Updates Flake8 and Mypy versions, fixes all errors. Replaces poetry instructions with uv

Author: sjoerdk

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
       - id: black
         language: python
   - repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+    rev: 7.3.0
     hooks:
       - id: flake8
         language: python

dicomtrolley/caching.py

@@ -189,13 +189,13 @@ class QueryCache:
 
     def __init__(self, cache: DICOMObjectCache):
         self.cache = cache
-        self.queries: Dict[Query, Tuple[DICOMObjectReference, ...]] = {}
+        self.queries: Dict[str, Tuple[DICOMObjectReference, ...]] = {}
 
     def add_response(self, query: Query, response: Sequence[DICOMObject]):
         """Cache response for this query"""
         self.cache.add_all(response)
         references = tuple(x.reference() for x in response)
-        self.queries[query.json()] = references
+        self.queries[query.model_dump_json()] = references
 
     def get_response(self, query: Query) -> List[Study]:
         """Obtain cached response for this query
@@ -206,7 +206,7 @@ def get_response(self, query: Query) -> List[Study]:
             If any of the results of query are not in cache or have expired
         """
         try:
-            references = self.queries[query.json()]
+            references = self.queries[query.model_dump_json()]
         except KeyError as e:
             raise NodeNotFound(
                 f"Query {query.to_short_string()} not found in cache"
@@ -221,7 +221,7 @@ def get_response(self, query: Query) -> List[Study]:
             return retrieved
         except NodeNotFound as e:
             # This query response is not (fully) cached anymore. Remove
-            self.queries.pop(query.json())
+            self.queries.pop(query.model_dump_json())
             raise NodeNotFound(
                 f"One or more response to {query.to_short_string()} "
                 f"was not in cache"

dicomtrolley/core.py

@@ -613,7 +613,7 @@ class Query(BaseModel):
     )  # to which depth to return results
     max_study_date: Optional[datetime] = None
     min_study_date: Optional[datetime] = None
-    include_fields: List[str] = Field([])  #
+    include_fields: Optional[List[str]] = Field(default_factory=list)
 
     class Config:
         extra = "forbid"  # raise ValueError when passing an unknown keyword to init
@@ -749,5 +749,5 @@ def find_study_by_id(
         )
 
 
-Instance.update_forward_refs()  # enables pydantic validation
-Series.update_forward_refs()
+Instance.model_rebuild()  # enables pydantic validation
+Series.model_rebuild()

dicomtrolley/fields.py

@@ -140,7 +140,6 @@ class StudyLevel:
         "InstitutionalDepartmentName",
         "NumberOfStudyRelatedSeries",
         "NumberOfStudyRelatedInstances",
-        "InstanceAvailability",
         "SOPClassesInStudy",
         "CurrentPatientLocation",
         "SourceApplicationEntityTitle",

docs/contributing.md

@@ -9,13 +9,13 @@ Report bugs at [https://github.com/sjoerdk/dicomtrolley/issues]()
 Fork this repo, create a feature branch
 
 ### Set up environment
-dicomtrolley uses [poetry](https://python-poetry.org/docs/) for dependency and package management 
+dicomtrolley uses [uv](https://docs.astral.sh/uv) for dependency and package management 
 
-* Install poetry (see [poetry docs](https://python-poetry.org/docs/#installation))
+* Install uv (see [uv docs](https://docs.astral.sh/uv/getting-started/installation/))
 
-* Create a virtual env. Go to the folder where cloned dicomtrolley and use 
+* Create a virtual env. Go to the folder where you cloned dicomtrolley and use 
   ```  
-  poetry install 
+  uv sync 
   ``` 
 
 * Install [pre-commit](https://pre-commit.com) hooks.

setup.cfg

@@ -68,6 +68,7 @@ ignore =
     W503
     # N815 allow mixedCase. Matching case of MINT API url parameters is clearer then renaming
     N815
+exclude:
     # I want to keep very long lines in long xml templates.
     # NOTE: this exlude is also set in pre-commit-config.yaml as pre-commit seems to ignore this here
     dicomtrolley/xml_templates.py

tests/mock_responses.py

@@ -393,7 +393,7 @@ def create_rad69_response(bytes_parts, soap_header=None):
     multi_part_soap_response = MultipartEncoder(
         fields=[("part1", soap_header)]
         + [
-            (f"part{idx+2}", ("filename", bytes_part, "application/dicom"))
+            (f"part{idx + 2}", ("filename", bytes_part, "application/dicom"))
             for idx, bytes_part in enumerate(bytes_parts)
         ],
     )

tests/test_dicom_qr.py

@@ -160,7 +160,7 @@ def test_find_study_with_basic_query():
     qr.parse_c_find_response = Mock()
 
     qr.find_studies(query=Query(PatientID="test"))
-    assert type(called[0]) == DICOMQuery
+    assert isinstance(called[0], DICOMQuery)
     assert called[0].PatientID == "test"
 
 

tests/test_examples.py

@@ -2,13 +2,13 @@
 from unittest.mock import Mock
 
 import pytest
-
-from dicomtrolley.storage import StorageDir
 from examples.go_shopping import go_shopping
 from examples.go_shopping_rad69 import go_shopping_rad69
 from examples.search_for_studies_dicom_qr import search_for_studies_dicom_qr
 from examples.search_for_studies_mint import search_for_studies_mint
 from examples.use_wado_only import use_wado_only
+
+from dicomtrolley.storage import StorageDir
 from tests.conftest import set_mock_response
 from tests.factories import create_c_find_image_response
 from tests.mock_responses import LOGIN_SUCCESS, MockUrls, RAD69_RESPONSE_ANY

tests/test_trolley.py

@@ -9,7 +9,6 @@
 from dicomtrolley.trolley import (
     Trolley,
 )
-
 from tests.conftest import create_mint_study
 from tests.factories import (
     StudyReferenceFactory,