Merge pull request #307 from emmo-repo/cwa/fix-306-ontodoc-rdflib-import

Fix ontoconvert rdflib import & add simple run tests for tools.

.github/workflows/ci_cd_updated_master.yml

@@ -65,7 +65,7 @@ jobs:
     - name: Release check
       run: |
         COMMIT_MSG="$(gh api /repos/${{ github.repository}}/commits/${{ env.DEFAULT_REPO_BRANCH }} --jq '.commit.message')"
-        if [[ "${COMMIT_MSG}" =~ ^Release\ v.*\ -\ Changelog$ ]]; then
+        if [[ "${COMMIT_MSG}" =~ ^Release\ v.*$ ]]; then
           echo "In a release - do not run this job !"
           echo "RELEASE_RUN=true" >> $GITHUB_ENV
         else

docs/developers/testing.md

@@ -0,0 +1,40 @@
+# Testing and tooling
+
+## Unit testing
+
+The [PyTest](https://pytest.org) framework is used for testing the EMMOntoPy package.
+It is a unit testing framework with a plugin system, sporting an extensive plugin library as well as a sound fixture injection system.
+
+To run the tests locally install the package with the `dev` extra (see the [developer's setup guide](setup.md)) and run:
+
+```console
+$ pytest
+=== test session starts ===
+...
+```
+
+To understand what options you have, run `pytest --help`.
+
+## Tools
+
+Several tools are used to maintain the package, keeping it secure, readable, and easing maintenance.
+
+### Mypy
+
+[Mypy](http://mypy-lang.org/) is a static type checker for Python.
+
+**Documentation**: [mypy.readthedocs.io](https://mypy.readthedocs.io/)
+
+The signs of this tool will be found in the code especially through the `typing.TYPE_CHECKING` boolean variable, which will be used in the current way:
+
+```python
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from typing import List
+```
+
+Since `TYPE_CHECKING` is `False` at runtime, the `if`-block will not be run as part of running the script or module or if importing the module.
+However, when Mypy runs to check the static typing, it forcefully runs these blocks, considering `TYPE_CHECKING` to be `True` (see the [`typing.TYPE_CHECKING` section](https://mypy.readthedocs.io/en/stable/runtime_troubles.html#typing-type-checking) in the Mypy documentation).
+
+This means the imports in the `if`-block are meant to *only* be used for static typing, helping developers to understand the intention of the code as well as to check the invoked methods make sense (through Mypy).

emmopy/emmocheck.py

@@ -411,13 +411,8 @@ def test_namespace(self):
         exceptions.update(self.get_config("test_namespace.exceptions", ()))
 
         def checker(onto, ignore_namespace):
-            if (
-                list(
-                    filter(
-                        onto.base_iri.strip("#").endswith, self.ignore_namespace
-                    )
-                )
-                != []
+            if list(
+                filter(onto.base_iri.strip("#").endswith, self.ignore_namespace)
             ):
                 print(f"Skipping namespace: {onto.base_iri}")
                 return
@@ -463,8 +458,19 @@ def checker(onto, ignore_namespace):
         checker(self.onto, self.ignore_namespace)
 
 
-def main():  # pylint: disable=too-many-locals,too-many-branches,too-many-statements
-    """Run all checks on ontology `iri`.  Default is 'http://emmo.info/emmo'."""
+def main(
+    argv: list = None,
+):  # pylint: disable=too-many-locals,too-many-branches,too-many-statements
+    """Run all checks on ontology `iri`.
+
+    Default is 'http://emmo.info/emmo'.
+
+    Parameters:
+        argv: List of arguments, similar to `sys.argv[1:]`.
+            Mainly for testing purposes, since it allows one to invoke the tool
+            manually / through Python.
+
+    """
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument("iri", help="File name or URI to the ontology to test.")
     parser.add_argument(
@@ -597,7 +603,7 @@ def main():  # pylint: disable=too-many-locals,too-many-branches,too-many-statem
         help="Stop the test run on the first error or failure.",
     )
     try:
-        args = parser.parse_args()
+        args = parser.parse_args(args=argv)
         sys.argv[1:] = args.unittest if args.unittest else []
         if args.verbose:
             sys.argv.append("-v")

tests/tools/conftest.py

@@ -0,0 +1,35 @@
+"""Pytest fixtures for the `tools` dir only."""
+from typing import TYPE_CHECKING
+
+import pytest
+
+if TYPE_CHECKING:
+    from types import ModuleType
+    from typing import Any, Dict
+
+
+@pytest.fixture
+def tool(request: "Dict[str, Any]") -> "ModuleType":
+    """Import a tool as a module."""
+    from copy import deepcopy
+    import importlib
+    from pathlib import Path
+    import sys
+
+    original_sys_path = deepcopy(sys.path)
+    original_tool_path: Path = (
+        Path(__file__).resolve().parent.parent.parent / "tools" / request.param
+    )
+
+    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(f"tools.{request.param}")
+    finally:
+        if tool_path and tool_path.exists():
+            tool_path.rename(tool_path.with_name(request.param))
+        sys.path = original_sys_path

tests/tools/test_emmocheck.py

@@ -0,0 +1,14 @@
+"""Test the `emmocheck` tool."""
+import pytest
+
+
+@pytest.mark.parametrize("tool", ["emmocheck"], indirect=True)
+def test_run(tool) -> None:
+    """Check that running `emmocheck` works."""
+    from pathlib import Path
+
+    test_file = (
+        Path(__file__).resolve().parent.parent / "testonto" / "models.ttl"
+    )
+
+    tool.main([str(test_file)])

tests/tools/test_ontoconvert.py

@@ -0,0 +1,14 @@
+"""Test the `ontoconvert` tool."""
+from pathlib import Path
+
+import pytest
+
+
+@pytest.mark.parametrize("tool", ["ontoconvert"], indirect=True)
+def test_run(tool, tmpdir: Path) -> None:
+    """Check that running `ontoconvert` works."""
+    test_file = (
+        Path(__file__).resolve().parent.parent / "testonto" / "models.ttl"
+    )
+
+    tool.main([str(test_file), str(tmpdir / "test.ttl")])

tests/tools/test_ontodoc.py

@@ -0,0 +1,15 @@
+"""Test the `ontodoc` tool."""
+from pathlib import Path
+
+import pytest
+
+
+@pytest.mark.skip("ontodoc is tested in other ways")
+@pytest.mark.parametrize("tool", ["ontodoc"], indirect=True)
+def test_run(tool, tmpdir: Path) -> None:
+    """Check that running `ontodoc` works."""
+    test_file = (
+        Path(__file__).resolve().parent.parent / "testonto" / "models.ttl"
+    )
+
+    tool.main([str(test_file), str(tmpdir / "test.md")])

tests/tools/test_ontograph.py

@@ -0,0 +1,14 @@
+"""Test the `ontograph` tool."""
+from pathlib import Path
+
+import pytest
+
+
+@pytest.mark.parametrize("tool", ["ontograph"], indirect=True)
+def test_run(tool, tmpdir: Path) -> None:
+    """Check that running `ontograph` works."""
+    test_file = (
+        Path(__file__).resolve().parent.parent / "testonto" / "models.ttl"
+    )
+
+    tool.main([str(test_file), str(tmpdir / "test.png")])

tests/tools/test_ontoversion.py

@@ -0,0 +1,14 @@
+"""Test the `ontoversion` tool."""
+import pytest
+
+
+@pytest.mark.parametrize("tool", ["ontoversion"], indirect=True)
+def test_run(tool) -> None:
+    """Check running `ontoversion` works."""
+    from pathlib import Path
+
+    test_file = (
+        Path(__file__).resolve().parent.parent / "testonto" / "testonto.ttl"
+    )
+
+    tool.main([str(test_file), "--format", "ttl"])

tools/ontoconvert

@@ -5,7 +5,8 @@ import argparse
 import os
 import warnings
 
-from rdflib.util import Graph, guess_format
+from rdflib.graph import Graph
+from rdflib.util import guess_format
 
 from ontopy.utils import (
     convert_imported,
@@ -17,8 +18,15 @@ from ontopy.utils import (
 from ontopy.factpluspluswrapper.factppgraph import FaCTPPGraph
 
 
-def main():
-    """Main run function."""
+def main(argv: list = None):
+    """Main run function.
+
+    Parameters:
+        argv: List of arguments, similar to `sys.argv[1:]`.
+            Mainly for testing purposes, since it allows one to invoke the tool
+            manually / through Python.
+
+    """
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument("input", help="IRI/file to OWL source.")
     parser.add_argument("output", help="Output file name.")
@@ -85,7 +93,7 @@ def main():
         ),
     )
 
-    args = parser.parse_args()
+    args = parser.parse_args(args=argv)
 
     # Inferred default input and output file formats
     if args.input_format:

tools/ontodoc

@@ -25,8 +25,15 @@ from ontopy.ontodoc import (
 import owlready2
 
 
-def main():
-    """Main run function."""
+def main(argv: list = None):
+    """Main run function.
+
+    Parameters:
+        argv: List of arguments, similar to `sys.argv[1:]`.
+            Mainly for testing purposes, since it allows one to invoke the tool
+            manually / through Python.
+
+    """
     parser = argparse.ArgumentParser(
         description="Tool for documenting ontologies.",
         epilog=(
@@ -192,7 +199,7 @@ def main():
             "debugging)."
         ),
     )
-    args = parser.parse_args()
+    args = parser.parse_args(args=argv)
 
     # Append to onto_path
     for paths in args.path:

tools/ontograph

@@ -18,8 +18,17 @@ from ontopy.utils import get_label
 import owlready2
 
 
-def main():  # pylint: disable=too-many-locals,too-many-branches,too-many-statements
-    """Main run function."""
+def main(
+    argv: list = None,
+):  # pylint: disable=too-many-locals,too-many-branches,too-many-statements
+    """Main run function.
+
+    Parameters:
+        argv: List of arguments, similar to `sys.argv[1:]`.
+            Mainly for testing purposes, since it allows one to invoke the tool
+            manually / through Python.
+
+    """
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument(
         "iri",
@@ -193,7 +202,7 @@ def main():  # pylint: disable=too-many-locals,too-many-branches,too-many-statem
     parser.add_argument(
         "--display", "-D", action="store_true", help="Whether to display graph."
     )
-    args = parser.parse_args()
+    args = parser.parse_args(args=argv)
 
     # Append to onto_path
     for paths in args.path:

tools/ontoversion

@@ -25,8 +25,15 @@ def infer_version(iri, version_iri):
     return version.lstrip("/").rstrip("/#")
 
 
-def main():
-    """Main run function."""
+def main(argv: list = None):
+    """Main run function.
+
+    Parameters:
+        argv: List of arguments, similar to `sys.argv[1:]`.
+            Mainly for testing purposes, since it allows one to invoke the tool
+            manually / through Python.
+
+    """
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument(
         "iri",
@@ -37,7 +44,7 @@ def main():
         "--format", "-f", default="xml", help='OWL format. Default is "xml".'
     )
     try:
-        args = parser.parse_args()
+        args = parser.parse_args(args=argv)
     except SystemExit as exc:
         sys.exit(exc.code)  # Exit without traceback on invalid arguments