From 62f451d848fad311833c4851275cf749e10c3a1a Mon Sep 17 00:00:00 2001 From: Mark Bonicillo Date: Tue, 9 Apr 2024 14:36:44 -0700 Subject: [PATCH 1/4] Move tests to root-level --- Makefile | 2 +- pyproject.toml | 4 +--- {hypernetx/algorithms/tests => tests/algorithms}/conftest.py | 0 .../algorithms/tests => tests/algorithms}/test_contagion.py | 0 .../algorithms/tests => tests/algorithms}/test_generative.py | 0 .../tests => tests/algorithms}/test_homology_mod_2.py | 0 .../tests => tests/algorithms}/test_laplacians_clustering.py | 0 .../algorithms/tests => tests/algorithms}/test_modularity.py | 0 .../tests => tests/algorithms}/test_s_centrality_measures.py | 0 {hypernetx/classes/tests => tests/classes}/conftest.py | 0 {hypernetx/classes/tests => tests/classes}/sample.csv | 0 {hypernetx/classes/tests => tests/classes}/test_hypergraph.py | 0 .../classes}/test_hypergraph_factory_methods.py | 0 .../classes/tests => tests/classes}/test_hypergraph_view.py | 0 .../classes/tests => tests/classes}/test_incidence_store.py | 0 .../classes/tests => tests/classes}/test_nx_hnx_agreement.py | 0 .../classes/tests => tests/classes}/test_property_store.py | 0 tox.ini | 2 +- 18 files changed, 3 insertions(+), 5 deletions(-) rename {hypernetx/algorithms/tests => tests/algorithms}/conftest.py (100%) rename {hypernetx/algorithms/tests => tests/algorithms}/test_contagion.py (100%) rename {hypernetx/algorithms/tests => tests/algorithms}/test_generative.py (100%) rename {hypernetx/algorithms/tests => tests/algorithms}/test_homology_mod_2.py (100%) rename {hypernetx/algorithms/tests => tests/algorithms}/test_laplacians_clustering.py (100%) rename {hypernetx/algorithms/tests => tests/algorithms}/test_modularity.py (100%) rename {hypernetx/algorithms/tests => tests/algorithms}/test_s_centrality_measures.py (100%) rename {hypernetx/classes/tests => tests/classes}/conftest.py (100%) rename {hypernetx/classes/tests => tests/classes}/sample.csv (100%) rename {hypernetx/classes/tests => tests/classes}/test_hypergraph.py (100%) rename {hypernetx/classes/tests => tests/classes}/test_hypergraph_factory_methods.py (100%) rename {hypernetx/classes/tests => tests/classes}/test_hypergraph_view.py (100%) rename {hypernetx/classes/tests => tests/classes}/test_incidence_store.py (100%) rename {hypernetx/classes/tests => tests/classes}/test_nx_hnx_agreement.py (100%) rename {hypernetx/classes/tests => tests/classes}/test_property_store.py (100%) diff --git a/Makefile b/Makefile index a6c38c9b..24742686 100644 --- a/Makefile +++ b/Makefile @@ -36,7 +36,7 @@ requirements.txt: ## Tests .PHONY: test test: - coverage run --source=hypernetx -m pytest + coverage run --source=hypernetx -m pytest tests coverage report -m ## Tests using Tox diff --git a/pyproject.toml b/pyproject.toml index 27c4cfb8..de924abf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -81,11 +81,9 @@ commitizen = {version = "^3.20.0", optional = true} requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" - [tool.pytest.ini_options] minversion = "6.0" addopts = "-ra" testpaths = [ - "hypernetx/classes/tests", - "hypernetx/algorithms/tests", + "tests" ] diff --git a/hypernetx/algorithms/tests/conftest.py b/tests/algorithms/conftest.py similarity index 100% rename from hypernetx/algorithms/tests/conftest.py rename to tests/algorithms/conftest.py diff --git a/hypernetx/algorithms/tests/test_contagion.py b/tests/algorithms/test_contagion.py similarity index 100% rename from hypernetx/algorithms/tests/test_contagion.py rename to tests/algorithms/test_contagion.py diff --git a/hypernetx/algorithms/tests/test_generative.py b/tests/algorithms/test_generative.py similarity index 100% rename from hypernetx/algorithms/tests/test_generative.py rename to tests/algorithms/test_generative.py diff --git a/hypernetx/algorithms/tests/test_homology_mod_2.py b/tests/algorithms/test_homology_mod_2.py similarity index 100% rename from hypernetx/algorithms/tests/test_homology_mod_2.py rename to tests/algorithms/test_homology_mod_2.py diff --git a/hypernetx/algorithms/tests/test_laplacians_clustering.py b/tests/algorithms/test_laplacians_clustering.py similarity index 100% rename from hypernetx/algorithms/tests/test_laplacians_clustering.py rename to tests/algorithms/test_laplacians_clustering.py diff --git a/hypernetx/algorithms/tests/test_modularity.py b/tests/algorithms/test_modularity.py similarity index 100% rename from hypernetx/algorithms/tests/test_modularity.py rename to tests/algorithms/test_modularity.py diff --git a/hypernetx/algorithms/tests/test_s_centrality_measures.py b/tests/algorithms/test_s_centrality_measures.py similarity index 100% rename from hypernetx/algorithms/tests/test_s_centrality_measures.py rename to tests/algorithms/test_s_centrality_measures.py diff --git a/hypernetx/classes/tests/conftest.py b/tests/classes/conftest.py similarity index 100% rename from hypernetx/classes/tests/conftest.py rename to tests/classes/conftest.py diff --git a/hypernetx/classes/tests/sample.csv b/tests/classes/sample.csv similarity index 100% rename from hypernetx/classes/tests/sample.csv rename to tests/classes/sample.csv diff --git a/hypernetx/classes/tests/test_hypergraph.py b/tests/classes/test_hypergraph.py similarity index 100% rename from hypernetx/classes/tests/test_hypergraph.py rename to tests/classes/test_hypergraph.py diff --git a/hypernetx/classes/tests/test_hypergraph_factory_methods.py b/tests/classes/test_hypergraph_factory_methods.py similarity index 100% rename from hypernetx/classes/tests/test_hypergraph_factory_methods.py rename to tests/classes/test_hypergraph_factory_methods.py diff --git a/hypernetx/classes/tests/test_hypergraph_view.py b/tests/classes/test_hypergraph_view.py similarity index 100% rename from hypernetx/classes/tests/test_hypergraph_view.py rename to tests/classes/test_hypergraph_view.py diff --git a/hypernetx/classes/tests/test_incidence_store.py b/tests/classes/test_incidence_store.py similarity index 100% rename from hypernetx/classes/tests/test_incidence_store.py rename to tests/classes/test_incidence_store.py diff --git a/hypernetx/classes/tests/test_nx_hnx_agreement.py b/tests/classes/test_nx_hnx_agreement.py similarity index 100% rename from hypernetx/classes/tests/test_nx_hnx_agreement.py rename to tests/classes/test_nx_hnx_agreement.py diff --git a/hypernetx/classes/tests/test_property_store.py b/tests/classes/test_property_store.py similarity index 100% rename from hypernetx/classes/tests/test_property_store.py rename to tests/classes/test_property_store.py diff --git a/tox.ini b/tox.ini index 1b8cfb70..27b3354f 100644 --- a/tox.ini +++ b/tox.ini @@ -29,7 +29,7 @@ commands_pre = poetry install --with test commands = env - poetry run coverage run --source=hypernetx -m pytest --junitxml=pytest.xml + poetry run coverage run --source=hypernetx -m pytest tests --junitxml=pytest.xml poetry run coverage report -m [testenv:notebooks-tests] From d3c61429b3719f3a1958484e9304598efa4b84ee Mon Sep 17 00:00:00 2001 From: Mark Bonicillo Date: Thu, 11 Apr 2024 11:19:52 -0700 Subject: [PATCH 2/4] Remove old notebooks --- .../classes/incidence_store_testing.ipynb | 226 ---- hypernetx/classes/property_stores.ipynb | 969 ------------------ 2 files changed, 1195 deletions(-) delete mode 100644 hypernetx/classes/incidence_store_testing.ipynb delete mode 100644 hypernetx/classes/property_stores.ipynb diff --git a/hypernetx/classes/incidence_store_testing.ipynb b/hypernetx/classes/incidence_store_testing.ipynb deleted file mode 100644 index 272b69bc..00000000 --- a/hypernetx/classes/incidence_store_testing.ipynb +++ /dev/null @@ -1,226 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "27fc8a9b", - "metadata": { - "toc": true - }, - "source": [ - "

Table of Contents

\n", - "
" - ] - }, - { - "cell_type": "markdown", - "id": "3c67cfb1", - "metadata": {}, - "source": [ - "# Notes\n", - "\n", - "going with regular dataframe for a few reasons:\n", - "* Can have column names to rely on that instead of position.\n", - "* using multi-indexing requires an additional row of \"data\" which is not needed.\n", - "* Code is more interpretable.\n", - "* it seems that it is more difficult to add new multi-indexes." - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "id": "6804bc42", - "metadata": {}, - "outputs": [], - "source": [ - "#!pytest incidence_store_tests.py" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "id": "adb60be4", - "metadata": { - "code_folding": [ - 15, - 21, - 30, - 43, - 49, - 62 - ] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "True\n", - "True\n", - "True\n", - "True\n", - "True\n", - "True\n" - ] - } - ], - "source": [ - "import pandas as pd\n", - "from incidence_store import IncidenceStore\n", - "\n", - "def test_iter():\n", - " # Test iteration over incidence pairs\n", - " data = pd.DataFrame({'nodes': [1, 2, 2, 3], 'edges': [1, 2, 3, 4]})\n", - " store = IncidenceStore(data)\n", - " expected_pairs = [(1, 1), (2, 2), (2, 3), (3, 4)]\n", - " actual_pairs = list(store)\n", - "\n", - " print(len(actual_pairs) == len(expected_pairs))\n", - " for i in range(len(actual_pairs)):\n", - " print(actual_pairs[i] == expected_pairs[i])\n", - "test_iter()\n", - "\n", - "def test_len():\n", - " # Test length of incidence store\n", - " data = pd.DataFrame({'nodes': [1, 2, 2, 3], 'edges': [1, 2, 3, 4]})\n", - " store = IncidenceStore(data)\n", - " print(len(store) == 4) # Should match the number of unique pairs\n", - "\n", - "def test_contains():\n", - " # Test if incidence pair exists\n", - " data = pd.DataFrame({'nodes': [1, 2, 2, 3], 'edges': [1, 2, 3, 4]})\n", - " store = IncidenceStore(data)\n", - "\n", - " assert (1, 1) in store\n", - " assert (2, 3) in store\n", - " assert (3, 5) not in store # Non-existent pair\n", - "\n", - "def test_neighbors():\n", - " # Test getting elements or memberships based on level and key\n", - " data = pd.DataFrame({'nodes': [1, 2, 2, 3], 'edges': [1, 2, 3, 4]})\n", - " store = IncidenceStore(data)\n", - "\n", - " assert store.neighbors(0, 1) == [1, 2] # Nodes in edge 1\n", - " assert store.neighbors(1, 2) == [2, 3] # Edges containing node 2\n", - " assert store.neighbors(0, 5) == [] # Non-existent edge\n", - " assert store.neighbors(2, 9) == [] # Non-existent node\n", - "\n", - " with pytest.raises(ValueError):\n", - " store.neighbors(3, 1) # Invalid level\n", - "\n", - "def test_edges():\n", - " # Test getting all edges\n", - " data = pd.DataFrame({'nodes': [1, 2, 2, 3], 'edges': [1, 2, 3, 4]})\n", - " store = IncidenceStore(data)\n", - " assert store.edges() == [1, 2, 3, 4]\n", - "\n", - "def test_nodes():\n", - " # Test getting all nodes\n", - " data = pd.DataFrame({'nodes': [1, 2, 2, 3], 'edges': [1, 2, 3, 4]})\n", - " store = IncidenceStore(data)\n", - " assert store.nodes() == [1, 2, 3]\n", - "\n", - "def test_dimensions():\n", - " # Test getting number of nodes and edges\n", - " data = pd.DataFrame({'nodes': [1, 2, 2, 3], 'edges': [1, 2, 3, 4]})\n", - " store = IncidenceStore(data)\n", - " print(store.dimensions() == (3, 4)) # (3 unique nodes, 4 unique edges)\n", - "test_dimensions()\n", - "\n", - "def test_restrict_to():\n", - " # Test restricting to a subset based on level and items\n", - " data = pd.DataFrame({'nodes': [1, 2, 2, 3], 'edges': [1, 2, 3, 4]})\n", - " store = IncidenceStore(data)\n", - "\n", - " # Inplace restriction\n", - " store.restrict_to(0, [1, 2], inplace=True)\n", - " assert store._data.equals(pd.DataFrame({'nodes': [1, 2], 'edges': [1, 2]}))\n", - " store = IncidenceStore(data) # Recreate initial store\n", - "\n", - " # Non-inplace restriction (returns new dataframe)\n", - " restricted_df = store.restrict_to(1, [2, 3], inplace=False)\n", - " assert not restricted_df.equals(store._data) # Should be a new dataframe\n", - " assert restricted_df.equals(pd.DataFrame({'nodes': [2, 3], 'edges': [2, 3]}))\n", - "\n", - " # Invalid level\n", - " with pytest.raises(ValueError):\n", - " store.restrict_to(3, [1]) # Invalid level should raise error\n", - "\n", - " # Non-existent items\n", - " store = IncidenceStore(data)\n", - " restricted_df = store.restrict_to(0, [5], inplace=False)\n", - " assert restricted_df.empty # Empty dataframe as no pairs with item 5\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "c4b333b3", - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.5" - }, - "toc": { - "base_numbering": 1, - "nav_menu": {}, - "number_sections": true, - "sideBar": false, - "skip_h1_title": false, - "title_cell": "Table of Contents", - "title_sidebar": "Contents", - "toc_cell": true, - "toc_position": {}, - "toc_section_display": true, - "toc_window_display": true - }, - "varInspector": { - "cols": { - "lenName": 16, - "lenType": 16, - "lenVar": 40 - }, - "kernels_config": { - "python": { - "delete_cmd_postfix": "", - "delete_cmd_prefix": "del ", - "library": "var_list.py", - "varRefreshCmd": "print(var_dic_list())" - }, - "r": { - "delete_cmd_postfix": ") ", - "delete_cmd_prefix": "rm(", - "library": "var_list.r", - "varRefreshCmd": "cat(var_dic_list()) " - } - }, - "types_to_exclude": [ - "module", - "function", - "builtin_function_or_method", - "instance", - "_Feature" - ], - "window_display": false - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/hypernetx/classes/property_stores.ipynb b/hypernetx/classes/property_stores.ipynb deleted file mode 100644 index 221000c0..00000000 --- a/hypernetx/classes/property_stores.ipynb +++ /dev/null @@ -1,969 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "id": "4f19fd90-bf5b-4669-972b-ebc1c7c18cde", - "metadata": { - "ExecuteTime": { - "end_time": "2024-03-12T23:45:02.971128Z", - "start_time": "2024-03-12T23:45:02.393051Z" - } - }, - "outputs": [], - "source": [ - "from property_store import PropertyStore\n", - "import pandas as pd" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "b0c4f4b20bfd82a8", - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-03-12T23:45:02.975967Z", - "start_time": "2024-03-12T23:45:02.972113Z" - } - }, - "outputs": [], - "source": [ - "LEVEL = 'level'\n", - "ID = 'id'\n", - "WEIGHT = 'weight'\n", - "PROPERTIES = 'misc_properties'\n", - "PROPERTIES_COLUMNS = [WEIGHT, PROPERTIES]\n", - "STRENGTH = 'strength'\n", - "HAIR_COLOR = 'hair_color'\n", - "INCIDENCES_PROPERTIES_COLUMNS = [WEIGHT, PROPERTIES, STRENGTH, HAIR_COLOR]\n" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "id": "8c21366f6624756b", - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-03-12T23:45:02.976761Z", - "start_time": "2024-03-12T23:45:02.974479Z" - } - }, - "outputs": [], - "source": [ - "edges = ['I', 'L', 'O', 'P', 'R', 'S']\n", - "\n", - "nodes = ['A', 'C', 'E', 'K', 'T1', 'T2', 'V']\n", - "\n", - "incidences = [('I', 'K'), ('I', 'T2'), ('L', 'C'), ('L', 'E'), ('O', 'T1'), ('O', 'T2'), ('P', 'A'), ('P', 'C'), ('P', 'K'), ('R', 'A'), ('R', 'E'), ('S', 'A'), ('S', 'K'), ('S', 'T2'), ('S', 'V')]" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "id": "73ac534aa8865bd8", - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-03-12T23:45:02.978411Z", - "start_time": "2024-03-12T23:45:02.976429Z" - } - }, - "outputs": [], - "source": [ - "ip_index = pd.MultiIndex.from_tuples(incidences, names=[LEVEL, ID])" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "7073a872bd5fcf69", - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-03-12T23:45:02.982736Z", - "start_time": "2024-03-12T23:45:02.980366Z" - } - }, - "outputs": [], - "source": [ - "# corresponding property store data\n", - "# uid, weight, properties\n", - "import uuid\n", - "edges_data = [(1, {}) for i in edges]\n", - "nodes_data = [(1, {}) for i in nodes]\n", - "inc_data = [(1, {}, 42, 'red') for _ in range(len(ip_index))]" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "4d89507e27fb39e1", - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-03-12T23:45:02.986955Z", - "start_time": "2024-03-12T23:45:02.983145Z" - } - }, - "outputs": [], - "source": [ - "# columns should map corresponding fields to the data\n", - "edges_index = pd.Index(edges, name=ID)\n", - "edges_df = pd.DataFrame(data=edges_data, index=edges_index, columns=[WEIGHT, PROPERTIES])\n", - "\n", - "nodes_index = pd.Index(nodes, name=ID)\n", - "nodes_df = pd.DataFrame(data=nodes_data, index=nodes_index, columns=PROPERTIES_COLUMNS)\n", - "\n", - "incidence_df = pd.DataFrame(data=inc_data, index=ip_index, columns=INCIDENCES_PROPERTIES_COLUMNS)" - 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" - }, - "execution_count": 23, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "incidence_df" - ] - }, - { - "cell_type": "code", - "execution_count": 24, - "id": "a048092e4b628b1c", - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-03-12T23:45:03.133724Z", - "start_time": "2024-03-12T23:45:03.091619Z" - } - }, - "outputs": [], - "source": [ - "inc_ps = PropertyStore(incidence_df)" - ] - }, - { - "cell_type": "code", - "execution_count": 25, - "id": "d94d9e5664364c0c", - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-03-12T23:45:03.134407Z", - "start_time": "2024-03-12T23:45:03.091958Z" - } - }, - "outputs": [ - { - "data": { - "text/plain": " weight misc_properties strength hair_color \\\nlevel id \nI K 1 {} 42 red \n T2 1 {} 42 red \nL C 1 {} 42 red \n E 1 {} 42 red \nO T1 1 {} 42 red \n T2 1 {} 42 red \nP A 1 {} 42 red \n C 1 {} 42 red \n K 1 {} 42 red \nR A 1 {} 42 red \n E 1 {} 42 red \nS A 1 {} 42 red \n K 1 {} 42 red \n T2 1 {} 42 red \n V 1 {} 42 red \n\n uid \nlevel id \nI K a9480e6d-b35d-4e85-aecf-281be8b4416d \n T2 746c4626-4bf8-4cac-9175-87609f4b9695 \nL C 954f8ab7-7b29-42d6-9faf-8076edb46fde \n E 56e812d7-5b78-45ba-a71a-5e5a3d14d57d \nO T1 ff55771d-872a-4c31-ad1a-a3429f38fdf4 \n T2 8eba7627-33c1-4ed6-b307-c845733975fc \nP A 20d7fc56-b4fe-44db-926e-bb3c15432878 \n C e484a40e-92f5-438b-b7fc-69c9a2b3e88e \n K 6b579df7-d440-41ab-908b-25e94f880b93 \nR A 3c057d33-9cae-427e-bfcf-3134e85b3219 \n E e110416d-db4b-4a62-9bb6-de9e80221da2 \nS A e410791f-3724-41cf-b5d6-10063741d916 \n K 72c7683b-2022-4360-bb35-0a6fef1ac2a3 \n T2 f3dab40a-5bf2-4ed7-8be8-d62f4b5da7a5 \n V 783873d6-f616-4a2d-bfc4-43c7c186dd05 ", - "text/html": "
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" - }, - "execution_count": 38, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "nodes_ps = PropertyStore(nodes_df, index=True)\n", - "nodes_ps.properties" - ] - }, - { - "cell_type": "code", - "outputs": [], - "source": [], - "metadata": { - "collapsed": false, - "ExecuteTime": { - "end_time": "2024-03-12T23:45:03.179151Z", - "start_time": "2024-03-12T23:45:03.112166Z" - } - }, - "id": "e32fbfed693fdf87", - "execution_count": 38 - } - ], - "metadata": { - "kernelspec": { - "display_name": "venv-hnx", - "language": "python", - "name": "venv-hnx" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.3" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} From 1d6eba423eeb32eccc5103db9e20110a4f6b8472 Mon Sep 17 00:00:00 2001 From: Mark Bonicillo Date: Mon, 15 Apr 2024 11:02:12 -0700 Subject: [PATCH 3/4] Update tests --- tests/classes/conftest.py | 326 ++++----------- tests/classes/test_hypergraph.py | 387 ++++++++++-------- .../test_hypergraph_factory_methods.py | 8 +- 3 files changed, 296 insertions(+), 425 deletions(-) diff --git a/tests/classes/conftest.py b/tests/classes/conftest.py index 2316f40b..02cf9931 100644 --- a/tests/classes/conftest.py +++ b/tests/classes/conftest.py @@ -7,17 +7,33 @@ from hypernetx import Hypergraph, HarryPotter, LesMis as LM from hypernetx.classes.helpers import create_dataframe -from collections import OrderedDict, defaultdict +from collections import OrderedDict, defaultdict, namedtuple class SevenBySix: """Example hypergraph with 7 nodes and 6 edges.""" - def __init__(self, static=False): + def __init__(self): + # Nodes + SBS_Nodes = namedtuple("SBS_Nodes", "A C E K T1 T2 V") a, c, e, k, t1, t2, v = nd = ("A", "C", "E", "K", "T1", "T2", "V") + self.nodes = SBS_Nodes(a, c, e, k, t1, t2, v) + + # Edges + SBS_Edges = namedtuple("SBS_Edges", "I L O P R S") i, l, o, p, r, s = ("I", "L", "O", "P", "R", "S") - self.edges = [{a, c, k}, {a, e}, {a, k, t2, v}, {c, e}, {t1, t2}, {k, t2}] - self.nodes = set(nd) + self.edges = SBS_Edges(i, l, o, p, r, s) + + # Labels + self.labels = OrderedDict( + [ + ("edges", list(self.edges)), + ("nodes", list(self.nodes)), + ] + ) + + # define edges + self.edges_list = [{a, c, k}, {a, e}, {a, k, t2, v}, {c, e}, {t1, t2}, {k, t2}] self.edgedict = OrderedDict( [ (p, {a, c, k}), @@ -28,7 +44,10 @@ def __init__(self, static=False): (i, {k, t2}), ] ) + self.dataframe = create_dataframe(self.edgedict) + # row = number of nodes = 6 + # columns = number of edges = 7 self.arr = np.array( [ [0, 0, 0, 1, 0, 1, 0], @@ -39,12 +58,6 @@ def __init__(self, static=False): [1, 0, 0, 1, 0, 1, 1], ] ) - self.labels = OrderedDict( - [ - ("edges", [i, l, o, p, r, s]), - ("nodes", [a, c, e, k, t1, t2, v]), - ] - ) self.data = np.array( [ @@ -66,7 +79,10 @@ def __init__(self, static=False): ] ) - self.dataframe = create_dataframe(self.edgedict) + +@pytest.fixture +def sbs() -> SevenBySix: + return SevenBySix() class TriLoop: @@ -76,26 +92,47 @@ def __init__(self): A, B, C, D = "A", "B", "C", "D" AB, BC, ACD = "AB", "BC", "ACD" self.edgedict = {AB: {A, B}, BC: {B, C}, ACD: {A, C, D}} - self.hypergraph = Hypergraph(self.edgedict, name="TriLoop") + + +@pytest.fixture +def triloop(): + return TriLoop() class TriLoop2: """Triloop example with redundant node and edge""" def __init__(self): + # Nodes A, B, C, D, E = "A", "B", "C", "D", "E" + # Edges AB, BC, ACD, ACD2 = "AB", "BC", "ACD", "ACD2" + self.nodes = set([A, B, C, D, E]) + self.edgedict = {AB: {A, B}, BC: {B, C}, ACD: {A, C, D, E}, ACD2: {A, C, D, E}} - self.hypergraph = Hypergraph(self.edgedict, name="TriLoop2") + self.name = "TriLoop2" + + +@pytest.fixture +def triloop2(): + return TriLoop2() class SBSDupes: def __init__(self): + # Nodes + a, c, e, f, k, t1, t2, v = nd = ("A", "C", "E", "F", "K", "T1", "T2", "V") + self.nodes = (a, c, e, f, k, t1, t2, v) + + # Edges + i, l, m, o, p, r, s = ("I", "L", "M", "O", "P", "R", "S") + self.edges = (i, l, m, o, p, r, s) + self.edgedict = OrderedDict( [ - ("I", {"K", "T2"}), - ("L", {"C", "E", "F"}), - ("M", {"C", "E", "F"}), + (i, {k, t2}), + (l, {c, e, f}), + (m, {c, e, f}), ("O", {"T1", "T2"}), ("P", {"A", "C", "K"}), ("R", {"A", "E", "F"}), @@ -106,6 +143,11 @@ def __init__(self): self.dataframe = create_dataframe(self.edgedict) +@pytest.fixture +def sbs_dupes(): + return SBSDupes() + + class LesMis: def __init__(self): self.edgedict = OrderedDict( @@ -136,98 +178,31 @@ def __init__(self): (8, {"FN", "JA", "JV", "PO", "SP", "SS"}), ] ) - self.hypergraph = Hypergraph(self.edgedict) - - -class Dataframe: - def __init__(self): - fname = os.path.join(os.path.dirname(__file__), "sample.csv") - self.df = pd.read_csv(fname, index_col=0) - - -class CompleteBipartite: - def __init__(self, n1, n2): - self.g = nx.complete_bipartite_graph(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) +def lesmis(): + return LesMis() @pytest.fixture -def sbs_labels(sbs): - return sbs.labels +def sample_df(): + fname = os.path.join(os.path.dirname(__file__), "sample.csv") + return pd.read_csv(fname, index_col=0) -@pytest.fixture -def triloop(): - return TriLoop() +#### Old fixtures not in use -@pytest.fixture -def triloop2(): - return TriLoop2() - - -@pytest.fixture -def sbs_hypergraph(sbs): - return Hypergraph(sbs.edgedict, name="sbsh", edge_col="edges", node_col="nodes") +class CompleteBipartite: + def __init__(self, n1, n2): + self.g = nx.complete_bipartite_graph(n1, n2) + self.left, self.right = nx.bipartite.sets(self.g) @pytest.fixture -def sbs_graph(sbs): +def sbs_graph(): + sbs = SevenBySix() edges = set() for _, e in sbs.edgedict.items(): edges.update(it.combinations(e, 2)) @@ -236,22 +211,6 @@ def sbs_graph(sbs): return G -@pytest.fixture -def sbsd(): - return SBSDupes() - - -@pytest.fixture -def sbsd_hypergraph(): - sbsd = SBSDupes() - return Hypergraph(sbsd.edgedict) - - -@pytest.fixture -def lesmis(): - return LesMis() - - @pytest.fixture def G(): return nx.karate_club_graph() @@ -275,11 +234,6 @@ def complete_bipartite_example(): return CompleteBipartite(2, 3).g -@pytest.fixture -def dataframe(): - return Dataframe() - - @pytest.fixture def dataframe_example(): M = np.array([[1, 1, 0, 0], [0, 1, 1, 0], [1, 0, 1, 0]]) @@ -288,148 +242,8 @@ def dataframe_example(): return pd.DataFrame(M, index=index, columns=columns) -@pytest.fixture -def harry_potter(): - return HarryPotter() - - @pytest.fixture def array_example(): return np.array( [[0, 1, 1, 0, 1], [1, 1, 1, 1, 1], [1, 0, 0, 1, 0], [0, 0, 0, 0, 1]] ) - - -####################Fixtures suite for test_hypergraph.py#################### -####################These fixtures are modular and thus have inter-dependencies#################### -@pytest.fixture -def les_mis(): - return LM() - - -@pytest.fixture -def scenes(): - return { - "0": ("FN", "TH"), - "1": ("TH", "JV"), - "2": ("BM", "FN", "JA"), - "3": ("JV", "JU", "CH", "BM"), - "4": ("JU", "CH", "BR", "CN", "CC", "JV", "BM"), - "5": ("TH", "GP"), - "6": ("GP", "MP"), - "7": ("MA", "GP"), - } - - -@pytest.fixture -def edges(scenes): - return list(set(list(scenes.keys()))) - - -@pytest.fixture -def nodes(scenes): - return list(set(list(np.concatenate([v for v in scenes.values()])))) - - -@pytest.fixture -def edge_properties(edges): - edge_properties = defaultdict(dict) - edge_properties.update( - {str(ed): {"weight": np.random.randint(2, 10)} for ed in range(0, 8, 2)} - ) - for ed in edges: - edge_properties[ed].update({"color": np.random.choice(["red", "green"])}) - return edge_properties - - -@pytest.fixture -def node_properties(les_mis, nodes): - return { - ch: { - "FullName": les_mis.dnames.loc[ch].FullName, - "Description": les_mis.dnames.loc[ch].Description, - "color": np.random.choice(["pink", "blue"]), - } - for ch in nodes - } - - -@pytest.fixture -def scenes_dataframe(scenes): - scenes_dataframe = ( - pd.DataFrame(pd.Series(scenes).explode()) - .reset_index() - .rename(columns={"index": "Scenes", 0: "Characters"}) - ) - scenes_dataframe["color"] = np.random.choice( - ["red", "green"], len(scenes_dataframe) - ) - scenes_dataframe["heaviness"] = np.random.rand(len(scenes_dataframe)) - - return scenes_dataframe - - -@pytest.fixture -def hyp_no_props(): - return Hypergraph( - pd.DataFrame( - np.array( - [ - np.random.choice(list("ABCD"), 50), - np.random.choice(list("abcdefghijklmnopqrstuvwxyz"), 50), - ] - ).T, # creates a transposed ndarray - columns=["Club", "Member"], - ) - ) - - -@pytest.fixture -def hyp_df_with_props(scenes_dataframe, node_properties, edge_properties): - return Hypergraph( - scenes_dataframe, - # cell_properties=["color"], - cell_weight_col="heaviness", - node_properties=node_properties, - edge_properties=edge_properties, - ) - - -@pytest.fixture -def hyp_dict_with_props(scenes): - scenes_with_cellprops = { - ed: { - ch: { - "color": np.random.choice(["red", "green"]), - "cell_weight": np.random.rand(), - } - for ch in v - } - for ed, v in scenes.items() - } - - return Hypergraph( - scenes_with_cellprops, - edge_col="Scenes", - node_col="Characters", - cell_weight_col="cell_weight", - cell_properties=scenes_with_cellprops, - ) - - -@pytest.fixture -def hyp_props_on_edges_nodes(scenes_dataframe, edge_properties, node_properties): - return Hypergraph( - setsystem=scenes_dataframe, - edge_col="Scenes", - node_col="Characters", - cell_weight_col="cell_weight", - cell_properties=["color"], - edge_properties=edge_properties, - node_properties=node_properties, - default_edge_weight=2.5, - default_node_weight=6, - ) - - -####################Fixtures suite for test_hypergraph.py#################### diff --git a/tests/classes/test_hypergraph.py b/tests/classes/test_hypergraph.py index 851d660f..ed3f1d01 100644 --- a/tests/classes/test_hypergraph.py +++ b/tests/classes/test_hypergraph.py @@ -8,65 +8,95 @@ from networkx.algorithms import bipartite from hypernetx.classes.property_store import PropertyStore +from tests.classes.conftest import SevenBySix -def test_hypergraph_from_iterable_of_sets(sbs): - H = Hypergraph(sbs.edges) - assert len(H.edges) == 6 - assert len(H.nodes) == 7 - assert H.degree("A") == 3 - assert H.number_of_edges() == 6 - assert H.number_of_nodes() == 7 +#################Tests on constructors and from_ ################################ -def test_hypergraph_from_dict(sbs): - H = Hypergraph(sbs.edgedict) - assert len(H.edges) == 6 - assert len(H.nodes) == 7 - assert H.degree("A") == 3 - assert H.size("R") == 2 - assert H.order() == 7 +@pytest.mark.parametrize( + "hg", + [ + Hypergraph(SevenBySix().edges_list), # list of edges + Hypergraph(SevenBySix().edgedict), # dictionary of edges to nodes + Hypergraph(SevenBySix().dataframe), # dataframe of edges to nodes + ], +) +def test_constructor_on_various_set_systems(hg): + sbs = SevenBySix() + assert len(hg.edges) == len(sbs.edges) + assert len(hg.nodes) == len(sbs.nodes) + assert hg.number_of_edges() == len(sbs.edges) + assert hg.number_of_nodes() == len(sbs.nodes) + assert hg.degree(sbs.nodes.A) == 3 + assert hg.order() == len(sbs.nodes) -def test_hypergraph_custom_attributes(sbs): - H = Hypergraph(sbs.edges) - assert isinstance(H.__str__(), str) - assert isinstance(H.__repr__(), str) - assert H.__contains__("A") - assert H.__len__() == 7 - nodes = [key for key in H.__iter__()] - assert sorted(nodes) == ["A", "C", "E", "K", "T1", "T2", "V"] - assert sorted(H.__getitem__("C")) == ["A", "E", "K"] +@pytest.mark.parametrize("h", [Hypergraph(), Hypergraph({})]) +def test_construct_empty_hypergraph(h): + h = Hypergraph() + assert h.shape == (0, 0) + assert h.edges.is_empty() + assert h.nodes.is_empty() -def test_get_linegraph(sbs): - H = Hypergraph(sbs.edges) - assert len(H.edges) == 6 - assert len(H.nodes) == 7 - assert len(set(H.get_linegraph(s=1)).difference(set([0, 1, 2, 3, 4, 5]))) == 0 + +def test_from_incidence_dataframe(lesmis): + h = Hypergraph(lesmis.edgedict) + df = h.incidence_dataframe() + hg = Hypergraph.from_incidence_dataframe(df) + assert hg.shape == (40, 8) + assert hg.size(3) == 8 + assert hg.degree("JA") == 3 + + +def test_from_numpy_array(sbs): + hg = Hypergraph.from_numpy_array(sbs.arr) + assert len(hg.nodes) == len(sbs.arr) + assert len(hg.edges) == len(sbs.arr[0]) + assert hg.dim("e5") == 2 + assert set(hg.neighbors("v2")) == {"v0", "v5"} + + +def test_from_bipartite(sbs): + hg = Hypergraph(sbs.edgedict) + hg_b = Hypergraph.from_bipartite(hg.bipartite()) + assert len(hg_b.edges) == len(sbs.edges) + assert len(hg_b.nodes) == 7 + + +#################tests on methods ################################ +def test_len(sbs): + hg = Hypergraph(sbs.edgedict) + assert len(hg) == len(sbs.nodes) -def test_hypergraph_from_incidence_dataframe(lesmis): - df = lesmis.hypergraph.incidence_dataframe() - H = Hypergraph.from_incidence_dataframe(df) - assert H.shape == (40, 8) - assert H.size(3) == 8 - assert H.degree("JA") == 3 +def test_contains(sbs): + hg = Hypergraph(sbs.edgedict) + assert sbs.nodes.A in hg -def test_hypergraph_from_numpy_array(sbs): - H = Hypergraph.from_numpy_array(sbs.arr) - assert len(H.nodes) == 6 - assert len(H.edges) == 7 - assert H.dim("e5") == 2 - assert set(H.neighbors("v2")) == {"v0", "v5"} +def test_iterator(sbs): + hg = Hypergraph(sbs.edgedict) + nodes = [key for key in hg] + assert sorted(nodes) == list(sbs.nodes) -def test_hypergraph_from_bipartite(sbsd_hypergraph): - H = sbsd_hypergraph - HB = Hypergraph.from_bipartite(H.bipartite()) - assert len(HB.edges) == 7 - assert len(HB.nodes) == 8 +def test_getitem(sbs): + hg = Hypergraph(sbs.edgedict) + nodes = hg[sbs.nodes.C] + assert sorted(nodes) == [sbs.nodes.A, sbs.nodes.E, sbs.nodes.K] + + +def test_get_linegraph(sbs): + hg = Hypergraph(sbs.edgedict) + assert len(hg.edges) == len(sbs.edges) + assert len(hg.nodes) == len(sbs.nodes) + + lg = hg.get_linegraph(s=1) + + diff = set(lg).difference(set(sbs.edges)) + assert len(diff) == 0 def test_add_edge_inplace(sbs): @@ -112,88 +142,129 @@ def test_add_edge_not_inplace(sbs): def test_remove_edges(sbs): - H = Hypergraph(sbs.edgedict) - assert H.shape == (7, 6) - # remove an edge without removing any nodes - H = H.remove_edges("P") - assert H.shape == (7, 5) - # remove an edge containing a singleton ear - H = H.remove_edges("O") - assert H.shape == (6, 4) + hg = Hypergraph(sbs.edgedict) + # shape returns (#nodes, #edges) + assert hg.shape == (len(sbs.nodes), len(sbs.edges)) + + # remove an edge containing nodes that are in other edges + # the number of nodes should not decrease + hg = hg.remove_edges(sbs.edges.P) + assert hg.shape == (len(sbs.nodes), len(sbs.edges) - 1) + + # remove an edge containing a singleton ear (i.e. a node not present in other edges) + # the number of nodes should decrease by exactly one + hg = hg.remove_edges(sbs.edges.O) + assert hg.shape == (len(sbs.nodes) - 1, len(sbs.edges) - 2) + + +def test_remove_nodes(sbs): + hg = Hypergraph(sbs.edgedict) + + assert sbs.nodes.A in hg.nodes + assert sbs.nodes.A in hg.edges[sbs.edges.P] + assert sbs.nodes.A in hg.edges[sbs.edges.R] + assert sbs.nodes.A in hg.edges[sbs.edges.S] + + hg_new = hg.remove_nodes(sbs.nodes.A) + + assert sbs.nodes.A not in hg_new.nodes + assert sbs.nodes.A not in hg_new.edges[sbs.edges.P] + assert sbs.nodes.A not in hg_new.edges[sbs.edges.R] + assert sbs.nodes.A not in hg_new.edges[sbs.edges.S] -@pytest.mark.skip("reason=remove has a new signature") def test_remove(triloop2): - H = triloop2.hypergraph - k = "ACD2" + H = Hypergraph(triloop2.edgedict, name=triloop2.name) + assert H.shape == (5, 4) - newH = H.remove(k, level=0) + duplicate_edge = ["ACD2"] + newH = H.remove(duplicate_edge, level=0) assert newH.shape == (5, 3) - newH = H.remove("E", level=1) + + assert H.shape == (5, 4) + newH = H.remove(["E"], level=1) assert newH.shape == (4, 4) - newH = H.remove("ACD", level=0) + + assert H.shape == (5, 4) + newH = H.remove(["ACD"], level=0) assert newH.shape == (5, 3) + + # remove incidence in which the node is associated with other edges + assert H.shape == (5, 4) + newH = H.remove([("ACD", "E")]) + assert newH.shape == (5, 4) + + # edge case: + # level defaults to 2, which handles the case of incidence pairs + # the list of incidence pairs must be a list of tuples + # if no tuples are given, the default behavior is to treat the list as a list of edges to be removed + # if one of the edges in the list doesn't exist, it is ignored + + # case 1: level defaults to 2, list of uids is a list of edges and nodes + assert H.shape == (5, 4) newH = H.remove(["ACD", "E"]) - assert newH.shape == (4, 3) - # with pytest.raises(TypeError): - # H.remove({"ACD": "edge"}) - - -def test_remove_nodes(): - a, b, c, d = "a", "b", "c", "d" - hbug = Hypergraph({0: [a, b], 1: [a, c], 2: [a, d]}) - assert a in hbug.nodes - assert a in hbug.edges[0] - assert a in hbug.edges[1] - assert a in hbug.edges[2] - hbug = hbug.remove_nodes(a) - assert a not in hbug.nodes - assert a not in hbug.edges[0] - assert a not in hbug.edges[1] - assert a not in hbug.edges[2] - - -def test_matrix(sbs_hypergraph): - H = sbs_hypergraph - assert H.incidence_matrix().todense().shape == (7, 6) - assert H.adjacency_matrix(s=2).todense().shape == (7, 7) - assert H.edge_adjacency_matrix().todense().shape == (6, 6) - aux_matrix = H.auxiliary_matrix(node=False) + assert newH.shape == (5, 3) + + # case 2: level defaults to 2, list of uids is a list of edges + # removing 2 edges that have the node B. Node B is not associated with any other edge + # new hypergraph should have 4 nodes and 2 edges + assert H.shape == (5, 4) + newH = H.remove(["AB", "BC"]) + assert newH.shape == (4, 2) + + # case 3: level defaults to 2, list of uids is a list of nodes + # no change + assert H.shape == (5, 4) + newH = H.remove(list(triloop2.nodes)) + assert newH.shape == (5, 4) + + +def test_matrix(sbs): + hg = Hypergraph(sbs.edgedict) + + assert hg.incidence_matrix().todense().shape == (len(sbs.nodes), len(sbs.edges)) + assert hg.adjacency_matrix(s=2).todense().shape == (7, 7) + assert hg.edge_adjacency_matrix().todense().shape == (6, 6) + + aux_matrix = hg.auxiliary_matrix(node=False) assert aux_matrix.todense().shape == (6, 6) -def test_collapse_edges(sbsd_hypergraph): - H = sbsd_hypergraph - assert len(H.edges) == 7 - HC = H.collapse_edges() - assert len(HC.edges) == 6 +def test_collapse_edges(sbs_dupes): + hg = Hypergraph(sbs_dupes.edgedict) + assert len(hg.edges) == len(sbs_dupes.edges) + + hc = hg.collapse_edges() + assert len(hc.edges) == len(sbs_dupes.edges) - 1 + + +def test_collapse_nodes(sbs_dupes): + hg = Hypergraph(sbs_dupes.edgedict) + assert len(hg.nodes) == len(sbs_dupes.nodes) + hc = hg.collapse_nodes() + assert len(hc.nodes) == len(sbs_dupes.nodes) - 1 -def test_collapse_nodes(sbsd_hypergraph): - H = sbsd_hypergraph - assert len(H.nodes) == 8 - HC = H.collapse_nodes() - assert len(HC.nodes) == 7 +def test_collapse_nodes_and_edges(sbs_dupes): + hg = Hypergraph(sbs_dupes.edgedict) + hc2 = hg.collapse_nodes_and_edges() -def test_collapse_nodes_and_edges(sbsd_hypergraph): - H = sbsd_hypergraph - HC2 = H.collapse_nodes_and_edges() - assert len(H.edges) == 7 - assert len(HC2.edges) == 6 - assert len(H.nodes) == 8 - assert len(HC2.nodes) == 7 + assert len(hg.edges) == len(sbs_dupes.edges) + assert len(hc2.edges) == len(sbs_dupes.edges) - 1 + assert len(hg.nodes) == len(sbs_dupes.nodes) + assert len(hc2.nodes) == len(sbs_dupes.nodes) - 1 -def test_restrict_to_edges(sbs_hypergraph): - H = sbs_hypergraph +def test_restrict_to_edges(sbs): + H = Hypergraph(sbs.edgedict) HS = H.restrict_to_edges(["P", "O"]) assert len(H.edges) == 6 assert len(HS.edges) == 2 -def test_restrict_to_nodes(sbs_hypergraph): - H = sbs_hypergraph +def test_restrict_to_nodes(sbs): + H = Hypergraph(sbs.edgedict) assert len(H.nodes) == 7 H1 = H.restrict_to_nodes(["A", "E", "K"]) assert len(H.nodes) == 7 @@ -203,9 +274,8 @@ def test_restrict_to_nodes(sbs_hypergraph): assert "C" not in H1.edges["P"] -# @pytest.mark.skip("reason=Deprecated method") def test_remove_from_restriction(triloop): - h = triloop.hypergraph + h = Hypergraph(triloop.edgedict) h1 = h.restrict_to_nodes(h.neighbors("A")).remove_nodes( "A" ) # Hypergraph does not have a remove_node method @@ -213,9 +283,9 @@ def test_remove_from_restriction(triloop): assert "A" not in h1.edges["ACD"] -def test_toplexes(sbsd_hypergraph): - H = sbsd_hypergraph - T = H.toplexes(return_hyp=True) +def test_toplexes(sbs_dupes): + h = Hypergraph(sbs_dupes.edgedict) + T = h.toplexes(return_hyp=True) assert len(T.nodes) == 8 assert len(T.edges) == 5 T = T.collapse_nodes() @@ -232,7 +302,6 @@ def test_is_connected(): assert h.is_connected(s=3, edges=True) is False -# @pytest.mark.skip("Deprecated methods") def test_singletons(): E = {1: {2, 3, 4, 5}, 6: {2, 5, 7, 8, 9}, 10: {11}, 12: {13}, 14: {7}} h = Hypergraph(E) @@ -298,7 +367,7 @@ def test_s_component_subgraphs(): def test_size(sbs): h = Hypergraph(sbs.edgedict) - assert h.size("S") == 4 + assert h.size(sbs.edges.S) == len(sbs.edgedict[sbs.edges.S]) assert h.size("S", {"T2", "V"}) == 2 assert h.size("S", {"T1", "T2"}) == 1 assert h.size("S", {"T2"}) == 1 @@ -309,6 +378,10 @@ def test_size(sbs): def test_diameter(sbs): h = Hypergraph(sbs.edgedict) assert h.diameter() == 3 + + +def test_diameter_should_raise_error(sbs): + h = Hypergraph(sbs.edgedict) with pytest.raises(Exception) as excinfo: h.diameter(s=2) assert "Hypergraph is not s-connected." in str(excinfo.value) @@ -317,7 +390,7 @@ def test_diameter(sbs): def test_node_diameters(sbs): h = Hypergraph(sbs.edgedict) assert h.node_diameters()[0] == 3 - assert h.node_diameters()[2] == [{"A", "C", "E", "K", "T1", "T2", "V"}] + assert h.node_diameters()[2] == [set(sbs.nodes)] def test_edge_diameter(sbs): @@ -329,67 +402,46 @@ def test_edge_diameter(sbs): assert "Hypergraph is not s-connected." in str(excinfo.value) -def test_bipartite(sbs_hypergraph): - assert bipartite.is_bipartite(sbs_hypergraph.bipartite()) +def test_bipartite(sbs): + hg = Hypergraph(sbs.edgedict) + assert bipartite.is_bipartite(hg.bipartite()) -def test_dual(sbs_hypergraph): - H = sbs_hypergraph - HD = H.dual() - assert isinstance(HD.nodes.property_store, PropertyStore) - assert isinstance(HD.edges.property_store, PropertyStore) - assert set(H.nodes) == set(HD.edges) - assert set(H.edges) == set(HD.nodes) - assert list(H.dataframe.columns) == list(HD.dataframe.columns) +def test_dual(sbs): + h = Hypergraph(sbs.edgedict) + hd = h.dual() + assert isinstance(hd.nodes.property_store, PropertyStore) + assert isinstance(hd.edges.property_store, PropertyStore) + assert set(h.nodes) == set(hd.edges) + assert set(h.edges) == set(hd.nodes) + assert list(h.dataframe.columns) == list(hd.dataframe.columns) @pytest.mark.filterwarnings("ignore:No 3-path between ME and FN") def test_distance(lesmis): - h = lesmis.hypergraph + h = Hypergraph(lesmis.edgedict) assert h.distance("ME", "FN") == 2 assert h.distance("ME", "FN", s=2) == 3 assert h.distance("ME", "FN", s=3) == np.inf def test_edge_distance(lesmis): - h = lesmis.hypergraph + h = Hypergraph(lesmis.edgedict) assert h.edge_distance(1, 4) == 2 h2 = h.remove([5], 0) assert h2.edge_distance(1, 4) == 3 assert h2.edge_distance(1, 4, s=2) == np.inf -def test_dataframe(lesmis): - h = lesmis.hypergraph +def test_incidence_dataframe(lesmis): + h = Hypergraph(lesmis.edgedict) df = h.incidence_dataframe() assert np.allclose(np.array(np.sum(df)), np.array([10, 9, 8, 4, 8, 3, 12, 6])) -def test_construct_empty_hypergraph(): - h = Hypergraph() - assert h.shape == (0, 0) - assert h.edges.is_empty() - assert h.nodes.is_empty() - assert isinstance(h.dataframe, pd.DataFrame) - - -def test_construct_hypergraph_from_empty_dict(): - h = Hypergraph({}) - assert h.shape == (0, 0) - assert h.edges.is_empty() - assert h.nodes.is_empty() - - -def test_construct_hypergraph_empty_dict(): - h = Hypergraph(dict()) - assert h.shape == (0, 0) - assert h.edges.is_empty() - assert h.nodes.is_empty() - - def test_static_hypergraph_s_connected_components(lesmis): - H = Hypergraph(lesmis.edgedict) - assert {7, 8} in list(H.s_connected_components(edges=True, s=4)) + h = Hypergraph(lesmis.edgedict) + assert {7, 8} in list(h.s_connected_components(edges=True, s=4)) def test_difference_on_same_hypergraph(lesmis): @@ -405,21 +457,24 @@ def test_difference_on_same_hypergraph(lesmis): assert hg_diff.incidence_dict == {} -def test_difference_on_empty_hypergraph(sbs_hypergraph): +def test_difference_on_empty_hypergraph(sbs): hg_empty = Hypergraph() + hg = Hypergraph(sbs.edgedict) + hg_diff = hg - hg_empty - hg_diff = sbs_hypergraph - hg_empty + assert len(hg_diff) == len(sbs.nodes) + assert len(hg_diff.nodes) == len(sbs.nodes) + assert len(hg_diff.edges) == len(sbs.edges) + assert hg_diff.shape == (len(sbs.nodes), len(sbs.edges)) - assert len(hg_diff) == 7 - assert len(hg_diff.nodes) == 7 - assert len(hg_diff.edges) == 6 - assert hg_diff.shape == (7, 6) + assert all(e in sbs.edges for e in hg_diff.edges) + assert all(n in sbs.nodes for n in hg_diff.nodes) - edges = ["I", "L", "O", "P", "R", "S"] - assert all(uid in edges for uid in hg_diff.incidence_dict.keys()) +def test_difference_on_similar_hypergraph(sbs): + hg = Hypergraph(sbs.edgedict) -def test_difference_on_similar_hypergraph(sbs_hypergraph): + # create a hypergraph based on hg, but remove the 'I' edge a, c, e, k, t1, t2, v = ("A", "C", "E", "K", "T1", "T2", "V") l, o, p, r, s = ("L", "O", "P", "R", "S") data = OrderedDict( @@ -427,12 +482,16 @@ def test_difference_on_similar_hypergraph(sbs_hypergraph): ) hg_similar = Hypergraph(data, edge_col="edges", node_col="nodes") - hg_diff = sbs_hypergraph - hg_similar + # returns a hypergraph with one edge and two nodes + hg_diff = hg - hg_similar assert len(hg_diff) == 2 assert len(hg_diff.nodes) == 2 assert len(hg_diff.edges) == 1 assert hg_diff.shape == (2, 1) - print(hg_diff.incidence_dict.keys()) - edges = ["I"] - assert all(uid in edges for uid in hg_diff.incidence_dict.keys()) + + edges_diff = ["I"] + assert all(edge in edges_diff for edge in hg_diff.edges) + + nodes_diff = ["K", "T2"] + assert all(node in nodes_diff for node in hg_diff.nodes) diff --git a/tests/classes/test_hypergraph_factory_methods.py b/tests/classes/test_hypergraph_factory_methods.py index 72ccea8d..316d8c1e 100644 --- a/tests/classes/test_hypergraph_factory_methods.py +++ b/tests/classes/test_hypergraph_factory_methods.py @@ -68,9 +68,7 @@ def test_from_dataframe_with_key(): assert "C" not in h.edges["a"] -def test_from_dataframe_with_transforms_and_fillna(dataframe): - df = dataframe.df - +def test_from_dataframe_with_transforms_and_fillna(sample_df): # @pytest.mark.skip() # def keymark.1(x): # return x**2 @@ -81,10 +79,10 @@ def test_from_dataframe_with_transforms_and_fillna(dataframe): # def keymark.3(x): # return (x > 0) * x - h = Hypergraph.from_incidence_dataframe(df) + h = Hypergraph.from_incidence_dataframe(sample_df) assert "A" in h.edges["a"] assert "A" not in h.edges["b"] - h = Hypergraph.from_incidence_dataframe(df, fillna=1) + h = Hypergraph.from_incidence_dataframe(sample_df, fillna=1) assert "A" in h.edges["b"] # h = Hypergraph.from_incidence_dataframe(df, transforms=[key1, key2]) # assert "A" in h.edges["c"] From 6fff6362e62ee02e492141d767acb1e2377b0fa1 Mon Sep 17 00:00:00 2001 From: Mark Bonicillo Date: Mon, 15 Apr 2024 17:04:08 -0700 Subject: [PATCH 4/4] Add test-core target --- Makefile | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/Makefile b/Makefile index 24742686..9d9dd79a 100644 --- a/Makefile +++ b/Makefile @@ -39,6 +39,12 @@ test: coverage run --source=hypernetx -m pytest tests coverage report -m +.PHONY: test-core +test-core: + coverage run --source=hypernetx/classes -m pytest tests/classes --verbose + coverage report -m + + ## Tests using Tox ## Includes linting, running tests on jupyter notebooks .PHONY: test-tox