_CONDUCT.md).
 
 ## License
-Released under the 3-Clause BSD license (see `license.md`)
+Released under the 3-Clause BSD license (see [`license.md`](license.md))
 
 Copyright (C) 2021 XGI Developers
+
 Nicholas Landry <[email protected]>
+
 Leo Torres <[email protected]>
 
 The XGI library has copied or modified code from the HyperNetX and NetworkX libraries, the licenses of which can be found in our [license file](license.md)
 
 ## Funding
-The XGI package has been supported by NSF Grant 2121905, ["HNDS-I: Using Hypergraphs to Study Spreading Processes in Complex Social Networks"](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2121905)
+The XGI package has been supported by NSF Grant 2121905, ["HNDS-I: Using Hypergraphs to Study Spreading Processes in Complex Social Networks"](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2121905).
 
 ## Other resources
 This library may not meet your needs and if this is this case, consider checking out these other resources:

docs/source/about.rst

@@ -1,6 +1,9 @@
 About
 =====
 
+.. image:: ../../logo/logo.svg
+  :width: 200
+
 The ``XGI`` library provides data structures and algorithms for modeling and analyzing
 complex systems with group (higher-order) interactions.
 
@@ -30,15 +33,13 @@ installed by ``pip`` during the installation process
 
 License
 -------
-
 This project is licensed under the `BSD 3-Clause License
 <https://github.com/ComplexGroupInteractions/xgi/blob/main/LICENSE.md>`__.
 Note that this excludes any images/pictures/figures shown here or in the
 documentation.
 
 Contributing
 ------------
-
 If you want to contribute to this project, please make sure to read the
 `code of conduct
 <https://github.com/ComplexGroupInteractions/xgi/blob/main/CODE_OF_CONDUCT.md>`__

docs/source/conf.py

@@ -24,7 +24,7 @@
 author = "Nicholas W. Landry and Leo Torres"
 
 # The full version, including alpha/beta/rc tags
-release = "0.1"
+release = "0.1.1"
 
 # -- General configuration ---------------------------------------------------
 

docs/source/index.rst

@@ -1,6 +1,9 @@
-=======
+===
 XGI
-=======
+===
+
+.. image:: ../../logo/logo.svg
+  :width: 200
 
 Description
 -----------

long_description.rst

@@ -0,0 +1,74 @@
+XGI
+===
+
+.. image:: https://github.com/ComplexGroupInteractions/xgi/blob/main/logo/logo.svg
+  :width: 200
+
+CompleX Group Interactions (XGI) is a Python package for the representation, manipulation,
+and study of the structure, dynamics, and functions of complex systems with group (higher-order) interactions.
+
+- **Source**: https://github.com/ComplexGroupInteractions/xgi
+- **Bug reports**: https://github.com/ComplexGroupInteractions/xgi/issues
+- **GitHub Discussions**: https://github.com/ComplexGroupInteractions/xgi/discussions
+- **Documentation**: https://xgi.readthedocs.io/en/latest/
+
+Installation
+------------
+XGI runs on Python 3.7 or higher.
+
+To install the latest version of XGI, run the following command
+.. code:: bash
+
+   pip install xgi
+
+To install this package locally:
+- Clone this repository
+- Navigate to the folder on your local machine
+- Run the following command
+.. code:: bash
+
+   pip install -e .["all"]
+
+
+Getting Started
+---------------
+To get started, take a look at the `tutorials <https://github.com/ComplexGroupInteractions/xgi/tree/main/tutorials>`_
+illustrating the library's basic functionality.
+
+Documentation
+-------------
+For more documentation, see our `Read The Docs <https://xgi.readthedocs.io/en/latest/>`_ page.
+
+Contributing
+------------
+Contributions are always welcome. Please report any bugs that you find `here <https://github.com/ComplexGroupInteractions/xgi/issues>`_.
+Or, even better, fork the repository on `GitHub <https://github.com/ComplexGroupInteractions/xgi>`_ and create a pull request (PR).
+We welcome all changes, big or small, and we will help you make the PR if you are new to `git`
+(just ask on the issue and/or see our `contributing guidelines <https://github.com/ComplexGroupInteractions/xgi/tree/main/CONTRIBUTING.md>`_.
+
+How to Cite
+-----------
+We acknowledge the importance of good software to support research, and we note
+that research becomes more valuable when it is communicated effectively. To
+demonstrate the value of XGI, we ask that you cite XGI in your work.
+Currently, the best way to cite XGI is to go to our
+`repository page <https://github.com/ComplexGroupInteractions/xgi>`_ and
+click the "cite this repository" button on the right sidebar. This will generate
+a citation in your preferred format, and will also integrate well with citation managers.
+
+Code of Conduct
+---------------
+Our full code of conduct, and how we enforce it, can be read in `our repository <https://github.com/ComplexGroupInteractions/xgi/tree/main/CODE_OF_CONDUCT.md>`_.
+
+License
+-------
+Released under the 3-Clause BSD license (see the `license file <https://github.com/ComplexGroupInteractions/xgi/tree/main/license.md>`_)
+
+Copyright (C) 2021 XGI Developers
+
+Nicholas Landry <[email protected]>
+
+Leo Torres <[email protected]>
+
+The XGI library has copied or modified code from the HyperNetX and NetworkX libraries, the licenses of which can be found in the
+`license file <https://github.com/ComplexGroupInteractions/xgi/tree/main/license.md>`_.

requirements/default.txt

@@ -1,5 +1,4 @@
-numpy>=1.19
-scipy>=1.5,!=1.6.1
-pandas>=1.1
-networkx>=2.5
-python>=3.7
+networkx>=2.2
+numpy>=1.19,<1.22
+scipy>=1.5
+pandas>=1.0

requirements/doc.txt → requirements/documentation.txt

@@ -1,3 +1,4 @@
 sphinx~=4.0
+sphinx-rtd-theme>=0.4.2
 numpydoc>=1.1
 pillow>=8.2

setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup
 import sys
 
-__version__ = "0.1"
+__version__ = "0.1.1"
 
 if sys.version_info < (3, 7):
     sys.exit("XGI requires Python 3.7 or later.")
@@ -18,37 +18,38 @@
     "xgi.utils",
 ]
 
-version = "0.1"
+version = "0.1.1"
 
 authors = "Nicholas Landry and Leo Torres"
 
 author_email = "[email protected]"
 
 url = "https://github.com/ComplexGroupInteractions/xgi"
 
-description = "XGI is a Python library for the representation and analysis of complex systems with group (higher-order) interaction."
+description = """XGI is a Python library for the representation
+and analysis of complex systems with group (higher-order) interactions."""
 
-install_requires = [
-    "networkx>=2.2,<3.0",
-    "numpy>=1.15.0,<2.0",
-    "scipy>=1.1.0,<2.0",
-    "pandas>=0.23",
-]
+with open("long_description.rst") as file:
+    long_description = file.read()
+
+
+def parse_requirements_file(filename):
+    with open(filename) as fid:
+        requires = [l.strip() for l in fid.readlines() if not l.startswith("#")]
+    return requires
 
-license = "3-Clause BSD license"
 
 extras_require = {
-    "testing": ["pytest>=4.0"],
-    "tutorials": ["jupyter>=1.0"],
-    "documentation": ["sphinx>=1.8.2", "sphinx-rtd-theme>=0.4.2"],
-    "all": [
-        "sphinx>=1.8.2",
-        "sphinx-rtd-theme>=0.4.2",
-        "pytest>=4.0",
-        "jupyter>=1.0",
-    ],
+    dep: parse_requirements_file("requirements/" + dep + ".txt")
+    for dep in ["developer", "documentation", "release", "test", "tutorial"]
 }
 
+extras_require["all"] = list({item for dep in extras_require.values() for item in dep})
+
+install_requires = parse_requirements_file("requirements/default.txt")
+
+license = "3-Clause BSD license"
+
 setup(
     name=name,
     packages=packages,
@@ -57,6 +58,7 @@
     author_email=author_email,
     url=url,
     description=description,
+    long_description=long_description,
     install_requires=install_requires,
     extras_require=extras_require,
 )

xgi/classes/function.py

@@ -2,10 +2,12 @@
 """
 
 from collections import Counter
+import numpy as np
 import xgi
 
 __all__ = [
     "degree_histogram",
+    "unique_edge_sizes",
     "freeze",
     "is_frozen",
     "create_empty_copy",
@@ -48,6 +50,28 @@ def degree_histogram(H):
     return [counts.get(i, 0) for i in range(max(counts) + 1)]
 
 
+def unique_edge_sizes(H, return_counts=False):
+    """A function that returns the unique edge sizes.
+
+    Parameters
+    ----------
+    H : Hypergraph object
+        The hypergraph of interest
+    return_counts : bool, default: False
+        Specifies whether to include the number of occurences of that edge size
+
+    Returns
+    -------
+    if return_counts:
+        numpy.ndarray, numpy.ndarray
+            Numpy arrays of the unique edge sizes and the number of each size respectively
+    else:
+        numpy.ndarray
+            A numpy array of the unique edge sizes
+    """
+    return np.unique(list(H.edge_size), return_counts=return_counts)
+
+
 def frozen(*args, **kwargs):
     """Dummy method that raises an error when trying to modify frozen hypergraphs
 

xgi/classes/hypergraph.py

@@ -24,6 +24,7 @@
 
 class Hypergraph:
     """A class to represent undirected hypergraphs."""
+
     node_dict_factory = dict
     node_attr_dict_factory = dict
     hyperedge_dict_factory = dict
@@ -883,25 +884,6 @@ def edge_size(self):
         """
         return EdgeSizeView(self)
 
-    def unique_edge_sizes(self, return_counts=False):
-        """A function that returns the unique edge sizes.
-
-        Parameters
-        ----------
-        return_counts : bool, default: False
-            Specifies whether to include the number of occurences of that edge size
-
-        Returns
-        -------
-        if return_counts:
-            numpy.ndarray, numpy.ndarray
-                Numpy arrays of the unique edge sizes and the number of each size respectively
-        else:
-            numpy.ndarray
-                A numpy array of the unique edge sizes
-        """
-        return np.unique(list(self.edge_degree), return_counts=return_counts)
-
     def clear(self):
         """Remove all nodes and edges from the graph.
 
@@ -1159,9 +1141,7 @@ def bunch_iter(nlist, nodes):
                     exc, message = e, e.args[0]
                     # capture error for non-sequence/iterator nbunch.
                     if "iter" in message:
-                        exc = XGIError(
-                            "nbunch is not a node or a sequence of nodes."
-                        )
+                        exc = XGIError("nbunch is not a node or a sequence of nodes.")
                     # capture error for unhashable node.
                     if "hashable" in message:
                         exc = XGIError(

xgi/classes/hypergraphviews.py

@@ -13,15 +13,14 @@
 """
 
 
-
 import xgi
 
 __all__ = ["generic_hypergraph_view", "subhypergraph_view"]
 
 
 def generic_hypergraph_view(H, create_using=None):
     """Create a read-only view of the hypergraph
-    
+
     The read-only view shares the same memory as the original hypergraph
     and "freezes" the hypergraph by removing the methods that can modify
     the hypergraph.
@@ -100,6 +99,8 @@ def subhypergraph_view(H, filtered_nodes=None, filtered_edges=None):
     newH._edge_attr = {edge: H._edge_attr[edge] for edge in newH._edge}
 
     # Add the filtered nodes with connections to the remaining edges after filtering
-    newH._node = {node: set(H._node[node]).intersection(newH._edge.keys()) for node in nodes}
+    newH._node = {
+        node: set(H._node[node]).intersection(newH._edge.keys()) for node in nodes
+    }
     newH._node_attr = {node: H._node_attr[node] for node in nodes}
     return newH

xgi/metadata.py

@@ -3,7 +3,7 @@
 Contains information about this package.
 """
 
-__version__ = "0.1"
+__version__ = "0.1.1"
 
 __author__ = "Nicholas W. Landry and Leo Torres"
 __copyright__ = "Copyright 2021-2022, " + __author__

xgi/readwrite/bipartite.py

@@ -1,4 +1,4 @@
-import  xgi
+import xgi
 from xgi.exception import XGIError
 
 __all__ = [