Merge pull request #239 from emmo-repo/cwa/close-220-tidy-up-tests

Ensure all produced files from tests are in a temp dir.

Add pytest fixtures for loading EMMO, as this is done in several
tests.
Add fixture for location to repo_dir, instantiating it only once per
pytest session.
Add a yield-fixture for creating a temporary directory that lives for
the lifetime of the test function.

This removes the possibility to check through the generated files
from the tests, keeping the unit tests being just that: unit tests.
However, I guess the generated files should be tested more now?

In short, the unit tests here should never rely on human inspection,
hence, they shouldn't produce any permanent files.

If examples are the motive for the tests (as it is explicitly stated for
one of them) it should be added to the examples/ folder and be
part of the documentation.

.gitignore

@@ -6,11 +6,6 @@ __pycache__
 MANIFEST
 dist
 build
-old
-test_graph2
-
-*.pdf
-*.xml
 
 # Documentation
 site/

MANIFEST.in

@@ -10,4 +10,4 @@ recursive-exclude examples/emmodoc old/** genfigs/** *.pdf *.html *~
 recursive-include demo *
 recursive-exclude demo old __pycache__ *~ *.pyc *.off
 
-recursive-include emmo/factpluspluswrapper/java *
+recursive-include ontopy/factpluspluswrapper/java **

tests/conftest.py

@@ -0,0 +1,34 @@
+"""Pytest fixtures and setup functions."""
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+import pytest
+
+if TYPE_CHECKING:
+    from ontopy.ontology import Ontology
+
+
+@pytest.fixture(scope="session")
+def repo_dir() -> Path:
+    """Absolute path to the repository directory."""
+    return Path(__file__).parent.parent.resolve()
+
+
+@pytest.fixture
+def emmo() -> "Ontology":
+    """Load and return EMMO."""
+    from emmopy import get_emmo
+
+    emmo = get_emmo()
+
+    return emmo
+
+
+@pytest.fixture
+def tmpdir() -> Path:
+    """Create a temporary directory that lasts the runtime of the test."""
+    from tempfile import TemporaryDirectory
+
+    res = TemporaryDirectory()
+    yield Path(res.name)
+    res.cleanup()

tests/test_basic.py

@@ -1,21 +1,14 @@
-def test_basic() -> None:
-    import sys
-    import os
-    import itertools
+from typing import TYPE_CHECKING
 
-    # Add emmo to sys path
-    thisdir = os.path.abspath(os.path.dirname(__file__))
-    sys.path.insert(1, os.path.abspath(os.path.join(thisdir, '..')))
-    from ontopy import get_ontology  # noqa: E402, F401
+if TYPE_CHECKING:
+    from ontopy.ontology import Ontology
 
-    import owlready2  # noqa: E402, F401
 
+def test_basic(emmo: "Ontology") -> None:
+    from ontopy import get_ontology
 
-    emmo = get_ontology()
-    emmo.load()
     emmo.sync_reasoner()
 
-
     onto = get_ontology('onto.owl')
     onto.imported_ontologies.append(emmo)
     onto.base_iri = 'http://emmo.info/examples/test#'
@@ -27,7 +20,7 @@ def test_basic() -> None:
 
         # Add entity using python classes
         class Oxygen(emmo.Atom):
-            pass
+            """Oxygen atom."""
 
         class H2O(emmo.Molecule):
             """Water molecule."""
@@ -37,19 +30,17 @@ class H2O(emmo.Molecule):
         # Create some
         H1 = onto.Hydrogen()
         H2 = onto.Hydrogen()
-        O = Oxygen()  # noqa: E741
-        w = H2O()
-        w.hasSpatialDirectPart = [H1, H2,  O]
-
-    onto.sync_attributes(name_policy='sequential', name_prefix='myonto_')
-    assert onto.base_iri + 'myonto_0' in onto
-    assert onto.base_iri + 'myonto_6' in onto
-
-    onto.sync_attributes(name_policy='uuid', name_prefix='onto_')
-    assert w.name.startswith('onto_')
-    assert len(w.name) == 5 + 36
-
-    # Remove all traces of onto such that they do not mess up other tests
-    # when running pytest
-    for e in itertools.chain(onto.classes(), onto.individuals()):
-        owlready2.destroy_entity(e)
+        O = Oxygen()
+        water = H2O()
+        water.hasSpatialDirectPart = [H1, H2, O]
+
+    name_prefix = "myonto_"
+    onto.sync_attributes(name_policy='sequential', name_prefix=name_prefix)
+    assert f"{onto.base_iri}{name_prefix}0" in onto
+    assert f"{onto.base_iri}{name_prefix}6" in onto
+
+    name_prefix = "onto_"
+    onto.sync_attributes(name_policy='uuid', name_prefix=name_prefix)
+    assert water.name.startswith('onto_')
+    # A UUID is 32 chars long + 4 `-` chars = 36 chars
+    assert len(water.name) == len(name_prefix) + 36

tests/test_catalog.py

@@ -1,41 +1,37 @@
-def test_catalog() -> None:
-    import sys
-    import os
-
-    # Add emmo to sys path
-    thisdir = os.path.abspath(os.path.dirname(__file__))
-    sys.path.insert(1, os.path.abspath(os.path.join(thisdir, '..')))
-    from ontopy.utils import read_catalog, ReadCatalogError  # noqa: E402, F401
-    from ontopy.utils import write_catalog  # noqa: E402, F401
-
-
-    ontodir = os.path.join(thisdir, 'testonto')
-    d_expected = {
-        'http://emmo.info/testonto/0.1.0': os.path.join(
-            ontodir, 'testonto.ttl'),
-        'http://emmo.info/testonto/0.1.0/models': os.path.join(
-            ontodir, 'models.ttl'),
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+
+def test_catalog(repo_dir: "Path", tmpdir: "Path") -> None:
+    from ontopy.utils import read_catalog, ReadCatalogError, write_catalog
+
+    ontodir = repo_dir / "tests" / 'testonto'
+    catalog_expected = {
+        'http://emmo.info/testonto/0.1.0': str(ontodir / 'testonto.ttl'),
+        'http://emmo.info/testonto/0.1.0/models': str(ontodir / 'models.ttl'),
     }
 
-    d = read_catalog(os.path.join(ontodir, 'catalog-v001.xml'))
-    assert d == d_expected
+    catalog = read_catalog(str(ontodir / 'catalog-v001.xml'))
+    assert catalog == catalog_expected
 
-    d = read_catalog(ontodir)
-    assert d == d_expected
+    catalog = read_catalog(str(ontodir))
+    assert catalog == catalog_expected
 
-    d = read_catalog(ontodir, recursive=True)
-    assert d == d_expected
+    catalog = read_catalog(str(ontodir), recursive=True)
+    assert catalog == catalog_expected
 
-    d, p = read_catalog(ontodir, return_paths=True)
-    assert d == d_expected
-    assert p == set([ontodir])
+    catalog, catalog_paths = read_catalog(str(ontodir), return_paths=True)
+    assert catalog == catalog_expected
+    assert catalog_paths == set([str(ontodir)])
 
-    d = read_catalog('https://raw.githubusercontent.com/emmo-repo/EMMO/master/'
+    catalog = read_catalog('https://raw.githubusercontent.com/emmo-repo/EMMO/master/'
                     'catalog-v001.xml')
-    assert any(v.endswith('/emmo.ttl') for v in d.values())
+    assert any(_.endswith('/emmo.ttl') for _ in catalog.values())
 
-    d = read_catalog('https://raw.githubusercontent.com/emmo-repo/EMMO/master')
-    assert any(v.endswith('/emmo.ttl') for v in d.values())
+    catalog = read_catalog('https://raw.githubusercontent.com/emmo-repo/EMMO/master')
+    assert any(_.endswith('/emmo.ttl') for _ in catalog.values())
 
     try:
         read_catalog(
@@ -46,17 +42,17 @@ def test_catalog() -> None:
         assert False, 'expected ReadCatalogError'
 
     try:
-        read_catalog(os.path.join(ontodir, 'does-not-exists'))
+        read_catalog(str(ontodir / 'does-not-exists'))
     except ReadCatalogError:
         pass
     else:
         assert False, 'expected ReadCatalogError'
 
-    d = read_catalog('https://raw.githubusercontent.com/emmo-repo/EMMO/master/'
+    catalog = read_catalog('https://raw.githubusercontent.com/emmo-repo/EMMO/master/'
                     'catalog-v001.xml', baseuri='/abc')
-    assert '/abc/emmo.ttl' in d.values()
-
+    assert '/abc/emmo.ttl' in catalog.values()
 
-    write_catalog(d, 'tmp-catalog.xml')
-    d2 = read_catalog('tmp-catalog.xml')
-    assert d2 == d
+    tmp_catalog_path = tmpdir / "tmp-catalog.xml"
+    write_catalog(catalog, output=tmp_catalog_path)
+    tmp_catalog = read_catalog(str(tmp_catalog_path))
+    assert tmp_catalog == catalog

tests/test_graph.py

@@ -1,35 +1,29 @@
-def test_graph() -> None:
-    import sys
-    import os
+from typing import TYPE_CHECKING
 
-    # Add emmo to sys path
-    thisdir = os.path.abspath(os.path.dirname(__file__))
-    sys.path.insert(1, os.path.abspath(os.path.join(thisdir, '..')))
-    from ontopy import get_ontology  # noqa: E402, F401
+if TYPE_CHECKING:
+    from pathlib import Path
 
+    from ontopy.ontology import Ontology
 
-    emmo = get_ontology()
-    emmo.load()
+def test_graph(emmo: "Ontology", tmpdir: "Path") -> None:
+        graph = emmo.get_dot_graph(relations='is_a')
+        graph.write_svg(tmpdir / 'taxonomy.svg')
+        graph.write_pdf(tmpdir / 'taxonomy.pdf')
 
-    graph = emmo.get_dot_graph(relations='is_a')
-    graph.write_svg('taxonomy.svg')
-    graph.write_pdf('taxonomy.pdf')
+        entity_graph = emmo.get_dot_graph('EMMO')
+        entity_graph.write_svg(tmpdir / 'taxonomy2.svg')
 
-    entity_graph = emmo.get_dot_graph('EMMO')
-    entity_graph.write_svg('taxonomy2.svg')
+        substrate_graph = emmo.get_dot_graph('Item', relations=True,
+                                            leafs=('Physical'), parents='Item',
+                                            style='uml')
+        substrate_graph.write_svg(tmpdir / 'merotopology_graph.svg')
 
-    substrate_graph = emmo.get_dot_graph('Item', relations=True,
-                                        leafs=('Physical'), parents='Item',
-                                        style='uml')
-    substrate_graph.write_svg('merotopology_graph.svg')
+        property_graph = emmo.get_dot_graph('Property')
+        property_graph.write_svg(tmpdir / 'property_graph.svg')
 
-    property_graph = emmo.get_dot_graph('Property')
-    property_graph.write_svg('property_graph.svg')
+        # Update the default style
+        emmo._default_style['graph']['rankdir'] = 'BT'
 
-
-    # Update the default style
-    emmo._default_style['graph']['rankdir'] = 'BT'
-
-    relations_graph = emmo.get_dot_graph('EMMORelation')
-    relations_graph.write_pdf('relation_graph.pdf')
-    relations_graph.write_png('relation_graph.png')
+        relations_graph = emmo.get_dot_graph('EMMORelation')
+        relations_graph.write_pdf(tmpdir / 'relation_graph.pdf')
+        relations_graph.write_png(tmpdir / 'relation_graph.png')