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src/gwas/tests/compression/test_arr.py

@@ -3,6 +3,7 @@
 
 import numpy as np
 import pandas as pd
+
 from gwas.compression.arr.base import FileArray, compression_methods
 from gwas.compression.arr.text import header_prefix
 from gwas.compression.pipe import CompressedTextReader

src/gwas/tests/compression/test_pipe.py

@@ -4,6 +4,7 @@
 
 import numpy as np
 import pytest
+
 from gwas.compression.pipe import (
     CompressedBytesReader,
     CompressedBytesWriter,

src/gwas/tests/conftest.py

@@ -5,14 +5,15 @@
 from typing import Literal, Mapping
 
 import pytest
+from psutil import virtual_memory
+from pytest import FixtureRequest
+
 from gwas.compression.convert import to_bgzip
 from gwas.log import add_handler, setup_logging_queue, teardown_logging
 from gwas.mem.wkspace import SharedWorkspace
 from gwas.tri.calc import calc_tri
 from gwas.utils import apply_num_threads, chromosome_to_int, chromosomes_set
 from gwas.vcf.base import VCFFile, calc_vcf, load_vcf
-from psutil import virtual_memory
-from pytest import FixtureRequest
 
 base_path: Path = Path(os.environ["DATA_PATH"])
 dataset: str = "opensnp"

src/gwas/tests/score/conftest.py

@@ -9,6 +9,8 @@
 
 import numpy as np
 import pytest
+from numpy import typing as npt
+
 from gwas.eig.base import Eigendecomposition
 from gwas.eig.calc import calc_eigendecompositions
 from gwas.mem.arr import SharedArray
@@ -30,7 +32,6 @@
     chromosomes_set,
 )
 from gwas.vcf.base import VCFFile
-from numpy import typing as npt
 
 from ..conftest import DirectoryFactory
 from .rmw_debug import rmw_debug

src/gwas/tests/score/rmw_debug.py

@@ -6,11 +6,12 @@
 
 import numpy as np
 import pytest
+from more_itertools import peekable
+from numpy import typing as npt
+
 from gwas.log import logger
 from gwas.raremetalworker.score import RaremetalworkerScoreCommand
 from gwas.utils import unwrap_which
-from more_itertools import peekable
-from numpy import typing as npt
 
 field_mapping: dict[str, str] = {
     "X:": "x",

src/gwas/tests/score/simulation.py

@@ -1,6 +1,7 @@
 from pathlib import Path
 
 import pytest
+
 from gwas.testing.convert import (
     convert_vcf_to_pfiles,
     get_pfile_variant_ids,

src/gwas/tests/score/test_cli.py

@@ -6,6 +6,8 @@
 
 import numpy as np
 import pandas as pd
+from pytest import FixtureRequest
+
 from gwas.compression.pipe import cache_suffix
 from gwas.eig.base import Eigendecomposition
 from gwas.mem.wkspace import SharedWorkspace
@@ -15,7 +17,6 @@
 from gwas.score.command import GwasCommand
 from gwas.score.job import SummaryCollection
 from gwas.vcf.base import VCFFile
-from pytest import FixtureRequest
 
 from ..conftest import chromosomes
 from ..utils import assert_both_close, check_bias

src/gwas/tests/score/test_ml.py

@@ -4,6 +4,8 @@
 
 import numpy as np
 import pytest
+from jax import numpy as jnp
+
 from gwas.log import logger
 from gwas.null_model.fastlmm import FaSTLMM
 from gwas.null_model.ml import MaximumLikelihood
@@ -13,7 +15,6 @@
     ProfileMaximumLikelihood,
 )
 from gwas.null_model.reml import RestrictedMaximumLikelihood
-from jax import numpy as jnp
 
 from ..utils import assert_both_close, check_bias, check_types
 from .rmw_debug import RmwDebug

src/gwas/tests/score/test_pheno.py

@@ -4,11 +4,12 @@
 
 import numpy as np
 import pandas as pd
-from gwas.mem.wkspace import SharedWorkspace
-from gwas.pheno import VariableCollection
 from numpy.testing import assert_array_equal
 from pytest import FixtureRequest
 
+from gwas.mem.wkspace import SharedWorkspace
+from gwas.pheno import VariableCollection
+
 from .simulation import missing_value_rate
 
 sample_count = 100

src/gwas/tests/score/test_rmw.py

@@ -3,6 +3,7 @@
 from time import time
 
 import numpy as np
+
 from gwas.compression.arr.base import (
     FileArray,
     TextCompressionMethod,

src/gwas/tests/score/test_score.py

@@ -7,6 +7,9 @@
 import pytest
 import scipy
 import seaborn as sns
+from matplotlib import pyplot as plt
+from numpy import typing as npt
+
 from gwas.eig.base import Eigendecomposition
 from gwas.eig.collection import EigendecompositionCollection
 from gwas.log import logger
@@ -17,8 +20,6 @@
 from gwas.score.calc import calc_u_stat, calc_v_stat
 from gwas.utils import make_sample_boolean_vectors
 from gwas.vcf.base import VCFFile
-from matplotlib import pyplot as plt
-from numpy import typing as npt
 
 from ..utils import check_bias
 from .conftest import RmwScore

src/gwas/tests/score/test_worker.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 import pytest
+
 from gwas.eig.base import Eigendecomposition
 from gwas.eig.collection import EigendecompositionCollection
 from gwas.mem.arr import SharedArray

src/gwas/tests/test_arr.py

@@ -2,6 +2,7 @@
 from pathlib import Path
 
 import numpy as np
+
 from gwas.mem.arr import SharedArray
 from gwas.mem.wkspace import SharedWorkspace
 

src/gwas/tests/test_eig.py

@@ -10,6 +10,7 @@
 import numpy as np
 import pytest
 import scipy
+
 from gwas.defaults import (
     default_kinship_minor_allele_frequency_cutoff,
     default_kinship_r_squared_cutoff,

src/gwas/tests/test_matrix_functions.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 import numpy as np
 import pytest
+
 from gwas._matrix_functions import dgesvdq, dimatcopy, set_tril, set_triu
 
 

src/gwas/tests/test_tri.py

@@ -5,11 +5,12 @@
 
 import numpy as np
 import pytest
+from numpy import typing as npt
+
 from gwas.mem.wkspace import SharedWorkspace
 from gwas.tri.base import Triangular, is_lower_triangular
 from gwas.tri.tsqr import scale
 from gwas.vcf.base import VCFFile
-from numpy import typing as npt
 
 sample_size_label = "large"
 chromosome = 22

src/gwas/tests/test_utils.py

@@ -1,14 +1,15 @@
 import logging
 from pathlib import Path
 
+from pytest import FixtureRequest, LogCaptureFixture
+
 from gwas.log import (
     logger,
     multiprocessing_context,
     setup_logging,
     teardown_logging,
 )
 from gwas.utils import Process
-from pytest import FixtureRequest, LogCaptureFixture
 
 
 class LogProcess(Process):

src/gwas/tests/test_var.py

@@ -5,14 +5,15 @@
 import numpy as np
 import pytest
 import scipy
+from jax import numpy as jnp
+
 from gwas.log import logger
 from gwas.null_model.ml import MaximumLikelihood
 from gwas.null_model.pml import (
     OptimizeInput,
     ProfileMaximumLikelihood,
 )
 from gwas.null_model.reml import RestrictedMaximumLikelihood
-from jax import numpy as jnp
 
 
 @pytest.mark.parametrize(

src/gwas/tests/test_vcf.py

@@ -6,14 +6,15 @@
 import numpy as np
 import pandas as pd
 import pytest
+from numpy import typing as npt
+from pytest_benchmark.fixture import BenchmarkFixture
+from tqdm.auto import tqdm
+
 from gwas.compression.pipe import CompressedTextReader
 from gwas.testing.convert import convert_vcf_to_bgen
 from gwas.tools import plink2
 from gwas.vcf.base import Engine, VCFFile
 from gwas.vcf.variant import Variant
-from numpy import typing as npt
-from pytest_benchmark.fixture import BenchmarkFixture
-from tqdm.auto import tqdm
 
 sample_size_label = "small"
 chromosome: int = 22

src/gwas/tests/test_wkspace.py

@@ -1,9 +1,10 @@
 # -*- coding: utf-8 -*-
 import numpy as np
 import pytest
+from numpy import typing as npt
+
 from gwas.mem.arr import SharedArray
 from gwas.mem.wkspace import SharedWorkspace
-from numpy import typing as npt
 
 
 def test_sw_merge() -> None:

src/gwas/tests/utils.py

@@ -2,11 +2,12 @@
 
 
 import numpy as np
-from gwas.log import logger
 from jaxtyping import jaxtyped
 from numpy import typing as npt
 from typeguard import typechecked as typechecker
 
+from gwas.log import logger
+
 check_types = jaxtyped(typechecker=typechecker)