Add test workflow, pytest script

.github/workflows/Test.yml

@@ -0,0 +1,61 @@
+name: Test
+
+# on: [push]
+on:
+  push:
+    branches: [main]
+    tags: ["*"]
+  pull_request:
+jobs:
+  build:
+    # runs-on: ubuntu-latest
+    name: Python ${{ matrix.python-version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          # - windows-latest
+        arch:
+          - x64
+          # - x86
+        # exclude:
+        #   # Exclude 32-bit macOS
+        #   - os: macOS-latest
+        #     arch: x86
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest
+          pip install -r requirements.txt
+      # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          # pytest
+          # python -m pytest
+          # coverage run -m pytest
+          python -m pytest --cov
+      - name: Generate coverage
+        run: |
+          coverage xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        # run: |
+          # curl -Os https://uploader.codecov.io/latest/linux/codecov
+          # chmod +x codecov
+          # ./codecov

src/main_dystonia_graph_and_ontology_method.py

@@ -68,7 +68,7 @@
 ########################################################
 
 
-def add_data_properties(g: nx.Graph):
+def add_data_properties(g: Graph):
    # Define the namespaces
     ex = Namespace("http://example.org/")
     g.bind("ex", ex)
@@ -136,7 +136,7 @@ def add_data_properties(g: nx.Graph):
     return (g)
 
 
-def add_object_properties (g: nx.Graph):
+def add_object_properties (g: Graph):
     ex = Namespace("http://example.org/")
     # Define an object property
     object_property_uri = ex['causes']
@@ -269,7 +269,7 @@ def plot_graph(G: nx.Graph):
     return
 
 
-def add_data_properties_to_nodes(g: nx.Graph):
+def add_data_properties_to_nodes(g: Graph, G: nx.Graph):
     # Define the namespaces
     ex = Namespace("http://example.org/")
     g.bind("ex", ex)
@@ -335,7 +335,7 @@ def add_data_properties_to_nodes(g: nx.Graph):
     return g
 
 
-def add_edges_to_RDF_graph(g: nx.Graph):
+def add_edges_to_RDF_graph(g: Graph, G: nx.Graph):
     # Define the namespaces
     ex = Namespace("http://example.org/")
     g.bind("ex", ex)
@@ -373,7 +373,7 @@ def add_edges_to_RDF_graph(g: nx.Graph):
     return(g)
 
 
-def add_nodes_to_RDF_graph(g: nx.Graph):
+def add_nodes_to_RDF_graph(g: Graph, G: nx.Graph):
     # Define the namespaces
     ex = Namespace("http://example.org/")
     g.bind("ex", ex)
@@ -396,10 +396,7 @@ def add_nodes_to_RDF_graph(g: nx.Graph):
     return(g)
 
 
-########################################################
-# Main Program Starts here                             #
-########################################################
-if __name__ == "__main__":
+def main():
     # G is networkX graph
     # g is an RDF graph
     # Declare a NetworkX graph
@@ -413,13 +410,24 @@ def add_nodes_to_RDF_graph(g: nx.Graph):
     g = Graph()
     g = add_object_properties(g)
     g = add_data_properties(g)
-    g = add_data_properties_to_nodes(g)
-    g = add_nodes_to_RDF_graph(g)
-    g = add_edges_to_RDF_graph(g)
+    g = add_data_properties_to_nodes(g, G)
+    g = add_nodes_to_RDF_graph(g, G)
+    g = add_edges_to_RDF_graph(g, G)
 
     # Serialize the updated RDF graph to an OWL file
     g.serialize(out_ontology, format="turtle")
     print('Graph and Ontology complete.')
     print(f'- {out_graph_file} has been written to file as a GraphML file')
     print(f'- {out_graph_image} has been written to file as a PNG file')
     print(f'- {out_ontology} has been written to file as an ontology')
+
+    return
+
+
+########################################################
+# Main Program Starts here                             #
+########################################################
+
+if __name__ == "__main__":
+
+    main()

tests/test_experiments.py

@@ -0,0 +1,26 @@
+"""
+    test_cvi.py
+
+# Description
+Runs each experiment within pytest to verify script functionality during CI.
+
+# Authors
+- Sasha Petrenko <[email protected]>
+"""
+
+# -----------------------------------------------------------------------------
+# TESTS
+# -----------------------------------------------------------------------------
+
+
+class TestExperiments:
+    """
+    Pytest class containing experiment unit tests.
+    """
+
+    def test_graph_ontology(self):
+        """
+        Tests the main function of `main_dystonia_graph_and_ontology_method.py`.
+        """
+        from src.main_dystonia_graph_and_ontology_method import main
+        main()