Isort all .py files

CHANGELOG.md

@@ -6,6 +6,7 @@
 - Modified code to support upgraded libraries
 - Rename a test file from `test_d4.py` to `test_handle_d4.py` and add 2 new tests to it
 - Fix return type of `get_intervals_completeness` function
+- Isort imports of the entire repo
 
 ## [1.2]
 ### Added

src/chanjo2/constants.py

@@ -1,9 +1,9 @@
 from typing import Callable, Dict, List
 
 from schug.load.ensembl import (
+    fetch_ensembl_exons,
     fetch_ensembl_genes,
     fetch_ensembl_transcripts,
-    fetch_ensembl_exons,
 )
 
 SAMPLE_NOT_FOUND: str = "One of more requested samples were not present in the database"

src/chanjo2/crud/cases.py

@@ -4,7 +4,7 @@
 from sqlalchemy.engine.cursor import CursorResult
 from sqlalchemy.orm import Session, query
 
-from chanjo2.models import SQLCase, SQLSample, CaseSample
+from chanjo2.models import CaseSample, SQLCase, SQLSample
 from chanjo2.models.pydantic_models import Case, CaseCreate
 
 

src/chanjo2/crud/intervals.py

@@ -5,14 +5,14 @@
 from sqlalchemy.orm import Session, query
 from sqlalchemy.sql.expression import Delete
 
+from chanjo2.models import SQLExon, SQLGene, SQLTranscript
 from chanjo2.models.pydantic_models import (
     Builds,
     ExonBase,
     GeneBase,
     TranscriptBase,
     TranscriptTag,
 )
-from chanjo2.models import SQLGene, SQLExon, SQLTranscript
 
 LOG = logging.getLogger("uvicorn.access")
 

src/chanjo2/crud/samples.py

@@ -1,4 +1,4 @@
-from typing import List, Optional, Union, Tuple
+from typing import List, Optional, Tuple, Union
 
 from fastapi import HTTPException, status
 from pyd4 import D4File
@@ -10,7 +10,7 @@
 from chanjo2.constants import SAMPLE_NOT_FOUND, WRONG_COVERAGE_FILE_MSG
 from chanjo2.crud.cases import filter_cases_by_name
 from chanjo2.meta.handle_d4 import get_d4_file
-from chanjo2.models import SQLCase, SQLSample, CaseSample
+from chanjo2.models import CaseSample, SQLCase, SQLSample
 from chanjo2.models.pydantic_models import SampleCreate
 
 

src/chanjo2/endpoints/cases.py

@@ -3,7 +3,7 @@
 from fastapi import APIRouter, Depends, HTTPException, status
 from sqlalchemy.orm import Session
 
-from chanjo2.crud.cases import create_db_case, get_case, get_cases, delete_case
+from chanjo2.crud.cases import create_db_case, delete_case, get_case, get_cases
 from chanjo2.dbutil import get_session
 from chanjo2.models.pydantic_models import Case, CaseCreate
 

src/chanjo2/endpoints/coverage.py

@@ -1,33 +1,30 @@
-from typing import List, Optional, Tuple, Dict
+from typing import Dict, List, Optional, Tuple
 
-from fastapi import APIRouter, HTTPException, status, Depends
+from fastapi import APIRouter, Depends, HTTPException, status
 from pyd4 import D4File
 from sqlalchemy.orm import Session
 
-from chanjo2.constants import (
-    WRONG_BED_FILE_MSG,
-    WRONG_COVERAGE_FILE_MSG,
-)
+from chanjo2.constants import WRONG_BED_FILE_MSG, WRONG_COVERAGE_FILE_MSG
 from chanjo2.crud.intervals import get_genes
 from chanjo2.crud.samples import get_samples_coverage_file
 from chanjo2.dbutil import get_session
 from chanjo2.meta.handle_bed import parse_bed
 from chanjo2.meta.handle_d4 import (
-    intervals_coverage,
-    get_intervals_mean_coverage,
     get_d4_file,
-    set_interval,
-    get_samples_sex_metrics,
     get_intervals_completeness,
+    get_intervals_mean_coverage,
     get_sample_interval_coverage,
+    get_samples_sex_metrics,
+    intervals_coverage,
+    set_interval,
 )
 from chanjo2.models import SQLExon, SQLGene, SQLTranscript
 from chanjo2.models.pydantic_models import (
-    SampleGeneIntervalQuery,
-    FileCoverageQuery,
     FileCoverageIntervalsFileQuery,
-    IntervalCoverage,
+    FileCoverageQuery,
     GeneCoverage,
+    IntervalCoverage,
+    SampleGeneIntervalQuery,
 )
 
 router = APIRouter()

src/chanjo2/endpoints/intervals.py

@@ -1,13 +1,11 @@
-from typing import List, Optional, Iterator
+from typing import Iterator, List, Optional
 
 from fastapi import APIRouter, Depends, HTTPException, Response, status
 from fastapi.responses import JSONResponse
 from sqlalchemy.orm import Session
 
-from chanjo2.constants import (
-    MULTIPLE_PARAMS_NOT_SUPPORTED_MSG,
-)
-from chanjo2.crud.intervals import get_genes, get_gene_intervals
+from chanjo2.constants import MULTIPLE_PARAMS_NOT_SUPPORTED_MSG
+from chanjo2.crud.intervals import get_gene_intervals, get_genes
 from chanjo2.dbutil import get_session
 from chanjo2.meta.handle_bed import resource_lines
 from chanjo2.meta.handle_load_intervals import (
@@ -20,9 +18,9 @@
     Builds,
     Exon,
     Gene,
-    Transcript,
-    GeneQuery,
     GeneIntervalQuery,
+    GeneQuery,
+    Transcript,
 )
 
 router = APIRouter()

src/chanjo2/endpoints/overview.py

@@ -1,7 +1,7 @@
 import logging
 from os import path
 
-from fastapi import APIRouter, Request, Depends
+from fastapi import APIRouter, Depends, Request
 from fastapi.encoders import jsonable_encoder
 from fastapi.responses import HTMLResponse
 from fastapi.templating import Jinja2Templates
@@ -11,10 +11,10 @@
 from chanjo2.dbutil import get_session
 from chanjo2.demo import DEMO_COVERAGE_QUERY_DATA
 from chanjo2.meta.handle_report_contents import (
-    get_report_data,
     get_gene_overview_coverage_stats,
+    get_report_data,
 )
-from chanjo2.models.pydantic_models import ReportQuery, GeneReportForm, GeneCoverage
+from chanjo2.models.pydantic_models import GeneCoverage, GeneReportForm, ReportQuery
 
 LOG = logging.getLogger("uvicorn.access")
 

src/chanjo2/endpoints/report.py

@@ -2,7 +2,7 @@
 from os import path
 from typing import Dict
 
-from fastapi import APIRouter, Request, Depends
+from fastapi import APIRouter, Depends, Request
 from fastapi.responses import HTMLResponse
 from fastapi.templating import Jinja2Templates
 from sqlalchemy.orm import Session

src/chanjo2/endpoints/samples.py

@@ -5,10 +5,10 @@
 
 from chanjo2.crud.samples import (
     create_sample_in_case,
+    delete_sample,
     get_case_samples,
     get_sample,
     get_samples,
-    delete_sample,
 )
 from chanjo2.dbutil import get_session
 from chanjo2.models.pydantic_models import Sample, SampleCreate

src/chanjo2/main.py

@@ -9,7 +9,7 @@
 
 from chanjo2 import __version__
 from chanjo2.dbutil import engine
-from chanjo2.endpoints import cases, intervals, samples, coverage, report, overview
+from chanjo2.endpoints import cases, coverage, intervals, overview, report, samples
 from chanjo2.models.sql_models import Base
 from chanjo2.populate_demo import load_demo_data
 

src/chanjo2/meta/handle_bed.py

@@ -1,4 +1,4 @@
-from typing import List, Tuple, Iterator
+from typing import Iterator, List, Tuple
 
 
 def resource_lines(file_path: str) -> Iterator[str]:

src/chanjo2/meta/handle_d4.py

@@ -1,17 +1,17 @@
 import logging
 from statistics import mean
-from typing import List, Optional, Tuple, Union, Dict
+from typing import Dict, List, Optional, Tuple, Union
 
 from pyd4 import D4File
 from sqlalchemy.orm import Session
 
 from chanjo2.crud.intervals import get_gene_intervals
 from chanjo2.models import SQLExon, SQLGene, SQLTranscript
 from chanjo2.models.pydantic_models import (
-    IntervalCoverage,
-    Sex,
     GeneCoverage,
+    IntervalCoverage,
     IntervalType,
+    Sex,
     TranscriptTag,
 )
 

src/chanjo2/meta/handle_load_intervals.py

@@ -1,5 +1,5 @@
 import logging
-from typing import Iterator, List, Union, Optional
+from typing import Iterator, List, Optional, Union
 
 import requests
 from schug.load.biomart import EnsemblBiomartClient

src/chanjo2/meta/handle_report_contents.py

@@ -1,22 +1,22 @@
 import logging
 from collections import OrderedDict
 from statistics import mean
-from typing import List, Dict, Tuple, Union, Set, Optional
+from typing import Dict, List, Optional, Set, Tuple, Union
 
 from pyd4 import D4File
 from sqlalchemy.orm import Session
 
 from chanjo2.crud.intervals import get_genes, get_hgnc_gene
 from chanjo2.crud.samples import get_sample
-from chanjo2.meta.handle_d4 import get_samples_sex_metrics, get_sample_interval_coverage
+from chanjo2.meta.handle_d4 import get_sample_interval_coverage, get_samples_sex_metrics
 from chanjo2.models import SQLExon, SQLGene, SQLSample, SQLTranscript
 from chanjo2.models.pydantic_models import (
+    GeneCoverage,
+    GeneReportForm,
+    IntervalType,
     ReportQuery,
     ReportQuerySample,
     SampleSexRow,
-    GeneCoverage,
-    IntervalType,
-    GeneReportForm,
 )
 
 LOG = logging.getLogger("uvicorn.access")

src/chanjo2/models/pydantic_models.py

@@ -3,17 +3,17 @@
 from datetime import datetime
 from enum import Enum
 from pathlib import Path
-from typing import Any, List, Optional, Dict
+from typing import Any, Dict, List, Optional
 
 import validators
-from pydantic import BaseModel, field_validator, model_validator, Field
+from pydantic import BaseModel, Field, field_validator, model_validator
 from pydantic_settings import SettingsConfigDict
 
 from chanjo2.constants import (
-    WRONG_COVERAGE_FILE_MSG,
-    MULTIPLE_GENE_LISTS_NOT_SUPPORTED_MSG,
     AMBIGUOUS_SAMPLES_INPUT,
     DEFAULT_COMPLETENESS_LEVELS,
+    MULTIPLE_GENE_LISTS_NOT_SUPPORTED_MSG,
+    WRONG_COVERAGE_FILE_MSG,
 )
 
 LOG = logging.getLogger("uvicorn.access")

src/chanjo2/models/sql_models.py

@@ -1,6 +1,6 @@
 from dataclasses import dataclass
 
-from sqlalchemy import Column, DateTime, Enum, ForeignKey, Integer, String, Index, Table
+from sqlalchemy import Column, DateTime, Enum, ForeignKey, Index, Integer, String, Table
 from sqlalchemy.orm import relationship
 from sqlalchemy.sql import func
 

src/chanjo2/populate_demo.py

@@ -1,4 +1,4 @@
-from typing import List, Tuple, Iterator
+from typing import Iterator, List, Tuple
 
 from schug.demo import (
     EXONS_37_FILE_PATH,
@@ -14,14 +14,14 @@
 from chanjo2.crud.cases import create_db_case
 from chanjo2.crud.samples import create_sample_in_case
 from chanjo2.dbutil import get_session
-from chanjo2.demo import DEMO_SAMPLE, DEMO_CASE
+from chanjo2.demo import DEMO_CASE, DEMO_SAMPLE
 from chanjo2.meta.handle_bed import resource_lines
 from chanjo2.meta.handle_load_intervals import (
+    update_exons,
     update_genes,
     update_transcripts,
-    update_exons,
 )
-from chanjo2.models.pydantic_models import CaseCreate, SampleCreate, Builds
+from chanjo2.models.pydantic_models import Builds, CaseCreate, SampleCreate
 
 db: sessionmaker = next(get_session())
 

tests/conftest.py

@@ -7,11 +7,10 @@
 from sqlalchemy import create_engine
 from sqlalchemy.orm import sessionmaker
 
-from chanjo2.constants import BUILD_38, BUILD_37
+from chanjo2.constants import BUILD_37, BUILD_38
 from chanjo2.crud.intervals import get_genes
 from chanjo2.dbutil import DEMO_CONNECT_ARGS, get_session
-from chanjo2.demo import DEMO_SAMPLE
-from chanjo2.demo import d4_demo_path, gene_panel_path
+from chanjo2.demo import DEMO_SAMPLE, d4_demo_path, gene_panel_path
 from chanjo2.main import Base, app, engine
 from chanjo2.meta.handle_bed import parse_bed
 from chanjo2.meta.handle_d4 import get_d4_file

tests/src/chanjo2/crud/test_crud_intervals.py

@@ -1,4 +1,4 @@
-from typing import List, Dict
+from typing import Dict, List
 
 from sqlalchemy.orm import sessionmaker
 

tests/src/chanjo2/endpoints/test_coverage.py

@@ -1,19 +1,19 @@
 import copy
-from typing import Type, Dict, List
+from typing import Dict, List, Type
 
 import pytest
 from fastapi import status
 from fastapi.testclient import TestClient
 
 from chanjo2.constants import (
-    WRONG_COVERAGE_FILE_MSG,
-    WRONG_BED_FILE_MSG,
-    MULTIPLE_GENE_LISTS_NOT_SUPPORTED_MSG,
     AMBIGUOUS_SAMPLES_INPUT,
+    MULTIPLE_GENE_LISTS_NOT_SUPPORTED_MSG,
+    WRONG_BED_FILE_MSG,
+    WRONG_COVERAGE_FILE_MSG,
 )
 from chanjo2.demo import gene_panel_path
-from chanjo2.models.pydantic_models import Builds, Sex, GeneCoverage, IntervalCoverage
-from chanjo2.populate_demo import DEMO_SAMPLE, DEMO_CASE
+from chanjo2.models.pydantic_models import Builds, GeneCoverage, IntervalCoverage, Sex
+from chanjo2.populate_demo import DEMO_CASE, DEMO_SAMPLE
 
 COVERAGE_COMPLETENESS_THRESHOLDS: List[int] = [10, 20, 30]
 

tests/src/chanjo2/endpoints/test_intervals.py

@@ -7,16 +7,11 @@
 
 from chanjo2.constants import MULTIPLE_PARAMS_NOT_SUPPORTED_MSG
 from chanjo2.meta.handle_bed import resource_lines
-from chanjo2.models.pydantic_models import (
-    Builds,
-    Exon,
-    Gene,
-    Transcript,
-)
+from chanjo2.models.pydantic_models import Builds, Exon, Gene, Transcript
 from chanjo2.populate_demo import (
+    BUILD_EXONS_RESOURCE,
     BUILD_GENES_RESOURCE,
     BUILD_TRANSCRIPTS_RESOURCE,
-    BUILD_EXONS_RESOURCE,
 )
 
 MOCKED_FILE_PARSER = "chanjo2.meta.handle_load_intervals.read_resource_lines"

tests/src/chanjo2/endpoints/test_overview.py

@@ -1,4 +1,4 @@
-from typing import Type, Dict, List
+from typing import Dict, List, Type
 
 from fastapi import status
 from fastapi.testclient import TestClient

tests/src/chanjo2/endpoints/test_samples.py

@@ -5,8 +5,7 @@
 from fastapi.testclient import TestClient
 from pytest_mock.plugin import MockerFixture
 
-from chanjo2.models.pydantic_models import Case
-from chanjo2.models.pydantic_models import WRONG_COVERAGE_FILE_MSG, Sample
+from chanjo2.models.pydantic_models import WRONG_COVERAGE_FILE_MSG, Case, Sample
 from chanjo2.populate_demo import DEMO_CASE, DEMO_SAMPLE