Merge pull request #181 from emmo-repo/cwa/add-Word

Add new `Word` content type.
Adds Word in a similar fashion as Code and similar.

---

When storing the Turtle file (cif-ddl.ttl) from Protégé it
changed the formatting. In order to understand the
actual change(s), I have split it up into several commits.

To see the purely formatting changes, see a34fd90.
To see the addition of Word, see d47bf00.

---

Updates to minimum v4.4.6 of PyCIFRW.

---

This PR goes a small step further and updates the cif-core.ttl
file under ontologies/ to the latest generated version of the
CIF-ontology according to the updated cif_core.dic in
COMCIFS and the newly added Word content type.

.gitignore

@@ -10,6 +10,11 @@ __pycache__
 *.dic
 *.cif
 
+dist/
+site/
+
+*.properties
+
 !test-cif/**/*.cif
 !tests/**/*.dic
 

dic2owl/dic2owl/cli.py

@@ -62,6 +62,14 @@ def main(argv: "Optional[List[str]]" = None) -> None:
             "to the CIF_DIC file."
         ),
     )
+    parser.add_argument(
+        "--local-ontologies",
+        action="store_true",
+        help=(
+            "Use local ontologies instead of the latest commit on GitHub. "
+            "This is mainly for debugging purposes."
+        ),
+    )
     parser.add_argument(
         "dicfile",
         metavar="CIF_DIC",
@@ -84,4 +92,8 @@ def main(argv: "Optional[List[str]]" = None) -> None:
         # downloaded.
         args.dicfile = str(args.dicfile)
 
-    dic2owl_run(dicfile=args.dicfile, ttlfile=args.ttlfile)
+    dic2owl_run(
+        dicfile=args.dicfile,
+        ttlfile=args.ttlfile,
+        local_ontologies=args.local_ontologies,
+    )

dic2owl/dic2owl/dic2owl.py

@@ -6,8 +6,6 @@
 from contextlib import redirect_stderr
 from os import devnull as DEVNULL
 from pathlib import Path
-
-# import textwrap
 import types
 from typing import TYPE_CHECKING
 import urllib.request
@@ -61,28 +59,35 @@ class MissingAnnotationError(Exception):
     """Raised when using a cif-dictionary annotation not defined in ddl"""
 
 
-# pylint: disable=too-few-public-methods
+# pylint: disable=too-few-public-methods,too-many-instance-attributes
 class Generator:
     """Class for generating CIF ontology from a CIF dictionary.
 
     Parameters:
         dicfile: File name of CIF dictionary to generate an ontology for.
         base_iri: Base IRI of the generated ontology.
         comments: Sequence of comments to add to the ontology itself.
+        local_ddl: If `True`, the CIF DDL ontology will be loaded from the
+            local repository.
 
     """
 
-    CIF_DDL = (
-        "https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/"
-        "ontology/cif-ddl.ttl"
-    )
+    cif_ddl: str
 
     def __init__(
         self,
         dicfile: "StrPath",
         base_iri: str,
         comments: "Sequence[str]" = (),
+        local_ddl: bool = False,
     ) -> None:
+        self.cif_ddl = (
+            (ONTOLOGY_DIR / "cif-ddl.ttl").as_uri()
+            if local_ddl
+            else "https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/"
+            "ontology/cif-ddl.ttl"
+        )
+
         self.dicfile = dicfile
         self.dic = CifDic(str(self.dicfile), do_dREL=False)
         self.comments = comments
@@ -92,7 +97,7 @@ def __init__(
         self.onto = self.world.get_ontology(base_iri)
 
         # Load cif-ddl ontology and append it to imported ontologies
-        self.ddl = self.world.get_ontology(self.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)
 
@@ -223,7 +228,9 @@ def _add_metadata(self) -> None:
 
 
 def main(
-    dicfile: "Union[str, Path]", ttlfile: "Union[str, Path]"
+    dicfile: "Union[str, Path]",
+    ttlfile: "Union[str, Path]",
+    local_ontologies: bool = False,
 ) -> Generator:
     """Main function for ontology generation.
 
@@ -238,6 +245,10 @@ def main(
 
             !!! important
                 The file will be overwritten if it already exists.
+        local_ontologies: If `True`, the ontologies used to generate the
+            ontology will be loaded from the local repository.
+            If `False`, the ontologies will be loaded from the latest commit in
+            the `main` branch on GitHub.
 
     Returns:
         The setup ontology generator class. This is mainly returned for
@@ -257,7 +268,9 @@ def main(
             # `file://` or similar.
             urllib.request.urlretrieve(baseurl + dic, dic)  # nosec
 
-    gen = Generator(dicfile=dicfile, base_iri=base_iri)
+    gen = Generator(
+        dicfile=dicfile, base_iri=base_iri, local_ddl=local_ontologies
+    )
     onto = gen.generate()
     onto.save(
         ttlfile if isinstance(ttlfile, str) else str(ttlfile.resolve()),

dic2owl/requirements.txt

@@ -1,2 +1,2 @@
 EMMOntoPy>=0.6.0,<1
-PyCifRW>=4.4.5,<5
+PyCifRW>=4.4.6,<5