Merge pull request #614 from emmo-repo/doctest

Added doctest

.github/workflows/ci_workflow.yml

@@ -88,7 +88,7 @@ jobs:
         pip install -U -e .[dev]
 
     - name: Test
-      run: pytest -vvv --cov=ontopy --cov=emmopy --cov-report=xml --cov-report=term
+      run: pytest -vvv --cov=ontopy --cov=emmopy --cov-report=xml --cov-report=term --doctest-modules
 
     - name: Upload coverage to Codecov
       if: matrix.python-version == '3.7' && github.repository == 'emmo-repo/EMMOntoPy'

examples/ontology-from-excel/make_microstructure_onto.py

@@ -1,11 +1,15 @@
 """
 python example for creating ontology from excel
 """
+from pathlib import Path
+
 from ontopy.excelparser import create_ontology_from_excel
 from ontopy.utils import write_catalog
 
+
+thisdir = Path(__file__).resolve().parent
 ontology, catalog, errdict = create_ontology_from_excel(
-    "tool/microstructure.xlsx"
+    thisdir / "tool/microstructure.xlsx"
 )
 
 ontology.save("microstructure_ontology.ttl", format="turtle", overwrite=True)

ontopy/manchester.py

@@ -94,7 +94,7 @@ def evaluate(ontology: owlready2.Ontology, expr: str) -> owlready2.Construct:
     Example:
     >>> from ontopy.manchester import evaluate
     >>> from ontopy import get_ontology
-    >>> emmo = get_ontology.load()
+    >>> emmo = get_ontology().load()
 
     >>> restriction = evaluate(emmo, 'hasPart some Atom')
     >>> cls = evaluate(emmo, 'Atom')

ontopy/patch.py

@@ -94,7 +94,7 @@ def _setitem(self, name, value):
     >>> emmo = get_emmo()
     >>> emmo.Atom['altLabel']
     ['ChemicalElement']
-    emmo.Atom['altLabel'] = 'Element'
+    >>> emmo.Atom['altLabel'] = 'Element'
     >>> emmo.Atom['altLabel']
     ['ChemicalElement', 'Element']
 

pyproject.toml

@@ -10,3 +10,6 @@ disable = [
 
 [tool.pylint.format]
 max-line-length = "80"
+
+[tool.pytest.ini_options]
+addopts = "--doctest-modules --ignore=demo --ignore=docs/demo --ignore=examples --ignore=docs/examples --ignore=site"

tests/ontopy_tests/test_graph.py

@@ -7,6 +7,9 @@
     from ontopy.ontology import Ontology
 
 
+@pytest.mark.filterwarnings(
+    "ignore:Style not defined for relation hasSpecialRelation:UserWarning"
+)
 def test_graph(testonto: "Ontology", tmpdir: "Path") -> None:
     """Testing OntoGraph on a small ontology
 

tests/test_basic.py

@@ -7,6 +7,7 @@
     from ontopy.ontology import Ontology
 
 
+@pytest.mark.filterwarnings("ignore:adding new IRI to ontology:UserWarning")
 def test_basic(emmo: "Ontology") -> None:
     from ontopy import get_ontology
     from ontopy.utils import LabelDefinitionError, EntityClassDefinitionError

tests/test_excelparser/test_excelparser.py

@@ -1,7 +1,8 @@
 """Test the Excel parser module."""
-import pytest
 from typing import TYPE_CHECKING
 
+import pytest
+
 from ontopy import get_ontology
 from ontopy.excelparser import create_ontology_from_excel
 from ontopy.utils import NoSuchLabelError
@@ -10,6 +11,11 @@
     from pathlib import Path
 
 
+@pytest.mark.filterwarnings("ignore:Ignoring concept :UserWarning")
+@pytest.mark.filterwarnings("ignore:Invalid parents for :UserWarning")
+@pytest.mark.filterwarnings(
+    "ignore:Not able to add the following concepts :UserWarning"
+)
 def test_excelparser(repo_dir: "Path") -> None:
     """Basic test for creating an ontology from an Excel file."""
     ontopath = (

tests/tools/test_excel2onto.py

@@ -1,12 +1,15 @@
 """Test the `ontograph` tool."""
 from typing import TYPE_CHECKING
 
+import pytest
+
 if TYPE_CHECKING:
     from pathlib import Path
     from types import ModuleType
     from typing import Callable
 
 
+@pytest.mark.filterwarnings("ignore::UserWarning")
 def test_run(get_tool: "Callable[[str], ModuleType]", tmpdir: "Path") -> None:
     """Check that running `excel2onto` works.