Bypass punning in ontodoc.

ontopy/ontodoc.py

@@ -392,23 +392,32 @@ def itemdoc(
         # Instances (individuals)
         if hasattr(item, "instances"):
             points = []
-            for entity in [
-                _ for _ in item.instances() if item in _.is_instance_of
-            ]:
-                points.append(
-                    point_style.format(
-                        point=asstring(entity, link_style), ontology=onto
+
+            for instance in item.instances():
+                if isinstance(instance.is_instance_of, property):
+                    warnings.warn(
+                        f'Ignoring instance "{instance}" which is both and '
+                        "indivudual and class. Ontodoc does not support "
+                        "punning at the present moment."
                     )
-                )
-            if points:
-                value = points_style.format(
-                    points="".join(points), ontology=onto
-                )
-                doc.append(
-                    annotation_style.format(
-                        key="Individuals", value=value, ontology=onto
+                    continue
+                if item in instance.is_instance_of:
+                    points.append(
+                        point_style.format(
+                            point=asstring(instance, link_style),
+                            ontology=onto,
+                        )
                     )
-                )
+                if points:
+                    value = points_style.format(
+                        points="".join(points), ontology=onto
+                    )
+                    doc.append(
+                        annotation_style.format(
+                            key="Individuals", value=value, ontology=onto
+                        )
+                    )
+
         return "\n".join(doc)
 
     def itemsdoc(self, items, header_level=3):

ontopy/utils.py

@@ -57,6 +57,10 @@ class UnknownVersion(EMMOntoPyException):
     """Cannot retrieve version from a package."""
 
 
+class IndividualWarning(EMMOntoPyWarning):
+    """A warning related to an individual, e.g. punning."""
+
+
 class NoSuchLabelError(LookupError, AttributeError, EMMOntoPyException):
     """Error raised when a label cannot be found."""
 

tests/testonto/testonto_w_individual.ttl

@@ -0,0 +1,24 @@
+@prefix : <http://emmo.info/testonto#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@base <http://emmo.info/testonto> .
+
+<http://emmo.info/testonto> rdf:type owl:Ontology ;
+                             owl:versionIRI <http://emmo.info/testonto/0.1.0> ;
+			     owl:versionInfo "0.1.0" .
+
+skos:prefLabel rdf:type owl:AnnotationProperty .
+skos:altLabel rdf:type owl:AnnotationProperty .
+
+:testclass rdf:type owl:Class ;
+    rdfs:subClassOf owl:Thing ;
+    skos:prefLabel "TestClass"@en .
+
+
+:testindividual rdf:type owl:NamedIndividual ,
+                           :testclass ;
+		skos:prefLabel "testindividual"@en .

tests/testonto/testonto_w_punning.ttl

@@ -0,0 +1,23 @@
+@prefix : <http://emmo.info/testonto#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@base <http://emmo.info/testonto> .
+
+<http://emmo.info/testonto> rdf:type owl:Ontology ;
+                             owl:versionIRI <http://emmo.info/testonto/0.1.0> ;
+			     owl:versionInfo "0.1.0" .
+
+skos:prefLabel rdf:type owl:AnnotationProperty .
+skos:altLabel rdf:type owl:AnnotationProperty .
+
+:testclass rdf:type owl:Class ;
+    rdfs:subClassOf owl:Thing ;
+    skos:prefLabel "TestClass"@en .
+
+
+:testclass rdf:type owl:NamedIndividual ,
+                           :testclass .

tests/tools/conftest.py

@@ -5,33 +5,110 @@
 
 if TYPE_CHECKING:
     from types import ModuleType
-    from typing import Any, Dict
+    from typing import Callable
 
 
-@pytest.fixture
-def tool(request: "Dict[str, Any]") -> "ModuleType":
-    """Import a tool as a module."""
+@pytest.fixture(scope="module", autouse=True)
+def rename_tools() -> None:
+    """Add a `.py` extension to all tools.
+
+    Run prior to all tests in this module.
+    First, rename all tools (adding a `.py` suffix) to make them importable as a
+    module. Then stop executing this fixture for a while (yield) and run all the tests
+    in the module. Then after they're done, rename the tools back (remove the `.py`
+    suffix) and also return `sys.path` to its original state prior to running the
+    tests.
+    To make the importability work, the `tools` folder had to be added to the
+    `sys.path`.
+    """
     from copy import deepcopy
-    import importlib
+    import os
     from pathlib import Path
+    import shutil
     import sys
 
     original_sys_path = deepcopy(sys.path)
-    original_tool_path: Path = (
-        Path(__file__).resolve().parent.parent.parent / "tools" / request.param
-    )
-    if str(original_tool_path.parent) not in sys.path:
-        sys.path.append(str(original_tool_path.parent))
-
-    assert (
-        original_tool_path.exists()
-    ), f"The requested tool ({request.param}) was not found in {original_tool_path.parent}"
-    try:
-        tool_path = original_tool_path.rename(
-            original_tool_path.with_name(f"{request.param}.py")
-        )
-        yield importlib.import_module(request.param)
-    finally:
-        if tool_path and tool_path.exists():
-            tool_path.rename(tool_path.with_name(request.param))
-        sys.path = original_sys_path
+    tools_path: Path = Path(__file__).resolve().parent.parent.parent / "tools"
+
+    if str(tools_path) not in sys.path:
+        sys.path.append(str(tools_path))
+
+    # Add ".py" suffix to all tools
+    for (
+        dirpath,
+        dirnames,
+        filenames,
+    ) in os.walk(tools_path):
+        if dirpath != str(tools_path):
+            continue
+
+        if dirnames:
+            for dirname in dirnames:
+                if dirname == "__pycache__":
+                    shutil.rmtree(
+                        Path(dirpath) / "__pycache__", ignore_errors=True
+                    )
+
+        for filename in filenames:
+            filepath = Path(dirpath) / filename
+            assert (
+                filepath.suffix == ""
+            ), f"A suffix was found (not expected) for file: {filepath}"
+
+            filepath.rename(filepath.with_suffix(".py"))
+
+    yield
+
+    # Remove ".py" suffix from all tools
+    for (
+        dirpath,
+        dirnames,
+        filenames,
+    ) in os.walk(tools_path):
+        if dirpath != str(tools_path):
+            continue
+
+        if dirnames:
+            for dirname in dirnames:
+                if dirname == "__pycache__":
+                    shutil.rmtree(
+                        Path(dirpath) / "__pycache__", ignore_errors=True
+                    )
+
+        for filename in filenames:
+            filepath = Path(dirpath) / filename
+            assert (
+                filepath.suffix == ".py"
+            ), f"A suffix was NOT found (not expected) for file: {filepath}"
+
+            filepath.rename(filepath.with_suffix(""))
+
+    sys.path = original_sys_path
+
+
+@pytest.fixture
+def get_tool() -> "Callable[[str], ModuleType]":
+    """Import a tool as a module.
+
+    Requires the fixture `rename_tools` to have been run already.
+    """
+    import importlib
+    from pathlib import Path
+    import sys
+
+    def _get_tool(name: str) -> "ModuleType":
+        """Import and return named tool."""
+        tool_path: Path = (
+            Path(__file__).resolve().parent.parent.parent / "tools" / name
+        ).with_suffix(".py")
+        assert (
+            str(tool_path.parent) in sys.path
+        ), f"'tools' dir not found in sys.path. Did `rename_tools` fixture run?\nsys.path: {sys.path}"
+
+        assert (
+            tool_path.exists()
+        ), f"The requested tool ({name}) was not found in {tool_path.parent}."
+
+        return importlib.import_module(name)
+
+    return _get_tool

tests/tools/test_emmocheck.py

@@ -1,14 +1,24 @@
 """Test the `emmocheck` tool."""
-import pytest
+from typing import TYPE_CHECKING
 
+if TYPE_CHECKING:
+    from types import ModuleType
+    from typing import Callable
 
-@pytest.mark.parametrize("tool", ["emmocheck"], indirect=True)
-def test_run(tool) -> None:
-    """Check that running `emmocheck` works."""
+
+def test_run(get_tool: "Callable[[str], ModuleType]") -> None:
+    """Check that running `emmocheck` works.
+
+    Parameters:
+        get_tool: Local module fixture to load a named tool as a module.
+            See the current folder's `conftest.py` file.
+
+    """
     from pathlib import Path
 
     test_file = (
         Path(__file__).resolve().parent.parent / "testonto" / "models.ttl"
     )
+    emmocheck = get_tool("emmocheck")
 
-    tool.main([str(test_file)])
+    emmocheck.main([str(test_file)])

tests/tools/test_excel2onto.py

@@ -1,12 +1,24 @@
 """Test the `ontograph` tool."""
-from pathlib import Path
-import os
-import pytest
+from typing import TYPE_CHECKING
 
+if TYPE_CHECKING:
+    from pathlib import Path
+    from types import ModuleType
+    from typing import Callable
+
+
+def test_run(get_tool: "Callable[[str], ModuleType]", tmpdir: "Path") -> None:
+    """Check that running `excel2onto` works.
+
+    Parameters:
+        get_tool: Local module fixture to load a named tool as a module.
+            See the current folder's `conftest.py` file.
+        tmpdir: A generic pytest fixture to generate a temporary directory, which will
+            exist only for the lifetime of this test function.
+
+    """
+    from pathlib import Path
 
-@pytest.mark.parametrize("tool", ["excel2onto"], indirect=True)
-def test_run(tool, tmpdir: Path) -> None:
-    """Check that running `excel2onto` works."""
     test_file = (
         Path(__file__).resolve().parent.parent
         / "test_excelparser"
@@ -17,10 +29,13 @@ def test_run(tool, tmpdir: Path) -> None:
         / "test_excelparser"
         / "onto_update.xlsx"
     )
+    excel2onto = get_tool("excel2onto")
 
-    tool.main([f"--output={str(tmpdir)}/onto.ttl", "--force", str(test_file)])
+    excel2onto.main(
+        [f"--output={str(tmpdir)}/onto.ttl", "--force", str(test_file)]
+    )
 
-    tool.main(
+    excel2onto.main(
         [
             f"--output={str(tmpdir)}/onto.ttl",
             "--force",
@@ -29,7 +44,7 @@ def test_run(tool, tmpdir: Path) -> None:
         ]
     )
 
-    tool.main(
+    excel2onto.main(
         [
             f"--output={str(tmpdir)}/ontology.ttl",
             "--force",

tests/tools/test_ontoconvert.py

@@ -1,14 +1,27 @@
 """Test the `ontoconvert` tool."""
-from pathlib import Path
+from typing import TYPE_CHECKING
 
-import pytest
+if TYPE_CHECKING:
+    from pathlib import Path
+    from types import ModuleType
+    from typing import Callable
 
 
-@pytest.mark.parametrize("tool", ["ontoconvert"], indirect=True)
-def test_run(tool, tmpdir: Path) -> None:
-    """Check that running `ontoconvert` works."""
+def test_run(get_tool: "Callable[[str], ModuleType]", tmpdir: "Path") -> None:
+    """Check that running `ontoconvert` works.
+
+    Parameters:
+        get_tool: Local module fixture to load a named tool as a module.
+            See the current folder's `conftest.py` file.
+        tmpdir: A generic pytest fixture to generate a temporary directory, which will
+            exist only for the lifetime of this test function.
+
+    """
+    from pathlib import Path
+
     test_file = (
         Path(__file__).resolve().parent.parent / "testonto" / "models.ttl"
     )
+    ontoconvert = get_tool("ontoconvert")
 
-    tool.main([str(test_file), str(tmpdir / "test.ttl")])
+    ontoconvert.main([str(test_file), str(tmpdir / "test.ttl")])