Pull request #144: Feature/hyp 367

Merge in HYP/hypernetx from feature/hyp-367 to develop

* commit '89c712bfff824b591422f0e15141bf6d7a36a24b': (108 commits)
  Fix formatting
  adding arithmetic for hypergraphs
  Bug fix: shouldn't require passing position for hyper-edges.
  Remove nwhy decorator reference
  Run linter; remove HNX_Paper
  updated hypergraph code class method constructors
  Remove references to warn_nwhy deprecation decorator
  Remove deprecated NetworkX functions
  Remove unnecessary hypergraph test
  Fix incidence_store bug; move, update, and fix incidence store tests;
  Remove EntitySet and tests
  add incidences reference to access _E HypergraphView
  removing hypergraph_outline to avoid versioning issues. new code is on hypergraph.py now
  centrality tutorial 5 is ready to go
  Updated the tutorials in basic 1,3,4 to work with new code..
  moved old hypergraph code into hypergraph_2.0 and  set hypergraph to match hypergraph_outline. updated dogsAndcats for testing
  updated tests to work with new hypergraph code. commented out _by_setsystem tests until they can be upgraded
  updated collapse in incidence to separate functions for equivalence classes and collapse identical elements. user can now specify keys when collapsing
  added is_empty to match old behavior
  Refactor set property
  ...

.gitignore

@@ -1,3 +1,4 @@
+.github/
 .DS_Store
 gitmerge.sh
 dist
@@ -39,3 +40,5 @@ docs/build
 coverage.xml
 cov.syspath.txt
 *.whl
+*dogsAndcats*
+.github/

.pre-commit-config.yaml

@@ -13,3 +13,7 @@ repos:
   - id: trailing-whitespace
     exclude: ^(docs/|hypernetx.egg-info/|setup.cfg)
   - id: check-merge-conflict
+- repo: https://github.com/psf/black
+  rev: 24.3.0
+  hooks:
+  - id: black

Makefile

@@ -11,7 +11,7 @@ lint: pylint flake8 mypy
 
 .PHONY: pylint
 pylint:
-	@$(PYTHON3) -m pylint --recursive=y --persistent=n --verbose hypernetx
+	@$(PYTHON3) -m pylint --recursive=y --persistent=n --verbose hypernetx --exit-zero
 
 .PHONY: mypy
 mypy:
@@ -129,3 +129,7 @@ test-deps:
 .PHONY: all-deps
 all-deps:
 	@$(PYTHON3) -m pip install .[all] --use-pep517
+
+.PHONY: install-develop
+install-develop:
+	@$(PYTHON3) -m pip install -e . --use-pep517

docs/source/conf.py

@@ -25,7 +25,7 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0 , os.path.abspath("../../hypernetx"))
+sys.path.insert(0, os.path.abspath("../../hypernetx"))
 
 
 # -- Project information -----------------------------------------------------
@@ -57,7 +57,7 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.todo",
     "sphinx.ext.viewcode",
-    'sphinx_copybutton',
+    "sphinx_copybutton",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -79,7 +79,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'en'
+language = "en"
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -239,8 +239,8 @@
     (
         master_doc,
         "HyperNetX.tex",
-        u"HyperNetX Documentation",
-        u"Brenda Praggastis, Dustin Arendt",
+        "HyperNetX Documentation",
+        "Brenda Praggastis, Dustin Arendt",
         "manual",
     ),
 ]
@@ -270,7 +270,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "hypernetx", u"HyperNetX Documentation", [author], 1)]
+man_pages = [(master_doc, "hypernetx", "HyperNetX Documentation", [author], 1)]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -285,7 +285,7 @@
     (
         master_doc,
         "HyperNetX",
-        u"HyperNetX Documentation",
+        "HyperNetX Documentation",
         author,
         "HyperNetX",
         "One line description of project.",
@@ -377,7 +377,7 @@
 
 # Remove the command prompts such as >>> when copying code snippets from copybutton
 # see https://sphinx-copybutton.readthedocs.io/en/latest/use.html
-copybutton_exclude = '.linenos, .gp'
+copybutton_exclude = ".linenos, .gp"
 
 #  tables and code-blocks are automatically numbered if they have a caption.
 # See https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-numfig

hypernetx/algorithms/contagion.py

@@ -308,6 +308,7 @@ def majority_vote(node, status, edge):
 
 # Auxiliary functions
 
+
 # The ListDict class is copied from Joel Miller's Github repository Mathematics-of-Epidemics-on-Networks
 class _ListDict_(object):
     r"""

hypernetx/algorithms/tests/test_contagion.py

@@ -12,6 +12,7 @@
 import hypernetx as hnx
 import random
 
+
 # Test the contagion functions
 def test_collective_contagion():
     status = {0: "S", 1: "I", 2: "I", 3: "S", 4: "R"}

hypernetx/algorithms/tests/test_generative.py

@@ -5,6 +5,7 @@
 import random
 from scipy.sparse import coo_matrix
 
+
 # Test the generative model functions
 def test_erdos_renyi():
     random.seed(42)

hypernetx/classes/__init__.py

@@ -1,4 +1,3 @@
-from hypernetx.classes.entityset import EntitySet
 from hypernetx.classes.hypergraph import Hypergraph
 
-__all__ = ["EntitySet", "Hypergraph"]
+__all__ = ["Hypergraph"]