sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
bb017011ad4c4f747387e320fb39a664ef24f33374be90f4872bf6d23289f4f1 | Python | 42,191 | 1,173 | """
This module includes the main classes that handle the training of the ANN models
as well as the predictions of the new chemical shifts.
"""
# Python import(s).
import warnings
import logging
import sys
from datetime import date
from gc import collect as collect_mem_garbage
from pathlib import Path
from time import... |
fd1e556055be55e2c16520c7cb25050a0479cdb297d4baee6fe7ef746e76dee9 | Python | 42,206 | 1,164 | #!/usr/bin/env python
#
# Copyright (c) 2014 10X Genomics, Inc. All rights reserved.
#
# Utilities for manipulating bam files
#
import os
import pysam
import log_subprocess
import random
import resource
import logging
import shutil
import math
import tenkit.bio_io as tk_io
import tenkit.seq as tk_seq
import csv
import ... |
9492a01d9f2a35b9eb452ea1379af721d26c1a32d231a955d4ae2f5d689d2305 | Python | 42,275 | 1,167 | """
Module for handling genomic regions such as chromosomes, bins, and restriction fragments.
The class :class:`~RegionsTable` is an implementation of the :class:`~RegionBased`
interface from the :mod:`genomic_regions` package. More details on how to use the
:class:`~genomic_regions.RegionBased` interface can be found... |
b0603e84a5409e72013b4ed01d7b476944dd6ed213b67d72a078ca73e78ade22 | Python | 42,284 | 1,063 | # MIT License
#
# Copyright (c) 2019-2024 The PyQMC Developers
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, m... |
e901905c51502a2d7205426f6af6f5ecb98aa62b5ee6fce2522e5a1cbd6d02b3 | Python | 42,305 | 952 | """
Manager and Serializer for Datasets.
"""
import glob
import logging
import os
from typing import (
Any,
Optional,
TypeVar,
)
from sqlalchemy import select
from galaxy import (
exceptions,
model,
)
from galaxy.datatypes import sniff
from galaxy.exceptions import ObjectInvalid
from galaxy.manag... |
a6b8a4bfeb834da3a7101b9995e31b49cb6d9465a1179d43618e045553cf4341 | Python | 42,355 | 1,444 | import pickle
from copy import deepcopy
import pytest
import networkx as nx
from networkx.classes import reportviews as rv
from networkx.classes.reportviews import NodeDataView
# Nodes
class TestNodeView:
@classmethod
def setup_class(cls):
cls.G = nx.path_graph(9)
cls.nv = cls.G.nodes # Nod... |
fd568d2300b3e7be46d5e0157f9177505b9d57bae6a06f5f7e75cc156a888589 | Python | 42,374 | 1,451 | from typing import Optional, Sequence, Union
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch import Tensor
from torch.nn.common_types import (
_size_any_t,
_size_1_t,
_size_2_t,
_size_3_t,
_ratio_any_t,
)
import numpy as np
from .. import base, functional
__all__ = ... |
74e32b8c85effb71a611bb4ff8d25cd39ed2bf5f4fed901d91efafd1305e362a | Python | 42,455 | 1,197 | # Copyright 2015,2016,2017 Nir Cohen
#
# 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 writi... |
5c1f4d56a4dd67b044bd7e439f307a8f27ad816b353cd3de7e002078f3d615d7 | Python | 42,458 | 840 | """
Created on Oct 12, 2022.
@author: voodoocode
"""
import numpy as np
import mne.forward
import mne.io.constants
import scipy.sparse
import finnpy.src_rec.utils # @UnresolvedImport
def compute(bem_mdl, cort_mdl, coreg, signal_type, rec_info = None, _mag_factor=1e-7, conductivity = None):
"""
Calculate th... |
6011111cb5174a0c891f2a48b3729e75bafe7c09d5fd828f925ad16cd21a260d | Python | 42,460 | 855 | # -*- coding: utf-8 -*-
"""
Created on Wed Feb 22 21:47:26 2019
@author: Zhiye
"""
from Model_construct import *
from generate_feature import *
import numpy as np
import os, sys, shutil, platform, time, pickle
from collections import defaultdict
from six.moves import range
import keras.backend as K
import tensorflow... |
54d949f51059fc22f69c75aa0639d1f4a2b73ebf05549e6e2aee74b1de2d7e29 | Python | 42,560 | 991 | #!/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 math
from typing import Any, cast
import pandas as pd
from ax.adapter.torch import TorchAdapte... |
712192862fdf2ee747dbd09d1c287f8fa8f52fe6d6b1eb73a3da340aa7d400b2 | Python | 42,595 | 1,040 | """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 copy
import os
from typing import Any
import ujson as json
from data_manager.models import Filter, FilterGroup, View
from data_manager.prep... |
8e854529c07f939aae8dfa5ebd4223ec30a4f9baefa358af2bf44a0d4690f676 | Python | 42,656 | 1,501 | # -*- coding: utf-8 -*-
"""
Slice
=====
This module provides basic handling of slicing of sources.
The main functionality is to virtually slice an array and return its
expected shape and order. Virtual slices can also be used as handles with
low communication overhead in parallel processing.
Example
-------
>>> im... |
122cceaedd9a1c0294e9ebca9c47e4e9fc2865171c06e3512ac7cc230f5cab69 | Python | 42,764 | 1,005 | # 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... |
b216d4aadd624d8a5892e70ee96d5b8af6110c0a89b1bd18b76a4274cbac7419 | Python | 42,797 | 1,098 | # 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... |
2054ec49e749abc007ebfbb5bcb40b200ac59618d10804dc01142414f7b46333 | Python | 42,840 | 1,254 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import itertools
import math
from abc import ABCMeta
from collections import Counter
from copy import deepcopy
from enum import StrEnum
from functools import cached_property, lru_cache
from io import StringIO
from ... |
e67ef3bd8462d436a8aa91f4371226a883a6a458d2b1a8ccaed3c966a8a63005 | Python | 42,909 | 1,307 | import math
import operator
from typing import AbstractSet, Callable, SupportsFloat, Tuple
import numpy
import pandas.core.computation.ops
from nl_expr import expression_walker as ew, type_system
from nl_expr.exceptions import (
NeuroLangException,
ProjectionOverMissingColumnsError,
RelationalAlgebraNotIm... |
0849666381eb718acaf9c8b29e98540d161ca389c130afc564fb3ab3011b5930 | Python | 42,977 | 1,150 | """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 json
from unittest.mock import patch
import pytest
from data_manager.models import View
from rest_framework import status
from ..utils imp... |
0c1fa1682e5e8b8bb5cfdbd0b3b02f93c19675934c255b30ccd8ed2182bc2b0a | Python | 43,099 | 1,122 | # -*- coding: utf-8 -*-
"""
From https://github.com/sbyrnes321/tmm (MIT license).
For information see the docstring of each function, and also see
manual.pdf (should be included with the distribution, otherwise get it
at http://sjbyrnes.com/fresnel_manual.pdf ). Physics background,
conventions, and derivations are at h... |
86c63070d2685137b1388e88c1812ff77150e44e7b8dd4b60e5117171406c822 | Python | 43,294 | 1,234 | """
========================
Cycle finding algorithms
========================
"""
from collections import defaultdict
from itertools import combinations, product
from math import inf
import networkx as nx
from networkx.utils import not_implemented_for, pairwise
__all__ = [
"cycle_basis",
"simple_cycles",
... |
56a2a2bf29829179b36d442d9b71a64f310d06ac986e4327014d33e1a32d2381 | Python | 43,348 | 1,377 | from __future__ import annotations
import itertools
import random
import warnings
from collections import Counter, defaultdict
from collections.abc import Mapping
from functools import partial, singledispatch, wraps
from importlib.metadata import version
from importlib.util import find_spec
from string import ascii_le... |
2ebd38cee2b293ee0f4e2ec343f922f3cc60c5d70891bace87a1f021ee076158 | Python | 43,418 | 1,077 | from .config import config
from .regions import Chromosome, Genome
from .matrix import RegionMatrixTable, RegionMatrixContainer, Edge, LazyEdge
from abc import abstractmethod, ABCMeta
from future.utils import with_metaclass, string_types, viewitems
from .tools.load import load
from .tools.general import distribute_inte... |
14ead9a90a94c09879acf9ebe645b57d66b1dbba4b2b45b21e7cf7fe4568e15d | Python | 43,545 | 1,072 | #!/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 import defaultdict
from collections.abc import Ca... |
fe5014600b969d2234968a44440e908bf7efe68bad1c89b326e86ceb7c7b9020 | Python | 43,552 | 1,104 | from typing import Callable, Optional, Union
import torch
import torch.nn as nn
import torch.nn.functional as F
from .. import base, monitor
from ..functional import learning as functional_learning
__all__ = [
"STDPLearner",
"MSTDPLearner",
"MSTDPETLearner",
]
def _check_open(learner) -> None:
if ... |
a984dab839dc673c7660e6e31452a7ccb6e4c515773a0ca7310712ed04680ac8 | Python | 43,573 | 1,236 | """
rgenetics datatypes
Use at your peril
Ross Lazarus
for the rgenetics and galaxy projects
genome graphs datatypes derived from Interval datatypes
genome graphs datasets have a header row with appropriate columnames
The first column is always the marker - eg columname = rs, first row= rs12345 if the rows are snps
su... |
68d1bd77ef731c8aedf9441736c0c77eaf477369c7c1e21133c8929dbc992400 | Python | 43,633 | 1,314 | import itertools as it
import operator
import pytest
import networkx as nx
from networkx.algorithms.isomorphism.vf2pp import (
_feasibility,
_feasible_look_ahead,
_feasible_node_pair,
_find_candidates,
_find_candidates_Di,
_GraphInfo,
_init_info,
_matching_order,
_restore_Tinout,
... |
c74e559feb46b3950379bc101da21b9571724e08fd0a07a51343f7217eaaa10a | Python | 43,649 | 817 | import torch
from torch import optim
from torch.utils.data.dataloader import DataLoader
from torch.utils.data import ConcatDataset
import numpy as np
import tqdm
import copy
from utils import get_data_loader,checkattr
from data.manipulate import SubDataset, MemorySetDataset
from models.cl.continual_learner import Conti... |
e4e6444680856ce13fa1cec71387f189c98fef4ceba95a6dd344786c0541bee3 | Python | 43,674 | 1,060 | # import libraries
import torch
from torch import nn
from math import sqrt
import argparse
class Reshape(nn.Module):
def __init__(self, in_features, out_channels):
super(Reshape, self).__init__()
self.in_features = in_features
self.out_channels = out_channels
self.k = 1 if self.in_f... |
3f35a0f552a9270665d7f220a913d17c42eb35f7aeca1c81ffeca24d4367ae21 | Python | 43,693 | 1,081 | from jinja2 import FileSystemLoader, Environment
import os
import importlib
import inspect
import re
import numpy as np
from brian2lava.utils.files import scrap_folder
from brian2 import get_device, Quantity, units, second
from brian2 import NeuronGroup, SpikeGeneratorGroup
from brian2.synapses.synapses import Synaptic... |
3c74f9683853a2fbfcfabe46d73274275657e8104f7f1fe5871e225bccbc42ed | Python | 43,717 | 1,004 | """
Base classes for job runner plugins.
"""
import datetime
import os
import string
import subprocess
import sys
import threading
import time
import traceback
import uuid
from queue import (
Empty,
Queue,
)
from typing import (
Any,
Generic,
Optional,
TYPE_CHECKING,
TypeVar,
Union,
)
... |
49afeb370f4147d68fe32fa17f5f77528706b6f31ad5444c12523c92897c6c57 | Python | 43,731 | 1,239 | #!/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 numbers
import warnings
from collections import OrderedDict
from collections.abc import Callabl... |
08910881cde10df061013320c3c5275f1998ae3817c34d805208845865af3541 | Python | 43,830 | 1,123 | from ..simulation import (
SimulatorAdapter,
SimulationComponent,
SimulationCell,
TargetsNeurons,
)
from ..models import ConnectivitySet
from ..helpers import ListEvalConfiguration, listify_input
from ..reporting import report, warn
from ..exceptions import *
import time, os, json, weakref, numpy as np
... |
55fc387b8af15568abc9ff1f23a1bef8ed83a566a07e8657dae8750df7f0dd2b | Python | 43,876 | 1,173 | """Generate and save cell densities
A density value is a non-negative float number corresponding to the number of cells in mm^3.
A density field is a 3D volumetric array assigning to each voxel a density value, that is
the mean cell density within this voxel.
In BBP terminology, a density field is often referred to a... |
fffb2e63da7602c96e57e33be4247eaa41bff103ff09bfc4dfa00b0c3262c579 | Python | 43,895 | 1,265 | """
Algorithms for finding k-edge-augmentations
A k-edge-augmentation is a set of edges, that once added to a graph, ensures
that the graph is k-edge-connected; i.e. the graph cannot be disconnected
unless k or more edges are removed. Typically, the goal is to find the
augmentation with minimum weight. In general, i... |
3c76e640e3bfe1618c42173a0f4dd8bbf582780a0000c51a55e6cf1ae7a8c151 | Python | 43,910 | 967 | import logging
from collections.abc import Callable
from typing import (
Any,
Literal,
Optional,
overload,
TYPE_CHECKING,
Union,
)
from zipfile import ZipFile
from sqlalchemy.orm import (
joinedload,
Query,
)
from galaxy import model
from galaxy.datatypes.registry import Registry
from ... |
20ab41ae96d6032de01b18d577ca637501f8c979def56655755737b77230b9cc | Python | 44,069 | 1,076 | '''
'''
#
# Adapted from MATLAB code written by S. Nishimoto (see Nishimoto, et al., 2011).
# Anwar O. Nunez-Elizalde (Jan, 2016)
#
# Updates:
# Anwar O. Nunez-Elizalde (Apr, 2020)
#
import itertools
import math
from PIL import Image
import numpy as np
from moten.backend import get_backend
from moten.backend._utils ... |
7f568c4364095e9d5c57fa077d16c7238e45c877d6ea9abab4ed4bdebf48aab3 | Python | 44,247 | 932 | import os
import importlib
import numpy as np
from brian2.core.namespace import get_local_namespace
from brian2.groups.neurongroup import NeuronGroup, StateUpdater
from brian2.synapses.synapses import Synapses
from brian2.input.spikegeneratorgroup import SpikeGeneratorGroup
from brian2.units import second
from brian2 ... |
0a66ea3b67745743887fc9d0c18ff70512f874d0d5a376570394a61a10524e56 | Python | 44,314 | 1,148 | """Functions for computing and verifying matchings in a graph."""
from itertools import repeat
import networkx as nx
from networkx.utils import not_implemented_for
__all__ = [
"is_matching",
"is_maximal_matching",
"is_perfect_matching",
"max_weight_matching",
"min_weight_matching",
"maximal_m... |
a4229670b51765185fe86d2041a25eff2c683f432b682ceadbc74d5daa624674 | Python | 44,314 | 1,148 | """Visualization functions for cerebellar cortical data.
Provides plotting in normal 3D and inflated 3D views using PyVista, as well as flatmap
view using Matplotlib.
"""
# ---------------------------------------------------------------------------
# Authors: John G Samuelson <johnsam@mit.edu>
# Christoph Din... |
a081166c8cb51bddcd6fe6a183069b99eef5b6642356939e90bc8c29f072bdca | Python | 44,412 | 953 | """
Custom tool creation agent for Galaxy.
"""
import asyncio
import logging
import re
from collections.abc import (
Callable,
Sequence,
)
from dataclasses import dataclass
from pathlib import Path
from typing import (
Any,
Literal,
Optional,
)
import yaml
from pydantic import (
BaseModel,
... |
8c6ea278f38d65173d1fe27c8ddd4c663fa0be710365c7c6c91bfc9a2f601299 | Python | 44,551 | 1,374 | import copy
from typing import Tuple, Generator, Optional, Callable
import torch
import torch.nn as nn
class StepModule:
r"""
**API Language** - :ref:`中文 <StepModule-cn>` | :ref:`English <StepModule-en>`
----
.. _StepModule-cn:
* **中文**
步进模式接口基类。
实现该接口的模块通过 ``step_mode`` 区分单步模式 ``"s"... |
f5dc8d298eba5ba50874dbba1942121454cae36334e47c2a389bd0360fc3a316 | Python | 44,730 | 704 | # 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... |
a7b77b24d4459eac8966872a328a49375be86ec334418fe0cd71f4912ae28d54 | Python | 44,746 | 1,291 | import gc
import pytest
import torch
import torch.nn as nn
from spikingjelly.activation_based import functional, layer, learning, neuron
def f_weight(x):
return torch.clamp(x, -1.0, 1.0)
def _count_alive_tensors():
gc.collect()
return sum(1 for obj in gc.get_objects() if torch.is_tensor(obj))
def _b... |
8ed6851220b7802d09c3a2e629fce91adcef662c7dce7de2d2626cd78cf7015a | Python | 44,785 | 1,111 | """
General purpose preprocessing library
=====================================
.. module:: lib_sconf
:platform: Linux
:synopsis: tool library to manage argument parsing, logging, path configuration, object saving, etc.
.. moduleauthor:: Jose M. Esnaola-Acebes <josemesnaola@gmail.com>
Parsing methods
--------... |
8c064f232b3f4794b631cce17ba2f6239e39e686c05733ce7432673e69b9a2e3 | Python | 44,846 | 980 | """Find bad channels."""
# Authors: The PyPREP developers
# SPDX-License-Identifier: MIT
import logging
import mne
import numpy as np
from mne.utils import check_random_state
from scipy import signal
from pyprep.ransac import find_bad_by_ransac
from pyprep.removeTrend import removeTrend
from pyprep.utils import _fi... |
5449c0c81159b0d6e8dac1cb10c6eee2f09cf7e1130339be7689fe2405e3e925 | Python | 44,925 | 1,236 | import bz2
import collections
import gzip
import inspect
import re
import threading
from collections import defaultdict
from os.path import splitext
from pathlib import Path
import networkx as nx
from networkx.utils import create_py_random_state, create_random_state
__all__ = [
"not_implemented_for",
"open_fi... |
fc66af4a7d84621dce824ed60f0b3eb7203a4e9cb8297352c8e330bef1fcbaab | Python | 45,078 | 1,043 | # 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 itertools
from collections.abc import Callable
from copy import deepcopy
from typing import Any
import numpy.typing a... |
87ec148559ad9f07281cdb1406a138153317b47e1fe944eecdb6b10b4e866a3c | Python | 45,098 | 952 | """
Classes for velocity-observing filters with D spatial dimentions.
The "logical" format for indexing is X[t,d,m] for time 't', spatial dimension 'd',
and motion source 'm'. However, for the implementation, we use X.reshape(T, D*M)
to obtain efficient matrix equations.
"""
import numpy as np
from . impor... |
bfcd014ea5f70ed0eb15396058a63af4007a7a4514def7c38d20928c7c2f8ccf | Python | 45,185 | 1,208 | """Read and write graphs in GEXF format.
.. warning::
This parser uses the standard xml library present in Python, which is
insecure - see :external+python:mod:`xml` for additional information.
Only parse GEFX files you trust.
GEXF (Graph Exchange XML Format) is a language for describing complex
network s... |
5998431c0d9e747e7c0b9a2f36bbf8801a43eb1ff2439a8609a15b7991bd45c7 | Python | 45,239 | 1,191 | """Playwright-backed implementation of the HasDriver abstraction layer.
This module provides a Playwright-based implementation that mirrors the API of
has_driver.py, allowing Galaxy tests to run with either Selenium or Playwright
backends with minimal code changes.
Overview
--------
HasPlaywrightDriver provides a hig... |
777ff194be438132a5d93f70c4c1cadde0435b794fb860d262143c2ce769ac33 | Python | 45,245 | 1,192 | from abc import ABC, abstractmethod
import warnings
from sklearn.base import BaseEstimator, RegressorMixin, MultiOutputMixin
from sklearn.utils.validation import check_is_fitted
from ._solvers import KERNEL_RIDGE_SOLVERS
from ._solvers import WEIGHTED_KERNEL_RIDGE_SOLVERS
from ._hyper_gradient import MULTIPLE_KERNEL_... |
110158c121eddc9316b4800302405ec573629a7b1e2faace22c0035cb0214b68 | Python | 45,299 | 1,453 | import numpy
import numpy as np
import pytest
from numpy.testing import assert_array_equal
import zarr
from zarr.indexing import (
make_slice_selection,
normalize_integer_selection,
oindex,
oindex_set,
replace_ellipsis,
PartialChunkIterator,
)
def test_normalize_integer_selection():
asse... |
5abfa1f7c7dc0078e33ea4ecec79334d8ba5fa9feefe9ac487e6ee871c31411e | Python | 45,489 | 1,397 | """Create portable serialized representations of Python objects.
See module cPickle for a (much) faster implementation.
See module copy_reg for a mechanism for registering custom picklers.
See module pickletools source for extensive comments.
Classes:
Pickler
Unpickler
Functions:
dump(object, file)
... |
039d30cf5a88a0846acb466aff3d17c9b449447bd3f2b4e884fade6b49347d4b | Python | 45,526 | 1,380 | """
Utilities to process intermediate representations of
Datalog programs.
"""
import collections
import operator
import typing
from typing import Iterable
import numpy as np
from scipy import sparse
from nl_expr.exceptions import (
RuleNotFoundError,
SymbolNotFoundError,
UnsupportedProgramError,
)
from... |
feb58256daece51f4c947e38eea3e1e579c2035c1cedeba7711e21a43d903247 | Python | 45,572 | 1,611 | """Functional interface to graph methods and assorted utilities."""
from collections import Counter
from itertools import chain
import networkx as nx
from networkx.utils import not_implemented_for, pairwise
__all__ = [
"nodes",
"edges",
"degree",
"degree_histogram",
"neighbors",
"number_of_no... |
47a47c980e88617ee843ba8ec295356b63c2389b8f65aa7597037aa93d93dd54 | Python | 45,669 | 1,058 | """
Created on Oct 12, 2022.
@author: voodoocode
"""
import functools
import numpy as np
import scipy.optimize
import scipy.spatial
import nibabel.freesurfer
import os
import mne
import warnings
import copy
import pyvista
import finnpy.src_rec.extract_anatomy # @UnresolvedImport
import finnpy.src_rec.utils # @Unre... |
6541c0f83be13c0b6bec55352f03f736daab18eae217d781d5283ebee6db7933 | Python | 45,805 | 1,368 | """
An attrs-inspired class annotation system, but my A stands for amateuristic.
"""
import builtins
import contextlib
import typing
from collections.abc import Mapping
from functools import wraps
import errr
from ..exceptions import (
BootError,
CastError,
CfgReferenceError,
ReferenceLambdaError,
... |
1104b49223df1a056e8a879af143ea59cd0843e7baaed76e8ba5108a2bc65a78 | Python | 45,847 | 1,197 | from dataclasses import dataclass, field
from typing import List
import marshmallow_dataclass
from marshmallow import validates, ValidationError
import json, yaml, os
from pathlib import Path
from typing import Union
from .package import VERSION
from ..utils import get_logger
DEFAULT_CONFIG_FILE_NAME = "clpipe_config.... |
d2f56e2090ad7f905e89af8e411b33da16913f17a9eebf908737dd33ddc65d67 | Python | 45,876 | 887 | import os
import numpy
from matplotlib import pyplot as plt
import numpy as np
import pandas as pd
import copy
from scipy import ndimage
from skimage.morphology import disk
from skimage import morphology as morph
from skimage import filters
from skimage import io
from pyneurite.neuriteanalyzer import Neuri... |
442a2d6a96930d82b932b17f3b90c2068abce3ba06418cbbe06efccb7e1e5dff | Python | 46,127 | 1,077 | import fanc
from fanc.config import config
from fanc.plotting.base_plotter import BasePlotterMatrix, BasePlotter1D, BasePlotter2D, ScalarDataPlot, \
PlotMeta, BaseOverlayPlotter
from fanc.plotting.helpers import append_axes, style_ticks_whitegrid
from fanc.tools.general import str... |
9923e417a6c91c392d3e08c74ada462955fd5771007525b8e5821c3dd046b92c | Python | 46,235 | 1,143 | """Functions for neighborhood enrichment analysis (permutation test, centralities measures etc.)."""
from __future__ import annotations
import warnings
from collections.abc import Sequence
from typing import Any, Literal, NamedTuple
import numpy as np
import pandas as pd
from anndata import AnnData
from fast_array_u... |
ada23c757f412317afaae8c95e514705adf93eba8f239246b30f66d0a4605b31 | Python | 46,386 | 1,206 | # 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 Mapping, Sequence
from logging import Logger
import numpy as np
import numpy.typing as npt
impor... |
02f9be6d2717ab47248a79d6fb5fb0d9cba836943e2aa570f0892e022225ed70 | Python | 46,418 | 909 | # 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... |
4262ca330ac0ab4e0e5ca8172bfe4f055f10e8af7657ab41390721ff07ccff2f | Python | 46,520 | 1,159 | """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."""
"""
Django Base settings for Label Studio.
For more information on this file, see
https://docs.djangoproject.com/en/3.1/topics/settings/
For the ... |
0fc7b2ecdc1193c3e0647e21fb43290572c15947a49e21ce8888d99e857b8494 | Python | 46,607 | 1,280 | from typing import Callable, Optional, Union
import torch
import torch.nn as nn
import torch.nn.functional as F
from . import base, neuron, quantize, surrogate
from .functional import neuron as functional
from spikingjelly.logger import logger
_hw_bits = 12
step_quantize = quantize.step_quantize
def quantize_8b... |
3f2ce1082729fc31a2266ed389da3ae6049bd2697382dc8b2f3b8b7a8f9aa570 | Python | 46,615 | 1,238 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import itertools
import json
from abc import ABC, abstractmethod
from collections import Counter
from collections.abc import Sequence
from copy import deepcopy
from typing import TYPE_CHECKING, Any, cast
import at... |
95c2233a58a53df2ece45f555f243e22e1ceafb61c1f368b68803880d52e3238 | Python | 46,698 | 998 | """
Likelihood function ICLex like described in
Model selection and clustering in stochastic block models with the exact integrated complete data likelihood
from Etienne Come and Pierre Latouche (2014)
"""
import math
from .objective_functions import ObjectiveFunction
# @formatter:off
def calculate_icl_ex_jeffrey_... |
116e87ec1c53e6598e027032e6963cab41a79e4c3d38579e839e54a8daff5d1e | Python | 46,702 | 1,000 | def val_pc_gauss(data_trans,alpha):
from timeawarepc.pcalg import estimate_skeleton, estimate_cpdag, causaleff_ida, ci_test_gauss
import networkx as nx
(g, sep_set) = estimate_skeleton(indep_test_func=ci_test_gauss,
data_matrix=data_trans,
... |
d7112c7ff462abf455cb4ee4f36761e5a927dd1efefb40849cf01a5219f249de | Python | 46,828 | 1,260 | import os
import numpy as np
import pytest
import tensorflow as tf
from learnMSA import Configuration
from learnMSA.align.align import align
from learnMSA.align.align_hits import HitAlignmentMode
from learnMSA.align.alignment_metadata import AlignmentMetaData
from learnMSA.align.alignment_model import AlignmentModel
... |
220966499dafbce90a668e99af4d1a474d70f62655b8d80616107e28a1a29dc3 | Python | 46,838 | 1,304 | """Convenience functions for storing and loading data."""
import io
import itertools
import os
import re
from collections.abc import Mapping, MutableMapping
from zarr._storage.store import data_root, meta_root, assert_zarr_v3_api_available
from zarr.core import Array
from zarr.creation import array as _create_array
fr... |
db1b02c3d90ee2c76f6c3a63b8325b33bfd40ef0ff600498c12e8831163fc8e5 | Python | 46,844 | 1,350 | """Functions to convert NetworkX graphs to and from common data containers
like numpy arrays, scipy sparse arrays, and pandas DataFrames.
The preferred way of converting data to a NetworkX graph is through the
graph constructor. The constructor calls the `~networkx.convert.to_networkx_graph`
function which attempts t... |
b44ff2dfa4a9c6a1160462ee6efd0650f3502ff0e417420377f73c3c0ad0ab9b | Python | 46,892 | 1,462 | """Algorithms for directed acyclic graphs (DAGs).
Note that most of these functions are only guaranteed to work for DAGs.
In general, these functions do not check for acyclic-ness, so it is up
to the user to check for that.
"""
import heapq
from collections import deque
from itertools import combinations, product
fro... |
9f4889dbdffb0d21f6bd80309c1ffaea3c67f3b88f935e7ddfb7324fc556c34e | Python | 46,894 | 1,138 | """
Manager and Serializer for histories.
Histories are containers for datasets or dataset collections
created (or copied) by users over the course of an analysis.
"""
import json
import logging
from typing import (
Any,
cast,
Literal,
Optional,
TYPE_CHECKING,
Union,
)
from uuid import UUID
f... |
85870fa9a75687dd2267a8c2a677dc0fd4d3697a981c398292aa1b1e4fd15fc5 | Python | 46,931 | 871 | import json
import logging
import os
from typing import (
Any,
Optional,
)
from sqlalchemy import or_
from galaxy import (
exceptions,
util,
)
from galaxy.tool_shed.galaxy_install.client import InstallationTarget
from galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager impor... |
a8cf763421ae1b2513a22783935e938724decbe34d0e7e71048b282cd61bb037 | Python | 47,055 | 1,222 | """
*************
VF2 Algorithm
*************
An implementation of VF2 algorithm for graph isomorphism testing.
The simplest interface to use this module is to call the
:func:`is_isomorphic <networkx.algorithms.isomorphism.is_isomorphic>`
function.
Introduction
------------
The GraphMatcher and DiGraphMatcher are r... |
7683c32645c79392b949bae3883eb64a719ac1d51ad8da8ee89149f40ffa848c | Python | 47,077 | 1,149 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
import logging
from itertools import product
from typing import Any
import torch
from ax.adapter.regi... |
d9e9f6366adc3b86a2f06777ba1936193732ff0364e3afdb2d5946207362a536 | Python | 47,162 | 1,232 | from dataclasses import dataclass, field
from typing import List
import marshmallow_dataclass
from marshmallow import validates, ValidationError
import json, yaml, os
from pathlib import Path
from typing import Union
from .package import VERSION
from ..utils import get_logger
DEFAULT_CONFIG_FILE_NAME = "clpipe_config.... |
760d4345ce40ad5307d654f4a04014f769943a77dd455913725721fb924183b4 | Python | 47,266 | 1,316 | """This module provides proxy objects around objects from the common
workflow language reference implementation library cwltool. These proxies
adapt cwltool to Galaxy features and abstract the library away from the rest
of the framework.
"""
import copy
import json
import logging
import os
from abc import (
ABCMet... |
37df0d7f13ad441ec9644691fdb272945c6af77ea4493c9453e61add0fa41dd7 | Python | 47,364 | 1,087 | # 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... |
b7ab4db38060ae4ed9f601e41be9d64b7adc0a205562b51883d0f0c9fb7e9650 | Python | 47,379 | 1,340 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
| Title:
cluster analysis on the WMH burden on the different JHU WM tracts
| Date:
2021-03-03
| Author(s):
Theodor Rumetshofer
| Description:
Performs cluster analysis on the WMH burden on the different JHU WM tracts
extr... |
3ce1d88cf5ed82822888ebe1e7e893faec75716c18b75ddc70ffd5ea7c10acea | Python | 47,425 | 1,161 | # -*- coding: utf-8 -*-
"""Module for reading, writing and validating SNIRF files.
SNIRF files are HDF5 files designed to facilitate the sharing of near-infrared
spectrocopy data. Their specification is defined at https://github.com/fNIRS/snirf.
This library wraps each HDF5 Group and offers a Pythonic interface on li... |
96522defb0a8e5aa86b53cd171868547444d9da1eea1271c0fe50fb415332d90 | Python | 47,459 | 1,316 | """
Algorithms for calculating min/max spanning trees/forests.
"""
from dataclasses import dataclass, field
from enum import Enum
from heapq import heappop, heappush
from itertools import count
from math import isnan
from operator import itemgetter
from queue import PriorityQueue
import networkx as nx
from networkx.... |
8522fca4edb8df2f95973554bfd204142ca00df4e83adce52c172b707519e1a2 | Python | 47,466 | 1,074 | """
Ring attractor network simulation library: auxiliary tools
==========================================================
.. module:: lib_ring
:platform: Linux
:synopsis: auxiliary library for the ring attractor network simulation
.. moduleauthor:: Jose M. Esnaola-Acebes <josemesnaola@gmail.com>
The Neural fi... |
d21bba8dd30cef331bb9a8f13f184c6e501fde7eff27e4dfa4d997b458956c54 | Python | 47,473 | 1,186 | # -*- coding:utf-8 -*-
import tensorflow as tf
from keras.api.layers import Layer, Dense, Dropout, BatchNormalization, Activation, Concatenate, Flatten, Input, \
Embedding, Lambda, Add, Conv2D, MaxPooling2D, SpatialDropout1D
# from tensorflow.python.keras.legacy_tf_layers.base import Layer
from keras import bac... |
81595837ac259be9abcd48522edf2ac22fa85981cab107d0c5ee8a109e32570f | Python | 47,478 | 707 | # Page layout for build_data_inventory.py (exec'd at the end of it, so every name defined there is available).
# One page, ordered for finding things: jump menu -> start here -> one searchable table -> browse by location
# -> repo files -> about. Maintainer notes go to a local, gitignored maintainer_notes.html, not the... |
1ed4eac0310363831e330493cc2162b74d18a1011c139446ec8386dc5e7ff60b | Python | 47,504 | 986 | # 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... |
e5af2c5fbcbe40ce1097ee5261dd8888e9430637b8789d4d43ec758cd7296ed9 | Python | 47,615 | 1,156 | # TODO: revisit ignoring type and write some tests for this, the multi-inheritance in this
# this file is challenging, it should be broken into true mixins.
"""
Constructive Solid Geometry file formats.
"""
import abc
import logging
import re
from typing import (
Optional,
TYPE_CHECKING,
)
from galaxy import ... |
e680e4cb89c1d6e1e060642c0c3682d09fc275d61b0f401fd3a45a56c599f61b | Python | 47,690 | 1,280 | import os
import numpy as np
import pytest
import tensorflow as tf
from learnMSA.config.language_model import LanguageModelConfig
from learnMSA.config.structure import StructureConfig
from learnMSA.hmm.util.value_set import PHMMValueSet
from learnMSA.hmm.util.value_set_emb import PHMMEmbeddingValueSet
import tests.hm... |
92741f3d085a7a7b53ab52b63f3c89452bab3d33faa9745ea06db7e5302bf591 | Python | 47,755 | 1,285 | # aggregator.py
# Authors: Jacob Schreiber <jmschreiber91@gmail.com>
# adapted from code written by Avanti Shrikumar
import numpy as np
from numba import njit
from . import affinitymat
from . import core
from . import forked
from . import precompile
from . import util
from collections import OrderedDict
@precomp... |
de167f8222c581e647943e8606413abfb83a3942af34e794add2557acb46786d | Python | 47,759 | 1,152 | import json
import shutil
import time
import warnings
from enum import Enum
from pathlib import Path
import numpy as np
import tensorflow as tf
from learnMSA.align.align_inserts import AlignedInsertions
from learnMSA.align.alignment_metadata import AlignmentMetaData
from learnMSA.align.align_hits import HitAlignmentM... |
4ecbf664d29212a7e35844bcfb3ea7663e4ac2fa0848c6eebda90b83c4fb37d3 | Python | 47,814 | 844 | import unittest
import h5py
import os
import sys
import time
from numbers import Number
from collections import deque
from collections.abc import Set, Mapping
import numpy as np
import shutil
try:
import snirf
from snirf import Snirf, validateSnirf, loadSnirf, saveSnirf
except ImportError:
sys.path.append(o... |
7e221f01a4ab58cac370779ab40dc1af9d80f5e8ced46cac98b136a99a818b34 | Python | 47,864 | 1,154 | # 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... |
30421d852a577fc2a81dcde99852cdd6bb18f9a06810d9aa4e44fc3a9d544062 | Python | 47,869 | 1,256 | """Tests for saving and viewing results in the interactive REPL."""
import io
from pathlib import Path
import numpy as np
import pandas as pd
import pytest
pytest.importorskip("prompt_toolkit")
pytest.importorskip("rich")
import nibabel as nib # noqa: E402
from rich.console import Console # noqa: E402
from neuro... |
e212e4d87d13725f41f6160ff365dd6a9a3249903fe8c32e4be494c6f3d4f27b | Python | 47,914 | 1,005 | # 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... |
a5ecc5f30d60ca42deee79f81df020f7abbc7b49620b3faab9c284fad905618f | Python | 47,928 | 1,294 | """Base class for MultiGraph."""
from copy import deepcopy
from functools import cached_property
import networkx as nx
from networkx import NetworkXError, convert
from networkx.classes.coreviews import MultiAdjacencyView
from networkx.classes.graph import Graph
from networkx.classes.reportviews import MultiDegreeView... |
18be6628753590771e02eed0b616fb4bc85927fdb92991d5f893108d5f62b762 | Python | 48,011 | 1,171 | """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 pathlib
from core.filters import NumberInFilter
from core.label_config import config_essential_data_has_changed
fr... |
b3921bfd0638e101c54886cfe85d5f5aee95a53597efd2ed51ec339958af93a5 | Python | 48,056 | 1,276 | """Utilities for discovering files to add to a model store.
Working with input "JSON" format used for Fetch API, galaxy.json
imports, etc... High-level utilities in this file can be used during
job output discovery or for persisting Galaxy model objects
corresponding to files in other contexts.
"""
import abc
import ... |
4844369971f064b60305f5a57baf0eb6babf394734ae76cd7ed7e64dc69f6c6e | Python | 48,059 | 1,151 | import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pickle as pk
import string, re
from scipy.signal import butter, filtfilt, cheby1
from sklearn.decomposition import PCA
from tqdm import tqdm
import parmap
import os
class EventTriggeredMaps():
def __init__(self):
pass
def... |
88dae36d7fdece067cae25dfb4947cf1b6fd1173f8e63c4dff0933415cccf323 | Python | 48,120 | 988 | from meld_classifier.paths import (
DEMOGRAPHIC_FEATURES_FILE,
BASE_PATH,
DK_ATLAS_FILE,
MELD_PARAMS_PATH,
)
import pandas as pd
import numpy as np
import nibabel as nb
import os
import h5py
import random
import csv
import json
import sys
import pickle
import shutil
from itertools import chain
import po... |
4be34d0df6cf5f33419257f579546712d78a9018a181ad530d485b9dcd100990 | Python | 48,428 | 1,241 | from .statistics import Statistics
from .plotting import plot_network
import numpy as np
import time
from .trees import TreeCollection
from .output import MorphologyRepository
from .helpers import map_ndarray, listify_input
from .models import CellType
from .connectivity import ConnectionStrategy
from warnings import w... |
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