sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
966eeb3258184bf9fee9dca657bc07ef09b95cde5b644961e246ad1ceb137a76 | Python | 58,007 | 1,219 | # Flat versions of objective functions described in Tiago P. Peixoto
# Nonparametric Bayesian inference of the microcanonical stochastic block model
# for more see in peixotos_hierarchical_sbm.py
# @formatter:off
import math
from .objective_functions import ObjectiveFunction
from .peixotos_hierarchical_sbm_tools imp... |
c41cb5ba09a12365fe11328f9fe6de795bc43d3d55d86b2aa148faa886be8316 | Python | 58,104 | 1,370 | # 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 json
from collections.abc import Iterable, Sequence
from logging import Logger
from typing import Any, cast, Literal, ... |
d9c15d1a05103407cbe157861c98b1cc6945cae2eb76fc9b3c90dd9512a28774 | Python | 58,333 | 1,511 | #!/usr/bin/env python
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
import numpy as np
import imageio
import sys
import os
from matplotlib.widgets import Slider, Button, RadioButtons, TextBox
from matplotlib.backend_bases import MouseButton
import time
import argparse
from gc_segment.utils import... |
98e61ea5fc62938a3864729ae5be20296da831c6fa32cdb42a94986949c58933 | Python | 58,432 | 1,388 | #!/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 math
import warnings
from collections.abc import Mapping, S... |
a6f7b4659e9b51748fa7db94b21348bc947562550d88c7f6766e86257df415ee | Python | 58,841 | 1,167 | """
Offload jobs to a Kubernetes cluster.
"""
import json # for debugging of API objects
import logging
import math
import os
import re
from dataclasses import dataclass
from datetime import datetime
from typing import (
Any,
TYPE_CHECKING,
TypedDict,
Union,
)
import yaml
from galaxy import model
fr... |
824e2afc1d2e1d9673502caee4c0bb163101bd982440793450b81d978e497e0a | Python | 58,933 | 1,635 | # Copyright (C) 2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
from collections.abc import Sequence
from enum import StrEnum
from typing import TYPE_CHECKING, Any, cast
from django.conf import settings
from django.shortcuts import get_ob... |
689b301c8deffe529e78537b80e19aef588a34fe5404ecf9e3367ad2d59233d1 | Python | 58,939 | 1,505 | """This module contains a linting functions for tool inputs."""
import ast
import re
import warnings
from copy import deepcopy
from typing import (
Iterator,
Optional,
Tuple,
TYPE_CHECKING,
)
from packaging.version import Version
from galaxy.tool_util.lint import Linter
from galaxy.tool_util_models.p... |
c68a20df9fa1f56e59cabebcee07f1fb8a1876b7b8b082972d66a35722726234 | Python | 59,142 | 1,527 | #!/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 collections.abc import Iterable, Mapping, Mut... |
65139e1ec54123720eb80858a9732e3053eaa95a55e5d7ce5644df9aed0c49c3 | Python | 59,396 | 1,313 | import argparse
import random
import os
from os import getcwd
from yaml import dump
from maxatac.utilities.system_tools import (get_version,
get_absolute_path,
get_cpu_count,
Mute,
... |
c74743dbde16ae6437d56b5d5378212931beb5935ab9d9322f16d6231b5218c8 | Python | 59,438 | 1,350 | #!/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 collections import OrderedDict
from collections.abc import Mapping, MutableMapping, S... |
f377610abeff1d322bebabf5818c908f0941b1cf9028f12e749f52989de2afbc | Python | 59,440 | 1,591 | #!/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 math
from abc import ABCMeta, abstractmethod
from copy impo... |
578fdc463849ced88c4669b414d54387a9f77e3a5bc2f298bee963103687f8d8 | Python | 59,466 | 1,712 | import copy
import math
import pytest
import torch
from spikingjelly.activation_based import functional, lava_exchange, neuron, surrogate
def _surrogate():
return surrogate.Sigmoid(alpha=4.0)
def _assert_close(actual, expected):
assert torch.allclose(actual, expected, atol=1e-6, rtol=1e-6)
@pytest.mark.... |
83028be607892a6b51e06788527a0c0168ec3cf1b7b553ff985c70fd2c7e8ac7 | Python | 59,681 | 1,756 | #
# Copyright (C) 2012-2017 The Python Software Foundation.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
import codecs
from collections import deque
import contextlib
import csv
from glob import iglob as std_iglob
import io
import json
import logging
import os
import py_compile
import re
import socket
try:
import ssl
... |
3bd37cd4afdf21c553f70a3d1026555c6888227bdbfb86c4086641360d84748f | Python | 59,849 | 1,461 | from __future__ import annotations
import warnings
from collections.abc import Callable, Iterable, Mapping, Sequence
from functools import partial
from numbers import Real
from typing import Any, Literal
import numpy as np
import pandas as pd
import scanpy as sc
from anndata import AnnData
from fast_array_utils.conv ... |
546157e458989116e04aaef611c7d4365b054059fa817df4268f44823e55bc2a | Python | 60,005 | 1,394 | #!/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 warnings
from collections.abc import Iterable
from functools import partial
from itertools impo... |
2d63ceacdc581a43306cb812529ad0aa1a841c736cc6c65eb7141b6ba1d9f5bf | Python | 60,026 | 1,460 | # 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... |
4f12761521a23352e7eb4735af5899b2ed6af1d43a40906c5c2389d3a711d4a5 | Python | 60,050 | 1,483 | import math
from pathlib import Path
import time
import sys
from typing import Any, Literal, Sequence, overload
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 learnMSA.hmm.tf.layer import PHMMLayer
from l... |
832290f25fc71e0eb906f00f22e737a8d5f4669513cd176f7be63f879f88eb96 | Python | 60,071 | 1,350 | #!/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, Mapping, Sequence
from copy ... |
1326a8bbb77a0111237e49e725ae81ee3a64222750647a6558b6af3924bf4ab2 | Python | 60,075 | 1,517 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from __future__ import annotations
import itertools
import logging
from collections.abc import Callab... |
88313a8ace0c9c8d31731e74fb2774144f05d3754ee68aed7c65e4501353fcee | Python | 60,623 | 1,906 | import operator
from typing import AbstractSet
import numpy as np
import pytest
from ...datalog import Fact
from nl_expr.exceptions import NonLiftableException, UnsupportedSolverError
from nl_expr.expressions import Constant, Symbol
from nl_expr.logic import Conjunction, Implication, Negation, Union
from ...relationa... |
1a2c9b9e41517145cbb847f42e4f6102f514cac12e27276229bafc6de4e40bf6 | Python | 60,777 | 1,924 | from __future__ import annotations
import warnings
from collections.abc import Hashable
from contextlib import nullcontext
from copy import deepcopy
from functools import partial, singledispatch
from importlib.metadata import version
from importlib.util import find_spec
from itertools import chain, permutations, produ... |
3b0f7d38b8376fdcdc702818789d5e21af2eef16adb348c43b78ac277e22d325 | Python | 60,859 | 1,707 | #!/home/arnab/atomate/pyenv395/bin/python
from pymatgen.io.vasp.sets import MPRelaxSet, MPStaticSet, MPSOCSet
from pymatgen.core import Structure
from pymatgen.core.periodic_table import Element
from pymatgen.analysis.magnetism.analyzer import MagneticStructureEnumerator, CollinearMagneticStructureAnalyzer
from pymatg... |
48b31c149af911f229954abc6da9e3527e7e04032ad40172ad34e021bb80bf54 | Python | 60,943 | 1,452 | from __future__ import division
import os
from fanc.config import config
from abc import abstractmethod, ABCMeta
import numpy as np
from scipy.stats import poisson
from collections import defaultdict, OrderedDict
import tables as t
from fanc.legacy.data.genomic import AccessOptimisedRegionMatrixTable, Edge, LazyEdge
fr... |
85f072af3af759d8552f1fd495ed5d41a6a386c5dd664fb798fd8a322e62b885 | Python | 61,170 | 1,448 | """Utilities defining "Galaxy Flavored Markdown".
This is an extension of markdown designed to allow rendering Galaxy object
references.
The core "Galaxy Flavored Markdown" format should just reference objects
by encoded IDs - but preprocessing should allow for instance workflow objects
to be referenced relative to t... |
49e20a8123800be2c74681177de3f4e864bd12e83005f21429c4d95c6ccc2175 | Python | 61,226 | 1,505 | """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 core.mixins import GetParentObjectMixin
from core.permissions import ViewClassPermission, all_permissions
from core.utils.comm... |
6de7352cd603eced4f23569753bad9321b466a0e8227281b64d06aaa50d404a3 | Python | 61,318 | 1,113 | import pandas as pd
import numpy as np
import h5py
import pathlib
from sklearn.model_selection import train_test_split
from sklearn.model_selection import StratifiedKFold
from pandas_plink import read_plink1_bin
from ..utils import helper_functions
from . import encoding_functions as enc
def prepare_data_files(data_... |
7337e52b09df7caa1d4a3def0990f279164311cbde61d87899391669f043a0fc | Python | 61,349 | 1,728 | """Clearing house for generic text datatypes that are not XML or tabular."""
import gzip
import json
import logging
import os
import re
import shlex
import subprocess
import tempfile
from html.parser import HTMLParser
from typing import (
IO,
Optional,
)
import ijson
import yaml
from galaxy.datatypes.data im... |
0f09803f91761e057f8dcb9ad2258af7378f329bd3499a54285df3ded6621cb1 | Python | 61,360 | 1,325 | """
Galaxy job handler, prepares, runs, tracks, and finishes Galaxy jobs
"""
import abc
import datetime
import os
from collections import defaultdict
from queue import (
Empty,
Queue,
)
from typing import (
Any,
Optional,
TYPE_CHECKING,
Union,
)
from sqlalchemy.exc import OperationalError
from... |
28a8859110b6de669c6cbf98f954940c939675519f566510b6533bcc87128c7e | Python | 61,562 | 1,298 | # 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... |
f6fa2721bdebe7f9adc363ce18ad2bdd052c57db7db8a2f7e525e29a824db08d | Python | 61,578 | 1,771 | """
Morphology module.
"""
# This is a note to myself, should expand into docs:
#
# It goes ``morphology-on-file`` into ``repository`` that the ``storage`` needs to provide
# support for. Then after a placement job has placed cells for a chunk, the positions are
# sent to a ``distributor`` that is supposed to use the ... |
45265db4b1dc52d6cad96f203c7fd420d98dec3a0903b870ba164b200913e628 | Python | 61,613 | 1,502 | """
Sequence classes
"""
import json
import logging
import math
import os
import re
import string
import subprocess
from collections.abc import (
Callable,
Iterable,
)
from itertools import islice
from typing import (
Any,
Optional,
)
import bx.align.maf
from markupsafe import escape
from galaxy impo... |
11e6afa64a234d242daf567ffb74b010472945d78795bbf5f7f690b14911619b | Python | 61,912 | 1,378 | """Job runner used to execute Galaxy jobs through Pulsar.
More information on Pulsar can be found at https://pulsar.readthedocs.io/ .
"""
import copy
import errno
import logging
import os
import re
import subprocess
from time import sleep
from typing import (
Any,
Optional,
TYPE_CHECKING,
Union,
)
im... |
c034c906d8cd79d20d707c2432a1982a7d486f5776de6f2a822adccd6eac80fa | Python | 61,951 | 1,493 | # 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... |
4b6e0c9febab4ee68a868723174e107280b74abb43390d186de65298ec0e9637 | Python | 62,109 | 1,879 | import atexit
import os
import sys
import pickle
import shutil
import tempfile
import textwrap
import unittest
import numpy as np
import pytest
try:
import ipytree
except ImportError: # pragma: no cover
ipytree = None
from numcodecs import Zlib
from numpy.testing import assert_array_equal
from zarr._storag... |
4529a6724938ba124abae0fca948815f647bdf1694f6795d8513f583622b766e | Python | 62,111 | 1,822 | """
Declarative engine registry for the neurolang-query CLI.
Engines are declared in :file:`engines/engines.yaml`, into whose entries
the files :file:`engines/<engine>/*.yaml` (their example queries and the
query assistant's guidance) are merged with OmegaConf. Each engine may
define:
* a **Python initialisation scr... |
20b666186157526d75ed8e5969e0ec8017e42a8e8f084ec31c9ef3eb4d8b5a81 | Python | 62,840 | 1,485 | import json
import logging
import mimetypes
import os
import shutil
import string
import tempfile
from collections.abc import (
Callable,
Generator,
Iterable,
)
from inspect import isclass
from typing import (
Any,
IO,
Literal,
Optional,
TYPE_CHECKING,
Union,
)
from markupsafe impor... |
8315e0894362be5d1d9e2cc5d96ed706c3bccf013818118e1ae4115a154bf60e | Python | 62,965 | 1,584 | #!/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 import OrderedDict
from collections.abc import Iterable, Mapping
from copy import dee... |
7689933866a9e8d0e0df179ac51c858e6bc68d0e5ba999b6e8c3a8e909221cdc | Python | 63,027 | 1,795 | import pytest
import os
from maxatac.utilities.system_tools import get_files
from maxatac.utilities.parser import (
get_synced_chroms,
parse_arguments
)
DATA_FOLDER = os.path.abspath(os.path.join(os.path.dirname(__file__), "temp"))
@pytest.mark.parametrize(
"chroms, filenames, ignore_regions, control_s... |
dc78ef162e4095a55392ef7342eb951ad3cd9e2997d9fbe4d26c095cb47f2dce | Python | 63,058 | 1,502 | import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pickle as pk
import glob
import sys
sys.path.append("/home/cat/code/widefield/") # Adds higher directory to python modules path.
import string, re
from scipy.signal import butter, filtfilt, cheby1
from sklearn.decomposition import PCA
impor... |
820d3a9601774db04573eba8518830e0cacf95fa86289afae74656be47071736 | Python | 63,196 | 1,653 | # 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... |
8f37cc8289f57c4e7246f7af39dda59ed54f3e98328c18c817a4894454ab9933 | Python | 63,281 | 1,511 | #!/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 dataclasses
import warnings
from collections import OrderedDict
from typing import Any
from uni... |
9849acecbdc533bcb57c6ce08416b031698a2cd7a38829cd353026c8f16081b4 | Python | 63,824 | 1,667 | # -*- coding: utf-8 -*-
"""
HDBSCAN: Hierarchical Density-Based Spatial Clustering
of Applications with Noise
"""
import numpy as np
from sklearn.base import BaseEstimator, ClusterMixin
from sklearn.metrics import pairwise_distances
from scipy.sparse import issparse
from sklearn.neighbors import KDTree, Ball... |
cb30af8fb124ce374f2c93b203b2d79cd15fe2f24ed4656798627513abce4472 | Python | 64,411 | 1,173 | import os, sys, fnmatch, struct, cdflib, configparser, logging
import xml.etree.ElementTree as ET
from .metadata import Metadata
from .fringe import Fringe
from ..utils import *
cp, np, convolve, gpuAvailable, freeMemory, e = checkForCupy()
def dataFormat(directory: str) -> str:
""" Check the format of the data w... |
9a46f97f75e30c5c235c0228c1da6abeb93513d0ddcb025321e1fc29d4ed9ac2 | Python | 64,424 | 1,615 | """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 base64
import datetime
import logging
import numbers
import os
import random
import traceback
import uuid
from typing import Any, Mapping, O... |
2df86ad19ed00bd6542c7b1d783b165442394a1d099ed7be30b47bedcd434991 | Python | 64,521 | 1,563 | #!/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 copy
import datetime
import json
import re
import warnings
from collections import OrderedDict
... |
82a7fb77c87d9326af51f80cd9a9f3ae4bfde2999d48ae6ef7bcc901c00bcebc | Python | 64,521 | 1,867 | # 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... |
4d353366b075fc07b360c3ff9fee092c82ecb2c4aea9de34b6c8bda365cc8d91 | Python | 64,733 | 1,556 | from __future__ import division
import os
from .config import config
from abc import abstractmethod, ABCMeta
import numpy as np
from scipy.stats import poisson
from collections import defaultdict, OrderedDict
import tables as t
from .matrix import RegionMatrixTable, Edge, LazyEdge
from .general import MaskFilter
import... |
fec5b74b50dbaac3a3f4f12947b9dfcbf64292f7c8df434be5d8148a404bd2d1 | Python | 65,029 | 1,131 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@title: Chemical classes
@description: classes for chemical objects, calculations, and simulations
@author: chrisarcadia
@created: 2018/06/03
"""
# units
# monoisotopic mass : Dalton [Da]
# concentration : moles per liter [mol/L] = [M]
# volume : liters [L]
# ... |
01ff2d5363ecbdaf7d7021e25ce006567db2afa884054eac55a9eef0a815f4fc | Python | 65,153 | 1,534 | # 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... |
5395a0744ea31a37cd8699a7b90595b0325375c99ba4b25a599f5b4739e09643 | Python | 65,548 | 1,895 | """
Code for merging/ concatenating AnnData objects.
"""
from __future__ import annotations
import uuid
import warnings
from collections import OrderedDict
from collections.abc import Mapping, MutableSet
from functools import partial, reduce, singledispatch
from itertools import repeat
from operator import and_, or_,... |
ef957867f82e70e27e2e90a18981e5fe61e58091d6b8c326ee87dd17d2a75854 | Python | 65,760 | 1,576 | # 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... |
09f3e1750bb0947df0cb550d2092d1169ab24b840d9d24239dff996610937b1e | Python | 65,773 | 1,220 | # -*- coding: utf-8 -*-
"""
Created on Sun Aug 18 16:52:50 2019
@author: schelskim
"""
# -*- coding: utf-8 -*-
"""
Created on Fri Jul 5 13:12:33 2019
@author: schelskim
"""
from .generaltools import generalTools
import numpy as np
from matplotlib import pyplot as plt
from skimage import morphology as morph
from sk... |
a905e16ef398d56f7e74143eaa96d8640dd04fbe2aafc95fe736fca37cf8f7ab | Python | 65,971 | 1,693 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import math
import textwrap
from collections.abc import Iterable, Iterator, Mapping
from enum import Enum
from typing import Any
from django.conf import settings as django_settings
from django.db import models as django_models
from django.db import ... |
27ed49e6038e400e26b9702bf758a03696b96392ec02e30439f562352876ee5b | Python | 66,314 | 1,416 | #!/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
"""
References
.. [Daulton2026bonsai]
S. Daulton, D. Eriksson, M. Balandat, and E. Bakshy. BONSAI... |
2efdcb139406a0e0a17e233aaca99338407266f04cf379eda5203f1f08d07f84 | Python | 66,349 | 1,783 | """
Saving and viewing of query results in the interactive REPL.
``.save PATH`` writes the last result as a table, or as a NIfTI image
when PATH ends with ``.nii`` or ``.nii.gz``; ``.view PATH`` shows a NIfTI
image, or the last result, in a browser: an HTML page of
:mod:`~neurolang_apps.utils.tui.brain_viewer`, whose ... |
d5ec59fdc93dde08b1cea6e4b35771ebfcd27e86f1469df38fe1da6abd94d6d5 | Python | 66,477 | 2,041 | """
******
Layout
******
Node positioning algorithms for graph drawing.
For `random_layout()` the possible resulting shape
is a square of side [0, scale] (default: [0, 1])
Changing `center` shifts the layout by that amount.
For the other layout routines, the extent is
[center - scale, center + scale] (default: [-1, ... |
a4ba525d997168cbc2f2f8349e2e1f0c9bb157ed40850313091556a8001c3ae6 | Python | 66,507 | 1,608 | """Experimental settings
Functions
---------
get_settings(experiment_name)
"""
__author__ = "Elizabeth A. Barnes and Noah Diffenbaugh"
__date__ = "25 March 2022"
def get_settings(experiment_name):
experiments = {
# ---------------------- MAIN SIMULATIONS ---------------------------
"exp15C_245":... |
c0be63c56e7e89a09c1d62c5e200452c9339215057671951d539842afc2dd594 | Python | 66,609 | 1,207 | # -*- coding: utf-8 -*-
"""
Created on Sun Aug 18 16:52:50 2019
@author: schelskim
"""
# -*- coding: utf-8 -*-
"""
Created on Fri Jul 5 13:12:33 2019
@author: schelskim
"""
from .generaltools import generalTools
import numpy as np
from matplotlib import pyplot as plt
from skimage import morphology... |
e21e7285f8c47cdf8b60f4bfa117bbe933b4a3806ce912e0c513e889b2d8c658 | Python | 66,629 | 1,731 | # Copyright (C) 2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import io
import itertools
import json
import operator
import xml.etree.ElementTree as ET
import zipfile
from copy import deepcopy
from datetime import datetime
from http import HTTPStatus
from io import BytesIO... |
69614bd1cea8c0678c7defa115956d363a4b379bb207d1443e7d1949c314112e | Python | 67,528 | 1,594 | #!/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 re
import warnings
from collections import defaultdict
from collections.abc import Callable
fro... |
c2ccbb4cf9a0ff7dd4b237b166c896d6ba6eeca233efd38818852136d1007efa | Python | 67,650 | 1,755 | # 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... |
7cdca3a40ea981a459b1ee0cd8745e53292ab8c46b426178a94aa204e4be17c6 | Python | 67,742 | 1,904 | """Tests for the neurolang-query CLI module."""
import json
import pytest
from nl_expr.exceptions import NeuroLangException, SymbolNotFoundError
from nl_expr.expressions import Constant, Symbol
from nl_core.datalog.pretty_printer import DatalogPrettyPrinter
from neurolang.frontend.datalog.squall_syntax_lark import p... |
52bb017d0012f9d202a1a3176265aca8615ad327d9d042a9ebee6f2c6656fce8 | Python | 67,780 | 1,688 | #!/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 dataclasses
import warnings
import pandas as pd
from ax.core.arm import Arm
from ax.core.obser... |
9d43b132652dfd3bf02090b810c21df27e57e60e5686f1869c65cc1cf5f3b2de | Python | 67,824 | 1,723 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""A graph generator based on the PC algorithm [Kalisch2007].
[Kalisch2007] Markus Kalisch and Peter Bhlmann. Estimating
high-dimensional directed acyclic graphs with the pc-algorithm. In The
Journal of Machine Learning Research, Vol. 8, pp. 613-636, 2007.
License: BSD
""... |
e7080668a93074d6c2ae5cff40bed0711aec0b487078a56d8f08ffcfee36782d | Python | 68,256 | 1,546 | import io
import pytest
import networkx as nx
from networkx.readwrite.graphml import GraphMLWriter
from networkx.utils import edges_equal, nodes_equal
class BaseGraphML:
@classmethod
def setup_class(cls):
cls.simple_directed_data = """<?xml version="1.0" encoding="UTF-8"?>
<!-- This file was written... |
640ff41e84533018e80bcff9590888767efc0d8d8bb79d78f386abbae99f6da5 | Python | 68,484 | 1,668 | from collections.abc import (
Callable,
Iterable,
)
from dataclasses import dataclass
from datetime import timedelta
from pathlib import Path
from types import SimpleNamespace
from typing import (
cast,
Optional,
TYPE_CHECKING,
Union,
)
from uuid import UUID
from sqlalchemy import (
delete,... |
94db7e783dd5dd78c12bf495a78c082d026ec84fb6b8d7bfc857697e5f873086 | Python | 69,047 | 1,727 | import itertools
import json
import logging
import math
import os
import re
import uuid
from typing import (
Any,
cast,
Dict,
Iterable,
List,
Optional,
Sequence,
Tuple,
TYPE_CHECKING,
)
from packaging.version import Version
from pydantic import TypeAdapter
from galaxy.tool_util.dep... |
17ad783cbb80e376954bc5129570da7ecc03038c85f87a40f6dce39bf592fae2 | Python | 69,248 | 1,407 | # 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... |
3d07792aedbfb7ab0154a0d96bfa673d09bf13910ea5d757c27e06954fead75a | Python | 69,328 | 1,473 | # -*- coding: utf-8 -*-
"""
Created on Sun Jul 14 09:22:35 2019
@author: sche... |
248b15f1f2a3f067abfb41147c27691576ce56280f83c61db48aba2c0b5780ab | Python | 69,756 | 1,722 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import itertools
import math
from collections import OrderedDict
from collections.abc import Callable, Hashable, Sequence
from functools import partial
from typing import Any, NamedTuple, TypeAlias, TypedDict, Type... |
1161114b3812d1d42ed377c4a290e049d1af9eaea6e427cd6c0886a597dbbaa9 | Python | 69,980 | 1,693 | #!/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 warnings
from collections.abc import Callable
from copy import deepcopy
from random import rand... |
8d6d54f074fab33388e4a4eee60b33171bf064b747e2dab6f0c7d7a9c35bdad5 | Python | 70,085 | 2,116 | # affinitymat.py
# Authors: Jacob Schreiber <jmschreiber91@gmail.com>
# adapted from code written by Avanti Shrikumar
import math
from concurrent.futures import ThreadPoolExecutor
import numpy as np
import scipy
from scipy.sparse import coo_matrix
import numba
from numba import njit
from numba import prange
from ... |
9f2a186df7c36e1e55e65c18bbc7edabbc4f035b700525ab0e14ac4107713863 | Python | 70,645 | 1,791 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""A graph generator based on the PC algorithm [Kalisch2007].
[Kalisch2007] Markus Kalisch and Peter Bhlmann. Estimating
high-dimensional directed acyclic graphs with the pc-algorithm. In The
Journal of Machine Learning Research, Vol. 8, pp. 613-636, 2007.
License: BSD
"... |
eb351c89a087b1937652376f11c0a7353942a32b61f0728158a947e3321590e7 | Python | 70,910 | 1,688 | """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 re
from dataclasses import dataclass
from datetime import datetime
from decimal import Decimal, InvalidOperation
from functoo... |
055b552948710fc9648db00f9a783f2ca8a1dd61402c3eff5acda67346dd4ee1 | Python | 71,011 | 1,738 | # 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 dataclasses
import itertools
import logging
import tempfile
from datetime import datetime
from itertools import produc... |
43ee006c083b467272f011510f71bb547ee9dd6a64ce83b3e684778d4151584b | Python | 71,028 | 1,482 | # -*- coding: utf-8 -*-
"""
Created on Sun Jul 14 09:22:35 2019
@author: ... |
42c0197ef310881bf07b078c6031e6a6d35fd551e77c4ac43b36bcba58f51011 | Python | 71,044 | 2,052 | """Base class for undirected graphs.
The Graph class allows any hashable object as a node
and can associate key/value attribute pairs with each undirected edge.
Self-loops are allowed but multiple edges are not (see MultiGraph).
For directed graphs see DiGraph and MultiDiGraph.
"""
from copy import deepcopy
from fu... |
be0eb0d4003d46356afc5de8a7e065110e3113a9301cf4f2d3cec84c27661b2c | Python | 71,337 | 1,554 | """
ISMAGS Algorithm
================
Provides a Python implementation of the ISMAGS algorithm. [1]_
ISMAGS does a symmetry analysis to find the constraints on isomorphisms if
we preclude yielding isomorphisms that differ by a symmetry of the subgraph.
For example, if the subgraph contains a 4-cycle, every isomorphis... |
f85079673c7fe1e97fac225a3fc1d5ef550e6d2cbe5463844c7d14240cd5a9ba | Python | 71,522 | 1,312 | #### script to make various plots for this project
import os
import numpy as np
import pandas as pd
import seaborn as sns
import nibabel as nib
import matplotlib.pyplot as plt
### thalpy is a lab-wide library for common funcitons we use in our lab
### see: https://github.com/HwangLabNeuroCogDynamics/thalpy
from thalpy.... |
f4064bd075b8381dcd4e32dd06d2593d49b0caec40aa65d05c86be18ad62e5e4 | Python | 71,658 | 1,578 | """
Universe configuration builder.
"""
# absolute_import needed for tool_shed package.
import configparser
import copy
import json
import locale
import logging
import logging.config
import os
import re
import socket
import string
import sys
import tempfile
import threading
from collections.abc import Callable
from d... |
0602041ea54731c0c50e0729bb34d3bfc70c03ef108a019c4b3bfe54ce65efc7 | Python | 72,683 | 2,107 | """Functions measuring similarity using graph edit distance.
The graph edit distance is the number of edge/node changes needed
to make two graphs isomorphic.
The default algorithm/implementation is sub-optimal for some graphs.
The problem of finding the exact Graph Edit Distance (GED) is NP-hard
so it is often slow. ... |
57c56ebd080d577a165e9d59a02b0bf1632a411a35ae7aaff45624577ede8b8e | Python | 72,825 | 2,308 | import matplotlib
#matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from matplotlib import gridspec
import parmap
import numpy as np
import pandas as pd
import os
import shutil
import cv2
import scipy.io as sio
import scipy.signal
import csv
from tqdm import trange
import glob, h5py
fr... |
e3d42b54b7d47cdc507baa64364e719d67094edae5da3523252aa6b973e75009 | Python | 73,202 | 1,797 | import argparse
import collections
import copy
import json
import logging
import math
import os
import re
import sys
from functools import reduce
from typing import (
Optional,
TYPE_CHECKING,
Union,
)
import numpy as np
import yaml
from galaxy.util import parse_xml
if TYPE_CHECKING:
from galaxy.model... |
8a9c2cf6a55bb9c69ac51d611e04c9e079516c62f18cb823b6c2c748dd0411ce | Python | 73,498 | 1,644 | import abc
import errno
import logging
import os
import string
import time
from collections import namedtuple
from errno import ENOENT
from typing import (
Any,
Dict,
FrozenSet,
List,
Optional,
Tuple,
TYPE_CHECKING,
Union,
)
from urllib.parse import urlparse
from uuid import UUID
from m... |
80dbaae19cc99cd9d6748adfab3a0316c2e5a5b07dd3fd09908df1a0e9beb653 | Python | 73,652 | 1,825 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""A graph generator based on the PC algorithm [Kalisch2007].
[Kalisch2007] Markus Kalisch and Peter Bhlmann. Estimating
high-dimensional directed acyclic graphs with the pc-algorithm. In The
Journal of Machine Learning Research, Vol. 8, pp. 613-636, 2007.
Licen... |
c1680d9ea7bd89a0145d5d3248849c6aabf63a13c41e8db8a41f1260fc6db445 | Python | 74,147 | 1,983 | """Polars backend for NeuroLang's Relational Algebra Set (RAS) system.
Uses pl.LazyFrame internally to defer materialization, allowing Polars'
query optimizer to handle chained operations efficiently.
"""
import builtins
from collections import OrderedDict, namedtuple
from typing import (
Callable,
Dict,
... |
06822bdb1de4edfd13fdc2cc219a15e75b4a0183f5107a44502985b8b34c004d | Python | 74,384 | 1,524 | import time
import networkx as nx
import csv
from MolRep.Interactions.link_models.CFLP.pysbm import sbm
from MolRep.Interactions.link_models.CFLP.pysbm.parallel_execution import parallel_execution
from MolRep.Interactions.link_models.CFLP.pysbm.parallel_execution import TEMP_DIRECTORY
from MolRep.Interactions.link_mo... |
de8505f06ee44dc292d77872c6452d9d36fa0d420bd37e7065acce2fed9ead8e | Python | 74,439 | 1,530 | import math
import random as rd
from unittest import TestCase
import networkx as nx
from pysbm import sbm
from pysbm.sbm.nxpartitiongraphbased import NxPartitionGraphBased
from pysbm.sbm.peixotos_flat_sbm import DeltaModelLogLikelihoodOfFlatMicrocanonicalDegreeCorrectedSbm
from pysbm.sbm.peixotos_flat_sbm import LogL... |
2f47c61cf341a3e48b81bf6d9924cafd0e71b7c7d07289d751cde110642019bb | Python | 74,605 | 2,236 | import copy
import importlib.metadata
import inspect
import json
import os.path
import pathlib
import pickle
import sys
import tempfile
import unittest
import numpy as np
from bsb_test import (
RandomStorageFixture,
get_data_path,
get_test_config,
list_test_configs,
)
from bsb_test.configs import get_t... |
2a57a037a7f2adacc1ffe803fe2b221bd734cea7013d78742941d9afb6865958 | Python | 75,215 | 2,397 | import matplotlib
#matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from matplotlib import gridspec
import parmap
import numpy as np
import pandas as pd
import os
import shutil
import cv2
import scipy.io as sio
import scipy.signal
import csv
from tqdm import trange
import glob, h5py
i... |
d5eb6c07e3e709ab4f57fcd7f4d108acc65b7252314c3ec8390eab906ecc7d41 | Python | 75,254 | 2,398 | import matplotlib
#matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from matplotlib import gridspec
import parmap
import numpy as np
import pandas as pd
import os
import shutil
import cv2
import scipy.io as sio
import scipy.signal
import csv
from tqdm import trange
import glob, h5py
fr... |
eecfc99bad95be72fe3e285129fc5485297fc9cf4620dd4bb0300c499d91c8cc | Python | 75,456 | 1,797 | """
Manage tool data tables, which store (at the application level) data that is
used by tools, for example in the generation of dynamic options. Tables are
loaded and stored by names which tools use to refer to them. This allows
users to configure data tables for a local Galaxy instance without needing
to modify the t... |
8e7f0e62d0a190e210d3d2aa34cee731cd0cb8c6525f01eae49723a86b6b3d9c | Python | 76,651 | 2,089 | # Copyright (C) 2021-2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import io
import json
import math
import operator
import os
import xml.etree.ElementTree as ET
import zipfile
from copy import deepcopy
from datetime import datetime
from http import HTTPStatus
from io impo... |
028a9894fd8ee94acca4a042ab7a0a09253ffeb10ac5e154dd9002819541e9ad | Python | 77,558 | 1,596 | # 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... |
e90932686b2eecfe74ee5287aa5325fa242200ee7b9a162ca560af696763c4b3 | Python | 79,009 | 2,079 | # 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 json
import math
import random
import tempfile
from collections.abc import Mapping
from pathlib import Path
from typin... |
77080e2e5c57dd9e304ec36c36a20d10b0447017b4eedfa598ff9246a75a1a8b | Python | 79,180 | 2,146 | """\
Main class and helper functions.
"""
from __future__ import annotations
from collections import OrderedDict, defaultdict
from collections.abc import Mapping, MutableMapping, Sequence
from copy import copy, deepcopy
from functools import singledispatchmethod
from pathlib import Path
from textwrap import dedent
fr... |
a567f15841e6c8d411282a474551d9c402c3cfdeb1e0242390c7f9cb6db995fd | Python | 79,394 | 1,813 | import sys
from openbabel import pybel, openbabel
from openbabel.openbabel import OBAtomAtomIter
import scipy
from collections import defaultdict
import os
from itertools import chain
import pandas as pd
import time
import itertools
import random
import math
from copy import deepcopy
class OutputGrabber(object):
... |
d8e81b91e003dab2e4717a9b72fa1fdc9e51ee54708cd2e80724b24e406d2a77 | Python | 79,852 | 2,419 | # Copyright 2007 Google Inc.
# Licensed to PSF under a Contributor Agreement.
"""A fast, lightweight IPv4/IPv6 manipulation library in Python.
This library is used to create/poke/manipulate IPv4 and IPv6 addresses
and networks.
"""
from __future__ import unicode_literals
import itertools
import struct
__version... |
bd50beebd2f73fec6ebbad3e5efc5428b22a8186864e260396ba5e106f88e641 | Python | 80,332 | 1,754 | import math
import torch
from torch.autograd.function import once_differentiable
from .._ops.first_spike import _cubic_value
from .._ops.tempotron import _roots, _states, _weight_gradient
from .._ops.tempotron.reference import _phi, _psp, _stationary, _voltage
from . import solver
__all__ = ["tempotron", "srm", "cu... |
774cd34b91a2f6fb7a2a92fd1f5dcf0c2fb6c09991dce63befac1c5c45806a21 | Python | 80,348 | 1,774 | import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from pylab import *
import numpy as np
import random
import math
import time
import os
import glob
# change the default font family
plt.rcParams.update({'font.family':'Arial'})
set_sigma_errors = False #True
data_sigma_errors = True # False
thismax... |
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