chore: bump dependencies and fix new linter errors (#1122)

.pre-commit-config.yaml

@@ -5,15 +5,15 @@
 repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.6
+    rev: v0.6.1
     hooks:
       - id: ruff
         args:
           - --ignore=A002  # builtin-argument-shadowing
           - --ignore=ARG001  # unused function argument
           - --ignore=D101  # undocumented-public-class
           - --ignore=D102  # undocumented-public-method
-          - --ignore=F841  # error suppression
+          - --ignore=F841  # unused-variable
           - --ignore=FIX002  # line-contains-to-do
           - --ignore=PLR0913  # too-many-arguments
           - --ignore=PLR2004  # magic-value-comparison

pyproject.toml

@@ -64,7 +64,7 @@ pytest-sugar = "^1.0.0"
 pandas-stubs = "^2.2.1.240316"
 types-networkx = "^3.2.1.20240331"
 requests-mock = "^1.12.1"
-testcontainers =  "^4.4.1"
+testcontainers =  "4.7.2"
 docker = "^7.1.0"
 types-docker = "^7.0.0.20240529"
 pytest-cov = "^5.0.0"
@@ -230,4 +230,3 @@ convention = "google"
 
 [tool.ruff.lint.isort]
 force-single-line = true
-known-first-party = ["dsp_tools"]

src/dsp_tools/commands/excel2json/properties.py

@@ -230,7 +230,7 @@ def _get_final_series(
         case None, None:
             return None
         case pd.Series(), pd.Series():
-            final_series = pd.Series(np.logical_or(mandatory_check, no_attribute_check))  # type: ignore[arg-type]
+            final_series = pd.Series(np.logical_or(mandatory_check, no_attribute_check))  # type: ignore[arg-type, assignment]
         case pd.Series(), None:
             final_series = mandatory_check  # type: ignore[assignment]
         case None, pd.Series():

test/conftest.py

@@ -8,7 +8,7 @@
 from dsp_tools.utils.logger_config import logger_config
 
 
-@pytest.fixture()
+@pytest.fixture
 def caplog(_caplog: pytest.LogCaptureFixture) -> Iterator[pytest.LogCaptureFixture]:  # noqa: F811 (redefinition)
     """
     The caplog fixture that comes shipped with pytest does not support loguru.

test/e2e/commands/ingest_xmlupload/test_ingest_xmlupload.py

@@ -28,7 +28,7 @@ def mapping_file() -> Iterator[Path]:
     mapping_file.unlink(missing_ok=True)
 
 
-@pytest.fixture()
+@pytest.fixture
 def _create_project() -> Iterator[None]:
     with get_containers():
         success = create_project(Path("testdata/json-project/test-project-e2e.json"), CREDS, verbose=True)

test/e2e/test_create_and_xmlupload.py

@@ -19,28 +19,28 @@
 RESCLASSES_IN_ONTO_JSON = 2
 
 
-@pytest.fixture()
+@pytest.fixture
 def _create_project() -> Iterator[None]:
     with get_containers():
         success = create_project(Path("testdata/json-project/test-project-e2e.json"), CREDS, verbose=True)
         assert success
         yield
 
 
-@pytest.fixture()
+@pytest.fixture
 def _xmlupload(_create_project: None) -> None:
     success = xmlupload(Path("testdata/xml-data/test-data-e2e.xml"), CREDS, ".")
     assert success
 
 
-@pytest.fixture()
+@pytest.fixture
 def auth_header(_create_project: None) -> dict[str, str]:
     payload = {"email": CREDS.user, "password": CREDS.password}
     token: str = requests.post(f"{CREDS.server}/v2/authentication", json=payload, timeout=3).json()["token"]
     return {"Authorization": f"Bearer {token}"}
 
 
-@pytest.fixture()
+@pytest.fixture
 def project_iri(_create_project: None) -> str:
     get_project_route = f"{CREDS.server}/admin/projects/shortcode/{PROJECT_SHORTCODE}"
     project_iri: str = requests.get(get_project_route, timeout=3).json()["project"]["id"]

test/integration/commands/excel2json/test_json_header.py

@@ -11,7 +11,7 @@
 from dsp_tools.models.exceptions import InputError
 
 
-@pytest.fixture()
+@pytest.fixture
 def filled_json_header() -> JsonHeader:
     test_path = Path("testdata/excel2json/new_excel2json_files/json_header.xlsx")
     return get_json_header(test_path)

test/integration/commands/excel2json/test_new_lists.py

@@ -10,14 +10,14 @@
 from dsp_tools.models.exceptions import InputError
 
 
-@pytest.fixture()
+@pytest.fixture
 def result_lists_correct() -> list[dict[str, Any]]:
     all_lists, _ = new_excel2lists(Path("testdata/excel2json/new_excel2json_files/lists"))
     all_lists = sorted(all_lists, key=lambda x: x["name"])
     return all_lists
 
 
-@pytest.fixture()
+@pytest.fixture
 def expected_lists() -> list[dict[str, Any]]:
     with open("testdata/excel2json/new-lists-output-expected.json", encoding="utf-8") as f:
         expected = json.load(f)

test/integration/commands/excel2json/test_project.py

@@ -8,14 +8,14 @@
 from dsp_tools.commands.excel2json.project import _validate_folder_structure_get_filenames
 
 
-@pytest.fixture()
+@pytest.fixture
 def expected_project() -> dict[str, Any]:
     with open("testdata/excel2json/excel2json-expected-output.json", encoding="utf-8") as f:
         proj = json.load(f)
         return cast(dict[str, Any], proj)
 
 
-@pytest.fixture()
+@pytest.fixture
 def returned_project() -> dict[str, Any]:
     excel_folder = "testdata/excel2json/excel2json_files"
     listfolder, onto_folders = _validate_folder_structure_get_filenames(excel_folder)

test/integration/commands/excel2xml/test_excel2xml_cli.py

@@ -9,7 +9,7 @@
 INVALID_EXCEL_DIRECTORY = "testdata/invalid-testdata/excel2xml"
 
 
-@pytest.fixture()
+@pytest.fixture
 def expected_output() -> str:
     with open("testdata/excel2xml/excel2xml-expected-output.xml", encoding="utf-8") as f:
         return f.read()

test/integration/commands/ingest_xmlupload/test_ingest_xmlupload.py

@@ -19,7 +19,7 @@ def _retrieve_mapping_file() -> Iterator[None]:
     Path(mapping_file.name).unlink()
 
 
-@pytest.fixture()
+@pytest.fixture
 def creds() -> ServerCredentials:
     return ServerCredentials(
         user="[email protected]",

test/integration/commands/project/test_create_project.py

@@ -17,21 +17,21 @@
 from dsp_tools.utils.shared import parse_json_input
 
 
-@pytest.fixture()
+@pytest.fixture
 def tp_systematic() -> dict[str, Any]:
     tp_systematic_file = "testdata/json-project/test-project-systematic.json"
     with open(tp_systematic_file, encoding="utf-8") as json_file:
         tp_systematic: dict[str, Any] = json.load(json_file)
     return tp_systematic
 
 
-@pytest.fixture()
+@pytest.fixture
 def tp_systematic_ontology(tp_systematic: dict[str, Any]) -> dict[str, Any]:
     onto: dict[str, Any] = tp_systematic["project"]["ontologies"][0]
     return onto
 
 
-@pytest.fixture()
+@pytest.fixture
 def tp_circular_ontology() -> dict[str, Any]:
     tp_circular_ontology_file = "testdata/invalid-testdata/json-project/circular-ontology.json"
     with open(tp_circular_ontology_file, encoding="utf-8") as json_file:

test/integration/commands/project/test_models_project.py

@@ -6,7 +6,7 @@
 from test.integration.commands.xmlupload.connection_mock import ConnectionMockBase
 
 
-@pytest.fixture()
+@pytest.fixture
 def project() -> Project:
     return Project(
         con=ConnectionMockBase(),

test/integration/commands/xmlupload/test_resource_creation.py

@@ -26,7 +26,7 @@
 from dsp_tools.utils.connection_live import ConnectionLive
 
 
-@pytest.fixture()
+@pytest.fixture
 def ingest_client_mock():  # type: ignore[no-untyped-def]
     return Mock(spec_set=AssetClient)
 

test/integration/utils/test_xml_utils.py

@@ -9,12 +9,12 @@
 from dsp_tools.utils.xml_utils import parse_and_clean_xml_file
 
 
-@pytest.fixture()
+@pytest.fixture
 def data_systematic_unclean() -> Path:
     return Path("testdata/xml-data/test-data-systematic.xml")
 
 
-@pytest.fixture()
+@pytest.fixture
 def data_systematic_cleaned() -> etree._Element:
     return parse_and_clean_xml_file(Path("testdata/xml-data/test-data-systematic.xml"))
 

test/unittests/commands/excel2json/json_header_fixtures.py

@@ -4,56 +4,56 @@
 import pytest
 
 
-@pytest.fixture()
+@pytest.fixture
 def prefixes_good() -> pd.DataFrame:
     return pd.DataFrame(
         {"prefixes": ["foaf:", "sdh"], "uri": ["http://xmlns.com/foaf/0.1/", "https://ontome.net/ns/sdhss/"]}
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def prefixes_missing_col() -> pd.DataFrame:
     return pd.DataFrame({"uri": ["http://xmlns.com/foaf/0.1/", "https://ontome.net/ns/sdhss/"]})
 
 
-@pytest.fixture()
+@pytest.fixture
 def prefixes_missing_val() -> pd.DataFrame:
     return pd.DataFrame(
         {"prefixes": ["foaf:", pd.NA], "uri": ["http://xmlns.com/foaf/0.1/", "https://ontome.net/ns/sdhss/"]}
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def prefixes_wrong_val() -> pd.DataFrame:
     return pd.DataFrame({"prefixes": ["foaf:", "sdh"], "uri": ["http://xmlns.com/foaf/0.1/", "not a uri"]})
 
 
-@pytest.fixture()
+@pytest.fixture
 def project_good_missing_zero() -> pd.DataFrame:
     return pd.DataFrame({"shortcode": [11], "shortname": ["name"], "longname": ["long"]})
 
 
-@pytest.fixture()
+@pytest.fixture
 def project_good_no_zero() -> pd.DataFrame:
     return pd.DataFrame({"shortcode": [1111], "shortname": ["name"], "longname": ["long"]})
 
 
-@pytest.fixture()
+@pytest.fixture
 def project_missing_col() -> pd.DataFrame:
     return pd.DataFrame({"shortname": ["name"], "longname": ["long"]})
 
 
-@pytest.fixture()
+@pytest.fixture
 def project_missing_val() -> pd.DataFrame:
     return pd.DataFrame({"shortcode": [pd.NA], "shortname": ["name"], "longname": ["long"]})
 
 
-@pytest.fixture()
+@pytest.fixture
 def project_too_many_rows() -> pd.DataFrame:
     return pd.DataFrame({"shortcode": [11, 0], "shortname": ["name", pd.NA], "longname": ["long", "other"]})
 
 
-@pytest.fixture()
+@pytest.fixture
 def description_good() -> pd.DataFrame:
     return pd.DataFrame(
         {
@@ -65,7 +65,7 @@ def description_good() -> pd.DataFrame:
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def description_too_many_rows() -> pd.DataFrame:
     return pd.DataFrame(
         {
@@ -78,32 +78,32 @@ def description_too_many_rows() -> pd.DataFrame:
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def description_missing_col() -> pd.DataFrame:
     return pd.DataFrame({"other": ["english"]})
 
 
-@pytest.fixture()
+@pytest.fixture
 def description_missing_val() -> pd.DataFrame:
     return pd.DataFrame({"other": ["english"], "description_en": [pd.NA]})
 
 
-@pytest.fixture()
+@pytest.fixture
 def keywords_good() -> pd.DataFrame:
     return pd.DataFrame({"keywords": ["one", pd.NA, "three"]})
 
 
-@pytest.fixture()
+@pytest.fixture
 def keywords_missing_col() -> pd.DataFrame:
     return pd.DataFrame({"other": [1]})
 
 
-@pytest.fixture()
+@pytest.fixture
 def keywords_missing_val() -> pd.DataFrame:
     return pd.DataFrame({"other": [1], "keywords": [pd.NA]})
 
 
-@pytest.fixture()
+@pytest.fixture
 def users_good() -> pd.DataFrame:
     return pd.DataFrame(
         {
@@ -118,7 +118,7 @@ def users_good() -> pd.DataFrame:
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def users_missing_col() -> pd.DataFrame:
     return pd.DataFrame(
         {
@@ -132,7 +132,7 @@ def users_missing_col() -> pd.DataFrame:
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def users_missing_val() -> pd.DataFrame:
     return pd.DataFrame(
         {
@@ -147,7 +147,7 @@ def users_missing_val() -> pd.DataFrame:
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def users_wrong_lang() -> pd.DataFrame:
     return pd.DataFrame(
         {
@@ -162,7 +162,7 @@ def users_wrong_lang() -> pd.DataFrame:
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def user_good() -> pd.Series[str]:
     return pd.Series(
         {
@@ -177,7 +177,7 @@ def user_good() -> pd.Series[str]:
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def user_wrong_lang() -> pd.Series[str]:
     return pd.Series(
         {
@@ -192,7 +192,7 @@ def user_wrong_lang() -> pd.Series[str]:
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def user_wrong_email() -> pd.Series[str]:
     return pd.Series(
         {
@@ -207,7 +207,7 @@ def user_wrong_email() -> pd.Series[str]:
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def user_wrong_role() -> pd.Series[str]:
     return pd.Series(
         {