Pull request #111: HYP-177 update tests suite for entityset

Merge in HYP/hypernetx from HYP-177-update-tests-suite-for-entityset to develop

* commit 'a249417bb8efe6d14e91e18b617a4af460f77d70': (27 commits)
  HYP-177 Reorg entityset tests
  HYP-353 Add deprecation warnings for property column args
  HYP-353 Remove option to customize misc cell props col
  HYP-353 Remove option to customize misc props column
  HYP-356 Add deprecate warnings to certain ES methods
  HYP-177 Update tox.ini script test deps
  HYP-177 Return none when property not found; update tests
  HYP-177 Refactor and fix set_cell_property
  HYP-177 Cleanup tests
  HYP-177 Modify helper method
  HYP-177 Update pytest and tox config
  HYP-177 Reorganize tests; cleanup fixtures
  HYP-177 Add tests for elements_by_column
  HYP-177 Add tests for collapse_identical_elements
  HYP-177 Update test config for CI
  HYP-177 Add tests for level method
  HYP-177 Fix set_cell_property bug
  HYP-177 Minor cleanup on assign_properties
  Add tests for assign_cell_properties
  HYP-177 Add tests for assign_properties, update docs
  ...

.coveragerc

@@ -1,5 +1,9 @@
 [run]
-omit = */tests/*
+omit =
+    */tests/*
+    */utils/toys/*
+    */utils/log.py
+
 [report]
 exclude_lines =
     _log

.gitignore

@@ -27,7 +27,7 @@ dist/
 *.egg-info*
 .tox/
 venv*
-.coverage
+.coverage*
 .idea
 *env*
 .venv*

MANIFEST.in

@@ -0,0 +1 @@
+include hypernetx/utils/toys/HarryPotter_Characters.csv

Makefile

@@ -11,27 +11,22 @@ test: test-deps
 	@$(PYTHON3) -m tox
 
 test-ci: test-deps
-	@$(PYTHON3) -m pip install 'pytest-github-actions-annotate-failures>=0.1.7'
 	pre-commit install
 	pre-commit run --all-files
-	@$(PYTHON3) -m tox -e py38 -r
+	@$(PYTHON3) -m tox
 
 test-ci-github: test-deps
 	@$(PYTHON3) -m pip install 'pytest-github-actions-annotate-failures>=0.1.7'
 	@$(PYTHON3) -m tox
 
-test-coverage: test-deps
-	coverage run --source=hypernetx -m pytest
-	coverage html
-
-.PHONY: test, test-ci, test-ci-github, test-coverage
+.PHONY: test, test-ci, test-ci-github
 
 ## Continuous Deployment
 ## Assumes that scripts are run on a container or test server VM
 
 ### Publish to PyPi
 publish-deps:
-	@$(PYTHON3) -m pip install -e .'[packaging]'
+	@$(PYTHON3) -m pip install -e .'[packaging]' --use-pep517
 
 build-dist: publish-deps clean
 	@$(PYTHON3) -m build --wheel --sdist
@@ -48,7 +43,7 @@ publish-to-pypi: publish-deps build-dist
 ### Update version
 
 version-deps:
-	@$(PYTHON3) -m pip install .'[releases]'
+	@$(PYTHON3) -m pip install .'[releases]' --use-pep517
 
 .PHONY: version-deps
 

hypernetx/classes/tests/conftest.py

@@ -6,6 +6,8 @@
 import numpy as np
 
 from hypernetx import Hypergraph, HarryPotter, EntitySet, LesMis as LM
+from hypernetx.classes.helpers import create_dataframe
+
 from collections import OrderedDict, defaultdict
 
 
@@ -40,31 +42,33 @@ def __init__(self, static=False):
         )
         self.labels = OrderedDict(
             [
-                ("edges", ["P", "R", "S", "L", "O", "I"]),
-                ("nodes", ["A", "C", "E", "K", "T1", "T2", "V"]),
+                ("edges", [p, r, s, l, o, i]),
+                ("nodes", [a, c, e, k, t1, t2, v]),
             ]
         )
 
         self.data = np.array(
             [
                 [0, 0],
                 [0, 1],
-                [0, 2],
+                [0, 3],
+                [1, 0],
                 [1, 2],
-                [1, 3],
                 [2, 0],
-                [2, 2],
-                [2, 4],
+                [2, 3],
                 [2, 5],
+                [2, 6],
                 [3, 1],
-                [3, 3],
+                [3, 2],
+                [4, 4],
                 [4, 5],
-                [4, 6],
-                [5, 0],
+                [5, 3],
                 [5, 5],
             ]
         )
 
+        self.dataframe = create_dataframe(self.edgedict)
+
 
 class TriLoop:
     """Example hypergraph with 2 two 1-cells and 1 2-cell forming a loop"""
@@ -100,6 +104,8 @@ def __init__(self):
             ]
         )
 
+        self.dataframe = create_dataframe(self.edgedict)
+
 
 class LesMis:
     def __init__(self):
@@ -146,11 +152,66 @@ def __init__(self, n1, n2):
         self.left, self.right = nx.bipartite.sets(self.g)
 
 
+@pytest.fixture
+def props_dataframe():
+    multi_index = pd.MultiIndex.from_tuples([(0, "P")], names=["level", "id"])
+    data = {
+        "properties": [{"prop1": "propval1", "prop2": "propval2"}],
+    }
+    return pd.DataFrame(data, index=multi_index)
+
+
+@pytest.fixture
+def cell_props_dataframe_multidx():
+    multi_index = pd.MultiIndex.from_tuples([("P", "A"), ("P", "C")], names=[0, 1])
+    data = {
+        "cell_properties": [
+            {"prop1": "propval1", "prop2": "propval2"},
+            {"prop1": "propval1", "prop2": "propval2"},
+        ]
+    }
+
+    return pd.DataFrame(data, index=multi_index)
+
+
+@pytest.fixture
+def cell_props_dataframe():
+    data = {
+        0: ["P", "P"],
+        1: ["A", "C"],
+        "cell_properties": [
+            {"prop1": "propval1", "prop2": "propval2"},
+            {"prop1": "propval1", "prop2": "propval2"},
+        ],
+    }
+    return pd.DataFrame(data)
+
+
 @pytest.fixture
 def sbs():
     return SevenBySix()
 
 
+@pytest.fixture
+def sbs_dataframe(sbs):
+    return sbs.dataframe
+
+
+@pytest.fixture
+def sbs_dict(sbs):
+    return sbs.edgedict
+
+
+@pytest.fixture
+def sbs_data(sbs):
+    return np.asarray(sbs.data)
+
+
+@pytest.fixture
+def sbs_labels(sbs):
+    return sbs.labels
+
+
 @pytest.fixture
 def triloop():
     return TriLoop()
@@ -176,6 +237,11 @@ def sbs_graph(sbs):
     return G
 
 
+@pytest.fixture
+def sbsd():
+    return SBSDupes()
+
+
 @pytest.fixture
 def sbsd_hypergraph():
     sbsd = SBSDupes()
@@ -217,6 +283,7 @@ def dataframe():
 
 @pytest.fixture
 def dataframe_example():
+    """NOTE: Do not use this dataframe as an input for 'entity' when creating an EntitySet object"""
     M = np.array([[1, 1, 0, 0], [0, 1, 1, 0], [1, 0, 1, 0]])
     index = ["A", "B", "C"]
     columns = ["a", "b", "c", "d"]