text stringlengths 12 6.59M |
|---|
import os
import datetime
import operator
import pytest
from doit import tools
from doit import task
def test_create_folder():
def rm_dir():
if os.path.exists(DIR_DEP):
os.removedirs(DIR_DEP)
DIR_DEP = os.path.join(os.path.dirname(__file__),"parent/child/")
rm_dir()
assert True ... |
# Copyright (c) 2015-2016 Vector 35 LLC
#
# 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, ... |
from AG_fft_tools import correlate2d
from agpy import gaussfitter
import warnings
import numpy as np
def cross_correlation_shifts_FITS(fitsfile1, fitsfile2, return_cropped_images=False, quiet=True, sigma_cut=False, **kwargs):
"""
Determine the shift between two FITS images using the cross-correlation
techn... |
import os
import csv
import sys
from optparse import make_option
from collections import Callable
from django.db.models import Q
from django.contrib.sites.models import Site
from django.db.models.loading import get_model
from django.core.management.base import LabelCommand, CommandError
DOMAIN = Site.objects.get_cur... |
import logging
import json
import requests
import datetime
import math
import time
# django modules
from django.views.decorators.csrf import csrf_exempt
from django.shortcuts import render, get_object_or_404
from django.views.generic import View, TemplateView, ListView, DetailView
from django.db.models import Q,Count
... |
"""
Internal tasks are tasks that are started from the teuthology infrastructure.
Note that there is no corresponding task defined for this module. All of
the calls are made from other modules, most notably teuthology/run.py
"""
from cStringIO import StringIO
import contextlib
import logging
import os
import time
impo... |
# -*- coding: utf-8 -*-
#
# pylast -
# A Python interface to Last.fm and Libre.fm
#
# Copyright 2008-2010 Amr Hassan
# Copyright 2013-2018 hugovk
#
# 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 Lice... |
{
'targets': [
{
'target_name': 'compiler',
'type': 'static_library',
'include_dirs': [
'include',
'src',
'externals/utf8proc',
'externals/json-parser',
],
'sources': [
'src/compiler/build_tables/build_parse_table.cc',
'src/compiler/bu... |
"""
Sphinx Documentation Automatic Builder
MIT License. See LICENSE for more details.
Copyright (c) 2013, Jonathan Stoppani
"""
import argparse
import os
import subprocess
import sys
import pty
import multiprocessing
from livereload import Server
from watchdog.observers import Observer
from watchdog.events import ... |
#!/usr/bin/env python
"""Run some linters on files of various types."""
USAGE = """%prog [options] [files] ...
Run linters over the given files, or the current directory tree.
By default -- if no commandline arguments are given -- this runs the
linters on all non-blacklisted python file under the current
directory... |
__version__ = "0.94"
import helpers
import os, shutil
module_dir = os.path.abspath(os.path.dirname(__file__))
default_params_str = """{
'fasta': '',
'csv': '',
'out_dir': '',
'protocol': 'gram_pos', # 'gram_neg'
#### Signal peptide and transmembrane helix prediction
'signalp4_bin': 'signalp_web',
# 'si... |
version = "1.2.2"
|
__version__ = '0.8'
__author__ = 'ArmedGuy'
import b3, time, threading, re, socket, thread, sys, pyircbot
from pyircbot import IrcEvent, IrcUser
from b3 import clients
import b3.events
import b3.plugin
import datetime, string
from b3 import functions
#------------------------------------------------------------------... |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2009 Benoit Chesneau <benoitc@e-engura.org>
#
# This software is licensed as described in the file LICENSE, which
# you should have received as part of this distribution.
#
import copy
from hashlib import md5
import os
import re
import shutil
import sys
from... |
import os
from ehive.runnable.IGFBaseProcess import IGFBaseProcess
from igf_data.utils.fileutils import get_temp_dir,remove_dir,check_file_path
from igf_data.utils.jupyter_nbconvert_wrapper import generate_ipynb_from_template,nbconvert_execute_in_singularity
class NotebookRunner(IGFBaseProcess):
'''
A runnable cla... |
import cv2
import matplotlib.pyplot as plt
import numpy as np
import os
import _init_paths
import caffe
caffe_root = os.path.join(os.path.dirname(__file__), '..', '..', 'caffe')
def get_map(image, verbose=False):
# caffe.set_device(0)
# caffe.set_mode_gpu()
caffe.set_mode_cpu()
model_def = os.path... |
from __future__ import print_function, unicode_literals
import re, time, json
from collections import defaultdict
from twisted.python import log
from twisted.internet import protocol
from twisted.protocols.basic import LineReceiver
from .database import get_db
SECONDS = 1.0
MINUTE = 60*SECONDS
HOUR = 60*MINUTE
DAY = 2... |
# Tai Sakuma <sakuma@fnal.gov>
import multiprocessing
import time
from ProgressReport import ProgressReport
##____________________________________________________________________________||
class ProgressReporter(object):
def __init__(self, queue, pernevents = 1000):
self.queue = queue
self.perneve... |
"""
This file is part of Arakoon, a distributed key-value store. Copyright
(C) 2010 Incubaid BVBA
Licensees holding a valid Incubaid license may use this file in
accordance with Incubaid's Arakoon commercial license agreement. For
more information on how to enter into this agreement, please contact
Incubaid (contact d... |
# Copyright 2013 The LUCI Authors. All rights reserved.
# Use of this source code is governed under the Apache License, Version 2.0
# that can be found in the LICENSE file.
"""Swarming bot main process.
This is the program that communicates with the Swarming server, ensures the code
is always up to date and executes ... |
"""Any shareable docstring components for rolling/expanding/ewm"""
from textwrap import dedent
from pandas.core.shared_docs import _shared_docs
_shared_docs = dict(**_shared_docs)
def create_section_header(header: str) -> str:
"""Create numpydoc section header"""
return "\n".join((header, "-" * len(header))... |
import logging
import requests
import urlparse
from selenium import common
from selenium import webdriver
from selenium.webdriver.common.action_chains import ActionChains
from selenium.webdriver.common.by import By
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.support.ui import WebDriverWait
... |
# Amara, universalsubtitles.org
#
# Copyright (C) 2012 Participatory Culture Foundation
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your op... |
#!/usr/bin/python
from lxml import etree
from StringIO import StringIO
from sfa.rspecs.rspec import RSpec
from sfa.util.xrn import *
from sfa.util.plxrn import hostname_to_urn
from sfa.util.config import Config
from sfa.rspecs.rspec_version import RSpecVersion
_version = {'type': 'ProtoGENI',
'version... |
#!/usr/bin/python
import copy
import gyp.common
import optparse
import os.path
import re
import shlex
import subprocess
import sys
# A list of types that are treated as linkable.
linkable_types = ['executable', 'shared_library', 'loadable_module']
# A list of sections that contain links to other targets.
dependency... |
from bda.plone.shop.interfaces import IShopExtensionLayer
from plone.app.users.browser.register import RegistrationForm, AddUserForm
from plone.app.users.browser.userdatapanel import UserDataPanel
from plone.supermodel import model
from plone.z3cform.fieldsets import extensible
from z3c.form import field
from zope impo... |
# -*- encoding: utf-8 -*-
from abjad.tools import systemtools
from abjad.tools import timespantools
import consort
import collections
def _make_timespan_inventory():
timespan_inventory = timespantools.TimespanInventory([
consort.PerformedTimespan(
start_offset=0,
stop_offset=20,
... |
#!/bin/env python
# Copyright (c) 2014 Hewlett-Packard Development Company, L.P.
#
# 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... |
print "Hello World!"
print "Goodby World..."
|
"""
Supplies Pane, Layout, NdLayout and AdjointLayout. Pane extends View
to allow multiple Views to be presented side-by-side in a NdLayout. An
AdjointLayout allows one or two Views to be ajoined to a primary View
to act as supplementary elements.
"""
from functools import reduce
from itertools import chain
import nu... |
# -*- coding: utf-8 -*-
# Copyright (C) 2014 Johannes Baiter <johannes.baiter@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your ... |
# -*- coding: utf-8 -*-
from datetime import datetime
import decimal
from decimal import Decimal as D
from hashlib import md5
import pickle
import sys
def get_bytes_buffer():
try:
# Python 2
from StringIO import StringIO
return StringIO()
except ImportError:
# Python 3
f... |
#
# spyne - Copyright (C) Spyne contributors.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This libra... |
# vim: ts=4 sw=4 expandtab
import os
import tempfile
import time
from collections import deque
from devops import xml
from xmlbuilder import XMLBuilder
def find(p, seq):
for item in seq:
if p(item): return item
class DeploymentSpec:
def __repr__(self):
return "<DeploymentSpec arch=\"%s\" os_t... |
"""Formatter producing CSV data."""
import sys
import csv
from collections import OrderedDict
import formatter
import executor
# TO BE DEFINED
# - wrong lines
# - return_code/code/section status
# - difference/similarity
class CSVFormatter(formatter.Formatter):
_RESULT_TABLE = {
executor.ER_OK: "ok",
... |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import inspect
# list of methods that check everything other than attributes
ALL_BUT_ATTRIBUTES = [
inspect.ismodule,
inspect.isclass,
inspect.ismethod,
inspect.isfunction,
inspect.isgeneratorfunction,
inspect.isgenerator,
inspect.istraceback,... |
import unittest
import saspy
import os
import pandas as pd
from IPython.utils.tempdir import TemporaryDirectory
from pandas.util.testing import assert_frame_equal
class TestSASdataObject(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.sas = saspy.SASsession(results='HTML') #cfgname='defa... |
import logging
import Hand, Utilities
# There's a few things to do about dragons.
# 1. When a card is played that has a triggered effect, >= 1 card in hand must be a dragon.
# 1a. If (at some later date) a card is played from that set which is a dragon, no information is known about the remaining cards.
# 1b. If (at s... |
#!/usr/bin/python3
from pkg_resources import parse_version
import json
import sys
import importlib
from importlib.machinery import SourceFileLoader
import traceback
import configparser
import datetime
from time import mktime
import argparse
import time
import logging
import os
import os.path
import glob
from websocket ... |
# Copyright 2018 The Bazel 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 la... |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import division, print_function
import emcee
import fitsio
import numpy as np
import matplotlib.pyplot as plt
from scipy.optimize import minimize
from plot_setup import setup, SQUARE_FIGSIZE, COLORS
import genrp
from genrp import terms
np.random.seed(42... |
# coding: utf-8
import unittest
import zeit.brightcove.connection
class ConnectionTest(unittest.TestCase):
# mix in some non-ASCII chars everywhere to guard against #10600
def test_strings_should_be_read_from_json_as_unicode(self):
conn = zeit.brightcove.connection.APIConnection(
None, No... |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Title: Dumpscript management command
Project: Hardytools (queryset-refactor version)
Author: Will Hardy (http://willhardy.com.au)
Date: June 2008
Usage: python manage.py dumpscript appname > scripts/scriptname.py
$Revision: 217 $
Descripti... |
# Copyright (c) 2012 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.
{
'variables': {
'conditions': [
[ 'toolkit_uses_gtk==1', {
# Link to system .so since we already use it due to GTK.
'use_sys... |
from restclients.wheniwork import WhenIWork
from restclients.models.wheniwork import WhenIWorkRequest, WhenIWorkUser
from restclients.wheniwork.users import Users
import dateutil.parser
from urllib import urlencode
class Requests(WhenIWork):
def get_request(self, request_id):
"""
Get Existing Requ... |
from nose.tools import *
import mock
from tests.factories import AuthUserFactory
from tests.factories import UserFactory, ProjectFactory
from framework.auth.decorators import Auth
from website.addons.dataverse.model import AddonDataverseUserSettings, \
AddonDataverseNodeSettings, DataverseFile
from website.addons.... |
# -*- coding: utf-8 -*-
from south.v2 import SchemaMigration
class Migration(SchemaMigration):
def forwards(self, orm):
managers = orm['fixmystreet.FMSUser'].objects.filter(manager=True)
#~ table_line_format = u"{0:5} {1:30.30} {2:15.15} {3:4} {4:4}"
#~ table_line_separator = ''.join(['-... |
from __future__ import annotations
import os
import shutil
import subprocess
from pathlib import Path
version = subprocess.run(
["poetry", "version", "-s"], capture_output=True, text=True
).stdout.rstrip()
dir: Path = Path(__file__).resolve().parents[1]
dist: Path = dir / "dist"
Path(dist / "gaphor").mkdir(paren... |
#!/usr/bin/python
from lxml import etree
from StringIO import StringIO
from sfa.rspecs.rspec import RSpec
from sfa.util.xrn import *
from sfa.util.plxrn import hostname_to_urn, xrn_to_hostname
from sfa.util.config import Config
from sfa.rspecs.rspec_version import RSpecVersion
_ad_version = {'type': 'ProtoGENI',
... |
#!/usr/bin/python
import copy
import gyp.common
import optparse
import os.path
import re
import shlex
import subprocess
import sys
# A list of types that are treated as linkable.
linkable_types = ['executable', 'shared_library', 'loadable_module']
# A list of sections that contain links to other targets.
dependency... |
#!/usr/bin/env python
from operator import itemgetter
import datetime
import sys
import usb.core
MAX_BYTES = 10 * 1000
STARTING_MESSAGE_SIZE = 48
ENDING_MESSAGE_SIZE = 64
MESSAGE_SIZE_STEP = 12
DATA_ENDPOINT = 0x81
class MessageDeviceBenchmarker(object):
def read(self):
data = self._read()
sel... |
#!/usr/bin/env python
#
# runtest.py - wrapper script for running SCons tests
#
# This script mainly exists to set PYTHONPATH to the right list of
# directories to test the SCons modules.
#
# By default, it directly uses the modules in the local tree:
# ./src/ (source files we ship) and ./etc/ (other modules we don't).... |
import mido
from Queue import Queue
from threading import Thread
import logging
from datetime import datetime
import os
import music
path = os.path.realpath(__file__)
dir_path = os.path.dirname(os.path.realpath(__file__))
# noinspection PyUnresolvedReferences
input_names = mido.get_output_names()
REFACE = 'reface DX... |
# DESCRIPTION: A script that contains the small, miscellaneous functions and
# classes that are used everywhere. Also contains the vector class.
# 50726f6772616d6d696e6720697320627265616b696e67206f66206f6e652062696720696d706f
# 737369626c65207461736b20696e746f207365766572616c207665727920736d616c6c20706f73
# 73696... |
from flask.ext.testing import TestCase
import unittest
import angular_flask
from flask import Flask, json, jsonify
from angular_flask import app, db, session
from angular_flask.models import User
class UserTestCase(TestCase):
STATUS_OK = "200 OK"
def create_app(self):
app = Flask(__name__)
app... |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
from frappe.utils import flt, cint
from frappe import _
from frappe.model.document import Document
class PackingSlip(Document):
def... |
#
# spyne - Copyright (C) Spyne contributors.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This libra... |
"""
map nifti image images to surface and extract parcels
"""
import os,sys,glob,shutil
from run_shell_cmd import run_shell_cmd
import tempfile
import nibabel.gifti.giftiio
import numpy
basedir=os.environ['MYCONNECTOME_DIR']
def get_data_from_parcels(volfile,outfile,save_gii=True):
surfaces={}
surfaces['mid... |
"""Formatter producing CSV data."""
import sys
import csv
from collections import OrderedDict
import formatter
import executor
# TO BE DEFINED
# - wrong lines
# - return_code/code/section status
# - difference/similarity
class CSVFormatter(formatter.Formatter):
_RESULT_TABLE = {
executor.ER_OK: "0",
... |
#!/usr/bin/env python
import datetime
import logging
import os
import re
from urllib.parse import urljoin
from bs4 import BeautifulSoup
from utils import utils, inspector
# http://www.archives.gov/oig/
archive = 2005
# options:
# standard since/year options for a year range to fetch from.
#
# Notes for IG's web t... |
#!/usr/bin/env python
# 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, software
# d... |
#!/usr/bin/env python
# Copyright (c) 2012 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.
"""Front end tool to manage .isolate files and corresponding tests.
Run ./isolate.py --help for more detailed information.
See mo... |
""" Flow class
"""
import pdb
from blackwidow.network.packet import AckPacket, DataPacket
from event import Event
class Flow(object):
"""Simple class for flows.
Flows will trigger host behavior.
"""
def __init__(self, flow_id, source, destination, amount, env, time):
""" Constructor for Flow c... |
from typing import Union, Optional
import numpy as np
from anndata import AnnData
from scipy.sparse import spmatrix
from .. import _utils
from .. import logging as logg
from ._utils import get_init_pos_from_paga
from .._compat import Literal
from .._utils import AnyRandom, _choose_graph
_LAYOUTS = ('fr', 'drl', 'kk... |
"""
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Real time animation of Wythoff construction with pyglet and glsl
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Code adapted from Matt Zucker's excellent shadertoy program at
"https://www.shadertoy.com/view/Md3yRB"
Matt's prog... |
import json
import logging
from collections import namedtuple
from distutils.version import LooseVersion
from django.core.exceptions import ObjectDoesNotExist
from django.core.exceptions import PermissionDenied
from django.core.exceptions import SuspiciousOperation
from django.core.files.storage import default_storage... |
import traceback
import datetime
from datetime import timedelta
import pytz
import astral
import random
import uuid
import re
import asyncio
import logging
from collections import OrderedDict
from copy import deepcopy
import appdaemon.utils as utils
from appdaemon.appdaemon import AppDaemon
class Scheduler:
def... |
import collections
import copy
import matplotlib.pyplot as plt
import numpy as np
from astromodels.parameter import Parameter
from astromodels.functions.functions import Uniform_prior
from astromodels.utils.valid_variable import is_valid_variable_name
from matplotlib.ticker import MaxNLocator
from mpl_toolkits.axes_gr... |
#!/usr/bin/env python
import base64
import logging
import os
import httplib2
import configparser
import time
import urllib
from datetime import date, timedelta
from functools import wraps
from apiclient import errors
from apiclient.discovery import build
from oauth2client.client import SignedJwtAssertionCredentials
... |
import time
import numpy as nm
import scipy.linalg as sla
from sfepy.base.base import output, get_default, Struct
from sfepy.solvers.solvers import make_get_conf, Solver, EigenvalueSolver
def eig(mtx_a, mtx_b=None, num=None, eigenvectors=True,
return_time=None, method='eig.scipy', **ckwargs):
"""
Uti... |
"""Base objects to be exported for use in Controllers"""
from paste.registry import StackedObjectProxy
from pylons.config import config
from pylons.legacy import h, jsonify, Controller, Response
__all__ = ['c', 'g', 'cache', 'request', 'response', 'session', 'jsonify',
'Controller', 'Response']
def __figu... |
import sys
import copy
from bento.parser.nodes \
import \
Node
# XXX: fix the str vs bool issue with flag variables
_LIT_BOOL = {"true": True, "false": False, True: True, False: False}
class Dispatcher(object):
def __init__(self, user_values=None):
self._d = {
"path_options": ... |
import re
import json
import subprocess
from bs4 import BeautifulSoup
from lib.utils.utils import appendQueries,iterate,connect,package
def absolute(myrange,domain,url,append):
if not append:
return None
if re.search("^//",append) != None:
return None
# If don't have http or https prefix... |
# Copyright 2015-2016 Yelp 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 agreed to in writin... |
#!/usr/bin/env python
# Copyright 2017 The Kubernetes 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 appli... |
from decimal import Decimal
import numpy as np
from BaseModel import BaseModel
class Statistic(BaseModel):
def __init__(self, param = {}):
BaseModel.__init__(self, "statistic", param)
def calc_variance(self, dataset):
'''Calculate E(x) and Var(x).
If dataset has no data, then return ... |
import threading
import datetime
from queue import Queue
from random import randint
import re
import sys
import traceback
import inspect
from datetime import timedelta
import logging
from appdaemon import utils as utils
from appdaemon.appdaemon import AppDaemon
class Threading:
def __init__(self, ad: AppDaemon, ... |
import datetime
import zmq
import json
from . import monitor
from panoptes.utils import logger, config, messaging, threads, serial
@logger.has_logger
@config.has_config
class CameraEnclosure(monitor.EnvironmentalMonitor):
"""
Listens to the sensors inside the camera enclosure
Args:
messaging (p... |
# Copyright (c) 2012 Jiri "NoxArt" Petruzelka
#
# 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, p... |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# protocol.py - Bitcoin protocol access for Bitnodes.
#
# Copyright (c) Addy Yeow Chin Heng <ayeowch@gmail.com>
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to de... |
from bountyfunding_api import app
from flask import Flask, url_for, render_template, make_response, redirect, abort, jsonify, request, g
from models import db, Issue, User, Sponsorship, Email, Payment, Change
from const import IssueStatus, SponsorshipStatus, PaymentStatus, PaymentGateway
from pprint import pprint
impor... |
import collections
import copy
from contextlib import contextmanager
import matplotlib.pyplot as plt
import numpy as np
from astromodels.parameter import Parameter
from astromodels.functions.functions import Uniform_prior
from astromodels.utils.valid_variable import is_valid_variable_name
from threeML.io.file_utils im... |
import click
@click.group()
@click.version_option()
def zephyr():
'''A command-line interface for Zephyr'''
@click.command()
@click.argument('projnm')
@click.confirmation_option(prompt='Are you sure you want to clean project outputs?')
def clean(projnm):
'''Clean up project results / outputs'''
... |
#!/usr/bin/env python
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
import os.path as op
auto_name = op.split(op.dirname(__file__))[-1]
config = Configuration(auto_name, parent_package, top_path)
config.add_data_files('matlab_eig.m')
... |
import logging
import os
from dart.client.python.dart_client import Dart
from dart.config.config import configuration
from dart.engine.redshift.metadata import RedshiftActionTypes
from dart.model.engine import Engine, EngineData
_logger = logging.getLogger(__name__)
def add_redshift_engine(config):
engine_config... |
import json
import re
from collections import Iterable
from copy import deepcopy
from datetime import datetime as dt
from datetime import timedelta as td
from functools import lru_cache
from http.client import HTTPResponse
from urllib import error, parse, request
from ruz.utils import (EMAIL_DOMAINS, EMAIL_PATTERN, RE... |
# importing modules
import csv
import pytest
import player
# tests
def test_given_player_apps_matches_total_returns_true():
with open('player_history.csv') as csvfile:
reader = csv.DictReader(csvfile)
for row in reader:
po = player.player(
row['Player Name'],
... |
#!/usr/bin/env python
# Copyright (c) 2011 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.
"""
lastchange.py -- Chromium revision fetching utility.
"""
import re
import optparse
import os
import subprocess
import sys
cla... |
class Event(object):
"""
Base event for all SQLObject events.
In general the sender for these methods is the class, not the
instance.
"""
class ClassCreateEvent(Event):
"""
Event raised before class creation. The sender is the superclass
(in case of multiple superclasses, the first su... |
"""
Linear mixed effects models.
The MixedLM class fits linear mixed effects models to data. This is a
group-based implementation that does not efficiently handle crossed
random effects.
The data are partitioned into disjoint groups. The probability model
for group i is:
Y = X*beta + Z*gamma + epsilon
where
* n_... |
from xml.etree import ElementTree
from wheelcms_axle.impexp import Importer
from wheelcms_axle.content import TypeRegistry, type_registry
from wheelcms_axle.tests.models import Type1, Type1Type
from wheelcms_categories.models import Category, CategoryType
import pytest
@pytest.fixture()
def cat1():
return Categ... |
"""Paster Commands, for use with paster in your project
The command(s) listed here are for use with Paste to enable easy creation of
various core Pylons templates.
Currently available commands are::
controller, restcontroller, shell
"""
import os
import sys
import paste.fixture
import paste.registry
import past... |
import requests
from django import forms
try: # Django < 1.5 doesn't have checks, so we'll just ignore that.
from django.core import checks
except ImportError:
pass
from django.core.cache import cache
from django.db.models.fields import Field
from django.core.files.base import File
from django.db.models.fie... |
#!/usr/bin/python
"""
Copyright (c) 2014 tilt (https://github.com/AeonDave/tilt)
See the file 'LICENSE' for copying permission
"""
import socket, re, source, util
from lib.logger import logger
def is_valid_ip(ip):
is_valid = re.match("^(([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])\.){3}([0-9]|[1-9][0-9]|1[0-... |
from hoomd.update.box_resize import BoxResize
# TODO remove when no longer necessary
class _updater:
pass
__all__ = ['BoxResize']
|
import unittest
import io
import VAPr.annovar_output_parsing as ns_test
# Most test info taken from test_files/test_out_csv_path/real_files/X7/X7.raw.11_annotated.hg19_multianno.txt'
class TestAnnovarTxtParser(unittest.TestCase):
ANNOVAR_ANNOTATION_CONTENT = """Chr Start End Ref Alt Func.knownGene Gene.knownGene... |
import re
import sys
import codecs
expressionData = sys.argv[1]
clinicalAnnotations = sys.argv[2]
dataOutFile = sys.argv[3]
metedataOutFile = sys.argv[4]
drugData = sys.argv[5]
profilingData = sys.argv[6]
#write outFile, clinical on left expression on Right
DrugDataDict = {}
with open(drugData, 'r') as f :
firs... |
print("Hello, welcome to the personalized passwordlist creator : ")
print("please enter the necessary information:")
print("!!! leave unknown information fields empty")
print(" ")
print("""1- info about subject
2- common number passwords
3- general password list
""")
wordlist = []
def shuffle():
lst =... |
# -*- coding: utf-8 -*-
"""Tests for core functions."""
import datetime
import json
import logging
import os
import re
import sys
import time
from io import BytesIO
from itertools import product
from unittest.mock import MagicMock, Mock, patch
from urllib.parse import parse_qs, quote, urlparse
import pytest
import ya... |
"""
An extension of scipy.stats.stats to support masked arrays
:author: Pierre GF Gerard-Marchant
:contact: pierregm_at_uga_edu
"""
# TODO : f_value_wilks_lambda looks botched... what are dfnum & dfden for ?
# TODO : ttest_reel looks botched: what are x1,x2,v1,v2 for ?
# TODO : reimplement ksonesamp
from __future__ ... |
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