sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3b0f3c01938a9a4483fa8d89bad66260dfba44c4a7b6a7cd6bc5f58b0a574489 | Python | 19,156 | 365 | ##############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
#... |
59b04997f0a80609455a5da659dcb30c72db8b6975641ce943001f926215d96f | Python | 19,159 | 478 | import copy
import filecmp
import json
import shutil
from pathlib import Path
from unittest.mock import MagicMock, patch
import numpy as np
import pandas as pd
import pytest
from omegaconf import OmegaConf
from PIL import Image
from lightning_pose.utils.cropzoom import (
_compute_bbox_df,
_crop_image,
cro... |
20f6ddf811eee0699224d886027a398fb2b24a6e7fafff4d91e30362ab34bfbf | Python | 19,162 | 452 | """Class for Grid Sampling Operator."""
import warnings
from collections.abc import Callable, Sequence
from typing import Literal
import torch
from typing_extensions import Self
from mrpro.data.SpatialDimension import SpatialDimension
from mrpro.operators.LinearOperator import LinearOperator
class _AdjointGridSamp... |
c75c95a9139a4b95961f768ebf8403bd734b71a7a56e37a87a5b29f8ae71b971 | Python | 19,162 | 478 | # 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... |
ac4326a263ea81dadd3cc564bdeb7c189c01a806bd7a1f4fc4ddc77ff170037c | Python | 19,164 | 599 | from datetime import datetime
import re
import zoneinfo
import numpy as np
import pytest
from pandas.errors import MergeError
import pandas as pd
import pandas._testing as tm
from pandas.core.reshape.concat import concat
@pytest.fixture
def left_no_dup():
return pd.DataFrame(
{"a": ["a", "b", "c", "d"]... |
ce58fde899f8d8b28611383859c8762ea83adb511d038d0449472ce1e416ffe9 | Python | 19,172 | 530 | from collections import abc
import email
from email.parser import Parser
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
class TestDataFrameToRecords:
def test_to_records_timeseries(self):
index = pd.date_range("1/1/2000", periods=10, unit="ns")
df = pd.DataFram... |
7aab68546226bec72e9ab3d8d3e4663ea254bda7928c097699b983cb327ea3fd | Python | 19,177 | 509 | # 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... |
6468ce1ccdbb330f677aeb069bd21b539a5ae6dbcf2ab5272d85b040ee8f1052 | Python | 19,183 | 495 | #!/usr/bin/env python
# coding: utf-8
import pandas as pd
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
from pyspark.sql import SparkSession
from pyspark.sql import dataframe
from pyspark.sql.types import StructType, StructField, DoubleType
import sklearn.model_selection as ms
from sklear... |
5578fb2beb1a7946b3de671251465193cff0da38178b56291478203abf2e412b | Python | 19,198 | 438 | import os
from . import conjugateGradient as cg, pointEvolution as evol
from . import surfaceMatching, surfaces
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from .affineBasis import *
## Main class for surface matching
# Template: sequence of surface classes (from surface.py); if not... |
6ecb07019b32e1d7cb3212bc5adb39cc67578f0050683164cecdd197671d15c7 | Python | 19,205 | 465 | import csv
import functools
import json
import os
import random
import warnings
import numpy as np
import torch
from pymatgen.core.structure import Structure
from torch.utils.data import Dataset, DataLoader
from torch.utils.data.dataloader import default_collate
from torch.utils.data.sampler import SubsetRandomSampler... |
7f2648903440a8ade78ad3190252b0aa114cae5fc624add0b3cb4f760db2bcd3 | Python | 19,216 | 418 | #!/usr/bin/env python
import sys, os, subprocess
import argparse
from argparse import RawTextHelpFormatter
###################################################
### 0. script description and parsing arguments ###
###################################################
synopsis1 = "\
- creates OrthNet with homologous loc... |
2fb7b5cf6f59f7ccdf585676bde71f282c2fce9a530b99ed154a891f5fedc82a | Python | 19,217 | 492 | import sys
import torch
import torch.nn as nn
import torch.nn.functional as F
import windseer.utils as utils
from .custom_modules import SparseConv
from .ModelBase import ModelBase
class ModelEDNN3D(ModelBase):
'''
Encoder/Decoder Neural Network to predict the wind.
It can be configured to a VAE structur... |
f3c5143b7e50a73bfcf53d64fe26e6a0c71d1dfcb6541eae642f438bb7bd6c0a | Python | 19,217 | 471 | # -*- coding: utf-8 -*-
import torch
import torch.nn.functional as func
class Quantizer(torch.autograd.Function):
@staticmethod
def forward(ctx, inputs):
"""
Performs the forward operation.
:param ctx: Autograd object with helper functions.
:param inputs: Input tensors.
... |
2e8d945ca7cdee62be9f03c5d919fc540902623f6a9c2fe5fc22cfdcd9f440cc | Python | 19,272 | 505 | # Copyright 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 agre... |
4764ec131796fb60d29d66b22ec6786b11b1ec0ec252d268535cb8202074b8c9 | Python | 19,272 | 531 | """Module containing utility functions for time series analysis"""
import math
import re
import warnings
from enum import Enum, IntEnum
from typing import Any, Dict, List, Optional, Tuple
import numpy as np
import pandas as pd
from sktime.param_est.seasonality import SeasonalityACF
from sktime.transformations.series.... |
6892665e6f8c2a1da819466346881d3f6fe63a9db325ff27ff3023cae3b1247a | Python | 19,292 | 561 | # 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... |
ed22e69bb2be97e317e699633d14a0d5f991d2f01d065c953997347b152fb37f | Python | 19,295 | 563 | """
evcouplings command-line app
Authors:
Thomas A. Hopf
.. todo::
Once there are different pipelines to run, there should
be individual commands for these, so will need to define additional
entry points for applications (e.g. evcomplex in addition to evcouplings).
"""
import re
from copy import deepc... |
a63f217cdf3be1d91a0cf42009615e07aa96693f0cc6b21e331f1446d78525a8 | Python | 19,303 | 466 | #!/usr/bin/env python
import sys, os, math, subprocess, datetime, argparse
from argparse import RawTextHelpFormatter
###################################################
### 0. script description and parsing arguments ###
###################################################
synopsis1 = "\
parses mRNA and CDS features... |
aef823c5a07e14d30ace3ebb4d620f152f989646408a6b5d967e07df80b23755 | Python | 19,309 | 384 | import os
import warnings
from datetime import datetime
class Messages:
FITTING_MODELS = "Fitting models on {n_models} response variables."
FITTING_MODEL = "Fitting model for {model_name}."
PREDICTING_MODELS = "Making predictions on {n_models} response variables."
PREDICTING_MODEL = "Making prediction... |
93b5e4a1462034060b7a7a84c4600f86bfe260e956e53f4f085b44e937e11199 | Python | 19,314 | 549 | import gc
import json
import shutil
from abc import ABC, abstractmethod
from itertools import chain
import numpy as np
import torch
import torch.nn as nn
from sklearn.metrics import accuracy_score, f1_score
from torch.nn.functional import softmax
from tqdm.autonotebook import tqdm
class BaseModelClass(nn.Module, ABC... |
c2ea29ab4027bd66e366b6522832ae85946da3ecfd6b32ab960423903f3b84a1 | Python | 19,323 | 579 | # 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... |
f5b290f7578d82b8f3114729c2e9de2c4cebde884dbd594be04c6c3d1c296b88 | Python | 19,323 | 530 | """
Test cases for concatenation stage of EVCouplings complex pipeline
Author:
Anna G. Green
"""
import unittest
import os
import tempfile
import pandas as pd
from unittest import TestCase
from copy import deepcopy
import ruamel.yaml as yaml
from evcouplings.complex.alignment import *
from evcouplings.complex.dis... |
14061799ea0cecb86bcbaa7afdb9788072e536b64b6f94179564676da6fd3843 | Python | 19,331 | 467 | import os
import numpy as np
import pandas as pd
import torch
from rdkit import Chem, DataStructs
from rdkit.Chem import AllChem
from torch_geometric.data import Data
from tqdm import tqdm
import sys
from sklearn.neighbors import KernelDensity
from scipy.stats import norm
sys.path.append("prepare_data")
from create_drp... |
6f0c87ee3b18a7c6e199a3d15cebb38b49789b7bee89f89b9e58feb243a74e70 | Python | 19,347 | 568 | """
Methods that can be shared by many array-like classes or subclasses:
Series
Index
ExtensionArray
"""
from __future__ import annotations
import operator
from typing import (
Any,
Self,
)
import numpy as np
from pandas._libs import lib
from pandas._libs.ops_dispatch import maybe_dispatch_ufunc... |
cc9cd82b549787b5e9039c5f43730b4c0170b9c7395779bc15dde2d07b9cb7d6 | Python | 19,350 | 344 | import sys
import os
import re
import argparse
import numpy as np
import pandas as pd
from cdr.config import Config
from cdr.util import sn
ENSEMBLE = re.compile('([^ ]+)\.m\d+')
CROSSVAL = re.compile('([^ ]+)\.CV([^.~]+)~([^.~]+)(\.m(\d+))?')
def new_row(system, results, tasks, base_partitions=None):
if base_... |
1d27de4e9c8780b837a7c59bab0352dee3c94ecf81cd36bd60a59c3b3685acf6 | Python | 19,368 | 363 | from typing import Iterator, List, Tuple
import torch
import math
import random
from tqdm import trange
import re
def generate_step(out, gen_idx, temperature=None, top_k=0, sample=False, valid_idx=None):
""" Generate a word from from out[gen_idx]
args:
- out (torch.Tensor): tensor of logits of siz... |
93774c84343f6d9cc6fb23e07fca701bde10b98ed8a3dfe47f36ed1dfde037de | Python | 19,374 | 463 | """Create ismrmrd datasets."""
import copy
import os
from pathlib import Path
from typing import BinaryIO, Literal
import ismrmrd
import ismrmrd.xsd
import torch
from einops import repeat
from ismrmrd.serialization import ProtocolSerializer
from mrpro.data import SpatialDimension
from mrpro.phantoms import EllipsePha... |
abd5ed55d986d1a9282d787480bb87f5ad0a0344e4e7c8754e33897bc317a6d0 | Python | 19,375 | 479 | """
This is the loadable seq2seq trainer library that is
in charge of training details, loss compute, and statistics.
See train.py for a use case of this library.
Note: To make this a general library, we implement *only*
mechanism things here(i.e. what to do), and leave the strategy
... |
bb8d66f71ae3809b0798eb8288f4ab10e7186164a05feb0468c959848e8b9860 | Python | 19,381 | 398 | """MR image data (IData) class."""
import datetime
import re
import warnings
from collections.abc import Iterable
from pathlib import Path
import nibabel
import numpy as np
import pydicom
import torch
from einops import rearrange, repeat
from pydicom import dcmread
from pydicom.dataset import Dataset
from pydicom.pix... |
f2ba0304e4a5ca377b917ede9831a4a33c684e854bca17252d2afacebaa20e64 | Python | 19,381 | 584 | # -*- coding: utf-8 -*-
import os
from PIL import Image
import os.path
import time
import torch
import torchvision.datasets as dset
import torchvision.transforms as trn
import torch.utils.data as data
import numpy as np
from PIL import Image
# /////////////// Data Loader ///////////////
IMG_EXTENSIONS = ['.jpg', '... |
d6709202c144e084c9b002567b9735352825bc5ff86b1f63aa1d3c38a04bdd6b | Python | 19,384 | 601 | import numpy as np
import pytest
from pandas.compat import HAS_PYARROW
from pandas.core.dtypes.dtypes import DatetimeTZDtype
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays import (
DatetimeArray,
IntervalArray,
NumpyExtensionArray,
PeriodArray,
SparseArray,
StringArr... |
2b90a805d5ee4eaf1291a002c8f69a14c9b7a209f8518e2cb03d5a28155b8548 | Python | 19,393 | 427 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Apr 4 23:20:47 2022
@author: wirrbel
"""
import os
import glob
import shutil
import numpy as np
import nibabel as nib
import multiprocessing as mp
import tempfile
import cv2
import datetime
from skimage import io, transform
from skimage.util import i... |
1df71afcfa83293331ecf054d77d0577be498618c1bbd4001d7136cd253f8e9c | Python | 19,396 | 552 | # 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... |
c8645e8e6c9484cf5725b4f3256f6519553c539b8af53425085c6d7c3be4cee8 | Python | 19,402 | 584 | # -*- coding: utf-8 -*-
import os
from PIL import Image
import os.path
import time
import torch
import torchvision.datasets as dset
import torchvision.transforms as trn
import torch.utils.data as data
import numpy as np
from PIL import Image
# /////////////// Data Loader ///////////////
IMG_EXTENSIONS = ['.jpg', '... |
3ef52ec1a8db73e80399bb3dc7ab88ac181a18ffe165a3e08e2fbd5986f2408c | Python | 19,409 | 520 | # 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... |
0cd9d647f6df6900d036d191eeb033d6f8b07c561f47a5c6dc741e12f1d9d443 | Python | 19,411 | 473 | import csv
import functools
import json
import os
import random
import warnings
from sklearn.preprocessing import OneHotEncoder
import numpy as np
import torch
from pymatgen.core.structure import Structure
from torch.utils.data import Dataset, DataLoader
from torch.utils.data.dataloader import default_collate
from torc... |
a8f485bd943d0b7b9037400f592a3d990a87bec81f37ded58e5253c837189a0e | Python | 19,421 | 444 | # 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... |
0502896fd062ac3f5c9c54db5118db612100e04a0d1d467447f1a85e8a813dce | Python | 19,433 | 515 | # 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... |
0a81ca49b7522c119d3b3cec54680119d300f38d99b681ea929b01c468d21dfd | Python | 19,439 | 483 | # 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... |
bb89b0ca365de76b68e30e0cbade2372d052bc017759ebe494042a8a417d16e6 | Python | 19,452 | 533 | import argparse
import matplotlib.pyplot as plt
import numpy as np
import h5py
from scipy.stats import pearsonr
import torch
from windseer.measurement_campaigns.predict import predict_case, masts_to_string
import windseer.plotting as plotting
import windseer.utils as utils
parser = argparse.ArgumentParser(
descri... |
870a27ca27c72a9da0591d844e959cb4af7ee6d03cda3f4a3fbcc9e5a837f263 | Python | 19,502 | 638 | # Copyright 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 agre... |
7376f596fa95cf790365c1b05274d73fb4dd7e4a97c40c74c034c150f050bd87 | Python | 19,503 | 570 | """
Methods that can be shared by many array-like classes or subclasses:
Series
Index
ExtensionArray
"""
from __future__ import annotations
import operator
from typing import (
Any,
Self,
)
import numpy as np
from pandas._libs import lib
from pandas._libs.ops_dispatch import maybe_dispatch_ufunc... |
adb2a65e8a7af92912b18915e5403ed9776d363403730b3e3acc9486db90de96 | Python | 19,505 | 357 | # Copyright (c) 2021-2023, NVIDIA Corporation
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of condit... |
cfe69b6b0b9e14bf352da1e9e7c7954ac0a63fae63652dd2b786f01af2334f26 | Python | 19,513 | 448 | """
Job management module for cptools2.
Handles experiment configuration, command generation, and result processing
for CellProfiler analysis on computing clusters.
"""
import os
from cptools2 import colours, commands, filelist, loaddata, splitter, utils
from cptools2.colours import pretty_print
class Job(object):... |
5e0a9f59255e71b7a4eadc605dc0006114a15d33ea86ec81177046bdbf9c6db9 | Python | 19,517 | 437 | import os
import numpy as np
import numpy.linalg as la
import logging
import h5py
import glob
from . import conjugateGradient as cg, kernelFunctions as kfun, pointEvolution as evol, bfgs
from . import surfaces
from . import surface_distances
from . import pointSets
from .surfaceMatching import SurfaceMatchingParam, Sur... |
1c030b0b7955f49e82891ade06f09266a71236a066c80a8d009a09550694f2e6 | Python | 19,528 | 603 | import numpy as np
import pytest
from pandas.compat import HAS_PYARROW
from pandas.core.dtypes.dtypes import DatetimeTZDtype
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays import (
DatetimeArray,
IntervalArray,
NumpyExtensionArray,
PeriodArray,
SparseArray,
StringArr... |
56b7c63719705c98d5e74ce834ee28746f4fde4ab547998e7fb76e809832f02b | Python | 19,535 | 524 | import os, torch, cv2, re
import numpy as np
from PIL import Image
import torch.nn.functional as F
import torchvision.transforms as T
from scipy.spatial.transform import Rotation as R
# Misc
img2mse = lambda x, y : torch.mean((x - y) ** 2)
mse2psnr = lambda x : -10. * torch.log(x) / torch.log(torch.Tensor([10.]))
t... |
00a10c7b7506ba91b423c75c43471ed62433bafb1ccd6187d90006f3402a7a85 | Python | 19,538 | 403 | #!/usr/bin/env python
__author__ = 'etseng@pacb.com'
import pdb
import os, sys
import itertools
from pickle import *
from collections import defaultdict, namedtuple
from Bio import SeqIO
from Bio.SeqIO import SeqRecord
from Bio.Seq import Seq
from bx.intervals.cluster import ClusterTree
from cupcake.io import BioRea... |
9b6b7333ae02b585a193297fb68c6bcd03b9c6dc5e4196963aa8b8aa8e31cb60 | Python | 19,545 | 408 | # Copyright (c) 2018-2023, NVIDIA Corporation
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of condit... |
b7f36f2602614145e1c833fa2b52a4115170201e4a469d284bff18788c72a80b | Python | 19,546 | 518 | import copy
from typing import Iterable, List, Literal, Optional, Union
import numpy as np
import pandas as pd
from anndata import AnnData
from mudata import MuData
def pair_peak_gene_sc(
adata_cc: AnnData,
adata: AnnData,
peak_annotation: Optional[pd.DataFrame] = None,
pvalue_adj_cutoff_cc: Optional... |
526795e0b857d6f2764c23103be46c5666102957ff4ab1eeffdadbe48fa5e072 | Python | 19,553 | 543 | """Tools for downloading datasets."""
import itertools
import json
import logging
import os
import os.path as op
import shutil
import tarfile
import time
import zipfile
from glob import glob
from io import BytesIO
from lzma import LZMAFile
from urllib.request import urlopen
import numpy as np
import pandas as pd
impor... |
93d9fe18317591cd9b08fd452cc084db71cfe6dc6e42d44fc5c682496581fbec | Python | 19,553 | 433 | """Transforms relate to tokenization/subword."""
from onmt.utils.logging import logger
from onmt.transforms import register_transform
from .transform import Transform, ObservableStats
class TokenizerTransform(Transform):
"""Tokenizer transform abstract class."""
def __init__(self, opts):
"""Initializ... |
0fc1dfb1330a93e70b0b5326c5942696e47f67a18fa1491966fcbe4df407ae2f | Python | 19,554 | 493 | '''
Created on Mar 8, 2012
@author: regger
'''
import numpy as np
from . import scalar_field
from model_data_base.mdbopen import mdbopen
class Edge(object):
'''
Edge object contains list of points,
diameter at each point, label,
string hocLabel, parentID
Used during reading of hoc files
'''
... |
d9a36c8010912400cad415a1fdc1fe042dd912f6ebd13af25925aab2fb1f53e7 | Python | 19,560 | 562 | #!/usr/bin/env python3
"""Small runtime checks shared by BASALT command modules."""
from __future__ import annotations
import fcntl
import hashlib
import os
import re
import shutil
import subprocess
from pathlib import Path
EXPECTED_MODEL_ENSEMBLES = 5
_CHECKPOINT_STEP = re.compile(r"^(\d+)")
_CHECKM2_METRIC_KEYS ... |
df09093a9956fc7681949f9b660debe76788c33227498ba68e60584fdf2aec36 | Python | 19,571 | 550 | from argparse import Namespace
from math import log2
from typing import Optional, Dict, Any, Union, TYPE_CHECKING, Tuple
import logging
import torch
import torch.nn.functional as F
import torch.nn as nn
from .hash_grid_torch import HashEmbedder
from ..transform import RigidTransform, ax_transform_points, mat_transform_... |
3f66103f207efc11539d64147f57f41c73fbd936b42a56acfaa4e5170f1839a9 | Python | 19,576 | 516 | from collections import ChainMap
import inspect
import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
class TestRename:
def test_rename_signature(self):
sig = inspect.signature(pd.DataFrame.rename)
parameters = set(sig.paramet... |
7c86df959e5e6ec7d30671ba884f327d4655423eeaf37981daa85af91b769966 | Python | 19,578 | 510 | # coding: utf-8
from atropos.adapters import *
from atropos.align import MatchInfo
from atropos.commands.trim.modifiers import *
from atropos.io.seqio import Sequence
from atropos.util import reverse_complement as rc
DUMMY_ADAPTER = Adapter("ACGT", FRONT)
def front_match(read):
match = Match(0, 2, 0, 2, 1, 0, Tr... |
5635fe213ecee55de83d2304807f4c3c9cb6dcf7436adaf5be38dca6e8b460ac | Python | 19,581 | 543 | """Tools for downloading datasets."""
import itertools
import json
import logging
import os
import os.path as op
import shutil
import tarfile
import time
import zipfile
from glob import glob
from io import BytesIO
from lzma import LZMAFile
from urllib.request import urlopen
import numpy as np
import pandas as pd
impor... |
57861f6ec1ebd7d8a3d727cf24be5e884708667976ce868e412a1f4fcf81e586 | Python | 19,585 | 517 | """Feature view."""
# -----------------------------------------------------------------------------
# Imports
# -----------------------------------------------------------------------------
import logging
import re
import numpy as np
from phylib.utils import Bunch, emit
from phy.plot.transform import Range
from ph... |
14543e0dd5c954ba3232728ec8c17806ee3f75dc66e9f42df70c08b3703b9e86 | Python | 19,593 | 508 | import math
import numpy as np
from sklearn.gaussian_process import GaussianProcessRegressor as GPR
from sklearn.gaussian_process.kernels import RBF, ConstantKernel
import time
import torch
def bin_log_data_binning(wind_data, grid_dimensions, verbose=False):
'''
Bins the input wind data into a grid specified ... |
c3dd9c5fa49345b3fe69f93cf56927f4eae08c92e9c8505c5379b784467eb710 | Python | 19,599 | 496 | # 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... |
cf3553ee4075c7439dea162161467b9da1859872d419a2bc816a92a67c660fb2 | Python | 19,607 | 639 | """
These benchmarks are for Series and DataFrame indexing methods. For the
lower-level methods directly on Index and subclasses, see index_object.py,
indexing_engine.py, and index_cached.py
"""
from datetime import datetime
import warnings
import numpy as np
from pandas import (
NA,
CategoricalIndex,
D... |
2787681a44be17219b5f12c86865f228e7edebb66e9d21ee6628ffc94809a9e9 | Python | 19,616 | 488 | # -*- coding: utf-8 -*-
'''
BOOSH_CLI
COMMAND LINE (CLI) VERSION FOR SPATIOTEMPORAL CLUSTERING OF MOLECULAR TRAJECTORY DATA USING 3D DBSCAN. TIME CONVERTED TO Z
THIS VERSION CLUSTERS THE INDIVIDUAL DETECTIONS RATHER THAN TRAJECTORY CENTROIDS
Design and coding: Tristan Wallis
Additional coding: Kyle Young, Alex McCann... |
06da353739df3ccf29adc4a7b9c41f80b752950c1636ffbeefd3c32873a398dd | Python | 19,622 | 502 | __all__ = [
"GlycoPeptideBranchMS2Data",
"GlycoPeptideBranchMS2Output",
"GlycoPeptideBranchMS2DataConverter",
"GlycoPeptideBranchMS2Dataset",
"GlycoPeptideBranchMS2DataBatch",
]
import itertools
from typing import (
Any,
List,
NamedTuple,
Sequence,
Tuple,
Union,
cast,
... |
8b91a50833f12bec71241d146a42e02d001ccf582e124929a15c132426d68b55 | Python | 19,622 | 429 | """
Title: stimulation_protocols.py
Author: Matus Tomko
Mail: matus.tomko __at__ fmph.uniba.sk
"""
import numpy as np
from neuron import h, gui
from CA1_plasticity.model.utils import Synapse
class StimulationProtocol:
"""
A class used to set a stimulation protocol
...
Attributes
----------
s... |
fee0dbe157de83728e5ec60a40d57be82b0b199af398636f960a3cb422784955 | Python | 19,625 | 540 | """
Tests for DatetimeIndex methods behaving like their Timestamp counterparts
"""
import calendar
from datetime import (
date,
datetime,
time,
)
import locale
import unicodedata
import numpy as np
import pytest
from pandas._libs.tslibs import timezones
from pandas.errors import Pandas4Warning
import pa... |
c20b19dcf4e1142788c64c7a621442c993ccd4182c4d3969bc256e2b86b2d0b5 | Python | 19,630 | 551 | # 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... |
93f22a70c8ae2d7d7ab0b4379753405e8259294f484707445a120e8ff80e2fc0 | Python | 19,631 | 502 | """Pure, immutable domain objects for AIND merge propositions.
This module deliberately knows nothing about Qt, files, spike arrays, or the
curation workflow. The controller and persistence layers exchange ordinary
JSON-compatible mappings through the codec functions below.
"""
from __future__ import annotations
fr... |
02693c5e12edc87aaefe0f058184ee997beb0b85ec50c2775aed9cb4e66cea02 | Python | 19,637 | 540 | #!/usr/bin/env python3
"""
Simple static site generator for the pandas web.
pandas_web.py takes a directory as parameter, and copies all the files into the
target directory after converting markdown files into html and rendering both
markdown and html files with a context. The context is obtained by parsing
the file `... |
23cb5d9b3dcff62a7ecaab6900ff941e8d5ce64b27959ae1f5b7479d0ae5ca05 | Python | 19,652 | 494 | # -*- coding: utf-8 -*-
"""
Created on Thu Nov 30 07:57:45 2023
@author: lonya
"""
#%% Load Data
import tkinter as tk
import tkinter.filedialog as fd
import numpy as np
import os
import matplotlib.pyplot as plt
import pandas as pd
import my_funcs as mf
import pickle
#%% Load single limb gait
root = tk.Tk()
filez = f... |
faaa39d293cec62806e8ec02db2c163e3d7203c7c33ade449f5161b852a5d913 | Python | 19,665 | 595 | #! /usr/bin/env python
# -*- coding: utf-8
#
# Copyright (c) 2023 Kenneth Atz, Clemens Isert & Gisbert Schneider (ETH Zurich)
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.nn import MessagePassing
from torch_geometric.typing import Adj, Size, Tensor
from dragonfly_gen.gml.pygm... |
47de1a8179fee848879e7d9f7c1c0e3e947cab7192b27cff8bbd403f7230a5b6 | Python | 19,670 | 431 | """Test datamodule functionality."""
from collections.abc import Sized
import numpy as np
import pytest
from lightning.pytorch.utilities import CombinedLoader
from torch.utils.data import RandomSampler
def test_base_datamodule(cfg, base_data_module):
im_height = cfg.data.image_resize_dims.height
im_width =... |
79d7585152f537b088beb4f00378a319dc291daedf5650087855254a357237f9 | Python | 19,671 | 440 | # Copyright (c) 2018-2023, NVIDIA Corporation
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of condit... |
868114fdbb8655c4c5a3d18ec2fd8010c5d4e693bbc4f01adb0d782300637e04 | Python | 19,673 | 414 |
from .utils import PheWebError, get_phenolist, chrom_order
from . import conf
from . import parse_utils
import io
import os
import csv
from contextlib import contextmanager
import json
import gzip
import datetime
from boltons.fileutils import AtomicSaver, mkdir_p
import pysam
import itertools, random
from pathlib imp... |
69ee5d8767d4e83f43ebcb70b9a3dfc4d474e2fa17aff7a1651a8df0aef7ef57 | Python | 19,678 | 505 | """Plot rendering endpoints.
The engine's ``pycaret.plots.*`` modules return ``plotly.graph_objects.Figure``
objects. These endpoints expose them over HTTP as JSON the React UI's
``react-plotly.js`` component can consume directly.
Two render styles:
- **Run-bound** (``GET /runs/{run_id}/plots/{kind}``): for screens ... |
cc77eccea6fd042afb05bda5fa63d31485092ea807014c3313b36c9a29248060 | Python | 19,688 | 506 | # 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... |
92cdbfdff0ae5472164ae25093b291ef7d4bc70394348543937db6d7d3ba35d5 | Python | 19,693 | 578 | import os
import argparse
import time
import csv
import sys
import json
import random
import numpy as np
import pprint
import yaml
import torch
import torch.multiprocessing as mp
import ray
from ray import tune
from matdeeplearn import models, process, training
######################################################... |
1454acc898fdbe73b1f916739cff6ffaaab56800adf78f8698e9fbe1bf4fd46a | Python | 19,700 | 486 | #MIT License
#
#Copyright (c) 2019 Iñigo Prada Luengo
#
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the "Software"), to deal
#in the Software without restriction, including without limitation the rights
#to use, copy, modify, merge,... |
a83ba1b2e8929535c8cc247fecc11d42bee1118ba313f9376895d2180f76c423 | Python | 19,717 | 460 | # 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... |
83dce05d45b73e08d00ebc241dcf87817344c5d490bd95762d8f524537f8238b | Python | 19,725 | 418 | # Copyright (c) 2018-2023, NVIDIA Corporation
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of condit... |
2465b63b6253e14d741956dbdf2fc53c1e341dc9460d822c27ed00c66669afcc | Python | 19,735 | 553 | """Base class and functions for implementing command-line interfaces for
Atropos subcommands.
"""
from argparse import ArgumentParser, ArgumentError, HelpFormatter
import copy
import logging
from multiprocessing import cpu_count
import operator
import os
import platform
import re
import sys
import textwrap
import urlli... |
5085e342acd07d69f81c4da6f4b3184460ac95c38452d880c3b5606017263132 | Python | 19,741 | 530 | import matplotlib.colors as colors
import matplotlib.cm as cm
import matplotlib.pyplot as plt
import numpy as np
from scipy.interpolate import griddata
from windseer.measurement_campaigns.measurements_line import get_tower_distances_on_line
def plot_measurement_campaign_scatter(ret):
'''
Plot the predictions... |
fcf3e9f52230fecc6210d6622d9376d6bdabb60434eadb8943cf50f6282b1894 | Python | 19,760 | 506 | #!/usr/bin/env python
from __future__ import print_function
import io
from math import trunc
from scipy import ndimage
import numpy as np
import os
import pandas as pd
import shutil
import tarfile
import time
import torch
import h5py
import sys
def change_dataset_compression(infile, outfile, s_hor=1, s_ver=1, compr... |
d2ac2a331368a11ca6864d28f57299c20201354685c561ceea1ab7aeabdbbbfa | Python | 19,763 | 426 | # Copyright 2019 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
83b3df2d152ef36779ca57e6cc9eebbb22e840293c8f9295ca487fe463735131 | Python | 19,767 | 550 | # Copyright 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 agre... |
d1c3f2cdc9944c5092dfc495b72c44346cba4a3e29295cf93ee4ab266e47995e | Python | 19,768 | 548 | """
Should always be faithful duplicate of sequence/BioReaders.py
Duplicated here for tofu installation. This one is called via cupcake.io.BioReaders.
"""
import re, sys, pdb
from collections import namedtuple
import pysam
Interval = namedtuple('Interval', ['start', 'end'])
class Sim... |
872509eadceec2124feb7d8c8b113388ef51169fdf8c3de482ed45b2ed09d0eb | Python | 19,786 | 541 | # 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... |
e2f9361580a623729f411137594bdc83c37192f66c3f211662609bc7d2eb1895 | Python | 19,789 | 574 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for GCPNet (https://github.com/BioinfoMachineLearning/GCPNet):
# ----------------------------------------------------------------------------------------------... |
f86151e02645b54ef3e9979dbc8ec2a0843e0189e3d973c55be533694ca447c4 | Python | 19,789 | 490 | """
Unit tests for transpiler function.
"""
from math import isclose
import pytest
import pennylane as qp
from pennylane import numpy as np
from pennylane.transforms.transpile import transpile
def build_qfunc_probs(wires):
def qfunc(x, y, z):
qp.Hadamard(wires=wires[0])
qp.RZ(z, wires=wires[2])... |
f5fa9c9f1af5cd68cd5d7508cdc641793816a3f43f768f1471d850317b5b92d2 | Python | 19,791 | 417 | #!/usr/bin/env python
__version__ = "1.08"
import os
import sys
import re
import shutil
import glob
import argparse
import textwrap
import pandas as pd
import operator
import time
from collections import defaultdict
from collections import Counter
from datetime import datetime
from Bio import SeqIO
class bcolors:
... |
0376841f4e2b667557eaaae9065c2b0cf12c89910ea5852076885b12a5795a58 | Python | 19,796 | 625 | """
Functions for arithmetic and comparison operations on NumPy arrays and
ExtensionArrays.
"""
from __future__ import annotations
import datetime
from functools import partial
import operator
from typing import (
TYPE_CHECKING,
Any,
)
import numpy as np
from pandas._libs import (
NaT,
Timedelta,
... |
2e0d1438bdcb6ff75ddc10cc325dc5f775a8794b983e94f1131c071349f8e86b | Python | 19,800 | 651 | """
Extend pandas with custom array types.
"""
from __future__ import annotations
import inspect
from typing import (
TYPE_CHECKING,
Any,
Self,
TypeVar,
cast,
overload,
)
import numpy as np
from pandas._libs import missing as libmissing
from pandas._libs.hashtable import object_hash
from pan... |
07b44a720dd80b56bb111beedf90806995f0a7ce2e3f1717ea01bdaa02c738ed | Python | 19,802 | 405 | import numpy as np
import torch
from torch.utils.data.dataset import TensorDataset
from torch.utils.data import DataLoader
import torch.nn.functional as F
from torch.autograd import Variable
import pickle as pkl
torch.set_default_dtype(torch.float64)
# input_B_AN_D, target_B_S_D, nodeIncomingEdges_B_S_IE_AE, rel_rec_... |
79e8e6ab310915a39732009cc01d311b30e0c67c7ecd4abc3b79221e03e0c058 | Python | 19,807 | 386 | # Copyright (c) 2021-2023, NVIDIA Corporation
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of condit... |
baa5fd9bd9edf926c5464b5cb05c7d08efcfe0852b7cade79f4e8a52a206d52b | Python | 19,820 | 692 | from datetime import (
datetime,
timedelta,
)
import operator
import zoneinfo
import numpy as np
import pytest
from pandas._libs.tslibs import iNaT
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
from pandas.core import roperator
from pandas.core.arrays import (
... |
f3fb8e9875102519ed391c89e2e6b0eb213d37820fba20dba18431449e9f6f71 | Python | 19,826 | 495 | """This script creates the group level figures."""
import os
from copy import deepcopy
import dill
import glmtools as glm
import h5py
import matplotlib as mpl
import matplotlib.pyplot as plt
import mne
import numpy as np
import osl
from anamnesis import obj_from_hdf5file
from matplotlib.lines import Line2D
from lemon... |
eff3bec26c34f4ab7b7818cd5b096b634a437a06d63224572a17eae41a68adc1 | Python | 19,836 | 514 | import numpy as np
import pytest
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
class TestDataFrameCov:
def test_cov(self, float_frame):
# min_periods no NAs (corner case)
expected = float_frame.cov()
result = float_frame.cov(min_periods=len(fl... |
177f87732da011dd411fc992b69591a39596c5a170e036be273204ce4a467000 | Python | 19,842 | 357 | # Copyright 2019 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
644623a500dbe0e2c7d4663489ffe42743751bb25b18a49c5c2b78d78a8a62e8 | Python | 19,862 | 411 | """
Reads a fasta file of individual protein sequences.
Uses ESM2 to infer MSA column-wise probabilities.
Writes a profile hmm in HHsearch 1.5 (.hhm) hmmer3 (.hmm) format.
"""
#TODO: figure out how to calculate cs219 files directly
#TODO: Apply Dirichlet priors to probabilities for hmmer3 output.
import to... |
3653f77364e83d5ddfdb1aff083be8bf978fd48e87f1016c17c17d85b81e722e | Python | 19,872 | 568 | import os
import subprocess
import sys
import textwrap
import numpy as np
import pytest
from pandas.compat import WASM
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.core.util.hashing import hash_tuples
from pandas.util import (
hash_array,
hash_pandas_... |
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