sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
37ffa35cb8dd2c1cc3e38a15693d8d1d214bac7f656a0630dc841b3778dd8850 | Python | 11,308 | 302 | # -*- coding: utf-8 -*-
"""
Created on Mon Dec 2 14:28:44 2019
@author: aaussel
"""
from brian2 import *
from scipy import signal
from cells.RS_FEF import *
from cells.FS_FEF_alt import *
from cells.SI_FEF import *
from cells.VIP_FEF import *
def generate_deepSI_and_gran_layers(theta_phase,N_SI,N_RS_gran,N_SI_gran... |
329beffb1af46c33d74b227ee7aa0c5db3528e41530e065d39af8a5772420f31 | Python | 11,315 | 302 | # -*- coding: utf-8 -*-
"""
Created on Mon Dec 2 14:28:44 2019
@author: aaussel
"""
from brian2 import *
from scipy import signal
from cells.RS_FEF import *
from cells.FS_FEF import *
from cells.SI_FEF import *
from cells.VIP_FEF import *
def generate_deepSI_and_gran_layers(theta_phase,N_SI,N_RS_gran,N_SI_gran,t_S... |
a2aaa37e01d5736a7ec51e316a94ef75e061d5bc298ca580fd6a99292460f0cb | Python | 11,316 | 296 | #!/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 unittest.mock import patch
from ax.core.base_trial import BaseTrial, TrialStatus
from ax.core.mu... |
edb40d9313c1baa6252b6be6c2ccdff0d187b40de113662f840613d5c22ef2d9 | Python | 11,318 | 364 | import subprocess
import numpy as np
import pandas as pd
import pysam
from ALLCools.utilities import parse_chrom_size, reverse_complement
from ._doc import *
def mode_mc_cov(table, mc, cov):
mc = table[mc].astype(int)
cov = table[cov].astype(int)
frac = np.round(mc / cov).astype(int)
values = pd.Da... |
4d98551c210223568f25eaf41f64f96853c362df2be2eb859ce7ddff1018e6fd | Python | 11,319 | 309 | # import libraries
import sys
sys.path.append('..')
import os
import torch
import torch.nn as nn
import numpy as np
import torchvision
from torchvision import transforms
import matplotlib.pyplot as plt
import time
import argparse
import copy
import json
from torch.utils.data import DataLoader
from utils.data_utils imp... |
fd0f49ef8d78fce73938ec12c651d9b605bcbcb6c7e9acb4f7e4cccab2aae3cd | Python | 11,322 | 311 | '''Compute total motion energy from greyscale videos.
'''
import numpy as np
from moten.utils import (iterator_func,
pointwise_square,
)
# Make tqdm optional
with_tqdm = True
try:
from tqdm import tqdm
except ImportError:
with_tqdm = False
def process_motion_... |
4e49576b8fdf063aed55363ce2800444f0c322a5888baad6fb12b1d79f978f7e | Python | 11,327 | 309 | # -*- coding: utf-8 -*-
"""
Created on Mon Dec 2 14:28:44 2019
@author: aaussel
"""
from brian2 import *
from scipy import signal
from cells.RS_FEF import *
from cells.FS_FEF import *
from cells.SI_FEF import *
from cells.VIP_FEF_alte import *
def generate_deepSI_and_gran_layers(theta_phase,N_SI,N_RS_gran,N_SI_gra... |
6e890c9d9440f92e29993a39098e5ee4f91d66f1a131b7a72bf7f50d78ef59a6 | Python | 11,331 | 311 | # NICE
# Copyright (C) 2017 - Authors of NICE
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program ... |
f11fa1dd183e09db452dd7a3ee6b80a695eef5298c918a70b8b762fa034635d4 | Python | 11,342 | 247 | """Utility functions to retrieve cell counts from the scientific literature.
Lexicon: AIBS stands for Allen Institute for Brain Science
https://alleninstitute.org/what-we-do/brain-science/
"""
from typing import TYPE_CHECKING, Dict, Union
import numpy as np
import pandas as pd
if TYPE_CHECKING: # pragme: no co... |
32a9983d7cb77da0e89954d9a8dd822b9ef4c3abe97f27f779ebeaf55873969f | Python | 11,343 | 255 | from __future__ import print_function
import os
import re
import copy
import random
import datetime
import timeit
import pdb
import PIL
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib import pyplot as plt
from sklearn.model_selection import train_test_split
from sklearn.metrics import roc_... |
56fdf3496f3d8842cdfbc28d6d47259a484e7b52f329d17b53fc37e27628bc8a | Python | 11,343 | 344 | import pytest
import networkx as nx
class TestLoadCentrality:
@classmethod
def setup_class(cls):
G = nx.Graph()
G.add_edge(0, 1, weight=3)
G.add_edge(0, 2, weight=2)
G.add_edge(0, 3, weight=6)
G.add_edge(0, 4, weight=4)
G.add_edge(1, 3, weight=5)
G.add_... |
1149cc9cf0548b0344a9c2530eddfce2c308a39e851c71e97d0f36cce7e89572 | Python | 11,347 | 270 | """Calculate the confidence intervals (through bootstrap tests) and significance
(through sign permutation tests) of the zero-shot identification analysis
results, and of the differences between the results and the noise ceiling.
Furthermore, fit a power-law function to the identification results to
extrapolate the ima... |
8aae1feb542ee2f9b8b25ffd97061f7a4111e6f83dd4e26133a641182d070e58 | Python | 11,347 | 303 | # -*- coding: utf-8 -*-
"""
Created on Mon Dec 2 14:28:44 2019
@author: aaussel
"""
from brian2 import *
from scipy import signal
from cells.RS_FEF import *
from cells.FS_FEF import *
from cells.SI_FEF import *
from cells.VIP_FEF import *
def generate_deepSI_and_gran_layers(theta_phase,N_SI,N_RS_gran,N_SI_gran,f_m... |
cac2fefd3c5c26396f550ba94388d832c683e6112db2b3ecb45d751096741f8e | Python | 11,347 | 302 | # -*- coding: utf-8 -*-
"""
Created on Mon Dec 2 14:28:44 2019
@author: aaussel
"""
from brian2 import *
from scipy import signal
from cells.RS_FEF import *
from cells.FS_FEF import *
from cells.SI_FEF import *
from cells.VIP_FEF_altd import *
def generate_deepSI_and_gran_layers(theta_phase,N_SI,N_RS_gran,N_SI_gra... |
a9dd52ad7eb89157658d803a4e49cde662b25e75c7bcd4aa557a788d61bf54dc | Python | 11,352 | 294 | """
The 'nodes' module contains methods to construct TF subgraphs computing the 1D or 2D DWT
or IDWT. Intended to be used if you need a DWT in your own TF graph.
"""
import tensorflow as tf
from tensorflow.keras.layers import *
def cyclic_conv1d_alt(input_node, filter_, mode):
"""
Alternative cyclic c... |
f8a213e26d6ba1bb52a22ee3aee28397b35f3090f171844a87b7a44d5ded8448 | Python | 11,352 | 210 | #!/usr/bin/env python
#
# Copyright (c) 2017 10X Genomics, Inc. All rights reserved.
#
import cellranger.analysis.io as analysis_io
import cellranger.analysis.constants as analysis_constants
import cellranger.h5_constants as h5_constants
import cellranger.io as cr_io
import cellranger.analysis.stats as analysis_stats
... |
b580df4c02e4c36bf4154fd9637ef64ff46ff0dd134cdb3f9b6fb57b9973c2e1 | Python | 11,364 | 384 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jun 5 13:55:26 2017
@author: virati
Stimulation artifact plotting and outlining
DISSERTATION FINAL
"""
#import Sim_Sig as SiSi
import numpy as np
#import prettyplotlib as ppl
import matplotlib.pyplot as plt
import matplotlib
import scipy.signal as sig
... |
68f6a6d97e972f05d9a881cebe6804e44255f7e14a8aa0f5428d014581d0dd48 | Python | 11,366 | 255 | #!/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 typing import TYPE_CHECKING
from ax.adapter.data_utils impor... |
d919facc3ee4b65b0d604da600279516fb0a655856fb1b3f3162af5f101eec43 | Python | 11,373 | 242 | # coding: utf-8
# 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"... |
c8c3c4f381c5a7d21346e6471801cf1865417a6f2f4215d9eb6e90384cddf700 | Python | 11,376 | 267 | # 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... |
2753a1f9faa7970ea86db993c072d5ee5c5d1b1ec1daa87112fb50459dcc162e | Python | 11,377 | 314 | '''Compute total motion energy from greyscale videos.
'''
import numpy as np
import moten
from moten.utils import (iterator_func,
pointwise_square,
)
# Make tqdm optional
with_tqdm = True
try:
from tqdm import tqdm
except ImportError:
with_tqdm = False
def pr... |
6cc504003cac24d53bae75cafe4e0eaa935718c585904e9bdc98ea1542dfd065 | Python | 11,378 | 339 | """Backing implementation for InstallRequirement's various constructors
The idea here is that these formed a major chunk of InstallRequirement's size
so, moving them and support code dedicated to them outside of that class
helps creates for better understandability for the rest of the code.
These are meant to be used... |
4f030f96273ae6c9d5f7fcb270d58007859a4fe7871d84b335754cccb80539b3 | Python | 11,382 | 306 | """
Closeness centrality measures.
"""
import functools
from collections import defaultdict
import networkx as nx
from networkx.utils.decorators import not_implemented_for
__all__ = ["closeness_centrality", "incremental_closeness_centrality"]
@nx._dispatchable(edge_attrs="distance")
def closeness_centrality(G, u=N... |
6cd7c8588db1c2c912b3b49a7db8fd11890d00874dce21041acd60d9d407c078 | Python | 11,394 | 333 | """
Transcript of a REPL session and the ``.transcript`` command.
Every entry of the session, a statement or a dot-command, is recorded
from the start with the plain text of the output it produced, so that
``.transcript PATH`` can write the session as a Markdown file and
``.transcript PATH --inputs`` the inputs that r... |
88799f5088002a08bbf64842d0b0d2ecfdd753fbd1d323da43f7e32a31544715 | Python | 11,399 | 295 | # 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 typing import Any, final
from ax.adapter.base import Adapter
from ax.analysis.anal... |
3f21ff6c17192efdbb81faaa6995be8f753f99960798c3563d713399fe4ccd4e | Python | 11,401 | 356 | """
Miscellaneous Utils
Nicholas Turner <nturner@cs.princeton.edu>, 2017
"""
import importlib
import datetime
import shutil
import types
import sys
import os
import re
import torch
from torch.utils.data import DataLoader
import tensorboardX
import numpy as np
import h5py
def make_required_dirs(args):
"""Sets up... |
581a1a10de6d28cbb35634da1a29f051cf6639b90a5837fced7c0ad62d19acbe | Python | 11,404 | 267 | #### All original code is copyright of Graham King, Trinity College Institute of Neuroscience.
## Code to create figures/plots of connectome stability (within participant spearman correlation across the two sessions)
## Last edited Oct 2022
import pandas as pd
import numpy as np
import glob
import os
import nilearn.s... |
3473f1adf7f8e655150ac2bb5dec874c79dc56fc11fc6e169881b78f27b20445 | Python | 11,413 | 318 | # -*- coding: utf-8 -*-
"""
Test data
"""
# Imports
import pandas as pd
from edbo.feature_utils import build_experiment_index
# Build data sets from indices
def aryl_amination(aryl_halide='ohe', additive='ohe', base='ohe', ligand='ohe', subset=1):
"""
Load aryl amination data with different features.
""... |
4d0745bf71562707fdce732d284eb62f08c044053238c3768fdcfabbcfe7d734 | Python | 11,415 | 290 | import importlib
import os
import threading
from functools import partial
from importlib import metadata
from typing import Callable, NamedTuple, Optional
import torch
from packaging.version import InvalidVersion, Version
from spikingjelly.logger import logger
from .native_loader import _check_native_device
_NEURO... |
487f8efc4c8ee4498907b8ab8b3bf211645d8b7657fca7afe73ea3d1408dbf43 | Python | 11,421 | 292 | """
Copyright © 2025 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
"""
import torch
from segment_anything import sam_model_registry
from torch import nn
import torch.nn.functional as F
from pathlib import Path
torch.backends.cuda.matmul.allow_tf32 = True
import logging
vit_logge... |
8fb62aefe902e53d6d48d00ee8758af6ae67e4162777e8c66cdeb5cc1cba5710 | Python | 11,435 | 306 | """
Object Store plugin for the Onedata Service.
"""
import logging
import os
from datetime import datetime
try:
from onedatafilerestclient import OnedataFileRESTClient
from onedatafilerestclient.errors import (
OnedataError,
OnedataRESTError,
)
except ImportError:
OnedataFileRESTClien... |
751d21aee7968560ae5ba35958f55b210ab0deb5aebf89c1d6d40d0756c514c3 | Python | 11,438 | 310 | #!/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 warnings import catch_warnings
import numpy as np
from ax.exceptions.core import UnsupportedErr... |
96ccdfd09d3933f1abfd2f3315e08965b88ffe21866156457c85aaac13719814 | Python | 11,451 | 286 | import typing
import errr
import numpy as np
from .. import config
from ..config import refs, types
from ..config._attrs import cfglist
from ..exceptions import (
IndicatorError,
LayoutError,
PlacementError,
PlacementRelationError,
)
from ..morphologies.selector import MorphologySelector
if typing.TY... |
93dfdc8901673c93aca159b454ba11de61e4157b2f80546fb19b8b608ab5b86a | Python | 11,457 | 402 | #!/usr/bin/env python
#
# Copyright (c) 2015 10X Genomics, Inc. All rights reserved.
#
import collections
import os
from cellranger.library_constants import GENE_EXPRESSION_LIBRARY_TYPE
Interval = collections.namedtuple('Interval', ['chrom', 'start', 'end', 'length', 'strand'])
Transcript = collections.namedtuple('Tra... |
1bfce640b1b4dfdd15413ee90bdff3534954f2c53850d22cf387ab46102cdce7 | Python | 11,461 | 360 | """Helper functions and constants for GCP Batch runner."""
import logging
import re
from humanfriendly import parse_timespan
log = logging.getLogger(__name__)
# Default values for GCP Batch runner configuration
DEFAULT_NFS_MOUNT_PATH = "/mnt/nfs"
DEFAULT_NFS_PATH = "/"
DEFAULT_MEMORY_MIB = 2048
DEFAULT_CPU_MILLI = ... |
f2933767bc1c7eaa9b645d7759129293d94be0f2b0e949b55d4bd325fd2dadc7 | Python | 11,470 | 259 | import tensorflow as tf
import os
import glob
import json
import pandas as pd
from collections import namedtuple
DataloaderParameters = namedtuple('DataloaderParameters', ('db_path_config', 'records_path', 'db_seq_len', 'seq_len', 'augment' ))
class DataLoaderGeneric():
"""Superclass for other dataset dataloaders... |
c71124268999ce7b3df9064a04e6b432843972d36892e4446f542a0f4d04734c | Python | 11,472 | 470 | # -*- coding: utf-8 -*-
"""
Source
======
This module provides the base class for data sources and sinks.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__ = 'GPLv3 - GNU General Pulic License v3 (see LICENSE.txt)'
__copyright__ = 'Copyright © 2020 by Christoph Kirst'
__webpage__ = '... |
cb2c8f29c7b7d4de51aa6eb7e347a2db414dd1d0ae5c604a13cc85e0bdfc6af2 | Python | 11,478 | 307 | #!/usr/bin/env python
"""
Scale Pyramid for Neuroglancer using Dask
This script builds a multi-resolution pyramid from a raw Zarr dataset.
It creates new downscaled datasets (s0, s1, s2, …) in the same container so that the data
can be efficiently viewed with neuroglancer.
Behavior is identical to the origina... |
cc6e133b5f7afab2d4404be74635dc185c0a1c587c4cbea843ac8d557fcbb560 | Python | 11,480 | 329 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from cogdl.layers import SELayer
from .. import BaseModel
from cogdl.layers import MLP, GATLayer, GINLayer
from cogdl.utils import batch_sum_pooling, batch_mean_pooling, batch_max_pooling
from cogdl.layers import Set2Set
class App... |
212365cd943bbda3967c8a2368b40e24e060fe0a7499dbce7c3116b394ab22ab | Python | 11,481 | 300 | import json
from typing import (
Any,
cast,
Dict,
List,
Optional,
Sequence,
Union,
)
from typing_extensions import get_args
from galaxy.tool_util_models.parameter_validators import (
AnyValidatorModel,
DatasetMetadataEqualParameterValidatorModel,
DatasetMetadataInDataTableParam... |
62c38744977c21068708aaccf6924e1274f2ad45f36d51e756575065a3b7316d | Python | 11,484 | 361 | """
This module provides a "Python implementation" of the camcoil
program (originally written in C) to estimate the random coil
chemical shift values from a sequence (string) of amino-acids.
The work is described in detail at:
1. Alfonso De Simone, Andrea Cavalli, Shang-Te Danny Hsu, Wim Vranken
and Michele Vend... |
9bb504905f91b1f6451f55f2e8fb0129e81d95168f14a37ca045227566284af1 | Python | 11,490 | 379 | from __future__ import annotations
from collections.abc import Sequence
from typing import Literal
import numpy as np
import pandas as pd
from anndata import AnnData
from numba import njit
from scanpy import logging as logg
from scipy.sparse import csc_matrix, csr_matrix, issparse, isspmatrix_csr, spmatrix
from sklea... |
4977a9c3c6fe0d59d2b53b2cec77dab0ed98bfcca3d8d8d449609eeb200c62a1 | Python | 11,492 | 376 | """Inferior and superior ranks, provided by the user, are passed to the kernel
function to provide a softer version of the rank filters. E.g.
``autolevel_percentile`` will stretch image levels between percentile [p0, p1]
instead of using [min, max]. It means that isolated bright or dark pixels will
not produce halos.
... |
30cfe2ae64918a0eb13f1297254e93031825a48f82c9024a678e87b29e60cc49 | Python | 11,494 | 250 | import torch
import torch.nn as nn
import rdkit.Chem as Chem
import torch.nn.functional as F
from MolRep.Explainer.Attribution.utils.fuseprop.nnutils import *
from MolRep.Explainer.Attribution.utils.fuseprop.encoder import GraphEncoder
from MolRep.Explainer.Attribution.utils.fuseprop.mol_graph import MolGraph
from MolR... |
2684d2fd963bbb87411c4b6d0f9e564f5a43e3b15cbc42c1133c3eb89422aafe | Python | 11,496 | 349 | import pytest
import networkx as nx
from networkx.utils import edges_equal, nodes_equal
# Note: SubGraph views are not tested here. They have their own testing file
class TestReverseView:
def setup_method(self):
self.G = nx.path_graph(9, create_using=nx.DiGraph())
self.rv = nx.reverse_view(self.... |
1a73fa832d74d14251be25009c0be78d99784fa7504068847756334432d3eb33 | Python | 11,497 | 295 | #!/usr/bin/env python
#
# Copyright (c) 2015 10X Genomics, Inc. All rights reserved.
#
import subprocess
import re
import os
import martian
import xml.etree.ElementTree as etree
import tenkit.constants as tk_constants
BCL2FASTQ_V1 = "OLD"
BCL2FASTQ_V2 = "NEW"
def get_bcl2fastq_v1(hostname):
try:
subproces... |
b144a045c0e80535ff5694ce11c5522f085e6009b362a475da2e49ac6adb5208 | Python | 11,502 | 315 | #!/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 ax.core.parameter import ChoiceParameter, ParameterType, RangeParameter
from ax.core.parameter_co... |
c7c9210afe9c3070dfe7a0e0ba8e46283f0d4df5afa117c1f65ef58bdcfcd147 | Python | 11,506 | 298 | # 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 typing import final
import pandas as pd
from ax.adapter.base import Adapter
from ax.analysis.analysis import Analysis
f... |
5459c1b416a46c3480384a2ad12031ce28a5aa4d715673a3bbdda01f09224490 | Python | 11,508 | 339 | # 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... |
f851bb99daf4ea20991b293b1db59998ebcbe351831da0d347c7a94fff9ecbdc | Python | 11,508 | 395 | """Strongly connected components."""
import networkx as nx
from networkx.utils.decorators import not_implemented_for
__all__ = [
"number_strongly_connected_components",
"strongly_connected_components",
"is_strongly_connected",
"kosaraju_strongly_connected_components",
"condensation",
]
@not_impl... |
ebf32b2a71bca89648e2046e5f7019156f56f16dc3f38661fa5acc88a5e27cad | Python | 11,509 | 251 | import logging
import os
from typing import (
Any,
Optional,
)
from sqlalchemy import false
from galaxy import util
from galaxy.model.tool_shed_install import ToolShedRepository
from galaxy.tool_shed.galaxy_install.client import InstallationTarget
from galaxy.tool_shed.galaxy_install.tools import tool_panel_m... |
5b466eab6f41faf90dc73888a20d6c89faeca304d2a25eaa9893a28102c3a882 | Python | 11,511 | 273 | #!/usr/bin/env python
#
# Copyright (c) 2015 10X Genomics, Inc. All rights reserved.
#
import os
import socket
import tenkit.log_subprocess as tk_subproc
import tenkit.preflight as tk_preflight
import cellranger.chemistry as cr_chem
import cellranger.constants as cr_constants
import cellranger.library_constants as lib_... |
246ea55a18a671cc13429306b4b1a4e046bed33d013e69744a593111939ac19a | Python | 11,513 | 288 | # Requriments - transformers, tokenizers
# Right now, the Smiles Tokenizer uses an exiesting vocab file from rxnfp that is fairly comprehensive and from the USPTO dataset.
# The vocab may be expanded in the near future
# Code from: https://github.com/deepchem/deepchem
import collections
import os
import re
import pkg... |
2cb772040391e9e830f25fa8303fe38421d2452a8640dbed97bf40562af19bf9 | Python | 11,514 | 375 | import re
import math
from functools import reduce
class CData:
def __init__(self, name):
self.name = name
self.timelist = []
self.deadlist = {} # dead objects
self.censoredlist = {} # censored objects
self.survpercent = []
self.survpercent_CI95 = []
... |
00373b1d4b91e739e51d8642b171acb31385597da4008a1cdb7a07583a09e8da | Python | 11,517 | 245 | # rmf 7.2.2020, last modified 4.14.2021
# cleaned up 3.1.2022
import sys, re
import svgwrite as svg
import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot as plot
import matplotlib._color_data as mcd
# FUNCTION: plots promoter and first intron, with any binding sites, for all transcripts in the group o... |
ab410288372a5c5c00d680d4c44bf4bba3e044aa3e0bfd959ccf83ddd232ea7f | Python | 11,517 | 323 | # %% import
import sys, os, platform
from src.pipelines import ComputeMinimumControlEnergy, Regression
from src.utils import rank_int, get_exact_p, get_null_p, get_p_val_string
from src.imaging_derivs import DataMatrix
from src.plotting import my_null_plot
from bct.algorithms.physical_connectivity import density_und
f... |
c32973b940ee8815c916a1c0d315d1a2e7492133a25806db331e57334f4bb90e | Python | 11,529 | 216 | from __future__ import division
import os
import argparse
import glob
import function as func
import operator
import fileinput
import pdb
import sys
import time
import itertools
from datetime import datetime
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from windows import *
from normalization... |
c3008803419f00259e3c841c50f60b939a01b1cb9ec93b76287ee7aaaaa131e8 | Python | 11,535 | 215 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@title: Plating.py
@author: chrisarcadia
@description: methods to assist in plate (container) preparation
@created: Thu May 31 10:00:03 2018
"""
import numpy
import scipy.special
from chemcpupy import Containers
# data related methods
def make_pe... |
cf37d985ef1931ffdb51864d5b58c2ee1ad7705e0f37dab349e5b13850c19a5d | Python | 11,536 | 408 | # -*- coding: utf-8 -*-
"""Docking_GD_Parallel.ipynb
Automatically generated by Colaboratory.
Original file is located at
https://colab.research.google.com/drive/1P4GssDPNRBrGwGPIuuTlIdHmC0J2TjxJ
"""
import os
import sys
import string
from pyrosetta import *
from rosetta import *
from rosetta.pro... |
e10441f263073f3c73c27d01fe52398ad0c5ca0277940655889ff3a6ce6e6341 | Python | 11,537 | 287 | #!/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 logging
from collections.abc import Callable
from typing im... |
27d91b21a502dabb9a55365ea4ea3bc925b91317e115cbfbf18a049b22744a72 | Python | 11,542 | 281 | # 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... |
bb1cbd350beb0d0473f47763ab3d30f485ab43063be5b948ac66e36376cc479f | Python | 11,547 | 290 | """Tests for mibitracker.helpers.
This tests for the retry and status checking utilities only.
Specific helper functions that make use of the MIBItracker API and can be
tested by running a local instance of the MIBItracker to ensure proper
integration. A set of examples can be found in
mibitracker/testing/MibiRequests... |
837d121e93579a280de09b9e73bd365261995638dc535d7e0d9d2186b2c262ca | Python | 11,568 | 283 | # 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... |
8fad97c7ec1cf269798831d7a0afd34a1acd32458e2189f14f38bbc9abf89725 | Python | 11,570 | 310 | import datetime
import getpass
import json
import os
import collections
import click
from pkg_resources import resource_stream, resource_filename
import shutil
def update_config_file(config_file=None):
"""Updates an existing configuration file with any new fields. Does not modify existing fields."""
new_confi... |
9386e5594f09fc01e0378302bcc1e8c053fa0654d9d66f7741bd735aafaad174 | Python | 11,573 | 390 | """Figure 1 plot - paradigm figure and behavior."""
# %%
# Imports
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib.lines import Line2D
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from config import ANALYSIS_DIR_LOCAL, STREAMS
from utils imp... |
2bd3693c634661dd513b4fabaee996055c56fb084773795d94eeed82291769c8 | Python | 11,575 | 310 | # 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... |
e933de654fb5e77b7d9b821fd1721853984ab5b9134a5a1d35286b40d6248df2 | Python | 11,576 | 319 | import functools
import logging
import os
from typing import (
TYPE_CHECKING,
Union,
)
from galaxy import model
from galaxy.jobs.runners import (
AsynchronousJobRunner,
AsynchronousJobState,
)
from galaxy.util import unicodify
if TYPE_CHECKING:
from galaxy.jobs import MinimalJobWrapper
CHRONOS_IM... |
f4ec8d41f9cc28da848e2a929d092b544c7e28b45938cf2c8e9414d84c0df8ea | Python | 11,585 | 330 | from __future__ import annotations
from spikingjelly.logger import logger
from typing import Optional
from weakref import ReferenceType, WeakKeyDictionary, ref
import torch.nn as nn
from .. import base
__all__ = [
"collect_reset_modules",
"detach_net",
"invalidate_reset_cache",
"reset_collected_mod... |
9241513a1def3e078509fe0a6dadedee18fc180114b81b97dff634d26d2b54e9 | Python | 11,607 | 358 | # -*- coding: utf-8 -*-
"""
Created on Mon Dec 2 14:28:44 2019
@author: aaussel
"""
from brian2 import *
from scipy import signal
from cells.RS_LIP import *
from cells.FS_LIP import *
from cells.SI_LIP import *
from cells.IB_soma_LIP import *
from cells.IB_axon_LIP import *
from cells.IB_apical_dendrite_LIP import *... |
d2127abc042691e29d2aea30a799f98a104a3af9d2adc86152e1db5d37fcd949 | Python | 11,610 | 406 | """Functions concerning tournament graphs.
A `tournament graph`_ is a complete oriented graph. In other words, it
is a directed graph in which there is exactly one directed edge joining
each pair of distinct nodes. For each function in this module that
accepts a graph as input, you must provide a tournament graph. The... |
63d64584a6193593f0e81b7ae563395c94f7c775a3692494198866f6c5bb625d | Python | 11,611 | 327 | import os
import json
import subprocess as sp
from argparse import ArgumentParser
from contextlib import ExitStack
from pathlib import Path
from typing import TYPE_CHECKING, Any
from learnMSA import Configuration
if TYPE_CHECKING:
from learnMSA.util import EmbeddingDataset, SequenceDataset
DEFAULT_FALLBACK_MEMO... |
11bbb0077348814f0fd7bb1eb7f33aafcb9cc458e3407774403c75810dbeb725 | Python | 11,617 | 358 | # -*- coding: utf-8 -*-
"""
Created on Mon Dec 2 14:28:44 2019
@author: aaussel
"""
from brian2 import *
from scipy import signal
from cells.RS_LIP_altd import *
from cells.FS_LIP_altd import *
from cells.SI_LIP import *
from cells.IB_soma_LIP import *
from cells.IB_axon_LIP import *
from cells.IB_apical_dendrite_LI... |
9ace2ebc6e5154dea333d76683fba0c268712561ebfe4667feecc4365815df54 | Python | 11,621 | 282 | from __future__ import annotations
from collections.abc import Iterator
from functools import reduce
from itertools import product
from typing import Any, cast
import numpy as np
import pandas as pd
from anndata import AnnData
from scanpy import logging as logg
from sklearn.metrics import DistanceMetric
from sklearn.... |
2101794fdfbc24d6dfabe89d2f1beee0af4f31234d8f3a6da56aa487dc521fa9 | Python | 11,632 | 277 | # Copyright (C) 2021-23 Intel Corporation
# SPDX-License-Identifier: BSD-3-Clause
# See: https://spdx.org/licenses/
import numpy as np
import typing as ty
from lava.magma.core.learning.constants import GradedSpikeCfg
from lava.magma.core.learning.learning_rule import LoihiLearningRule
from lava.magma.core.process.con... |
7b7ff9e219063b780d6c9cd084e54582ef065b0a86628c11576120ba78ac1478 | Python | 11,632 | 350 | # -*- coding: utf-8 -*-
"""
Created on Wed Dec 4 11:35:36 2019
@author: aaussel
"""
from cells.RE_mdPul import *
from cells.TC_mdPul import *
#from cells.HTC_mdPul import *
from cells.HTC_buffer_mdPul_Destxhe_tests import *
from scipy import signal
prefs.codegen.target = 'numpy'
defaultclock.dt = 0.01*ms
runtime... |
ad0db999c765427fa9f8db4e7a4757f99e3c357013a0da239f2f5be5bc7318fa | Python | 11,632 | 355 | import pathlib
import numpy as np
from scipy import linalg
from sklearn.utils.extmath import safe_sparse_dot
from sklearn.linear_model import LinearRegression
_DEFAULT_ALPHAS = np.logspace(-1, 3, 9)
def _preprocess(X, Y, feat_penalty=None):
new_X = np.empty((X.shape[0], X.shape[1] + 1), dtype=X.dtype)
ne... |
7125b51aa7511b0a9fd6e21374e74704b2691221e74ce43df9663b94fe07fb17 | Python | 11,634 | 303 | #!/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 copy import deepcopy
from ax.adapter.base import DataLoaderConfig
from ax.adapter.data_utils imp... |
e5fdeb18423db0da26072f9faace9af21fb4f64a477def1dcbc33e148bb54ab2 | Python | 11,644 | 240 | """aggregate_matched_control.py - collapses the per-subject matched-registration control into a
per-ROI cohort comparison of V1 orientation divergence, and reports the Results 3.6 correlation
between that divergence and the between-model field difference.
Trap: baseline tensor_divergence.csv (08_tensor_divergence.py) ... |
9992d1a92f3bdc44f4a038877345fa88e0f983f7d46fa52de2a9bd004a5273e4 | Python | 11,651 | 426 | # Original author: D. Eppstein, UC Irvine, August 12, 2003.
# The original code at http://www.ics.uci.edu/~eppstein/PADS/ is public domain.
"""Functions for reading and writing graphs in the *graph6* format.
The *graph6* file format is suitable for small graphs or large dense
graphs. For large sparse graphs, use the *... |
a983ceae26be5b6b0113b58078c720eb03b061c9dbc6a080beaf6fd6a1cf2aea | Python | 11,651 | 354 | # -*- coding: utf-8 -*-
# Imports
import random
import pandas as pd
import numpy as np
from pyclustering.cluster.kmedoids import kmedoids
from pyclustering.cluster import cluster_visualizer
from pyclustering.utils.metric import distance_metric, type_metric
from sklearn.cluster import KMeans
from sklearn.metrics impor... |
fc1f33c0284b32397d1ad7bc567c430b2b712ec8e6d9b77899bc69bd6ef685ac | Python | 11,661 | 330 | """
Mixin blender module for the scaffold object. When scaffold.for_blender() is called
all the public callable objects of this module are bound to the instance.
"""
import bpy as _bpy, numpy as _np
from .. import blender as _main
def create_network(self, scene, name):
"""
Creates the root collectio... |
793c68366e38b306e98528455391b0f440ebb49f32f3a02980d08c3512ef96e8 | Python | 11,663 | 305 | """
Copyright © 2025 Howard Hughes Medical Institute, Authored by Carsen Stringer , Michael Rariden and Marius Pachitariu.
"""
import logging
import numpy as np
from tqdm import trange
from . import transforms, utils
import torch
TORCH_ENABLED = True
core_logger = logging.getLogger(__name__)
tqdm_out = utils.TqdmToL... |
b937f954f3f3bbc44b961de00fca6ec26aa0f2dc1c62dbe14558eb95fc2f5989 | Python | 11,669 | 357 | import pytest
import sklearn.utils.estimator_checks
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import StandardScaler
from sklearn.exceptions import NotFittedError
from sklearn.base import clone
from himalaya.backend import set_backend
from himalaya.backend import ALL_BACKENDS
from himalaya.u... |
caa11e4b5d9d01d58908bedad8e6a1618aa535186ef2d7acbdfabab3790904cb | Python | 11,675 | 292 | from jinja2 import Environment, FileSystemLoader, select_autoescape
from yapf.yapflib.yapf_api import FormatFile
import requests
from unidecode import unidecode
from pathlib import Path
from datetime import date, datetime
import getpass
import os
import sys
import re
from pylint import lint
"""
Generates SNIRF interf... |
c9361438bf165a29ea7086b593f3a118327342aab1a481b06ac0d169978d0067 | Python | 11,682 | 290 | #!/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 copy import deepcopy
from math import sqrt
import numpy as np
from ax.adapter.base import DataLo... |
86a9ae2d86219a61e9832d36337ee6ffbfcf3317a0d7d2004161e96af6a5d352 | Python | 11,683 | 377 | # -*- coding: utf-8 -*-
"""
FilterKernel
=============
Implementation of various volumetric filter kernels.
.. _FilterTypes:
Filter Type
-----------
Filter types defined by the ``ftype`` key include:
=============== =====================================
Type Descrition
=============== ================... |
619eda95f0032ca8cbc04f9a8d9c6bb1450d509ca3fc2e41aa4c412d5179606a | Python | 11,684 | 331 | import os
import uuid
from collections.abc import Callable
from functools import (
lru_cache,
wraps,
)
from multiprocessing import get_context
from threading import (
local,
Lock,
)
from typing import (
Any,
)
import pebble
from celery import (
Celery,
shared_task,
Task,
)
from celery.s... |
d6bf5d395487b22eedf77ab66a7b892a3649a32d4ab6af2b8a8bc327cbf25ee6 | Python | 11,684 | 318 | import typing
from collections import deque
from typing import Iterable, Optional, Union
import errr
from ._util import get_location_name
from .definitions import CableType, ModelDefinition
from .exceptions import ConstructionError, FrozenError, ModelDefinitionError
if typing.TYPE_CHECKING:
from build... |
320812ab187de73a7eb8962da7b1e81918a8be991a42fd6ff1f129013ab426cd | Python | 11,685 | 352 | import sys
sys.path.append('../')
import pyedflib
import utils
from data.data_utils import *
from constants import INCLUDED_CHANNELS, FREQUENCY
from utils import StandardScaler
from torch.utils.data import Dataset, DataLoader
import torch
import math
import h5py
import numpy as np
import os
import pickle
import scipy
i... |
4f1368455092014a6fa4eed05cded966378094f1f06bee2a5bc7d2ed926d552d | Python | 11,689 | 362 | from collections.abc import Iterable, Mapping, MutableMapping, MutableSet, Set
from typing import AbstractSet, Tuple
from nl_expr.expression_walker import ReplaceExpressionsByValues
from nl_expr.expressions import Constant, FunctionApplication
from nl_expr.type_system import Unknown, get_args
from ..utils.relational_a... |
cf26a8973b2d45aa877266006792e4f6d2d13b7e1fb2d98e1f332fbd3cb06e2c | Python | 11,689 | 350 | from sklearn.preprocessing import StandardScaler
import math
import pandas as pd
import numpy as np
import re
import pyBigWig
import pickle
import multiprocessing as mp
import time
import os
import sys
from keras.models import load_model
class DNArepresent:
def __init__(self, sequence, chrom, start, stop, strand... |
ac0314d6b755b9ae6f479659b733d632a50464a147de445a9d03d57722394a4b | Python | 11,691 | 529 | #!/usr/bin/env python
# coding: utf-8
# # Data analysis for our study on the transparency and open science standards in the policies of medical and health science journals
# The protocol and details of our study is openly availble via the OSF [here](https://osf.io/h2xud/).
# In[1]:
# import libraries required for ... |
b3d642806c57a9d68b2961b142483caefa53d8b3a5230b34ee972bb8d73a3755 | Python | 11,695 | 266 | # 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... |
f0faaf927bf3346e5d1d04127cad956d17c1a19cada1949d9b733dddcbdd3cf6 | Python | 11,697 | 351 | #!/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 Callable, Generator
from contextlib im... |
59ce3d70191c532b014784d9d9b8ef78868f3b5e4646c075af108389528c2c42 | Python | 11,700 | 278 | # -*- coding: utf-8 -*-
"""
Created on Mon Jan 10 23:22:40 2022
@author: Danny
"""
import pandas as pd
import numpy as np
from datetime import datetime
from scipy.stats import mannwhitneyu
def days_between(d1, d2):
d1 = datetime.strptime(d1, "%Y-%m-%d")
d2 = datetime.strptime(d2, "%Y-%m-%d")
... |
db4555860b3f7b0844c975f419b9b721c5bf462ac1cae20c2c2c9bdf588c3b10 | Python | 11,701 | 348 | # -*- coding: utf-8 -*-
"""
Implementation of various volumetric filter kernels
.. _FilterTypes:
Filter Type
-----------
Filter types defined by the ``ftype`` key include:
=============== =====================================
Type Descrition
=============== =====================================
``mean`... |
ea7603f17ef40de1f5c67a38c44e36262362490cc159046b5456b2c84e04edb3 | Python | 11,707 | 261 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon August 6 2018
@author: chrisarcadia
@description: script to review a library platesheet and to optionally
generate a mass list and Andrew recipe for that library
"""
# Import python libraries
import chemcpupy
import csv
i... |
f461dc5f24d4935e9cdb5176441c6b30a2cf756f660b18f1fa3e9786e2bd90e5 | Python | 11,710 | 364 | """
This module provides a "Python implementation" of the camcoil
program (originally written in C) to estimate the random coil
chemical shift values from a sequence (string) of amino-acids.
The work is described in detail at:
1. Alfonso De Simone, Andrea Cavalli, Shang-Te Danny Hsu,
Wim Vranken and Michele Vend... |
777905371919632ff35dc9c73267076f1ec4ab2544c81da4fbfd41cddcc76c90 | Python | 11,720 | 321 | """Short Term Storage service for Galaxy.
This service is used to store files for a short period of time (e.g. a few minutes, hours or days)
and then serve them to the client. This is useful for large files that take a long time to
generate and are not worth storing permanently.
"""
# TODO: Move it to its own package... |
f3501f88a324342fab45c514580ae1760f3940e58382eb52d33194f9a9fe8e8d | Python | 11,720 | 287 | """This file and its contents are licensed under the Apache License 2.0. Please see the included NOTICE for copyright information and LICENSE for a copy of the license."""
import logging
from datetime import datetime
from core.current_request import CurrentContext
from core.permissions import AllPermissions
from core... |
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