gt stringclasses 1
value | context stringlengths 2.49k 119k |
|---|---|
#!/usr/bin/env python
'''
Evaluate VCFs against BAMSurgeon "Truth" VCFs
Adam Ewing, adam.ewing@mater.uq.edu.au
Requires PyVCF (https://github.com/jamescasbon/PyVCF)
and PySAM
'''
import sys, os
import vcf
import argparse
import pysam
from collections import OrderedDict
def match(subrec, trurec, vtype='SNV'):
ass... | |
# -*- coding: utf-8 -*-
# Generated by the protocol buffer compiler. DO NOT EDIT!
# source: tcav_results/results.proto
import sys
_b=sys.version_info[0]<3 and (lambda x:x) or (lambda x:x.encode('latin1'))
from google.protobuf import descriptor as _descriptor
from google.protobuf import message as _message
from google... | |
"""Extract reference documentation from the NumPy source tree.
"""
import inspect
import textwrap
import re
import pydoc
try:
from StringIO import StringIO
except ImportError:
from io import StringIO
from warnings import warn
class Reader(object):
"""A line-based string reader.
"""
def __init... | |
# Copyright 2020 Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: Apache-2.0
"""Tests the network latency of a Firecracker guest."""
import logging
import platform
import re
import pytest
import host_tools.network as net_tools
from conftest import ARTIFACTS_COLLECTION
from framework.... | |
# util/deprecations.py
# Copyright (C) 2005-2019 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Helpers related to deprecation of functions, methods, classes, other
functio... | |
from urllib import quote_plus
from django.contrib import messages
from django.http import HttpResponse, HttpResponseRedirect, Http404, JsonResponse
try:
from django.utils import simplejson as json
except ImportError:
import json
from django.shortcuts import render, get_object_or_404, redirect
from django.utils ... | |
# Licensed to the StackStorm, Inc ('StackStorm') 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 use th... | |
#
# The Python Imaging Library.
# $Id$
#
# Windows Icon support for PIL
#
# History:
# 96-05-27 fl Created
#
# Copyright (c) Secret Labs AB 1997.
# Copyright (c) Fredrik Lundh 1996.
#
# See the README file for information on usage and redistribution.
#
# This plugin is a refactored version of Win32IconImageP... | |
'''Wrapper for the github API.
This maintains an on-disk cache of API calls and maps github API calls onto
Python functions.
'''
import sys
import logging
import json
import re
import os
import hashlib
import cPickle
import requests
GITHUB_API_ROOT = 'https://api.github.com'
WHITESPACE_RE = re.compile(r'^[ \t\n\r... | |
# Copyright 2013 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# TODO(nduca): Rewrite what some of these tests to use mocks instead of
# actually talking to the device. This would improve our coverage quite
# a bit.
imp... | |
#
# GtkHelp.py -- customized Gtk widgets
#
# Eric Jeschke (eric@naoj.org)
#
# Copyright (c) Eric R. Jeschke. All rights reserved.
# This is open-source software licensed under a BSD license.
# Please see the file LICENSE.txt for details.
#
from __future__ import print_function
import time
import math
from ginga.gtkw ... | |
import json
import requests
import pytest
import demistomock as demisto
# Disable insecure warnings
requests.packages.urllib3.disable_warnings()
BASE_URL = 'https://localhost:6078'
API_TOKEN = 'apitoken'
params = {
'base_url': BASE_URL,
'token': API_TOKEN,
'insecure': True,
'mirror_direction': 'Both... | |
# subprocess - Subprocesses with accessible I/O streams
#
# For more information about this module, see PEP 324.
#
# Copyright (c) 2003-2005 by Peter Astrand <astrand@lysator.liu.se>
#
# Licensed to PSF under a Contributor Agreement.
# See http://www.python.org/2.4/license for licensing details.
r"""Subprocesses with ... | |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2010-today OpenERP SA (<http://www.openerp.com>)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms o... | |
# Copyright 2016 Capital One Services, LLC
#
# 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... | |
# copyright 2003-2010 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This file is part of logilab-common.
#
# logilab-common is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as publ... | |
#!/usr/bin/env python
"""
MHC Epitope analysis
Created September 2013
Copyright (C) Damien Farrell
"""
import sys, os, shutil, string, types
import csv, glob, pickle, itertools
import re
import time, random
from collections import OrderedDict
from operator import itemgetter
#import matplotlib
#matplotlib.... | |
#!/usr/bin/python2.7
# Copyright 2011 Google Inc. All Rights Reserved.
#
# 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 requi... | |
import collections
import string
import numpy
import six
import cupy
from cupy import carray
from cupy import elementwise
from cupy import util
six_range = six.moves.range
six_zip = six.moves.zip
_broadcast = elementwise._broadcast
_check_args = elementwise._check_args
_decide_params_type = elementwise._decide_par... | |
"""
parser.http package (imdb package).
This package provides the IMDbHTTPAccessSystem class used to access
IMDb's data through the web interface.
the imdb.IMDb function will return an instance of this class when
called with the 'accessSystem' argument set to "http" or "web"
or "html" (this is the default).
Copyright... | |
from collections import Iterable
import copy
from numbers import Real, Integral
import sys
import numpy as np
from openmc import Mesh
from openmc.summary import Summary
import openmc.checkvalue as cv
if sys.version_info[0] >= 3:
basestring = str
_FILTER_TYPES = ['universe', 'material', 'cell', 'cellborn', 'su... | |
"""
.. _tut_erp:
EEG processing and Event Related Potentials (ERPs)
==================================================
.. contents:: Here we cover the specifics of EEG, namely:
:local:
:depth: 1
"""
import mne
from mne.datasets import sample
from mne.channels import combine_channels
#########################... | |
# coding=utf-8
# Copyright 2018 The Google AI Language Team Authors.
#
# 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 ... | |
# Copyright 2012 OpenStack Foundation
# All Rights Reserved.
#
# 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 requ... | |
import zmq
import Queue
import threading
import msgpack
import snappy
import traceback
import time
def _unpack(str) :
if str[0] == 'S':
tmp = snappy.uncompress(str[1:])
obj = msgpack.loads(tmp)
elif str[0] == '\0':
obj = msgpack.loads(str[1:])
else:
return None
#print ... | |
"""
Bundle subcommands.
"""
import logging
import sys
import typing as ty
import click
from git_pw import api
from git_pw import utils
LOG = logging.getLogger(__name__)
_list_headers = ('ID', 'Name', 'Owner', 'Public')
_sort_fields = ('id', '-id', 'name', '-name')
def _get_bundle(bundle_id: str) -> dict:
"""... | |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import argparse
import libvirt
import logging
from ovm.configuration import Configuration
from ovm.utils.logger import logger
from ovm.vmcli.management import * # noqa
def add_subparsers(parser):
subparsers = parser.add_subparsers()
# console
subcommand =... | |
# Copyright (c) 2012-2013 Mitch Garnaat http://garnaat.org/
# Copyright 2012-2014 Amazon.com, Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http... | |
import weakref
from twisted.internet import task
from twisted.trial import unittest
from axiom import store
from imaginary import iimaginary, objects, events, action
from imaginary.test import commandutils
from examplegame import mice
from examplegame import japanese
class MouseChallengeMixin(object):
"""
... | |
# Copyright 2013 the Neutrino authors (see AUTHORS).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
# Neutrino syntax tree definitions
from abc import abstractmethod
import data
import plankton
# Syntax tree visitor. The default behavior of each visit method is to apply
# the visitor recursively.
cl... | |
# Copyright 2013 Rackspace Hosting Inc.
# All Rights Reserved.
#
# 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 applic... | |
# -*- coding: utf-8 -*-
from scipy.interpolate import griddata
import numpy as np
import logging
from .helpers import get_latex_table_frame
class Comparison(object):
def __init__(self, parent):
self.parent = parent
self._logger = logging.getLogger("chainconsumer")
def dic(self):
r"""... | |
from __future__ import print_function, absolute_import
from ctypes import (c_char_p, byref, POINTER, c_bool, create_string_buffer,
c_void_p, c_size_t, cast, string_at)
from . import ffi
from .linker import link_modules
from .common import _decode_string, _encode_string
from .value import ValueRef
... | |
# Copyright 2014 Netflix, Inc.
#
# 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... | |
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
import numpy as np
import matplotlib
from matplotlib.testing.decorators import image_comparison, knownfailureif, cleanup
import matplotlib.pyplot as plt
from matplotlib import patches, path, transf... | |
"""
work queue specification
"""
import re
import types
from six import iteritems
from pandaserver.taskbuffer.GlobalShares import Share
RESOURCE = 'Resource'
ACTIVE_FUNCTIONS = [RESOURCE]
class WorkQueue(object):
# attributes
_attributes = ('queue_id', 'queue_name', 'queue_type', 'VO', 'queue_share', 'qu... | |
# encoding=utf8
"""
Module for computing various vector and matrix norms. Vector norms define a measure
of distance for vectors. Matrix norms are measures of distance in the space of the
matrix. The most common vector norm is the 2-norm, the equivalent matrix norm
is the Frobenius norm.
"""
import numpy as np
impor... | |
#!/usr/bin/env python
"""Convert SeqAn profiling information into PDF graphic.
USAGE: profile2pdf.py <program.profile.txt> <out.pdf>
"""
from __future__ import with_statement
__author__ = 'Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>'
import math
import sys
import cairo
IGNORE_LIMIT = 0.00001
# Automatic le... | |
###############################################################################
#
# Copyright (c) 2011 Ruslan Spivak
#
# 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, inc... | |
import json
import boto3
import sure # noqa # pylint: disable=unused-import
from botocore.exceptions import ClientError
import pytest
from moto import mock_iam, mock_ec2, mock_s3, mock_sts, mock_elbv2, mock_rds
from moto.core import set_initial_no_auth_action_count
from moto.core import ACCOUNT_ID
from uuid import ... | |
import json
import os
from subprocess import PIPE
from subprocess import Popen
from time import sleep
from unittest import TestCase
import requests
from sqlalchemy import create_engine
from sqlalchemy.orm import sessionmaker
from api.decorator import threaded, retry_on_fail
from database.dictionary import Base, Defin... | |
# coding: utf-8
#-------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for
# license information.
#----------------------------------------------------------------------... | |
#===----------------------------------------------------------------------===##
#
# Part of the LLVM Project, under the Apache License v2.0 with LLVM Exceptions.
# See https://llvm.org/LICENSE.txt for license information.
# SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
#
#===----------------------------------... | |
#!/usr/bin/env python
import os.path
import argparse
import math
import random
import numpy as np
import sympy as sp
import matplotlib.pyplot as plt
plt.rc('text', usetex=True)
plt.rc('font', family='serif')
import stats.methods as methods
from stats.utils import *
################
# Declarations #
################... | |
""" Selective Kernel Networks (ResNet base)
Paper: Selective Kernel Networks (https://arxiv.org/abs/1903.06586)
This was inspired by reading 'Compounding the Performance Improvements...' (https://arxiv.org/abs/2001.06268)
and a streamlined impl at https://github.com/clovaai/assembled-cnn but I ended up building somet... | |
"""
.. module:: pdf
:synopsis: This module implements Probability Density Functions (PDFs)."
.. moduleauthor:: Martin Hunt <mmh@Purdue.edu>
This file is part of PUQ
Copyright (c) 2013 PUQ Authors
See LICENSE file for terms.
"""
from __future__ import absolute_import, division, print_function
import numpy as np
i... | |
# Copyright 2012 Nebula, Inc.
#
# 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 agree... | |
from __future__ import unicode_literals
import logging
from PIL import Image
from os import path
import os.path
try:
from io import BytesIO
except ImportError:
from cStringIO import StringIO as BytesIO
from django.db import models
from django.db.models import signals
from django.utils.translation import uget... | |
# -*- coding: utf-8 -*-
#
# Copyright 2012 Canonical Ltd.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful, but
# W... | |
# Copyright 2014 The Oppia Authors. All Rights Reserved.
#
# 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 ... | |
"""
HTML Widget classes
"""
from __future__ import unicode_literals
import copy
import datetime
import re
from itertools import chain
from django.conf import settings
from django.forms.utils import flatatt, to_current_timezone
from django.utils import datetime_safe, formats, six
from django.utils.datastructures impo... | |
from flask import Flask, render_template, request, redirect, url_for, flash, jsonify
from flask_pagination import Pagination
from db import *
from flask_login import LoginManager, login_user
import consts
import md5
# system consts
records_per_page = 10
md5_salt = 'coersive control'
app = Flask(__name__)
app.secret_... | |
from __future__ import absolute_import, unicode_literals
import datetime
import os
from decimal import Decimal
from django import forms
from django.core.files.uploadedfile import SimpleUploadedFile
from django.core.validators import ValidationError
from django.db import connection
from django.forms.models import mode... | |
'''
Alternate strategies to find IAC+SE in a bytestring.
The payload looks like a 4+ byte blob:
IAC SB <zero or more payload bytes> IAC SE
The tricky part is that an IAC in the payload is escaped to IAC IAC.
So the terminting IAC+SE is really the first SE that is preceded by
an *odd* number of IACs.
These function... | |
###############################################################################
##
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary for... | |
# -*- coding: utf-8 -*-
"""
celery.backends.base
~~~~~~~~~~~~~~~~~~~~
Result backend base classes.
- :class:`BaseBackend` defines the interface.
- :class:`KeyValueStoreBackend` is a common base class
using K/V semantics like _get and _put.
"""
from __future__ import absolute_import
import... | |
# adding this to suppress sklearn DeprecationWarnings...
def warn(*args, **kwargs):
pass
import warnings
warnings.warn = warn
import numpy as np
import os
import time
import pickle
import datetime
from datetime import timedelta
from optparse import OptionParser
from sklearn.model_selection import cross_val_score, ... | |
# Copyright (C) 2013 Google Inc. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the ... | |
# swift_build_support/cmake.py - Detect host machine's CMake -*- python -*-
#
# This source file is part of the Swift.org open source project
#
# Copyright (c) 2014 - 2017 Apple Inc. and the Swift project authors
# Licensed under Apache License v2.0 with Runtime Library Exception
#
# See https://swift.org/LICENSE.txt f... | |
"""Support for UK public transport data provided by transportapi.com."""
from datetime import datetime, timedelta
import logging
import re
import requests
import voluptuous as vol
from homeassistant.components.sensor import PLATFORM_SCHEMA, SensorEntity
from homeassistant.const import CONF_MODE, HTTP_OK, TIME_MINUTES... | |
#!/usr/bin/env
"""
Based on waveletanalysis.py
For P. Stabeno
Using Anaconda packaged Python
modifications for confidence intervals based on wave_matlab at
http://paos.colorado.edu/research/wavelets/
### License ###
The MIT License (MIT)
Copyright (c) 2013 Aaron O'Leary (dev@aaren.me)
Permission... | |
import scores_db
import mock
import redis_client
import control
from twisted.internet import defer
import yaml
# Unit tests
## ScoresDB access
def test_set_scores():
fake_connection = mock.Mock()
fake_connection.set = mock.Mock()
with mock.patch('redis_client.connection', fake_connection):
scores... | |
import mock
import os
import pytest
import tempfile
from datetime import datetime
from django.conf import settings
from django.core import mail
from django.test.utils import override_settings
from freezegun import freeze_time
from olympia import amo
from olympia.activity.models import ActivityLog
from olympia.addons... | |
# -*- coding: utf-8 -
#
# This file is part of restkit released under the MIT license.
# See the NOTICE for more information.
import base64
import urllib
import time
import random
import urlparse
import hmac
import binascii
try:
from urlparse import parse_qs, parse_qsl
except ImportError:
from cgi import par... | |
#!/usr/bin/env python
'''
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")... | |
# Copyright (c) 2014 Adafruit Industries
# Author: Tony DiCola
#
# 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... | |
# -*- test-case-name: pyflakes -*-
# (c) 2005-2010 Divmod, Inc.
# See LICENSE file for details
import __builtin__
import os.path
import _ast
import re
from pyflakes import messages
interpol = re.compile(r'%(\([a-zA-Z0-9_]+\))?[-#0 +]*([0-9]+|[*])?'
r'(\.([0-9]+|[*]))?[hlL]?[diouxXeEfFgGcrs%]')
... | |
"""Storage for auth models."""
import asyncio
from collections import OrderedDict
from datetime import timedelta
import hmac
from logging import getLogger
from typing import Any, Dict, List, Optional
from homeassistant.auth.const import ACCESS_TOKEN_EXPIRATION
from homeassistant.core import HomeAssistant, callback
fro... | |
# coding=utf-8
# Copyright 2018 The Google AI Language Team Authors.
#
# 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 ... | |
'''
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 use this ... | |
"""Adds support for generic hygrostat units."""
import asyncio
import logging
from homeassistant.components.humidifier import PLATFORM_SCHEMA, HumidifierEntity
from homeassistant.components.humidifier.const import (
ATTR_HUMIDITY,
DEVICE_CLASS_DEHUMIDIFIER,
DEVICE_CLASS_HUMIDIFIER,
MODE_AWAY,
MODE_... | |
#!/usr/bin/env python
# Licensed to Cloudera, Inc. under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. Cloudera, Inc. licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you ma... | |
"""Tests of http client with custom Connector"""
import asyncio
import http.cookies
import gc
import socket
import unittest
import ssl
import tempfile
import shutil
import os.path
from unittest import mock
import aiohttp
from aiohttp import web
from aiohttp import client
from aiohttp import helpers
from aiohttp.clien... | |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# 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... | |
# Author: Travis Oliphant 2001
# Author: Nathan Woods 2013 (nquad &c)
import sys
import warnings
from functools import partial
from . import _quadpack
import numpy
from numpy import Inf
__all__ = ['quad', 'dblquad', 'tplquad', 'nquad', 'quad_explain',
'IntegrationWarning']
error = _quadpack.error
class ... | |
# encoding: utf-8
import socket
from functools import partial
from pprint import pformat
from marrow.server.http.testing import HTTPTestCase, CRLF, EOH
from marrow.util.compat import unicode
log = __import__('logging').getLogger(__name__)
from applications import *
class TestHTTP11Protocol(HTTPTestCase):
... | |
import sys, re, os, time, math
from datetime import datetime
from dateutil.parser import parse as dtparse
import pickle, json
from pprint import pformat
import asyncio
from functools import partial
import biothings.utils.mongo as mongo
import biothings.utils.aws as aws
from biothings.utils.common import timesofar
fro... | |
"""
Test module for Flask-htpasswd extension
"""
from __future__ import absolute_import, unicode_literals
import base64
import os
import unittest
from flask import request, Flask, g
from itsdangerous import JSONWebSignatureSerializer as Serializer
import mock
from flask_htpasswd import HtPasswdAuth
class TestAuth(u... | |
#!/usr/bin/env python
"""
Integration (not unit) tests for pylast.py
"""
import time
import unittest
import pylast
from .test_pylast import TestPyLastWithLastFm
class TestPyLastNetwork(TestPyLastWithLastFm):
def test_scrobble(self):
# Arrange
artist = "test artist"
title = "test title"
... | |
############################################################################
# Copyright (c) Wolf Vollprecht, Johan Mabille and Sylvain Corlay #
# Copyright (c) QuantStack #
# #
# Distribute... | |
##########################################################################
#
# Copyright (c) 2013, Image Engine Design Inc. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistrib... | |
#!/usr/bin/env python3
# Written by Devon Mack April-May 2017
# This program takes a 5 parameters in the config file and runs a SNVPhyl in galaxy fully automatically
# Parameters (when it doubt, delete the config.json file and the program will create it for you with defaults):
# config.json
# api_key: The API key wh... | |
__author__ = 'woolly_sammoth'
from kivy.config import Config
Config.set('graphics', 'borderless', '0')
Config.set('graphics', 'resizable', '1')
Config.set('graphics', 'fullscreen', '0')
Config.set('input', 'mouse', 'mouse,disable_multitouch')
from kivy.app import App
from kivy.uix.boxlayout import BoxLayout
from kiv... | |
# 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... | |
# -*- coding: utf-8 -*-
# Copyright (c) 2014, 2015 Mitch Garnaat
#
# 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 appl... | |
'''tzinfo timezone information for Africa/Cairo.'''
from pytz.tzinfo import DstTzInfo
from pytz.tzinfo import memorized_datetime as d
from pytz.tzinfo import memorized_ttinfo as i
class Cairo(DstTzInfo):
'''Africa/Cairo timezone definition. See datetime.tzinfo for details'''
zone = 'Africa/Cairo'
_utc_tr... | |
#this python file runs the non-iterative and iterative versions of
#the A and B versions of the trace simplification algorithm,
#where:
# A - Blocks are considered alone
# B - Blocks of like thread segments are condensed into single blocks
# this aims to simplify even in the case of incremental failure
import ... | |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# 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 applica... | |
# (C) Datadog, Inc. 2013-2017
# (C) Brett Langdon <brett@blangdon.com> 2013
# All rights reserved
# Licensed under Simplified BSD License (see LICENSE)
# stdlib
import re
import time
import urllib
import urlparse
from collections import defaultdict
# 3p
import requests
from requests.exceptions import RequestException... | |
# Copyright (c) 2006-2012 Mitch Garnaat http://garnaat.org/
# Copyright (c) 2010, Eucalyptus Systems, Inc.
# Copyright (c) 2012 Amazon.com, Inc. or its affiliates.
# All rights reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation file... | |
import json
import locale
import logging
import os
import re
import string
from zipfile import ZipFile, ZipInfo
from tarfile import TarFile, TarInfo
from pyp2rpm import utils
logger = logging.getLogger(__name__)
def generator_to_list(fn):
"""This decorator is for flat_list function.
It converts returned ge... | |
import calendar
import time
from dataclasses import dataclass
from typing import Any, Dict, List, Optional, Tuple
from django.conf import settings
from django.http import HttpRequest
from django.utils import translation
from two_factor.utils import default_device
from zerver.context_processors import get_apps_page_ur... | |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import logging
import os
import re
from datetime import datetime
import cPickle
import tempfile
from contextlib import closing
from string import Template
import wsgiref.util
import cgi
from urllib import quote_plus, unquote_plus
import hashlib
import random
class Request... | |
"""
The contents of this file are taken from
https://github.com/niwinz/django-jinja/blob/master/django_jinja/management/commands/makemessages.py
Jinja2's i18n functionality is not exactly the same as Django's.
In particular, the tags names and their syntax are different:
1. The Django ``trans`` tag is replaced by a... | |
# SPDX-FileCopyrightText: 2015 Eric Larson
#
# SPDX-License-Identifier: Apache-2.0
"""
The httplib2 algorithms ported for use with requests.
"""
import logging
import re
import calendar
import time
from email.utils import parsedate_tz
from pip._vendor.requests.structures import CaseInsensitiveDict
from .cache import... | |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2012-2021 SoftBank Robotics. All rights reserved.
# Use of this source code is governed by a BSD-style license (see the COPYING file).
""" Test QiPkg """
from __future__ import absolute_import
from __future__ import unicode_literals
from __future__ import pr... | |
# Copyright (c) 2015 Xilinx Inc.
#
# 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, modify, merge, publish, distrib... | |
import collections
import copy
import multiprocessing as mp
from operator import gt, lt
import random
from random import randint, uniform, shuffle
import pysal as ps
from pysal.region.components import check_contiguity
import numpy as np
from numpy.random import RandomState
class LocalSearch(mp.Process):
"""
... | |
"""A multi-producer, multi-consumer queue."""
from _pydev_imps._pydev_time import time as _time
from _pydev_imps import _pydev_thread
try:
from _pydev_imps import _pydev_threading as _threading
except ImportError:
import dummy_threading as _threading
from collections import deque
import heapq
__all__ = ['Empt... | |
# $Id: TemplateExpand.py 1053 2008-07-30 12:03:29Z landrgr1 $
#
# Created by Greg Landrum August, 2006
#
#
from __future__ import print_function
from rdkit import RDLogger as logging
logger = logging.logger()
logger.setLevel(logging.INFO)
from rdkit import Chem
from rdkit.Chem import Crippen
from rdkit.Chem import All... |
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