Merge pull request #62 from emmo-repo/close_57_unit-tests-dic2owl

Unit tests for `dic2owl` CLI and setup testing framework.

Update pre-commit hooks and extend when `dic2owl` CI
runs.

.github/workflows/dic2owl_ci.yml

@@ -4,6 +4,8 @@ on:
   push:
     paths:
       - 'dic2owl/**'
+      - 'tests/**'
+      - '.github/**'
 
 jobs:
 
@@ -41,5 +43,5 @@ jobs:
       - name: Lint with MyPy
         run: mypy --ignore-missing-imports --scripts-are-modules dic2owl/dic2owl
 
-      # - name: Run unittests
-      #   run: pytest --cov dic2owl/dic2owl tests/
+      - name: Run unit tests with PyTest
+        run: pytest --cov dic2owl tests/

.gitignore

@@ -5,8 +5,10 @@ __pycache__
 *.pyc
 
 .mypy*
+.coverage
 
 *.dic
 *.cif
 
 !test-cif/**/*.cif
+!tests/**/*.dic

.pre-commit-config.yaml

@@ -7,14 +7,14 @@ repos:
     exclude: .*(\.md|\.ttl|\.cif)$
 
 - repo: https://github.com/ambv/black
-  rev: 21.7b0
+  rev: 21.11b1
   hooks:
   - id: black
     args:
       - --config=dic2owl/pyproject.toml
 
 - repo: https://github.com/pycqa/pylint
-  rev: 'v2.10.1'
+  rev: 'v2.12.1'
   hooks:
   - id: pylint
     args:

dic2owl/dic2owl/__init__.py

@@ -10,7 +10,10 @@
 terminal.
 """
 # pylint: disable=line-too-long
+from .dic2owl import Generator
 
 __version__ = "0.2.0"
 __author__ = "Jesper Friis <jesper.friis@sintef.no>, Casper Welzel Andersen <casper.w.andersen@sintef.no>, Francesca Lønstad Bleken <francesca.l.bleken@sintef.no>"
 __author_email__ = "cif@emmo-repo.eu"
+
+__all__ = ("Generator",)

dic2owl/dic2owl/cli.py

@@ -5,13 +5,14 @@
 ontology-generation tool for CIF `.dic`-files.
 """
 import argparse
-import logging
+
+# import logging
 from pathlib import Path
 
 
-LOGGING_LEVELS = [
-    logging.getLevelName(level).lower() for level in range(0, 51, 10)
-]
+# LOGGING_LEVELS = [
+#     logging.getLevelName(level).lower() for level in range(0, 51, 10)
+# ]
 
 
 def main(argv: list = None) -> None:
@@ -33,18 +34,18 @@ def main(argv: list = None) -> None:
         help="Show the version and exit.",
         version=f"dic2owl version {__version__}",
     )
-    parser.add_argument(
-        "--log-level",
-        type=str,
-        help="Set the stdout log-level (verbosity).",
-        choices=LOGGING_LEVELS,
-        default="info",
-    )
-    parser.add_argument(
-        "--debug",
-        action="store_true",
-        help="Overrule log-level option, setting it to 'debug'.",
-    )
+    # parser.add_argument(
+    #     "--log-level",
+    #     type=str,
+    #     help="Set the stdout log-level (verbosity).",
+    #     choices=LOGGING_LEVELS,
+    #     default="info",
+    # )
+    # parser.add_argument(
+    #     "--debug",
+    #     action="store_true",
+    #     help="Overrule log-level option, setting it to 'debug'.",
+    # )
     parser.add_argument(
         "-o",
         "--output",

dic2owl/dic2owl/dic2owl.py

@@ -9,7 +9,7 @@
 
 # import textwrap
 import types
-from typing import Any, Set, Union, Sequence
+from typing import TYPE_CHECKING
 import urllib.request
 
 from CifFile import CifDic
@@ -19,24 +19,29 @@
 with open(DEVNULL, "w") as handle:  # pylint: disable=unspecified-encoding
     with redirect_stderr(handle):
         from emmo import World
-        from emmo.ontology import Ontology
 
         from owlready2 import locstr
 
 
+if TYPE_CHECKING:
+    from _typeshed import StrPath
+    from typing import Any, Sequence, Set, Union
+
+    from emmo.ontology import Ontology
+
 # Workaround for flaw in EMMO-Python
 # To be removed when EMMO-Python doesn't requires ontologies to import SKOS
-import emmo.ontology  # noqa: E402
+import emmo.ontology  # pylint: disable=wrong-import-position
 
 emmo.ontology.DEFAULT_LABEL_ANNOTATIONS = [
     "http://www.w3.org/2000/01/rdf-schema#label",
 ]
 
-"""The absolute, normalized path to the `ontology` directory in this
-repository"""
 ONTOLOGY_DIR = (
     Path(__file__).resolve().parent.parent.parent.joinpath("ontology")
 )
+"""The absolute, normalized path to the `ontology` directory in this
+repository"""
 
 
 def lang_en(string: str) -> locstr:
@@ -67,40 +72,41 @@ class Generator:
 
     """
 
+    CIF_DDL = (
+        "https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/"
+        "ontology/cif-ddl.ttl"
+    )
+
     # TODO:
     # Should `comments` be replaced with a dict `annotations` for annotating
     # the ontology itself?  If so, we should import Dublin Core.
 
     def __init__(
         self,
-        dicfile: str,
+        dicfile: "StrPath",
         base_iri: str,
-        comments: Sequence[str] = (),
+        comments: "Sequence[str]" = (),
     ) -> None:
         self.dicfile = dicfile
-        self.dic = CifDic(dicfile, do_dREL=False)
+        self.dic = CifDic(str(self.dicfile), do_dREL=False)
         self.comments = comments
 
         # Create new ontology
         self.world = World()
         self.onto = self.world.get_ontology(base_iri)
 
         # Load cif-ddl ontology and append it to imported ontologies
-        cif_ddl = (
-            "https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/"
-            "ontology/cif-ddl.ttl"
-        )
-        self.ddl = self.world.get_ontology(str(cif_ddl)).load()
+        self.ddl = self.world.get_ontology(self.CIF_DDL).load()
         self.ddl.sync_python_names()
         self.onto.imported_ontologies.append(self.ddl)
 
         # Load Dublin core for metadata and append it to imported ontologies
         # dcterms = self.world.get_ontology('http://purl.org/dc/terms/').load()
         # self.onto.imported_ontologies.append(dcterms)
 
-        self.items: Set[dict] = set()
+        self.items: "Set[dict]" = set()
 
-    def generate(self) -> Ontology:
+    def generate(self) -> "Ontology":
         """Generate ontology for the CIF dictionary.
 
         Returns:
@@ -194,7 +200,7 @@ def _add_data_value(self, item: dict) -> None:
 
         self._add_annotations(cls, item)
 
-    def _add_annotations(self, cls: Any, item: dict) -> None:
+    def _add_annotations(self, cls: "Any", item: dict) -> None:
         """Add annotations for dic item `item` to generated ontology
         class `cls`.
 
@@ -228,7 +234,9 @@ def _add_metadata(self) -> None:
         )
 
 
-def main(dicfile: Union[str, Path], ttlfile: Union[str, Path]) -> Generator:
+def main(
+    dicfile: "Union[str, Path]", ttlfile: "Union[str, Path]"
+) -> Generator:
     """Main function for ontology generation.
 
     Parameters:

dic2owl/requirements_dev.txt

@@ -2,3 +2,5 @@ bandit~=1.7.0
 mypy==0.910
 pre-commit~=2.15
 pylint~=2.11
+pytest~=6.2
+pytest-cov~=2.12