Linter/formatter changes (min. Python now 3.9)

src/voc4cat/convert.py

@@ -1,7 +1,7 @@
 import logging
 from itertools import chain
 from pathlib import Path
-from typing import Dict, Literal, Union
+from typing import Literal, Union
 
 import pyshacl
 from colorama import Fore, Style
@@ -242,10 +242,10 @@ def rdf_to_excel(
         modified=holder["modified"],
         creator=holder["creator"],
         publisher=holder["publisher"],
-        version=holder.get("versionInfo", None),
-        provenance=holder.get("provenance", None),
-        custodian=holder.get("custodian", None),
-        pid=holder.get("pid", None),
+        version=holder.get("versionInfo"),
+        provenance=holder.get("provenance"),
+        custodian=holder.get("custodian"),
+        pid=holder.get("pid"),
     )
     cs.to_excel(wb)
 
@@ -366,7 +366,7 @@ def rdf_to_excel(
     return dest
 
 
-def format_log_msg(result: Dict, colored: bool = False) -> str:
+def format_log_msg(result: dict, colored: bool = False) -> str:
     from rdflib.namespace import SH
 
     formatted_msg = ""

src/voc4cat/convert_043.py

@@ -1,5 +1,4 @@
 import logging
-from typing import List, Tuple
 
 from curies import Converter
 from openpyxl import Workbook
@@ -51,7 +50,7 @@ def extract_concepts_and_collections(
     s: Worksheet,
     prefix_converter: Converter,
     vocab_name: str = "",
-) -> Tuple[List[models.Concept], List[models.Collection]]:
+) -> tuple[list[models.Concept], list[models.Collection]]:
     concepts = []
     collections = []
     # Iterating over the concept page and the additional concept page

src/voc4cat/fields.py

@@ -8,7 +8,8 @@
 
 import logging
 import re
-from typing import Any, ClassVar, Generator
+from collections.abc import Generator
+from typing import Any, ClassVar
 
 import base32_crockford
 from pydantic import BaseConfig, HttpUrl

src/voc4cat/models.py

@@ -2,7 +2,7 @@
 import logging
 import os
 from itertools import chain
-from typing import List, Union
+from typing import Union
 
 from curies import Converter
 from openpyxl import Workbook
@@ -289,19 +289,19 @@ def to_excel(self, wb: Workbook):
 
 class Concept(BaseModel):
     uri: AnyHttpUrl
-    pref_label: Union[str, List[str]]
-    alt_labels: List[str] = []
-    pl_language_code: List[str] = []
-    definition: Union[str, List[str]]
-    def_language_code: List[str] = []
-    children: List[AnyHttpUrl] = []
+    pref_label: Union[str, list[str]]
+    alt_labels: list[str] = []
+    pl_language_code: list[str] = []
+    definition: Union[str, list[str]]
+    def_language_code: list[str] = []
+    children: list[AnyHttpUrl] = []
     source_vocab: AnyHttpUrl | None = None
     provenance: str | None = None
-    related_match: List[AnyHttpUrl] = []
-    close_match: List[AnyHttpUrl] = []
-    exact_match: List[AnyHttpUrl] = []
-    narrow_match: List[AnyHttpUrl] = []
-    broad_match: List[AnyHttpUrl] = []
+    related_match: list[AnyHttpUrl] = []
+    close_match: list[AnyHttpUrl] = []
+    exact_match: list[AnyHttpUrl] = []
+    narrow_match: list[AnyHttpUrl] = []
+    broad_match: list[AnyHttpUrl] = []
     vocab_name: str = Field("", exclude=True)
 
     # We validate with a reusable (external) validators. With a pre-validator,
@@ -477,7 +477,7 @@ class Collection(BaseModel):
     uri: AnyHttpUrl
     pref_label: str
     definition: str
-    members: List[AnyHttpUrl]
+    members: list[AnyHttpUrl]
     provenance: str | None = None
     vocab_name: str = Field("", exclude=True)
 
@@ -528,8 +528,8 @@ def to_excel(self, wb: Workbook, row_no: int):
 
 class Vocabulary(BaseModel):
     concept_scheme: ConceptScheme
-    concepts: List[Concept]
-    collections: List[Collection]
+    concepts: list[Concept]
+    collections: list[Collection]
 
     def to_graph(self):
         g = self.concept_scheme.to_graph()

tests/conftest.py

@@ -10,7 +10,7 @@ def datadir():
     return Path(__file__).resolve().parent / "data"
 
 
-@pytest.fixture()
+@pytest.fixture
 def temp_config():
     """
     Provides a temporary config that can be safely changed in test functions.

tests/test_check.py

@@ -10,6 +10,7 @@
     CS_SIMPLE,
     CS_SIMPLE_TURTLE,
 )
+
 from voc4cat.checks import Voc4catError
 from voc4cat.cli import main_cli
 from voc4cat.utils import ConversionError

tests/test_checks.py

@@ -8,6 +8,7 @@
 
 import pytest
 from rdflib import RDF, SKOS, Graph
+
 from voc4cat.checks import (
     Voc4catError,
     check_for_removed_iris,
@@ -263,9 +264,12 @@ def test_check_for_removed_iris(  # noqa: PLR0913
     )
     config.load_config(config=config.IDRANGES)
 
-    with caplog.at_level(logging.ERROR), pytest.raises(
-        Voc4catError,
-        match=r"Forbidden removal of 1 concepts\/collections detected. See log for IRIs.",
+    with (
+        caplog.at_level(logging.ERROR),
+        pytest.raises(
+            Voc4catError,
+            match=r"Forbidden removal of 1 concepts\/collections detected. See log for IRIs.",
+        ),
     ):
         check_for_removed_iris(original, reduced)
     assert log_text in caplog.text

tests/test_cli.py

@@ -4,6 +4,7 @@
 from unittest import mock
 
 import pytest
+
 from voc4cat.checks import Voc4catError
 from voc4cat.cli import main_cli, run_cli_app
 
@@ -105,8 +106,11 @@ def test_valid_config(monkeypatch, datadir, caplog, tmp_path, temp_config):
 def test_invalid_outdir(monkeypatch, datadir, tmp_path, caplog):
     monkeypatch.chdir(datadir)
     shutil.copy(datadir / "README.md", tmp_path)
-    with caplog.at_level(logging.ERROR), pytest.raises(
-        Voc4catError, match="Outdir must be a directory but it is a file."
+    with (
+        caplog.at_level(logging.ERROR),
+        pytest.raises(
+            Voc4catError, match="Outdir must be a directory but it is a file."
+        ),
     ):
         main_cli(["transform", "--outdir", str(tmp_path / "README.md"), CS_SIMPLE])
     assert "Outdir must be a directory but it is a file." in caplog.text

tests/test_convert.py

@@ -3,12 +3,13 @@
 from pathlib import Path
 
 import pytest
-import voc4cat
 from test_cli import (
     CS_CYCLES,
     CS_CYCLES_TURTLE,
     CS_SIMPLE,
 )
+
+import voc4cat
 from voc4cat.checks import Voc4catError
 from voc4cat.cli import main_cli
 

tests/test_dag_util.py

@@ -1,4 +1,5 @@
 import pytest
+
 from voc4cat.checks import Voc4catError
 from voc4cat.dag_util import (
     dag_from_indented_text,

tests/test_docs.py

@@ -8,6 +8,7 @@
 from test_cli import (
     CS_CYCLES_TURTLE,
 )
+
 from voc4cat.checks import Voc4catError
 from voc4cat.cli import main_cli
 
@@ -32,9 +33,10 @@ def test_build_docs_pylode_ci_no_git(monkeypatch, datadir, tmp_path, caplog):
     shutil.copy(datadir / "valid_idranges.toml", dst / "idranges.toml")
     outdir = dst / "pylode"
 
-    with caplog.at_level(logging.ERROR), mock.patch(
-        "voc4cat.gh_index.subprocess"
-    ) as subprocess:
+    with (
+        caplog.at_level(logging.ERROR),
+        mock.patch("voc4cat.gh_index.subprocess") as subprocess,
+    ):
         subprocess.Popen.return_value.returncode = 1
         main_cli(
             ["docs", "--force", "--style", "pylode", "--outdir", str(outdir), str(dst)]
@@ -51,8 +53,9 @@ def test_build_docs_pylode_ci_no_config(monkeypatch, datadir, tmp_path, caplog):
     shutil.copy(datadir / CS_CYCLES_TURTLE, dst)
     outdir = dst / "pylode"
 
-    with caplog.at_level(logging.ERROR), pytest.raises(
-        Voc4catError, match="Config file not found"
+    with (
+        caplog.at_level(logging.ERROR),
+        pytest.raises(Voc4catError, match="Config file not found"),
     ):
         main_cli(
             ["docs", "--force", "--style", "pylode", "--outdir", str(outdir), str(dst)]

tests/test_fields.py

@@ -2,6 +2,7 @@
 
 import pytest
 from pydantic import BaseModel, ValidationError
+
 from voc4cat.fields import Orcid, Ror
 
 

tests/test_merge_vocab.py

@@ -4,6 +4,7 @@
 
 import pytest
 from test_cli import CS_CYCLES_TURTLE, CS_SIMPLE_TURTLE
+
 from voc4cat.merge_vocab import main_cli
 
 
@@ -61,9 +62,10 @@ def test_main_merge_split_vocab_dir(datadir, tmp_path, caplog):
     shutil.copy(datadir / CS_SIMPLE_TURTLE, ttl_inbox / "splitvoc")
     shutil.copy(datadir / CS_SIMPLE_TURTLE, vocab / "splitvoc")
 
-    with caplog.at_level(logging.DEBUG), mock.patch(
-        "voc4cat.merge_vocab.subprocess"
-    ) as subprocess:
+    with (
+        caplog.at_level(logging.DEBUG),
+        mock.patch("voc4cat.merge_vocab.subprocess") as subprocess,
+    ):
         subprocess.Popen.return_value.returncode = 1
         exit_code = main_cli([str(ttl_inbox), str(vocab)])
     assert "Entering directory" in caplog.text

tests/test_models.py

@@ -5,6 +5,7 @@
 import pytest
 from pydantic.error_wrappers import ValidationError
 from rdflib import Graph
+
 from voc4cat import config
 from voc4cat.models import Concept, ConceptScheme, reset_curies
 

tests/test_template043.py

@@ -3,8 +3,9 @@
 from unittest import mock
 
 import pytest
-import voc4cat
 from rdflib import SKOS, Graph, Literal, URIRef, compare
+
+import voc4cat
 from voc4cat import convert
 from voc4cat.utils import ConversionError
 

tests/test_transform.py

@@ -15,6 +15,7 @@
     CS_SIMPLE,
     CS_SIMPLE_TURTLE,
 )
+
 from voc4cat.checks import Voc4catError
 from voc4cat.cli import main_cli
 
@@ -671,8 +672,11 @@ def test_join_with_invalid_envvar(monkeypatch, datadir, tmp_path, caplog):
     # join files again as test
     cmd = ["transform", "-v", "--join"]
     cmd.append(str(tmp_path))
-    with caplog.at_level(logging.ERROR), pytest.raises(
-        Voc4catError, match="Invalid environment variable VOC4CAT_VERSION"
+    with (
+        caplog.at_level(logging.ERROR),
+        pytest.raises(
+            Voc4catError, match="Invalid environment variable VOC4CAT_VERSION"
+        ),
     ):
         main_cli(cmd)
     assert 'Invalid environment variable VOC4CAT_VERSION "2.0"' in caplog.text

tests/test_utils.py

@@ -1,5 +1,6 @@
 from openpyxl import Workbook, load_workbook
 from openpyxl.worksheet.table import Table
+
 from voc4cat.utils import adjust_length_of_tables, split_and_tidy