build(lint): sort imports with Ruff's isort rules

mypy_stubs/biocommons/seqrepo/fastadir/fastadir.pyi

@@ -1,4 +1,5 @@
 from typing import Any, Iterator, Optional
+
 from biocommons.seqrepo.fastadir.bases import BaseReader, BaseWriter
 
 class FastaDir(BaseReader, BaseWriter):

mypy_stubs/biocommons/seqrepo/seqaliasdb/seqaliasdb.pyi

@@ -1,5 +1,5 @@
-from typing import Any, Iterator, Optional
 import sqlite3
+from typing import Any, Iterator, Optional
 
 class SeqAliasDB(object):
     _db_path: str

mypy_stubs/mavehgvs/variant.pyi

@@ -1,5 +1,5 @@
-from typing import Any, Callable, List, Mapping, Optional, Sequence, Tuple, Union
 from re import Match
+from typing import Any, Callable, List, Mapping, Optional, Sequence, Tuple, Union
 
 from .position import VariantPosition
 

pyproject.toml

@@ -145,4 +145,4 @@ line-length = 120
 
 # Ruff's default rule set changes between minor releases, so it is written out here; widen it in its own commit.
 [tool.ruff.lint]
-select = ["E4", "E7", "E9", "F"]
+select = ["E4", "E7", "E9", "F", "I"]

src/mavedb/lib/alleles.py

@@ -25,7 +25,6 @@
 from mavedb.models.score_set import ScoreSet
 from mavedb.models.variant import Variant
 
-
 # How many variants a whole-set builder loads per round of batched queries. Bounds both the size of each
 # query's IN list (a variant's record links can fan out to dozens of reverse-translation members) and the
 # number of ORM rows held at once.

src/mavedb/lib/annotation/study_result.py

@@ -12,8 +12,8 @@
 from mavedb.lib.annotation.method import (
     publication_identifiers_to_method,
 )
-from mavedb.lib.vrs import vrs_object_from_mapped_variant
 from mavedb.lib.variants import variant_score
+from mavedb.lib.vrs import vrs_object_from_mapped_variant
 
 
 def variant_impact_study_result(

src/mavedb/lib/annotation_status_manager.py

@@ -19,9 +19,9 @@
 from sqlalchemy.orm import Session
 from sqlalchemy.sql import desc
 
+from mavedb.models.annotation_event import ALLELE_SUBJECT_TYPES, VARIANT_SUBJECT_TYPES, AnnotationEvent
 from mavedb.models.enums.annotation_type import AnnotationType
 from mavedb.models.enums.disposition import Disposition
-from mavedb.models.annotation_event import ALLELE_SUBJECT_TYPES, VARIANT_SUBJECT_TYPES, AnnotationEvent
 
 logger = logging.getLogger(__name__)
 

src/mavedb/lib/clingen/content_constructors.py

@@ -1,11 +1,11 @@
 from datetime import datetime
-from uuid import uuid4
 from urllib.parse import quote_plus
+from uuid import uuid4
 
 from mavedb import __version__
 from mavedb.constants import MAVEDB_BASE_GIT, MAVEDB_FRONTEND_URL
-from mavedb.lib.types.clingen import LdhContentLinkedData, LdhContentSubject, LdhEvent, LdhSubmission
 from mavedb.lib.clingen.constants import LDH_ENTITY_NAME, LDH_SUBMISSION_TYPE
+from mavedb.lib.types.clingen import LdhContentLinkedData, LdhContentSubject, LdhEvent, LdhSubmission
 from mavedb.models.allele import Allele
 from mavedb.models.mapping_record import MappingRecord
 from mavedb.models.variant import Variant

src/mavedb/lib/csv/deprecated_params.py

@@ -16,7 +16,6 @@
 from mavedb.lib.csv.namespaces import CsvNamespace
 from mavedb.lib.deprecation import deprecation_headers, record_deprecated_usage
 
-
 DROP_NA_COLUMNS_DESCRIPTION = (
     "Deprecated: use `drop_unused_hgvs_columns`, which names what it actually does. This parameter only"
     " ever dropped the HGVS coordinate columns a score set does not use, never every NA column. It will"

src/mavedb/lib/csv/variant.py

@@ -26,11 +26,11 @@
     AvailableCsvNamespaceEntry,
     calibration_can_annotate,
     calibration_namespace_entries,
+    calibration_viewer,
     clinvar_namespace_entries,
     clinvar_release_namespaces,
     score_sets_have_current_mappings,
     static_namespace_entry,
-    calibration_viewer,
 )
 from mavedb.lib.csv.fetch import fetch_variant_csv_data
 from mavedb.lib.csv.namespaces import (
@@ -39,8 +39,8 @@
     clinvar_namespace_sort_key,
 )
 from mavedb.lib.mave.utils import NA_VALUE
-from mavedb.lib.urns import score_set_urn_sort_key, variant_urn_sort_key
 from mavedb.lib.permissions.score_calibration import ScoreCalibrationViewer
+from mavedb.lib.urns import score_set_urn_sort_key, variant_urn_sort_key
 from mavedb.models.allele import Allele
 from mavedb.models.mapping_record import MappingRecord
 from mavedb.models.mapping_record_allele import MappingRecordAllele

src/mavedb/lib/experiments.py

@@ -4,8 +4,8 @@
 from sqlalchemy import func, not_, or_
 from sqlalchemy.orm import Session
 
-from mavedb.lib.logging.context import logging_context, save_to_logging_context
 from mavedb.lib.collections import readable_official_collections
+from mavedb.lib.logging.context import logging_context, save_to_logging_context
 from mavedb.lib.permissions import Action
 from mavedb.lib.score_sets import find_superseded_score_set_tail
 from mavedb.lib.types.authentication import UserData

src/mavedb/lib/oddspaths.py

@@ -1,6 +1,6 @@
 from typing import Optional
 
-from mavedb.lib.acmg import StrengthOfEvidenceProvided, ACMGCriterion
+from mavedb.lib.acmg import ACMGCriterion, StrengthOfEvidenceProvided
 
 
 def oddspaths_evidence_strength_equivalent(

src/mavedb/lib/score_calibrations.py

@@ -29,8 +29,8 @@
 from mavedb.lib.validation.exceptions import ValidationError
 from mavedb.lib.validation.utilities import inf_or_float
 from mavedb.lib.variants import score_from_variant_data
-from mavedb.models.enums.functional_classification import FunctionalClassification
 from mavedb.models.calibration_control import CalibrationControl
+from mavedb.models.enums.functional_classification import FunctionalClassification
 from mavedb.models.enums.score_calibration_relation import ScoreCalibrationRelation
 from mavedb.models.score_calibration import ScoreCalibration
 from mavedb.models.score_calibration_functional_classification import ScoreCalibrationFunctionalClassification

src/mavedb/lib/seqrepo.py

@@ -6,17 +6,17 @@
 
 import os
 import re
-from base64 import urlsafe_b64encode, urlsafe_b64decode
-from binascii import unhexlify, hexlify
+from base64 import urlsafe_b64decode, urlsafe_b64encode
+from binascii import hexlify, unhexlify
 
 # TODO (https://github.com/VariantEffect/mavedb-api/issues/354). We need pydantic upgraded to use this package.
 # from ga4gh.core.identifiers import is_ga4gh_identifier, CURIE_NAMESPACE as ga4gh_namespace
 from typing import Generator, Optional
 
-from biocommons.seqrepo import SeqRepo, __version__ as seqrepo_dep_version
+from biocommons.seqrepo import SeqRepo
+from biocommons.seqrepo import __version__ as seqrepo_dep_version
 from bioutils.accessions import infer_namespaces
 
-
 DEFAULT_CHUNK_SIZE = 8192
 
 

src/mavedb/lib/uniprot/id_mapping.py

@@ -1,13 +1,13 @@
-import requests
-import time
 import logging
+import time
+from typing import Any, Dict, List, Optional
 
+import requests
 from requests.adapters import HTTPAdapter, Retry
-from typing import List, Optional, Dict, Any
 
 from mavedb.lib.logging.context import logging_context, save_to_logging_context
-from mavedb.lib.uniprot.constants import UNIPROT_ID_MAPPING_API_URL, SWISS_PROT_ENTRY_TYPE
 from mavedb.lib.types import uniprot
+from mavedb.lib.uniprot.constants import SWISS_PROT_ENTRY_TYPE, UNIPROT_ID_MAPPING_API_URL
 
 logger = logging.getLogger(__name__)
 

src/mavedb/lib/validation/dataframe/variant.py

@@ -1,23 +1,23 @@
 import logging
 import warnings
-from typing import Hashable, Optional, TYPE_CHECKING
+from typing import TYPE_CHECKING, Hashable, Optional
 
 import pandas as pd
 from fqfa.validator import dna_bases_validator
 from mavehgvs.exceptions import MaveHgvsParseError
 from mavehgvs.variant import Variant
 
-from mavedb.lib.validation.exceptions import ValidationError
+from mavedb.lib.validation.constants.target import strict_valid_sequence_types as valid_sequence_types
 from mavedb.lib.validation.dataframe.column import (
+    construct_target_sequence_mappings,
     generate_variant_prefixes,
+    validate_hgvs_column_properties,
     validate_variant_column,
     validate_variant_formatting,
-    validate_hgvs_column_properties,
-    construct_target_sequence_mappings,
 )
-from mavedb.lib.validation.constants.target import strict_valid_sequence_types as valid_sequence_types
-from mavedb.models.target_sequence import TargetSequence
+from mavedb.lib.validation.exceptions import ValidationError
 from mavedb.models.target_accession import TargetAccession
+from mavedb.models.target_sequence import TargetSequence
 
 if TYPE_CHECKING:
     from cdot.hgvs.dataproviders import RESTDataProvider

src/mavedb/lib/vrs_utils.py

@@ -14,6 +14,7 @@
 from itertools import cycle
 from typing import Any
 
+from biocommons.seqrepo import SeqRepo
 from ga4gh.core import ga4gh_identify
 from ga4gh.vrs.extras.translator import AlleleTranslator
 from ga4gh.vrs.models import (
@@ -28,8 +29,6 @@
 )
 from ga4gh.vrs.normalize import normalize
 
-from biocommons.seqrepo import SeqRepo
-
 from mavedb.lib.hgvs import extract_accession, split_cis_phased_hgvs
 from mavedb.lib.logging.context import logging_context
 from mavedb.lib.seqrepo import AmbiguousSequenceError, SequenceNotFoundError, resolve_refget

src/mavedb/models/clinical_control_mapped_variant.py

@@ -1,8 +1,7 @@
-from sqlalchemy import Column, Table, ForeignKey
+from sqlalchemy import Column, ForeignKey, Table
 
 from mavedb.db.base import Base
 
-
 mapped_variants_clinical_controls_association_table = Table(
     "mapped_variants_clinical_controls",
     Base.metadata,

src/mavedb/models/collection_user_association.py

@@ -1,15 +1,15 @@
 # Prevent circular imports
 from typing import TYPE_CHECKING
 
-from sqlalchemy import Enum, Column, ForeignKey, Integer
+from sqlalchemy import Column, Enum, ForeignKey, Integer
 from sqlalchemy.orm import Mapped, relationship
 
 from mavedb.db.base import Base
 from mavedb.models.enums.contribution_role import ContributionRole
 
 if TYPE_CHECKING:
-    from mavedb.models.user import User
     from mavedb.models.collection import Collection
+    from mavedb.models.user import User
 
 
 class CollectionUserAssociation(Base):

src/mavedb/models/gnomad_variant_mapped_variant.py

@@ -1,8 +1,7 @@
-from sqlalchemy import Column, Table, ForeignKey
+from sqlalchemy import Column, ForeignKey, Table
 
 from mavedb.db.base import Base
 
-
 gnomad_variants_mapped_variants_association_table = Table(
     "gnomad_variants_mapped_variants",
     Base.metadata,

src/mavedb/models/score_calibration_publication_identifier.py

@@ -1,7 +1,7 @@
 # Prevent circular imports
 from typing import TYPE_CHECKING
 
-from sqlalchemy import Column, ForeignKey, Integer, Enum
+from sqlalchemy import Column, Enum, ForeignKey, Integer
 from sqlalchemy.orm import Mapped, relationship
 
 from mavedb.db.base import Base

src/mavedb/routers/experiments.py

@@ -11,9 +11,9 @@
 from mavedb import deps
 from mavedb.lib.authentication import get_current_user
 from mavedb.lib.authorization import get_principal, require_current_user, require_current_user_with_email
+from mavedb.lib.collections import readable_official_collections
 from mavedb.lib.contributors import find_or_create_contributor
 from mavedb.lib.exceptions import NonexistentOrcidUserError
-from mavedb.lib.collections import readable_official_collections
 from mavedb.lib.experiments import enrich_experiment_with_num_score_sets
 from mavedb.lib.experiments import search_experiments as _search_experiments
 from mavedb.lib.identifiers import (

src/mavedb/routers/variants.py

@@ -3,8 +3,8 @@
 from typing import Annotated, Any, List, Optional
 
 from fastapi import APIRouter, Depends, Path, Query, Response
-from fastapi.exceptions import HTTPException
 from fastapi.encoders import jsonable_encoder
+from fastapi.exceptions import HTTPException
 from fastapi.responses import JSONResponse, StreamingResponse
 from ga4gh.core.identifiers import GA4GH_IR_REGEXP
 from ga4gh.va_spec.acmg_2015 import VariantPathogenicityStatement

src/mavedb/scripts/audit_allele_identifiers.py

@@ -45,11 +45,10 @@
 from datetime import datetime
 from typing import Any, Optional, Sequence
 
+import asyncclick as click
 from ga4gh.core import ga4gh_identify
 from ga4gh.vrs.models import Allele as VrsAllele
 from ga4gh.vrs.models import CisPhasedBlock, SequenceLocation
-
-import asyncclick as click
 from sqlalchemy import select
 from sqlalchemy.orm import Session
 

src/mavedb/scripts/export_public_data.py

@@ -29,11 +29,11 @@
 from sqlalchemy import select
 from sqlalchemy.orm import Session, joinedload, lazyload
 
+from mavedb.lib.allele_annotations import get_allele_cross_references
+from mavedb.lib.alleles import get_live_record_allele_links, with_chunk_inputs
 from mavedb.lib.annotation.annotate import variant_highest_level_annotation
 from mavedb.lib.annotation.conformance import serialize_annotation
 from mavedb.lib.annotation.context import load_annotation_context_inputs
-from mavedb.lib.allele_annotations import get_allele_cross_references
-from mavedb.lib.alleles import get_live_record_allele_links, with_chunk_inputs
 from mavedb.lib.cat_vrs import build_categorical_variant
 from mavedb.lib.csv.entries import score_sets_have_current_mappings
 from mavedb.lib.csv.namespaces import CsvNamespace

src/mavedb/scripts/export_sweep.py

@@ -37,13 +37,13 @@
 from sqlalchemy import func, select
 from sqlalchemy.orm import Session
 
+from mavedb.lib.alleles import with_chunk_inputs
 from mavedb.lib.annotation.annotate import (
     variant_functional_impact_statement,
     variant_pathogenicity_statement,
     variant_study_result,
 )
 from mavedb.lib.annotation.conformance import AnnotationRoundTripError, round_trip_annotation
-from mavedb.lib.alleles import with_chunk_inputs
 from mavedb.lib.annotation.context import VariantAnnotationContext, load_annotation_context_inputs
 from mavedb.lib.annotation.exceptions import EXPECTED_ABSENCE_EXCEPTIONS
 from mavedb.lib.csv.score_set import available_score_set_csv_namespaces, get_score_set_variants_as_csv

src/mavedb/scripts/mapped_gene_from_mapped_variant.py

@@ -1,17 +1,16 @@
 import json
 import logging
-import requests
-from typing import Sequence, Optional
+from typing import Optional, Sequence
 
 import click
+import requests
 from sqlalchemy import select
 from sqlalchemy.orm import Session
 
-from mavedb.models.score_set import ScoreSet
 from mavedb.models.mapped_variant import MappedVariant
+from mavedb.models.score_set import ScoreSet
 from mavedb.models.target_gene import TargetGene
 from mavedb.models.variant import Variant
-
 from mavedb.scripts.environment import script_environment, with_database_session
 
 logger = logging.getLogger(__name__)

src/mavedb/scripts/migrate_mapped_variants_to_allele_substrate.py

@@ -127,19 +127,18 @@
 
 import sqlalchemy as sa
 from biocommons.seqrepo import SeqRepo
+from pydantic import ValidationError
 from sqlalchemy.exc import IntegrityError
 from sqlalchemy.orm import Session, configure_mappers
 
-from mavedb.models import *  # noqa: F401,F403  pylint: disable=wildcard-import  — register all mappers for configure_mappers()
+from mavedb.data_providers.services import seqrepo
 from mavedb.db.session import SessionLocal
 from mavedb.lib.annotation_status_manager import AnnotationStatusManager
-from pydantic import ValidationError
-
-from mavedb.data_providers.services import seqrepo
 from mavedb.lib.hgvs import extract_accession
 from mavedb.lib.seqrepo import AmbiguousSequenceError, SequenceNotFoundError, resolve_refget
 from mavedb.lib.variants import get_hgvs_from_post_mapped
 from mavedb.lib.vrs_utils import CANONICAL_ACCESSION_PREFIXES, canonical_variation_document, location_refgets
+from mavedb.models import *  # noqa: F401,F403  pylint: disable=wildcard-import  — register all mappers for configure_mappers()
 from mavedb.models.allele import Allele
 from mavedb.models.annotation_event import AnnotationEvent
 from mavedb.models.clinvar_allele_link import ClinvarAlleleLink

src/mavedb/view_models/base/base.py

@@ -1,5 +1,4 @@
 from humps import camelize
-
 from pydantic import BaseModel as PydanticBaseModel
 from pydantic import field_validator
 

src/mavedb/view_models/doi_identifier.py

@@ -1,5 +1,4 @@
 import idutils
-
 from pydantic import field_validator
 
 from mavedb.lib.validation.exceptions import ValidationError

src/mavedb/view_models/experiment_controlled_keyword.py

@@ -1,7 +1,7 @@
 from typing import Optional
-from typing_extensions import Self
 
 from pydantic import model_validator
+from typing_extensions import Self
 
 from mavedb.lib.validation import keywords
 from mavedb.view_models import keyword, record_type_validator, set_record_type

src/mavedb/view_models/external_gene_identifier.py

@@ -1,7 +1,7 @@
 from typing import Optional
-from typing_extensions import Self
 
 from pydantic import field_validator, model_validator
+from typing_extensions import Self
 
 from mavedb.lib.validation import identifier as identifier_validator
 from mavedb.view_models import record_type_validator, set_record_type