Make separate test environments for full version and minimal version …

…without dependencies

A new environment for testing only with core dependencies installed is added to the ci_tests workflow.

All tests are moved to separate functions instead of test scripts.

Tests that require additiona  dependencies are skipped if the required dependency is not installed.

.github/workflows/ci_tests.yml

@@ -85,3 +85,30 @@ jobs:
     - name: Run doctest on tutorial
       run: |
         python -m doctest docs/tutorial.md
+
+  pytest-no-extra-dependencies: # Test for basic version, without extras installed
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+    - name: Checkout tripper
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        sudo apt install graphviz
+        python -m pip install -U pip
+        pip install -U setuptools wheel flit
+        pip install -e .[testing-core]
+
+    - name: Test with pytest, but without other extra dependencies
+      run: pytest -vvv tests/

pyproject.toml

@@ -57,6 +57,10 @@ testing = [
     "DLite-Python >=0.4.0,<1",
     "graphviz ~= 0.20",
 ]
+testing-core = [
+    "pytest ~=7.4",
+    "pytest-cov ~=4.1",
+]
 dev = [
     "mike ~=1.1",
     "mkdocs ~=1.5",

tests/convert/test_convert.py

@@ -1,55 +1,61 @@
 """Test convertions."""
 # pylint: disable=invalid-name
-from tripper import Triplestore
-from tripper.convert import load_container, save_container
-
-ts = Triplestore(backend="rdflib")
-EX = ts.bind("ex", "http://example.com/ex#")
-
-
-config1 = {
-    "downloadUrl": "http://example.com/somedata.txt",
-    "mediaType": "application/text",
-    "anotherField": "More info...",
-}
-
-config2 = {
-    "downloadUrl": "http://example.com/somedata.txt",
-    "mediaType": "application/text",
-    "anotherField": "More info...",
-    "configurations": {
-        "key1": "val1",
-        "key2": 2,
-        "key3": 3.14,
-        "key4": None,
-        "key5": True,
-        "key6": False,
-        "key7": ["a", 1, 2.2, True, None],
-    },
-}
-
-# Store dictionaries to triplestore
-save_container(ts, config1, EX.config1)
-save_container(ts, config2, EX.config2)
-
-# Print content of triplestore
-# print(ts.serialize())
-
-# Load dictionaries from triplestore
-d1 = load_container(ts, EX.config1)
-d2 = load_container(ts, EX.config2)
-
-# Check that we got back what we stored
-assert d1 == config1
-assert d2 == config2
-
-
-# Now, test serialising using recognised_keys
-save_container(ts, config1, EX.config1b, recognised_keys="basic")
-save_container(ts, config2, EX.config2b, recognised_keys="basic")
-
-d1b = load_container(ts, EX.config1b, recognised_keys="basic")
-d2b = load_container(ts, EX.config2b, recognised_keys="basic")
-
-assert d1b == config1
-assert d2b == config2
+
+import pytest
+
+
+def test_convertions():
+    """Test convertions. Uses rdflib as triplestore backend"""
+
+    pytest.importorskip("rdflib")
+    from tripper import Triplestore
+    from tripper.convert import load_container, save_container
+
+    ts = Triplestore(backend="rdflib")
+    EX = ts.bind("ex", "http://example.com/ex#")
+
+    config1 = {
+        "downloadUrl": "http://example.com/somedata.txt",
+        "mediaType": "application/text",
+        "anotherField": "More info...",
+    }
+
+    config2 = {
+        "downloadUrl": "http://example.com/somedata.txt",
+        "mediaType": "application/text",
+        "anotherField": "More info...",
+        "configurations": {
+            "key1": "val1",
+            "key2": 2,
+            "key3": 3.14,
+            "key4": None,
+            "key5": True,
+            "key6": False,
+            "key7": ["a", 1, 2.2, True, None],
+        },
+    }
+
+    # Store dictionaries to triplestore
+    save_container(ts, config1, EX.config1)
+    save_container(ts, config2, EX.config2)
+
+    # Print content of triplestore
+    # print(ts.serialize())
+
+    # Load dictionaries from triplestore
+    d1 = load_container(ts, EX.config1)
+    d2 = load_container(ts, EX.config2)
+
+    # Check that we got back what we stored
+    assert d1 == config1
+    assert d2 == config2
+
+    # Now, test serialising using recognised_keys
+    save_container(ts, config1, EX.config1b, recognised_keys="basic")
+    save_container(ts, config2, EX.config2b, recognised_keys="basic")
+
+    d1b = load_container(ts, EX.config1b, recognised_keys="basic")
+    d2b = load_container(ts, EX.config2b, recognised_keys="basic")
+
+    assert d1b == config1
+    assert d2b == config2

tests/mappings/test_function.py

@@ -1,42 +1,47 @@
-"""Test mapping function.
+"""Test mapping function."""
 
-We have two data sources:
-  - literal number 3.2 mapped to ex:A
-  - vector mapped to ex:B
 
-We also have two mapping functions; first() and sum()
-  - first(): ex:B[0] -> ex:C
-  - sum(): ex:A + ex:C -> ex:D
+def test_mapping():
+    """Test mapping function.
 
-The test asks for the value of an individual of ex:D
-"""
-# pylint: disable=unused-argument,invalid-name
-from tripper import Literal, Tripper
+    We have two data sources:
+      - literal number 3.2 mapped to ex:A
+      - vector mapped to ex:B
 
-tp = Tripper(backend="rdflib")
-EX = tp.bind("ex", "http://example.com/onto#")
+    We also have two mapping functions; first() and sum()
+      - first(): ex:B[0] -> ex:C
+      - sum(): ex:A + ex:C -> ex:D
 
+    The test asks for the value of an individual of ex:D
 
-def first(vector):
-    """Return first element of the vector."""
-    return vector[0]
+    Uses rdflib as backend
+    """
+    # pylint: disable=unused-argument,invalid-name
+    import pytest
 
+    pytest.importorskip("rdflib")
+    from tripper import Literal, Tripper
 
-def add(a, b):
-    """Return the sum of `a` and `b`."""
-    return a + b
+    tp = Tripper(backend="rdflib")
+    EX = tp.bind("ex", "http://example.com/onto#")
 
+    def first(vector):
+        """Return first element of the vector."""
+        return vector[0]
 
-def vector(iri, configurations, triplestore):
-    """Return a vector."""
-    return [0.5, 1.2, 3.4, 6.6]
+    def add(a, b):
+        """Return the sum of `a` and `b`."""
+        return a + b
 
+    def vector(iri, configurations, triplestore):
+        """Return a vector."""
+        return [0.5, 1.2, 3.4, 6.6]
 
-tp.add_data(Literal(3.2), EX.A)
-tp.add_data(vector, EX.B)
+    tp.add_data(Literal(3.2), EX.A)
+    tp.add_data(vector, EX.B)
 
-tp.add_function(first, expects=EX.B, returns=EX.C)
-tp.add_function(add, expects=(EX.A, EX.C), returns=EX.D)
+    tp.add_function(first, expects=EX.B, returns=EX.C)
+    tp.add_function(add, expects=(EX.A, EX.C), returns=EX.D)
 
-tp.map(EX.indv, EX.D)
-assert tp.get_value(EX.indv) == 3.7
+    tp.map(EX.indv, EX.D)
+    assert tp.get_value(EX.indv) == 3.7

tests/mappings/test_mappings.py

@@ -1,52 +1,57 @@
 #!/usr/bin/env python
 """Test mappings."""
-from pathlib import Path
 
-from tripper import Triplestore
-from tripper.mappings import mapping_routes
+# pylint: disable=invalid-name
 
-# Configure paths
-thisdir = Path(__file__).parent.absolute()
+import pytest
 
-ts = Triplestore(backend="rdflib")
 
+def test_mappings():
+    """Test mappings.
+    Uses rdflib as backend
+    """
 
-# Define some prefixed namespaces
-CHEM = ts.bind("chem", "http://onto-ns.com/onto/chemistry#")
-MOL = ts.bind("mol", "http://onto-ns.com/meta/0.1/Molecule#")
-MOL2 = ts.bind("mol2", "http://onto-ns.com/meta/0.1/Molecule2#")
-SUB = ts.bind("sub", "http://onto-ns.com/meta/0.1/Substance#")
+    pytest.importorskip("rdflib")
 
+    from tripper import Triplestore
+    from tripper.mappings import mapping_routes
 
-# Add mappings from data models to ontology
-ts.add_mapsTo(CHEM.Identifier, MOL.name)
-ts.add_mapsTo(CHEM.Identifier, SUB.id)
+    ts = Triplestore(backend="rdflib")
 
-ts.add_mapsTo(CHEM.GroundStateEnergy, MOL.groundstate_energy)
-ts.add_mapsTo(CHEM.GroundStateEnergy, MOL2.energy)
-ts.add_mapsTo(CHEM.GroundStateEnergy, SUB.molecule_energy)
+    # Define some prefixed namespaces
+    CHEM = ts.bind("chem", "http://onto-ns.com/onto/chemistry#")
+    MOL = ts.bind("mol", "http://onto-ns.com/meta/0.1/Molecule#")
+    MOL2 = ts.bind("mol2", "http://onto-ns.com/meta/0.1/Molecule2#")
+    SUB = ts.bind("sub", "http://onto-ns.com/meta/0.1/Substance#")
 
+    # Add mappings from data models to ontology
+    ts.add_mapsTo(CHEM.Identifier, MOL.name)
+    ts.add_mapsTo(CHEM.Identifier, SUB.id)
 
-routes = mapping_routes(
-    target=SUB.molecule_energy,
-    sources={MOL.groundstate_energy: 1.0},
-    triplestore=ts,
-)
+    ts.add_mapsTo(CHEM.GroundStateEnergy, MOL.groundstate_energy)
+    ts.add_mapsTo(CHEM.GroundStateEnergy, MOL2.energy)
+    ts.add_mapsTo(CHEM.GroundStateEnergy, SUB.molecule_energy)
 
-assert routes.number_of_routes() == 1
-assert routes.output_iri == (
-    "http://onto-ns.com/meta/0.1/Substance#molecule_energy"
-)
-assert routes.cost == 2.0
-assert (
-    routes.visualise(0).strip()
-    == """
+    routes = mapping_routes(
+        target=SUB.molecule_energy,
+        sources={MOL.groundstate_energy: 1.0},
+        triplestore=ts,
+    )
+
+    assert routes.number_of_routes() == 1
+    assert routes.output_iri == (
+        "http://onto-ns.com/meta/0.1/Substance#molecule_energy"
+    )
+    assert routes.cost == 2.0
+    assert (
+        routes.visualise(0).strip()
+        == """
 digraph G {
   "mol:groundstate_energy" -> "chem:GroundStateEnergy" [label="mapsTo"];
   "chem:GroundStateEnergy" -> "sub:molecule_energy" [label="inverse(mapsTo)"];
 }
 """.strip()
-)
+    )
 
-# Commented out, to avoid dependencies of Graphviz
-# routes.visualise(0, output="graph.png", format="png", dot="dot")
+    # Commented out, to avoid dependencies of Graphviz
+    # routes.visualise(0, output="graph.png", format="png", dot="dot")