sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
349c29cbecc0af0b837bf25610223e62da2c190f2edac9bc72fd198d95c5c814 | Python | 26,736 | 755 | # Copyright 2020 DeepMind Technologies Limited.
#
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agre... |
fdbc0297a0be4a55ad5233ab09a74b00ca69342c82cefb3be5ccbbe45f7f800e | Python | 26,752 | 744 | import sys
import numpy as np
import os.path as op
import json
from argparse import ArgumentParser, RawDescriptionHelpFormatter
import bids
from bids.layout import BIDSLayout
from bids.config import set_option
from pathlib import Path
from rsHRF import spm_dep, fourD_rsHRF, utils
from packaging.version import Version
... |
9baeba095f4a596ad1385ccd2e582151552c97a5631ea11355e43a37f6ef2716 | Python | 26,772 | 686 | """
Maximum flow (and minimum cut) algorithms on capacitated graphs.
"""
import networkx as nx
from .boykovkolmogorov import boykov_kolmogorov
from .dinitz_alg import dinitz
from .edmondskarp import edmonds_karp
from .preflowpush import preflow_push
from .shortestaugmentingpath import shortest_augmenting_path
from .u... |
905dd657e0cc392ed6f3452e958d6ff5c0192372b805e8999e61e7cc24f95c18 | Python | 26,783 | 795 | """Tests for the core of the interactive REPL."""
import re
import pandas as pd
import pytest
pytest.importorskip("prompt_toolkit")
pytest.importorskip("rich")
from neurolang_apps.utils.tui import ( # noqa: E402
InteractiveTuiApp,
TuiSettings,
)
from neurolang_apps.utils.tui.results import rows_table # n... |
875bc8a44bf890b66a470e25a0b010eb6b54d0c5aa1584578485183f54d0219a | Python | 26,795 | 747 | """Unit tests for the :mod:`networkx.algorithms.community.quality`
module.
"""
from typing import NamedTuple
import pytest
import networkx as nx
from networkx import barbell_graph
from networkx.algorithms.community import (
constant_potts_model,
map_equation,
modularity,
overlapping_modularity,
... |
e3d49b8d773665ddb3af01208202821949d8a46e22a2dd2f9a17c8fef08a7344 | Python | 26,804 | 547 | #!/usr/bin/env python3
import os
import numpy as np
import time
import torch
from torch import optim
# -custom-written libraries
import utils
from utils import checkattr
from data.load import get_context_set
from models import define_models as define
from models.cl.continual_learner import ContinualLearner
from models.... |
76d2781b68d95cb2354ef802bf18cdf050d368873a7e15c6caa66f8e54482edc | Python | 26,812 | 623 | #!/usr/bin/env python
#
# Copyright (c) 2015 10X Genomics, Inc. All rights reserved.
#
import collections
import cPickle
import csv
import itertools
import json
import math
import numpy as np
import os
import subprocess
import sys
import re
import tenkit.log_subprocess as tk_subproc
import tenkit.safe_json as tk_safe_j... |
84018750f956f126b8054eb45980cf92138a91080926cfa790e19ce6a9ce7f45 | Python | 26,827 | 727 | """\
This module implements on disk sparse datasets.
This code is based on and uses the conventions of h5sparse_ by `Appier Inc.`_.
See the copyright and license note in this directory source code.
.. _h5sparse: https://github.com/appier/h5sparse
.. _Appier Inc.: https://www.appier.com/
"""
# TODO:
# - think about s... |
e2b4eb4c227488fe09c6b4e02723b4f0b3495679b412df2d34520b21dd521e28 | Python | 26,878 | 679 | import json
from collections.abc import MutableMapping
from copy import deepcopy
from typing import (
Any,
cast,
Dict,
List,
Optional,
Tuple,
Union,
)
import packaging.version
from pydantic import TypeAdapter
from galaxy.tool_util.deps import requirements
from galaxy.tool_util.parameters.c... |
d3abca25c9e47982dc7c5b2f87a316041f9c894ea9062ffaa81afe6c8a0c9c2c | Python | 26,882 | 539 | import time
import os
import numpy as np
from cellpose import io, utils, models, dynamics
from cellpose.transforms import normalize_img, random_rotate_and_resize
from pathlib import Path
import torch
from torch import nn
from tqdm import trange
import logging
train_logger = logging.getLogger(__name__)
def _loss_fn_c... |
c12f62d3eb1bf1915829c2aaf801244553804c91f1f4b22ca3c8e97ed1e7b215 | Python | 26,921 | 718 | # Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from collections.abc import Callable
from unittest.mock import patch
import pandas as pd
from ax.adapter.registry import Gen... |
6084b4651841b8fac1bdfd7d24b0e70112c9e15c95483c5e16d67d746e5173a5 | Python | 26,928 | 689 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
25d27dced472e0773e6f9f954bbe31de752d744215aff381bccb086fc3b6b237 | Python | 26,964 | 788 | # -*- coding: utf-8 -*-
#
# Copyright (C) 2012 The Python Software Foundation.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
"""Access to Python's configuration information."""
import codecs
import os
import re
import sys
from os.path import pardir, realpath
try:
import configparser
except ImportError:
import Conf... |
9a7a42ca9802668c3ad0776cf3a28d9bba11f000aa442ad6395a789d472144ae | Python | 26,967 | 776 | 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
import torch.nn as nn
from torch.autograd import Variable
import numpy as np
import scipy.linalg as slin
import scipy.sparse as sp
import networkx as nx
import panda... |
692918da2bd066b23e355b0616ac3935d52d1ec9b67d8e59caccb98c7b5ecbd1 | Python | 26,972 | 677 | from __future__ import annotations
import copy
import functools
import inspect
from typing import Callable
import torch
from .. import base
from spikingjelly.logger import logger
__all__ = ["FlexSN"]
def _as_tuple(value) -> tuple:
return (value,) if isinstance(value, torch.Tensor) else tuple(value)
def _con... |
7d038081131d0b64878b58549e866e9109df70d92ec74507ce81ce6329125b6d | Python | 26,993 | 645 | from cogdl.datasets.grb_data import Cora_GRBDataset
from attack.modification import *
from attack.injection import *
from attack.modification import RAND as RAND_Modify
from attack.injection import RAND as RAND_Inject
from attack.modification import PGD as PGD_Modify
from attack.injection import PGD as PGD_Inject
from ... |
ea8cb78a5373c1fb813d548343242b4f3ddddcb025e83c04e05c343cd751f743 | Python | 27,019 | 819 | import pathlib
import subprocess
import numpy as np
import pandas as pd
import pyBigWig
import xarray as xr
from numba import njit
from ALLCools.utilities import parse_mc_pattern
def _mvalue(mc, cov, alpha=0.1):
m = np.log2((mc + alpha) / (cov - mc + alpha))
return m
def _frac(mc, cov, alpha=0.001):
f... |
f7abb1e853402113ac17dec4998a2d39bd07f3a9c85b763e8b0a3bdfb3052110 | Python | 27,020 | 519 | # -*- coding: utf-8 -*-
import os
import click
import random
import logging
import pandas as pd
import numpy as np
from datetime import datetime, timedelta
from tqdm import tqdm
from itertools import chain
from definitions import DATA_DIR, ROOT_DIR
from src.omni.functions import save_pickle, load_pickle, save_list2csv... |
8540c30c813f28d10a6bcb8452d942b8948a45688c51489b03c21eb79851b6a7 | Python | 27,031 | 524 | import itertools
import numpy as np
import pandas as pd
pd.set_option("compute.use_numexpr", False)
import tenkit.stats as tk_stats
import sys
import cellranger.analysis.diffexp as cr_diffexp
import cellranger.library_constants as lib_constants
import os
import cellranger.io as cr_io
import collections
DIFFERENTIAL_EX... |
285d2510d0f482184b0b2f8fcca0ee53e383d5a3b38a14d4ff32c71ebc260e8b | Python | 27,043 | 580 | """Consolidated model quality-control checks for Human-GEM.
A single entry point for the structural checks. Each check writes a detailed,
diff-friendly CSV under data/testResults/ so that whatever is wrong is spelled
out in a committed file (not only in the workflow log), and buildReport.py turns
the same files into t... |
ae4c5ae9fbe5de68ae2f34a2e80a54e3c3e0e6445b7357769140028459c19e5b | Python | 27,060 | 610 | """
Actions to be run at job completion (or output hda creation, as in the case of
immediate_actions listed below.
"""
import datetime
from markupsafe import escape
from galaxy.model import PostJobActionAssociation
from galaxy.util import send_mail
from galaxy.util.custom_logging import get_logger
log = get_logger(... |
25589e4024394bfe5dc9b3f23eca34ef324e8203dec0e82efb51792c91982b24 | Python | 27,075 | 645 | """
Copyright © 2025 Howard Hughes Medical Institute, Authored by Carsen Stringer, Michael Rariden and Marius Pachitariu.
"""
import sys, pathlib, warnings
from qtpy import QtGui, QtCore
from qtpy.QtWidgets import QApplication, QScrollBar, QCheckBox, QLabel, QLineEdit
import pyqtgraph as pg
import numpy as np
from s... |
13c0814173b9c111de18533bb5b1ded88b37c072ee0eab01e95b44f947704f5e | Python | 27,087 | 781 | from __future__ import annotations
import copy
import warnings
from dataclasses import dataclass, field
from math import ceil, isfinite, prod
from numbers import Real
from typing import Any
import torch
import torch.nn as nn
from ..neuron.base_node import BaseNode
from ..neuron.integrate_and_fire import IFNode
from ... |
d282059cd452310f5f04ed6b0f009f65b5376c7f12b4d556616212e2d1a6f12e | Python | 27,108 | 841 | # -*- coding: utf-8 -*-
# Imports
import pandas as pd
import numpy as np
from scipy.stats import norm
import math
from random import sample as random_sample
from .pd_utils import to_torch, join_to_df, argmax, complement, sample, torch_to_numpy
# Main acquisition class
class acquisition:
"""Class represents the... |
c2815e12b62ffcb15776739f728ac691799d8f5ab9daf4857d93b0a68f8fa52b | Python | 27,121 | 688 | """
Flow based cut algorithms
"""
import itertools
import networkx as nx
from networkx.algorithms.approximation.connectivity import (
local_node_connectivity as approx_local_node_connectivity,
)
# Define the default maximum flow function to use in all flow based
# cut algorithms.
from networkx.algorithms.flow im... |
36610875fdbb75c95c60114a95fbacba9add89401dc261db218f05bd2464bef6 | Python | 27,126 | 603 | # Copyright (c) MONAI Consortium
# 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 in writing, so... |
7fb6f44da49cb1fc0dee1abc9df4a5b19c4ce2965ed1ef61a5409315e7790fdd | Python | 27,132 | 791 | from collections.abc import Mapping
from copy import deepcopy
from functools import partial
from random import choices
from string import ascii_lowercase
from anndata import AnnData
from anndata.experimental import AnnCollection
import numpy as np
import pandas as pd
import synthetic_spatial_datagen
import xarray as xr... |
2267c7c0a1370d1f3868305938517daef312cd393d96c6ecec7ad77683d13d65 | Python | 27,145 | 915 | import abc
import builtins
import inspect
import math
from weakref import WeakKeyDictionary
import numpy as np
from packaging.requirements import Requirement
from ..exceptions import (
CastError,
ClassMapMissingError,
InvalidReferenceError,
NoneReferenceError,
RequirementError,
TypeHandlingErr... |
02d3f0ddaa25197957852947088afabdf19ad0c8affd4bf65377e6f993ed1797 | Python | 27,150 | 797 | # -*- coding: utf-8 -*-
"""
Created on Tue Feb 22 17:09:31 2022
@author: marcomau
"""
import os
import numpy as np
import torch
import torch.nn.functional as F
from torch_geometric.data import Data
import model_RGNN_evolution1 as model
from utils_RGNN_evolution1 import*
from sklearn.preprocessing import S... |
1652371f8f11022eb39233be2a1dc15b4a8b9440c40e5264237a52be62c12002 | Python | 27,152 | 981 | import argparse
import textwrap
def fancplot_parser():
usage = '''fancplot [<fancplot global parameters>] <region> [<region> ...]
--plot <plot type> [<plot parameters>] <plot data file(s)> [...]
Run fancplot --plot <plot type> -h for help on a specific subplot.\n\nPlot types:\n\n'''
... |
ea618efcd87becaa1f36ba3ed55c51b7cb423a24f8b48270fb3926ae98260165 | Python | 27,166 | 535 | import errno
import logging
from typing import (
Any,
)
from galaxy.exceptions import RequestParameterInvalidException
from galaxy.tool_shed.galaxy_install.client import InstallationTarget
from galaxy.tool_shed.util.basic_util import strip_path
from galaxy.tool_shed.util.repository_util import get_repository_owner... |
56ce77f8ac0e1f758a0bece88ad2ee1ef66a4dc599b22dd566b82921729e4e1f | Python | 27,189 | 807 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# ex: set sts=4 ts=4 sw=4 et:
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See the COPYING file distributed along with the smile package for the
# copyright and license terms.
#
# ## ### ### ### ### ### ... |
3c0e13f8ca045677f2d7ae344412a0b7f3534f755d3505bf8ff60cf35cb7a02f | Python | 27,192 | 677 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from __future__ import annotations
import itertools
import warnings
from collections.abc import Calla... |
dc39e4ca1ed3bfd6365b35089b2f982d3c18344a263d6789e8824baad2b3d62a | Python | 27,203 | 548 | import numpy as np
import torch
import torch.nn as nn
import random
import scipy
import time
import matplotlib.pyplot as plt
import seaborn as sns
from scipy.stats import norm
from datasets import load_aux_patterns
def set_seed(manualSeed):
np.random.seed(manualSeed)
random.seed(manualSeed)
... |
36ff236ca5dc5d7a7ae61f1096856539c77b6bd8e6163cf7bc3152a3f980e70e | Python | 27,257 | 810 | # -*- coding: utf-8 -*-
"""
BlockProcessing
===============
Module to process data in parallel for large data sets
This strategy allows memory intensive processing of larger data sets.
Example
-------
>>> import numpy as np
>>> import ClearMap.IO.IO as io
>>> import ClearMap.ParallelProcessing.BlockProcessing as bp... |
91633735860745002d8411021434c75e10b2d104086a3e654a4d13fce8282d05 | Python | 27,281 | 692 | """Helper class for making and retrying requests to the MIBItracker.
Copyright (C) 2021 Ionpath, Inc. All rights reserved."""
import datetime
import io
import json
import os
import warnings
import requests
from requests.adapters import HTTPAdapter
from requests.exceptions import HTTPError
from skimage import io as ... |
1ab8fd62c27079641333ceb062be8c48f220ba469bca70292c9bdbcf94bd0a02 | Python | 27,291 | 955 | from __future__ import absolute_import, division
import copy
import numbers
import numpy as np
import zarr
import h5py
import json
import logging
logger = logging.getLogger(__name__)
class Freezable(object):
__isfrozen = False
def __setattr__(self, key, value):
if self.__isfrozen and not hasattr(... |
2cfa516236049811fd5a0c2b4f7e1b1eb6559be46910c4bd36bdd007c76b826c | Python | 27,292 | 521 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thur August 30 2018
@author: chrisarcadia
@description: script to review a composite library sourceplatesheet and to optionally
generate a mass list and Echo recipe for that library
Composite Library Style #1
... |
7ba32942452e555570f4d0e7682e45be232e17e2b19f2f678ef9f376d016a9ef | Python | 27,309 | 756 | """
The LLM query assistant in the REPL: ``.ask`` and ``.llm``.
``.ask <question>`` turns the question into a query of the session's
language with an LLM (see :mod:`neurolang_apps.utils.llm`), printing the
steps of the agent as they run. The query is not run: it is put in the
next prompt, to be read, edited and run wi... |
11a85b03d8bd8089942bfc88d7b07b75df75d3786806c04a04ff409b53a75c00 | Python | 27,320 | 570 | # Copyright 2019, Mukesh Mithrakumar. All Rights Reserved.
#
# 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... |
5551ab8d5e413ad348637dab4fb1f549e67be763141e8655e9a3e8b42ad88e8b | Python | 27,381 | 638 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from __future__ import annotations
from collections.abc import Mapping
from itertools import groupby
... |
c666d9fdf359135bddc60e2f71a58c48628e976cd012c5f11f1ca2811cd6e5bc | Python | 27,381 | 753 | #!/usr/bin/env python
"""Build a mulled image for specified conda targets.
Examples
Build a mulled image with:
mulled-build build 'samtools=1.3.1--4,bedtools=2.22'
"""
import json
import logging
import os
import platform as _platform_module
import shutil
import stat
import string
import subprocess
import sys
f... |
b1687b8848095fb531ae52f00718c71a08f5403bfa9e282f5c98c85ba730c7e6 | Python | 27,399 | 682 | import bisect
import os
import pathlib
import warnings
from abc import ABC, abstractmethod
from itertools import combinations
from typing import List, Literal, Protocol, runtime_checkable
import natsort as ns
import feather
import numpy as np
import pandas as pd
from alpineer.io_utils import list_files, validate_paths
... |
fc6f1c67e6188ab2e2fd9f83328638d158b26cd521289668c86f8483dd476e53 | Python | 27,432 | 688 | """Tests for MSA to HMM conversion functionality."""
import os
import numpy as np
import pytest
from learnMSA.hmm.util.transition_index_set import PHMMTransitionIndexSet
from learnMSA.hmm.util.value_set import PHMMValueSet
from learnMSA.util.aligned_dataset import AlignedDataset
def test_msa_to_counts() -> None:
... |
a5c08ba2692ad778e60e7e13dfa91cfb243ab66f4bad1b5905a829b7972b95a0 | Python | 27,434 | 682 | """Client-centric CWL-related utilities.
Used to share code between the Galaxy test framework
and other Galaxy CWL clients (e.g. Planemo)."""
import abc
import hashlib
import io
import json
import os
import tarfile
import tempfile
import urllib.parse
from collections import namedtuple
from typing import (
Any,
... |
5e5c5a2541c5f4c24dd48a3accda9be5cb80086766e71d9640668a513f2a4da1 | Python | 27,494 | 905 | r"""
Query Resolution Expression
===========================
Declares FrontEnd Expression class and subclasses.
Those classes are used to build Datalog programs
in an ergonomic manner, and attention is paid to their representation
"""
import operator as op
from functools import wraps
from types import BuiltinFunctionTy... |
b98d745fb5edd0fdc253677e71a5959e129599fdf8d66f3b1820f1407fb0cbb6 | Python | 27,530 | 621 | # -*- coding: utf-8 -*-
"""
Functions for generating workflow methods reports
Note: all text contained within this module is released under a `CC-0 license
<https://creativecommons.org/publicdomain/zero/1.0/>`_.
"""
import logging
import numpy as np
from . import __version__
from .datasets import check_donors, fetc... |
ee4556069b260ea619035a1e5362ec1c581db4f73c97ed1c5dc79b43ef3e39a5 | Python | 27,530 | 818 | """Functions for finding and manipulating cliques.
Finding the largest clique in a graph is NP-complete problem, so most of
these algorithms have an exponential running time; for more information,
see the `Wikipedia article on the clique problem <clique_wiki_>`_.
.. _clique_wiki: https://en.wikipedia.org/wiki/Clique_... |
455816c8f69542e4678de11ab042d9bac7f7f05eb504ac382e1861ba7fd21c4a | Python | 27,534 | 723 | # -*- coding: utf8 -*-
"""
All loaders for mice datasets.
"""
__all__ = [
'load_meta_blood',
'load_full_meta',
'sanity_check',
'filter_CBC_dataset',
'load_lifespan_itp'
]
import os
import glob
import pandas as pd
import numpy as np
_GLOBAl_DIR_PATH = os.path.dirname(__file__) + '/raw'
_GLOBAl_DATA... |
33b90af66b5e437d618f44c0eeb5fd828b931182d82032e799e31adddc3b408e | Python | 27,540 | 558 | for key in list(globals().keys()):
if (not key.startswith("__")) and (key != "key"):
globals().pop(key)
del key
from typing import Any, Iterable, Mapping, Sequence, Tuple, Union
import anndata
import numpy as np
import logging
from scipy.sparse import spmatrix
from rpy2 import robjects
from joblib import Paralle... |
3719d0db08c77ed64f4446e88e3d8984fc52f7708571ea32ab0e7257e0bba153 | Python | 27,545 | 724 | # -*- coding: utf8 -*-
"""
All loaders for mice datasets.
"""
__all__ = [
'load_meta_blood',
'load_full_meta',
'sanity_check',
'filter_CBC_dataset',
'load_lifespan_itp',
'fill_wbc_counts'
]
import os
import glob
import pandas as pd
import numpy as np
_GLOBAl_DIR_PATH = os.path.dirname(__file__... |
c5d0a56123b94c173668c47ebe75e2be9ff857ab0d0bf1622521f43df61ce5de | Python | 27,612 | 739 | """Provides functions for computing minors of a graph."""
from itertools import chain, combinations, permutations, product
import networkx as nx
from networkx import density
from networkx.utils import arbitrary_element
__all__ = [
"contracted_edge",
"contracted_nodes",
"equivalence_classes",
"identif... |
677d7acdb936ab17a8b33302ef25a2081b17774e86bddec968341db970dc4b64 | Python | 27,635 | 943 | # encoding: utf-8
"""
NRRD
====
IO interface to NRRD volumetric image data files.
Note
----
The interface is based on nrrd.py for reading and writing nrrd files.
See 'this link <http://teem.sourceforge.net/nrrd/format.html>`_ for
specifications.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.co... |
026983d450d76697f77889b50bdbc15dba688bee26b5297300c2297365c1a6c3 | Python | 27,646 | 501 | """Functions that either provide an instruction flow or a string to display."""
import os
import os.path as op
import numpy as np
import pandas as pd
import sp_experiment
from sp_experiment.utils import get_final_choice_outcomes
from sp_experiment.define_settings import (txt_color,
... |
7248edf96a89b13634bbdb36a03ef03d1490067c10fe6fa281e93a99a68f103b | Python | 27,710 | 667 | # Copyright 2020 DeepMind Technologies Limited.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed... |
04b24f44c92ea77865fdeff50b48486879bc7d716679e72f8b28bde7ee60e382 | Python | 27,723 | 754 | import functools
import hashlib
import json
import logging
import os
import platform
import re
import shutil
import sys
import tempfile
from typing import (
Any,
Callable,
Dict,
Iterable,
Iterator,
List,
Optional,
Tuple,
TYPE_CHECKING,
Union,
)
from packaging.version import Vers... |
d2e517dcca816420f7570ed9e200db8e6961b49b5db1e10a3589c06d2b843ef5 | Python | 27,765 | 634 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jun 17 14:32:49 2022
@author: akshay
"""
from dash import dcc,html,dash_table
import dash_bootstrap_components as dbc
from app import app
from dash.dependencies import Input, Output,State
import dash_uploader as du
import dash
from plots import *
from b... |
8a97d69c6c57be063999c3b3a28c90942dadca16bca9103db273d30cf9d32618 | Python | 27,783 | 551 | from itertools import combinations
from itertools import chain
import numpy as np
import pandas as pd
import numpy as np
from collections import defaultdict
from itertools import combinations
from itertools import chain
import itertools
import pickle
from feature import *
import os
import warnings
def us... |
aaee48e45294d2831031c9eebb338172e5494c1b8e01cbb9bcb74eeb02e4a0f0 | Python | 27,837 | 621 | import copy
import warnings
from typing import List
import re
import numpy as np
import pandas as pd
import xarray as xr
from alpineer import io_utils, load_utils, misc_utils
from skimage.measure import regionprops, regionprops_table
import ark.settings as settings
from ark.segmentation import segmentation_utils
from... |
87a3dedae620096def47b71c3d13e267dd124041a5de891f90b518e762c0e515 | Python | 27,845 | 695 | import sys
from collections.abc import Sequence
if sys.version_info >= (3, 12):
from typing import override
else:
from typing_extensions import override
import numpy as np
import tensorflow as tf
from hidten.hmm import HMMConfig
from hidten.tf.util import T_initializer, setup_initializer
from hidten.tf.emitte... |
2cee60a031a2bfe1e883e8170ef6eb4bd756527a4514c2bfeaeff8c966af7a28 | Python | 27,857 | 794 | import jax
import jax.numpy as jnp
import numpy as np
from functools import partial
import pyqmc.wftools
from typing import NamedTuple
class BasisParameters(NamedTuple):
"""
These are parameters for the basis functions (polypade and cusp).
"""
beta_a: float
beta_b: float
ion_cusp: list
rc... |
79eb3eac0f1b94be618b45c09af034483e8274e0e0067912c912cc4e8565f88d | Python | 27,871 | 792 | import os
from shutil import copyfile
import sys
import logging
import argparse
import json
import re
import yaml
import numpy as np
import torch
import tensorboardX
import gunpowder as gp
import incasem as fos
SCRIPT_DIR = os.path.dirname(__file__)
REPO_ROOT = os.path.abspath(os.path.join(SCRIPT_DI... |
71ac3b79df80669718377c52da7cd0e2cd6eb1a30b9bd83884a92d5612467f0a | Python | 27,881 | 1,032 | # -*- coding: utf-8 -*-
"""
IO
==
IO interface to read files as sources.
This is the main module to distribute the reading and writing of
individual data formats to the specialized sub-modules.
See :mod:`ClearMap.IO` for details.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__ =... |
dc9537ea2b36c290bca7794ba688918048479885c2c9f7e284b9cf49f3c1815c | Python | 27,921 | 549 | # -*- coding: utf-8 -*-
import pandas as pd
import os
import copy
import numpy as np
import time
import re
from skimage import io
from scipy import ndimage
from scipy.ndimage import morphology
from matplotlib import pyplot as plt
input_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
... |
68226cf15e4f1619048dbd4b92a30b2e7e821002a05c1b2adf6b0cfb54165b36 | Python | 27,927 | 699 | r"""
*****
LaTeX
*****
Export NetworkX graphs in LaTeX format using the TikZ library within TeX/LaTeX.
Usually, you will want the drawing to appear in a figure environment so
you use ``to_latex(G, caption="A caption")``. If you want the raw
drawing commands without a figure environment use :func:`to_latex_raw`.
And if... |
6c07ec270608ca6bc95db69232e3f09c3d7502c67bb60bd34f2791c6e2a83704 | Python | 27,943 | 844 | # -*- coding: utf-8 -*-
"""
Interface to Elastix for alignment of volumetric data
The elastix documentation can be found `here <http://elastix.isi.uu.nl/>`_.
In essence, a transformation :math:`T(x)` is sought so that for a fixed image
:math:`F(x)` and a moving image :math:`M(x)`:
.. math::
F(x) = M(T(x))
Once... |
d3d2d399e3a38dead59f23279000256e7fb0298091aa81cd80134ce20739e9b4 | Python | 27,943 | 706 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
bf4061900adae4cbe56dcee64a43888d4a73a41f25f9e5fc059127ffa2a76e96 | Python | 27,951 | 532 | import unittest
import pysnirf2
from pysnirf2 import Snirf, validateSnirf
import h5py
import os
import sys
import time
from numbers import Number
from collections import deque
from collections.abc import Set, Mapping
import numpy as np
import shutil
VERBOSE = True # Additional print statements in each test
# Need to... |
06a0f575694c4370fb3a6c7e63e99b8e78fff959f50a3301758b8bb1141395de | Python | 27,975 | 846 | """
CLI defined here
When adding new function:
1. add a func_register_subparser function to register the subparser
2. add a condition in main func about this new func name, import the real func as func in main
"""
import argparse
import inspect
import logging
import os
import subprocess
import sys
import ALLCools
f... |
bce9b475da1a2913a27cb6fad55aece0bc27ac3510b981122e859e390f32cf82 | Python | 27,976 | 680 | #Contains MeldCohort and MeldSubject classes
from contextlib import contextmanager
from meld_classifier.paths import (
DEMOGRAPHIC_FEATURES_FILE,
CORTEX_LABEL_FILE,
SURFACE_FILE,
DEFAULT_HDF5_FILE_ROOT,
NVERT,
BASE_PATH,
MELD_PARAMS_PATH
)
import pandas as pd
import numpy as np
import nibab... |
4aa3b01a53714a1d14d6dbfbf1a749a63441fe2b2c417e1ac8d7d3c73fcf54f9 | Python | 28,018 | 582 | # -*- coding: utf-8 -*-
import numpy as np
import pandas as pd
import os
import copy
import seaborn as sb
from matplotlib import pyplot as plt
from scipy.signal import argrelextrema
from scipy import stats
from scipy.stats import linregress
def smoothen(row,new_growth_data,radius,column):
#calculat... |
1777b957771fc272276582f56903a3e3baed02c15316a6a4e044dd7272b90e41 | Python | 28,075 | 726 | '''
'''
#
# Adapted from MATLAB code written by S. Nishimoto (see Nishimoto, et al., 2011).
# Anwar O. Nunez-Elizalde (Jan, 2016)
#
# Updates:
# Anwar O. Nunez-Elizalde (Apr, 2020)
#
#
# Implementation notes:
#
# The terminology here is "pyramid" and "filters".
# In moten.core, the termilogy is inconsistent.
#
# TODO:... |
3c018694d76ee1917ff0b9bf7e7352af97ae082fd5708bd2c9c8ddff7c654071 | Python | 28,075 | 576 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
import logging
from math import ceil
from typing import Any
import torch
from ax.adapter.registry imp... |
59f75e2b36e8136e7c22d987f777eb24d9e003d1a449932de103df0a5eaa8129 | Python | 28,089 | 680 | """This module contains a linting functions for tool tests."""
from io import StringIO
from typing import (
Iterator,
List,
Set,
Tuple,
TYPE_CHECKING,
)
from packaging.version import Version
from galaxy.tool_util.lint import Linter
from galaxy.tool_util.parameters import validate_test_cases_for_t... |
e6e798113b224856b2669a0e4d153d02acb2173582801d3bed92e8a3daaa1034 | Python | 28,106 | 705 | import cv2
import numpy as np
import xlrd
import random
import os
# tolist
def get_data():
# 此函数读取datasets文件夹下的图片，并和excel表格的标签一一对应
# 返回数据与标签，单个数据为1维向量形式，非图片的矩阵形式
data = []
label = []
# 先得到标签集
workbook = xlrd.open_workbook('weight.xls')
Data_sheet = workbook.sheets()[0]
rowNum = Data_she... |
2e13ba41046137298063f3bef20514a88732c2dadff61b37c93aa24f97d6a0c9 | Python | 28,116 | 755 | from ...simulation import (
SimulatorAdapter,
SimulationComponent,
SimulationCell,
TargetsNeurons,
TargetsSections,
SimulationResult,
SimulationRecorder,
SimulationDevice,
)
from ...helpers import get_configurable_class
from ...reporting import report, warn
from ...models import Connecti... |
86085ef265a3f283508b1a2bf474f0ac905e9c3dac727808b461e3064632f30a | Python | 28,158 | 674 | import abc
import builtins
import os
from datetime import (
datetime,
timezone,
)
from enum import Enum
from typing import (
Any,
ClassVar,
Generic,
Optional,
TYPE_CHECKING,
)
from galaxy.exceptions import (
ConfigurationError,
ItemAccessibilityException,
RequestParameterInvalid... |
d4d5eef9c22338c21f3d03f3170aa75b03e1ecccf608335bc9a847754b853135 | Python | 28,163 | 721 | """
Created on Dec 29, 2020.
This module provides different functions to estimate sfc between two signals from the time domain.
@author: voodoocode
"""
import numpy as np
import scipy.signal
def dac_td(data_1, data_2, f_min, f_max, fs, nperseg, nfft, return_signed_conn = True, minimal_angle_thresh = 10, volume_con... |
925163bbc3a42738ba6cebe13ffe2aca7187c553068fd3973776cd19289f5f9d | Python | 28,217 | 782 | from pathlib import Path
import sys
from learnMSA.run.args import parse_args
from learnMSA.run.args_to_config import args_to_config
class TestArgsToConfig:
"""Tests for converting argparse Namespace to Configuration."""
def test_args_to_config_with_minimal_args(self):
"""Test conversion with only re... |
19c324d6d3d6c97314976d5f1a0a0241ff1dd1626648f9c7f606163d32a7d90c | Python | 28,354 | 714 | from __future__ import division
from fanc.config import config
from fanc.regions import RegionsTable, GenomicRegion
from fanc.matrix import RegionMatrixTable
from fanc.legacy.architecture.architecture import ArchitecturalFeature, calculateondemand, \
_get_pytables_data_type
from fanc.general import MaskFilter
from ... |
a31c19e4c62b37d9715b8f4abf4458ce799064e55636637135f171bc99cc9916 | Python | 28,374 | 681 | # Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
import copy
import math
from typing import cast
from unittest.mock import patch
import torch
from ax.adapter.base import Ad... |
f416b67399751436ffa2333405e9e984a91d5fad4860c206dc44214c3d58de46 | Python | 28,393 | 717 | import time
from collections import deque
from itertools import chain
import numpy as np
import torch
import sys
import os
import copy
from scipy import stats
import torch.nn as nn
from src.utils import get_argparser
from src.encoders_ICA import NatureCNN
import pandas as pd
import datetime
from src.lstm_attn import s... |
93e3985e68eb64074fac3b813a5c76d2d4662c7005d10d40d86562faac7884f3 | Python | 28,428 | 1,212 | """
adapted from
https://github.com/lab-cosmo/sphericart/blob/main/sphericart/include/macros.hpp
https://doi.org/10.1063/5.0156307
Filippo Bigi Guillaume Fraux Nicholas J. Browning Michele Ceriotti
J. Chem. Phys. 159, 064802 (2023)
Hard-coded expressions for low-l Cartesian spherical harmonics and their
deriva... |
567dd49e86622d91648780594f23e74917285d6eb37f8cf8683d8aee3625cdcf | Python | 28,454 | 711 | import os
import tempfile
from shutil import rmtree
import feather
import numpy as np
import pandas as pd
import pytest
import skimage.io as io
from alpineer import image_utils, io_utils, load_utils, misc_utils, test_utils
from pytest_cases import parametrize_with_cases
# import ark.phenotyping.pixie_preprocessing as... |
d19b2cc11dcdf1cbc6e55f79f18b7abf0edb991f3eaa2fc4cb38764b2029fa36 | Python | 28,507 | 540 | """Class for the network model and for the input tuning functions. Assumes D=2 spatial dims."""
import numpy as np
from . import log, asciiL
from functools import lru_cache
from . import FilterStrinfAdiabaticDiagonalSigma
from . import LinearPopulationCode, OneToOnePopulationCode, LinearInputPopulationCode
from scip... |
54c95fa389e43f75e6dddf91b1bbb690e04976ac9d890d268fd0200528f2e0bb | Python | 28,513 | 535 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on July 27, 2020
@author: chris3arcadia
@description: script to review a composite library sourceplatesheet and to optionally
generate a mass list and Echo recipe for that library
Composite Library Style #4... |
7a4e7507468d0a750dd14b0650c23b8c3ec645e76f412ebd2734788d86297418 | Python | 28,585 | 814 | import argparse
from contextlib import contextmanager
import json
import time
from dataclasses import asdict, dataclass
from pathlib import Path
from typing import Any, Iterator
import torch
import torch.nn as torch_nn
import torch.nn.functional as F
if __package__:
from .fp8_coverage import _FP8CoverageTracker
e... |
7bb5b893b0b8e218a2797a32ba2ee81afbc55a03edceb9e7e4fec273d027e964 | Python | 28,585 | 758 | # Copyright (c) MONAI Consortium
# 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 in writing, so... |
9f818a7cfabea5e6dbb05143727568c0af4592fb557283d0bdb5dcf59a2a21a8 | Python | 28,669 | 653 | """
Tool recommendation agent for suggesting appropriate Galaxy tools.
Despite the historical name, this agent recommends both atomic Galaxy tools
and end-to-end IWC workflows. Atomic asks ("which tool sorts a BAM?") still
get a tool back; analysis-shaped asks ("RNA-seq from FASTQ to differential
expression") get a wo... |
c57e16a12271cdeccffdbc2ba41477ef8c6c951c37ed541463e26fba64cea7dd | Python | 28,686 | 532 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on July 27, 2020
@author: chris3arcadia
@description: script to review a composite library sourceplatesheet and to optionally
generate a mass list and Echo recipe for that library
Composite Library Style #5... |
a75661f00c0a475ab9dd91058d1dfab518d3bb4faefc0f93d06f33a2274368ef | Python | 28,702 | 907 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
GraphProcessing
===============
Module providing tools to create and manipulate graphs. Functions include graph
construction from skeletons, simplification, reduction and clean-up of graphs.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__licens... |
11d4306445b693abd14db91232d8c6f63a51ec0bb6901ec7c10e0177a81e9872 | Python | 28,762 | 531 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thur August 30 2018
@author: chrisarcadia
@description: script to review a composite library sourceplatesheet and to optionally
generate a mass list and Echo recipe for that library
Composite Library Style #3
... |
3fcb96a69faf6c1ef1de710fab3b4120e6c88de79ede2b0102dc5b9483a63694 | Python | 28,767 | 728 | """Plot the correlation analysis results.
Parameters
----------
project_dir : str
Directory of the project folder.
"""
import argparse
import os
import numpy as np
import matplotlib
from matplotlib import pyplot as plt
# =============================================================================
# Input argumen... |
c11019a45f9fdfb1592d06deffac0b88e6e2f29f766d3f9ad2654dbeceaad4c4 | Python | 28,836 | 633 | import random as rd
import unittest as ut
import networkx as nx
import numpy as np
from pysbm import sbm
class TestSBMInference(ut.TestCase):
""" Test Class for SBMInference and subclasses """
# noinspection PyPep8Naming
def __init__(self, methodName='runTest'):
super(TestSBMInference, self).__... |
eade76393adc1072e4aa90c3fdd39b32142fbdf0c4f485b3f9b6f12332dfc6fe | Python | 28,842 | 752 | from __future__ import division
import tables
import logging
import operator
from collections import defaultdict
from genomic_regions import GenomicRegion, as_region
from future.utils import string_types
from ..tools.general import RareUpdateProgressBar
from ..regions import RegionsTable
from ..matrix import RegionMa... |
318e4b44c2377ec6b4c2dc9fe71f2d819d05e238fabd7adc233d53f55f6b61f5 | Python | 28,930 | 681 | import sys
import copy
from PyQt5 import QtGui
from PyQt5 import QtCore
from PyQt5 import QtWidgets
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt5agg import \
NavigationToolbar2QT as NavigationToolbar
from matplotlib.figure import Figu... |
e03a2081a068606d9b805f6b1027167f1608244ae3c3c5749175c09ca69106c6 | Python | 28,932 | 763 | import os
import glob
import click
import pandas
import nibabel as nib
import json
import numpy
import gc
import psutil
import re
from pkg_resources import resource_filename
from .postprocutils.utils import (
get_scrub_vector,
calc_filter,
apply_filter,
regress,
scrub_data,
notch_filter,
)
fro... |
36c9e49f6f1b232c736e2da4002f86c38d28a6a650848b95321fc679af4046df | Python | 28,933 | 763 | import os
import glob
import click
import pandas
import nibabel as nib
import json
import numpy
import gc
import psutil
import re
from pkg_resources import resource_filename
from .postprocutils.utils import (
get_scrub_vector,
calc_filter,
apply_filter,
regress,
scrub_data,
notch_filter,
)
fro... |
e5ac77255406c3bfe914c14d29657d9b7923d79313bb846aaadaffab78378ba8 | Python | 28,965 | 774 | from spikingjelly.logger import logger
from typing import Callable, Optional, Tuple
import os
from pathlib import Path
import multiprocessing
from concurrent.futures import ThreadPoolExecutor
from functools import partial
import math
import h5py
import numpy as np
from torchvision.datasets.utils import extract_archive... |
670641030f2e23498566449400d72f6a23526ca175ab40908b3f82c931a5e100 | Python | 28,971 | 526 |
import os
import json
import numpy as np
import pandas as pd
from rdkit import Chem
from pathlib import Path
from sklearn.model_selection import train_test_split, StratifiedKFold, KFold
from MolRep.Evaluations.data_split import scaffold_split, defined_split
from MolRep.Featurization.Graph_embeddings import GraphEmb... |
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