sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
ccf6d57fb2c962b1083a02dcdb12407485ed0417cc31d018c36f8e1654194d8f | Python | 14,541 | 392 | # -*- coding: utf-8 -*-
"""
Created on Fri Nov 22 10:46:47 2019
@author: Amelie Aussel
"""
from brian2 import *
defaultclock.dt = 0.01*ms
prefs.codegen.target = 'numpy'
eq_HTC_buffer_mdPul='''
dV/dt=(-INa-IK-IL-IKL-IH-ITLT-ITHT-IAHP-IGJ-Iapp-Iapp2-J-Isyn-Itheta)/Cm_HTC : volt
J : amp * meter ** -2
... |
7d37513d941d451432c81e3aa2796faa67740f15553285e4d41eb44a5326655c | Python | 14,555 | 273 | # 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... |
7e7be2719951cdadf8fba3d303afe213d80a14780692cebdc8ae4601276ab956 | Python | 14,590 | 412 | from __future__ import annotations
import copy
import functools
import traceback
from typing import Any
import torch
from spikingjelly.logger import logger
from .triton_runtime import (
is_fp8_dtype,
normalize_cuda_device,
normalize_triton_compute_dtype_name,
normalize_triton_storage_dtype,
reso... |
025a35ab8bd3c5dc3624476e903bc320092d482040122dd76314883e2061580b | Python | 14,597 | 423 | from typing import Optional
import torch
from .. import functional, surrogate
from .base_node import BaseNode
__all__ = ["QIFNode", "EIFNode"]
class QIFNode(BaseNode):
def __init__(
self,
tau: float = 2.0,
v_c: float = 0.8,
a0: float = 1.0,
v_threshold: float = 1.0,
... |
c57f1b852e70f06b30a2d24e5d7882aebf9a307b74fe6831d969085ee62eba96 | Python | 14,612 | 407 | """Flow based node and edge disjoint paths."""
from itertools import filterfalse as _filterfalse
import networkx as nx
# Define the default maximum flow function to use for the underlying
# maximum flow computations
from networkx.algorithms.flow import (
edmonds_karp,
preflow_push,
shortest_augmenting_pa... |
0c56e29d5f3413c5ae85b17d11aaa230602799e3ed3b6f72b6a1ebc0fde9ee96 | Python | 14,623 | 391 | # -*- coding: utf-8 -*-
"""
MeasurePointList
================
Measurements on a subset of points in large arrays.
Paralllel measuremnts at specified points of the data only.
Useful to speed up processing in large arrays and only a smaller number
of measurement points.
See also
--------
:mod:`ClearMap.Analysis.Measu... |
2f7836b3b35b91f5d7e9c05bc48f8ab3d137aba05ebecbcfb2f7a85fc4c3b5e7 | Python | 14,635 | 357 | from spikingjelly.logger import logger
import os
from pathlib import Path
import time
from typing import Callable, Optional, Tuple, Union
import numpy as np
from . import utils
from .base import (
EventBuilder,
FrameCustomIntegrateBuilder,
FrameFixedDurationBuilder,
FrameFixedNumberBuilder,
Neurom... |
e7f22b33efc7e5713b9f74fa8c215243adc6187e9c1445afa16de2d914842b61 | Python | 14,635 | 415 | import random
from copy import copy
import pytest
import networkx as nx
from networkx.utils import (
PythonRandomInterface,
PythonRandomViaNumpyBits,
arbitrary_element,
create_py_random_state,
create_random_state,
dict_to_numpy_array,
discrete_sequence,
edges_equal,
flatten,
gr... |
727bfa830c9193fc0b12076c200831448844194e4c3bdd8e5c30dae2cf6156b0 | Python | 14,640 | 438 | """
Dot-commands of the interactive REPL.
Commands are registered in :data:`COMMANDS` with the :func:`command`
decorator, which records the handler together with its usage and help
text. A handler is called with the REPL application and the text that
follows the command name.
"""
import difflib
import re
from typing ... |
c83a7fd4330527c298fb403a4cc58582354a736ae219c5c650d144f40171def0 | Python | 14,643 | 406 | import sys
import numpy as np
import tensorflow as tf
import tensorflow.keras.layers as KL
import tensorflow.keras.backend as K
class NCC:
"""
Local (over window) normalized cross correlation loss.
"""
def __init__(self, win=None, eps=1e-5):
self.win = win
self.eps = eps
def ncc(... |
c75d396045587a8757d0dd7878c6632826638769f0cfdc18f2566cf94bf91475 | Python | 14,664 | 412 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Feb 7 00:25:29 2023
@author: wirrbel
"""
#load modules
import nrrd
import pandas as pd
import numpy as np
import os
from PIL import Image
import tifffile
output_dir = os.path.join("/home/wirrbel/2022-11-09_cortical_flatmap_test/","2023-02-06_colo... |
40077d25f16b2a857c097bb045d74a0d64cfc02714508ca1587f48b975010bbb | Python | 14,673 | 340 |
import tensorflow as tf
import numpy as np
from evoten.backend_tf import BackendTF
from evoten.expm_gtr import expm_gtr, precompute_gtr, expm_gtr_from_decomp
backend = BackendTF()
class SubstitutionModel(tf.keras.layers.Layer):
"""
A utility class for handling parametrization of substitution models for
... |
7d8518f25cae3a4140d45d2f484e645e9d0b3df11f87ad1aaa6fde0b5cbb2739 | Python | 14,685 | 430 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 12 16:23:57 2020
@author: amelie
"""
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 11 13:56:08 2020
@author: amelie
"""
from brian2 import *
from scipy import signal
from FEF_full import *
from LIP_full import *
from mdP... |
d18e88c3c95d72cbc4058f6909838465d2045340ba11a68e7d1cc1760e9c1af9 | Python | 14,690 | 281 | #!/usr/bin/python
# conc_effect.py by Patrick D Roberts (2022)
# Calculate concentrations and effects on Wilson-Cowan model parameters from dose
# import neural_mech.dose_to_model as dose2model
# d2m = dose2model.Dose_Conversion()
import numpy as np
import pandas as pd
def seperate_clinical_pre_post(clinical_data):
... |
e3efde8fad4093bcd8c81e8f0e7193e21669b0b8ffdacda86e822076b3aed3e5 | Python | 14,690 | 452 | """ Module containing custom layers
Code taken from -> https://github.com/akanimax/BMSG-GAN
"""
import torch as th
# ==========================================================
# Equalized learning rate blocks:
# extending Conv2D and Deconv2D layers for equalized learning rate logic
# ================================... |
b26c70dd0f20c0c1e5d90921503dedbbacf392fa246460ed2256df01f5898d29 | Python | 14,697 | 418 | from __future__ import annotations
from contextlib import contextmanager
from functools import partial, singledispatch
from pathlib import Path
from typing import TYPE_CHECKING, overload
import h5py
import numpy as np
import pandas as pd
import zarr
from scipy import sparse
import anndata as ad
from anndata._core.fi... |
b8bbab67a6eb2e4691f68d5967bfee7ec6dc6237d02ccc40f9ec3c34483d5227 | Python | 14,697 | 480 | from cogdl.data import Graph
import scipy.sparse as sp
import torch
import numpy as np
import scipy
def getGRBGraph(graph: Graph):
features = graph.x
if hasattr(graph, "grb_adj") and graph.grb_adj is not None:
adj = graph.grb_adj
else:
edge_index = graph.edge_index
edge_attr = gra... |
9b964b077033bdc0a6600f101ad14cb914484c322693798bb07261cbe5d88876 | Python | 14,699 | 401 | """
This contains some utility functions for reading files, searching for entities,
and other basic tasks.
The functions to_conll_iob, read_conll and get_NER_tagcounts were modified from
http://nlpforhackers.io/named-entity-extraction/
"""
import codecs
import os
from collections import Counter
try:
import Config... |
564232c453f0eda58e6624f7d8106cd64fcb16d97c1e360b5724bf1f6f12afcd | Python | 14,701 | 404 | """Functions for generating grid graphs and lattices
The :func:`grid_2d_graph`, :func:`triangular_lattice_graph`, and
:func:`hexagonal_lattice_graph` functions correspond to the three
`regular tilings of the plane`_, the square, triangular, and hexagonal
tilings, respectively. :func:`grid_graph` and :func:`hypercube_g... |
9f491f38330019b26d47cc2f0d50d179598132b51e94acf42a8911eae5004eac | Python | 14,713 | 415 | # 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... |
06c0b92a9ddb0c3ff517820f5eca3822868919cb939ba2060bd7eeea09d3faca | Python | 14,720 | 455 | import abc
import os
from collections.abc import MutableMapping
from string import ascii_letters, digits
from typing import Any, List, Mapping, Optional, Union
from zarr.meta import Metadata2, Metadata3
from zarr.util import normalize_storage_path
# v2 store keys
array_meta_key = '.zarray'
group_meta_key = '.zgroup'
... |
2bda7c7730851b5a2f563e2ae313060a0c0e3c017d382140b113bf37613cf0b2 | Python | 14,732 | 358 | """Tests for bipartite community detection and quality functions."""
import pytest
import networkx as nx
from networkx.algorithms import bipartite
from networkx.algorithms.bipartite.community import (
_bipartite_modularity_merge_delta,
)
from networkx.algorithms.community.quality import NotAPartition
class Test... |
a5f4458f6ca19a35cf519c9d9fd74b981e6467f4f1d06cd0d6c4c18b2efe7964 | Python | 14,738 | 345 | # -*- 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_buffer_mdPul_Destxhe_tests import *
from mdPul_one_column_v3 import *
from scipy import signal
prefs.codegen.target = 'numpy'
defaultclock.dt = 0.01*ms
run... |
3b11ea7de7f46416d864a29bd545aca2a7b034e173aae3bb5e0f4341eb2d0494 | Python | 14,741 | 466 | """
This module includes the main class that handles the detection
of the aromatic rings.
"""
# Python import(s).
from collections import namedtuple
import numpy as np
# Private import(s).
from src.chemical_shifts.auxiliaries import ACCEPTED_RES, RES_3_TO_1
# Add documentation to the NamedTuple.
__pdoc__ = {}
# Mod... |
e528988bf5ef833df8ca89fe39056bfa923cbe39f45ffd4237c504634e2a330d | Python | 14,743 | 496 | # -----------------------------------------------------------------------------
# download_AMBA.py
# Authors: Antoine Beauchamp, Yohan Yee
"""
Download in-situ hybridization data sets from the Allen Mouse Brain Atlas
"""
# Packages --------------------------------------------------------------------
import os
import... |
35564c9a59e4771830c0dc39183adcf3068d11171d0aee76c9d1dc05d380fe1c | Python | 14,744 | 406 | """Swap edges in a graph."""
import math
import networkx as nx
from networkx.utils import py_random_state
__all__ = ["double_edge_swap", "connected_double_edge_swap", "directed_edge_swap"]
@nx.utils.not_implemented_for("undirected")
@py_random_state(3)
@nx._dispatchable(mutates_input=True, returns_graph=True)
def ... |
bd7837977b8a408d6bf68c3e1e51bde4b4c7c82e77cd71db82d13c7d3d31a9f5 | Python | 14,747 | 371 | import multiprocessing
import os
from functools import partial
from shutil import move, rmtree
from typing import Any, Callable, Tuple
import feather
from alpineer import io_utils, misc_utils
from pyarrow.lib import ArrowInvalid
from ark.phenotyping import cluster_helpers, pixel_cluster_utils
multiprocessing.set_sta... |
b434dee822bd7a16c00ca52628d1862319d0afa166d209c727d58595965f44f0 | Python | 14,764 | 403 | import enum
from typing import Sequence
import sys
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.tf.prior.dirichlet import T_TFTensor, TFDirichletPrior, TFPrior
from hidten.tf.util import epsilon, ... |
6d989e71b728a9c6af43ff8eed8ed8dc39de8bf34107a49f099b263899fd2787 | Python | 14,769 | 516 | from __future__ import annotations
import pickle
import sys
import warnings
from abc import ABC, ABCMeta
from collections.abc import Callable, Mapping, Sequence
from functools import wraps
from itertools import product
from pathlib import Path
import anndata as ad
import geopandas as gpd
import matplotlib
import matp... |
ab70df09de3931b57c53c7cb993297aaeebc7c8c914687cccfbb0e4c368f5cd3 | Python | 14,769 | 450 | import unittest as ut
import six
from pysbm import additional_types as at
class TestSetDict(ut.TestCase):
""" Test Class SetDict """
# noinspection PyPep8Naming
def __init__(self, methodName='runTest'):
super(TestSetDict, self).__init__(methodName)
def setUp(self):
self.list = at.S... |
21a3209f0388b2bf563d40c7efa7e861741cf7c01d906a93d482002fd1982907 | Python | 14,772 | 419 | """
Error formatting and reporting for NeuroLang frontend.
Provides readable error messages for Datalog and SQUALL parse and semantic
errors, with source context, location pointers and actionable suggestions.
"""
import difflib
import os
import re
import sys
from functools import partial
from typing import Callable, ... |
170e30260384b9387de4b08967254d5738ee44591d0fd016891e19431d396982 | Python | 14,781 | 396 | #!/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 time
from asyncio import iscoroutinefunction
from functools import partial
from logging import ... |
292f2b321ab88cb25fd8cc006c2a31c5e056ce0b3b6557efc936aec52d636be6 | Python | 14,782 | 364 | """
Utilities for encrypting sensitive headers using Galaxy's Vault system.
This module provides functionality to:
1. Identify sensitive headers that should be encrypted based on configuration
2. Encrypt/decrypt headers using the vault
3. Transform data structures to use vault references for sensitive headers
This ca... |
c97b6d76550552e11a28a50b3717084273b298992136bfb31ed8de204aad5a60 | Python | 14,784 | 458 | import re
from collections import namedtuple, OrderedDict, defaultdict
from copy import deepcopy
import numpy as np
import pandas as pd
HMMER_PREFIX_WARNING = "# WARNING: seq names have been made unique by adding a prefix of"
class DefaultOrderedDict(OrderedDict):
"""
Source:
http://stackoverflow.com/que... |
f2dc17bb666e250f392980045073ef1c25531cad51a9db13ca2d6f6d06db59fc | Python | 14,788 | 326 | # 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... |
b5f6e04b666232a38901e46322b97900e753c902a565a521a0a3f631fef63817 | Python | 14,791 | 534 | import os
import pathlib
import random
import tempfile
import pytest
import networkx as nx
from networkx.utils.decorators import (
argmap,
not_implemented_for,
np_random_state,
open_file,
py_random_state,
)
from networkx.utils.misc import PythonRandomInterface, PythonRandomViaNumpyBits
def test_... |
40a3064ee587332c39cda821db086b0c170434beede29be9b7fb9cd3f754f7af | Python | 14,794 | 387 | """Opt-in Nsight Systems ranges for SNN training and inference scripts."""
from contextlib import ExitStack, contextmanager
import json
from pathlib import Path
from typing import Iterator, Optional, Sequence
import torch
from torch import nn
from spikingjelly.activation_based.base import StepModule
__all__ = ["cap... |
38817577cd8b7322d98703e38b60d968021dd99cc53d36f40dd0068cf52f0b1e | Python | 14,804 | 385 | #!/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 collections.abc import Iterable, Sequence
from typing import Any, Self
from ax.core.arm import A... |
e830edc8802ac9f7374d81b84b60cdc48c6c5f6405db8b879edaedb0cdcd911f | Python | 14,812 | 378 | # 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 math
from itertools import product
from unittest.mock import Mock
import numpy as np
import pandas as pd
from ax.benc... |
d474db8ba20fdff74179618fbbbd0594a47109f6828f474dec2189791def8442 | Python | 14,824 | 393 | #!/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.metric import Metric
from ax.exceptions.core import OptimizationNotConfiguredError, UserI... |
b680658cc16dc4e5acd63ea7b1bb5025181c4c68b62332aae2fda9c7c5e78db7 | Python | 14,845 | 441 | # Test for Moody and White k-components algorithm
import pytest
import networkx as nx
from networkx.algorithms import flow
from networkx.algorithms.connectivity.kcomponents import (
_consolidate,
_generate_partition,
_reconstruct_k_components,
build_k_number_dict,
)
FLOW_FUNCS = (
flow.boykov_kolm... |
5e584ff458c2f58ad818c17658a983e1372b504d51918e4d80aca8e852d6fcaa | Python | 14,851 | 446 | import logging
from abc import (
ABC,
abstractmethod,
)
from collections.abc import Sequence
from contextlib import contextmanager
from typing import (
Any,
Optional,
)
import sqlalchemy as sa
from alembic import (
context,
op,
)
from sqlalchemy.exc import OperationalError
log = logging.getLog... |
fec36d3e2bf81a9259d517e3444d362dd642c91cb3e3b38f1a0a852c85f4af9e | Python | 14,855 | 386 | import warnings
import numpy as np
import pandas as pd
from copy import deepcopy
from src.utility import get_reconstruct_coords, read_thunderstorm_drift_json
import os
import json
try:
from third_party.dme.dme import dme_estimate
from third_party.dme.rcc import rcc3D
except:
print("unable to load dme drift ... |
bf7f09ef32097fc40888bea0b915673516895af611d00b6de5a075ed7843a055 | Python | 14,871 | 350 | import numpy as np
from brian2 import get_device
from brian2.synapses.synapses import SynapticPathway, Synapses
from brian2lava.utils.math import check_convert_to_int32
from brian2lava.utils.const import LOIHI2_SPECS, EPSILON
from brian2 import get_logger
class LavaParameters:
"""
This class holds essential, static... |
514a9761f4f2074e0d5b495b1aa701f5023cb3dae7e8254f2d8466ac1f3e9233 | Python | 14,874 | 478 | """
This module contains the classes required to construct options.
"""
import argparse
import contextlib
import copy
import functools
import os
import pathlib
import tempfile
import toml
from .exceptions import OptionError
from .reporting import warn
class OptionDescriptor:
"""
Base option property descri... |
8b254a9691cb5a5857e925a2a23be7b017ac1335662f5e0b75b8ccd9307bdfca | Python | 14,893 | 289 | # 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... |
628a10ad92ad659f89489f57c4bc9bd90b3fb3a7332e19a636c1d5cee595f273 | Python | 14,917 | 513 | from collections import Counter
import numpy as np
from scipy import ndimage
from scipy import sparse
from . import _seg_utils
from .. import bbox
def relabel_data(d, mapping, copy=True):
"""
Relabel data according to a mapping dict.
Modify the entries of :param:d according to a :param:mapping dictiona... |
187a8a8346c86cf9af670e0d592beb075b4f1297dfdd405ddaa8f2259d0deb8a | Python | 14,922 | 332 | #!/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 copy import deepcopy
import numpy as np
from ax.adapter.base... |
8b185c8cc6317cc86fdec015501bf8ef1d648412c0100fa79352e93227f50cf5 | Python | 14,936 | 393 | # 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 Sequence
from typing import final
import pandas as pd
from ax.adapter.base import Adapter
from a... |
0a05f388ee7a258b661f0690e395e66f2793893cb06bb250b92706dd1a5ac3cf | Python | 14,944 | 343 | # 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... |
558ac431642cc7484acb4d38fcc253e347ca5393e70eaf9338e8d83ee3f5432a | Python | 14,960 | 327 | # -*- coding: utf-8 -*-
"""
Created on 2020.05.19
@author: Jiahua Rao, Weiming Li, Hui Yang, Jiancong Xie
Code based on:
Errica, Federico, et al. "A fair comparison of graph neural networks for graph classification." (ICLR 2020). -> https://github.com/diningphil/gnn-comparison
"""
import time
from datetime import ti... |
f7934aebee9a0336a782a4a68f10881d53743f984200b8da3825d43e7513ffd9 | Python | 14,963 | 415 | # -*- coding: utf-8 -*-
"""Useful functions for the pke module."""
from __future__ import division
from __future__ import absolute_import
from __future__ import print_function
import os
import sys
import csv
import pickle
import gzip
import json
import codecs
import logging
from collections import defaultdict
from... |
fcd1aeb9779450c45919458bc709b3dd5ee350834c3ce26a92a6f1703e5a3fdb | Python | 14,971 | 346 | # -*- coding: utf-8 -*-
"""
Created on 2020.05.19
@author: Jiahua Rao, Weiming Li, Hui Yang, Jiancong Xie
Code based on:
Yang et al "Analyzing Learned Molecular Representations for Property Prediction" & "A Deep Learning Approach to Antibiotic Discovery" -> https://github.com/chemprop/chemprop
"""
from argparse impo... |
7e4bd233d895b94f0aa75028e62281e0bf4c212f2da8907e286d950a10a9ab8a | Python | 14,985 | 364 | """Detecting communities based on the Louvain Community Detection algorithm"""
import itertools
from collections import defaultdict, deque
import networkx as nx
from networkx.algorithms.community import modularity
from networkx.utils import py_random_state
__all__ = ["louvain_communities", "louvain_partitions"]
@p... |
48d7fed3b9b4d0d9c272af88e00474764edb8dc418b9f1c384d7e9430757e07a | Python | 14,986 | 401 | """Borrowed from:
https://github.com/AllenYolk/flash-snn/tree/main/flashsnn/utils
https://github.com/fla-org/flash-linear-attention/blob/main/fla/utils.py
"""
import functools
import torch
from spikingjelly import configure
from spikingjelly.logger import logger
from . import triton_missing as dummy
triton_op = to... |
a397e458bac5929d9fb7eddab78f2c140cf13375fbac42c161ac70ed1711dd1f | Python | 14,990 | 390 | """This module contains a linting functions for tool outputs."""
import ast
from typing import TYPE_CHECKING
from packaging.version import Version
from galaxy.tool_util.lint import Linter
from ._util import is_valid_cheetah_placeholder
from ..parser.output_collection_def import NAMED_PATTERNS
if TYPE_CHECKING:
... |
7bbe3680bc54ffd8636cf9f90a04103c8fe18a7d9865062806444f7291ba0a47 | Python | 15,001 | 358 | import pytest
import networkx as nx
from networkx.generators.classic import empty_graph
from networkx.utils import edges_equal, nodes_equal
class TestRelabel:
def test_convert_node_labels_to_integers(self):
# test that empty graph converts fine for all options
G = empty_graph()
H = nx.con... |
882d018e78c78b2e635da295401d57f797d4e7940a4c7b919cf54ddbb8bc1e4b | Python | 15,002 | 410 | """Tests related to awkward arrays"""
from __future__ import annotations
import warnings
import numpy as np
import numpy.testing as npt
import pandas as pd
import pytest
from awkward.operations import str as ak_str
import anndata
from anndata import AnnData, ImplicitModificationWarning, read_h5ad
from anndata.compa... |
39859fa612bb6a9095789e1b36eddd66a2d2fadc5c9636aff45a28f0463c9e23 | Python | 15,014 | 389 | import json
import logging
from unittest.mock import patch
import projects.api
import pytest
from django.test import TestCase
from django.urls import reverse
from projects.tests.factories import ProjectFactory
from rest_framework.test import APIClient
@pytest.mark.django_db
class TestProjectSampleTask(TestCase):
... |
a5833897e90617e5485f80f11ec016d3d314798c1780ef6f348c15df3c9fcd53 | Python | 15,016 | 348 | #!/usr/bin/env python
# Copyright Michael Fonder 2021. All rights reserved.
# ==============================================================================
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from utils.custom_layers import *
from m4depth_model... |
b9c533d2af7a14d09ee20a8cd5d6d4c6743070b9a135042501ad08187dc34630 | Python | 15,032 | 356 | #!/usr/bin/env python3
import sys
import os
import numpy as np
# -expand module search path to parent directory
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
# -custom-written code
import main
from params.param_stamp import get_param_stamp_from_args
from params.param_values import chec... |
c099077982855a1ab51bb12ca8715f8f95d6b8c4e1effa8b9f2b43cc3bfd7645 | Python | 15,036 | 436 | """
#########################################################################################################
Author: Álvaro Fernández García
Date: 24 - Marzo - 2019
Description: Validación cruzada del clasficador encargado de detectar las Glándulas.
#####################################################################... |
010216a85bd23d59ee75f81c3fce2eb6b4504850dbe29132211232bead74f6c7 | Python | 15,037 | 377 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Classes and functions for training and saving models
Created on Wed May 19 09:54:16 2021
@author: townesf
"""
import numpy as np
import tensorflow as tf
from time import time,process_time
from contextlib import suppress
from tempfile import TemporaryDirectory
from o... |
a1beff411ef264435782fd4dd3fd7467111d3dbddf5ffff2062ed1eea502db54 | Python | 15,038 | 417 | import copy
from typing import Callable, Tuple
import torch
import torch.nn as nn
import torch.nn.functional as F
from .. import base
from ..functional.net_config import detach_net
__all__ = [
"fptt_online_training_init_w_ra",
"fptt_online_training",
"ottt_online_training",
]
def fptt_online_training_... |
d25bafaaab7751351e3d75a8dca8326db1901c150dc2ed4ded594985b2f2a5a7 | Python | 15,046 | 481 | # gapped_kmer.py
# Authors: Jacob Schreiber <jmschreiber91@gmail.com>
# adapted from code written by Avanti Shrikumar
import scipy
import numpy as np
from concurrent.futures import ThreadPoolExecutor
from numba import njit
from numba import uint64
import numba
from . import precompile
_FIBONACCI = np.uint64(11400... |
3f90c2a9797c505877ab1acc63fa1464abdc8bb31cdf8ab7ea589da7bf087efe | Python | 15,050 | 339 | import copy
import functools
import warnings
import numpy as np
import pandas as pd
import spatial_lda.featurization as ft
from sklearn.cluster import KMeans, MiniBatchKMeans
from sklearn.metrics import silhouette_score
from sklearn.model_selection import train_test_split
from tqdm.notebook import tqdm
import ark.uti... |
15842d89a982f2daa15e948c21da1585474f0d39c47846a34d5c9a7222fb29b6 | Python | 15,055 | 415 | import os
import pathlib
from glob import glob
import numpy as np
import torch
import torch.nn.functional as F
from torch.utils.data import Dataset
from ..utils import import_attr
from . import norms
class FieldDataset(Dataset):
"""Dataset of lists of fields.
`in_patterns` is a list of glob patterns for the... |
e4c91ee097552b88c931a580ed64a375574e6375b0cac274f2d58985948a60a9 | Python | 15,058 | 491 | import pytest
import numpy as np
from ..sFIR import smooth_fir
def test_regress():
val1 = np.random.randint(1, 10)
val2 = np.random.randint(11, 200)
y = np.random.random((val2))
X = np.random.random((val2, val1))
out = smooth_fir.regress(y, X)
assert type(out) == type(np.asarray([]))
asser... |
12cee3b966ef7ea81b42ea1ea1170ed83a832cfdd4b14ceb37ddfb964e7415fc | Python | 15,066 | 375 | """Tests for tiling segmentation QC metrics."""
from __future__ import annotations
import dask.array as da
import numpy as np
import pytest
import xarray as xr
import squidpy as sq
from squidpy.experimental.im._tiling import compute_cell_info, compute_cell_info_tiled
from tests.conftest import PlotTester, PlotTester... |
d9bbc645fc40dafcdfb8af626c479ba4d331b2765275cb7e20d6f01d04bb99d7 | Python | 15,074 | 427 | """Qwen2.5 dense versus public-recipe SNN inference efficiency runner."""
from __future__ import annotations
import argparse
import gc
import hashlib
import math
import os
import statistics
import subprocess
import sys
import time
from pathlib import Path
from typing import Dict, List, Mapping, Optional
import torch... |
cb0752a1015a62ae4efbb84f44be963c4488e2b7b369619ce83307ac07d47178 | Python | 15,075 | 509 | # 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... |
e47bed5f6da169d35971276666a5268ecea6fd330da51f0bf895c4bc1252e021 | Python | 15,079 | 390 | """Offline CUDA implementation calibration; production never runs this search."""
import argparse
import csv
import hashlib
import importlib
import json
import math
import os
from pathlib import Path
import statistics
import subprocess
import time
import torch
FAMILIES = (
"if",
"lif",
"plif",
"qif"... |
d84cf6bbdd0ff6459a3a97a592eb64ef094c47cdbeec8d7bebaaebf8f5dec85b | Python | 15,087 | 404 | import os
import time
import numpy as np
import tensorflow as tf
import pickle
import librosa
from tensorflow.python.keras import backend as K
from .dataset import DataSet
from tqdm import tqdm
# ----------------------------------------------------------------------------
default_opt = {'alg': 'adam', 'lr': 1e-4, '... |
ec65dc0d9b0f3da8df00eeecc0c7ec1f971600d445ec72361ad74a1bf2d19326 | Python | 15,096 | 444 | import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
from pylab import *
import numpy as np
import random
import math
import time
import os
import glob
import copy
plottest = False # True
Nrms = 10 # Number of averages
DR_estimates = np.zeros(Nrms)
Dz_es... |
78f42bb53675bb8260b629d87383992e2c7cb3640a3a00a6b02aa04405f87cec | Python | 15,098 | 312 | import numpy as np
import torch
from torch.nn import functional as F
from models.fc.layers import fc_layer, fc_multihead_layer
from models.fc.nets import MLP, MLP_gates
from models.conv.nets import ConvLayers
from models.cl.memory_buffer_stream import MemoryBuffer
from models.cl.continual_learner import ContinualLearne... |
3e00e39e4f1495d3b4f9436f3b278b43a2a1aebf52f8df23582eee3cb457c21c | Python | 15,101 | 418 | import warnings
import itertools
import numpy as np
from ..utils import compute_lipschitz_constants
from ..progress_bar import bar, ProgressBar
from ..backend import get_backend
from ..scoring import r2_score
from ..validation import check_cv
def solve_sparse_group_lasso_cv(X, Y, groups=None, l21_regs=[0.05],
... |
9054137ac362c0fa7a65e428f551de50eedbf2a03efe5dc19c4ac200e10fa384 | Python | 15,105 | 411 | from __future__ import absolute_import
import time
import logging
from collections import namedtuple
from itertools import takewhile
import email
import re
from ..exceptions import (
ConnectTimeoutError,
MaxRetryError,
ProtocolError,
ReadTimeoutError,
ResponseError,
InvalidHeader,
)
from ..pack... |
fcc013783ade78141f5c9b711aa0417944cfa04ee9830aec821b10c1485a2798 | Python | 15,117 | 490 | import pytest
from clpipe.config.options import ProjectOptions, ScrubColumn, ScrubTimepoints
from clpipe.postprocutils.image_workflows import *
from clpipe.postprocutils.global_workflows import *
def test_build_postprocessing_wf(
artifact_dir,
request,
sample_raw_image,
sample_raw_image_mask,
sam... |
b119d52108d7741ba3253e25f5de6a13c2621cf52118532125e87d3b786a4876 | Python | 15,121 | 447 | from __future__ import annotations
import importlib
import importlib.resources
import json
from collections.abc import Callable, Sequence
from typing import TYPE_CHECKING
import jsonschema
import pandas as pd
import pytest
from referencing import Registry, Resource
from anndata import AnnData
from anndata.acc import... |
a8cd50a874b67e876da0feff1a8ad0efcb0cd3d4c459fb53f1068775769e2a1c | Python | 15,124 | 380 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Classes and functions for training and saving models
Created on Wed May 19 09:54:16 2021
@author: townesf
"""
import numpy as np
import tensorflow as tf
from time import time,process_time
from contextlib import suppress
#from shutil import rmtree
from tempfile impor... |
f7587ae286e6b4b783da742d5cf022fb6a401f29f6cc1188c8e672b1459cfda9 | Python | 15,138 | 398 | #!/usr/bin/env python
# Identification of potential RNA G-quadruplexes by G4RNA screener.
# Copyright (C) 2018 Jean-Michel Garant
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundatio... |
b22effd5102f9579e53debe81021697e8380fa43e83cf8fc55d16506507b7c54 | Python | 15,140 | 408 | from typing import Optional
import torch
import torch.nn as nn
import torch.nn.functional as F
from .. import functional, surrogate
from .base_node import BaseNode
__all__ = ["MPBNBaseNode", "MPBNLIFNode"]
class MPBNBaseNode(BaseNode):
def __init__(
self,
v_threshold: float = 1.0,
v_res... |
fd40e7a798e4e85c69c24e319c80aa013291cadcbe34b5e15382390a12eebc3d | Python | 15,140 | 418 | from typing import Any, Callable, Dict, Optional
import torch
import torch.nn as nn
from .. import functional, layer, neuron
from ..layer.attention import QKAttention, SpikingSelfAttention
from .._neuron import _make_multi_step_neuron
__all__ = ["QKFormer", "qkformer_10_384"]
class _PatchEmbedInit(nn.Module):
... |
3233e990114d6d1703345828b5a85c6b0e41ee68909efd5f0ed3e6d211334d39 | Python | 15,146 | 380 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Classes and functions for training and saving models
Created on Wed May 19 09:54:16 2021
@author: townesf
"""
import numpy as np
import tensorflow as tf
from time import time,process_time
from contextlib import suppress
#from shutil import rmtree
from tempfile impor... |
a659d10d33fecb103e28430fd441ce75bbbe7e60e5528d22637acf9a781986e5 | Python | 15,147 | 352 | """
Manager and Serializer for libraries.
"""
import logging
from typing import (
Optional,
)
from sqlalchemy.exc import (
MultipleResultsFound,
NoResultFound,
)
from sqlalchemy.orm import Query
from galaxy import exceptions
from galaxy.managers.folders import FolderManager
from galaxy.model import (
... |
8b8a416f9038366682b25951d578b3ca1513a1a40532e2d9f89af2c2440575b5 | Python | 15,155 | 491 | import pytest
import networkx as nx
from networkx.utils import edges_equal
def test_tensor_product_raises():
with pytest.raises(nx.NetworkXError):
P = nx.tensor_product(nx.DiGraph(), nx.Graph())
def test_tensor_product_null():
null = nx.null_graph()
empty10 = nx.empty_graph(10)
K3 = nx.comp... |
dd9dbef83ed820b98f36dbc40ce393afce55ecd621fce9f94fed1a9f6fc5d451 | Python | 15,159 | 428 | import warnings
import pytest
from ..context import EngineContext
from ..examples import Example
from ..validation import (
_undefined_predicates,
arity_errors,
check_query,
run_preview,
)
def symbols(nl):
"""Return the names of the symbols of the engine."""
return {getattr(s, "name", s) for... |
00fc5415c86bec88f0df3c184345b2a362b8e8e69dc8f260f301df8d760edeca | Python | 15,168 | 336 | # -*- coding: utf-8 -*-
"""
Created on 2020.05.19
@author: Jiahua Rao, Weiming Li, Hui Yang, Jiancong Xie
Code based on:
Errica, Federico, et al. "A fair comparison of graph neural networks for graph classification." (ICLR 2020). -> https://github.com/diningphil/gnn-comparison
"""
import time
from datetime import ti... |
e1b2114e026623dcb6b92b84e18ac12a9101041f235dfb0ca493a1c08db48f33 | Python | 15,179 | 447 | import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
from pylab import *
import numpy as np
import random
import math
import time
import os
import glob
import copy
plottest = False # True
Nrms = 10 # Number of averages
DR_estimates = np.zeros(Nrms)
Dz_es... |
2c34b97f8ea1f0e6401789eb31da2d37fe3215f7142745dd405aaa2dba730428 | Python | 15,185 | 371 | import json
import logging
from collections.abc import (
Callable,
Iterable,
)
from typing import (
Any,
Optional,
TYPE_CHECKING,
Union,
)
from urllib.parse import (
urlsplit,
urlunsplit,
)
from sqlalchemy import (
Column,
create_engine,
delete,
insert,
Integer,
... |
0e78d2456156b3f2aa20e82c1deafb08e4096b4613b302d4fa56ef47c4fb3eca | Python | 15,188 | 471 | import abc
import dataclasses
import typing
from abc import abstractmethod
from ._util import Assert, Copy, Iterable, MechId, MechIdTuple, Merge
from .exceptions import ModelDefinitionError
if typing.TYPE_CHECKING:
from .parameter import Parameter
@dataclasses.dataclass
class CableProperties(Copy, ... |
4f2e0f76b6741d594915b7f3d338e79840af8de43a7d80c95d27499d3f13b38d | Python | 15,194 | 352 | # 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... |
9a24e2c495209b51aa57da9b265e68075af99ea7289fecd6336ec51a6e02baa3 | Python | 15,194 | 303 | import torch
from typing import Tuple
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence, pad_sequence
from torch import nn
import torch.nn.functional as F
import numpy as np
class RNNClassifier(nn.Module):
def __init__(self, arch: str, static_input_size: int, dynamic_input_size: int, static... |
3b97d9961a5944b58bdcceaf6820772740fa2cb417921eed3055349e44da09e6 | Python | 15,213 | 503 | import numpy as np
import matplotlib.pyplot as plt
import theory_curve
import scipy as sp
import math
import scipy.special
import matplotlib as mpl
from cycler import cycler
from tqdm import tqdm
myaxis_font = 8
myfont = 6
mpl.rcParams['axes.prop_cycle'] = cycler(color='bgrcmyk')
plt.rcParams.update({'font.size': myf... |
561330663cabc563cd55cc4e22ad33ababc5fe7c337811b9d37f0bf3920cd90e | Python | 15,213 | 522 | import pytest
from brian2 import NeuronGroup,Synapses, run, ms
from brian2.utils.logger import catch_logs
from numpy.testing import assert_array_equal, assert_equal, assert_allclose
import numpy as np
from brian2lava.tests.utils import *
def _compare(synapses, expected):
conn_matrix = np.zeros((len(synapses.sourc... |
a6d00b27fd56520f08ebbbf8f6b492f5bf9e1b8cdd5bd8d859694410031c4bf1 | Python | 15,216 | 359 | """Independent two-GPU DP/DDP/PP capture and correctness workload.
Run DP with Python and DDP/PP with torchrun (two workers). Manual control uses
ready/go/done/exit files in --gate-dir so the shell controls the NSYS session.
No profiling interface is added to SpikingJelly distributed training.
"""
from __future__ imp... |
6bfe6fe57f58e676cf03fb0a5cc5c727118d7547ac1828074b0111a79e56de19 | Python | 15,220 | 416 | # 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... |
f8485dfa593c43630cec5134fba0899edbee177a1ebf14357553def4e042bc33 | Python | 15,221 | 361 | # 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
"""
Functions that create ``BenchmarkProblem``s based on BoTorch test functions.
"""
from collections.abc import Mapping
fro... |
68dcdf4902779624d09495831bfed5290fa2fa3e10d90931ac6f446ab4d12c50 | Python | 15,222 | 508 | """ Synapse Assignment by Voxel Association Networks """
import random
import copy
import operator
import itertools
import torch
import numpy as np
import scipy.ndimage as ndimage
import pandas as pd
from ...types import bbox
from ... import seg_utils
from .. import colnames as cn
from . import locs
from . import ... |
d0b4f7aa3303f230a549156a07569d74159d8953958284f09043307f7bffc2cc | Python | 15,222 | 469 | # -*- coding: utf-8 -*-
"""
Smoothing
=========
Smooth a binary image based on the local configuration of voxels in a cube.
See also
--------
The algortihm has similarities to the skeletonization algorithm using
parallel thinning (:mod:`~ClearMap.ImageProcessing.Skeletonization`).
"""
__author__ = 'Christoph Kirst... |
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