Add unit tests (#11)

* Update .gitignore

* Create requirements.txt

* Add Github action

* format with isort and black

* set up basic test

* fix small GHA issue

* added pytest as a requirement

* fix file path

* Update conftest.py

* fix file paths

* add tests

* fix tests

.github/workflows/test.yml

@@ -0,0 +1,31 @@
+name: Test schema
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+
+    - name: Install packages
+      run: |
+        python -m pip install --upgrade pip wheel setuptools
+        python -m pip install -r requirements.txt
+        python -m pip list
+
+    - name: Test schema
+      run: |
+        # run test suite
+        pytest --color=yes

.gitignore

@@ -160,3 +160,5 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+test.*

requirements.txt

@@ -0,0 +1,3 @@
+fastjsonschema
+pytest
+requests

schemas/HIF_schemas.ipynb

@@ -121,7 +121,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "schema = json.load(open(\"hif_schema_v0.1.0.json\",\"r\"))\n",
+    "schema = json.load(open(\"hif_schema_v0.1.0.json\", \"r\"))\n",
     "schema"
    ]
   },
@@ -182,7 +182,7 @@
    "source": [
     "# %%timeit #5.55 ms ± 101 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n",
     "hif = to_hif(lm)\n",
-    "json.dump(hif,open(\"../examples/lesmis_hif.json\",\"w\"),allow_nan=False)"
+    "json.dump(hif, open(\"../examples/lesmis_hif.json\", \"w\"), allow_nan=False)"
    ]
   },
   {
@@ -194,7 +194,7 @@
    "source": [
     "# %%timeit #742 µs ± 2.52 µs per loop (mean ± std. dev. of 7 runs, 1,000 loops each)\n",
     "try:\n",
-    "    validator(hif);\n",
+    "    validator(hif)\n",
     "except Exception as e:\n",
     "    print(e)"
    ]
@@ -214,12 +214,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
     "from copy import deepcopy\n",
+    "\n",
     "hiftest = deepcopy(hif)\n",
-    "hiftest['network-type'] = \"ordered\"\n",
+    "hiftest[\"network-type\"] = \"ordered\"\n",
     "try:\n",
-    "    validator(hiftest);\n",
+    "    validator(hiftest)\n",
     "except Exception as e:\n",
     "    print(e)\n",
     "validator(hiftest);"
@@ -381,7 +381,7 @@
    "outputs": [],
    "source": [
     "try:\n",
-    "    validator(hshif);\n",
+    "    validator(hshif)\n",
     "except Exception as e:\n",
     "    print(e)"
    ]
@@ -414,7 +414,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert hshyp == newhshyp ## this checks that the structure is the same"
+    "assert hshyp == newhshyp  ## this checks that the structure is the same"
    ]
   },
   {
@@ -424,7 +424,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "json.dump(hshif,open(\"../examples/contacts_high_school_hif.json\",\"w\"),allow_nan=False)"
+    "json.dump(\n",
+    "    hshif, open(\"../examples/contacts_high_school_hif.json\", \"w\"), allow_nan=False\n",
+    ")"
    ]
   },
   {

schemas/performance_testing.py

@@ -1,32 +1,33 @@
-'''
+"""
 Datasets to use:  
 
 1. http://bigg.ucsd.edu/models/e_coli_core    (xgi.load_big_data ecoli dataset from this website)]
 2. https://github.com/HGX-Team/data/tree/main/contacts/high-school
-'''
+"""
 
-import timeit
-import sys
-import hypernetx as hnx
-import xgi
-import pandas as pd
-import fastjsonschema
+import datetime as dtm
 import json
+import sys
+import timeit
 import warnings
-import datetime as dtm
 from time import perf_counter
 
-
+import fastjsonschema
+import hypernetx as hnx
+import pandas as pd
+import xgi
 
 warnings.simplefilter("ignore")
-sys.stdout = open('performance_testing_output.txt','a')
+sys.stdout = open("performance_testing_output.txt", "a")
+
 
 def marktime(msg=None):
     temp = dtm.datetime.now()
-    print(temp.strftime("%d/%m/%y %H:%M:%S"),": ",msg,flush=True)
+    print(temp.strftime("%d/%m/%y %H:%M:%S"), ": ", msg, flush=True)
     return temp
 
-schema = json.load(open("hif_schema_v0.1.0.json","r"))
+
+schema = json.load(open("hif_schema_v0.1.0.json", "r"))
 validator = fastjsonschema.compile(schema)
 
 ### high_school data as dataframes for hnx;
@@ -39,8 +40,9 @@ def marktime(msg=None):
 hs_nodedf = pd.DataFrame(hs["nodes"])
 hs_nodedf = hs_nodedf.set_index("id").reset_index().fillna("")
 
+
 ### HNX constructors
-def hnx_hypergraph(df,nodedf=None,edgedf=None):
+def hnx_hypergraph(df, nodedf=None, edgedf=None):
     return hnx.Hypergraph(df, node_properties=nodedf)
 
 
@@ -66,21 +68,22 @@ def hnx_from_hif(hif):
     incidences = pd.DataFrame(hif["incidences"])
     return hnx.Hypergraph(incidences, node_properties=nodes, edge_properties=edges)
 
+
 marktime("Begin Run")
 
 start = perf_counter()
-h = hnx_hypergraph(hs_df,nodedf=hs_nodedf)
+h = hnx_hypergraph(hs_df, nodedf=hs_nodedf)
 finish = perf_counter()
-print('hnx_high_school ',f'{finish - start:.5f} ns',flush=True)
+print("hnx_high_school ", f"{finish - start:.5f} ns", flush=True)
 
 start = perf_counter()
 hif = hnx_to_hif(h)
 finish = perf_counter()
-print('hnx_to_hif high_school ',f'{finish - start:.5f} ns',flush=True)
+print("hnx_to_hif high_school ", f"{finish - start:.5f} ns", flush=True)
 
 start = perf_counter()
 newh = hnx_from_hif(hif)
 finish = perf_counter()
-print('hnx_from_hif high_school ',f'{finish - start:.5f} ns',flush=True)
+print("hnx_from_hif high_school ", f"{finish - start:.5f} ns", flush=True)
 
 marktime("Run Complete \n")

tests/conftest.py

@@ -0,0 +1,35 @@
+import json
+
+import pytest
+import requests
+
+schema_location = "https://raw.githubusercontent.com/pszufe/HIF_validators/main/schemas/hif_schema_v0.1.0.json"
+json_dir = "tests/test_files"
+
+
+@pytest.fixture
+def schema():
+    r = requests.get(schema_location)
+
+    if r.ok:
+        return r.json()
+
+
+@pytest.fixture
+def empty():
+    return json.load(open(f"{json_dir}/empty.json", "r"))
+
+
+@pytest.fixture
+def bad_top_level_field():
+    return json.load(open(f"{json_dir}/bad_top_level_field.json", "r"))
+
+
+@pytest.fixture
+def metadata_as_list():
+    return json.load(open(f"{json_dir}/metadata_as_list.json", "r"))
+
+
+@pytest.fixture
+def empty_hypergraph():
+    return json.load(open(f"{json_dir}/empty_hypergraph.json", "r"))

tests/test_files/bad_top_level_field.json

@@ -0,0 +1 @@
+{"test": {"prop1": "test"}, "incidences": []}

tests/test_files/empty.json

@@ -0,0 +1 @@
+{}

tests/test_files/empty_hypergraph.json

@@ -0,0 +1 @@
+{"incidences": []}

tests/test_files/metadata_as_list.json

@@ -0,0 +1 @@
+{"metadata": [0, 1, 2], "incidences": []}

tests/test_schema.py

@@ -0,0 +1,25 @@
+import fastjsonschema
+import pytest
+
+
+def test_empty(schema, empty):
+    validator = fastjsonschema.compile(schema)
+    with pytest.raises(ValueError):
+        validator(empty)
+
+
+def test_bad_top_level_field(schema, bad_top_level_field):
+    validator = fastjsonschema.compile(schema)
+    with pytest.raises(ValueError):
+        validator(bad_top_level_field)
+
+
+def test_metadata_as_list(schema, metadata_as_list):
+    validator = fastjsonschema.compile(schema)
+    with pytest.raises(ValueError):
+        validator(metadata_as_list)
+
+
+def test_empty_hypergraph(schema, empty_hypergraph):
+    validator = fastjsonschema.compile(schema)
+    validator(empty_hypergraph)