ruff format

src/fusor/__init__.py

@@ -1,4 +1,5 @@
 """Provide computable object representation and validation for gene fusions"""
+
 from fusor.fusor import FUSOR
 
 from .version import __version__

src/fusor/examples/__init__.py

@@ -1,4 +1,5 @@
 """Provide programmatic access to example objects."""
+
 import json
 from pathlib import Path
 

src/fusor/fusor.py

@@ -1,4 +1,5 @@
 """Module for modifying fusion objects."""
+
 import logging
 import re
 from urllib.parse import quote

src/fusor/models.py

@@ -1,4 +1,5 @@
 """Model for fusion class"""
+
 from abc import ABC
 from enum import Enum
 from typing import Any, Literal
@@ -120,9 +121,9 @@ class BaseStructuralElement(ABC, BaseModel):
 class TranscriptSegmentElement(BaseStructuralElement):
     """Define TranscriptSegment class"""
 
-    type: Literal[
+    type: Literal[FUSORTypes.TRANSCRIPT_SEGMENT_ELEMENT] = (
         FUSORTypes.TRANSCRIPT_SEGMENT_ELEMENT
-    ] = FUSORTypes.TRANSCRIPT_SEGMENT_ELEMENT
+    )
     transcript: CURIE
     exon_start: StrictInt | None = None
     exon_start_offset: StrictInt | None = 0
@@ -212,9 +213,9 @@ def check_exons(cls, values):
 class LinkerElement(BaseStructuralElement, extra="forbid"):
     """Define Linker class (linker sequence)"""
 
-    type: Literal[
+    type: Literal[FUSORTypes.LINKER_SEQUENCE_ELEMENT] = (
         FUSORTypes.LINKER_SEQUENCE_ELEMENT
-    ] = FUSORTypes.LINKER_SEQUENCE_ELEMENT
+    )
     linker_sequence: SequenceDescriptor
 
     @field_validator("linker_sequence", mode="before")
@@ -260,9 +261,9 @@ class TemplatedSequenceElement(BaseStructuralElement):
     product.
     """
 
-    type: Literal[
+    type: Literal[FUSORTypes.TEMPLATED_SEQUENCE_ELEMENT] = (
         FUSORTypes.TEMPLATED_SEQUENCE_ELEMENT
-    ] = FUSORTypes.TEMPLATED_SEQUENCE_ELEMENT
+    )
     region: LocationDescriptor
     strand: Strand
 
@@ -340,9 +341,9 @@ class MultiplePossibleGenesElement(BaseStructuralElement):
     MultiplePossibleGenesElement.
     """
 
-    type: Literal[
+    type: Literal[FUSORTypes.MULTIPLE_POSSIBLE_GENES_ELEMENT] = (
         FUSORTypes.MULTIPLE_POSSIBLE_GENES_ELEMENT
-    ] = FUSORTypes.MULTIPLE_POSSIBLE_GENES_ELEMENT
+    )
 
     model_config = ConfigDict(
         json_schema_extra={"example": {"type": "MultiplePossibleGenesElement"}},

src/fusor/nomenclature.py

@@ -1,4 +1,5 @@
 """Provide helper methods for fusion nomenclature generation."""
+
 from biocommons.seqrepo.seqrepo import SeqRepo
 from ga4gh.vrsatile.pydantic.vrs_models import SequenceLocation
 

src/fusor/tools.py

@@ -1,4 +1,5 @@
 """Provide miscellaneous tools for fusion modeling."""
+
 import logging
 
 from biocommons.seqrepo.seqrepo import SeqRepo

src/fusor/version.py

@@ -1,2 +1,3 @@
 """Define library version."""
+
 __version__ = "0.1.0"

tests/conftest.py

@@ -1,4 +1,5 @@
 """Module containing methods and fixtures used throughout tests."""
+
 import logging
 
 import pytest

tests/test_fusor.py

@@ -1,4 +1,5 @@
 """Module for testing the FUSOR class."""
+
 import copy
 
 import pytest
@@ -817,9 +818,9 @@ def test_templated_sequence_element(
     assert tsg.model_dump() == templated_sequence_element.model_dump()
 
     expected = copy.deepcopy(templated_sequence_element.model_dump())
-    expected["region"]["location"][
-        "sequence_id"
-    ] = "ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"
+    expected["region"]["location"]["sequence_id"] = (
+        "ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"
+    )
     expected["region"]["location_id"] = "ga4gh:VSL.bL1N-PQfp4dGlEz6PEd34fGxdxo82Zkb"
     tsg = fusor_instance.templated_sequence_element(
         100,

tests/test_models.py

@@ -1,4 +1,5 @@
 """Module for testing the fusion model."""
+
 import copy
 
 import pytest

tests/test_nomenclature.py

@@ -1,4 +1,5 @@
 """Test nomenclature generation."""
+
 import pytest
 
 from fusor.models import AssayedFusion, CategoricalFusion, TranscriptSegmentElement

tests/test_tools.py

@@ -1,4 +1,5 @@
 """Test FUSOR tools."""
+
 import pytest
 
 from fusor.exceptions import IDTranslationException