setup.cfg -> pyproject.toml

Set line-length to 79 (80) in `black` (`pylint`) tools.

.github/static/get_dic2owl_deps.py

@@ -24,7 +24,9 @@ def main(argv_input: list = None) -> Set[str]:
     )
     args = parser.parse_args(argv_input)
 
-    requirements_regex = re.compile(r"^(?P<name>[A-Za-z0-9_-]+)(~=|>=|==).*\n$")
+    requirements_regex = re.compile(
+        r"^(?P<name>[A-Za-z0-9_-]+)(~=|>=|==).*\n$"
+    )
     dependencies = set()
     for file in args.requirements_files:
         if not file.exists():
@@ -34,7 +36,10 @@ def main(argv_input: list = None) -> Set[str]:
                 match = requirements_regex.fullmatch(line)
                 if match is None:
                     raise ValueError(
-                        f"Couldn't determine package name from line:\n\n  {line}"
+                        (
+                            "Couldn't determine package name from line:\n\n  "
+                            f"{line}"
+                        )
                     )
                 dependencies.add(match.group("name"))
     return dependencies

.github/workflows/dic2owl_ci.yml

@@ -31,7 +31,7 @@ jobs:
         run: bandit -r dic2owl/dic2owl
 
       - name: Run PyLint
-        run: pylint --rcfile=dic2owl/setup.cfg dic2owl/dic2owl
+        run: pylint --rcfile=dic2owl/pyproject.toml dic2owl/dic2owl
 
       - name: Run safety
         run: |

.pre-commit-config.yaml

@@ -10,13 +10,13 @@ repos:
   rev: 21.7b0
   hooks:
   - id: black
+    args:
+      - --config=dic2owl/pyproject.toml
 
 - repo: https://github.com/pycqa/pylint
   rev: 'v2.10.1'
   hooks:
   - id: pylint
     args:
-      - --rcfile
-      - dic2owl/setup.cfg
-      - --disable
-      - import-error
+      - --rcfile=dic2owl/pyproject.toml
+      - --disable=import-error

dic2owl/dic2owl/__init__.py

@@ -3,9 +3,11 @@
 
 This is a tool to generate ontologies from a CIF `.dic`-file.
 
-It can be used either by importing and using the `dic2owl.dic2owl.main` function or running it via
-the `dic2owl` CLI, which will be automatically installed when `pip install`-ing this package.
-For more information on how to run the CLI, run `dic2owl --help` in your terminal.
+It can be used either by importing and using the `dic2owl.dic2owl.main`
+function or running it via the `dic2owl` CLI, which will be automatically
+installed when `pip install`-ing this package.
+For more information on how to run the CLI, run `dic2owl --help` in your
+terminal.
 """
 
 __version__ = "0.1.0"

dic2owl/dic2owl/cli.py

@@ -1,15 +1,17 @@
 """
 # `dic2owl` CLI
 
-The `dic2owl` command line interface (CLI) is an easy way of running the ontology-generation tool
-for CIF `.dic`-files.
+The `dic2owl` command line interface (CLI) is an easy way of running the
+ontology-generation tool for CIF `.dic`-files.
 """
 import argparse
 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:
@@ -50,24 +52,31 @@ def main(argv: list = None) -> None:
         dest="ttlfile",
         type=Path,
         help=(
-            'The generated output file. Example "--output cif_core.ttl". If output is not '
-            "provided, the filename will be taken to be similar to the CIF_DIC file."
+            'The generated output file. Example "--output cif_core.ttl". If '
+            "output is not provided, the filename will be taken to be similar "
+            "to the CIF_DIC file."
         ),
     )
     parser.add_argument(
         "dicfile",
         metavar="CIF_DIC",
         type=Path,
-        help="The CIF dictionary file from which to generate an OWL ontologized Turtle file.",
+        help=(
+            "The CIF dictionary file from which to generate an OWL ontologized"
+            " Turtle file."
+        ),
     )
 
     args = parser.parse_args(argv)
 
     if args.ttlfile is None:
-        args.ttlfile = args.dicfile.resolve().name[: -len(args.dicfile.suffix)] + ".ttl"
+        args.ttlfile = (
+            args.dicfile.resolve().name[: -len(args.dicfile.suffix)] + ".ttl"
+        )
 
     if not args.dicfile.resolve().exists():
-        # The dic-file does not exist, use it as a string instead so it can be downloaded.
+        # The dic-file does not exist, use it as a string instead so it can be
+        # downloaded.
         args.dicfile = str(args.dicfile)
 
     dic2owl_run(dicfile=args.dicfile, ttlfile=args.ttlfile)

dic2owl/dic2owl/dic2owl.py

@@ -35,7 +35,9 @@
 
 """The absolute, normalized path to the `ontology` directory in this
 repository"""
-ONTOLOGY_DIR = Path(__file__).resolve().parent.parent.parent.joinpath("ontology")
+ONTOLOGY_DIR = (
+    Path(__file__).resolve().parent.parent.parent.joinpath("ontology")
+)
 
 
 def lang_en(string: str) -> locstr:
@@ -218,7 +220,9 @@ def _add_metadata(self) -> None:
 
         for comment in self.comments:
             self.onto.metadata.comment.append(comment)
-        self.onto.metadata.comment.append(f"Generated with dic2owl from {self.dicfile}")
+        self.onto.metadata.comment.append(
+            f"Generated with dic2owl from {self.dicfile}"
+        )
 
 
 def main(dicfile: Union[str, Path], ttlfile: Union[str, Path]) -> Generator:
@@ -250,7 +254,8 @@ def main(dicfile: Union[str, Path], ttlfile: Union[str, Path]) -> Generator:
     for dic in ("ddl.dic", "templ_attr.cif", "templ_enum.cif", dicfile):
         if not Path(dic).resolve().exists():
             print("downloading", dic)
-            # Since `baseurl` is used, the retrieved URL will never be a `file://` or similar.
+            # Since `baseurl` is used, the retrieved URL will never be a
+            # `file://` or similar.
             urllib.request.urlretrieve(baseurl + dic, dic)  # nosec
 
     gen = Generator(dicfile=dicfile, base_iri=base_iri)