Merge pull request #91 from pnnl/updated-master

Update master

.gitignore

@@ -25,3 +25,5 @@ tutorials/h2d-hnx-why_v5.tar.gz
 vis_develop
 dist/
 *.egg-info*
+.tox/
+venv*

Makefile

@@ -0,0 +1,30 @@
+
+SHELL = /bin/bash
+
+# Variables
+VENV = venv_test
+PYTHON = $(VENV)/bin/python
+
+## Environment
+
+venv:
+	@rm -rf VENV;
+	@python -m venv $(VENV);
+
+deps:
+	@$(PYTHON) -m pip install tox
+
+.PHONY: venv deps
+
+## Test
+
+test: venv deps
+	rm -rf .tox
+	@$(PYTHON) -m tox
+
+.PHONY: test
+
+clean:
+	rm -rf .out .pytest_cache .tox *.egg-info dist build
+
+.PHONY: clean

hypernetx/classes/hypergraph.py

@@ -2302,7 +2302,7 @@ def dataframe(self, sort_rows=False, sort_columns=False, cell_weights=True):
 
     @classmethod
     def from_bipartite(
-        cls, B, set_names=("nodes", "edges"), name=None, static=False, use_nwhy=False
+        cls, B, set_names=("edges", "nodes"), name=None, static=False, use_nwhy=False
     ):
         """
         Static method creates a Hypergraph from a bipartite graph.
@@ -2356,7 +2356,7 @@ def from_bipartite(
         if static:
             elist = []
             for e in list(B.edges):
-                if e[0] in nodes:
+                if e[0] in edges:
                     elist.append([e[0], e[1]])
                 else:
                     elist.append([e[1], e[0]])

hypernetx/classes/tests/test_hypergraph_constructors.py

@@ -1,9 +1,11 @@
+from collections import OrderedDict
+
 import pytest
 import numpy as np
 import pandas as pd
 import networkx as nx
-from hypernetx import Hypergraph, Entity, EntitySet
-from hypernetx import HyperNetXError
+from hypernetx import Hypergraph, EntitySet
+
 
 
 def test_from_bipartite():
@@ -17,6 +19,25 @@ def test_from_bipartite():
     assert "Hypergraph is not s-connected." in str(excinfo.value)
 
 
+@pytest.mark.parametrize("static", [(True), (False)])
+def test_hypergraph_from_bipartite_and_from_constructor_should_be_equal(seven_by_six, static):
+    edgedict = OrderedDict(seven_by_six.edgedict)
+
+    bipartite_graph = Hypergraph(edgedict).bipartite()
+    hg_from_bipartite = Hypergraph.from_bipartite(bipartite_graph, static=static)
+
+    entityset = EntitySet("_", edgedict)
+    hg_from_constructor = Hypergraph(entityset, static=static)
+
+    assert hg_from_bipartite.isstatic == hg_from_constructor.isstatic
+
+    assert hg_from_bipartite.shape == hg_from_constructor.shape
+
+    incidence_dict_hg_from_bipartite = {key: sorted(value) for key, value in hg_from_bipartite.incidence_dict.items()}
+    incidence_dict_hg_from_constructor = {key: sorted(value) for key, value in hg_from_constructor.incidence_dict.items()}
+    assert incidence_dict_hg_from_bipartite == incidence_dict_hg_from_constructor
+
+
 def test_from_numpy_array():
     M = np.array([[0, 1, 1, 0, 1], [1, 1, 1, 1, 1], [1, 0, 0, 1, 0], [0, 0, 0, 0, 1]])
     h = Hypergraph.from_numpy_array(M)

setup.cfg

@@ -1,3 +1,3 @@
 [metadata]
-description-file=README.md
+description_file=README.md
 

setup.py

@@ -32,6 +32,7 @@
         "pandas>=0.23",
         "python-igraph>=0.9.6",
         "celluloid>=0.2.0",
+        "decorator>=5.1.1"
     ],
     license="3-Clause BSD license",
     long_description="""

tox.ini

@@ -0,0 +1,13 @@
+# tox (https://tox.readthedocs.io/) is a tool for running tests
+# in multiple virtualenvs. This configuration file will run the
+# test suite on all supported python versions. To use it, "pip install tox"
+# and then run "tox" from this directory.
+
+[tox]
+envlist = py37
+
+[testenv]
+deps =
+    pytest
+commands =
+    pytest hypernetx/ -v --disable-warnings