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#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Unit tests for data_ingestion.py script."""
#
# (C) Pywikibot team, 2012-2015
#
# Distributed under the terms of the MIT license.
#
from __future__ import unicode_literals
__version__ = '$Id$'
import os
from tests import _data_dir
from tests import _images_dir
from tests.... | valhallasw/pywikibot-core | tests/data_ingestion_tests.py | Python | mit | 4,020 | [
"CRYSTAL"
] | 1c7ddb920343cee472b56cf83459d9c1574edc920b7a8ff4fb67e0bad0d52614 |
from collections import OrderedDict
from django.utils import timezone
from edc_registration.models import RegisteredSubject
from edc_base.utils import convert_from_camel
from edc_constants.constants import YES, POS, NEG, IND, NEVER, UNKNOWN, DWTA, OTHER
from edc_dashboard.subject import RegisteredSubjectDashboard
fro... | botswana-harvard/tshilo-dikotla | td_dashboard/classes/maternal_dashboard.py | Python | gpl-2.0 | 11,690 | [
"VisIt"
] | cb72f5504a472b6eb014474ede2e134768c431a21d6d2f3be1431ba52b02af90 |
import classes
import io
import numpy as np
import scipy.fftpack as fftpack
import scipy.signal as signal
from scipy.signal import butter, lfilter
def dec2base(num, base, l):
'''
Converts a decimal number into an array of l digits in a given base.
Input:
num - number to be converted
base - conversio... | epfl-lts2/room_transfer_function_toolkit | room_transfer_function_toolkit_python/room_transfer_function_toolkit/other_methods.py | Python | gpl-3.0 | 2,391 | [
"Gaussian"
] | 7141ade7634c7ad0c43ed8703c52d8301962af7edbd0458b48b1a1ee983c5541 |
#!/usr/bin/env python
#Corey Brune 08 2016
#This script creates an environment
#requirements
#pip install docopt delphixpy
#The below doc follows the POSIX compliant standards and allows us to use
#this doc to also define our arguments for the script.
"""Create Host Environment
Usage:
dx_environment.py (--type <na... | mcbrune/delphixpy-automation | v1_8_0/dx_environment.py | Python | mit | 27,209 | [
"ASE"
] | 798aba623bfbf94be46c37b245708077c928d206241e2c0bca0d796d4dfa92fe |
#!/usr/bin/env python
# coding: utf-8
import librosa
import logging
import numpy as np
from scipy.spatial import distance
from scipy import signal
from scipy.ndimage import filters
import pylab as plt
import msaf
from msaf.algorithms.interface import SegmenterInterface
def median_filter(X, M=8):
"""Median filter... | urinieto/msaf | msaf/algorithms/foote/segmenter.py | Python | mit | 4,176 | [
"Gaussian"
] | 64a4a220ada30184590a22ce73a584b659feaeb26c06606d2b5125b5772ccff2 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetR... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/General/Testing/Python/TestClipClosedSurface.py | Python | gpl-3.0 | 2,401 | [
"VTK"
] | ec9d2a78feeebc171666317322839490610a03b073c1736590860f3772e0750b |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/songs/forms/songmaintenancedialog.py | Python | gpl-2.0 | 10,254 | [
"Brian"
] | 681887acb76577d668e07dab1dd095936b2a11f125436831f56c9e1852754ce7 |
#! /usr/bin/env python
"""
Change current DIRAC File Catalog working directory
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
from COMDIRAC.Interfaces import critical
from COMDIRAC.Interfaces import DSession
from COMDIRAC.Interfaces import D... | DIRACGrid/COMDIRAC | src/COMDIRAC/Interfaces/scripts/dcd.py | Python | gpl-3.0 | 1,668 | [
"DIRAC"
] | 65c77d53a6b749365a351162a2180e4e23c285203c3cccd460e0ca61a925f832 |
#!/usr/bin/env python
#Processes uploads from the user.
# WARNING: Changes in this tool (particularly as related to parsing) may need
# to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools
import subprocess, time
import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile
from galaxy import eg... | cogsys-tuebingen/SBVC | dist/BioPax2SBML_webservice/ECCBPaperVersion/upload_biopax.py | Python | lgpl-3.0 | 11,705 | [
"Galaxy"
] | e3aed85a7c85e6d513e3dc7e57206050fa2da2655d48c9cc43313d5afa20e896 |
#!/usr/bin/env python
import logging
from numpy import absolute, asfortranarray, diff, ones, inf, empty_like, isfinite
from scipy.optimize import minimize
from scipy.interpolate import interp1d
from numpy.linalg import norm
from time import time
from warnings import warn
#
from .transcararc import getColumnVER
from .p... | scienceopen/histfeas | histfeas/FitVER.py | Python | gpl-3.0 | 6,256 | [
"Gaussian"
] | cafabd694672c2c69c4026587204d46c5bf723f025576779215ef301fe01e0f9 |
#Calculate vertical integrals of area mean, annual mean specific humidity for whole atmosphere and levels above 100hPa (strat wv)
#Could set a threshold to determine spin-up end, e.g. require changes of less than 1% seems plausible. Need more data to confirm this is appropriate however
from netCDF4 import Dataset
impo... | Alexander-P/Isca | src/extra/python/scripts/general_spinup_fn.py | Python | gpl-3.0 | 5,122 | [
"NetCDF"
] | 9e473da7a035cc019e3288800e9ad998217e5de43dc159d697903931f860eeed |
#
# 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 us... | iemejia/incubator-beam | sdks/python/apache_beam/pipeline_test.py | Python | apache-2.0 | 29,763 | [
"VisIt"
] | 60340b5ae3403b5c1571a47ce050aa2aecec6b63e02cbd0b29c7f4a8f3007423 |
class ObjectionFrame(object):
DEFENSE_CHARACTERS = {
"Apollo Justice": 60,
"Mia Fey": 15,
"Miles Edgeworth (Defense)": 690,
"Phoenix Wright": 1,
}
PROSECUTION_CHARACTERS = {
"Franziska von Karma": 21,
"Godot": 175,
"Klavier Gavin": 65,
"Manfr... | 4Kaylum/SkyBot | cogs/utils/objection_frame.py | Python | gpl-3.0 | 3,991 | [
"MOE"
] | bab11da7a52c224c95580559fa840d524e4f9910e42fb5e24a6ab467d11a2901 |
import numpy as np
from .control import model_setup
from .cp_confocal import threed
from .cp_triplet import trip
# 3D + Triplet Gauß
# Model 6013
def CF_Gxyz_gauss_3DTT(parms, tau):
u""" Three-dimensional free diffusion
with a Gaussian laser profile, including two triplet components.
The triplet ... | paulmueller/PyCorrFit | pycorrfit/models/model_confocal_tt_3d.py | Python | gpl-2.0 | 3,436 | [
"Gaussian"
] | 737b91904f3496378ffd94d1f258b6844f29b0e51816294f48c119437a30449c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
'''
Created on Mar 5, 2012
'''
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Sh... | matk86/pymatgen | pymatgen/alchemy/tests/test_transmuters.py | Python | mit | 4,522 | [
"pymatgen"
] | 0242f34a44207ee935a7fee4c98a5911bbe4d912190f9df3ca69d808099b759b |
# -*- coding: utf-8 -*-
"""Generate graphs with a given degree sequence or expected degree sequence.
"""
# Copyright (C) 2004-2016 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
from __future__ import divisi... | goulu/networkx | networkx/generators/degree_seq.py | Python | bsd-3-clause | 31,101 | [
"Brian"
] | 18a21626391b566a2ac9761db73cab1ed923b3cb60b20a4db7712d8fe55086b0 |
from __future__ import print_function
import ast
class TreeChopperTransform(ast.NodeTransformer):
def visit(self, node):
print("node %s" % node)
stump_node = ast.Pass()
return stump_node
| ucb-sejits/ast_tool_box | ast_tool_box/transformers/tree_chopper.py | Python | mit | 218 | [
"VisIt"
] | 179c0a30691abfb2df85f270e4a86e30a93696e1fd6ffa2af0c6b07201eb1c89 |
from __future__ import print_function
__author__ = ['Michele Cappellari', 'lposti']
"""
#####################################################################
Copyright (C) 2001-2014, Michele Cappellari
E-mail: cappellari_at_astro.ox.ac.uk
Updated versions of the software are available from my web page
http://purl.or... | lposti/pyfJmod | fJmodel/voronoi.py | Python | bsd-3-clause | 30,219 | [
"Galaxy"
] | 9e1ef757c5d9bd761466a57cf73bf25c83fded7d8e07ffc43e3f1e4318c8c729 |
#!/usr/bin/env python
import sys, os, argparse
import pdb
from .agglo import Rag
from .imio import read_image_stack
from .morpho import juicy_center
from numpy import zeros, bool, hstack, vstack, newaxis, array, savetxt
from scipy.ndimage.filters import median_filter, gaussian_filter
from scipy.ndimage.measurements im... | jni/gala | gala/stitch.py | Python | bsd-3-clause | 4,607 | [
"Gaussian"
] | 06b5778d74565f2ba6d29acd8fa93bf5b3afe470f3a336bfa70666127a090f24 |
# $Id$
#
# Copyright (C) 2005-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import random
from rdkit.six.moves impo... | soerendip42/rdkit | rdkit/Chem/Randomize.py | Python | bsd-3-clause | 1,688 | [
"RDKit"
] | 31e9eb5a52372ad369f0a70c1b29f4058ebb04f3647eab3edaf74442bab8a419 |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathem... | sknepneklab/SAMoS | analysis/batch_nematic/batch_analyze_nematic_phi1.0b.py | Python | gpl-3.0 | 2,489 | [
"VTK"
] | c901dc112712a8ba93198b6971ba2c43dd5ac62346957c6ac6d94e9742c9c590 |
# !usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-06-28 15:32:49
# @Last modified by: Brian Cherinka
# @Last Modified time: 2018-07-10 15:31:48
from __future__ import print_function, division, absolute_import
import os
import datetim... | albireox/marvin | python/marvin/web/settings.py | Python | bsd-3-clause | 3,941 | [
"Brian"
] | edb1c9c41a485edbca69407a1eceaa52bd83f545da57cf99d298855b471b4fcb |
########################################################################
# File : TaskQueueDirector.py
# Author : Stuart Paterson, Ricardo Graciani
########################################################################
""" The TaskQueue Director Agent controls the submission of pilots via the
PilotDirectors. ... | marcelovilaca/DIRAC | WorkloadManagementSystem/Agent/TaskQueueDirector.py | Python | gpl-3.0 | 19,111 | [
"DIRAC"
] | 24092663e43c662d219f0f99757d1e1317ee6e708f67672bfda88e1547b301a5 |
import importlib
from typing import List, Type # noqa
import warnings
from pandas.util._decorators import Appender
from pandas.core.dtypes.common import is_integer, is_list_like
from pandas.core.dtypes.generic import ABCDataFrame, ABCSeries
import pandas
from pandas.core.base import PandasObject
# Trigger matplotl... | toobaz/pandas | pandas/plotting/_core.py | Python | bsd-3-clause | 55,261 | [
"Gaussian"
] | 6418007fe0b20792d73b9519fef83b546529214635d559a1e0b604df3efe14a7 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-affy/package.py | Python | lgpl-2.1 | 2,130 | [
"Bioconductor"
] | 850528596fbbb7c16f7c13efe83cb2ee15d520d9d4e1b51ef93d1892a0c51c44 |
# Plot a histogram
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
from util import get_data, plot_data, compute_daily_returns
def test_run():
# Read data and plot
dates = pd.date_range('2009-01-01', '2012-12-31')
symbols = ['SPY', 'XOM', 'GLD', 'GOOG']
initialize = 'n' # toggle... | liggettla/jubilant-pancake | 6_histograms/histograms.py | Python | mit | 3,180 | [
"Gaussian"
] | 827d0fa8dfa58e8a27a242511c54aa8ef60f6bb5ed3e305d5d193a254d629940 |
from numpy.random import multivariate_normal as mv_norm
from ..geometry import PointAt, BoundingBox
def boundingbox_type_checked(value) -> BoundingBox:
if type(value) is not BoundingBox:
raise TypeError('Bounds must be of type <BoundingBox>!')
return value
def gaussian(bounds: BoundingBox) -> PointA... | yedivanseven/LPDE | sklKDE/producers/distributions.py | Python | gpl-3.0 | 617 | [
"Gaussian"
] | 7453db4c937a6fc89d02d34d6d957ba52c41a8f2af57814b5b85edc1dce046b8 |
# Copyright 2015 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.
"""Dummy benchmarks for the bisect FYI integration tests.
The number they produce aren't meant to represent any actual performance
data of the browser. For m... | axinging/chromium-crosswalk | tools/perf/benchmarks/dummy_benchmark.py | Python | bsd-3-clause | 1,676 | [
"Gaussian"
] | a37534359ab239857eba376d86415c8dbaf616bf05dac8602ce9f655330c1dcb |
import csv
import os
import sys
from io import BytesIO
import cStringIO
from urlparse import urlparse
import xml.etree.ElementTree as XMLParser
import pycurl
import codecs
class NcMLConverter(object):
'''Convert NcML metadata files produced by ncdump to a summarized CSV table.'''
def __init__(se... | DataONEorg/sem-prov-design | docs/science-scenarios/example-files/mstmip/NetCDFSummary/mstmip/NcMLConverter.py | Python | apache-2.0 | 10,890 | [
"NetCDF"
] | e4308fc3f4b731f0e6a1827c588053e376ee24ce9fb25503d96fd23c2f91ced7 |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
from scipy._lib.six import string_types, exec_
import sys
import keyword
import re
import inspect
import types
import warnings
from scipy.misc impor... | jonycgn/scipy | scipy/stats/_distn_infrastructure.py | Python | bsd-3-clause | 112,903 | [
"Gaussian"
] | 40892844c2164e2a6907fccb384739f06d27ed70698e0308186216e33686b644 |
"""
@ Andrew Li and Arul Prasad, PRIMES 2014
@ Script purpose: Given several objects, lengths, the location of drug resistant SNPs within the proteins, and arrays of ranges of disorder within the protein, the program will output two textfiles of distances from the SNPs to every other amino acid in each protein.
This wa... | GilAlterovitz/andrewarul | snpToDisorder.py | Python | mit | 7,432 | [
"PyMOL"
] | d11979847614c312583bdff76d4e80db04c3bcf1a859df2c2c705d2f098c737d |
"""
Views for the verification flow
"""
import json
import logging
import decimal
import datetime
from collections import namedtuple
from pytz import UTC
from ipware.ip import get_ip
from django.conf import settings
from django.core.urlresolvers import reverse
from django.http import (
HttpResponse, HttpResponse... | dkarakats/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 52,731 | [
"VisIt"
] | 8181fd4a88a9d0e22be748f9234b74bee84446dbfbebd86f240d10595751199b |
# (C) British Crown Copyright 2014, Met Office
#
# This file is part of Iris.
#
# Iris 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 3 of the License, or
# (at your option) any later ve... | Jozhogg/iris | lib/iris/tests/experimental/ugrid/test_ugrid.py | Python | lgpl-3.0 | 1,702 | [
"NetCDF"
] | 036774116e4f70ef43287495294d39a891f5bd02319ff11c6c24ed4708769b15 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ---------------------... | JWDebelius/scikit-bio | skbio/parse/sequences/tests/test_iterator.py | Python | bsd-3-clause | 12,217 | [
"scikit-bio"
] | cd7ad44cc13a761ea33df0fc930c4530fb18dd96e52f70e988f71c61dc7fc047 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible 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
# ... | andreaso/ansible | lib/ansible/modules/network/lenovo/cnos_backup.py | Python | gpl-3.0 | 11,140 | [
"VisIt"
] | 5133a41a96e27bf1b02361acb075a8ed05b1a5d19d90fb361d5ccfdc563d6b29 |
#!/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... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/powerstate.py | Python | gpl-2.0 | 5,096 | [
"VisIt"
] | fd3a445fe2cc99429e28470e2add62621e365f74e15cb26cf3393a4328bdee0e |
#
# @file TestCompartment_newSetters.py
# @brief Compartment unit tests for new set function API
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automat... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestCompartment_newSetters.py | Python | bsd-3-clause | 10,681 | [
"VisIt"
] | d79ddc7accb70ebeea65824318bb774d1995d59e8f78edc9260f5d29da84c41c |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible 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... | rghe/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 45,863 | [
"VisIt"
] | 3d23eb6b8de7d06c5fd9272bd91df94244bffa2c9535bdd35ff763cd544f465e |
import logging
import requests
from dateutil import parser
from lxml import etree
from . import TransportRTIProvider
from requests.exceptions import RequestException
from moxie.core.exceptions import ServiceUnavailable
from datetime import datetime
logger = logging.getLogger(__name__)
class ODSLiveBusRtiProvider(Tr... | ox-it/moxie | moxie/transport/providers/odslive.py | Python | apache-2.0 | 6,080 | [
"VisIt"
] | 84b4290dcc7f96145e14710cb52028db6b012fa62f712880b1bd339b5a87fe94 |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Sof... | andrebellafronte/stoq | stoqlib/gui/utils/logo.py | Python | gpl-2.0 | 1,345 | [
"VisIt"
] | 655cccb1cce832c7c8e2def320288cbffb14bac091a7421868e47b9fff36003c |
import sys
def pgp_words_from_bytes(list_of_bytes):
# Use the PGP wordlist to convert bytes to words
#
# `list_of_bytes` should look like
# ['de', 'ad', 'be', 'ef', '17', 5e']
# PGP word list from https://en.wikipedia.org/wiki/PGP_word_list
# Hex: [Even Word, Odd Word]
pgp_words = {
'00': ['aardva... | jbaber/phrase_from_bytes | phrase_from_bytes.py | Python | gpl-2.0 | 29,847 | [
"Elk",
"MOE",
"ORCA"
] | 742b5d8b80db8523ddf2bc06e01e6f3a002c7e8cc5cea1e473d4838aa4f36f8d |
# Asynchronous sockets in Jython.
#
# Copyright (c) 2002 brian zimmer <mailto:bzimmer@ziclix.com>
'''
Generate the errno module by extracting the values from CPython.
Better windows error messages could be derived by parsing:
http://www.sockets.com/err_lst1.htm#DetailedErrorDescriptions
http://msdn.microsoft.com/li... | tunneln/CarnotKE | jyhton/Misc/make_errno.py | Python | apache-2.0 | 3,525 | [
"Brian"
] | dd3a1cabf7d63f7e9cde5646ef42547a9ee5922d8921d83f56f6bb00cc8844b0 |
# -*- python -*-
# Package : omniidl
# __init__.py Created on: 1999/11/3
# Author : David Scott (djs)
#
# Copyright (C) 2002-2008 Apasphere Ltd
# Copyright (C) 1999 AT&T Laboratories Cambridge
#
# This file is part of omniidl.
#
# omniidl is free software; you ... | ogata-lab/rtmsdk-mac | x86_64/lib/python2.7/site-packages/omniidl_be/cxx/__init__.py | Python | lgpl-2.1 | 12,403 | [
"VisIt"
] | 0db58acd0ba76a79e464b3a8bdcb1b7e757cd023d850aac33b3a1d8d2376bee2 |
#
# Copyright 2016 The BigDL 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 applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/tfpark/utils.py | Python | apache-2.0 | 3,134 | [
"ORCA"
] | 0fa95279af68357c09da581af13f9302dfe8a51740779bede7895e797326f539 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose-examples | snippets/gssaCylinderDiffusion.py | Python | gpl-2.0 | 6,565 | [
"MOOSE"
] | 1ceda7308ce1b4b5af6e86f113372bdd81409e6b3c9055fca6518ef9a36ef63f |
# 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... | sasukeh/neutron | neutron/tests/unit/agent/linux/test_ip_lib.py | Python | apache-2.0 | 53,330 | [
"Brian"
] | fdfa7799986ad1526a98d2ec064c7b47a2fb07ecbfcd863be1aa820dc1c613c6 |
import openpathsampling as paths
from openpathsampling.netcdfplus import StorableNamedObject
import openpathsampling.engines as peng
try:
import plumed
except ImportError:
pass
import numpy as np
import warnings
import copy
import os
import sys
class PLUMEDCV(paths.collectivevariable.CoordinateFunctionCV):
... | choderalab/openpathsampling | openpathsampling/collectivevariables/plumed_wrapper.py | Python | lgpl-2.1 | 12,322 | [
"MDTraj"
] | 402cf301c90d3853871363e904ac54e00f64f9ff69f994b0d659140159daf6a6 |
import ast
import math
import unittest
from math import sqrt, sin, cos
from numpy import array, eye, roll, tile
from openmdao.main.api import Assembly, Component, set_as_top
from openmdao.main.datatypes.api import Float, List, Slot, Dict
from openmdao.main.datatypes.array import Array
from openmdao.main.expreval impor... | DailyActie/Surrogate-Model | 01-codes/OpenMDAO-Framework-dev/openmdao.main/src/openmdao/main/test/test_evalexpr.py | Python | mit | 31,609 | [
"VisIt"
] | e36cf265797991ce9cacdfbaa89b45a8cb29f340f108d64bf118277fd92b74c4 |
from . import fwio
from . import utils
from . import db
import numpy as np
import ase
try:
import decaf
import ckutil
except(ImportError):
pass
def get_potential_energy(
calculator,
in_file='input.traj',
out_file='pw.pwo'):
"""Performs a ASE get_potential_energy() call with a c... | jboes/CatKit | catkit/flow/fwase.py | Python | gpl-3.0 | 4,808 | [
"ASE",
"ESPResSo"
] | 87200143db5abf77a4eb4be1e960e651fa37dbb1f99af16fb268aae6d11a4462 |
"""Extract list of URLs in a web page
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.2 $"
__date__ = "$Date: 2004/05/05 21:57:19 ... | nopressurelabs/privacypy | urllister.py | Python | gpl-3.0 | 839 | [
"VisIt"
] | d7550b869d79491c62a893e07e4a51e366968ae78a840cc0965a0cc5485753ea |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | wdwvt1/scikit-bio | skbio/util/_testing.py | Python | bsd-3-clause | 5,279 | [
"scikit-bio"
] | ca28ca920f29032e34da2f272d8b802451cc41c6e0af6a41558267a7e54d10f9 |
import tsfc
import coffee
import json
import numpy as np
def create_form(form_string, family, degree, dimension, operation):
from firedrake import dx, inner, grad
import firedrake as f
f.parameters['coffee']['optlevel'] = 'O3'
f.parameters['pyop2_options']['opt_level'] = 'O3'
f.parameters['pyop2_... | dham/sum_factorisation_scaling_tests | test_count.py | Python | mit | 1,778 | [
"VisIt"
] | 826c632a4b3bdf5bca61277ea4e48dc34b60b662be512713d176f3c949a6a722 |
"""
Implementation of all of the individual 'twill' commands available through
twill-sh.
"""
import sys
import _mechanize_dist as mechanize
from _mechanize_dist import ClientForm
from _mechanize_dist._headersutil import is_html
OUT=None
ERR=sys.stderr
# export:
__all__ = ['get_browser',
'reset_browser',
... | jasrusable/fun | venv/lib/python2.7/site-packages/twill/commands.py | Python | gpl-2.0 | 23,001 | [
"VisIt"
] | 4f6d9eb04dfc9a2b69ea85a51340e69a2f2258da936c5d2d45c3308415ba4028 |
#
# Copyright 2016 The BigDL 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 applicable law or agreed to in ... | yiheng/BigDL | pyspark/bigdl/nn/keras/layer.py | Python | apache-2.0 | 106,700 | [
"Gaussian"
] | 7ad268d3dcb68647b8128d3d451f104fcbf2b7ed00e152ecd333320e9a6970df |
# Author: Travis Oliphant, 2002
#
# Further updates and enhancements by many SciPy developers.
#
from __future__ import division, print_function, absolute_import
import math
import warnings
from . import statlib
from . import stats
from .stats import find_repeats
from . import distributions
from numpy import isscala... | juliantaylor/scipy | scipy/stats/morestats.py | Python | bsd-3-clause | 52,106 | [
"Gaussian"
] | c3c132f7b0d5d0769eebd75e6a584648a57df633748d6cbe0f027ccbc104d9a9 |
from brian.stdunits import *
from brian.units import *
F = 1
N_SUBPOP = 6
INTERCO_RATE = .2
INTERCO_STRENGTH = 0.
PARAMETERS = {
'Common':
{'simu_dt' : 0.05*msecond,
'simu_length' : 3000*msecond,
'resample_dt': 0.5*msecond,
'N_subpop' : N_SUBPOP,
'N_mitral' : N_SUBPOP*100*F,
'int... | neuro-lyon/multiglom-model | src/paramsets/std_beta_6glom_ring.py | Python | mit | 5,024 | [
"Brian"
] | 27c8b4a4552268d850b17de1debf883dbcedcd425165f38e86301a37f35f393d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
r"""Utilities for reproducing Harrold et al 2015 on SDSS J160036.83+272117.8.
"""
# Import standard packages.
from __future__ import absolute_import, division, print_function
import collections
import copy
import pdb
import re
import warnings
# Import installed packages.... | stharrold/2015_Harrold_SDSSJ1600 | code/utils.py | Python | mit | 81,416 | [
"Gaussian"
] | f785fb837f7b1ef33bd42cf831f17f5088ef45fd45c6eb9e67154449d73484a2 |
import img_scale
import pyfits as pyf
import pylab as pyl
from mpl_toolkits.axes_grid1 import axes_grid
import cPickle as pickle
import os
from scipy.stats import scoreatpercentile
def mk_image(galaxy):
base = './../../../images_v5/GS_2.5as_matched/gs_all_'
i_img = pyf.getdata(base+str(galaxy)+'_I.fits')
... | boada/ICD | sandbox/lowerSN/plot_icd_mass_montage.py | Python | mit | 3,646 | [
"Galaxy"
] | 567a95117242b3a355c2356d3de3fd67dfadab9c6c75a407d745961345ed778b |
import pytest
from pysisyphus.helpers import geom_loader
from pysisyphus.testing import using
from pysisyphus.run import run_from_dict
@pytest.fixture
def run_dict():
return {
"geom": {
"fn": "lib:hcn_iso_ts_opt_xtb.xyz",
},
"irc": {
"type": "eulerpc",
... | eljost/pysisyphus | tests/test_endopt_barriers/test_endopt_barriers.py | Python | gpl-3.0 | 1,426 | [
"xTB"
] | e2f7bd51ce835a504d4aff5c1b89a0fd438dcdd3ca645b8ddc17f1637cc5f775 |
from ase import Atoms, Atom
from ase.units import Hartree, Bohr
from gpaw import GPAW, debug, dry_run, Mixer, MixerDif, PoissonSolver
from gpaw.poisson import FixedBoundaryPoissonSolver
from gpaw import restart as restart_gpaw
from gpaw.grid_descriptor import GridDescriptor
from gpaw.transformers import Transformer
fr... | qsnake/gpaw | gpaw/transport/calculator.py | Python | gpl-3.0 | 109,051 | [
"ASE",
"GPAW"
] | 4e83fa6c1225358208b6295dc4f57cbdabd872fff04da5f28dc9aa3d05c42b7b |
# 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... | kou/arrow | python/pyarrow/util.py | Python | apache-2.0 | 4,642 | [
"VisIt"
] | 04a08eb27b22457bb231360acc64752d0f6a0fb5f246f7297eb031e2005cae37 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/p4util/__init__.py | Python | gpl-2.0 | 1,167 | [
"Psi4"
] | 5b23e5734e46a3c4a0bfbe2f7df27535fb64129b8f0a08469d3ef09c5c4c3118 |
#Clustering
from sklearn.cluster import AffinityPropagation #Perform Affinity Propagation Clustering of data.
from sklearn.cluster import AgglomerativeClustering #Agglomerative Clustering
from sklearn.cluster import Birch #Implements the Birch clustering algorithm.
from sklearn.cluster import DBSCAN #Perform DBSCAN clu... | dmccloskey/python_statistics | python_statistics/scikitLearn_dependencies.py | Python | mit | 22,642 | [
"Gaussian"
] | 4682fa12a83d9bc9c8f895edb78f29ec6088968c8eb704d98c22e98ec3d75f86 |
"""
test views
"""
import datetime
import json
import re
import pytz
import ddt
from mock import patch, MagicMock
from nose.plugins.attrib import attr
from capa.tests.response_xml_factory import StringResponseXMLFactory
from courseware.courses import get_course_by_id # pyline: disable=import-error
from courseware.fie... | atsolakid/edx-platform | lms/djangoapps/ccx/tests/test_views.py | Python | agpl-3.0 | 26,487 | [
"VisIt"
] | 317dd6851423224397349895db1da747855dfbc3a01116f32338d7aae1211de7 |
# Copyright 2017-2020 The GPflow Contributors. 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 appli... | GPflow/GPflow | gpflow/kernels/convolutional.py | Python | apache-2.0 | 4,443 | [
"Gaussian"
] | d33051acfb528a981dd0d10cacf793b0cccd244c58a6bb950ce8995cbe5d432f |
#!/usr/bin/env
"""
Chuckchi_Winds_NARR_model_prep.py
Retrieve NARR winds for one locations
Filter NARR winds with a triangular filter (1/4, 1/2, 1/4) and output every 3hrs
Provide U, V
Save in EPIC NetCDF standard
#Added subsample routine that uses mod function (%) to pull out times that is divisible by... | shaunwbell/FOCI_Analysis | ReanalysisRetreival_orig/Chuckchi_Winds/Chuckchi_Winds_NARR_model_prep.py | Python | mit | 10,114 | [
"NetCDF"
] | a05ff83743720ad0a2c2f1797c627e1e89b70a695d8c80eb08a7b7c55b1b8f34 |
import logging
import click
from readtagger.findcluster import ClusterManager
from readtagger import VERSION
import multiprocessing_logging
@click.command()
@click.option('-i',
'--input_path',
help='Find cluster in this BAM file.',
type=click.Path(exists=True),
... | bardin-lab/readtagger | readtagger/cli/findcluster.py | Python | mit | 3,798 | [
"BWA"
] | 12542f9352c5e9a4cbf0e2f00cadefd9541d554ae1ffa16fcf6b4ac45ed40cc3 |
# This new verion (6/11/10) hasn't been tested yet.
# Can't run unit tests on my MacPro w/o Nio.
#---------------------------------------------------
# S.D. Peckham
# May, June 2010
import os
import sys
import time
import numpy
import file_utils
# import Nio # (a module in the PyNIO package)
#---------------... | mdpiper/topoflow | topoflow/utils/ncts_files_Nio.py | Python | mit | 24,549 | [
"NetCDF"
] | 098563065d650e4e377809ce15f84daa560ff1e6457bedb800b82d6c952204ad |
'''
libChEBIpy (c) University of Manchester 2015-2020
libChEBIpy is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=superfluous-parens
# pylint: disable=too-many-public-methods
import math
import sys
from ._ba... | libChEBI/libChEBIpy | libchebipy/_chebi_entity.py | Python | mit | 9,599 | [
"VisIt"
] | cb74d640804959cbab390d13c14ece31b4d82edc5b13cc0f452c1c56f776e638 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Created on Mar 18, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "S... | nisse3000/pymatgen | pymatgen/apps/borg/tests/test_hive.py | Python | mit | 4,772 | [
"pymatgen"
] | f9b48f70c4c8e7b5900c1e4eff7355ad27081635c1d0ad2d0f56038460235500 |
import enum
FGNodeType = enum.Enum('FGNodeType','component libraryfunction librarymethod input output assignment literal forward unknown')
class FGNode(object):
def __init__(self, nodeid, nodetype, ref=None, inputs=[]):
self.nodeid = nodeid
self.type = nodetype
self.ref = ref
self.inputs = inputs
... | Planet-Nine/cs207project | pype/fgir.py | Python | mit | 4,224 | [
"VisIt"
] | 18e3bc38dcd76c4d5f8347cc7c390bf93ef43bf3985f0c846666e3c8399b2246 |
# Author: Samuel Genheden samuel.genheden@gmail.com
"""
Program to make the molecules in a datafile whole
The default output is the input data file with a "_whole" string appended
Example:
lmp_makewhole.py data.128dopc_4232wat
"""
import argparse
import os
import sys
import numpy as np
from sgenlib import lammp... | SGenheden/Scripts | Lammps/lmp_makewhole.py | Python | mit | 1,436 | [
"LAMMPS"
] | 870318c43e9aadb5635b8e14b7f020020d5e274069c69d9da6cc313afeed0aec |
from geopy.distance import vincenty
import requests
def get_distance(lat_orig, lng_orig, lat_des, lng_des):
# Use the vincenty method (geopy.distance) to return the distance between two sets of coordinates.
# Args:
# lat_orig (float): latitude of origin
# lng_orig (float): longitude of origin
... | mkudija/Map-Tools | map_functions.py | Python | mit | 1,427 | [
"COLUMBUS"
] | fedf09794018fd05c18db9fe7e0c9703607e3caa2501812ae1c4f1576aaee100 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
gnpy.core.info
==============
This module contains classes for modelling :class:`SpectralInformation`.
"""
from __future__ import annotations
from collections import namedtuple
from collections.abc import Iterable
from typing import Union
from numpy import argsort, ... | Telecominfraproject/gnpy | gnpy/core/info.py | Python | bsd-3-clause | 9,462 | [
"ASE"
] | a9ca4dddbd7e757336da371c10b776c0fc7fed6c35ed1512b2f67c9e46e4d6ed |
import pandas as pd
from sklearn.ensemble import RandomForestClassifier
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.ensemble import BaggingClassifier
from sklearn.ensemble import AdaBoostClassifier
from sklearn.ensemble import ExtraTreesClassifier
from sklearn.neural_network import MLPClassifie... | rupakc/Kaggle-Compendium | Carvana - Dont Get Kicked/carvana-baseline.py | Python | mit | 3,518 | [
"Gaussian"
] | 126a5835fa0adece24771757588817bf45046cab2512f9d203d59bb7565e74cc |
# -*- coding: utf-8 -*-
{
"'Cancel' will indicate an asset log entry did not occur": "'Abbrechen' wird angeben, dass ein Asset Log Eintrag nicht eingetreten ist",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that... | devinbalkind/eden | languages/de.py | Python | mit | 255,654 | [
"VisIt"
] | 1325f40acc47c8817bf51055e8f493daff2dd77d34be111d71494fb3fbb63b46 |
########################################################################
# $Id$
# File : InProcessComputingElement.py
# Author : Stuart Paterson
########################################################################
""" The simplest Computing Element instance that submits jobs locally.
"""
__RCSID__ = "$Id$"
fro... | avedaee/DIRAC | Resources/Computing/InProcessComputingElement.py | Python | gpl-3.0 | 4,528 | [
"DIRAC"
] | 555194d93c20b0c2a7f78a3b6e17d9d1f9f4e8a30ba51d0b14efce69c27f072a |
#!/usr/local/sci/bin/python2.7
#*****************************
#
# merge _day and _night netCDF files
#
#
#************************************************************************
'''
Author: Robert Dunn
Created: March 2016
Last update: 12 April 2016
Location: /project/hadobs2/hadisdh/marine/PROGS/Build
--------------... | Kate-Willett/HadISDH_Marine_Build | EUSTACE_SST_MAT/merge_day_night.py | Python | cc0-1.0 | 27,657 | [
"NetCDF"
] | f0535b4611c404ad8e3a2d58a686a2e9e43736a1b8eec8ea6eccd6ae0c0a357c |
from __future__ import unicode_literals
import logging
from django.contrib.auth.models import User
from django.core.cache import cache
from django.core.exceptions import ObjectDoesNotExist
from django.db import models
from django.db.models import Count, Q
from django.utils import six, timezone
from django.utils.trans... | KnowNo/reviewboard | reviewboard/reviews/models/review_request.py | Python | mit | 38,197 | [
"VisIt"
] | 38d24de247f98f6760c56c4cb380273defe17f462e87afa94f3049aa549843f1 |
"""
In this test we want to check if Tornado generate the same credentials dictionnary as DIRAC.
It also test if the correct certificates are sended by client.
To run this test you must have the handlers who returns credentials dictionnary.
Handlers are diracCredDictHandler and tornadoCredDictHandler j... | DIRACGrid/DIRAC | tests/DISET_HTTPS_migration/TestClientReturnedValuesAndCredentialsExtraction.py | Python | gpl-3.0 | 3,744 | [
"DIRAC"
] | e36561ccc14097b65f5630e6ba890dfd0ecfcf24b8d34d9ce4a1951f7085535e |
#!/usr/bin/python
"""This simple demo calculates the total energy of CO molecules
using once LDA and once PBE as xc-functional. Obviously
some parts in this scripts are longer than necessary, but are shown
to demonstrate some more features."""
import ase
import ase.calculators.castep, ase.io.castep
calc = ase.calcula... | conwayje/ase-python | doc/ase/calculators/ase_castep_demo.py | Python | gpl-2.0 | 1,977 | [
"ASE",
"CASTEP"
] | 6e50eab476e62573c3ce53e954a7d91064697d4430c8746cbb18ff8f4b96416d |
import datetime
import httplib
import json
import time
import urllib
class Site:
def __init__(self, name, site_token, url):
self._name = name
self._site_token = site_token
self._url = url
def get_name(self):
return self._name
def get_site_token(self):
return self.... | kjiwa/optify-api-client-python | optify.py | Python | mit | 19,155 | [
"VisIt"
] | 14688f61d6142f06763c9252785137e44b2e732ccd5bb65de437ecb735fc1a7a |
#!/usr/bin/env python3
"""
Main interface.
"""
import numpy as np
from numpy import pi
import matplotlib as mpl
import matplotlib.pyplot as plt
from scipy.constants import arcmin
from argparse import ArgumentParser
from os import path
from constants import c
import density
import lens
import potential
import times
fr... | dwysocki/GravLens | src/main.py | Python | mit | 7,320 | [
"Galaxy"
] | 1dc90074b5ebc8bca8bbdccb47b78e214d8ea88f414445dcad99b9fd94ba65f6 |
# Name: mapper_occci_online.py
# Purpose: Nansat mapping for OC CCI data, stored online in THREDDS
# Author: Anton Korosov
# Licence: This file is part of NANSAT. You can redistribute it or modify
# under the terms of GNU General Public License, v.3
# http://www.gnu.o... | nansencenter/nansat | nansat/mappers/mapper_opendap_siwtacsst.py | Python | gpl-3.0 | 2,417 | [
"NetCDF"
] | 441913c3f110956f1de77a24ec3e153f05b5ce78585c88c0e7c35a5dfcc4b4cb |
# Copyright (c) Charl P. Botha, TU Delft.
# All rights reserved.
# See COPYRIGHT for details.
import config
from install_package import InstallPackage
import os
import re
import shutil
import sys
import utils
BASENAME = "VTK"
GIT_REPO = "http://vtk.org/VTK.git"
GIT_TAG = "v5.6.1"
VTK_BASE_VERSION = "vtk-5.6"
# this... | nagyistoce/devide.johannes | install_packages/ip_vtk56.py | Python | bsd-3-clause | 9,152 | [
"VTK"
] | 87855ad653a5d4dc8045d28744f3438dbddc7cca9b23f15cf5c25ed0609161ef |
#!/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/servicelistreload.py | Python | gpl-2.0 | 5,232 | [
"VisIt"
] | 77f99c633ca3d5c553900214d4f73a81a1174cf08f7b5e77f5619844a1e41916 |
""" TransformationPlugin is a class wrapping the supported transformation plugins
"""
import re
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.SiteSEMapping import getSitesForSE, getSEsForSite
from DIRAC.Core.Utilities.List import breakListIntoChunks,... | avedaee/DIRAC | TransformationSystem/Agent/TransformationPlugin.py | Python | gpl-3.0 | 12,854 | [
"DIRAC"
] | c0cb66bf2ff3d7b9e284c59c461a571b8aa3fe0e6b27687500b2c0e72c978d5c |
import numpy as np
from mpl_toolkits.basemap import pyproj
from datetime import datetime
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import pyroms
def make_remap_grid_file(Bgrd, Bpos='t'):
#create remap file
remap_filename = 'remap_grid_' + Bgrd.name + '_' + Bpos + '.nc'
nc = netCD... | dcherian/pyroms | pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/make_remap_grid_file.py | Python | bsd-3-clause | 3,434 | [
"NetCDF"
] | 008867ef53aff5570fb81b96f8ec457679b2d1e7838452014ae1da65a531dcae |
"""
Tests install_django_app_trusty.py script
"""
import getpass
import io
import re
import os
import sys
import shutil
import subprocess
import datetime
from unittest import mock
from unittest.mock import call
import djangoapp
from djangoapp import InstallDjangoApp, main
from tests.conf_tests import GIT_REPO, APP_HOM... | globz-eu/infrastructure | chef-repo/cookbooks/install_scripts/files/scripts/tests/test_djangoapp.py | Python | gpl-3.0 | 50,017 | [
"Biopython"
] | 58c2574608003bf5e0fdf0717267e88fbb23f742d0b932506c5da60d7cfddcdd |
# Copyright 2017 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... | ppwwyyxx/tensorflow | tensorflow/python/data/experimental/kernel_tests/sql_dataset_test.py | Python | apache-2.0 | 22,756 | [
"MOE"
] | b7412cc34c82fc5b4dd650f9ca8c38924d749b1a4007f878468f0b3e9eb7a0e9 |
from generators.symmetricpoints import SymmetricPointsGenerator
from core.settings import Settings
from core.datacontainer import DataContainer
from bio.brainregion import BrainRegion
from bio.neuron import Neuron
from bio.neuralconnection import NeuralConnection
from vis.visneuralconnection import VisNeuralConnection
... | zibneuro/brainvispy | bio/brain.py | Python | bsd-3-clause | 7,603 | [
"NEURON"
] | 2b41e1052e2fa4424ddb7db0fc3d11772dadd07d94420a8055dea57088dfcd1b |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to
# submit large numbers of jobs on supercomputers. It provides a python interface to physical input,
# ... | pylada/pylada-light | tests/espresso/test_extract.py | Python | gpl-3.0 | 5,368 | [
"CRYSTAL",
"ESPResSo",
"VASP"
] | a364457455b4a0fdc29fd1f58e3164115690993d59946fafe5ff2e8f54cfbbb3 |
# 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.
"""Provides an interface to start and stop Android emulator.
Emulator: The class provides the methods to launch/shutdown the emulator with
... | s20121035/rk3288_android5.1_repo | external/chromium_org/build/android/pylib/utils/emulator.py | Python | gpl-3.0 | 14,376 | [
"Galaxy"
] | 3996f9d71c7aaf6583f6096e001fc1a2f684832c301824152e18a1627692939a |
'''
Broken (piecewise continuous) random field generation using rft1d.randn1d
Note:
When FWHM gets large (2FWHM>nNodes), the data should be padded
using the *pad* keyword.
'''
import numpy as np
from matplotlib import pyplot
from spm1d import rft1d
#(0) Set parameters:
np.random.seed(12345)
nResponses = 5
nNode... | 0todd0000/spm1d | spm1d/rft1d/examples/random_fields_broken_1.py | Python | gpl-3.0 | 873 | [
"Gaussian"
] | 0001bec7f62b63f58d850d9b917b25af231a529047c555eefd1eb4e5212570a3 |
# -*- coding: utf-8 -*-
import os
import unittest
from StringIO import StringIO
from antlr3.tree import CommonTreeAdaptor, CommonTree, INVALID_TOKEN_TYPE
from antlr3.treewizard import TreeWizard, computeTokenTypes, \
TreePatternLexer, EOF, ID, BEGIN, END, PERCENT, COLON, DOT, ARG, \
TreePatternParser, \
... | arruda/ANTLR3-python | unittests/testtreewizard.py | Python | bsd-3-clause | 20,910 | [
"VisIt"
] | 301e7c1c35b9feccd38fb8910fe1bffacd008f77f6e1b304b1fe81e98e8fd6bb |
# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. 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.
import os
import unittest
from Bio.PopGen import SimCoal
from Bio.PopGen.... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_PopGen_SimCoal.py | Python | gpl-2.0 | 2,075 | [
"Biopython"
] | 1e15c36950ce82d3c70db3bd808d4f87fe280cde4a26a20570e11e4e2be46145 |
import urllib
from galaxy import exceptions
from galaxy import web, util
from galaxy.web import _future_expose_api_anonymous
from galaxy.web.base.controller import BaseAPIController
from galaxy.web.base.controller import UsesVisualizationMixin
from galaxy.web.base.controller import UsesHistoryMixin
from galaxy.visuali... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/api/tools.py | Python | gpl-3.0 | 20,638 | [
"Galaxy"
] | 74c9ba5d63148eade9f2402e0510b65504b4262ea57a021ab2105847878aea3c |
# ashworth
# useful selection groups for protein-DNA interfaces
from pymol import cmd,util
# shortcut command for pymol's "color by chains (e. c)"
def color_by_chains():
for obj in cmd.get_names('objects'):
util.color_chains('%s and e. c' %obj)
cmd.extend('cbce',color_by_chains)
#class DNA_selections:
# def __ini... | weitzner/Dotfiles | pymol_scripts/DNAselections.py | Python | mit | 1,773 | [
"PyMOL"
] | e022debc616bafce9669b2844d1ea8f108cd344bb6961e42813fa161e14af551 |
import param
import topo.pattern.basic
import topo.pattern.random
import __main__
import os
import contrib
import topo
from topo.transferfn.misc import PatternCombine
from topo.transferfn.misc import HalfRectify
from topo import numbergen
from topo.pattern.basic import Gaussian
from topo.numbergen import UniformRandom... | jesuscript/topo-mpi | contrib/JanA/surrounnd_model_design.py | Python | bsd-3-clause | 15,847 | [
"Gaussian"
] | 31a6d7861c8f300d01d0f7aa2c1f6fc961b1fabe4904d3a31d0e2b3feb95ca25 |
# coding=utf-8
"""
Tests for the course home page.
"""
from __future__ import absolute_import
from datetime import datetime, timedelta
import ddt
import mock
import six
from django.conf import settings
from django.http import QueryDict
from django.urls import reverse
from django.utils.http import urlquote_plus
from d... | jolyonb/edx-platform | openedx/features/course_experience/tests/views/test_course_home.py | Python | agpl-3.0 | 46,167 | [
"VisIt"
] | 81b58892b3b7ec6891779a3c0fee4dbcf80e79c79b17f305777c33610bbdf4f7 |
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