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# coding: utf-8
from __future__ import unicode_literals
from ariadne import actions, stories, config, runners
from ariadne.context import browsers, flask
from . import flask_app
# Configuration
class ExampleConfig(config.BaseConfig):
def context_processors(self):
return [
flask.FlaskApp(flas... | tricoder42/python-ariadne | tests/functional/tutorial/scenario_user_login.py | Python | mit | 806 | [
"VisIt"
] | 70d5c9f398aa8d43b72fb687340bc1f144330182b65d3ca790a1b466d8abe517 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import subp... | nuclear-wizard/moose | python/TestHarness/tests/test_Expect.py | Python | lgpl-2.1 | 1,947 | [
"MOOSE"
] | 5184c9667a0f143631e86f59b695a8b048cfaf1c45e36c8cd30b222ab33c42a5 |
import numpy as np
# Set-up a simple matrix in parallel, diagonalize using ScaLAPACK
# D&C driver then compare *eigenvalues* with serial LAPACK diagonlize
from time import time
from gpaw.blacs import BlacsGrid, parallelprint
from gpaw.mpi import world, rank, size
from gpaw.utilities import compiled_with_sl
from gpaw.... | qsnake/gpaw | gpaw/test/parallel/scalapack_diag_simple.py | Python | gpl-3.0 | 2,221 | [
"GPAW"
] | 02037adc072ac7a4fc1b4d9e6242b5d526d9afeb4f41917adc9c5b605186caec |
########################################################################
# File : ProxyProviderFactory.py
# Author : A.T.
########################################################################
""" The Proxy Provider Factory instantiates ProxyProvider objects
according to their configuration
"""
from DIRAC im... | chaen/DIRAC | Resources/ProxyProvider/ProxyProviderFactory.py | Python | gpl-3.0 | 2,090 | [
"DIRAC"
] | 7ed582a006e40b7a7279ce4e996dca6e67bcfc8ddbeccbd2d64ea1fcf39bf617 |
#!/usr/bin/env python
import sys
import time
from operator import itemgetter
import os
import subprocess
def main():
python_dir = "/mnt/wigclust5/data/safe/kendall/Python-2.7.1"
bowtie_dir = "/mnt/wigclust5/data/safe/kendall/bowtie-0.12.7"
tophat2_dir = "/mnt/wigclust5/data/safe/kendall/tophat-2.0.4.L... | maggiecrow/scCoexp | process.rna01.py | Python | mit | 6,811 | [
"Bowtie"
] | c35e658df8e2bdbeca5903666aff164536ac58f83e3b6ba70cb28280ad1cba67 |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | waterponey/scikit-learn | sklearn/cluster/k_means_.py | Python | bsd-3-clause | 59,590 | [
"Gaussian"
] | a66c04c61c7daae5ad0a123fa6300f3bac30b31dab2fa3ca32ddaa084d0cfcd6 |
import os
import re
import shutil
import sys
if sys.version_info[:2] < (2, 7):
sys.exit('virtualenv requires Python 2.7 or higher.')
try:
from setuptools import setup
from setuptools.command.test import test as TestCommand
class PyTest(TestCommand):
user_options = [('pytest-args=', 'a', "Argu... | yougov/yg-buildpack-python3 | vendor/virtualenv-16.0.0/setup.py | Python | mit | 4,047 | [
"Brian"
] | be4c6d59b708d362274770a0e2c399e7882f4c4a4e39334c6dffeff9aec59ffe |
#!/usr/local/bin/python
import Tkinter as TK
import random
import itertools
class Card:
SUITS = ["Hearts", "Clubs", "Diamonds", "Spades"]
RANKS = ['A', '2', '3', '4', '5', '6', '7', '8', '9', '10', 'J', 'Q', 'K']
def __init__(self, rank, suit):
self.suit = suit
self.rank = rank
def __str__(self):
... | pedros80/blackjack | blackjack.py | Python | gpl-3.0 | 6,308 | [
"CASINO"
] | 88fc8e8bfcec781c4c9fdf8c0d720ff334b67d0c9201c9f8c4b43143deaf35f1 |
from netCDF4 import Dataset, stringtochar, chartostring
import random, numpy
# test utilities for converting arrays of fixed-length strings
# to arrays of characters (with an extra dimension), and vice-versa.
# netCDF does not have a fixed-length string data-type (only characters
# and variable length strings). The c... | Unidata/netcdf4-python | examples/test_stringarr.py | Python | mit | 1,883 | [
"NetCDF"
] | 8a2a500e0100819fc54b17178e2e937343ca4121b82c958778653914bf860658 |
#!/usr/bin/env python
# This example demonstrates the use of fields and use of
# vtkProgrammableDataObjectSource. It creates fields the hard way (as
# compared to reading a vtk field file), but shows you how to
# interface to your own raw data.
import os
import re
import vtk
from vtk.util.misc import vtkGetDataRoot
V... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/DataManipulation/Python/FinancialField.py | Python | gpl-3.0 | 8,599 | [
"VTK"
] | 0ea63716e1b0f0d79254bdea7a26807bca3f2b0e7346618438b01cd860b8b18f |
# Copyright (c) 2017 Brian Ginsburg, Julie Rutherford-Fields
# This work is available under the "3-clause ('new') BSD License”.
# Please see the file COPYING in this distribution
# for license terms.
#debug config
DEBUG = True
SQLALCHEMY_ECHO = True
| thuselem/teergrube | instance/config.py | Python | bsd-3-clause | 253 | [
"Brian"
] | b57465b79cfaba696b18f112b70d8c07843e0875b6f05baa3182c68fec30965f |
#!python3
import os
import os.path
import re
import sys
import subprocess
import enum
__version__ = "1.2"
CREDENTIALS_FILE = "/var/_xcsbuildd/githubcredentials"
def warning(*objs):
with open("/tmp/cavejohnson.log", "a") as file:
file.write(" ".join(objs))
file.write("\n")
def reSignIPAArgs(arg... | kiancheong/CaveJohnson | cavejohnson/__init__.py | Python | mit | 26,762 | [
"VisIt"
] | 518861521d9e3a0598d0d010792dc7f2971f3c5cf942283f66c3d05af0491ab4 |
# Copyright 2014 Diamond Light Source Ltd.
#
# 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 t... | FedeMPouzols/Savu | savu/plugins/filters/base_fitter.py | Python | gpl-3.0 | 7,877 | [
"Gaussian"
] | 2820b98daf134f44bf60fffd51caab7f19235f9556a6cad95b15955f48b2ab69 |
# -*- coding: UTF8 -*-
# Este arquivo é parte do programa Enplicaw
# Copyright 2013-2015 Carlo Oliveira <carlo@nce.ufrj.br>,
# `Labase <http://labase.selfip.org/>`__; `GPL <http://is.gd/3Udt>`__.
#
# Enplicaw é um software livre; você pode redistribuí-lo e/ou
# modificá-lo dentro dos termos da Licença Pública Geral GNU... | labase/eica | src/analisys/enplicow.py | Python | gpl-2.0 | 21,612 | [
"NEURON"
] | 59007621ebc57e08202296ca2c46fa20b62c88e1c8ea502004902eb9eba71139 |
#!/usr/bin/python
"""
# Created on Aug 12, 2016
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com) GitHub ID: grastogi23
#
# module_check: not supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
"... | alxgu/ansible | lib/ansible/modules/network/avi/avi_api_session.py | Python | gpl-3.0 | 8,328 | [
"VisIt"
] | 61f77e5bdc97db5772237c4f5a53bcd59afcbd11e8ee2dfd69e8da4989716e7e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to perform fitting of molecule with arbitrary
atom orders.
This module is supposed to perform exact comparisons without the atom order
correspondence prerequisite, while molecu... | davidwaroquiers/pymatgen | pymatgen/analysis/molecule_matcher.py | Python | mit | 47,660 | [
"pymatgen"
] | c0280d31ade8a1fbf6439795fc2e6ebafaaffe6f9d646f4345e8c05f9e66aed3 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/analysis/XDensity.py | Python | gpl-3.0 | 1,583 | [
"ESPResSo"
] | 3f56a015a54025e90669b255e7137214022ba189338fda526c7eb8c29e99d069 |
import vtk
def main():
colors = vtk.vtkNamedColors()
sphere = vtk.vtkSphere()
sphere.SetCenter(0, 0, 0)
sphere.SetRadius(0.5)
# The sample function generates a distance function from the implicit
# function. This is then contoured to get a polygonal surface.
sample = vtk.vtkSampleFunctio... | lorensen/VTKExamples | src/Python/ImplicitFunctions/Sphere.py | Python | apache-2.0 | 1,494 | [
"VTK"
] | 12e4c60b34b59e37753fd2a08a044a0f68699014f62c77b65841272010574c11 |
"""
Authorize Sauce
===============
The secret sauce for accessing the Authorize.net API. The Authorize APIs for
transactions, recurring payments, and saved payments are all different and
awkward to use directly. Instead, you can use Authorize Sauce, which unifies
all three Authorize.net APIs into one coherent Pythoni... | davejmac/authorizesauce-wsdl | setup.py | Python | mit | 3,361 | [
"VisIt"
] | 422ec090fa8268b0b20af73111f87f5609f36696f4f116f6cfecff0a36db7533 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Create a MANIFEST file for distributing soruces with distutils."""
from __future__ import print_function
import glob
... | gaursagar/cclib | manifest.py | Python | bsd-3-clause | 970 | [
"cclib"
] | fea40863d8f012693347ba1f18e2ecfaa3c5eff04a41ccf2d5c8cba98ead2f86 |
from __future__ import unicode_literals
from django.db import models
from django.conf import settings
import pprint
from Bio.Phylo.TreeConstruction import _DistanceMatrix, DistanceTreeConstructor
from Bio import Phylo
import StringIO
import json
STATUS = {'PENDING':1,'RUNNING':2,'ERROR':3,'COMPLETE':4}
STATUS_CHOICES... | hamzakhanvit/update_iv | webui/models.py | Python | gpl-3.0 | 23,347 | [
"BLAST"
] | 7da0543476bf367a6be039377c65bbe5e26a4e0a392b3da4e21a181e09997be6 |
#!/usr/bin/env python
# Copyright 2013 The Swarming 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.
"""Client tool to trigger tasks or retrieve results from a Swarming server."""
__version__ = '0.8.2'
import collection... | Teamxrtc/webrtc-streaming-node | third_party/webrtc/src/chromium/src/tools/swarming_client/swarming.py | Python | mit | 46,560 | [
"VisIt"
] | 9406ad4fdf86217431bda6630e545c96bdd1f127c6ac6d18a11712b80d67c149 |
"""
Executes a set of implementations as a program.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import _, logger
import os, sys
from string import Template
from zeroinstall import support
from zeroin... | slovenwd/0install | zeroinstall/injector/run.py | Python | lgpl-2.1 | 12,325 | [
"VisIt"
] | 63d2d7c52ca2dcfa39704f0d1e51de7c8ae2bfad7b587c5a84234216048a20b1 |
import pathlib
import numpy as np
import pytest
from util import full
from loprop.core import penalty_function, AU2ANG
from loprop.dalton import MolFragDalton
from . import hcl_absorption_data as ref
thisdir = pathlib.Path(__file__).parent
case = "hcl_absorption"
tmpdir = thisdir / case / "tmp"
@pytest.fixture
d... | vahtras/loprop | tests/test_hcl_absorption.py | Python | gpl-3.0 | 2,805 | [
"Dalton"
] | de79fea8b361652b5f5249425b09e2c7efd030e4a936db67b7c0165061e75c04 |
# -*- coding: utf-8 -*-
import sys
PY3 = False
if sys.version_info[0] >= 3: PY3 = True; unicode = str; unichr = chr; long = int
if PY3:
import urllib.parse as urllib # Es muy lento en PY2. En PY3 es nativo
else:
import urllib ... | alfa-addon/addon | plugin.video.alfa/channels/puyasubs.py | Python | gpl-3.0 | 20,434 | [
"MOE"
] | 2579a26632f687ad0c24565cfb99bc1ab9749b003650612daa1238eb6e0ce2d3 |
# -*- coding: utf-8 -*-
# ufloat - fast python floats with physical units
# Copyright (C) 2015 Christoph Gohle <christoph.gohle@mpq.mpg.de>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software ... | chrisgee/ufloat | ufloat/constants.py | Python | gpl-3.0 | 18,303 | [
"Avogadro"
] | a1977a2486ae30383093eb5d2942ce704b0c669a75bf62c802941b7c41028df3 |
# Copyright (c) 2003-2014 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, o... | tianzhihen/python-mode | pymode/libs/pylama/lint/pylama_pylint/pylint/checkers/variables.py | Python | lgpl-3.0 | 33,153 | [
"VisIt"
] | fa65bcba5eb6cc8e1848ff681e17828707e55ff251f988060262f788a24fcc30 |
from saddam import *
from behave import *
from splinter import Browser
browser = Browser('flask', app=app)
@then(u'show text "{text}"')
def step_impl(context, text):
assert text in browser.html, browser.html
@given(u'load page: "{page}"')
def step_impl(context, page):
browser.visit(page) | dimh/saddam | features/steps/saddam_step.py | Python | gpl-3.0 | 302 | [
"VisIt"
] | c37686897af31f54f24bcb8a8447f29432a1e4dc73f6830c46e713bbb6127afc |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# This module is also sponsored by E.T.A.I. (www.etai.fr)
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version... | kvar/ansible | lib/ansible/modules/cloud/vmware/vmware_guest.py | Python | gpl-3.0 | 146,525 | [
"VisIt"
] | ac0ad68033463ab2d649cbd271d8c12d4f6722ef471a86317dc8bf064f6b8eba |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# module builder script
#
import os, sys, shutil, tempfile, subprocess, platform
template_dir = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
support_dir = os.path.join(template_dir, 'support')
sdk_dir = os.path.dirname(template_dir)
common_dir = ... | pinnamur/titanium_mobile | support/module/builder.py | Python | apache-2.0 | 8,026 | [
"VisIt"
] | 63305680d1ae9d0c6730dbaf64f9698c27942d9e6abdf77e6ba90b7dff29c675 |
#!/usr/bin/env python
# encoding: utf-8
'''
Created by Brian Cherinka on 2016-04-28 14:07:58
Licensed under a 3-clause BSD license.
Revision History:
Initial Version: 2016-04-28 14:07:58 by Brian Cherinka
Last Modified On: 2016-04-28 14:07:58 by Brian
'''
from __future__ import print_function
from __future__... | sdss/marvin | python/marvin/web/controllers/plate.py | Python | bsd-3-clause | 3,911 | [
"Brian"
] | b3e334c9ee30e4818dad9a05fd56fdbbd9e1ff831de333efdfd4ace6d3383fad |
"""
Utilities for ESPEI
Classes and functions defined here should have some reuse potential.
"""
from typing import Any, Dict, Type
import importlib
import itertools
import re
from collections import namedtuple
import numpy as np
import symengine
from distributed import Client
from pycalphad import Model, variables ... | PhasesResearchLab/ESPEI | espei/utils.py | Python | mit | 15,054 | [
"pycalphad"
] | e2527e449b45685d40789ee131e51ea99b1f5a1cabf6a51fa237aeb31dddec16 |
import numpy as np
from matplotlib import pyplot
import rft1d
eps = np.finfo(float).eps
def here_anova1(Y, X, X0, Xi, X0i, df):
Y = np.matrix(Y)
### estimate parameters:
b = Xi*Y
eij = Y - X*b
R = eij.T*eij
### reduced design:
b0 = X0i*Y
eij0 = Y - X0*b0
R... | 0todd0000/rft1d | rft1d/examples/val_upx_2_F_set.py | Python | gpl-3.0 | 2,513 | [
"Gaussian"
] | 47199ce7f12b7ebbf6214704ce92deaffaf43912b2ff83a8851bc202ce179086 |
#
# Copyright (C) 2022 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later vers... | espressomd/espresso | testsuite/python/mpiio_exceptions.py | Python | gpl-3.0 | 5,235 | [
"ESPResSo"
] | 3fc1010f5c35f556b4b47a4cebd9aa4edf293da7f3a2456412b11ace58f5d21c |
# 2015.11.16, LI Yunsheng
from math import floor, ceil, sqrt
from queue import PriorityQueue
import cv2
import numpy as np
from scipy.interpolate import interp1d
from scipy.optimize import fsolve
class Vehicle():
def __init__(self, wheelbase=2.94, front_offset=0.988, rear_offset=1.28, width=2.029, traje... | bourbakilee/PyMPL | Environment.py | Python | gpl-3.0 | 24,905 | [
"Gaussian"
] | f31f204a84237d137c958b880e15b57a164917c73753b668a549dec0290ee9f5 |
# vim: expandtab:ts=4:sw=4
"""
This module contains an image viewer and drawing routines based on OpenCV.
"""
import numpy as np
import cv2
import time
import pymotutils
def is_in_bounds(mat, roi):
"""Check if ROI is fully contained in the image.
Parameters
----------
mat : ndarray
An ndarray... | nwojke/pymotutils | pymotutils/visualization/opencv.py | Python | gpl-3.0 | 19,204 | [
"Gaussian"
] | 7872641e1ee5729942da7d5a3d289623ab9700e19c623d044aedb81f5d2451d8 |
# Copyright 2001 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Maximum Entropy code.
Uses Improved Iterative Scaling.
"""
# TODO Define terminology
from... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/MaxEntropy.py | Python | gpl-2.0 | 10,383 | [
"Biopython"
] | ef731c7660578c2b7944d7d8af49d851db6c4afdb21f41f21ced5deb31afa1fc |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
3D visualization of activation maps using Mayavi
"""
# Author: Gael Varoquaux <gael dot varoquaux at normalesup dot org>
# License: BSD
# Standard library imports
import os
# Standard scientific lib... | bthirion/nipy | nipy/labs/viz_tools/anat_cache.py | Python | bsd-3-clause | 3,380 | [
"Mayavi"
] | e0c5a290e4715befcd4e6730a89db78561a0ed44faf3dc2de3785a540f38afad |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | tests/licensedcode/test_models.py | Python | apache-2.0 | 9,134 | [
"VisIt"
] | 5401320f7c13ab36bc8ecb6b2003d370ae2d98a930440ae372f93365a1bd62f5 |
#!/usr/local/bin/python
# ========================================================================
# Classes which define connections to devices
#
# Brian Landers <blanders@sapient.com>
# 07.07.2001
#
# $Id: connections.py,v 1.11 2002/06/19 22:59:40 bluecoat93 Exp $
# ==============================================... | hdecreis/netdevicelib | src/netdevicelib/connections.py | Python | lgpl-2.1 | 33,036 | [
"Brian"
] | b54e31da5e2491b3a662de427dfedabd4028c74f91982464830a1fa480391353 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | kyleabeauchamp/mdtraj | mdtraj/tests/test_reporter.py | Python | lgpl-2.1 | 8,000 | [
"MDTraj",
"OpenMM"
] | 8cae8d01e57c8818aa396ffd7f83644acccb774a7e4f53f1151e544f6794bbe3 |
# -*- coding: utf-8 -*-
import matplotlib.pyplot as plt
from probfit.pdf import gaussian
from probfit.plotting import draw_pdf
bound = (-10, 10)
arg = dict(mean=2, sigma=1)
draw_pdf(gaussian, arg=arg, bound=bound, label=str(arg), density=True)
arg = dict(mean=-3, sigma=2)
draw_pdf(gaussian, arg=arg, bound=bound, la... | iminuit/probfit | doc/pyplots/pdf/gaussian.py | Python | mit | 404 | [
"Gaussian"
] | 8d5c7737faef4b88141974ced3b1adb769fd0d2728e21560cf2dbf42cc74e8f3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''Views tests for the OSF.'''
from __future__ import absolute_import
import unittest
import json
import datetime as dt
import mock
import httplib as http
from nose.tools import * # noqa PEP8 asserts
from tests.test_features import requires_search
from modularodm import... | revanthkolli/osf.io | tests/test_views.py | Python | apache-2.0 | 158,857 | [
"Brian"
] | 5662d89b98a3fb4036621383566988629ea7e12eacde51d66bae64d6d017ada3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Pairdist creates a neighbor-joining tree from a set of sequences,
using maximum likelihood distances based on pairwise sequence
alignments.
"""
__author__ = "Frank Kauff <frank.kauff@gmx.de>"
# This program is free software: you can redistribute it and/or modify
# it... | frederic-mahe/pairdist | pairdist.py | Python | gpl-3.0 | 12,476 | [
"Biopython"
] | fc78d759669fdde388d7c2570a053da4e54941b8351fc1d6ed052e1df036dfb9 |
""" IdProvider based on OAuth2 protocol
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import re
import six
import time
import pprint
import requests
from authlib.jose import JsonWebKey, jwt
from authlib.common.urls import url_decode
from authlib.common... | ic-hep/DIRAC | src/DIRAC/Resources/IdProvider/OAuth2IdProvider.py | Python | gpl-3.0 | 21,419 | [
"DIRAC"
] | d612f149850a4103ddcc074354e6d5e88491bfd68319e77f052508f08cb71f3d |
from sys import exit
from random import randint
class Scene(object):
def enter(self):
print "This scene is not yet configured. Subclass it and implement enter()."
exit(1)
class Engine(object):
def __init__(self, scene_map):
print "Engine __init__ has scene_map", scene_map
s... | krmaxwell/lpthw | ex43/ex43.py | Python | gpl-3.0 | 3,762 | [
"BLAST"
] | f766f5756d5248880c0d4c8529f31826a21e189c6732eb03ffe1fc65add51a56 |
#!/usr/bin/env python
desc="""Align pairs/mates onto contigs and run SSPACE scaffolder.
"""
epilog="""Author:
l.p.pryszcz+git@gmail.com
19/06/2012 Dublin/Warsaw
"""
import os, subprocess, sys, tempfile
from datetime import datetime
def _unload_sam(sam):
return sam[0], int(sam[1]), sam[2], int(sam[3]), int(sam[4])... | lpryszcz/redundans | bin/fastq2sspace.py | Python | gpl-2.0 | 13,995 | [
"BWA"
] | d2ff00769c25502c9900af2480e644dc878c9a4d012ab2be51be10889511fd40 |
"""MSMBuilder: Statistical models for Biomolecular Dynamics
"""
from __future__ import print_function, absolute_import
DOCLINES = __doc__.split("\n")
import os
import sys
import glob
import traceback
import numpy as np
from os.path import join as pjoin
from setuptools import setup, Extension, find_packages
try:
... | dotsdl/msmbuilder | setup.py | Python | lgpl-2.1 | 6,961 | [
"Gaussian",
"MDTraj"
] | 1ae1e9c2f2bc49390d170d39fee94a06b19cd546c3a901b35cfee45a349b273e |
#
# pyFlow - a lightweight parallel task engine
#
# Copyright (c) 2012-2015 Illumina, 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:
#
# 1. Redistributions of source code must retain the a... | Illumina/HapMix | pyflow/demo/bclToBwaBam/bwaworkflow.py | Python | gpl-3.0 | 23,953 | [
"BWA"
] | 06e842f1befaeceae7515caa3b52f270f1ae817c9d059f77b9a6dea21d4e9c73 |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2014 CRS4.
#
# This file is part of blast-python.
#
# blast-python is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option)
# ... | crs4/blast-python | BlastPython/IO_interface.py | Python | gpl-3.0 | 1,287 | [
"BLAST"
] | b54d911febbd7ad17430f2f024de3e993872162981ae977060632a8857ebd492 |
from typing import Callable, Dict, Union
import jax
import blackjax.adaptation as adaptation
import blackjax.mcmc as mcmc
import blackjax.smc as smc
from blackjax.base import AdaptationAlgorithm, SamplingAlgorithm
from blackjax.types import Array, PRNGKey, PyTree
__all__ = [
"adaptive_tempered_smc",
"hmc",
... | blackjax-devs/blackjax | blackjax/kernels.py | Python | apache-2.0 | 13,951 | [
"Gaussian"
] | a06c9ba4f4ae52de4817ecfae14ba6eaae4fa6d0b14489f3d90f24ac35cac55a |
#!/usr/bin/python
"""
Copyright 2016 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester 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 th... | druss316/G-Harvestor | html/ghLists.py | Python | gpl-3.0 | 4,822 | [
"Galaxy"
] | 9336add061c184be6a93970cd9a89f8081ff918f5b2ceefd8a450dc6c6dec085 |
#!/usr/bin/env python
### prend en entree une e-value et un fichier xml
### renvoit un fichier xml ne contenant que les hits positifs,
### dont la evalue est superieure au seuil et ayant une
### longueur d'alignement superieure a 33 (defaut dans blast2go)
import string
import os
import sys
blastfile = sys.argv[2] # ... | alunem/bioman | blast/bmn-ParseBlastXml_changeId.py | Python | gpl-2.0 | 3,557 | [
"BLAST"
] | 3623b9ead958b769136cf0c9c5e48abb10be55b7c38a4c4f2c20495d2c65dfdd |
"""
simple, elegant templating
(part of web.py)
Template design:
Template string is split into tokens and the tokens are combined into nodes.
Parse tree is a nodelist. TextNode and ExpressionNode are simple nodes and
for-loop, if-loop etc are block nodes, which contain multiple child nodes.
Each node can emit som... | jacintos/my-wahi | web/template.py | Python | mit | 44,962 | [
"VisIt"
] | 6b7776681bec76298220c1f81db70d3f3f336879434ac66c2cadb281b32c0a72 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2007-2009 Stephane Charette
# Copyright (C) 2009 Gary Burton
# Contribution 2009 by Bob Ham <rah@bash.sh>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012-2013 Paul Franklin
#
# This ... | pmghalvorsen/gramps_branch | gramps/gui/plug/report/_graphvizreportdialog.py | Python | gpl-2.0 | 10,911 | [
"Brian"
] | ca86b337b0c84fabd17cc23236a317c19f75d2cfb1eae31828c6107645334587 |
from __future__ import division, unicode_literals
import inspect
import time
import serial
from .util import to_two_bytes, two_byte_iter_to_str, pin_list_to_board_dict
# Message command bytes (0x80(128) to 0xFF(255)) - straight from Firmata.h
DIGITAL_MESSAGE = 0x90 # send data for a digital pin
ANALOG_MESSAGE ... | JoseU/pyFirmata | pyfirmata/pyfirmata.py | Python | mit | 19,963 | [
"CRYSTAL"
] | e050afe83b1ad8a1e2f7ba226a4c299cc967cdbbe75cefb4710bf756f557f32c |
"""
orthopoly.py - A suite of functions for generating orthogonal polynomials
and quadrature rules.
Copyright (c) 2014 Greg von Winckel
All rights reserved.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
... | FEniCS/fiat | FIAT/orthopoly.py | Python | lgpl-3.0 | 10,895 | [
"Gaussian"
] | 52ef334baaec6cd2378817d275ec6841e8a9049961a57dba4ecf85155a3f963c |
from chemlab.core import System, Atom, Molecule
from chemlab.io import datafile, add_default_handler
from chemlab.io.handlers import GromacsIO
from chemlab.io.handlers import EdrIO
from nose.tools import assert_raises
from nose.plugins.skip import SkipTest
import numpy as np
def test_datafile():
add_default_hand... | swails/chemlab | tests/test_io.py | Python | gpl-3.0 | 3,909 | [
"GAMESS",
"Gromacs",
"cclib"
] | 4ecd1221c073e42f2ec9a92f62775afe83a4645d6b48736f86102c29f9d17125 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import copy
import glob
import json
import os
from unittest import TestCase
import unittest
from pymatgen import Molecule
from pymatgen.io.qchem import QcTask, QcInput,... | migueldiascosta/pymatgen | pymatgen/io/tests/test_qchem.py | Python | mit | 74,331 | [
"pymatgen"
] | 6e5d102bc3e4cd6264ba2c1836c743c9d63d95548f3fd5ca5a56ff293655d5a9 |
""" Aliases gather aliasing informations. """
from pythran.analyses.global_declarations import GlobalDeclarations
from pythran.intrinsic import Intrinsic, Class, UnboundValue
from pythran.passmanager import ModuleAnalysis
from pythran.tables import functions, methods, MODULES
from pythran.unparse import Unparser
from ... | serge-sans-paille/pythran | pythran/analyses/aliases.py | Python | bsd-3-clause | 27,510 | [
"VisIt"
] | 1b904756ec37248bbf1a6a008b9ab38e7e666e0452de9d86a2f2ac611e9a601f |
"""
Acceptance tests for studio related to the outline page.
"""
from datetime import datetime, timedelta
import itertools
from pytz import UTC
from bok_choy.promise import EmptyPromise
from ...pages.studio.overview import CourseOutlinePage, ContainerPage, ExpandCollapseLinkState
from ...pages.studio.utils import add_... | olexiim/edx-platform | common/test/acceptance/tests/studio/test_studio_outline.py | Python | agpl-3.0 | 70,926 | [
"VisIt"
] | 8d113b49f3c25597d7d3a3ff18d7ca75cefe94eb096379114b103f83634a9a95 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008-2011 Kees Bakker
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2013-2017 Alois Poettker
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Publi... | sam-m888/gramps | gramps/plugins/lib/libprogen.py | Python | gpl-2.0 | 84,225 | [
"Brian"
] | d878097f4ac108c41506b5fa56dc3e1d60be265ae0ca1740951596ddf5c32b27 |
#!/usr/bin/env python
'''
This example shows how to access the data stored in checkpoint file,
Also how to quickly update an object using the data from the checkpoint file.
'''
import numpy
import h5py
from pyscf import gto, scf, ci
from pyscf.lib import chkfile
mol = gto.M(atom='N 0 0 0; N 0 0 1.2', basis='ccpvdz')... | gkc1000/pyscf | examples/misc/02-chkfile.py | Python | apache-2.0 | 1,392 | [
"PySCF"
] | 81f7fb270a3d080d573e3fe097a84b69464dd742cbecfeff412d50eb58e3c22f |
"""
Courseware views functions
"""
import logging
import urllib
import json
import cgi
from datetime import datetime
from collections import defaultdict
from django.utils import translation
from django.utils.translation import ugettext as _
from django.utils.translation import ungettext
from django.conf import setti... | DNFcode/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 46,173 | [
"VisIt"
] | c447c95fd571817918c7692d405e77f04379a921f28e96d36ba9b7fdef7f2102 |
#!/usr/bin/env python
"""A class for handling 5C read data."""
import os
import sys
import numpy
import h5py
try:
import pysam
except:
pass
class FiveCData(object):
"""
This class handles interaction count data for 5C experiments.
The FiveCData class contains all of the interaction informati... | bxlab/HiFive_Paper | Scripts/hifive-1.1.3/hifive/fivec_data.py | Python | bsd-3-clause | 20,850 | [
"pysam"
] | 973a74f722999ddef4329f1c8449f57e24dd34bd237a7a3cb1d031b5b5756fe6 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Created on Apr 25, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Apr 25, 20... | materialsproject/pymatgen | pymatgen/vis/tests/test_structure_vtk.py | Python | mit | 1,142 | [
"pymatgen"
] | afda9b593dc70c344af3db4207e8161ae963ea9e7804c375c51e2d12e585822f |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | swails/mdtraj | mdtraj/tests/test_xtc.py | Python | lgpl-2.1 | 9,090 | [
"MDTraj"
] | d4440c22e8aee2fb0e24cefe91922098edce35ff77aa51c702f97ac3bd64a37f |
# Copyright 2012 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of ngs_crumbs.
# ngs_crumbs is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, ... | JoseBlanca/ngs_crumbs | crumbs/vcf/prot_change.py | Python | gpl-3.0 | 10,970 | [
"Biopython"
] | 54c22f4b55cf308c45ff7c19506fd6dc312e57bb3975556c14d0358a33856933 |
import sys
try:
import numpy
except ImportError:
print("Numpy (http://numpy.scipy.org) not found.")
print("This test requires numpy!")
sys.exit(0)
import vtk
import vtk.numpy_interface.dataset_adapter as dsa
import vtk.numpy_interface.algorithms as algs
w = vtk.vtkRTAnalyticSource()
bp = vtk.vtkBrow... | keithroe/vtkoptix | Common/Core/Testing/Python/TestNumpyInterface.py | Python | bsd-3-clause | 7,853 | [
"VTK"
] | 76c5592a14f6a64761341527594992f2296797d0a60cee1e47c3f3b488f46a91 |
#!/usr/bin/env python
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2018 Raik Gruenberg & Johan Leckner
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Softwar... | graik/biskit | archive_biskit2/scripts/Biskit/am_restartMD.py | Python | gpl-3.0 | 4,056 | [
"Amber"
] | 5dea62450efbdb06c7019680f997027ae23f930a398120836e5a218fd6dc4c87 |
tests=[
("python","SDSupply.py",{}),
("python","SmartsMolFilter.py",{}),
("python","SmartsRemover.py",{}),
("python","SmilesDupeFilter.py",{}),
("python","SmilesOutput.py",{}),
("python","SmilesSupply.py",{}),
]
longTests=[
]
if __name__=='__main__':
import sys
from rdkit import TestRunner
f... | adalke/rdkit | rdkit/VLib/NodeLib/test_list.py | Python | bsd-3-clause | 399 | [
"RDKit"
] | 969486600b05e12859c1c7686cd5c01c2edc2560edd3a334bb58844096526dbe |
##########################################################################
#
# This file is part of OCEMR.
#
# OCEMR is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License,... | ph1l/ocemr | ocemr/forms.py | Python | gpl-3.0 | 30,494 | [
"VisIt"
] | 57de071476a635cb21c719895e29a6fe8cbf2e24d284a7986f522dbd55a84f5c |
#!C:\OSGEO4~1\bin\python.exe
# -*- coding: utf-8 -*-
###############################################################################
# $Id: gdal_pansharpen.py 7464f4b11b93bb2d1098d1b962907228932bf8c1 2018-05-03 19:56:49 +1000 Ben Elliston $
#
# Project: GDAL scripts
# Purpose: Perform a pansharpening operatio... | kubaszostak/gdal-dragndrop | osgeo/apps/Python27/Scripts/gdal_pansharpen.py | Python | mit | 11,339 | [
"NetCDF"
] | 3d08a7ceb7ca59fbc360103e2d551d740eed31cad7226608d03d3bd6f84f3079 |
##
# Copyright 2009-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | boegel/easybuild-easyblocks | easybuild/easyblocks/o/openfoam.py | Python | gpl-2.0 | 26,813 | [
"ParaView"
] | 1cbbbbcef7e061bfad3d06c8b7b2a520c3fc60915ca6bac28f829f8a9e4b6291 |
"""Mayavi/traits GUI for converting data from KIT systems."""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
from collections import Counter
import os
import queue
import sys
from threading import Thread
import numpy as np
from mayavi.core.ui.mayavi_scene import MayaviScene
fr... | kambysese/mne-python | mne/gui/_kit2fiff_gui.py | Python | bsd-3-clause | 28,793 | [
"Mayavi"
] | 2c8b8a9d1d9b0c10387f1508063bc2c7866ad7d5a33f6de21287b97a7d8255fa |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import glob
import itertools
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import time
import urllib
import urllib2
import urlparse
import xmlrpclib
import zlib
from xml.etree import ElementTree
from cStri... | grap/OCB | addons/web/controllers/main.py | Python | agpl-3.0 | 70,114 | [
"VisIt"
] | bd59cb2b7bcd0ee93214b22b70df122b23e1466ba80766d994c04e06f82d2136 |
# Copyright 2017 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 required by applicable law or a... | jtk54/spinnaker | dev/validate_bom__deploy.py | Python | apache-2.0 | 44,900 | [
"ORCA"
] | df9c317f249f71929111e78d0d4909bcd433da9c4ed20eb891d41ce7f3fb8633 |
#!/usr/bin/env python
# B a r a K u d a
#
# Prepare 2D maps (monthly) that will later become a GIF animation!
# NEMO output and observations needed
#
# L. Brodeau, november 2016
import sys
import os
import numpy as nmp
from string import replace
from netCDF4 import Dataset
import barakuda_tool as bt
impor... | brodeau/barakuda | python/exec/prepare_movies.py | Python | gpl-2.0 | 7,287 | [
"ORCA"
] | 3304cfdc9f944247eda535dc12e226ec9ff1a941f77f233bd43b6b05a4ceb126 |
#!/usr/bin/env python2
'''
Generate blast_results.json file, used by Kablammo to list all BLAST result
sets available on the server.
Usage: simply run generate_list.py with no arguments. data/blast_results.json
will then list all XML files in the data/ directory.
'''
import os
import json
def main():
results_dir = ... | jwintersinger/kablammo | data/generate_list.py | Python | mit | 703 | [
"BLAST"
] | 02c6e4ffce0aded51df3fdbe9f8249703856902c8761e2bf1ed689aa8abd669d |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2017 The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this s... | jasperges/blenderseed | ui/__init__.py | Python | mit | 3,042 | [
"VisIt"
] | f4c07699543945f747a6cf646022ebe72ed75db97a9edd742c15950d86af47e4 |
"""Rewrite assertion AST to produce nice error messages"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import ast
import errno
import imp
import itertools
import marshal
import os
import re
import string
import struct
import sys
import types
import atom... | hackebrot/pytest | src/_pytest/assertion/rewrite.py | Python | mit | 40,925 | [
"VisIt"
] | d0e3b135e5e6d3245f2fa56b95d8cb033b567381c5140fb74ec32d7aca07b3e6 |
#-*- coding: utf-8 -*-
"""
ohp
~~~
A collection of interview questions
1) performing outer_joins on csv files
2) least square regression
:copyright: (c) 2012 by Mek
:license: BSD, see LICENSE for more details.
"""
import csv
import random
import string
from operator import add
from itertools i... | mekarpeles/ohp | ohp/ohp.py | Python | bsd-3-clause | 5,553 | [
"Brian"
] | 1723b24e5f2af498b47390a045ecc75d29bfd54b46f3fd6c6aeae190e96b0dec |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
# pylint: disable=too-many-branches,too-many-... | mganeva/mantid | Framework/PythonInterface/plugins/algorithms/AngularAutoCorrelationsSingleAxis.py | Python | gpl-3.0 | 12,513 | [
"NetCDF"
] | 8ef4f63d19ff50334cb38a07225ee2e881ea28387f7f4d71fd1e43798ebd79e1 |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (gregory_r_warnes@groton.pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
###################... | intip/da-apps | plugins/da_centrallogin/modules/soappy/SOAPpy/Server.py | Python | gpl-2.0 | 26,498 | [
"Brian"
] | be2b0cc329759d51092ef40b8e82c0c658600d6421c672774639bd782326c3e5 |
#!/usr/bin/python3.5
from analysis import getPctChange, getPrice
from emailActions import send_email
import cfg
from os import environ
cfg.run_setup()
sender = environ['CRYPTOALERT_EMAIL']
pwd = environ['CRYPTOALERT_PWD']
#if abs(1) > 0:
#body = 'The price for Bitcoin has changed by %s in the last hour. The c... | pmt210/CryptoAlerts | main.py | Python | mit | 588 | [
"Brian"
] | d069398a00df4cb05322920d44b48247f49f9e2d0a815caf9275fbf9a34c0da5 |
from typing import Dict, List, Optional, Tuple, Union, Sequence
import numpy as np
import tensorflow as tf
from typing_extensions import Literal
from odin.networks import Networks, TrainStep
from odin.backend import TensorType
from odin.utils import as_tuple
from scipy import sparse
from tensorflow.python.data.ops.da... | imito/odin | odin/bay/vi/_base.py | Python | mit | 14,586 | [
"Gaussian"
] | e866db68048a1cc9caf114340600dc3856ae10fabf6280e3fa75c25c6329a38f |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019-2021, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
"""Installed collections management package."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import errno
import f... | ghjm/ansible | lib/ansible/galaxy/collection/__init__.py | Python | gpl-3.0 | 56,626 | [
"Galaxy"
] | 416c6dd9f3fb6fb4e194a992e47c6bb5eff01848a8265d29bf0f34805402ba6c |
"""
Copyright (C) 2014, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Maintainer: Rudolf Streif (rstreif@jaguarlandrover.com)
"""
"""
Django settings for rvi p... | PDXostc/rvi_backend | settings.py | Python | mpl-2.0 | 7,038 | [
"Jaguar"
] | 388084702d0db97997d5d68d4a0022377e99b852699159a28cdafe7522e392e9 |
"""
Functionality for dealing with dbkeys.
"""
#dbkeys read from disk using builds.txt
from galaxy.util import read_dbnames
from galaxy.util.json import loads
import os.path
class GenomeBuilds( object ):
default_value = "?"
default_name = "unspecified (?)"
def __init__( self, app, data_table_name="__dbke... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/util/dbkeys.py | Python | gpl-3.0 | 5,080 | [
"Galaxy"
] | 608125c7f0ab7f419c60acf612ab9e8a0ccfe7a7b20eb2a8c735971fed8ce115 |
##Uses a PFG form to select and merge various PDFs to create a custom viewbook for prospective students
##The PFG form should send a unique username and up to 6 majors and/or areas of interests in the query string
from pyPdf import PdfFileWriter, PdfFileReader
from Products.CMFPlone.utils import _createObjectByType
imp... | uwosh/Scripts | mergePDFs.py | Python | gpl-2.0 | 5,885 | [
"VisIt"
] | 59dcb0aaa552ea64e1e360b711a04f3c4677007caeb0a744ba01541b89b88769 |
# -*- coding: utf-8 -*-
from django.db import models
import datetime
class status_history(models.Model):
comment = models.TextField(null=True, blank=True)
status = models.CharField(max_length=250)
entity_name = models.CharField(max_length=250)
created_at = models.DateTimeField()
order = models.Fore... | akiokio/centralfitestoque | src/salesReport/models.py | Python | bsd-2-clause | 8,831 | [
"VMD"
] | d5a4f5a112ea2cc6c868b3b9b8efbaa39cbc1ea0c68db68b28fd3749856f3d88 |
import re
import urllib
import urllib2
import cherrypy
import smtplib
from email import Message
from pytz import utc
from datetime import datetime, timedelta
from model.User import User
from model.Group import Group
from model.Notebook import Notebook
from model.Note import Note
from model.Password_reset import Passwor... | osborne6/luminotes | controller/Users.py | Python | gpl-3.0 | 70,288 | [
"VisIt"
] | 5773c01e8025f3427885ef019abb26c35acc592e3dc49683b0b649a01daf4315 |
from alta.workflows import Wms
from alta.bims import Bims
from alta.objectstore import build_object_store
class Client:
def __init__(self, conf, logger):
self.conf = conf
self.logger = logger
self.gi = None
self.bk = None
self.ir = None
logger.debug('conf: '.format... | gmauro/presta | presta/client.py | Python | mit | 1,716 | [
"Galaxy"
] | f91ea1c600df0baa8fe946c4df0be7936a9d3a9966ffdd2655c0d798e22956c3 |
"""
General helper functions that don't fit neatly under any given category.
They provide some useful string and conversion methods that might
be of use when designing your own game.
"""
import os, sys, imp, types, math, re
import textwrap, datetime, random, traceback, inspect
from inspect import ismodule
from colle... | TaliesinSkye/evennia | src/utils/utils.py | Python | bsd-3-clause | 31,873 | [
"VisIt"
] | 0efdf0d19ea0b9a7c19c96edda7745af66143d3f00d8e648adeb23a9e2beea78 |
#Copyright ReportLab Europe Ltd. 2000-2012
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/pdfbase/cidfonts.py
#$Header $
__version__=''' $Id: cidfonts.py 3959 2012-09-27 14:39:39Z robin $ '''
__doc__="""CID (Asian multi-byte) font support.
... | nakagami/reportlab | src/reportlab/pdfbase/cidfonts.py | Python | bsd-3-clause | 18,829 | [
"Brian"
] | e45c6b90f3c507d42ea1d22ef805d9da20f95118a32ea44188b912231e229a72 |
#!/usr/bin/env python
# -*- coding: latin-1 -*-
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Kyle A. Beauch... | kyleabeauchamp/mdtraj | mdtraj/nmr/scalar_couplings.py | Python | lgpl-2.1 | 4,491 | [
"MDTraj"
] | 5e85691e63ae8de7b4d9d89cd8ef0bf0c28196323497426b062e7beadd915a9f |
#!/usr/bin/env
"""
Wavelt Coherence and X-wavelet transform
For P. Stabeno
Using Anaconda packaged Python
Based on
--------
xwt from - "Crosswavelet and wavelet coherence software were provided by
A. Grinsted." (C) Aslak Grinsted 2002-2004
modifications for confidence intervals b... | jeepsterboy/waveletanalysis | xwt_wavelet_analy_GOA.py | Python | mit | 17,017 | [
"NetCDF"
] | d378cf925773558132812a86e2b36a8e5b899e488da9434ba84144af45985d5a |
#!/usr/bin/python3
import sys
import argparse
import re
def logs():
print 'Running script {}'.format(sys.argv[0])
print 'Check 00_logs folder to see output for this script\n\n'
sys.stdout = open('../00_logs/10_{}_analyzed.out'.format(sys.argv[1]), 'w')
print 'Input file was:', sys.argv[1]
print
... | CoderMatthias/ortholog-assignment | 05_scripts/10_ortho_analysis.py | Python | gpl-2.0 | 9,985 | [
"BLAST"
] | 42a7576f0485e5c48c89874a6454ca66106a89d076700cc60f0d902b9573d122 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/messageanswer.py | Python | gpl-2.0 | 5,200 | [
"VisIt"
] | ea7ff051ad080d781794bb398d535e60f4015f6b2e9465878544efadbbababc0 |
import os
import nest
import logging
import datetime
from time import clock
from parameters import *
from data import *
times = []
spikegenerators = {} # dict name_part : spikegenerator
spikedetectors = {} # dict name_part : spikedetector
multimeters = {} # dict name_part : multimeter
SYNAPSES = 0
FORM... | magnastrazh/NEUCOGAR | nest/dopamine/integrated/scripts/func.py | Python | gpl-2.0 | 11,963 | [
"NEURON"
] | 8cf9a152983a4a9b57f48a66ee44535709eae6cb0ba4cc23149f8f0f792faffa |
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