text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
"""
Interval datatypes
"""
import pkg_resources
pkg_resources.require( "bx-python" )
import logging, os, sys, time, tempfile, shutil
import data
from galaxy import util
from galaxy.datatypes.sniff import *
from galaxy.web import url_for
from cgi import escape
import urllib
from bx.intervals.io import *
from galaxy.da... | volpino/Yeps-EURAC | lib/galaxy/datatypes/interval.py | Python | mit | 49,885 | [
"Galaxy"
] | 8876f9419789060c98d0de90d8ffbfcab061981644c8b0464921d65a881744f7 |
"""
An updated CRYSTAL logs parser
wrapping a standalone parser called pycrystal
Authors: Evgeny Blokhin and Andrey Sobolev
"""
import os.path
from pycrystal import CRYSTOUT as _CRYSTOUT, CRYSTOUT_Error
from tilde.parsers import Output
class CRYSTOUT(Output):
def __init__(self, filename):
Output.__init__... | tilde-lab/tilde | tilde/parsers/CRYSTAL/CRYSTAL.py | Python | mit | 2,021 | [
"CRYSTAL"
] | 7bbe20ecd42ed751fdcf064b7d08fdd4fc92cedbf04a6df7afacf5488b4c646e |
#! /usr/bin/env python
import json, urllib2, re
from urllib2 import Request, urlopen, URLError
from datetime import datetime, timedelta
def removeNonAscii(s):
s = s.replace("&", "and")
return "".join([x if ord(x) < 128 else '_' for x in s])
req = Request('http://api.tvmaze.com/schedule')
try:
print 'Visi... | heyted/tvmaze2xml | tvmaze2xml.py | Python | gpl-2.0 | 2,255 | [
"VisIt"
] | 8fb961a82830a7d60b4f8ba4e0ecc5d718886fb52fdb6012ef6fcfef4b68b2af |
'''
MFEM example 20
See c++ version in the MFEM library for more detail
'''
import os
import mfem.ser as mfem
from mfem.ser import intArray
from os.path import expanduser, join, dirname
import numpy as np
from numpy import sin, cos, exp, sqrt
m_ = 1.0
k_ = 1.0
def run(order=1,
prob=0,
nste... | mfem/PyMFEM | examples/ex20.py | Python | bsd-3-clause | 6,639 | [
"Gaussian"
] | 4a830bf12b62aa71e5793adf7061f23d1c02dd685044c2bbf2882e17b53c9c2d |
import glob
import os
from time import sleep
import hashlib
from subprocess import call
path_to_ase = "path\\to\\aseprite.exe"
def main():
while True:
for filename in glob.glob("*.ase"):
# Try to find an existing instance for that file
file = AseFile.find_file(filename)
... | scambier/aseprite-autoexport | converter.py | Python | mit | 1,450 | [
"ASE"
] | 9803c33bc98ce2282d32e95d1c846f62ab9e1abfb1ebe6b9100e4063d44cab46 |
import glob
from setuptools import setup, find_packages
setup(
name='seroba',
version='1.0.2',
description='SEROBA: Serotyping for illumina reads',
packages = find_packages(),
author='Lennard Epping',
author_email='path-help@sanger.ac.uk',
url='https://github.com/sanger-pathogens/seroba',
... | sanger-pathogens/seroba | setup.py | Python | gpl-3.0 | 868 | [
"Biopython"
] | 4962afab145f1d9939c9639c45d3234b33bb380bd26ccfff0212ff8f45f75f28 |
# ----------------------------------------------------------------------------
# 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/stats/tests/test_misc.py | Python | bsd-3-clause | 1,791 | [
"scikit-bio"
] | 5f0f7573e5d0e0998ea2344dc3ce5993a6a93c0b0a775faea9c691182c21841d |
#!/usr/local/bin/python3
#
# archlinux.py
from chrubix.distros import Distro
from chrubix.utils import system_or_die, chroot_this, wget, logme, do_a_sed, \
call_makepkg_or_die, abort_if_make_is_segfaulting
import os
class ArchlinuxDistro( Distro ):
def __init__( self , *args, **kwargs ... | ReubenAbrams/Chrubix | src/chrubix/distros/archlinux.py | Python | gpl-3.0 | 15,622 | [
"MOOSE"
] | 29d80d2e15dfca001b9c28dc8ddd5487d548d578cb0c0387bcf951b41a0ea8e6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2010, 2011 Brian E. Granger
#
# This file is part of pyzmq.
#
# pyzmq is free software; you can redistribute it and/or modify it under
# the terms of the Lesser GNU General Public License as published by
# the Free Software Foundation; eithe... | svpcom/pyzmq-ctypes | zmq/tests/test_socket.py | Python | lgpl-3.0 | 3,625 | [
"Brian"
] | c8713cf3bc8e992efc224a192a535c2526d33a4b28d12c2c3a6fe86b2fda44bf |
# -*- coding: utf-8 -*-
"""
Utilities for smoothing the 0.5 level-set of binary arrays.
"""
import logging
from typing import Tuple
import numpy as np
from scipy import sparse
from scipy import ndimage as ndi
__all__ = [
'smooth',
'smooth_constrained',
'smooth_gaussian',
'signed_distance_function'
]... | pmneila/PyMCubes | mcubes/smoothing.py | Python | bsd-3-clause | 9,699 | [
"Gaussian"
] | 6cdbbbe3253b3c85f85a2b8048b2f5950248b48598d6cee9240f9de73b1632e5 |
# -*- coding: utf-8 -*-
#
# futures documentation build configuration file, created by
# sphinx-quickstart on Wed Jun 3 19:35:34 2009.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All... | santegoeds/pythonfutures | docs/conf.py | Python | bsd-2-clause | 6,302 | [
"Brian"
] | e194cf57e674a44a0586ba1e958da1e5b70c7b1f26b8b1d36015cf852dd212d8 |
from pylab import plot,grid,title,subplot,xlabel,ylabel,text,subplots_adjust,fill_between,mean,connect,show
from shogun.Kernel import GaussianKernel
from shogun.Classifier import LibSVM, LDA
from shogun.Evaluation import ROCEvaluation
import util
util.set_title('ROC example')
util.DISTANCE=0.5
subplots_adjust(hspace=0... | ratschlab/ASP | examples/undocumented/python_modular/graphical/roc.py | Python | gpl-2.0 | 1,515 | [
"Gaussian"
] | 9a0d5b3512a3b586dbcc78f0b11b15de594498a675f310e64257107b67a324f6 |
"""
DataFrame
---------
An efficient 2D container for potentially mixed-type time series or other
labeled data series.
Similar to its R counterpart, data.frame, except providing automatic data
alignment and a host of useful data manipulation methods having to do with the
labeling information
"""
from __future__ import... | jreback/pandas | pandas/core/frame.py | Python | bsd-3-clause | 329,625 | [
"Elk"
] | b4dcc302d1221ea7a38194c21e20605df297d62a4e9b9e835d591084866b509d |
# 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... | junghans/espressopp | src/esutil/GammaVariate.py | Python | gpl-3.0 | 1,699 | [
"ESPResSo"
] | ccddc97412530b126e7cb2909c2f5afa1bd53168cd22dae1effff91fe912058f |
# -*- coding: utf-8 -*-
#
# This file is part of EventGhost.
# Copyright © 2005-2019 EventGhost Project <http://www.eventghost.org/>
#
# EventGhost 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 versio... | topic2k/EventGhost | eg/Classes/CheckUpdate.py | Python | gpl-2.0 | 5,663 | [
"VisIt"
] | 36e8a38eaae20d99f153202a8755970b7207558c5aa00219b8d023dbd9552fcd |
from pathlib import Path
import xarray
from typing import Union, Tuple, Dict, Sequence
from typing.io import TextIO
from datetime import datetime, timedelta
import logging
from .rio import rinexinfo
from .obs2 import rinexobs2
from .obs3 import rinexobs3
from .nav2 import rinexnav2
from .nav3 import rinexnav3
from .sp... | scienceopen/pyrinex | src/georinex/base.py | Python | mit | 7,443 | [
"NetCDF"
] | 878e070904036c8b8a0382a95a908f7fe5ded9158afef4169cdf9a8f639b35bc |
from neuron import h
h.nrn_load_dll("E:\\Google Drive\\Github\\Spinal-Cord-Modeling\\nrnmech.dll")
import helper_functions as hf
from Ia_template import Ia
from Mn_template import Mn
class Ia_network:
def __init__(self, N = 2, syn_w = 0.15, syn_delay = 1):
self._N = N;
self.cells = [] ... | penguinscontrol/Spinal-Cord-Modeling | Python/Ia_network.py | Python | gpl-2.0 | 2,666 | [
"NEURON"
] | d839eac962f06b714573fae5a220a125a105c8eabb4285c9b88d6fa04088073e |
# encoding: utf-8
'''
Created on Nov 26, 2015
@author: tal
Based in part on:
Learn math - https://github.com/fchollet/keras/blob/master/examples/addition_rnn.py
See https://medium.com/@majortal/deep-spelling-9ffef96a24f6#.2c9pu8nlm
'''
from __future__ import print_function, division, unicode_literals
import os
imp... | MajorTal/DeepSpell | keras_spell.py | Python | mit | 24,924 | [
"Gaussian"
] | f46d65c5fdbb66c1e9f12d910226c413498dd23abd89b7ac8de8f5e659ec9383 |
#!/usr/bin/env python
import sys
import os
import PyQt4
import vtk
from vtk.test import Testing
class TestvtkQtTableView(Testing.vtkTest):
def testvtkQtTableView(self):
sphereSource = vtk.vtkSphereSource()
tableConverter = vtk.vtkDataObjectToTable()
tableConverter.SetInput(sphereSource.GetOutput())
... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/GUISupport/Qt/Testing/Python/TestvtkQtTableView.py | Python | gpl-3.0 | 817 | [
"VTK"
] | 95aa2081b2fec025fa0622583dfca1f8da171106f156fdcafcc8665017e7868c |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
# Denis A. Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
from copy import deepcopy
from distutils.version import LooseVersion
import itertools as itt
from math import log
import ... | rkmaddox/mne-python | mne/cov.py | Python | bsd-3-clause | 79,191 | [
"Gaussian"
] | 52cf8276a909f1c49c5902078aa4493a49aaa9bb9f0febe2843519cbea6060bf |
#!/usr/bin/env python
#JSON {"lot": "UKS/6-31G*",
#JSON "scf": "CDIISSCFSolver",
#JSON "linalg": "CholeskyLinalgFactory",
#JSON "difficulty": 6,
#JSON "description": "UKS DFT example with LDA and numerical Hartree"}
from horton import *
# Load the coordinates from file.
# Use the XYZ file from HORTON's test data ... | eustislab/horton | data/examples/hf_dft/uks_methyl_numlda.py | Python | gpl-3.0 | 2,789 | [
"Gaussian"
] | bf1cbd905c42925b394999f2df72085af94c68996d679febecde124088c09426 |
from django.shortcuts import render_to_response, redirect
from django.template import RequestContext
from django.template.loader import render_to_string
from django.core.mail import send_mail, mail_managers, EmailMessage
from django.contrib.auth.decorators import login_required
from django.contrib import messages
from ... | azavea/Open-Data-Catalog | OpenDataCatalog/contest/views.py | Python | mit | 5,512 | [
"VisIt"
] | a24d34326865a8c85ebbcc979b6756c834896e75ccea6570d3e60d0deb45df56 |
"""
Migration script to rename the sequencer information form type to external service information form
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
from sqlalchemy.exc import *
from galaxy.model.custom_types import *
import datetime
now = datetime.d... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py | Python | gpl-3.0 | 1,102 | [
"Galaxy"
] | 2761fe721d9f4756c74a6a9f81032751c4978531e176ab8757be50f2beef8d12 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from tweepy import Stream
from tweepy import OAuthHandler
from tweepy.streaming import StreamListener
from pprint import pprint
# Visit https://apps.twitter.com/ to obtain the data
#import credentials.py
import tweepy
import importlib.machinery
import sys
sys.path.insert(0, ... | davidam/python-examples | nlp/tweepy-example.py | Python | gpl-3.0 | 693 | [
"VisIt"
] | 461a0f0815b7045efa89d080d43a44228c3a3b348107e147a2e95f79184f30f4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
FIXME: Proper module docstring
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.co... | dongsenfo/pymatgen | pymatgen/entries/tests/test_entry_tools.py | Python | mit | 2,233 | [
"pymatgen"
] | 15cef8eb84ed387ac3e8d642ca0d5dd5c702206b4f66df179ba6af55854d3658 |
#
# Copyright (C) 2013-2019 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... | fweik/espresso | src/python/espressomd/checkpointing.py | Python | gpl-3.0 | 9,661 | [
"ESPResSo"
] | 112e4e6269c5c9cf0e608f411444cfa0ba2febdfcc54fcfb6f41c70ff2509fc9 |
#################################################################
# $HeadURL$
#################################################################
"""
Usage of ThreadPool
ThreadPool creates a pool of worker threads to process a queue of tasks
much like the producers/consumers paradigm. Users just need to fill the queue
w... | Andrew-McNab-UK/DIRAC | Core/Utilities/ThreadPool.py | Python | gpl-3.0 | 11,411 | [
"DIRAC"
] | 8d638e2cebd563fa11d99335992d21e8a5f915f3118be927fdba7b2b00cafc5b |
# -*- coding: utf-8 -*-
# Test scripts are always called from BUILD directory by cmake.
import os
import sys
import numpy as np
import time
import test_difshells as td
import chan_proto
import param_chan
import moose
print('Using moose from %s' % moose.__file__ )
difshell_no = 3
difbuf_no = 0
script_dir_ = os.path.... | dilawar/moose-core | tests/core/test_hsolve_externalCalcium.py | Python | gpl-3.0 | 2,762 | [
"MOOSE",
"NEURON"
] | 3812899b0f5ae3b223ac6fffa368664c9d45198323e2451b432bacf358ae5a5b |
import functools
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import DictCache
from inspect import getcallargs
from DIRAC.Core.DISET.RPCClient import RPCClient
__remoteMethods__ = []
def RemoteMethod( method ):
__remoteMethods__.append( method.__name__ )
@functools.wraps( method )
def w... | DIRACGrid/RESTDIRAC | RESTSystem/Client/OAToken.py | Python | gpl-3.0 | 6,296 | [
"DIRAC"
] | 35d0f55eabb70c2bf92b75e4cec4f2d5ae93b3e48f26c72f22711ef0956ec933 |
# license-expression is a free software tool from nexB Inc. and others.
# Visit https://github.com/nexB/license-expression for support and download.
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and http://aboutcode.org
#
# This software is licensed under the Apache License versio... | all3fox/license-expression | tests/test_license_expression.py | Python | apache-2.0 | 65,726 | [
"VisIt"
] | 6b2f58527a7c4c8665f6f59ec90adc2720ebc9a88d2a94e7604c093941422507 |
#!/usr/bin/env python
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your op... | chouseknecht/galaxy | setup.py | Python | apache-2.0 | 3,620 | [
"Galaxy"
] | 43419e4b4e8486a615c8a72f7e1f8809cf62b924e010b8df7df20b89b453d626 |
# Copyright 2016 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... | npuichigo/ttsflow | third_party/tensorflow/tensorflow/python/ops/distributions/special_math.py | Python | apache-2.0 | 14,747 | [
"Gaussian"
] | 331c8a913a0ebe85b7a7db4768352b24b3383f6438936645599ebc5948d89fd6 |
#!/usr/bin/env python
#
# Copyright 2013 Tristan Bereau and Christian Kramer
#
# 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
#
# U... | MMunibas/FittingWizard | scripts/draw_pics.py | Python | bsd-3-clause | 8,080 | [
"Gaussian"
] | c0fbbff279283a90d008d0805aceeeaab0783dca78447cf01342f29779ecdbec |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Jason Swails
# Contributors:
#
# This code for reading Amber r... | msultan/mdtraj | mdtraj/formats/amberrst.py | Python | lgpl-2.1 | 33,271 | [
"Amber",
"MDTraj",
"NetCDF"
] | bc4d93d27f3ebab7543e790fb27a72c3d11e4bab0a2857bfe00361e9cef06a2d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import ast
import inspect
from grafo import Grafo
def foo(a): # função a ser testada
b = 2 + a
if (b > 2):
print a
print b
if (a > b):
print 3
if(a == 4):
print "asd"
else:
print a
... | hugo-tavares/python-cfg | ast_walker.py | Python | gpl-3.0 | 1,991 | [
"VisIt"
] | 6fdcfc32239a9684f95d569787249fa9c919f6fe43ef39db1ddec1fbf310b86f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2014 Liang Wang <liang.wang@cs.helsinki.fi>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
#
# Liang Wang @ CS Dept, Helsinki Univ, Finland
# 2014.05.01
#
import logging
import numpy
import tempfile
from scipy import linalg
fr... | beni55/panns | panns/utils.py | Python | gpl-2.0 | 5,074 | [
"Gaussian"
] | 5ce2357d5c71f8a37c872285bda24875c52a368033b9436a4bc877bbd5c91976 |
import os
import warnings
import numpy as np
from ..core import indexing
from ..core.dataarray import DataArray
from ..core.utils import is_scalar
from .common import BackendArray
from .file_manager import CachingFileManager
from .locks import SerializableLock
# TODO: should this be GDAL_LOCK instead?
RASTERIO_LOCK ... | pydata/xarray | xarray/backends/rasterio_.py | Python | apache-2.0 | 15,484 | [
"NetCDF"
] | c9332eb9787854ab132f0f08764011adcfde2de0db81c181b9d5b0465b2caa7f |
import numpy as np
from ase import Atom, Atoms
from ase.units import Hartree
from gpaw.mpi import size
from gpaw import GPAW
from gpaw.response.bse import BSE
GS = 1
bse = 1
casida = 1
compare = 1
if GS:
d = 2.89
cluster = Atoms([Atom('Na', (0, 0, 0)),
Atom('Na', (0, 0, d)),
... | robwarm/gpaw-symm | gpaw/test/bse_vs_lrtddft.py | Python | gpl-3.0 | 1,536 | [
"ASE",
"GPAW"
] | d6401351e702652f2bcb77e73a64ac9924172a03662990727acbfa28aa3fdd33 |
"""Implementation of the WebSocket protocol.
`WebSockets <http://dev.w3.org/html5/websockets/>`_ allow for bidirectional
communication between the browser and server.
WebSockets are supported in the current versions of all major browsers,
although older versions that do not support WebSockets are still in use
(refer ... | allenl203/tornado | tornado/websocket.py | Python | apache-2.0 | 61,445 | [
"VisIt"
] | 8620f036fc9ec4eb584b2a6f170f323db8ea4b2421324690d008891f33a249b6 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# !! This is the configuration of Nikola. !!#
# !! You should edit it to your liking. !!#
# ! Some settings can be different in different languages.
# ! A comment stating (translatable) is used to denote those.
# ! There are two ways to s... | s2hc-johan/nikola | tests/data/translated_titles/conf.py | Python | mit | 27,281 | [
"VisIt"
] | d3dad1cc443c4522cd1d0e2e894f4a4918dbe2b23e037a9aa8ad402bb0339a72 |
#!/usr/bin/env python
# encoding: utf-8
"""
Get HDF5 patch results on VOSpace and combine them into a single HDF5 file.
Run as fetch_patch_results.py phat_field_starfish.hdf5 --vodir phat/fields
2015-06-16 - Created by Jonathan Sick
"""
import os
import argparse
import vos
import h5py
import numpy as np
from astro... | jonathansick/androcmd | scripts/fetch_patch_results.py | Python | mit | 6,784 | [
"Galaxy"
] | 40df406b16e6a73f6e8ba5e1faf3bc6d74769a8ba5f3b8d1518d63f7d1eb571a |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | alejob/mdanalysis | package/MDAnalysis/lib/NeighborSearch.py | Python | gpl-2.0 | 4,172 | [
"Biopython",
"MDAnalysis"
] | 0c1faac07b226cb656afb1d836fe4f223f1a21ee47878b2be5ff3afee887b2f8 |
'''
*** SHED SKIN Python-to-C++ Compiler ***
Copyright 2005-2013 Mark Dufour; License GNU GPL version 3 (See LICENSE)
cpp.py: output C++ code
output equivalent C++ code, using templates and virtuals to support data and OO polymorphism.
class GenerateVisitor: inherits visitor pattern from compiler.visitor.ASTVisitor,... | shedskin/shedskin | shedskin/cpp.py | Python | gpl-3.0 | 114,119 | [
"VisIt"
] | fdddbea94458e2f9c10171e699a996c1ca22bef8f2a5d692c222ef21a8aae21e |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/songusage/forms/songusagedetaildialog.py | Python | gpl-2.0 | 5,627 | [
"Brian"
] | 403623af4c5de9f336d653ef45d691ab257d4bd8f12c23f649c0d46de7bd791f |
"""
Robust location and covariance estimators.
Here are implemented estimators that are resistant to outliers.
"""
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import warnings
import numbers
import numpy as np
from scipy import linalg
from scipy.stats import chi2
from . import empir... | BiaDarkia/scikit-learn | sklearn/covariance/robust_covariance.py | Python | bsd-3-clause | 31,108 | [
"Gaussian"
] | 124a451691f249fca0b762bb6d986617d40d6a9e2209b2a9a19ab1bf19ce7395 |
# Line too long - pylint: disable=C0301
# Copyright (c) Greenplum Inc 2011. All Rights Reserved.
from contextlib import closing
import os
import platform
import shutil
import sys
import tarfile
try:
from gppylib import gplog
from gppylib.commands import gp
from gppylib.commands.base import Command, REMOTE... | lintzc/gpdb | gpMgmt/bin/gppylib/operations/package.py | Python | apache-2.0 | 53,482 | [
"ORCA"
] | a66bbcdbce75c7dcc38000e376de29b45d08286c5f95c8a903b4791b52b558d0 |
# Models implement the base Local Inspector Value-Entry Specification (LIVES)
# v1.0 - http://www.yelp.com/healthscores
from django.contrib.gis.db import models
from django.utils.translation import ugettext_lazy
class Establishment(models.Model):
"""Business or restaurant property"""
STATUS_CHOICES = (('dele... | codefordurham/Durham-Restaurants | inspections/models.py | Python | bsd-3-clause | 8,811 | [
"VisIt"
] | c2dcb0f3bcb652a32ad4c4c2ffbd413bc204350e6c0c1bcea88bdf69fe93047f |
__author__ = 'tonycastronova'
import unittest
from models.ueb import ueb
from utilities.gui import parse_config
import wrappers
from coordinator.engine import Coordinator
import time
from transform import space
class testUEB(unittest.TestCase):
def setup(self):
pass
def test_run(self):
#... | Castronova/EMIT | models/ueb/test/test_ueb.py | Python | gpl-2.0 | 2,649 | [
"NetCDF"
] | 64407e3fe03ca0b4fb8c6bee76bc1577209e87ddd41116905aae9f5176448f31 |
"""
The B{0install} command-line interface.
"""
# Copyright (C) 2011, 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 optparse import OptionParser
import logging
from zeroinstall import SafeEx... | linuxmidhun/0install | zeroinstall/cmd/__init__.py | Python | lgpl-2.1 | 4,696 | [
"VisIt"
] | 6d77aa0836ca0a9e7361a8c4a4b105a8d50fa6b04ce9da2481b86da36b62a5ec |
#
# Copyright (C) 2013,2014,2015,2016 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)... | tbereau/espresso | samples/python/p3m.py | Python | gpl-3.0 | 6,612 | [
"ESPResSo"
] | 7aaa1e3affa5d283d5d715a908d23d97bbfca4f25b59fa24618fd5ce25e7f89c |
import re
positive_words = set([
"addicting", "addictingly", "admirable", "admirably", "admire", "admires", "admiring", "adorable",
"adorably", "adore", "adored", "adoring", "amaze", "amazed", "amazes", "amazing",
"angelic", "appeal", "appealed", "appealing", "appealingly", "appeals", "attentive", "attracted",
"att... | mortardata/mortar-examples | udfs/jython/twitter_sentiment.py | Python | apache-2.0 | 11,076 | [
"exciting"
] | 15ef53d41c12faf022cf83311ff7cf3e69cdd6b622f8c88c92dbccae27d497a4 |
#!/usr/bin/python
# BayesMRInumpy.py: Calculate the Bayes Factor associated with a given group-level fMRI t-stat map
# This version makes use of the NumPy and NiBabel packages to perform image calculations without FSL
# Written by Tom Johnstone (2016) itjohnstone@gmail.com
# Based on code provided by Zoltan_Dienes (ht... | TomEmotion/BayesMRI | BayesMRI_numpy.py | Python | gpl-3.0 | 9,348 | [
"Gaussian"
] | 2439aaddcb8f574670d2bf6d87d5afdbd11f6c8d78a9d0f3aefd0af554fb22d7 |
#!/usr/bin/env python
# ***** BEGIN LICENSE BLOCK *****
# Version: MPL 1.1/GPL 2.0/LGPL 2.1
#
# The contents of this file are subject to the Mozilla Public License
# Version 1.1 (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.mozil... | archifix/settings | sublime/Packages/SublimeCodeIntel/libs/textinfo.py | Python | mit | 88,877 | [
"VisIt"
] | e35f466bd338e6936e8aead5f3782e7a3a07c07e81bace0fa728f6ca97a36188 |
# coding: utf-8
"""Test mdn.kumascript."""
from __future__ import unicode_literals
from django.utils.six import text_type
from mdn.html import HTMLText
from mdn.kumascript import (
Bug, CSSBox, CSSxRef, CompatAndroid, CompatChrome, CompatGeckoDesktop,
CompatGeckoFxOS, CompatGeckoMobile, CompatIE, CompatNightl... | mdn/browsercompat | mdn/tests/test_kumascript.py | Python | mpl-2.0 | 39,220 | [
"VisIt"
] | ee2d782e5fcce79bb452ff7c167834f904ab1dbe21fc35489448e729c8d58247 |
print("How old are you?", end=' ')
age = input()
print("How tall are you?", end=' ')
height = input()
print("How much do you weigh?", end=' ')
weight = input()
print(f"So, you're {age} old, {height} tall and {weight} heavy.")
name = input("What's your surname? ")
print(f"""Nice to meet you Mr. {name}, we've been expe... | jpilorget/lpthw | ex11.py | Python | gpl-3.0 | 549 | [
"VisIt"
] | 6187a55151a359401013f0d69d85deaf4d84431fc4215e06ed25018c2d115a2f |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/magic/sources/galaxyfinder.py | Python | mit | 24,200 | [
"Galaxy"
] | 980691a7bdfb9ac12faacbeb24fc10b783471996b6d5c1ddc55d748bcfb8ab93 |
# -*- coding: utf-8 -*-
#
# pulsepacket.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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, or... | QJonny/CyNest | pynest/examples/pulsepacket.py | Python | gpl-2.0 | 5,355 | [
"Gaussian",
"NEURON"
] | 3b64956c86b47996a57b0a07b6c4a1fb90570432e0959cab418c39f482c91494 |
## \file
## \ingroup tutorial_roofit
## \notebook -nodraw
## Organization and simultaneous fits: creating and writing a workspace
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
import ROOT
# Create model and dataset
# ---------------------------------------------... | root-mirror/root | tutorials/roofit/rf502_wspacewrite.py | Python | lgpl-2.1 | 2,078 | [
"Gaussian"
] | 9168faf5d5b1af774b2c806056f1cbbd2a0f21ab4f41c0dcc76d0c461373bbfe |
# The MIT License (MIT)
# Copyright (c) 2016, 2017 by the ESA CCI Toolbox development team and contributors
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including wi... | CCI-Tools/cate-core | cate/ops/outliers.py | Python | mit | 7,222 | [
"NetCDF"
] | 936a104a34785f504481362069c674d7d1182b48592f3f42d58e55b387738a01 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | fullprogramaciondev/portal | config/urls.py | Python | bsd-3-clause | 1,324 | [
"VisIt"
] | 04d6f7890a7d2a0a49805480741a470b964cb3b9b2ee7673b24f54faa6f2872c |
# Copyright 2020 The TensorFlow Probability 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 o... | tensorflow/probability | tensorflow_probability/python/experimental/mcmc/preconditioned_hmc_test.py | Python | apache-2.0 | 35,324 | [
"Gaussian"
] | 55881753f3ba21f812c518782abfe9ee4bbebb157510907a1f8dee98f1ff2f0b |
import numpy as np
import matplotlib as mpl
import matplotlib.pylab as plt
def sigma_from_waist(w):
return w/np.sqrt(2)
class Params:
'''
gt_scale_factor : "Greater than" scale factor
w0 : Gaussian Beam waist
'''
def __init__(self,w,l_scale_factor,eps_scale_factor):
## P... | deot95/Tesis | Monografía Física/Workspace/Code/Python/adz.py | Python | mit | 1,843 | [
"Gaussian"
] | 2582523733e93b35cbf34d92e818071e55b7d202feead79eeb693df5c18f23b1 |
#!/usr/bin/env python
# (C) Copyright IBM Corporation 2004, 2005
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# ... | execunix/vinos | xsrc/external/mit/MesaLib/dist/src/mapi/glapi/gen/gl_x86_asm.py | Python | apache-2.0 | 9,401 | [
"Brian"
] | f359cfcd462f9e7a9abec490d4db32a8980fba4cf72ff6677bbd08c6889ff3f5 |
#!/usr/bin/python
"""
Pull RGID information (from CCCB NextSeq naming scheme) from FASTQ.
"""
import argparse
import gzip
__author__ = 'dkdeconti'
__copyright__ = "Copyright 2017"
__credits__ = ["Derrick DeConti"]
__license__ = "MIT"
__maintainer__ = "Derrick DeConti"
__email__ = "deconti@jimmy.harvard.edu"
__stat... | dkdeconti/HLA_epitope_prediction_from_WES | get_RGID_from_FASTQ.py | Python | mit | 1,730 | [
"BWA"
] | f9f76bc25bd5bd0dac06ba781111fb4fb2573c492557d3f0c3073c14a6c82ce0 |
from django.conf.urls import patterns, url
from django.contrib.auth.decorators import login_required
from django.views.decorators.csrf import ensure_csrf_cookie
from django.views.generic import TemplateView
# For adding explicit grouping resource endpoints in API documentation.
from rest_framework_swagger.urlparser im... | aschampion/CATMAID | django/applications/catmaid/urls.py | Python | gpl-3.0 | 24,476 | [
"NEURON"
] | 37d1b409b9d591dd4f92fc507b1db9ca5535aa92cc2a3ab12b5944bb7a49b54a |
# coding: utf-8
#############################
#### Various experiments ####
#############################
import numpy as np
import pickle
import time
from os import listdir
from learning import build_translation, extract_name, extract_features
from skimage.io import imread
from sklearn.multiclass import OneVsRestCl... | rmonat/princess-or-frog | src/exps.py | Python | gpl-3.0 | 3,123 | [
"Gaussian"
] | 8a176d0b09b1300d4483e4e17cb37896d5f3b53185b9bf450c5830735d0bd57e |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011 CERN.
##
## Invenio 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, or (at your opt... | kaplun/Invenio-OpenAIRE | modules/bibedit/lib/refextract_tests.py | Python | gpl-2.0 | 29,629 | [
"DIRAC"
] | 2aaaa3c9d70b503d2edb9fa9b826183df03f756e4ac818c881fe0b5621601663 |
#!/usr/bin/env python
#
# $File: backwardMigrate.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistr... | BoPeng/simuPOP | docs/backwardMigrate.py | Python | gpl-2.0 | 2,439 | [
"VisIt"
] | 2e3d71f0946aeb9f3cccfe6c20f059c8271a65f64247b05759e1b494e72260be |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.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 version 3 of the License, or
# (at your option) an... | HuaweiSwitch/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 30,728 | [
"Galaxy",
"MOOSE"
] | cd8f5e11a47df981f9831d65c296ad83ce06e2b151b682c0d993b80b6caf1ba8 |
# -----------------------------------------------------------------------------
# Download data:
# - Browser:
# http://midas3.kitware.com/midas/folder/10409 => VisibleMale/vm_head_frozenct.mha
# - Terminal
# curl "http://midas3.kitware.com/midas/download?folders=&items=235235" -o vm_head_frozenct.mha
# ----... | Kitware/arctic-viewer | scripts/examples/vtk/medical/head-ct-volume.py | Python | bsd-3-clause | 3,622 | [
"VTK"
] | b13581c5f1bfa2a5ee64bff47a1c81906bb7cd0115aa1603dc25fcce5e0dcbf3 |
# The code is rewritten based on source code from tensorflow tutorial for Recurrent Neural Network.
# https://www.tensorflow.org/versions/0.6.0/tutorials/recurrent/index.html
# You can get source code for the tutorial from
# https://github.com/tensorflow/tensorflow/blob/master/tensorflow/models/rnn/ptb/ptb_word_lm.py
#... | JSLBen/KnowledgeTracing | reference_py/student_model.py | Python | mit | 13,536 | [
"Gaussian"
] | 7a22f6619f87ed49636dec6d65de0b1bf422e5d7e31f297fd3cccdddf891d6f9 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* 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
... | nuclear-wizard/moose | python/chigger/tests/line_sample/line_sample_elem.py | Python | lgpl-2.1 | 1,166 | [
"MOOSE"
] | ed5efa658ab7d57981e22f9cafabf9ba42f65d77d2d99e6655eeae5da126a19a |
#!/usr/bin/env python
"""This is the setup.py file for the GRR client.
This is just a meta-package which pulls in the minimal requirements to create a
full grr server.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import unicode_literals
import itertools
import os
import s... | dunkhong/grr | grr/server/setup.py | Python | apache-2.0 | 7,769 | [
"GULP"
] | de368e7d4df4383106f1842132681a7131073458a5187f461ca5ee4c8abc5eb5 |
# calculate CO dimer
from ase import *
from hotbit import Hotbit
for SCC in [False,True]:
calc=Hotbit(SCC=SCC,width=0.05,txt='test.cal')
atoms=Atoms('CO',positions=[(0,0,0),(1.13,0,0)],cell=(10,10,10),pbc=False)
atoms.center(vacuum=10) #not necessary
atoms.set_calculator(calc)
print(atoms.get_pote... | pekkosk/hotbit | hotbit/doc/examples/CO.py | Python | gpl-2.0 | 336 | [
"ASE"
] | 647305caddf234d2bc4e08a3e6d197f187e899b9bbf4e7df11071c02bdd74879 |
"""
ALFAFA "source" .sav file
"""
import idlsave
try:
import astropy.io.fits as pyfits
except ImportError:
import pyfits
import pyspeckit
import numpy as np
def read_alfalfa_file(filename):
"""
Read the contents of a whole ALFALFA source file
"""
savfile = idlsave.read(filename)
source_dic... | bsipocz/pyspeckit | pyspeckit/spectrum/readers/alfalfa.py | Python | mit | 2,331 | [
"Gaussian"
] | ce81ff803a09435b0b1f9f9c205a7169c9fa4c270d28a99ea006f2eaf45368a1 |
# -*- coding:utf-8; mode:python -*-
"""
Each time Sunny and Johnny take a trip to the Ice Cream Parlor, they pool together dollars for ice cream. On any given day, the parlor offers a line of flavors. Each flavor, , is numbered sequentially with a unique ID number from to and has a cost, , associated with it.
Given th... | wkmanire/StructuresAndAlgorithms | pythonpractice/hackerrank/icecreamparlor.py | Python | gpl-3.0 | 5,208 | [
"VisIt"
] | 252d45072953f962ba2b275dbc8bead13a6b77a940e30e342215c9006249ff8b |
#!/usr/bin/python
"""Test of column header output."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
sequence.append(KeyComboAction("End"))
sequence.append(KeyComboAction("<Shift>Right"))
sequence.append(KeyComboAction("Down"))
sequence.append(KeyComboAction("Down"))
sequence.append(KeyComb... | pvagner/orca | test/keystrokes/gtk3-demo/role_column_header.py | Python | lgpl-2.1 | 4,640 | [
"ORCA"
] | e02f2246ae026622142ce033d0e781631bd72ea16cf716675729b65c4e51b0ca |
# -*- coding: utf-8 -*-
"""
This file is part of pyCMBS.
(c) 2012- Alexander Loew
For COPYING and LICENSE details, please refer to the LICENSE file
"""
from cdo import Cdo
from pycmbs.data import Data
import tempfile as tempfile
import copy
import glob
import os
import sys
import numpy as np
from pycmbs.benchmarking ... | pygeo/pycmbs | pycmbs/benchmarking/models/mpi_esm.py | Python | mit | 41,720 | [
"NetCDF"
] | b4b2489ef2ae5f1756aa475d6e9f1c9c9f4b634a58ea1b7fb1d287dcfd89eba3 |
"""Traits-based GUI for head-MRI coregistration"""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
from ..externals.six.moves import queue
import re
from threading import Thread
import warnings
import numpy as np
from scipy.spatial.distance import cdist
# allow import... | cmoutard/mne-python | mne/gui/_coreg_gui.py | Python | bsd-3-clause | 53,969 | [
"Mayavi"
] | d959f1e6603fe24c25fffd01610ae4f3d845f4c5c930ec60b6d7f11ffcf262fa |
from ase import Atoms
a = Atoms('H2', positions=[(0, 0, 0), (0, 0, 1.1)])
a.pbc[0] = 1
assert a.pbc.any()
assert not a.pbc.all()
a.pbc = 1
assert a.pbc.all()
a.cell = (1, 2, 3)
a.cell *= 2
a.cell[0, 0] = 3
assert not (a.cell.diagonal() - (3, 4, 6)).any()
| grhawk/ASE | tools/ase/test/properties.py | Python | gpl-2.0 | 257 | [
"ASE"
] | 57c93f1b712ece72971761e5123382df76b53c48b7a7f204e3f67b6141381d36 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Common test support for pymatgen test scripts.
This single module should provide all the common functionality for pymatgen
tests in a single location, so that test scripts can just import it and work
right... | gmatteo/pymatgen | pymatgen/util/testing.py | Python | mit | 7,709 | [
"pymatgen"
] | d7c35b26d923b75a8c37ea62ad16b90f6e3366bdf77f5c5846707cf4deb86067 |
""" Accounting class to stores network metrics gathered by perfSONARs.
Filled by "Accounting/Network" agent
"""
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseAccountingType
class Network(BaseAccountingType):
"""
Accounting type to stores network metrics gathered by perfSONARs.
... | DIRACGrid/DIRAC | src/DIRAC/AccountingSystem/Client/Types/Network.py | Python | gpl-3.0 | 1,178 | [
"DIRAC"
] | d0e8376f23123d2b4af09ce823b4c574edaf2f76d82b1fd834378d4f0527b467 |
from datetime import timedelta
from django import forms
from edc_constants.constants import YES, NO, UNKNOWN, OTHER, NOT_APPLICABLE
from .constants import ONGOING
from .models import Enrollment, EntryToCare
from ba_namotswe.models.subject_visit import SubjectVisit
from dateutil.relativedelta import relativedelta
comp... | botswana-harvard/ba-namotswe | ba_namotswe/validators.py | Python | gpl-3.0 | 9,291 | [
"VisIt"
] | 339cc26b47d169f59392bedef6757d90f95b4ad532753c96efd10b867a0ab5e7 |
#!/usr/bin/python2.7
import logging
import gzip
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
import pysam
from optparse import OptionParser
import os
import re
import sys
from progressbar import Bar, Timer, Percentage, ProgressBar
def main():
... | AlgoLab/PIntron-scripts | Preprocessing/splitBAM.py | Python | agpl-3.0 | 11,950 | [
"pysam"
] | b33114b46fd11f7fb149be55f4489c08037fdb9739982a88e17411f32a084d13 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013-2014 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 Lesser General Public License as published by
## the Free Softw... | andrebellafronte/stoq | stoqlib/gui/dialogs/inventorydetails.py | Python | gpl-2.0 | 5,391 | [
"VisIt"
] | 305dd3f9c7ba8ec4197f7debea0a8bc76d55476999a61dc503116d2751a4eac3 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/core/test_updating_atomgroup.py | Python | gpl-2.0 | 9,338 | [
"MDAnalysis"
] | 762b5b8e8b6464a8a24198ed3a2212cd2c2bc82a2a2231ff51bb6396af386301 |
import copy
import gc
import pickle
import sys
import unittest
import weakref
import inspect
from test import support
try:
import _testcapi
except ImportError:
_testcapi = None
# This tests to make sure that if a SIGINT arrives just before we send into a
# yield from chain, the KeyboardInterrupt is raised i... | kikocorreoso/brython | www/src/Lib/test/test_generators.py | Python | bsd-3-clause | 59,919 | [
"VisIt"
] | d5f77a99f8b22a81ea303e09ed69981b7ee0beb6fe896f7fea060429da7c63ce |
# Copyright(C) 2011-2019 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 ve... | psci2195/espresso-ffans | testsuite/python/ek_charged_plate.py | Python | gpl-3.0 | 6,187 | [
"ESPResSo"
] | 26a7e150b076d9407395fe71de297ccaef7aa9f876384a6f9aec42e3ef2226df |
from time import sleep
from lettuce import *
from rapidsms.contrib.locations.models import LocationType, Location
from survey.features.page_objects.household_member import NewHouseholdMemberPage, EditHouseholdMemberPage, DeleteHouseholdMemberPage
from survey.features.page_objects.households import HouseholdDetailsPage
... | unicefuganda/uSurvey | survey/features/household_member-steps.py | Python | bsd-3-clause | 4,202 | [
"VisIt"
] | 22cc1d0c1d8abd4bc51ed85914b6198234e292bc0f35acb235a54f4e0036ad96 |
from collections import OrderedDict
import re
import copy
import numpy as np
import pandas as pd
import xarray as xr
import matplotlib as mpl
import matplotlib.patches as mpatches
import matplotlib.pyplot as plt
from matplotlib.ticker import FuncFormatter
from matplotlib.colors import LinearSegmentedColormap
import ti... | ceos-seo/data_cube_utilities | data_cube_utilities/plotter_utils.py | Python | apache-2.0 | 125,683 | [
"Gaussian"
] | 5d1b528a6fb103174c5e092d3cfc4f0fa43d9dd69112dcb07511daa30cd67b8d |
##############################################################################
#
# Author: Alejandro Molina-Sanchez
# Run real-time simulations with yambo
#
# Warning: Real-time simulations requires several data folders for running
# properly. Before using this scripts compulsively is recommended
# to understand the d... | henriquemiranda/yambopy | tutorial/si/map-symm.py | Python | bsd-3-clause | 1,693 | [
"Yambo"
] | 63d6ce3c4489d416df53c99cea866b09e3cb801527da549aad6c1bc7b2a0e4d6 |
""" This is a test of the ProxyDB
It supposes that the DB is present and installed in DIRAC
"""
# pylint: disable=invalid-name,wrong-import-position,protected-access
import os
import re
import sys
import stat
import shutil
import tempfile
# TODO: This should be modernised to use subprocess(32)
import subprocess as... | DIRACGrid/DIRAC | tests/Integration/Framework/Test_ProxyDB.py | Python | gpl-3.0 | 29,670 | [
"DIRAC"
] | 14fc779ce5a525827fb6cd766a3d849d202447a889b35f229e046492977ed9e8 |
#
# @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/qcdb/molpro.py | Python | gpl-2.0 | 14,111 | [
"Psi4"
] | 0fdcf54512b2a4cfb6d78c2f12f223e9e2e698b22344b5e9a7898b10d612ecf6 |
#from ctx_base import StandardBaseContext
from .libmp.backend import basestring, exec_
from .libmp import (MPZ, MPZ_ZERO, MPZ_ONE, int_types, repr_dps,
round_floor, round_ceiling, dps_to_prec, round_nearest, prec_to_dps,
ComplexResult, to_pickable, from_pickable, normalize,
from_int, from_float, from_npfl... | FreeCAD/FreeCAD-AppImage | conda/modifications/ctx_mp_python.py | Python | lgpl-2.1 | 38,113 | [
"Gaussian"
] | bd42f2641281f966ba579e05d4a14a62ea4d4ccd93d4db6c34e3fa79106a90ad |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. 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
#
# U... | sunqm/pyscf | pyscf/x2c/sfx2c1e_hess.py | Python | apache-2.0 | 16,870 | [
"PySCF"
] | 7f440f158f3a5d1cca7b4e006aa1c14da53a995a313b6d87ead57d54bbff1a88 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.community.AvailabilityReportPerGroup | ZenPacks/community/AvailabilityReportPerGroup/reports/plugins/AvailabilityByGroup.py | Python | gpl-2.0 | 7,751 | [
"VisIt"
] | dcd412c0492b570d6079ff2e0c4d8cc421bdfdc822d6789670fe86202942298d |
# 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/standard_system/Default.py | Python | gpl-3.0 | 2,072 | [
"ESPResSo"
] | c823f3daba32e2993f4e0448305366b8e4d2aa491098953548032a408a82b4cd |
"""Reference implementation for building a nengo.Network."""
import collections
import logging
import numpy as np
import nengo.decoders
import nengo.neurons
import nengo.objects
import nengo.utils.distributions as dists
import nengo.utils.numpy as npext
from nengo.utils.compat import is_callable, is_integer
logger ... | ZeitgeberH/nengo | nengo/builder.py | Python | gpl-3.0 | 37,766 | [
"NEURON"
] | f4ed77863bad87a5012b40ba4e376956b2795ac7b4f276f7d359c81584ed23d6 |
'''
MMD functions implemented in tensorflow.
'''
from __future__ import division
import tensorflow as tf
from tf_ops import dot, sq_sum
_eps=1e-8
################################################################################
### Quadratic-time MMD with Gaussian RBF kernel
def _mix_rbf_kernel(X, Y, sigmas, wts=N... | dougalsutherland/opt-mmd | gan/mmd.py | Python | bsd-3-clause | 5,045 | [
"Gaussian"
] | ee87e14d544134bfbe45500a732cef6212007b5c89b9e0d94119521534970d39 |
#!/usr/bin/python
#collect_metrics_seqXTo2d.py
import sys
import re
import argparse
from argparse import RawTextHelpFormatter
import logging
import pprint
import yaml
import json
from collections import OrderedDict
import os
import numpy
#from Bio import SeqIO
import ast
pp = pprint.PrettyPrinter(indent=4, width=10)... | tiennes/misc-bio-stuff | scripts/collect_metrics_seqXTo2d.py | Python | gpl-3.0 | 18,986 | [
"HTSeq"
] | c88d157ff74b71834abcead611d89d9989e22403ed76f0ec0b5dcf69ddcf3e8b |
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