Pull request #132: Hotfix/HYP-364 address joss related issues

Merge in HYP/hypernetx from hotfix/HYP-364-address-joss-related-issues to master

* commit '838f33a019d0eab94f03a1c757708433855fa2ad':
  bump: version 2.1.2 → 2.1.3
  HYP-364 Add html support for eacute character in tutorial 1
  Remove unnecessary dependencies for documentation
  HYP-364 Fix math syntax
  HYP-364 Fix doctrings
  HYP-364 Add acute accents on certain French words
  HYP-364 Fix hyperlink typo
  HYP-364 Fix contributing typos

.cz.toml

@@ -1,6 +1,6 @@
 [tool.commitizen]
 name = "cz_conventional_commits"
-version = "2.1.2"
+version = "2.1.3"
 version_files = [
     "setup.py",
     "docs/source/conf.py",

CONTRIBUTING.md

@@ -4,7 +4,7 @@ If you have ideas for improving this project, we would love to hear from you!
 
 ## Orientation
 
-The world of open source is wide; it can be a lot to take in!  If this is your first time working with an open source project, then welcome!    If you're an experienced contributor, then welcome back!  Either way, this online resource might help you [get oriented, or bursh up](https://opensource.guide/how-to-contribute/) on the process.
+The world of open source is wide; it can be a lot to take in!  If this is your first time working with an open source project, then welcome!    If you're an experienced contributor, then welcome back!  Either way, this online resource might help you [get oriented, or brush up](https://opensource.guide/how-to-contribute/) on the process.
 
 ## Report an issue, bug, or feature request
 
@@ -36,4 +36,4 @@ If you're stuck or don't know where to begin, then you're in good company -- we'
 
 # Code of conduct
 
-Our shared values as software developers guide us in our day-to-day interactions and decision-making. Our open source projects are no exception. Trust, respect, collaboration and transparency are core values we believe should live and breathe within our projects. Our community welcomes participants from around the world with different experiences, unique perspectives, and great ideas to share.  Our  [code of conduct](CODE_OF_CONDUCT) describes these values, and our standards for contributing.
+Our shared values as software developers guide us in our day-to-day interactions and decision-making. Our open source projects are no exception. Trust, respect, collaboration and transparency are core values we believe should live and breathe within our projects. Our community welcomes participants from around the world with different experiences, unique perspectives, and great ideas to share.  Our  [code of conduct](CODE_OF_CONDUCT.md) describes these values, and our standards for contributing.

docs/source/conf.py

@@ -19,7 +19,7 @@
 import os
 
 
-__version__ = "2.1.2"
+__version__ = "2.1.3"
 
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -57,8 +57,6 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.todo",
     "sphinx.ext.viewcode",
-    "nb2plots",
-    "texext",
     'sphinx_copybutton',
 ]
 

docs/source/hypergraph101.rst

@@ -295,7 +295,7 @@ can also measure the size of the intersection
 :math:`W` we can not only talk about its length :math:`N`, but also
 define its **width** :math:`s(W) = \min_{0 \le i \le N} s_i` as the size
 of the smallest such intersection. When a walk :math:`W` has width
-:math:`s`, we call it an **:math:`s`-walk**. It follows that all walks
+:math:`s`, we call it an :math:`s`-walk. It follows that all walks
 in a graph are 1-walks with width 1. In Fig. `5 <#swalks>`__ we see two
 walks in a hypergraph. While both have length 2 (counting edgewise, and
 recalling origin zero), the one on the left has width 1, and that on the

hypernetx/__init__.py

@@ -11,4 +11,4 @@
 from hypernetx.utils import *
 from hypernetx.utils.toys import *
 
-__version__ = "2.1.2"
+__version__ = "2.1.3"

hypernetx/algorithms/homology_mod2.py

@@ -1,4 +1,4 @@
-"""
+r"""
 Homology and Smith Normal Form
 ==============================
 The purpose of computing the Homology groups for data generated
@@ -541,7 +541,7 @@ def reduced_row_echelon_form_mod2(M):
 
 
 def boundary_group(image_basis):
-    """
+    r"""
     Returns a csr_matrix with rows corresponding to the elements of the
     group  generated by image basis over $\mathbb{Z}_2$
 
@@ -734,7 +734,7 @@ def betti_numbers(h, k=None):
 
 
 def homology_basis(bd, k=None, boundary=False, **kwargs):
-    """
+    r"""
     Compute a basis for the kth-simplicial homology group, $H_k$, defined by a
     chain complex $C$ with boundary maps given by bd $= \{k:\partial_k \}$
 

hypernetx/algorithms/laplacians_clustering.py

@@ -39,7 +39,7 @@
 
 
 def prob_trans(H, weights=False, index=True, check_connected=True):
-    """
+    r"""
     The probability transition matrix of a random walk on the vertices of a hypergraph.
     At each step in the walk, the next vertex is chosen by:
 

setup.cfg

@@ -50,6 +50,7 @@ license_files =
 	LICENSE.rst
 
 [options]
+include_package_data=True
 packages =
 	hypernetx
 	hypernetx.algorithms
@@ -66,6 +67,7 @@ install_requires =
 	scikit-learn>=0.20.0
 	pandas>=1.5.3
 	decorator>=5.1.1
+	typing-extensions>=4.8.0
 
 [options.extras_require]
 releases =
@@ -76,18 +78,19 @@ linting =
     pylint-exit>=1.2.0
     black>=23.3.0
 testing =
+	pytest>=7.2.2
+	pytest-cov>=4.1.0
+	pytest-lazy-fixture>=0.6.3
+	pytest-xdist>=3.2.1
+	pytest-env
 	tox>=4.4.11
-    pre-commit>=3.2.2
+	nbmake>=1.4.1
+	pre-commit>=3.2.2
     pylint>=2.17.2
     pylint-exit>=1.2.0
     black>=23.3.0
-	pytest>=7.2.2
-	coverage>=7.2.2
 	celluloid>=0.2.0
 	igraph>=0.10.4
-	nbmake>=1.4.1
-	pytest-lazy-fixture>=0.6.3
-	pytest-xdist>=3.2.1
 tutorials =
 	jupyter>=1.0
 	python-igraph>=0.10.4
@@ -99,7 +102,6 @@ widget =
 	jupyter-nbextensions-configurator>=0.6.2
 documentation =
 	sphinx<7
-	nb2plots>=0.6.1
 	sphinx-rtd-theme>=1.2.1
 	sphinx-autobuild>=2021.3.14
 	sphinx-copybutton>=0.5.1
@@ -115,9 +117,8 @@ all =
 	sphinx-autobuild>=2021.3.14
 	sphinx-copybutton>=0.5.1
 	pytest>=7.2.2
-	coverage>=7.2.2
+	pytest-cov>=4.1.0
 	jupyter>=1.0
-	python-igraph>=0.10.4
+	igraph>=0.10.4
 	partition-igraph>=0.0.6
 	celluloid>=0.2.0
-	igraph>=0.10.4

setup.py

@@ -1,5 +1,5 @@
 from setuptools import setup
 
-__version__ = "2.1.2"
+__version__ = "2.1.3"
 
 setup(version=__version__)

tutorials/Tutorial 1 - HNX Basics.ipynb

@@ -27,7 +27,9 @@
    "source": [
     "# Data\n",
     "\n",
-    "The data in several of our notebooks are taken from the [jean.dat dataset](http://ftp.cs.stanford.edu/pub/sgb/jean.dat) available from the Stanford GraphBase at https://www-cs-faculty.stanford.edu/~knuth/sgb.html. This data gives character scene incidence information from the novel **Les Miserables** by Victor Hugo.\n"
+    "The data in several of our notebooks are taken from the [jean.dat dataset](http://ftp.cs.stanford.edu/pub/sgb/jean.dat) available from the Stanford GraphBase at https://www-cs-faculty.stanford.edu/~knuth/sgb.html. \n",
+    "\n",
+    "<p>This data gives character scene incidence information from the novel Les Mis&eacuterables by Victor Hugo.</p>"
    ]
   },
   {
@@ -437,7 +439,7 @@
     "* `s_components`\n",
     "* `s_component_subgraphs`.\n",
     "\n",
-    "To learn more about some of our research in this area,  check out our paper, [Hypernetwork science via high order hypergraph walks](https://epjdatascience.springeropen.com/articles/10.1140/epjds/s13688-020-00231-0\")\n",
+    "To learn more about some of our research in this area,  check out our paper, [Hypernetwork science via high order hypergraph walks](https://epjdatascience.springeropen.com/articles/10.1140/epjds/s13688-020-00231-0)\n",
     "\n",
     "`s_components` returns a generator object which iterates through the edge sets for each s-connected component.  "
    ]