Merge branch 'main' into setuptools-scm

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.0
+    rev: v0.5.0
     hooks:
       - id: ruff-format
       - id: ruff

pyproject.toml

@@ -36,7 +36,7 @@ dynamic=["version"]
 
 [project.optional-dependencies]
 tests = ["pytest", "pytest-cov", "pytest-asyncio"]
-dev = ["pre-commit", "pytest", "pytest-cov", "pytest-asyncio", "ruff==0.2.0"]
+dev = ["pre-commit", "pytest", "pytest-cov", "pytest-asyncio", "ruff==0.5.0"]
 
 [project.urls]
 Homepage = "https://github.com/cancervariants/fusor"
@@ -84,16 +84,22 @@ select = [
     "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
     "T10",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
     "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+    "LOG",  # https://docs.astral.sh/ruff/rules/#flake8-logging-log
     "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+    "INP",  # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
     "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
     "T20",  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
     "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
     "Q",  # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
     "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
     "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+    "SLF",  # https://docs.astral.sh/ruff/rules/#flake8-self-slf
     "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+    "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
     "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
     "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+    "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
+    "FURB",  # https://docs.astral.sh/ruff/rules/#refurb-furb
     "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
 ]
 fixable = [
@@ -104,15 +110,19 @@ fixable = [
     "ANN",
     "B",
     "C4",
+    "LOG",
     "G",
     "PIE",
     "PT",
     "RSE",
     "SIM",
-    "RUF"
+    "PERF",
+    "FURB",
+    "RUF",
 ]
-# ANN101 - missing-type-self
 # ANN003 - missing-type-kwargs
+# ANN101 - missing-type-self
+# ANN102 - missing-type-cls
 # D203 - one-blank-line-before-class
 # D205 - blank-line-after-summary
 # D206 - indent-with-spaces*
@@ -128,7 +138,7 @@ fixable = [
 # S321 - suspicious-ftp-lib-usage
 # *ignored for compatibility with formatter
 ignore = [
-    "ANN101", "ANN003",
+    "ANN003", "ANN101", "ANN102",
     "D203", "D205", "D206", "D213", "D300", "D400", "D415",
     "E111", "E114", "E117", "E501",
     "W191",
@@ -144,5 +154,10 @@ ignore = [
 # S101 - assert
 # B011 - assert-false
 # N805 - invalid-first-argument-name-for-method
-"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011"]
+# INP001 - implicit-namespace-package
+# SLF001 - private-member-access
+"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011", "INP001", "SLF001"]
 "src/fusor/models.py" = ["ANN201", "N805", "ANN001", "ANN2", "ANN102"]
+
+[tool.ruff.format]
+docstring-code-format = true

src/fusor/__init__.py

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

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

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