sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
91cb77f2207814128a3efca4626a40d0964aa0a398ee90cb12b427ca192882a3 | Python | 33,927 | 773 | """Tests for bbox coordinate transformation utilities."""
import numpy as np
import pandas as pd
import pytest
import torch
from lightning_pose.data.bboxes import (
as_bbox_df_list,
crop_and_resize_frames,
crop_views,
frame_to_model,
frame_to_model_batch,
frame_to_norm,
full_frame_bbox,
... |
9875a8d2f37c5225bc6f65b11443deb1e1642116706a23ac3b58ca1349f965c6 | Python | 33,956 | 987 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
80984a5eb806e005cedf9338c761453d573909879adbefe6556c52420f730e88 | Python | 34,000 | 852 | import math
from typing import Optional
import numpy as np
import pandas as pd
import pytorch_lightning as pl
import SimpleITK as sitk
import torch
import torch.nn as nn
import torchmetrics
from .landmark_localizer import CombinedLandmarkLocalizer
from .utils import (
TABULAR_NAMES,
MEASUREMENT_NAMES,
Inv... |
f8a7af5de356c4dab3efcab159b96f2ed37b269b6fe44944eff4fc1d2f257abd | Python | 34,015 | 828 | import numpy as np
import pandas as pd
class TestCategoricalReprWithFactor:
def test_print(self, using_infer_string):
factor = pd.Categorical(["a", "b", "b", "a", "a", "c", "c", "c"], ordered=True)
dtype = "str" if using_infer_string else "object"
expected = [
"['a', 'b', 'b',... |
09000b912c2ad0119cce954b83ecd2cabb247989aa5e84e976bed34c59a04c63 | Python | 34,016 | 1,031 | #panel_apps.py
from initialization.config import *
from initialization.initialization import *
import numpy as np
import pandas as pd
import os
# matplotlib imports
import matplotlib.pyplot as plt
plt.rcParams.update({
"figure.facecolor": (1.0, 1.0, 1.0, 1.0),
"axes.facecolor": (1.0, 1.0, 1.0, 1.0),
... |
a40a5da9b9a495cd08c5b3645bceb86ea8ba1e385d8f2cd7db492e7b7e1f5f9a | Python | 34,030 | 926 | import torch
from torch.nn import Module
import windseer.utils as utils
import sys
import warnings
import re
import copy
class CombinedLoss(Module):
'''
Loss which can combine all of the different loss functions into one using learnable homoscedastic uncertainty factors.
Based on Geometric Loss Functions ... |
13011aa0966f2694c4f12d72301e42d923b527ea9843e83615868419ad59ed99 | Python | 34,047 | 948 | import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
class TestDataFrameSortValues:
@pytest.mark.parametrize("dtype", [np.uint8, bool])
def test_sort_values_sparse_no_warning(self, dtype):
# GH#45618
ser = pd.Series(pd.Cat... |
b0e7e029fe2c3a81774b7a5436e7edf183852850e55c95d083fc699a5ee772c8 | Python | 34,073 | 867 | import numpy as np
from numba import jit
from . import diffeo
import logging
from pykeops.numpy import LazyTensor
import pykeops
from . import kernelFunctions_util as ku
def haussdorffDist(fv1, fv2):
dst = ((fv1.vertices[:, np.newaxis, :] - fv2.vertices[np.newaxis, :, :] )**2).sum(axis=2)
res = np.amin(dst, ax... |
f863811cdde1c88cbb6c7a21cd72c2c0fe44487cc01af887d8e747ae5ab17808 | Python | 34,074 | 1,039 | import pathlib
from textwrap import (
dedent,
indent,
)
import numpy as np
import pytest
import pandas as pd
jinja2 = pytest.importorskip("jinja2")
from pandas.io.formats.style import Styler
@pytest.fixture
def env():
project_dir = pathlib.Path(__file__).parent.parent.parent.parent.parent.resolve()
... |
97c28c3238a672a24890127e2f49f84b6a27135d390ba0917944f6e8b1585836 | Python | 34,075 | 1,037 | """
Tests dtype specification during parsing
for all of the parsers defined in parsers.py
"""
from collections import defaultdict
from io import StringIO
import numpy as np
import pytest
from pandas._libs import lib
from pandas.compat.pyarrow import pa_version_under25p0
from pandas.errors import (
EmptyDataError... |
85e4ce242ff101cf612f508d6d73829c54665177403a17d418da42594fa71dec | Python | 34,081 | 942 | # coding: utf-8
"""Routines for printing a text report. This is the legacy code for generating
text-based reports. This will eventually be deprecated in favor of the Jinja2
and MultiQC reports.
"""
from abc import ABCMeta, abstractmethod
import math
import textwrap
from atropos.io import open_output
from atropos.util ... |
36d93a2ab8cf7f44462ad41127a1826deb8b5f41d828cf1d1b956b2c14caaf71 | Python | 34,114 | 672 | #! /usr/bin/env python
# gen-inclusions.py : generate .tex inclusions for user guide
#
# usage: gen-inclusions.py
# or: gen-inclusions.py <top_builddir> <top_srcdir>
#
# Runs the tutorial examples in the user guide and extracts output
# snippets for inclusion in .tex files. This saves having to manually
# updat... |
07295abc667a8a2b38fc80bd400a0863a7e0a1c5a6bd11b16fdbf30a34db42d6 | Python | 34,122 | 879 | import os
import pysam
import multiprocessing
import collections
def convert_benchmark_vcf_into_vapor_bed(vcf_path):
index = 1
for record in pysam.VariantFile(vcf_path):
sv_chrom = record.contig
sv_start = record.start + 1
sv_type = record.info["SVTYPE"]
sv_length = record... |
eafa08ec1e989bda797532891883763dd3406512ac36228d80a1c62c905db9a1 | Python | 34,134 | 927 | # --------------------------------------------------------
# Based on BEiT, timm, DINO and DeiT code bases
# https://github.com/microsoft/unilm/tree/master/beit
# https://github.com/rwightman/pytorch-image-models/tree/master/timm
# https://github.com/facebookresearch/deit
# https://github.com/facebookresearch/dino
# --... |
6b46d4d18b3da98cbd3c7a3c06965730e403c549eec318ac8ff56fe45eb953da | Python | 34,152 | 1,027 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
931755d70fe4a9f79139f9fd2741a7104664cf8d7e0cb0cff659584344c33e09 | Python | 34,161 | 926 | #!/usr/bin/env python
"""REST Translation server."""
import codecs
import sys
import os
import time
import json
import threading
import re
import traceback
import importlib
import torch
import onmt.opts
from itertools import islice, zip_longest
from copy import deepcopy
from collections import defaultdict
from argpars... |
b58a1ab0ad816a297fdb2c5feaf6699c5b099f18b92cd5557f7d38dfd007e502 | Python | 34,189 | 732 | """Data pipelines based on efficient video reading by nvidia dali package.
Import warning
--------------
``nvidia-dali-cuda110`` is not installed on CPU-only machines (macOS, GPU-less Linux), so
importing this module at the top level of any other module will raise ``ImportError`` on those
platforms and break ``import ... |
dd656b25e3c68605f97753720e5293b88501935eb39fc5a0cb9894e13a2bd7f2 | Python | 34,223 | 814 | """
From https://github.com/mouthful/ClofNet/blob/master/newtonian
"""
import numpy as np
import matplotlib.pyplot as plt
import time
class SpringSim(object):
def __init__(self, n_balls=5, box_size=5., loc_std=.5, vel_norm=.5,
interaction_strength=.1, noise_var=0.):
self.n_balls = n_ball... |
657732d17d63943999e00860ac4a0c2245b21595b7fac5fff40df26fd539a3c8 | Python | 34,253 | 995 | """test the scalar Timestamp"""
import calendar
from datetime import (
UTC,
datetime,
timedelta,
)
import locale
import re
import time
import unicodedata
import zoneinfo
from dateutil.tz import (
tzlocal,
tzutc,
)
import numpy as np
import pytest
from pandas._libs.tslibs.dtypes import NpyDatetime... |
acecfe93a4aec675906641a556fa6989c76cea5659c86f90842a645d5ad263bf | Python | 34,274 | 997 | # Copyright 2018-2022 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
c18371554698039ec518d2c707f9e6ce1669923ff90d34b52f22221780411ae4 | Python | 34,285 | 1,102 | from datetime import datetime
import re
import numpy as np
import pytest
from pandas._libs import lib
from pandas._libs.tslibs import Day
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
from pandas.core.indexes.datetimes import date_range
@pytest.fixture
def dti():
ret... |
8913adb4d92973f512095ba69df06a4b9282285aa691b02d7372717153f0571f | Python | 34,316 | 896 | # Copyright 2025 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
77a3d1ed06bbcc22ac6eae0c425aa0f924d526d8098e9b7f520acb05bd95addb | Python | 34,324 | 813 | # Copyright 2025 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
1d697324fe7ef8c940d20ec555d20a1cf3681616952d3cc747cb3768be311bc2 | Python | 34,328 | 969 | import numpy as np
import pytest
from pandas.errors import (
InvalidIndexError,
OutOfBoundsDatetime,
Pandas4Warning,
)
import pandas as pd
import pandas._testing as tm
from pandas.tests.frame.common import _check_mixed_float
class TestFillNA:
def test_fillna_dict_inplace_nonunique_columns(self):
... |
261d1c420dd971208d107aa76da7fa23228f5df49e8d66f06a695b8900c99de4 | Python | 34,363 | 940 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
@pytest.fixture(
params=[["linear", "single"], ["nearest", "table"]], ids=lambda x: "-".join(x)
)
def interp_method(request):
"""(interpolation, method) arguments for quantile"""
return request.param
class TestDataFrameQu... |
84c1ba0a6075b5f0cd8e7e2a8ba326508a328033eafdcdb4d6b32d2ee77147cd | Python | 34,373 | 784 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
1d525fbdd8dc54b76ac775395ac904fd6f3690bb78aa4d83a594425c66f29c17 | Python | 34,380 | 627 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
81ef67aa463f30d86b3742d64e39ad18c3bf2edbeb00a5d71edb5c2623d7a945 | Python | 34,571 | 890 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
2a562693e96779d82fe4efe0f073687eca53f36e0de6d0eb147f88caaea06dbd | Python | 34,574 | 961 | # Copyright 2022 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
0a8cab855730450c93418d8bf82c35d1a933611725e572205471c1487a05bdc8 | Python | 34,598 | 674 | # We begin by importing all necessary libraries.
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import scipy.stats as sts
from matplotlib.cm import register_cmap
from random import choices
from collections import Counter
from scipy.linalg import norm as nrm
from sklearn.dec... |
1109016062f2965701952d019e2ee92f3b2e793a7f9d1d750e5c05246356df03 | Python | 34,603 | 889 | from datetime import (
datetime,
timedelta,
)
from importlib import reload
import re
import string
import sys
import warnings
import numpy as np
import pytest
from pandas._libs.tslibs import iNaT
from pandas.errors import (
OutOfBoundsDatetime,
OutOfBoundsTimedelta,
Pandas4Warning,
)
import pandas... |
4b03b1e6950d288d2caca2d49577a31a3a1a78460f76373bae48aafb3b3790ad | Python | 34,604 | 787 | import sys, os
import multiprocessing
import math
import time
import numpy as np
from pathlib import Path
ROOT_DIR = Path(__file__).parent
import tensorflow as tf
from tensorflow import keras
from tensorflow.keras import backend as K
#tf.config.run_functions_eagerly(True) #eager tf is dummy slow
from apnet.keras_pai... |
e97e9129eeca55cb44f51aa7c8beb786538c0d578f85452fb8787b71684f08a1 | Python | 34,632 | 839 | """Dataset analysis and config recommendation logic backing ``litpose recommend``.
Given a directory (or single CSV file) of DLC-format labeled frames, this module inspects
the dataset and available hardware to recommend a starting-point lightning-pose config:
model type, backbone, image resize dimensions, batch size,... |
ef0570b16cc4dd68c45b352bb0d98c28e0b7f6593096cd72023613b3a7a13127 | Python | 34,759 | 860 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
ac3bcdb769c6240fda40430f273a5c305e84bbae47c2e47b3d6b2221522c91cf | Python | 34,764 | 757 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
11adc12774c1214eb7cf7d9325d3f9b7bd6f1fd4903536e0c9838e34155f7d02 | Python | 34,803 | 772 | import cv2
import numpy as np
import os
import h5py
import RSL as RSL_File
import matplotlib
import tensorflow.python.keras as keras
import matplotlib.pyplot as plt
from scipy import stats
from tensorflow.python.keras.models import model_from_json
from ImSetNorm import Normalize
import warnings
import copy
... |
1f7ad4901f0f0fe5e1dfe59549f93d9acc3a4ecce9508c7e69fed31417a344aa | Python | 34,827 | 961 | """Test cases for misc plot functions"""
import os
import numpy as np
import pytest
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.tests.plotting.common import (
_check_colors,
_check_legend_labels,
_check_plot_works,
_check_text_labels,
_c... |
c8b14011b9cea12e35646c77cd33a7338a47926190d12f15303cd7d2999f037b | Python | 34,877 | 811 | """PCA class to assist with computing PCA losses."""
import logging
import warnings
from typing import Any, Literal, cast
import numpy as np
import torch
from jaxtyping import Float
from omegaconf import ListConfig
from sklearn.decomposition import PCA
from sklearn.decomposition._pca import _infer_dimension
from skle... |
b4f066d8cbfcba25e5faad1a15849290902fc1df81c88dd5b2bacd7a1e16c613 | Python | 34,892 | 1,021 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
d8c58aab76e580ecc05c01b3b23acbfc08397a5aba8e09b604ccfe03e5d94a70 | Python | 34,927 | 947 | import matplotlib.pyplot as plt
import numpy as np
import neuron
from neuron import h, gui, load_mechanisms
from CA1_plasticity.model.utils import RecordingVector
from CA1_plasticity.model.utils import Synapse
import sys
class CA1:
def __init__(self, hoc_model, path_mods, setting, ttx=False):
self.settin... |
1acaf521b977c16763c652c2f174c5a1e171f19f229bfca47da8db9f3ad394a2 | Python | 34,975 | 907 | """Functions and classes for computing nearest neighbors."""
from __future__ import annotations
import contextlib
import sys
from inspect import signature
from textwrap import indent
from typing import TYPE_CHECKING
if sys.version_info < (3, 15):
from types import MappingProxyType as frozendict # noqa: N813
im... |
9e26a5bd51f4c92aa384c292c6ae8b5b8b7174da6f8084b7c77020c3ad22d615 | Python | 34,981 | 906 | import json
from pathlib import Path
from typing import Tuple, Union
import os, shutil
import warnings
from concurrent.futures import ThreadPoolExecutor
import time
from scipy.io import loadmat
import numpy as np
import torch
from torch.fft import fft, ifft, fftshift
from kilosort import CCG
from kilosort.preprocessi... |
96c6f2ac82cf6db9c9cd579df567c6c169de096bdab5bed40a6cc04315ea6322 | Python | 34,997 | 1,043 | """
Tools for interfacing with AQuA datasets from uncaging experiments
Designed to accompany the paper "Network-level encoding of local
neurotransmitters in cortical astrocytes" (DOI: TODO)
"""
## ------------------------------------------------------------------------ ##
## Imports
## ------------------------------... |
f9b0a42cbb14421f67b0dccc2976d9252cf0df69aefc5f3a8ba3b7542374a23f | Python | 35,002 | 879 | # Copyright 2023 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
551322a8170cb6183b0fa1dba17bd010aa6c100003bf1ffda96e5c9956439507 | Python | 35,060 | 1,070 | # import modules
from __future__ import print_function
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from sequence_models.constants import DIST_BINS, THETA_BINS, PHI_BINS, OMEGA_BINS
from sequence_models.structure import Attention1d
from sequence_models.layers import Positiona... |
f1fb1e7e35c47b58025a441d71bd795fb361ceb97c79267288e0202eaa329015 | Python | 35,088 | 485 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
119c9cbb4047a5a7c4b14042778340385b5539f9d2ace8c83bbc1ab24f9092e0 | Python | 35,122 | 876 | """CBMA methods from the ALE and MKDA families."""
import logging
from abc import abstractmethod
from hashlib import md5
import nibabel as nib
import numpy as np
import pandas as pd
from joblib import Parallel, delayed
from scipy import ndimage
from tqdm.auto import tqdm
from nimare.base import Estimator
from nimare.... |
eefbac8fb8c2dbbd52ff85b2d03f2230682619d5b2080f4c7ac2ffeaa6039751 | Python | 35,122 | 900 | import datetime
import numpy as np
import pytest
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
@pytest.fixture(
params=[
"linear",
"index",
"values",
"nearest",
"slinear",
"zero",
"quadratic",
"cubic",
... |
72700e7983955bbdfa165e133e7557996376fe1f80adbfa317d8c352a9565022 | Python | 35,161 | 911 | from datetime import datetime
import re
import numpy as np
import pytest
from pandas.errors import OutOfBoundsDatetime
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays import IntervalArray
class TestSeriesReplace:
def test_replace_explicit_none(... |
923ec5fc0bc09fed607df689cc3168b7a86537ecb74f2da0ae799b435f676a10 | Python | 35,196 | 905 | # cython: language_level=3
# Time-stamp: <2024-10-22 16:26:57 Tao Liu>
"""Module for ReadAlignment collection
Copyright (c) 2024 Tao Liu
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file COPYING included
with the distribution).
@status: experiment... |
aa595f719b4e699b3da81d33b833f204dbbcee82d211ac30afd9cc26e5b15d90 | Python | 35,204 | 996 | import time
import itertools
from functools import partial
from copy import deepcopy
import numpy as np
import torch
from torch import nn
import torch.nn.functional as F
from utils import time_to_string, to_torch_var
from criterions import dsc_binary_loss, tp_binary_loss, tn_binary_loss
from criterions import focal_los... |
2a8483963f809181b51b0b7b3089d242ac913bba6b4cfd8a18b704b22f065d7e | Python | 35,213 | 855 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
8107b6b020f978278bde4051785c4b6d8a1e0758a563082ecc33e62f06553ea3 | Python | 35,224 | 984 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
3ddae299fddcc8d0ef1451f509e0b9b27816d885d8179b836d798b0b14aef828 | Python | 35,228 | 1,065 | import pathlib
from textwrap import (
dedent,
indent,
)
import numpy as np
import pytest
import pandas as pd
jinja2 = pytest.importorskip("jinja2")
from pandas.io.formats import style_render
from pandas.io.formats.style import Styler
@pytest.fixture
def env():
project_dir = pathlib.Path(__file__).paren... |
16ebe55993534b72ae1dc9bed2b9529fce29b5dc4fec5d8e06bf19d9d34a2683 | Python | 35,232 | 959 | # Copyright 2018-2020 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
8b4c8c3c49f5639c64e0c353e760a87c68bff262a5d2ab461d569dab635cf5be | Python | 35,234 | 1,043 | """
The tests in this package are to ensure the proper resultant dtypes of
set operations.
"""
from datetime import datetime
import operator
import numpy as np
import pytest
from pandas._config import using_string_dtype
from pandas._libs import lib
import pandas.util._test_decorators as td
from pandas.core.dtypes.... |
c965db097f72c370b2234edf8d237abe25ce3f5fa33b09f4cb20cc626667e0ed | Python | 35,258 | 944 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
6588a0e8f840e376786b67833866fa45ac9790beead2c8809bf8d19f501a701d | Python | 35,297 | 1,137 | """
Routines for filling missing data.
"""
from __future__ import annotations
from functools import wraps
from typing import (
TYPE_CHECKING,
Any,
Literal,
cast,
overload,
)
import numpy as np
from pandas._config import is_nan_na
from pandas._libs import (
NaT,
algos,
lib,
)
from pa... |
892793a7aec5a7c5334f4c0c9da2df33b2de82b15513a7e10638f8b322b1671d | Python | 35,307 | 742 | __author__ = 'etseng@pacb.com'
import pdb
from collections import defaultdict, namedtuple, Counter
from csv import DictReader
import vcf
import pysam
from Bio.Seq import Seq
from Bio import SeqIO
from cupcake.io.BioReaders import GMAPSAMReader
from .coordinate_mapper import get_base_to_base_mapping_from_sam
__VCF_EX... |
056c32d7cceb83b4ea51fda862e92bad3c392f5c3eca5bb204c3115162137527 | Python | 35,315 | 1,088 | """
Functions for preparing various inputs passed to the DataFrame or Series
constructors before passing them to a BlockManager.
"""
from __future__ import annotations
from collections import abc
from typing import (
TYPE_CHECKING,
Any,
)
import warnings
import numpy as np
from numpy import ma
from pandas._... |
b1e6ffda6ae02b24496b1b42a20646ebb250f7b89f513a12a4730bf31422431e | Python | 35,371 | 840 | """Test loss classes."""
import math
from typing import Literal
import numpy as np
import pytest
import torch
from kornia.geometry.subpix import spatial_softmax2d
from lightning_pose.data.heatmaps import generate_heatmaps
from lightning_pose.losses.losses import (
HeatmapJSLoss,
HeatmapKLLoss,
HeatmapMSE... |
c587fe4a38c32240e9907173d93eb2f01cc6f50c4b763388420944d2e2b06bc5 | Python | 35,377 | 912 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
c673469fdb1cfb6b652b129e3cc3e22127dd9bb52311dda1d5c768ee834f6408 | Python | 35,389 | 773 | # this is to set the parameters for the pregnancy model for the rat
# note that diabetes and unx has not been characterized so then there are no diabetes/unx options in this file
import re
from defs import *
from values import *
import time
# pick out compartment IDs. E.g. given label=Area_Lumen_Cell, it would return
... |
c2d7c25bf3ab03f8bab2edf7a848499b9747addf16489f64fb4c641464e85bfd | Python | 35,460 | 764 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
a68f5b4783c7bf5a8ec758e1855c66fbf3d1c395dea81d6a897d454b6a0c9622 | Python | 35,495 | 800 | """Model execution-backend logic: eager checkpoint loading, ``torch.compile()``, and
ONNX/TensorRT export and runtime attachment.
`_RuntimeMixin` is mixed into `lightning_pose.api.model.Model`. It owns every method
that changes *how* a loaded model executes -- eager weight loading, compilation, and
export/attachment o... |
e46093df74490c5e445919ee097810814dd87362d052d262c8c19d2b7d01b29f | Python | 35,499 | 953 | # Copyright 2018-2020 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
e79544749638c848e6a9ceb0265845a79959e76949c5498dfdbecfd3f66adae8 | Python | 35,590 | 979 | """Test cases for misc plot functions"""
import os
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.tests.plotting.common import (
_check_colors,
_check_legend_labels,
_check_plot_works,
_check_text_labels,
_check_ticks_props,
)
mpl = pytest.importors... |
8fc2c80d471ee5c1eff42db92382c3f8d4f5e60a728a433ae493c57a6c53e93a | Python | 35,592 | 1,023 | """
Utilities for conversion to writer-agnostic Excel representation.
"""
from __future__ import annotations
import functools
import itertools
import re
from typing import (
TYPE_CHECKING,
Any,
cast,
)
import warnings
import numpy as np
from pandas._libs.lib import is_list_like
from pandas.util._excepti... |
482848c472cc1c5ce224a3384e825625e6df7682ae07cb6882aebabc5354c912 | Python | 35,607 | 846 | # Copyright 2025 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
adaef54bb8ed620e31b4ba5c2c783bf2f102ddd452c0f9ba4e5076a8ffedc658 | Python | 35,610 | 1,107 | """
Expose public exceptions & warnings
"""
from __future__ import annotations
import abc
import ctypes
from pandas._config.config import OptionError
from pandas._libs.tslibs import (
IncompatibleFrequency,
OutOfBoundsDatetime,
OutOfBoundsTimedelta,
)
from pandas.util.version import InvalidVersion
cl... |
23b59bc52051acd4df3ec68902d093f6038e95cf00651003ed4dd5b346553245 | Python | 35,631 | 1,108 | """
Expose public exceptions & warnings
"""
from __future__ import annotations
import abc
import ctypes
from pandas._config.config import OptionError
from pandas._libs.tslibs import (
IncompatibleFrequency,
OutOfBoundsDatetime,
OutOfBoundsTimedelta,
)
from pandas.util.version import InvalidVersion
cl... |
155325629b5bf6ce2daff36a831654bd44f368836d4c08b68cd8b535e4930aaf | Python | 35,643 | 897 | import re
import numpy as np
import pytest
from pandas._libs.tslibs.period import IncompatibleFrequency
from pandas.errors import (
OutOfBoundsDatetime,
Pandas4Warning,
)
from pandas.core.dtypes.dtypes import PeriodDtype
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays import PeriodA... |
f3241b1a7ef4fa62830450c183e3c6cb7fb82ce070da0417ca2d9af7e646023f | Python | 35,669 | 550 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import argparse
from sdna.coordinator import SDNA
class SDNAArgs:
def __init__(self):
"""
Class is used to correctly parse the arguments for the tool.
"""
self.parser = argparse.ArgumentParser(
prog="sDNA",
de... |
22a8c8f90e63d2c9e7af4c6155ca5ea451e1576dddbe90edb9c95cfe7372a52d | Python | 35,690 | 704 | #! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this wo... |
15a43d6ea706eac00af8712862fe3759781c52f9c5ab2ad6d6250ec5deb1f145 | Python | 35,703 | 999 | #Pytorch
import torch
from torch import nn
from torch.nn import functional as F
import torchvision.models as models
from torch import Tensor
from typing import Type, Any, Callable, Union, List, Optional
class AdaptiveConcatPool2d(nn.Module):
"Layer that concats `AdaptiveAvgPool2d` and `AdaptiveMaxPool2d`." # fro... |
1e9ff55217352fdf233e5017037bbf6c58e7b95329ea465673883535c9d59b5b | Python | 35,704 | 1,073 | import numpy as np
import pytest
from pandas.core.dtypes.common import ensure_platform_int
import pandas as pd
import pandas._testing as tm
import pandas.core.indexes.range as range_module
from pandas.core.indexes.range import min_fitting_element
class TestRangeIndex:
@pytest.fixture
def simple_index(self):... |
39d7f3c24885802c8036b061eb0bc478726b603e2b08ab7becdd779b15d8466f | Python | 35,712 | 759 | # We begin by importing all necessary libraries.
import numpy as np
import scipy as sp
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import scipy.stats as sts
from matplotlib.lines import Line2D
import matplotlib.patches as mpatches
from matplotlib.cm import register_cmap
from random import ... |
b5b896f61bfa27968f4bf11e6a10deb3865ea8257efcb87d0489562683db9e71 | Python | 35,756 | 1,372 | from __future__ import annotations
from io import (
BytesIO,
StringIO,
)
import os
import numpy as np
import pytest
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.io.common import get_handle
from pandas.io.xml import read_xml
# CHECKLIST
# [x] - Val... |
33325c8fdde6e26b7a01a09cd1df085eed36f9e015b2d81a1dc9c13c3e9c70cd | Python | 35,772 | 974 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
6db74c299560b244b482699d7a6019936e3d1fe420eea5d6227c3a520e067b7f | Python | 35,775 | 907 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
3fc89534aa7a8dfabf724daf79f83c92e173427625cd662086b8e1d603dd8792 | Python | 35,808 | 910 | from __future__ import print_function
from itertools import chain
import json
import os
import vtk, qt, ctk, slicer, logging
import numpy
from slicer.i18n import tr as _
from slicer.i18n import translate
from slicer.ScriptedLoadableModule import *
import SimpleITK as sitk
import sitkUtils
import traceback
#
# Slicer... |
ff2ff573fbf3ca23f2f3addcf873c47829654a35dfb534335db81052c16d83d1 | Python | 35,831 | 819 | """
Apache-2.0 license
Copyright (c) 2023 Quentin Uhl, Ileana O. Jelescu
Please cite my latest NEXI paper or ISMRM abstract if not yet available.
"""
# Implementation of the Neurite Exchange Imaging model in scipy
import numpy as np
import scipy.integrate
# utilitary functions for jacobian, hessian and MSE jacobia... |
9496408d7c2a50c90b7784d0d3980b2efc4c4328e870fc3c6fd5808308a3d287 | Python | 35,833 | 989 | # Copyright 2018-2022 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
d4fff3e1922daaaa691f6e3d94b95efe62509957c80e4206c1abacfcf3abed95 | Python | 35,876 | 236 |
"""
# # # # # # STEP: germline
python SVision-pro.py --target_path /data/DATA/Human_genomes/reference_based_analysis/aligned_reads/GIAB/HG002/GIAB.HG002.GRCh37.HiFi.minimap2.bam --access_path ./src/pre_process/hg19.access.10M.bed --model_path /data/home/songbo/workspace/svision-pro/sim_train_ccs/models/model_liteune... |
a5081fa80b5297b40de2588be17c698756b58a2c6a74c7416d6c9d8baab1a79a | Python | 35,887 | 896 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
6ddae0f655d28573d5a31359b7325d7ce9e4f7f0a42e2cd8a772c8abef4da290 | Python | 35,917 | 869 | import copy
import importlib.util
import json
from pathlib import Path
from types import SimpleNamespace
import pytest
import torch
from pyaging.utils import resolve_feature_ranges
ROOT = Path(__file__).resolve().parents[1]
CLOCKS_DIR = Path(__file__).resolve().parents[1] / "clocks"
METADATA_DIR = ROOT / "clocks" / ... |
a56d6fc9f686e366aeec37664beaec80d2e39c503e1e440dc1846234b80db011 | Python | 35,919 | 911 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
e1251956bf51e9f3338f176b2911b71a04d88667c15c7e4531035462351f34a9 | Python | 35,922 | 771 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
74f4bab25aaab680263965a66750df821f88d85067cd48fc84fb4f70b8ca89b6 | Python | 35,928 | 876 | from defs import *
from values import *
from set_params import set_torq_params
import math
import flux
import copy
import numpy as np
# parameters
dx = 1e-3
PI = 3.14159265
cell = membrane()
celln = membrane()
count=0
def conservation_init (my_cell0, my_cell1,my_celln, my_dx):
# global parameters
global dx... |
0677266065ea25354418d916b1bdcdf4df63de03940a6420a1e9bc67781a7fd8 | Python | 35,975 | 798 | import cv2
import numpy as np
import os
import h5py
import matplotlib
import tensorflow.python.keras as keras
import matplotlib.pyplot as plt
from scipy import stats
from tensorflow.python.keras.models import model_from_json
from ImSetNorm import Normalize
import warnings
warnings.filterwarnings("ignore", ... |
a9b667a79da2493f6c780c92d88902cb5c9815f342b6a400bdab0ac4a729d4e8 | Python | 35,976 | 1,038 | """
Provide user facing operators for doing the split part of the
split-apply-combine paradigm.
"""
from __future__ import annotations
from itertools import pairwise
from typing import (
TYPE_CHECKING,
final,
)
import warnings
import numpy as np
from pandas._libs import (
algos as libalgos,
)
from panda... |
4daef017c483914752a3948d3eee6f47bdf12370b6398f97f02d37dbf3fe22e3 | Python | 36,013 | 881 | import numpy as np
import logging
import pyfftw
from numba import prange, jit, int64
from multiprocessing import cpu_count
c_ = np.array([[1,0,0,0,0],
[1,1,0,0,0],
[1,1,1/3,0,0],
[1,1,0.4,1/15,0],
[1,1,3/7,2/21,1/105]])
c1_ = np.array([[0,0,0,0],
... |
37a2692fef89cbe7cb761f798535142e39d4cd8f5f96fbf33e2ede9f8ecef238 | Python | 36,068 | 947 | # Copyright 2020-2023 Xupeng Chen, Ran Wang
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to ... |
dba6ab57c26d707a5ba938f13ef760a0ba5d7f7f7c639f4d8188f2c767c607b7 | Python | 36,115 | 1,004 | """
test with the TimeGrouper / grouping with datetimes
"""
from datetime import (
UTC,
datetime,
timedelta,
)
import numpy as np
import pytest
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.core.groupby.grouper import Grouper
from pandas.core.grou... |
777afb70c2c232b1e76a09bd30379dab6a900696acd2ea8fe84aca272d2a350e | Python | 36,137 | 913 | import re
import numpy as np
import pytest
from pandas._libs.tslibs.period import IncompatibleFrequency
from pandas.errors import (
OutOfBoundsDatetime,
Pandas4Warning,
)
from pandas.core.dtypes.dtypes import PeriodDtype
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays import PeriodA... |
0276272f48f61d205a25bd0a43fd062fc1414d41c0af0f54577882aeb37ff104 | Python | 36,168 | 985 | """Test cases for .hist method"""
import re
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.tests.plotting.common import (
_check_ax_scales,
_check_axes_shape,
_check_colors,
_check_legend_labels,
_check_patches_all_filled,
_check_plot_works,
... |
3b8997d7a053e9c20d12106587d7081d3871305304528aaf40cb0b5ca84ebaf9 | Python | 36,234 | 940 | from itertools import permutations
import re
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
import pandas.core.common as com
class TestIntervalIndex:
index = pd.IntervalIndex.from_arrays([0, 1], [1, 2])
def create_index(self, closed="right"):
return pd.IntervalInd... |
e20a97f0e73e9181cc87a0c0f5dc8264b55df34b90437f05d379b425fa35811b | Python | 36,239 | 995 | #!/usr/bin/env python
# -*- coding: UTF-8 -*-
# Created by Roberto Preste
from sqlalchemy import Column, String, Integer, Float, ForeignKey
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import relationship
Base = declarative_base()
class Main(Base):
__tablename__ = "Main"
id = ... |
72245759c1446ac081cd0eac6191fb29130320d9d812d26ff59630222d265b2e | Python | 36,258 | 1,158 | from datetime import datetime
import re
import numpy as np
import pytest
from pandas._libs import lib
from pandas._libs.tslibs import Day
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
from pandas.core.indexes.datetimes import date_range
@pytest.fixture
def dti():
ret... |
c3d150756704a0354ba86dd459ebf451b35ded9c7497f7585d13da4dc1a09742 | Python | 36,260 | 978 | # Copyright 2022 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agre... |
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