isort, warn from tight_layout

limix/__init__.py

@@ -7,9 +7,7 @@
 The official documentation together with examples and tutorials can be found
 at https://limix.readthedocs.io/.
 """
-from . import __config__
-
-from . import vardec, her, io, plot, qc, qtl, sh, stats, threads
+from . import __config__, her, io, plot, qc, qtl, sh, stats, threads, vardec
 from ._cli import cli
 from ._config import config
 from ._example import file_example

limix/_cli/_cli.py

@@ -3,8 +3,8 @@
 from .download import download
 from .estimate_kinship import estimate_kinship
 from .extract import extract
-from .remove import remove
 from .qtl import qtl
+from .remove import remove
 from .see import see
 
 

limix/_cli/download.py

@@ -1,4 +1,5 @@
 import click
+
 import limix
 
 

limix/_cli/estimate_kinship.py

@@ -1,4 +1,5 @@
 import click
+
 import limix
 
 

limix/_cli/extract.py

@@ -1,4 +1,5 @@
 import click
+
 import limix
 
 

limix/_cli/qtl.py

@@ -1,6 +1,7 @@
 import click
-from .st_sscan import st_sscan
+
 from .scan import scan
+from .st_sscan import st_sscan
 
 
 # @click.command(cls=OrderedCommand)

limix/_cli/remove.py

@@ -1,6 +1,7 @@
-import limix
 import click
 
+import limix
+
 
 @click.command()
 @click.pass_context

limix/_cli/scan.py

@@ -1,4 +1,5 @@
 import click
+
 from ._click import OrderedCommand
 
 

limix/_cli/see.py

@@ -1,6 +1,7 @@
-import limix
 import click
 
+import limix
+
 
 @click.command()
 @click.pass_context

limix/_cli/st_sscan.py

@@ -1,4 +1,5 @@
 import click
+
 from ._click import OrderedCommand
 
 

limix/_cli/test/test_pipeline.py

@@ -1,13 +1,14 @@
 import os
 
-import limix
-from limix._cli.pipeline import Pipeline
-from limix._cli.preprocess import normalize, where, impute
-from limix.io._fetch import fetch
 from numpy import nan
 from numpy.random import RandomState
 from numpy.testing import assert_allclose
 
+import limix
+from limix._cli.pipeline import Pipeline
+from limix._cli.preprocess import impute, normalize, where
+from limix.io._fetch import fetch
+
 
 def test_pipeline_where_filter():
 

limix/_data/test/test_data_asarray.py

@@ -1,9 +1,10 @@
 import numpy as np
 import pytest
 import xarray as xr
-from limix._data import asarray
 from numpy.testing import assert_array_equal as assert_eq, assert_string_equal
 
+from limix._data import asarray
+
 
 def test_asarray():
     from limix._data._conf import CONF

limix/_display/__init__.py

@@ -1,6 +1,6 @@
+from ._core import blue, bold, green, red, width
+from ._display import add_title_header, banner, indent, session_block, session_line
 from ._exception import print_exc
-from ._display import banner, session_block, session_line, add_title_header, indent
-from ._core import bold, blue, red, green, width
 
 __all__ = [
     "print_exc",

limix/_display/_exception.py

@@ -1,5 +1,6 @@
 import sys
-from ._display import bold, red, pprint
+
+from ._display import bold, pprint, red
 
 
 def print_exc(stack, e):

limix/her/_estimate.py

@@ -1,5 +1,5 @@
-from .._display import session_block, session_line
 from .._data import conform_dataset, normalize_likelihood
+from .._display import session_block, session_line
 from ..qc._lik import normalise_extreme_values
 from ..qtl._assert import assert_finite
 

limix/io/test/test_fetch.py

@@ -1,14 +1,16 @@
-import limix
-from limix.io._fetch import fetch
-import pytest
 import sys
+
+import pytest
 from numpy.testing import (
     assert_allclose,
     assert_array_equal,
     assert_equal,
     assert_string_equal,
 )
 
+import limix
+from limix.io._fetch import fetch
+
 _samples = [
     "HG00111",
     "HG00112",

limix/io/test/test_readers.py

@@ -1,7 +1,6 @@
 from numpy.testing import assert_allclose, assert_equal
 
-from limix import io
-from limix import file_example
+from limix import file_example, io
 from limix.sh import extract
 
 

limix/plot/__init__.py

@@ -24,15 +24,15 @@
 from limix_plot import (
     ConsensusCurve,
     box_aspect,
+    get_pyplot,
+    image,
     kinship,
     load_dataset,
     manhattan,
     normal,
     pca,
     power,
     qqplot,
-    image,
-    get_pyplot,
     show,
 )
 

limix/qc/_impute.py

@@ -1,6 +1,7 @@
-from limix._bits import dask, get_shape, numpy, pandas, xarray
 import warnings
 
+from limix._bits import dask, get_shape, numpy, pandas, xarray
+
 
 def mean_impute(X, axis=-1, inplace=False):
     """

limix/qc/_mean_std.py

@@ -1,6 +1,7 @@
-from limix._bits import dask, numpy, pandas, xarray
 import warnings
 
+from limix._bits import dask, numpy, pandas, xarray
+
 
 def mean_standardize(X, axis=-1, inplace=False):
     """

limix/qc/test/test_allele.py

@@ -1,11 +1,10 @@
 import dask.array as da
 import xarray as xr
+from bgen_reader import allele_expectation, compute_dosage, example_files, read_bgen
 from numpy import array_equal, ndarray
 from numpy.random import RandomState
 from numpy.testing import assert_, assert_allclose
 from pandas import DataFrame, Series
-from bgen_reader import read_bgen, allele_expectation, example_files
-from bgen_reader import compute_dosage
 
 from limix.qc import compute_maf
 

limix/qc/test/test_impute.py

@@ -1,14 +1,16 @@
 import pytest
-from limix.qc import mean_impute
 from numpy import asarray, nan
 from numpy.random import RandomState
+
+from limix.qc import mean_impute
+
 from .util import (
+    assert_dask_array,
+    assert_dask_dataframe,
     assert_ndarray_1d,
     assert_ndarray_2d,
-    assert_pandas_series,
     assert_pandas_dataframe,
-    assert_dask_array,
-    assert_dask_dataframe,
+    assert_pandas_series,
     assert_xarray_dataarray,
 )
 

limix/qc/test/test_indep_pairwise.py

@@ -1,8 +1,9 @@
 from dask.array import from_array
-from limix.qc import indep_pairwise
 from numpy.random import RandomState
 from numpy.testing import assert_equal
 
+from limix.qc import indep_pairwise
+
 
 def test_indep_pairwise():
     random = RandomState(0)

limix/qc/test/test_linalg.py

@@ -1,6 +1,7 @@
-from numpy import zeros, ones
+from numpy import ones, zeros
 from numpy.random import RandomState
 from numpy.testing import assert_allclose
+
 from limix.qc import remove_dependent_cols
 
 

limix/qc/test/test_mean_standardize.py

@@ -1,15 +1,16 @@
 import pytest
-from numpy import nan
-from limix.qc import mean_standardize
-from numpy import array
+from numpy import array, nan
 from numpy.random import RandomState
+
+from limix.qc import mean_standardize
+
 from .util import (
+    assert_dask_array,
+    assert_dask_dataframe,
     assert_ndarray_1d,
     assert_ndarray_2d,
-    assert_pandas_series,
     assert_pandas_dataframe,
-    assert_dask_array,
-    assert_dask_dataframe,
+    assert_pandas_series,
     assert_xarray_dataarray,
 )
 

limix/qc/test/test_missing.py

@@ -1,8 +1,9 @@
+import dask.array as da
+from numpy import nan
 from numpy.random import RandomState
 from numpy.testing import assert_array_equal
-from numpy import nan
+
 from limix.qc import count_missingness
-import dask.array as da
 
 
 def test_count_missingness():

limix/qc/test/test_quantile_gaussianize.py

@@ -1,14 +1,16 @@
 import pytest
-from limix.qc import quantile_gaussianize as qg
 from numpy import asarray, nan
 from numpy.random import RandomState
+
+from limix.qc import quantile_gaussianize as qg
+
 from .util import (
+    assert_dask_array,
+    assert_dask_dataframe,
     assert_ndarray_1d,
     assert_ndarray_2d,
-    assert_pandas_series,
     assert_pandas_dataframe,
-    assert_dask_array,
-    assert_dask_dataframe,
+    assert_pandas_series,
     assert_xarray_dataarray,
 )
 

limix/qc/test/test_unique.py

@@ -1,7 +1,8 @@
+import dask.array as da
 from numpy.random import RandomState
 from numpy.testing import assert_array_equal
+
 from limix.qc import unique_variants
-import dask.array as da
 
 
 def test_unique_variants():

limix/qc/test/util.py

@@ -1,8 +1,8 @@
-from numpy.testing import assert_allclose, assert_, assert_array_equal
-import xarray as xr
 import dask.array as da
 import dask.dataframe as dd
 import pandas as pd
+import xarray as xr
+from numpy.testing import assert_, assert_allclose, assert_array_equal
 
 
 def assert_ndarray_1d(func, data1d):

limix/qtl/_iscan.py

@@ -1,11 +1,12 @@
 import sys
 
 from limix._display import session_line
+
 from .._bits import unvec
 from .._data import asarray as _asarray, conform_dataset, normalize_likelihood
 from .._display import session_block
-from ._result import IScanResultFactory
 from ._assert import assert_finite
+from ._result import IScanResultFactory
 
 
 def iscan(G, y, lik="normal", K=None, M=None, idx=None, E0=None, E1=None, verbose=True):

limix/qtl/_result/__init__.py

@@ -1,5 +1,5 @@
-from ._st_factory import STScanResultFactory
-from ._mt_factory import MTScanResultFactory
 from ._ifactory import IScanResultFactory
+from ._mt_factory import MTScanResultFactory
+from ._st_factory import STScanResultFactory
 
 __all__ = ["STScanResultFactory", "MTScanResultFactory", "IScanResultFactory"]

limix/qtl/_scan.py

@@ -1,6 +1,7 @@
 import sys
 
 from limix._display import session_line
+
 from .._data import asarray as _asarray, conform_dataset, normalize_likelihood
 from .._display import session_block
 from ._assert import assert_finite

limix/qtl/test/test_qtl_iscan.py

@@ -1,9 +1,10 @@
 import scipy.stats as st
-from limix.qc import normalise_covariance
-from limix.qtl import iscan
 from numpy import exp, eye, zeros
 from numpy.random import RandomState
 
+from limix.qc import normalise_covariance
+from limix.qtl import iscan
+
 
 def _test_qtl_iscan_three_hypotheses(lik):
     random = RandomState(0)

limix/qtl/test/test_qtl_scan.py

@@ -1,8 +1,5 @@
 import pytest
 import scipy.stats as st
-from limix.qc import normalise_covariance
-from limix.qtl import scan
-from limix.stats import linear_kinship
 from numpy import (
     argmin,
     array,
@@ -20,6 +17,10 @@
 from numpy.testing import assert_allclose
 from pandas import DataFrame
 
+from limix.qc import normalise_covariance
+from limix.qtl import scan
+from limix.stats import linear_kinship
+
 
 def _test_qtl_scan_st(lik):
     random = RandomState(0)