Merge branch 'main' of github.com:HippocampusGirl/RAMP

Author: HippocampusGirl

.pre-commit-config.yaml

@@ -20,7 +20,7 @@ repos:
         exclude_types:
           - diff
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.6
+    rev: v0.6.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

src/gwas/tests/compression/test_arr.py

@@ -4,6 +4,8 @@
 import numpy as np
 import pandas as pd
 import pytest
+from upath import UPath
+
 from gwas.compression.arr.base import (
     Blosc2CompressionMethod,
     FileArray,
@@ -14,7 +16,6 @@
 from gwas.compression.arr.text import header_prefix
 from gwas.compression.pipe import CompressedTextReader
 from gwas.utils import cpu_count
-from upath import UPath
 
 try:
     import blosc2 as blosc2

src/gwas/tests/compression/test_pipe.py

@@ -2,14 +2,15 @@
 
 import numpy as np
 import pytest
+from upath import UPath
+
 from gwas.compression.pipe import (
     CompressedBytesReader,
     CompressedBytesWriter,
     CompressedTextReader,
     CompressedTextWriter,
 )
 from gwas.utils import cpu_count
-from upath import UPath
 
 
 @pytest.mark.parametrize("compression", ["zst", "xz", "gz", "bz2", "lz4"])

src/gwas/tests/conftest.py

@@ -4,6 +4,12 @@
 import numpy as np
 import pandas as pd
 import pytest
+from numpy import typing as npt
+from psutil import virtual_memory
+from pytest import FixtureRequest
+from tqdm.auto import tqdm
+from upath import UPath
+
 from gwas.compression.convert import to_bgzip
 from gwas.compression.pipe import CompressedTextReader
 from gwas.log import add_handler, setup_logging_queue, teardown_logging
@@ -12,11 +18,6 @@
 from gwas.utils import apply_num_threads, chromosome_to_int, chromosomes_set, cpu_count
 from gwas.vcf.base import VCFFile, calc_vcf, load_vcf
 from gwas.vcf.variant import Variant
-from numpy import typing as npt
-from psutil import virtual_memory
-from pytest import FixtureRequest
-from tqdm.auto import tqdm
-from upath import UPath
 
 base_path: UPath = UPath(os.environ["DATA_PATH"])
 dataset: str = "opensnp"

src/gwas/tests/score/conftest.py

@@ -6,6 +6,9 @@
 
 import numpy as np
 import pytest
+from numpy import typing as npt
+from upath import UPath
+
 from gwas.eig.base import Eigendecomposition
 from gwas.eig.calc import calc_eigendecompositions
 from gwas.mem.arr import SharedArray
@@ -29,8 +32,6 @@
     get_global_lock,
 )
 from gwas.vcf.base import VCFFile
-from numpy import typing as npt
-from upath import UPath
 
 from ..conftest import DirectoryFactory
 from .rmw_debug import rmw_debug

src/gwas/tests/score/simulation.py

@@ -1,4 +1,6 @@
 import pytest
+from upath import UPath
+
 from gwas.testing.convert import (
     convert_vcf_to_pfiles,
     get_pfile_variant_ids,
@@ -7,7 +9,6 @@
 from gwas.testing.simulate import SimulationResult, simulate
 from gwas.utils import cpu_count
 from gwas.vcf.base import VCFFile
-from upath import UPath
 
 from ..conftest import DirectoryFactory
 

src/gwas/tests/score/test_cli.py

@@ -3,6 +3,9 @@
 
 import numpy as np
 import pandas as pd
+from pytest import FixtureRequest
+from upath import UPath
+
 from gwas.compression.cache import cache_suffix
 from gwas.eig.base import Eigendecomposition
 from gwas.mem.wkspace import SharedWorkspace
@@ -12,8 +15,6 @@
 from gwas.score.command import GwasCommand
 from gwas.score.job import SummaryCollection
 from gwas.vcf.base import VCFFile
-from pytest import FixtureRequest
-from upath import UPath
 
 from ..conftest import chromosomes
 from ..utils import assert_both_close, check_bias

src/gwas/tests/score/test_ml.py

@@ -2,6 +2,8 @@
 
 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
@@ -11,7 +13,6 @@
     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

@@ -1,11 +1,12 @@
 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 upath import UPath
 
+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

@@ -2,13 +2,14 @@
 
 import numpy as np
 import pytest
+from upath import UPath
+
 from gwas.compression.arr.base import (
     FileArray,
     compression_methods,
 )
 from gwas.log import logger
 from gwas.utils import cpu_count
-from upath import UPath
 
 from .conftest import RmwScore
 

src/gwas/tests/score/test_score.py

@@ -4,6 +4,10 @@
 import pytest
 import scipy
 import seaborn as sns
+from matplotlib import pyplot as plt
+from numpy import typing as npt
+from upath import UPath
+
 from gwas.eig.base import Eigendecomposition
 from gwas.eig.collection import EigendecompositionCollection
 from gwas.log import logger
@@ -14,9 +18,6 @@
 from gwas.score.calc import calc_u_stat, calc_v_stat
 from gwas.utils import get_global_lock, make_sample_boolean_vectors
 from gwas.vcf.base import VCFFile
-from matplotlib import pyplot as plt
-from numpy import typing as npt
-from upath import UPath
 
 from ..utils import check_bias
 from .conftest import RmwScore

src/gwas/tests/score/test_worker.py

@@ -1,4 +1,5 @@
 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

@@ -1,7 +1,8 @@
 import numpy as np
+from upath import UPath
+
 from gwas.mem.arr import SharedArray
 from gwas.mem.wkspace import SharedWorkspace
-from upath import UPath
 
 
 def test_sa(tmp_path: UPath) -> None:

src/gwas/tests/test_eig.py

@@ -7,6 +7,8 @@
 import numpy as np
 import pytest
 import scipy
+from upath import UPath
+
 from gwas.defaults import (
     default_kinship_minor_allele_frequency_cutoff,
     default_kinship_r_squared_cutoff,
@@ -21,7 +23,6 @@
 from gwas.tri.tsqr import scale
 from gwas.utils import cpu_count, get_global_lock
 from gwas.vcf.base import VCFFile
-from upath import UPath
 
 from .conftest import chromosomes
 

src/gwas/tests/test_matrix_functions.py

@@ -1,5 +1,6 @@
 import numpy as np
 import pytest
+
 from gwas._matrix_functions import dgesvdq, dimatcopy, set_tril, set_triu
 
 

src/gwas/tests/test_tri.py

@@ -2,13 +2,14 @@
 
 import numpy as np
 import pytest
+from numpy import typing as npt
+from upath import UPath
+
 from gwas.mem.wkspace import SharedWorkspace
 from gwas.tri.base import Triangular, is_lower_triangular
 from gwas.tri.tsqr import scale
 from gwas.utils import cpu_count
 from gwas.vcf.base import VCFFile
-from numpy import typing as npt
-from upath import UPath
 
 sample_size_label = "large"
 chromosome = 22

src/gwas/tests/test_utils.py

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

src/gwas/tests/test_var.py

@@ -4,14 +4,15 @@
 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

@@ -4,12 +4,13 @@
 import numpy as np
 import pandas as pd
 import pytest
+from pytest_benchmark.fixture import BenchmarkFixture
+from upath import UPath
+
 from gwas.mem.wkspace import SharedWorkspace
 from gwas.testing.convert import convert_vcf_to_bgen
 from gwas.tools import plink2
 from gwas.vcf.base import Engine, VCFFile
-from pytest_benchmark.fixture import BenchmarkFixture
-from upath import UPath
 
 from .conftest import ReadResult
 from .utils import check_bias

src/gwas/tests/test_wkspace.py

@@ -1,8 +1,9 @@
 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
 import scipy
-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 = partial(jaxtyped, typechecker=typechecker)