From d6fc39a42a4c255e219a4fef19251dd63381ed5a Mon Sep 17 00:00:00 2001 From: Mark Bonicillo Date: Fri, 8 Dec 2023 12:36:24 -0800 Subject: [PATCH 1/8] HYP-364 Fix contributing typos --- CONTRIBUTING.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 97893fc7..ccc6d8fa 100644 --- a/CONTRIBUTING.md +++ b/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. From 5d20ae229efdf3fa83ca24f8d30ca386bd484d4d Mon Sep 17 00:00:00 2001 From: Mark Bonicillo Date: Fri, 8 Dec 2023 12:38:41 -0800 Subject: [PATCH 2/8] HYP-364 Fix hyperlink typo --- tutorials/Tutorial 1 - HNX Basics.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/Tutorial 1 - HNX Basics.ipynb b/tutorials/Tutorial 1 - HNX Basics.ipynb index 06a33c71..ce8c35b4 100644 --- a/tutorials/Tutorial 1 - HNX Basics.ipynb +++ b/tutorials/Tutorial 1 - HNX Basics.ipynb @@ -437,7 +437,7 @@ "* `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. " ] From 62ea04ae88a85a4f5d90a87a2af8c824bd784239 Mon Sep 17 00:00:00 2001 From: Mark Bonicillo Date: Fri, 8 Dec 2023 12:43:08 -0800 Subject: [PATCH 3/8] HYP-364 Add acute accents on certain French words --- tutorials/Tutorial 1 - HNX Basics.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/Tutorial 1 - HNX Basics.ipynb b/tutorials/Tutorial 1 - HNX Basics.ipynb index ce8c35b4..b4b8097b 100644 --- a/tutorials/Tutorial 1 - HNX Basics.ipynb +++ b/tutorials/Tutorial 1 - HNX Basics.ipynb @@ -27,7 +27,7 @@ "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. This data gives character scene incidence information from the novel **Les Misérables** by Victor Hugo.\n" ] }, { From 59ddab7772e8510f1385f21586a7a41e2ec2aedf Mon Sep 17 00:00:00 2001 From: Mark Bonicillo Date: Fri, 8 Dec 2023 12:58:09 -0800 Subject: [PATCH 4/8] HYP-364 Fix doctrings --- hypernetx/algorithms/homology_mod2.py | 6 +++--- hypernetx/algorithms/laplacians_clustering.py | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/hypernetx/algorithms/homology_mod2.py b/hypernetx/algorithms/homology_mod2.py index a987d922..06cc1966 100644 --- a/hypernetx/algorithms/homology_mod2.py +++ b/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 $= \{k:\partial_k \}$ diff --git a/hypernetx/algorithms/laplacians_clustering.py b/hypernetx/algorithms/laplacians_clustering.py index 8ff66b49..a411ca33 100644 --- a/hypernetx/algorithms/laplacians_clustering.py +++ b/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: From ee1693f9a99b40f751f6e54be497c559c2f543ba Mon Sep 17 00:00:00 2001 From: Mark Bonicillo Date: Fri, 8 Dec 2023 13:09:06 -0800 Subject: [PATCH 5/8] HYP-364 Fix math syntax --- docs/source/hypergraph101.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/hypergraph101.rst b/docs/source/hypergraph101.rst index fd5ff15d..02f0b5aa 100644 --- a/docs/source/hypergraph101.rst +++ b/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 From a29cf8d2763eb56bb40afb7892f7c9afc9c1a767 Mon Sep 17 00:00:00 2001 From: Mark Bonicillo Date: Fri, 3 Nov 2023 15:15:26 -0700 Subject: [PATCH 6/8] Remove unnecessary dependencies for documentation --- docs/source/conf.py | 2 -- setup.cfg | 21 +++++++++++---------- 2 files changed, 11 insertions(+), 12 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index e8a60ff3..b5f7d905 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -57,8 +57,6 @@ "sphinx.ext.napoleon", "sphinx.ext.todo", "sphinx.ext.viewcode", - "nb2plots", - "texext", 'sphinx_copybutton', ] diff --git a/setup.cfg b/setup.cfg index d076ab0f..110d528b 100644 --- a/setup.cfg +++ b/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 From c46247b5eadb84eaf64091688ca3b1b42d719f5c Mon Sep 17 00:00:00 2001 From: Mark Bonicillo Date: Fri, 8 Dec 2023 13:26:52 -0800 Subject: [PATCH 7/8] HYP-364 Add html support for eacute character in tutorial 1 --- tutorials/Tutorial 1 - HNX Basics.ipynb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tutorials/Tutorial 1 - HNX Basics.ipynb b/tutorials/Tutorial 1 - HNX Basics.ipynb index b4b8097b..37f53e0b 100644 --- a/tutorials/Tutorial 1 - HNX Basics.ipynb +++ b/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 Misérables** 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", + "

This data gives character scene incidence information from the novel Les Misérables by Victor Hugo.

" ] }, { From 838f33a019d0eab94f03a1c757708433855fa2ad Mon Sep 17 00:00:00 2001 From: Mark Bonicillo Date: Fri, 8 Dec 2023 13:33:24 -0800 Subject: [PATCH 8/8] =?UTF-8?q?bump:=20version=202.1.2=20=E2=86=92=202.1.3?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .cz.toml | 2 +- docs/source/conf.py | 2 +- hypernetx/__init__.py | 2 +- setup.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.cz.toml b/.cz.toml index fcc7476e..70ea04bb 100644 --- a/.cz.toml +++ b/.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", diff --git a/docs/source/conf.py b/docs/source/conf.py index b5f7d905..4d9094dc 100644 --- a/docs/source/conf.py +++ b/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, diff --git a/hypernetx/__init__.py b/hypernetx/__init__.py index b9bacb2c..e06e64ab 100644 --- a/hypernetx/__init__.py +++ b/hypernetx/__init__.py @@ -11,4 +11,4 @@ from hypernetx.utils import * from hypernetx.utils.toys import * -__version__ = "2.1.2" +__version__ = "2.1.3" diff --git a/setup.py b/setup.py index 4f311f32..51888922 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ from setuptools import setup -__version__ = "2.1.2" +__version__ = "2.1.3" setup(version=__version__)