Package: src:python-bioregistry Version: 0.11.12-4 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202610/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:python-bioregistry, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] .. todo:: IRI with weird embedding, like ones that end in .html """ > prefix, identifier = self.converter.parse_uri(uri) ^^^^^^^^^^^^^^^^^^ E TypeError: cannot unpack non-iterable NoneType object bioregistry/resource_manager.py:344: TypeError =============================== warnings summary =============================== bioregistry/schema_utils.py:61: 1778 warnings tests/test_contexts.py: 1778 warnings tests/test_manager.py: 19558 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/schema_utils.py:61: PydanticDeprecatedSince20: The `parse_obj` method is deprecated; use `model_validate` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ return {prefix: Resource.parse_obj(value) for prefix, value in data.items()} bioregistry/schema/struct.py:648: 7112 warnings tests/test_api.py: 7 warnings tests/test_collections.py: 58 warnings tests/test_contexts.py: 209240 warnings tests/test_data.py: 230996 warnings tests/test_data_slow.py: 334389 warnings tests/test_identifiers_org.py: 1497 warnings tests/test_manager.py: 422132 warnings tests/test_metaregistry.py: 245 warnings tests/test_resolve.py: 8418 warnings tests/test_web/test_api.py: 4180 warnings tests/test_web/test_ui.py: 13217 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/schema/struct.py:648: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ return self.dict().get(metaprefix) or dict() tests/test_web/test_api.py:13 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/tests/test_web/test_api.py:13: StarletteDeprecationWarning: Using `httpx` with `starlette.testclient` is deprecated; install `httpx2` instead. from starlette.testclient import TestClient bioregistry/app/api.py:137 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/app/api.py:137: FastAPIDeprecationWarning: `example` has been deprecated, please use `examples` instead prefix: str = Path( bioregistry/app/api.py:185 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/app/api.py:185: FastAPIDeprecationWarning: `example` has been deprecated, please use `examples` instead METAPREFIX_PATH = Path( bioregistry/app/api.py:353 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/app/api.py:353: FastAPIDeprecationWarning: `example` has been deprecated, please use `examples` instead identifier: str = Path( bioregistry/app/api.py:405 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/app/api.py:405: FastAPIDeprecationWarning: `example` has been deprecated, please use `examples` instead identifier: str = Path(title="Context Key", description="The context key", example="obo"), bioregistry/app/impl.py:14 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/app/impl.py:14: StarletteDeprecationWarning: starlette.middleware.wsgi is deprecated and will be removed in a future release. Please refer to https://github.com/abersheeran/a2wsgi as a replacement. from starlette.middleware.wsgi import WSGIMiddleware tests/test_api.py: 7 warnings tests/test_collections.py: 18 warnings tests/test_contexts.py: 31539 warnings tests/test_data.py: 43942 warnings tests/test_data_slow.py: 47708 warnings tests/test_identifiers_org.py: 778 warnings tests/test_manager.py: 48395 warnings tests/test_metaregistry.py: 56 warnings tests/test_resolve.py: 3454 warnings tests/test_web/test_api.py: 2727 warnings tests/test_web/test_ui.py: 5177 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/schema/struct.py:673: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ rv = self.dict().get(key) tests/test_collections.py: 13 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/tests/test_collections.py:31: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ collection = collection_pydantic.dict() tests/test_data.py::TestRegistry::test_keys /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/tests/test_data.py:83: PydanticDeprecatedSince20: The `__fields__` attribute is deprecated, use the `model_fields` class property instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ keys = set(Resource.__fields__.keys()) tests/test_data.py: 1404 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/tests/test_data.py:875: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ for key, value in publication.dict().items(): tests/test_manager.py: 3021 warnings tests/test_web/test_api.py: 38 warnings tests/test_web/test_ui.py: 31 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/schema/struct.py:2853: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ records = [publication.dict(exclude_none=True) for publication in publications] tests/test_manager.py: 99 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/schema/struct.py:1296: PydanticDeprecatedSince20: The `parse_obj` method is deprecated; use `model_validate` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ publications.append(Publication.parse_obj(publication)) tests/test_metaregistry.py: 32 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/tests/test_metaregistry.py:84: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ invalid_keys = set(registry.dict()).difference(Registry.__fields__) tests/test_metaregistry.py: 32 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/tests/test_metaregistry.py:84: PydanticDeprecatedSince20: The `__fields__` attribute is deprecated, use the `model_fields` class property instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ invalid_keys = set(registry.dict()).difference(Registry.__fields__) tests/test_web/test_api.py::TestWeb::test_api_collection tests/test_web/test_api.py::TestWeb::test_api_metaresource tests/test_web/test_api.py::TestWeb::test_api_resource /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/app/api.py:57: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ content = content.dict( tests/test_web/test_api.py: 2390 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/schema/utils.py:30: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ return sanitize_dict(base_model.dict(**kwargs)) tests/test_web/test_api.py: 3556 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/tests/test_web/test_api.py:59: PydanticDeprecatedSince20: The `parse_obj` method is deprecated; use `model_validate` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ return {key: Resource.parse_obj(resource) for key, resource in data} tests/test_web/test_api.py: 1778 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/tests/test_web/test_api.py:93: PydanticDeprecatedSince20: The `parse_obj` method is deprecated; use `model_validate` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ return {key: Resource.parse_obj(resource) for key, resource in data} tests/test_web/test_api.py::TestWeb::test_external_registry_mappings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/tests/test_web/test_api.py:237: PydanticDeprecatedSince20: The `parse_obj` method is deprecated; use `model_validate` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ res_parsed = MappingResponse.parse_obj(res.json()) tests/test_web/test_api.py::TestWeb::test_iri_mapping /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/tests/test_web/test_api.py:255: PydanticDeprecatedSince20: The `parse_obj` method is deprecated; use `model_validate` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ data = URIResponse.parse_obj(res.json()) tests/test_web/test_api.py::TestWeb::test_ui_resource_rdf tests/test_web/test_ui.py::TestUI::test_ui_collection_rdf tests/test_web/test_ui.py::TestUI::test_ui_registry_rdf /usr/lib/python3/dist-packages/rdflib/plugins/parsers/notation3.py:2063: DeprecationWarning: Dataset.default_context is deprecated, use Dataset.default_graph instead. conj_graph.default_context = graph # TODO: CG __init__ should have a tests/test_web/test_api.py: 42 warnings tests/test_web/test_ui.py: 34 warnings /usr/lib/python3/dist-packages/rdflib/graph.py:2228: DeprecationWarning: Dataset.default_context is deprecated, use Dataset.default_graph instead. c = self.default_context if default else None tests/test_web/test_ui.py::TestUI::test_ui /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/app/ui.py:274: PydanticDeprecatedSince20: The `schema` method is deprecated; use `model_json_schema` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ schema=Context.schema(), tests/test_web/test_ui.py::TestUI::test_ui /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/app/ui.py:288: PydanticDeprecatedSince20: The `schema` method is deprecated; use `model_json_schema` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ schema=Context.schema()["properties"], tests/test_web/test_ui.py: 22 warnings /usr/lib/python3/dist-packages/jinja2/environment.py:490: PydanticDeprecatedSince20: The `__fields__` attribute is deprecated, use the `model_fields` class property instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ return getattr(obj, attribute) tests/test_web/test_ui.py::TestUI::test_ui_collection_json /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/app/utils.py:181: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ json.dumps(data.dict(exclude_unset=True, exclude_none=True), ensure_ascii=False), tests/test_web/test_ui.py::TestUI::test_ui_collection_json /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bioregistry/app/utils.py:186: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/ yaml.safe_dump(data.dict(exclude_unset=True, exclude_none=True), allow_unicode=True), -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_web/test_api.py::TestWeb::test_iri_mapping - TypeError: can... = 1 failed, 124 passed, 6 skipped, 6 deselected, 1450917 warnings in 146.16s (0:02:26) = E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build; python3.14 -m pytest -k 'not test_url and not test_url_banana and not test_obolibrary_example and not test_usages ' dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.14 --parallel=2 returned exit code 13 make: *** [debian/rules:12: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 --------------------------------------------------------------------------------
