sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
cd9fb7e7b014d41b5646b5d95d655c9f31d658640b2a95856fa65ff5c45f054e | Python | 18,499 | 446 | #!/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 Sequence
from typing import Any
from ax.core.optimization_config import M... |
828ea238d2939464287fe006db8a568f3245fb992aead4b2893127100502e96f | Python | 18,501 | 520 |
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains t... |
aa53fd3ae998c6026061b99a867424e8023298d39d5d0da1d29e8b5eb09a9a6f | Python | 18,510 | 473 | """
Created on 15/07/2014
@author: Andrew Robinson
Modification on 24/10/2022
Addition of LDAP3 auth provider using the ldap3 module. The original LDAP auth provider uses the python-ldap library which
has external dependencies like openldap client libs. ldap3 is a pure Python LDAP v3 client library.
@author: Mahend... |
23fc1ea7fcb531af73ae4c28d8fc7f70f11a289df36ed840b1c37dc6a1b85a8a | Python | 18,519 | 437 | """This module is responsible for converting between Galaxy's tool
input description and the CWL description for a job json."""
import json
import logging
import os
from enum import Enum
from typing import (
Any,
NamedTuple,
Optional,
)
from galaxy.exceptions import RequestParameterInvalidException
from g... |
066f7d03438fecc427835105af97f089ba998b1ca81bf838182bf221d835aa76 | Python | 18,526 | 489 | import torch.nn as nn
import torch
import torch.nn.functional as F
from torch.autograd import Variable
import torch.optim as optim
import dgl
from dgl.nn import GATConv
from blitz.modules import BayesianLinear
import math, random
import numpy as np
class ConvLSTMCell(nn.Module):
def __init__(self, input_dim, hidd... |
185e057094a1704b0be9195d8e285eb60355a1649ed69f349e68ead1d350d89e | Python | 18,527 | 429 | # -*- coding: utf-8 -*-
"""
Created on 2020.05.19
@author: Jiahua Rao, Weiming Li, Hui Yang, Jiancong Xie
Code based on:
Shang et al "Edge Attention-based Multi-Relational Graph Convolutional Networks" -> https://github.com/Luckick/EAGCN
Coley et al "Convolutional Embedding of Attributed Molecular Graphs for Physical... |
a3446f8cf0dfb09139f94b38a1c9d6bcbd1e475b1dc7a747a5afff9e4e136bd0 | Python | 18,533 | 352 | # -*- coding: utf-8 -*-
"""
Created on Mon Jul 29 14:07:09 2019
@author: schelskim
"""
from .generaltools import generalTools
import sys
import os
import numpy as np
import pandas as pd
from skimage import io
from skimage import morphology as morph
from scipy import ndimage
from skimage import measur... |
ba5c3db9fd234bd81043a68ecb02c9fc27d1e59bd569e05b0db0da01a3ee6637 | Python | 18,547 | 473 | # 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... |
c9711f18aa2aae1a0fb8039fa2239e634cbacee783d050fdf93c5edf56c2f1eb | Python | 18,566 | 568 | import abc, numpy as np, pickle, h5py, math, itertools
from .helpers import ConfigurableClass
from .voxels import VoxelCloud, detect_box_compartments, Box
from sklearn.neighbors import KDTree
from .exceptions import *
from .reporting import report
class Compartment:
"""
Compartments are line segments with a r... |
fd8afb30e93bf6bea04beea9a8dfede35ebe017659f523c899c1391859d72769 | Python | 18,573 | 496 | """Utilities to help job and tool code setup jobs."""
import json
import os
import shutil
import threading
from typing import (
Any,
cast,
NamedTuple,
Optional,
Union,
)
from galaxy.files import (
ConfiguredFileSources,
DictFileSourcesUserContext,
FileSourcesUserContext,
)
from galaxy.... |
4098a65f3aad40d1f7e1e192fa47d884ad9049442f6aea3ea1f8aaa032aa548c | Python | 18,593 | 289 | import multiprocessing
import os
from typing import Optional, Tuple, Union
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
import numpy as np
import pandas as pd
from simba.mixins.geometry_mixin import GeometryMixin
from simba.plotting.geometry_plotter import Geometr... |
4e67793c6c99e32cba1ff0f24f148a78d3423a6d82185555fcb951fe4c8f5896 | Python | 18,632 | 564 | import jax
import jax.numpy as jnp
import logging
from functools import partial
from typing import Generator
import itertools
import numpy as np
log = logging.getLogger()
def angular_momentum_xyz(ell: int) -> Generator[tuple[int, int, int], None, None]:
for lx in reversed(range(ell + 1)):
for ly in rever... |
6e431574f931881fd5e209f014b75a1453c19c7efdace5218b19c1ff27c8f064 | Python | 18,645 | 564 | """Provide utility functions for the main experiment.
Only functions that do not need a direct psychopy import.
main file: sp.py
other utilities: psychopy_utils.py
"""
import os.path as op
from collections import OrderedDict
from time import perf_counter
import numpy as np
import pandas as pd
tr = None # noqa: E4... |
ef7fa958fa55ffd9bd6b48789e6fbba72d808073e1e996ff12a3553e23906538 | Python | 18,645 | 506 | import itertools
import pytest
import networkx as nx
from networkx.algorithms import flow
from networkx.algorithms.connectivity import (
local_edge_connectivity,
local_node_connectivity,
)
flow_funcs = [
flow.boykov_kolmogorov,
flow.dinitz,
flow.edmonds_karp,
flow.preflow_push,
flow.short... |
7bdb2f2121d25e80ea9915909f56a36002496d80b2cedc5151155a2d7a3b677b | Python | 18,646 | 491 | """A more modern version of the S3 object store based on boto3 instead of boto."""
import logging
import os
import re
from typing import (
Any,
Callable,
ClassVar,
Dict,
Set,
TYPE_CHECKING,
)
from typing_extensions import (
Literal,
NotRequired,
TypedDict,
)
if TYPE_CHECKING:
... |
3c954bed6493ff9c5d2989670b02eede1c1abadbc9c436ae01415d779a46e2ba | Python | 18,657 | 534 | """
Classes for wrapping Objects and Sanitizing string output.
"""
import copyreg
import inspect
import logging
import string
from collections import UserDict
from collections.abc import Callable
from numbers import Number
from types import (
BuiltinFunctionType,
BuiltinMethodType,
CodeType,
FrameType,... |
910e45e5c855069e687dd18d720c42e6169647ca759416bcacd0619936615097 | Python | 18,665 | 526 | # This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains th... |
98c1b076198f03f0c1ef2225057f0e5df2feb7381a51bde552427f244c83c30a | Python | 18,676 | 561 | # ----------------------------------------------------------------------------
# train_multilayer_perceptron.py
# Author: Antoine Beauchamp
# Created: December 15th, 2020
"""
Train a multi-layer perceptron
Description
-----------
This script trains a multi-layer perceptron neural network to classify mouse
voxels int... |
6fac5ceba337e717e26d3d099376a711696d0d8d8815c3b6eabf9484b627ea14 | Python | 18,709 | 417 | #!/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 data.labelstream import SharpBoundaryStream, RandomStream, FuzzyBoundaryStream
from data.datastream import ... |
ff10a3af4bc9649898486d6c810e97a0afa58c1d051bd6550565eefc9fbb445c | Python | 18,713 | 484 | import pathlib
import subprocess
from collections import defaultdict
from concurrent.futures import ProcessPoolExecutor, as_completed
from math import ceil
import numpy as np
import pandas as pd
import scipy.sparse as ss
import xarray as xr
from .._allc_to_region_count import batch_allc_to_region_count
from .._doc im... |
a79bd5ef49bccc9b57de71fda2c746f5e12fcbe8eca9f44b79f133d9375a225e | Python | 18,719 | 369 | import function as func
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import pdb
import os
import math
import pysam
import sys
import random
import lockfile
from time import sleep
## Variables
global_var_dict = func.global_variables()
SAMPLE = global_var_dict['SAMPLE']
CNV_CHR ... |
da0d4bc17639c97114ea0f05618bbc98a5a61405e3fb484a434b16e3609476ca | Python | 18,753 | 422 | import abc
import logging
import os
import shutil
from typing import (
NamedTuple,
Optional,
Union,
)
from sqlalchemy.orm import Session
from sqlalchemy.orm.exc import DetachedInstanceError
from galaxy.datatypes.sniff import (
convert_function,
FilePrefix,
should_convert_text,
stream_url_t... |
f793f2e9193586be51cf505f300c57ded63a3a673ea8c7daafc2cd8ae8dfa147 | Python | 18,760 | 478 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 14 23:47:22 2022
@author: wirrbel
"""
import nrrd
import os
import json
import matplotlib.pyplot as plt
import numpy as np
from scipy.ndimage import gaussian_filter
import tifffile
import sys
sys.path.append('../cortical_flatmaps/ccf_streamline... |
35ffaeb1d4d91c590eaa71f04e38108c99509268ae4c82e5541a8c0b2f863205 | Python | 18,762 | 565 | #!/usr/bin/env python
# how to use this function...
# PYTHONPATH=lib python lib/galaxy/model/dataset_collections/types/semantics.py
import argparse
import ast
import os
import re
import sys
from io import StringIO
from typing import (
Annotated,
Any,
Literal,
NamedTuple,
Optional,
Union,
)
imp... |
d2f1503b744225a069cd7be74337566bfa982c7368fc8f432026213d924d50c9 | Python | 18,777 | 528 | from collections import UserDict
import pytest
import networkx as nx
from networkx.utils import edges_equal
from .test_graph import BaseAttrGraphTester
from .test_graph import TestGraph as _TestGraph
class BaseMultiGraphTester(BaseAttrGraphTester):
def test_has_edge(self):
G = self.K3
assert G.... |
aa7b2ea0b8348b4bc84417b6eb4f5d8461e91039b6a4ef130c93737e09d3474e | Python | 18,797 | 413 | """
Plot Figure 7 (Network)
"""
import numpy as np
import pylab as pl
import strinf as si
from strinf.plotting import truncate_colormap
# # # PARAMETERS # # #
ZOOM = 1.5
SAVE = True
SHOW = True
PANEL = ("D", "G", "H", "I", "J", "M") # The sketches in A, B, C, E, F, H, K, L are always plotted.
MT_tuning = {
... |
dfb3a5a5f95772e3b54bf4569111596e24b8bba0290ddb9969dc8ce38d0998b6 | Python | 18,808 | 541 | import copy
import os
from typing import (
Any,
Callable,
cast,
Dict,
Iterable,
Iterator,
List,
Optional,
Tuple,
Union,
)
from typing_extensions import (
get_args,
Literal,
)
from galaxy.tool_util_models.tool_source import JavascriptRequirement
from galaxy.util import (... |
c3c2e4ff5aef85a9924cebb59aa09f584fa81d8403091e20d1e5f789cf53982e | Python | 18,822 | 533 |
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains t... |
a6c84487ca66347767c2b430fff9d02b3e7e7dc41a3322fb425d407a15ba2721 | Python | 18,832 | 379 | # 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... |
c119d1b71396ed5fb84c6984909d167b2a27326c916160dba5f96840fe88592b | Python | 18,833 | 525 | import logging
import os
from collections import defaultdict
from collections.abc import Callable
from datetime import datetime
from typing import (
Any,
NamedTuple,
Optional,
Protocol,
)
from galaxy import exceptions
from galaxy.files.sources import (
BaseFilesSource,
PluginKind,
)
from galaxy... |
849f92d7910e356468e43e4839b328b8dd1c781be07a4870297d5a05818b0048 | Python | 18,835 | 541 | # -*- coding:utf-8 -*-
__author__ = 'yangjian'
"""
"""
import copy
import pandas as pd
import pickle
from deeptables.models.config import ModelConfig
from deeptables.models.deeptable import DeepTable
from deeptables.models.preprocessor import DefaultPreprocessor
from deeptables.utils import dt_logging, fs, consts as... |
49f5e435223de6a49ae85fc7dbcd1ec2506b44745b73bc95ae9c30551dabb46f | Python | 18,839 | 415 | import math
import numpy as np
import random
import torch
from torch.optim.optimizer import Optimizer
from torch.nn.utils import parameters_to_vector, vector_to_parameters
import torch.nn as nn
import torch.nn.functional as F
from models.fc import excitability_modules as em
## This code has been based upon: https://g... |
8cc5642f57bbe873310f924e4f7486f11a41d43e20b74e47ea41a8af2583ac65 | Python | 18,839 | 508 | #! /usr/bin/env python3
### Get the FES estimate from reweighting. 1D or 2D only ###
# uses a weighted kernel density estimation, so it requires the bandwidth sigma
# usage is similar to plumed sum_hills
# NB: in case of multiple walkers one should combine them in a single file
# when using --stride or --skiprows one... |
2c5d7d57b3792fae12fc400e9718a70a84e3bfeec9a0d3ffb2c725117fb78590 | Python | 18,845 | 625 | import base64
import copy
import json
import numpy as np
import pytest
from zarr.codecs import Blosc, Delta, Pickle, Zlib
from zarr.errors import MetadataError
from zarr.meta import (ZARR_FORMAT, decode_array_metadata, decode_dtype,
decode_group_metadata, encode_array_metadata,
... |
63f21ba363342a4b5dc11ef57951ce2f6d50c40cc822a44142d53f4e665045f6 | Python | 18,846 | 464 | # 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... |
a99c46f2e4c1a8da9d6cd7c51a225b1b63123751468579c83e478a7a65956748 | Python | 18,850 | 423 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Oct 14 02:13:31 2022
@author: wirrbel
"""
# We begin by adding the current path to sys.path to make sure that the imports work correctly
import sys
sys.path.append('/home/wirrbel/brainrender_update_2022-01/')
import os
import pandas as pd
import numpy ... |
904a0fed7a47bd39b8bdce88648fc90a0b35947ef2616831f90c449c83fbe2dc | Python | 18,857 | 464 | """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."""
from enum import Enum
from typing import Any, List, Optional, Union
from django.conf import settings
from pydantic import BaseModel, Field, Strict... |
d2ff19c136628c98587b689b4cd14fd6603bd367ca8b6511da9d00e5dc03c709 | Python | 18,865 | 524 | """Cell-aware tiling for large images.
Splits a label image into overlapping tiles such that every cell is fully
contained in exactly one tile. Cells are assigned to tiles by centroid:
the tile whose non-overlapping base region contains the centroid owns the
cell. Non-owned cells are zeroed out in each tile's mask s... |
43f9b23a0d74ba6331bfcf851798e32b7eb5914f14edfe2c4c991475c4564ad0 | Python | 18,873 | 476 | import random
import time
import numpy as np
import scipy.sparse as sp
import torch
import torch.nn as nn
import torch.nn.functional as F
from tqdm.auto import tqdm
from ..base import InjectionAttack, EarlyStop
from cogdl.utils.grb_utils import eval_acc, feat_preprocess, adj_preprocess, getGraph, getGRBGraph
class T... |
38e01b8697a0bc4c7adcf73bc184ee6cac8a51aa94493b4be7f6537ff776242d | Python | 18,875 | 459 | #!/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 warnings
from typing import cast, TYPE_CHECKING
import num... |
6235f16fd00cf5043f60e3a0073841d85062f1e5fced50e3460b9259e8111b2a | Python | 18,904 | 383 | # 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... |
43b8a0dcd3ed5b11bc52a22ebb3c6e6b732fea5a8d0e95225dd1d9a1e96242b7 | Python | 18,907 | 575 | from __future__ import annotations
from contextlib import contextmanager
from copy import deepcopy
from functools import reduce, singledispatch
from importlib.util import find_spec
from typing import TYPE_CHECKING, Literal
import numpy as np
import pandas as pd
from pandas.api.types import is_bool_dtype
from scipy im... |
8343ee6eb7c6cd68cb12d74da5ca7dda0e61841872eb4c39e71f7c96f6d80e5e | Python | 18,910 | 577 | import collections
import operator
from typing import AbstractSet, Iterable
import numpy
from nl_core.relational_algebra import str2columnstr_constant
from ..datalog import WrappedRelationalAlgebraSet
from ..datalog.expression_processing import (
EQ,
UnifyVariableEqualities,
conjunct_formulas,
extrac... |
520a6b48527a7146cf5ec7aedb8fae39cd7ae290a4bbe4111b4f8022e835849b | Python | 18,917 | 417 | import statsmodels.api as sm
import statsmodels.stats.outliers_influence as sm_diagnostics
import statsmodels.stats as sm_stats
import matplotlib.pyplot as plt
import scipy as scipy
import pandas as pd
import seaborn as sns
import os
# https://www.statsmodels.org/dev/examples/notebooks/generated/regression_pl... |
938abd44c09701baa2693fbca5ddfdc19a6a8070d14137b004fd3edb5ed1309f | Python | 18,947 | 438 | # -*- coding: utf-8 -*-
"""
Created on 2020.05.19
@author: Jiahua Rao, Weiming Li, Hui Yang, Jiancong Xie
Code based on:
Shang et al "Edge Attention-based Multi-Relational Graph Convolutional Networks" -> https://github.com/Luckick/EAGCN
Coley et al "Convolutional Embedding of Attributed Molecular Graphs for Physical... |
17a5874b05dd420a3dc9299f782b4deeec611c2d676910902821fd94529f5e31 | Python | 18,951 | 533 | """
This file is modified from methylpy https://github.com/yupenghe/methylpy.
Author: Yupeng He
Notes added on 07/03/2022 - Difference between bismark and hisat-3n
Read mpileup doc first: http://www.htslib.org/doc/samtools-mpileup.html
For Bismark SE mapping:
Bismark converted the reads orientation based on their co... |
950c3036b508e85a67fbd476fe1af4bdf895922b89314ea800d64b48810e3416 | Python | 18,972 | 525 | 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... |
9c66b8493e720fc19af3b7f3e7a1e61c1b9c498e51afb5dd975482da7fa3ed69 | Python | 18,979 | 466 | import unittest, os, sys, numpy as np, h5py, importlib
sys.path.insert(0, os.path.join(os.path.dirname(__file__), ".."))
from bsb.core import Scaffold
from bsb.config import JSONConfig
from bsb.simulators.nest import NestCell
from bsb.models import Layer, CellType
from bsb.exceptions import *
def relative_to_tests_f... |
481a3586b00b38d06a82e20a6d9dd2e0e4fd127356705c9f1d199aa75897dacc | Python | 19,008 | 489 | import numpy as np
import warnings
import math
from tqdm import tqdm
from skimage.measure import regionprops
from skimage.draw import polygon
from csbdeep.utils import _raise, axes_check_and_normalize, axes_dict
from itertools import product
from .geometry import polygons_to_label
OBJECT_KEYS = set(('prob', 'points... |
64161ca714e8c89ed0631b3a6dac92e2e62df20ca290804b0b7b8595d90960a7 | Python | 19,042 | 553 | import numpy as np
from scipy import stats
from scipy import sparse
from scipy.spatial import distance
from sklearn.utils.estimator_checks import check_estimator
from hdbscan import (
HDBSCAN,
BranchDetector,
detect_branches_in_clusters,
approximate_predict_branch,
)
from hdbscan.tests.test_hdbscan impo... |
3d9fefd368207ca0ad1a9eda29d7b9d6f3c7d4681bed573cb1c96c13772a2735 | Python | 19,047 | 499 | #!/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
"""
Module containing a registry of standard models (and generators, samplers etc.)
such as Sobol gene... |
69cc4d5f8d5d9f992ec2e27298d17ec7aed17d36c0a8f9fea77bad04d1d7cbf4 | Python | 19,048 | 412 | # Protobuffer files handler
#
# Author : Michael Fonder
#
# This file contains the scripts necessary to encode some data samples into
# protobuffer files (ProtoBufSerializer class) and to extract minibatches out
# of a protobuffer database (ProtoBufDeserializer class).
#
# ==============================================... |
68159e64f95560df8da93296a0e86421d27fb1d283a99279c14195f80fccb57f | Python | 19,065 | 508 | """
Some of the functions are modified from methylpy https://github.com/yupenghe/methylpy.
Original Author: Yupeng He
"""
import gc
import logging
import os
import resource
import shlex
import subprocess
from concurrent.futures import ProcessPoolExecutor, as_completed
import numpy as np
import psutil
from pysam impo... |
df1378c3106cfbbab91bf55a1558e40b3004e67b3b01eee0f0f2c8f59ceda165 | Python | 19,073 | 535 | """
Mask R-CNN
Train on the nuclei segmentation dataset from the
Kaggle 2018 Data Science Bowl
Licensed under the MIT License (see LICENSE for details)
Written by Waleed Abdulla
Heavily modified by Carsen Stringer for general datasets (12/2019)
------------------------------------------------------------
Usage: impor... |
fe45bf02a09e0317a3253649656820a6f53b6871df9aa552562d30d604c02342 | Python | 19,076 | 600 | """Basic algorithms for breadth-first searching the nodes of a graph."""
from collections import deque
import networkx as nx
__all__ = [
"bfs_edges",
"bfs_tree",
"bfs_predecessors",
"bfs_successors",
"descendants_at_distance",
"bfs_layers",
"bfs_labeled_edges",
"generic_bfs_edges",
]
... |
d2727031b24a46bf4a1c93897a55952e8c5377f12aa78991681ec137e6694b70 | Python | 19,089 | 411 | import tensorflow as tf
from tifffile import TiffFile as TIF
import numpy as np
import os
import matplotlib.pyplot as plt
import scipy.ndimage
from src.factory import Factory,Kernel
import copy
from astropy.convolution import Gaussian2DKernel
from src.utility import get_root_path
from astropy.convolution import Gaussia... |
29f4d5db56cc6f9dfc05e2c67e44649086df56947f46d54c62526856a38dfea9 | Python | 19,093 | 405 | import pandas as pd
import numpy as np
import pickle
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Descriptors
from rdkit.Chem import rdMolDescriptors
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Draw
from rdkit.Chem.Draw import rdMolDraw2D
import kerastuner... |
cd135ba4a41438f6704f257e427373c05f225783924b7914eec6fb81268de7a8 | Python | 19,105 | 528 | import argparse
import os
import sys
import glob
import pandas
import numpy
import nipy.modalities.fmri.hrf
import matplotlib.pyplot as plt
from nipy import load_image
from subprocess import call
from nipy.core.image.image import Image
from nipy import save_image
import scipy.stats
from scipy.ndimage import convolve1d
... |
1514f544ae4945ce993c1854225c74d13263e6300b6821995d783e454482ea1b | Python | 19,117 | 458 | from copy import deepcopy
import numpy as np
import xarray as xr
from skimage.draw import disk
def generate_test_dist_matrix(num_A=100, num_B=100, num_C=100,
distr_AB=(10, 1), distr_random=(200, 1),
seed=None):
"""
This function will return a random... |
a5a0285f3884456fc7e841e211393298cccec2b82a336fde7999fae4ddafa9ea | Python | 19,147 | 475 | from __future__ import annotations
import warnings
from collections.abc import Hashable, Mapping, Sized
from dataclasses import dataclass
from functools import wraps
from typing import TYPE_CHECKING, overload
import numpy as np
import pandas as pd
from anndata._warnings import warn
from ..compat import XDataArray, ... |
8f84bb0b3dac337a3df56e9529fcd45dc34883d7a4570c5aeb76e26f8fff8aad | Python | 19,156 | 556 | # -*- coding: utf-8 -*-
"""
Functions for calculating DDLS
"""
import math
import time
import warnings
import cv2
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import tools.image.post_processing as pp
warnings.filterwarnings("error")
def point_on_circle(center, radius, angle):
'''
... |
052dcd8d51855b1c0932f0cb05b26e817e5fb88bbe7e3790adab08df75951e9e | Python | 19,168 | 578 | import re
import sys
import os
import math
from numpy import *
output= open(r'E:\OneDrive\学术\博士论文\fig\Part 2\co-expression\SPTBN2 matrix.txt','w+')
p2 = [[],[],[],[],[],[],[],[],[],[],[],[],[],[],[],[]]
p3 = [[],[],[],[],[],[],[],[],[],[],[],[],[],[],[],[]]
p4 = [[],[],[],[],[],[],[],[],[],[],[],[],[],[],[],... |
227ca77746e233ef8a138a74676bbcd69a3f5b35de06cb97fec7babea8735c57 | Python | 19,172 | 618 | # -*- coding: utf-8 -*-
# Imports
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib
from scipy.stats import spearmanr
from scipy.cluster import hierarchy
from .math_utils import model_performance
from .pd_utils import to_torch
# Scatter plot for pred-obs
def plot2d(x,y,expor... |
6627aa2efae116564d5901a8b59354def0baec91fe582fbbc92d09ed57fb6bfb | Python | 19,175 | 467 | """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
import os
import uuid
from collections import Counter
import ijson
import pandas as pd
try:
import ujson as json
except: # no... |
89c73dcbe3777034344a936fb1417407d69dfad44d652048d7a2b1b20734a3be | Python | 19,184 | 392 | """
Contains library functions
"""
import json
import logging
import os.path
from markupsafe import escape
from galaxy import (
exceptions,
util,
)
from galaxy.managers.collections_util import (
api_payload_to_create_params,
dictify_dataset_collection_instance,
)
from galaxy.model import (
Histor... |
263226ba7dc8e1b352bb0a5efa1ddee8fb96c6f9a430ae438869528e162a950e | Python | 19,185 | 589 | """
Provides utilities for working with GFF files.
"""
import copy
from bx.intervals.io import (
GenomicInterval,
GenomicIntervalReader,
MissingFieldError,
NiceReaderWrapper,
ParseError,
)
from bx.tabular.io import (
Comment,
Header,
)
from galaxy.util import unicodify
FASTA_DIRECTIVE = ... |
68a7d63941e44f4a91573ce10e08d4f10a80f01ec6869b1456eff319ce6fb387 | Python | 19,199 | 466 | import logging
import os
import shutil
import tempfile
from contextlib import contextmanager
from datetime import datetime
from typing import (
Any,
Iterator,
Optional,
)
from galaxy.exceptions import (
ObjectInvalid,
ObjectNotFound,
)
from galaxy.objectstore import ConcreteObjectStore
from galaxy.... |
677b12e5efa465a9665c6f628a891445913b1b4bc6a2769f2012a3ca097f6c1e | Python | 19,217 | 488 | # 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... |
a136ea7f1f5fd2c5fd7f2854b9ce9e07276be1b3abf639cb26cb8e87f47fe5e4 | Python | 19,241 | 658 | import pytest
import sys
import shutil
import json
from pathlib import Path
from bids import BIDSLayout, BIDSLayoutIndexer
from clpipe.bids import get_bids
import nibabel as nib
import nipype.pipeline.engine as pe
from nilearn import plotting
from nilearn.image import load_img, index_img
sys.path.append("../clpipe")... |
8bf745c2d4d2e20be03be68403031b966ab802dddf34dad044a35031e4688b9d | Python | 19,245 | 467 | import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
import spatial_lda.visualization as sv
from alpineer import misc_utils
from ark.utils.spatial_lda_utils import make_plot_fn
def draw_boxplot(cell_data, col_name, col_split=None,
split_vals=None, dpi=None, sa... |
251e8475e75c33c943d0bd1384e74c66a15d667b46e23153403544e5774bf5b9 | Python | 19,261 | 540 | import itertools
import itertools as it
import time
import typing
import arbor
import numpy as np
from arbor import units as U
from bsb import (
AdapterError,
Chunk,
SimulationData,
SimulatorAdapter,
UnknownGIDError,
report,
warn,
)
if typing.TYPE_CHECKING: # pragma: nocover
from .sim... |
7afcfb2dcbaa84c33bbff5a8aa6912d2f942ba476d967c941f5932d3e1e74573 | Python | 19,263 | 381 | '''
The script to test trained models
'''
import os
os.environ["CUDA_DEVICE_ORDER"]="PCI_BUS_ID"
os.environ["CUDA_VISIBLE_DEVICES"] = "0"
import numpy as np
import torch
from torch.autograd import Variable
from matplotlib import pyplot as plt
import pickle as pkl
from torch.optim import Adam
from tqdm import tqdm
impo... |
6f4397b4abd4606cc3c41ae721b3e1f00defa378e6458385cd6d36315496620a | Python | 19,320 | 678 | import pytest
import networkx as nx
def test_square_clustering_adjacent_squares():
G = nx.Graph([(1, 2), (1, 3), (2, 4), (3, 4), (3, 5), (4, 6), (5, 6)])
# Corner nodes: C_4 == 0.5, central face nodes: C_4 = 1 / 3
expected = {1: 0.5, 2: 0.5, 3: 1 / 3, 4: 1 / 3, 5: 0.5, 6: 0.5}
assert nx.square_cluste... |
42b5c247652486fdcf3563ae211883380f0f24b0279be814e174d6a0015985d6 | Python | 19,333 | 476 | #!/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
import os
import random
import string
from unittest.mock import patch
import sqlalchemy... |
c075a7e0556e5a2f7a46bd6f052b7959ff2b61e19eaae3f62ef2884d758b4dd7 | Python | 19,361 | 601 | from typing import Any, Callable, Dict, Optional
import torch
import torch.nn as nn
from .. import functional, layer, neuron, surrogate
from .._neuron import _make_multi_step_neuron
__all__ = [
"MSResNet",
"MaxResNet",
"ms_resnet18",
"ms_resnet34",
"max_resnet18",
]
def _conv3x3(in_channels: in... |
3b030dd3a7f6bf86d5f765d8218283edf65cdc39c0c9eb93b93176a3ffa2350d | Python | 19,366 | 618 | from collections import Counter
import pytest
import networkx as nx
from networkx.algorithms.planarity import (
check_planarity_recursive,
get_counterexample,
get_counterexample_recursive,
)
class TestLRPlanarity:
"""Nose Unit tests for the :mod:`networkx.algorithms.planarity` module.
Tests thr... |
cc70de8fabec736937dd1fa1471118968888f6a4acb5dbae291982add216e3cf | Python | 19,369 | 559 | # -*- coding: utf-8 -*-
"""models
Defines network models using PyTorch .Module inheritance
"""
# Contributions and Changelog accessed via a private git repository:
# https://github.com/philipwijesinghe/deep-learning-lsm.git
# philip.wijesinghe@gmail.com
# Copyright (c) 2020 Philip Wijesinghe@University of St Andrews... |
89be34f62f8aac0d0751e33ff0527f71c30e3e85338caee920432757ef62a89f | Python | 19,373 | 547 | import base64
import itertools
from collections.abc import Mapping
import numcodecs
import numpy as np
from numcodecs.abc import Codec
from zarr.errors import MetadataError
from zarr.util import json_dumps, json_loads
from typing import cast, Union, Any, List, Mapping as MappingType, Optional
ZARR_FORMAT = 2
ZARR_F... |
69b9be293b60e3b757f53f2816db98e2aa80373744a2cb5c0380f7872e6a2229 | Python | 19,382 | 396 | # -*- coding: utf-8 -*-
"""
Created on Wed Feb 22 21:41:28 2022
@author: Zhiye
"""
from six.moves import range
import keras.backend as K
from keras.engine.topology import Layer
from keras.layers import Input, Dense, Reshape, Activation, Flatten, Dropout, Lambda, add, concatenate, Concatenate, Add, average, ... |
6eb3585f2b71968015845af437b0c25a734a92c6cead65faa8a113c2d5ba7178 | Python | 19,386 | 610 | from ast import Index
import numpy as np
from scipy import stats
import torch
from torch.optim.lr_scheduler import LambdaLR
import math
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torch.utils.data.sampler import SubsetRandomSampler
import torchvision
import torchvision.transfo... |
dfb26d6c7f96ebbff61a54b1ac51fb5963b0c255b442b262aea7f52c056207de | Python | 19,392 | 427 | import numpy as np
import matplotlib.pyplot as plt
from PIL import Image
from PIL import ImageFile
ImageFile.LOAD_TRUNCATED_IMAGES = True
import ptitprince as pt
from meld_classifier.paths import EXPERIMENT_PATH
from meld_classifier.meld_cohort import MeldCohort
import os
import glob
import pandas as pd
from statsmo... |
5e5cf3046c01edc0526cab37ac2cfd2ad37b37f88de2ca4b727e9e6a5f68d69d | Python | 19,400 | 569 | # ----------------------------------------------------------------------------
# mlp_validation_resampling.py
# Author: Antoine Beauchamp
# Created: February 3rd, 2021
"""
Description
-----------
"""
# Packages -------------------------------------------------------------------
import sys
import argparse
import o... |
d339e7a4ec556e17efd223ec2aebfd26f28a0a6fefa23fd8fba7f4a09dc06bf8 | Python | 19,410 | 434 | """Public, ``sdata``-aware entry points for stain normalization.
The single integration boundary for the stain module: the only file that
reads ``sdata.images[...]``, writes back via :class:`Image2DModel`, and is
re-exported publicly. Everything it calls is a pure DataArray-layer
primitive (:mod:`._reinhard`, :mod:`._... |
4e5a01c9f7b7be1ec5c9872defb8ec9fbf88703731c080edbe6c8252a85de844 | Python | 19,428 | 517 | import logging
import os
import h5py
import numpy as np
import pandas
import cooler
from genomic_regions import GenomicRegion
from ..tools.sambam import natural_cmp
from functools import cmp_to_key
import tempfile
import warnings
from ..tools.files import tmp_file_name
from ..tools.general import str_to_int
import shu... |
0404e119afcfb09ec58f28c70ca06f4970ce7562f811c8d8081d3843e3e10ea5 | Python | 19,438 | 534 | import glob
import json
import logging
import pathlib
import subprocess
import warnings
from typing import Union
import numpy as np
import pandas as pd
import xarray as xr
import yaml
log = logging.getLogger()
def calculate_posterior_mc_frac(mc_da, cov_da, var_dim=None, normalize_per_cell=True, clip_norm_value=10):... |
2dfd2e03ab2e5145a4b61bbf354f4b827fe6547def552bf1b61af51cbae865dc | Python | 19,443 | 559 | """Optimisers eliminating, simplifying and pushing projections."""
from itertools import permutations
from nl_expr import expression_walker as ew
from nl_expr.expressions import Constant, FunctionApplication, Symbol
from nl_expr.utils.orderedset import OrderedSet
from ..relational_algebra import (
COUNT,
Colu... |
8ff06d9bace96e0083af0b7a4cf94f086be1e838679ff0e5f4aa181e4ed06359 | Python | 19,460 | 520 | import pytest
from django.contrib.auth import get_user_model
from label_studio_sdk import LabelStudio
from projects.tests.factories import ProjectFactory
from tasks.tests.factories import TaskFactory
User = get_user_model()
class TestSDKPredictionValidation:
"""Comprehensive tests for prediction validation using... |
f9dae833f8cc8c5c22364445492a8a62674b3a68bea65d79dc768676f64950a2 | Python | 19,473 | 425 | import os
import pandas as pd
import numpy as np
from sklearn.ensemble import RandomForestClassifier
from sklearn.model_selection import cross_validate
from sklearn.svm import SVC
from sklearn import metrics
from sklearn.metrics import make_scorer, get_scorer
from tqdm import tqdm
import pprint
import random
import jso... |
2ecf61387409ce16464861eb62cfaefa75f355c77d48f3360489b6996f38c8cf | Python | 19,491 | 525 | # 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... |
7b786a7f4e8df949e9d09cc597672d44d213776c488266e9fb96087e50651353 | Python | 19,521 | 471 | #!/usr/bin/env python
# -*- coding:utf-8 -*-
import argparse
import numpy as np
import voxelmorph as vxm
import tensorflow as tf
import neurite as ne
import tensorflow.keras.backend as K
#import tensorflow_scientific as tfs
from voxelmorph.tf import tensorflow_scientific as tfs
import os
from skimage.metrics import st... |
86d4abb316a9f6a3e666a11a1a26e861dedd4d4f2db13bec86ef0f3495d34251 | Python | 19,526 | 464 | import torch
import torch.nn as nn
from torch.nn import functional as F
from torch.nn.parameter import Parameter
from torch.nn import Module
from torch.nn.modules.transformer import _get_clones
from torch.nn.modules.linear import Linear
from torch.nn.modules.dropout import Dropout
from torch.nn.modules.normalization i... |
6c89b45345d3926d7061709a25a2a7d92191712ca72ab390521ecab2727b5577 | Python | 19,529 | 430 | from __future__ import print_function, unicode_literals, absolute_import, division
import numpy as np
import warnings
import math
from tqdm import tqdm
from csbdeep.models import BaseConfig
from csbdeep.internals.blocks import unet_block
from csbdeep.utils import _raise, backend_channels_last, axes_check_and_normaliz... |
993e0050046f8de78e9cdd3d8d267022aed393c8db2c8184c9b6bba0333d75c9 | Python | 19,530 | 535 | """
FSM utility functions.
This module provides:
1. UUID7 utilities for time-series optimization (uses uuid-utils library)
2. FSM-specific helper functions for organization resolution and state management
UUID7 provides natural time ordering and global uniqueness, making it ideal
for INSERT-only architectures with mi... |
ab97fe9a681e529175a963a17de03aac99e553645dd894485c347d61b5476d7f | Python | 19,534 | 470 | import json
import logging
import time
from typing import (
Any,
Optional,
)
from urllib.parse import quote
from galaxy import exceptions
from galaxy.files import (
ConfiguredFileSources,
FileSourcesUserContext,
)
from galaxy.files.models import (
FilesSourceOptions,
PartialFilesSourcePropertie... |
74af8881a519682752b73228e73c57e8f4764a59ace3f72214d3ab87c2977d18 | Python | 19,536 | 479 | import pytest
import networkx as nx
np = pytest.importorskip("numpy")
pytest.importorskip("scipy")
class TestLaplacian:
@classmethod
def setup_class(cls):
deg = [3, 2, 2, 1, 0]
cls.G = nx.havel_hakimi_graph(deg)
cls.WG = nx.Graph(
(u, v, {"weight": 0.5, "other": 0.3}) for... |
7b67a11ecedc06e196cbd846c820625dbc6e0dedb80dc02b8cedffa26dfac571 | Python | 19,542 | 564 | #!/usr/bin/env python
# % brew vinstall samtools 1.0
# % brew vinstall samtools 0.1.19
# % brew vinstall samtools 1.1
# % brew env samtools 1.1
# PATH=/home/john/.linuxbrew/Cellar/htslib/1.1/bin:/home/john/.linuxbrew/Cellar/samtools/1.1/bin:$PATH
# export PATH
# LD_LIBRARY_PATH=/home/john/.linuxbrew/Cellar/htslib/1.1/... |
cf4781a96591eaea8951b99eae086ab0de6519eb9f2c5f132121894a238a16be | Python | 19,553 | 375 | import argparse
import logging
import os
import copy
from collections import defaultdict
from typing import List
import numpy as np
import torch
from sklearn import metrics
from torch.nn.utils.rnn import pad_sequence
from torch.utils.data.dataloader import DataLoader
from training.models import RNNClassifier
from opera... |
b3895e6822b05f82df76b37f371d98260f1e04ff10dabc2c34bae43289de5413 | Python | 19,572 | 625 | # util.py
# Authors: Jacob Schreiber <jmschreiber91@gmail.com>, Ivy Raine <ivy.ember.raine@gmail.com>
# adapted from code written by Avanti Shrikumar
from enum import Enum
from operator import attrgetter
import textwrap
from typing import List
import numpy as np
from numba import njit
from . import precompile
clas... |
27bb569b040136c88a595c69068c5583cb50f1077e93e3eb6efad1648b59c93a | Python | 19,581 | 465 | #!/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 pathlib
from collections.abc import Callable
from typing import Any
import torch
from ax.adapt... |
cf6737e91bb5a145c4129a11cb79e381707f3ae257d27925bcb26c4cde992de9 | Python | 19,581 | 439 | from typing import (
Optional,
Union,
)
from galaxy import model
from galaxy.exceptions import RequestParameterInvalidException
from galaxy.jobs.manager import JobManager
from galaxy.managers.context import ProvidesUserContext
from galaxy.managers.export_tracker import StoreExportTracker
from galaxy.managers.h... |
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