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#!/usr/bin/env python
#import math
#math.pi
import scipy
import scipy.constants as const
import time
import datetime
import sys
"""
THIS PROGRAM COMPUTE A SCANNING SEQUENCE FOR PF/SAM/SOAR
Philippe Amram
last update: 2015, March, 19
NOTATIONS:
epais = distance between the two plates
gap = th... | b1quint/samfp | samfp/old/create_scan_script.py | Python | bsd-3-clause | 24,668 | [
"Galaxy"
] | ee9011b062e95a3e989cd0cf695152c897a64aa99dd3d2387ce6123b3528a7af |
import pytest
from .addons import hardware_nvidia_gpu, using_dftd3, using_gcp, using_cppe
import json
import qcengine as qcng
from qcengine.testing import using
import psi4
pytestmark = pytest.mark.quick
using_ambit = pytest.mark.skipif(psi4.addons("ambit") is False,
reason="Psi4 no... | dgasmith/psi4 | tests/pytests/test_addons.py | Python | lgpl-3.0 | 54,634 | [
"CFOUR",
"GAMESS",
"Molpro",
"Psi4",
"Q-Chem"
] | d4f81dabca169344730da2b56c95c3151b4c541cf830e519e70c44cbb0757168 |
#!/usr/bin/env python
"""Several utility functions that do not seem to fit somewhere
else.
"""
# Copyright 2009-2013 Max J. Hoffmann (mjhoffmann@gmail.com)
# This file is part of kmos.
#
# kmos is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License ... | mhoffman/kmos | kmos/utils/__init__.py | Python | gpl-3.0 | 19,100 | [
"ASE",
"Jmol"
] | 2395aadc8f75300140704a088ba89bea19f1868a2d9339e022d9456a014c51d7 |
# coding: utf-8
"""
# XDMF Generator
We want a script that can look at the files in a folder and generate a nice
XDMF output for them.
The XDMF/XMF structure for Underworld is as such:
- XDMF.temporalFields.xmf points to XDMF.FilesField.xdmf
- XDMF.FilesField.xdmf has a list of all the XDMF.Fields.**timestep**.xmf... | OlympusMonds/lithospheric_modelling_recipe | scripts/xdmf_generator.py | Python | gpl-3.0 | 3,039 | [
"ParaView"
] | 105f5976a94fc5a3bd675316cff6c626b63624f94b595a6b04744820725ef857 |
import math, nanopores, dolfin
# @Benjamin, Gregor TODO:
# -) check permittivity and surface charge of ahem
# -) what biased voltage to use?
# some default values for parameters
### geo params [nm]
geo_name = "aHem"
domscale = 1.
l4 = 15.
l3 = 15.
R = 20.
r0 = 5.
z0 = 10.
exit_i = 1
badexit = {"upperbulkb"}
goodexit... | mitschabaude/nanopores | nanopores/scripts/ahemIV.py | Python | mit | 3,751 | [
"FEFF"
] | 4692442b819da7b3d105010d83adf9865b1f2b74fe215d5ecaf85af0d7278e79 |
#!/usr/bin/env python
# ________ _______________ ____________
# ___ __/__ ____(_)_ /__ /______________ ___/_ /__________________ _______ ___
# __ / __ | /| / /_ /_ __/ __/ _ \_ ___/____ \_ __/_ ___/ _ \ __ `/_ __ `__ \
# _ / __ |/ |/ /_ / / /_... | ActianCorp/twitter-streaming | python/twitter_kafka_direct.py | Python | apache-2.0 | 4,589 | [
"VisIt"
] | 073143f2a2c15eea95504b40cdc5c6d9467d6a96ae7fc0c44e9982f134feb3d5 |
from vtk.vtkCommonDataModel import vtkDataObject
from vtk.vtkCommonExecutionModel import vtkAlgorithm
from vtk.vtkCommonExecutionModel import vtkDemandDrivenPipeline
from vtk.vtkCommonExecutionModel import vtkStreamingDemandDrivenPipeline
from vtk.vtkFiltersPython import vtkPythonAlgorithm
class VTKAlgorithm(object):
... | msmolens/VTK | Wrapping/Python/vtk/util/vtkAlgorithm.py | Python | bsd-3-clause | 9,207 | [
"VTK"
] | bf35306b61f3f33e5c3c78f7b076e070c93c517d192ef300f6a14a635d891570 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2009 Douglas S. Blank
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as p... | arunkgupta/gramps | gramps/plugins/quickview/samesurnames.py | Python | gpl-2.0 | 6,487 | [
"Brian"
] | 5777d6ceb854e59dcfdf53f3abb5c43f51ecf6ace8483295a1d87b11ca1170de |
# Copyright (C) 2020(H)
# Jozef Stefan Institute
# Max Planck Institute for Polymer Research
# Copyright (C) 2012,2013,2017,2018(H)
# Max Planck Institute for Polymer Research
# Copyright (C) 2019
# Max Planck Computing and Data Facility
# This file is part of ESPResSo++ > Powered by HeSpaDDA al... | espressopp/espressopp | src/tools/decomp.py | Python | gpl-3.0 | 36,762 | [
"ESPResSo"
] | 4e22bff0b0b7819293de694f19706870234a93689d08e1d9c2aeef7e861d3b8e |
from builtins import str
from builtins import range
from paraview.simple import *
import fabric
from invoke.context import Context
from fabric import Connection
from zutil import analysis
import logging
log = logging.getLogger("paramiko.transport")
sh = logging.StreamHandler()
sh.setLevel(logging.DEBUG)
log.addHand... | zCFD/zutil | zutil/post/pvserver.py | Python | mit | 10,372 | [
"ParaView"
] | 73bd29f3430cdcc7a63205c42ada1f9b93fff7c930e3777b6912c32db364d1a9 |
import base64
import functools
import random
import string
import urllib.parse
from datetime import datetime
from datetime import timedelta
from typing import Dict
from typing import List, Mapping, Optional
from typing import Tuple
from cachetools import TTLCache
from requests.structures import CaseInsensitiveDict
fr... | sk89q/Plumeria | plumeria/core/oauth/manager.py | Python | mit | 16,496 | [
"VisIt"
] | 8c36650b4de38985114a90b83a063d229eb454cf79dd98ac4c1b453ecda47847 |
# -*- coding: utf-8 -*-
### BEGIN LICENSE
# Copyright (C) 2010-2012 Kevin Mehall <km@kevinmehall.net>
#This program is free software: you can redistribute it and/or modify it
#under the terms of the GNU General Public License version 3, as published
#by the Free Software Foundation.
#
#This program is distributed in th... | hephaestus9/Radio | pithos/pithos.py | Python | mit | 32,244 | [
"Brian"
] | 915a50d68d146be41c17eb1ea452ae2b66d457303de3bcbcff94ba0ccda63923 |
from __future__ import division
import sys
import math
import random
import copy
from annsp import annsp
from tools import Functions
from QDA import QDA
from compiler.ast import flatten
funcs_ = Functions()
sys.dont_write_bytecode = True
class pwperceptrons(object):
"""inits - some necessary preprocessing"""
... | saifuddin778/pwperceptrons | pwperceptrons.py | Python | mit | 7,277 | [
"NEURON"
] | 082188ba4bbddc97dc76b6105e3b5ec87c03f8935352f350b99b444cb27f8fbc |
"""
Constructs a data source for the ga4gh server by downloading data from
authoritative remote servers.
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import argparse
import gzip
import os
import requests
import shutil
import subprocess
import tempfil... | macieksmuga/server | scripts/download_example_data.py | Python | apache-2.0 | 16,559 | [
"BWA",
"pysam"
] | c3b7792123704dce499f63510bb1c64b970b07816ce91e2a6ef523e9a3943652 |
import matplotlib
matplotlib.use('Agg')
import numpy as np
import netCDF4
from datetime import datetime
import pyroms
import pyroms_toolbox
import sys
year = int(sys.argv[1])
def create_HYCOM_file(name):
global nc
print 'Creating file %s' %name
#create netCDF file
nc = netCDF4.Dataset(name, 'w', fo... | kshedstrom/pyroms | examples/NWGOA3/Fetch_Pacific/get_pacific_zeta.py | Python | bsd-3-clause | 5,138 | [
"NetCDF"
] | 50592e238d271c2c32c8448da413f2c67b3b3eddca51632dbcc1c5548e8e8b75 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import copy
import pprint
import proteindf_bridge as bridge
import logging
logger = logging.getLogger(__name__)
class TaskObject(object):
"""Task management base class
- create task directory
name: Name of the task. It is used for the work direct... | ProteinDF/QCLObot | qclobot/taskobject.py | Python | gpl-3.0 | 8,034 | [
"Amber"
] | 700725c642096a4af8f66212c57fca80022e3c3985ab6e7fdb152c0a638362c6 |
# -*- test-case-name: twisted.trial.test.test_runner -*-
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
"""
A miscellany of code used to run Trial tests.
Maintainer: Jonathan Lange
"""
__all__ = [
'suiteVisit', 'TestSuite',
'DestructiveTestSuite', 'DryRunVisitor',
'ErrorHolder',... | nlloyd/SubliminalCollaborator | libs/twisted/trial/runner.py | Python | apache-2.0 | 28,076 | [
"VisIt"
] | 336ac547085dc00f685dc06494d466b723c5ebf88bc93153a927c3be0cbbb6ff |
# -*- coding: utf-8 -*-
#
# documentation build configuration file, created by
# sphinx-quickstart on Sat Sep 27 13:23:22 2008-2009.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# The contents of this file are pickled, so don't put values in the namespace
# that aren't pickleab... | ericzolf/ansible | docs/docsite/sphinx_conf/core_conf.py | Python | gpl-3.0 | 11,119 | [
"Galaxy"
] | 7fff8c6ea42b6c4757066948f117ffa1cc0f0342c171999a1d904dd7d403a891 |
# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
import re
from lxml.cssselect import CSSSelector
from zope.testbrowser.browser import Browser
from splinter.element_list import Element... | devenbansod/SWD-Query | splinter/driver/zopetestbrowser.py | Python | gpl-2.0 | 12,097 | [
"VisIt"
] | c9df280ac1c125960e46af840079ae11cd3cd6c95c1faf7a79d57eee364c7eaf |
""" StorageManagerHandler is the implementation of the StorageManagementDB in the DISET framework """
__RCSID__ = "$Id$"
from types import IntType, DictType, ListType, StringTypes, LongType
from DIRAC import gLogger, S_OK
from DIRAC.Core.DISET.RequestHandler ... | andresailer/DIRAC | StorageManagementSystem/Service/StorageManagerHandler.py | Python | gpl-3.0 | 14,238 | [
"DIRAC"
] | 7bc06ee1ce1a5ef22c7856114dd5834a5b50893b5fabbe52161c94cc40679706 |
import itertools
import random
import math
class FeedForwardNet(object):
"""A backpropagating feed forward neural network."""
def __init__(self, layers):
self._layers = layers
@classmethod
def fromfuncs(cls, neuroncounts, learningrate,
biasfunc=lambda: random.uniform(-1, 1... | tmerr/trevornet | trevornet/trevornet/feedforward.py | Python | mit | 8,286 | [
"NEURON"
] | ddeac626dfc99be7419359230734e9f5f15ab03d060681f28a22ec7fededbd01 |
# 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... | kobejean/tensorflow | tensorflow/contrib/timeseries/python/timeseries/ar_model.py | Python | apache-2.0 | 47,539 | [
"Gaussian"
] | f2e1d6a093ed0e3687454954e1bab05f89c925f055c93c69fe0b2ef5eabe733b |
#
# 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... | darionyaphet/spark | python/pyspark/ml/regression.py | Python | apache-2.0 | 87,373 | [
"Gaussian"
] | 3ee7e7874f5b28f37f95a560718b6f9a32d878a7e6fbf487deeb5126ae712560 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyGsd(PythonPackage):
"""The GSD file format is the native file format for HOOMD-blue. GSD... | iulian787/spack | var/spack/repos/builtin/packages/py-gsd/package.py | Python | lgpl-2.1 | 1,144 | [
"HOOMD-blue"
] | 031483a592ad9bccc14b1383e820ef03748d2996c836ae537ce081a7359b37d9 |
# $Id$
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
import wx # needs this for wx.OPEN, we need to make this constant available
# elsewhere
class pngWRT(ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
... | nagyistoce/devide | modules/writers/pngWRT.py | Python | bsd-3-clause | 3,025 | [
"VTK"
] | 3d3a9bde77133be36af89fc9ff176e4ab7da3048e193e75d9971dd24859010c1 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/sequence/_repr.py | Python | bsd-3-clause | 4,193 | [
"scikit-bio"
] | 72c54b2e344195797f9221027109cdee99d85ca0e02bd6045df6d720732445da |
# -*- coding:utf-8 mode:python; tab-width:4; indent-tabs-mode:nil; py-indent-offset:4 -*-
import argparse
import cPickle as pickle
import glob
import os
import StringIO
import sys
import yaml
try:
from pBabel import XYZFile_ToSystem, XYZFile_FromSystem, SystemGeometryTrajectory
from pCore import TextLogFileWrit... | mattbernst/polyhartree | pdynamo-runner.py | Python | gpl-3.0 | 14,903 | [
"GAMESS",
"NWChem"
] | 6855d0010d1f1dec991920c1acbb5f034822dfc301f3fd69ca0ee0d0656de935 |
########################################################################
# File : SSHComputingElement.py
# Author : Dumitru Laurentiu
########################################################################
""" SSH (Virtual) Computing Element: For a given list of ip/cores pair it will send jobs
directly through ... | vmendez/DIRAC | Resources/Computing/SSHBatchComputingElement.py | Python | gpl-3.0 | 7,526 | [
"DIRAC"
] | f079655be67048e20cd95c5debeeb434ba3aaf18e7dd1891fef79a78c80e72b7 |
__all__ = ['vol', 'vol_fold']
import os
import numpy as np
from tempfile import mktemp
import scipy.misc
import time
from tempfile import mktemp
import numpy as np
import scipy.misc
from .. import core
from .. import utils
from ..core import ants_image as iio
from ..core import ants_image_io as iio2
_view_map = {... | ANTsX/ANTsPy | ants/viz/volume.py | Python | apache-2.0 | 26,238 | [
"VTK"
] | 5d835a89428db20846fa3c4d10bde0230bde89f7850f3ae23c8c5e3fb17662ed |
#!/usr/bin/env python
from random import randrange, choice, shuffle, randint, seed, random
from math import sqrt
from collections import deque, defaultdict
from fractions import Fraction
import operator
from game import Game
from copy import deepcopy
try:
from sys import maxint
except ImportError:
from sys im... | ZJvandeWeg/bugfree-batman | tools/ants.py | Python | gpl-2.0 | 72,214 | [
"VisIt"
] | 727f7d9e3144d39c7d1e76159439fee89a0420ba95b3b126706796b76e35c3e4 |
# $Id$
#
# Copyright (C) 2004-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
#
from __future__ import print_function
from rdkit import RDConfig
import os,sys,copy
import unittest
import math
from rdkit import Chem
from rdkit.Chem import rdMolAlign,rdMolTransforms,rdMolDescriptors,rdDistGeom,ChemicalFo... | soerendip42/rdkit | Code/GraphMol/MolAlign/Wrap/testMolAlign.py | Python | bsd-3-clause | 18,815 | [
"RDKit"
] | cba59d9e41546c6a973aa596cb83be23d678a3f9244daa036478977655145168 |
#!/usr/bin/python2
"""
bootalert
Sends email with hostname and IP address
Brian Parsons <brian@pmex.com>
"""
import ConfigParser
import datetime
import re
import smtplib
import socket
import sys
import urllib2
# Get Hostname
hostname = socket.gethostname()
# Get current IP
try:
ipsite = urllib2.urlopen('http... | bparsons/bootalert | bootalert.py | Python | mit | 2,055 | [
"Brian"
] | 90614123df62ba7adf086453014bbb7559e0c78666858fcc6fa7182c3e211e00 |
#
# 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)... | Marcello-Sega/espresso | tools/mpiio2blockfile.py | Python | gpl-3.0 | 3,724 | [
"ESPResSo"
] | fab422c512b4941c5302a05078b7586f2e23ba08b666927b578385882637081f |
# Copyright 2021 Red Hat, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | openstack/python-tripleoclient | tripleoclient/v1/overcloud_restore.py | Python | apache-2.0 | 5,424 | [
"VisIt"
] | 6b5ae5c0b87f70120b20a614794bed683c02b0f9bce3dce426f6d7b3e950a293 |
###########################################################################
#
# 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... | anksp21/Community-Zenpacks | ZenPacks.AndreaConsadori.Netasq/ZenPacks/AndreaConsadori/Netasq/modeler/plugins/NetasqDeviceMap.py | Python | gpl-2.0 | 1,318 | [
"VisIt"
] | 2399bde9c69d4c0c7bb1b0eaea5442afe70bc671579165dec729b2f2c6c0a9a2 |
import time
#import numpy as np
#import scipy
#import pandas as pd
from scipy.signal import convolve, gaussian
# from sklearn import linear_model
#import matplotlib.pyplot as plt
#import seaborn as sns
for i in range(100):
print('TAIA')
time.sleep(100)
| nate-russell/TAIA | MC/taia.py | Python | mit | 264 | [
"Gaussian"
] | bd50bff308bc4e35467057745c9a8672eb83cb275bc0829ca7b6417cb120e535 |
# -*- coding: utf-8 -*-
r"""
Keypoints are stored in the invA format by default.
Unfortunately many places in the code reference this as A instead of invA
because I was confused when I first started writing this.
to rectify this I am changing terminology.
Variables:
invV : maps from ucircle onto an ellipse (perdo... | Erotemic/vtool | vtool_ibeis/keypoint.py | Python | apache-2.0 | 82,616 | [
"Gaussian"
] | adad79fbafe878efeed4450c29336dc1552e49b604d013cf07bc9f8b433fda2c |
##./parallel_manager.sh ./create_skysub_delink_para.sh ${SUBARUDIR}/${cluster}/${filter} SCIENCE ${ending} ".sub" TWOPASS
global tmpdir
import os
#os.system('mkdir -p ' + tmpdir)
astrom = 'solve-field'
import traceback, tempfile, re, commands, MySQLdb
global test
test = 'test_'
mysqldb_params = {'db' : 'subaru',
... | deapplegate/wtgpipeline | calc_test_save.py | Python | mit | 557,343 | [
"Galaxy"
] | ea4f2cab295d519394cc5981bb0b6e4791a475ab79628044fc200e9bd55c36fb |
"""
Optimization procedure/task
"""
from typing import List, Optional
import qcelemental as qcel
import qcengine as qcng
from .base import BaseTasks
from ..interface.models import Molecule, OptimizationRecord, QCSpecification, ResultRecord, TaskRecord, KeywordSet
from ..interface.models.task_models import PriorityEn... | psi4/DatenQM | qcfractal/procedures/optimization.py | Python | bsd-3-clause | 11,924 | [
"Psi4"
] | c1d43f9f98285ab84b9cdfe441fb86183c69dc18b30591671e2755f14daf38c2 |
from common.tests.selenium.base import SeleniumTestCase
class TestCanGoToCommonPages(SeleniumTestCase):
"""
Automated visual tests to visit common pages
"""
def test_can_goto_home_page(self):
self.browser.get(self.live_server_url)
welcome = self.browser.find_element_by_tag_name('h1').... | payal97/portal | systers_portal/common/tests/selenium/test_can_goto_common_pages.py | Python | gpl-2.0 | 1,221 | [
"VisIt"
] | 77bd8d7ce67ee26ba546601719dd18abf3ef00829a5cf3c9038216d8480d5738 |
# (c) 2015 J Miguel Farto, jmfarto@gmail.com
r'''
Aditional static paths
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import os
from flask import Blueprint
from flask import current_app as app
from flask.helper... | damahou/sagewui | sagewui/blueprints/static_paths.py | Python | gpl-3.0 | 1,622 | [
"Jmol"
] | cf8e8b8920f89a915da6b4fd74def1eac2b301eed731cc2134b5887145a3c14f |
#!/usr/bin/env python
"""
Extracts data from reference files or calculates FF data.
Takes a sequence of keywords corresponding to various
datatypes (ex. mb = MacroModel bond lengths) followed by filenames,
and extracts that particular data type from the file.
Note that the order of filenames IS IMPORTANT!
Used to ma... | arosale4/q2mm | q2mm/calculate.py | Python | mit | 83,824 | [
"Amber",
"Gaussian",
"Jaguar",
"MacroModel",
"TINKER"
] | 3ad9fb4efc2c27f70dd64c9258290bacb5876259f5d39579f8086bb90f613903 |
"""Module for SOP classes of the SEG modality."""
import logging
from collections import defaultdict, OrderedDict
from copy import deepcopy
from os import PathLike
from typing import (
Any, cast, Dict, List, Optional, Sequence, Union, Tuple, BinaryIO
)
import numpy as np
from pydicom.dataset import Dataset
from py... | MGHComputationalPathology/highdicom | src/highdicom/seg/sop.py | Python | mit | 123,481 | [
"VisIt"
] | 38fdcfaacd6a0ecb44446b071110aef2180e5c756932dea2409f1ee9b6c96ca5 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
import sys
class Hdf(AutotoolsPackage):
"""HDF4 (also known as HDF) is a library and multi-object
file... | LLNL/spack | var/spack/repos/builtin/packages/hdf/package.py | Python | lgpl-2.1 | 9,229 | [
"NetCDF"
] | aadd9a19f665fa6e4aba63b52d24f25013e57d87540b117dfe0d5d1dc6145927 |
#!/usr/bin/env python3
# (C) 2016, Markus Wildi, wildi.markus@bluewin.ch
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
#
# ... | jstrobl/rts2 | scripts/u_point/u_point/quick_analysis.py | Python | lgpl-3.0 | 7,630 | [
"VisIt"
] | 61f274b185fd811e8a56af0dae0b128ac7194ab3131dc78cf871c6e7bb5d3dba |
# $Id$
#
# Copyright (C)2003-2010 greg Landrum and 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.
#
""" Hybrid EState-VSA de... | greglandrum/rdkit | rdkit/Chem/EState/EState_VSA.py | Python | bsd-3-clause | 3,549 | [
"MOE",
"RDKit"
] | 05d65db5de664bb10f9ce749a166f7a75a494eba52cfc867bf2af59184098a42 |
#!/usr/bin/env python
import fnmatch
import os
from pathlib import Path
import re
import shlex
import shutil
import subprocess
import sys
import tempfile
import time
from concurrent.futures import ThreadPoolExecutor
from contextlib import contextmanager
from typing import Optional
import click
import git
import typer
... | DIRACGrid/DIRAC | integration_tests.py | Python | gpl-3.0 | 24,355 | [
"DIRAC"
] | 7af6e206465425009ea9cb616e94a0d173fc9cbb8a7e30c51221d48ce7c55eda |
import numpy as np
import matplotlib.pyplot as plt
from scipy.special import erfc
import lmfit
import logging
from pycqed.analysis import analysis_toolbox as a_tools
from pycqed.analysis.tools import data_manipulation as dm_tools
import string
#################################
# Fitting Functions Library #
#######... | DiCarloLab-Delft/PycQED_py3 | pycqed/analysis/fitting_models.py | Python | mit | 51,750 | [
"Gaussian"
] | 7b7ed485bcf8142d4bb7046169b8c6801cd8f95462d6d7c030a0c7545f51f13f |
from PyQt4 import QtGui
import qimage2ndarray #http://kogs-www.informatik.uni-hamburg.de/~meine/software/qimage2ndarray/doc/#converting-ndarrays-into-qimages
from PyQt4 import QtCore
import numpy as np
import dnfpy.view.plotArrayQt as plotArrayQt
import pyqtgraph as pg
from scipy import signal
from scipy import ndimage... | bchappet/dnfpy | src/dnfpy/view/arrayView.py | Python | gpl-2.0 | 6,177 | [
"Gaussian"
] | e0e07dc921c02d67f82f0f3cd71d02338a5b8a5f3312cfde8bb676781ee8e547 |
########################################################################
# $HeadURL$
# File : OcciImage.py
# Author : Victor Mendez ( vmendez.tic@gmail.com )
########################################################################
# DIRAC
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
# VMDIRAC
from VMDIRAC.Work... | myco/VMDIRAC | WorkloadManagementSystem/Client/OcciImage.py | Python | gpl-3.0 | 8,147 | [
"DIRAC"
] | 7a243f255934acedfc77803550d33d428fdb03fae5b21f63efb0d3edc19a97ad |
import unittest
from pymock import *
from dalton.config import Rule
from dalton.updater import SecurityGroupUpdater
class FakeSecurityGroup(object):
def __init__(self, id, name):
self.id, self.name = id, name
class SecurityGroupUpdaterTest(PyMockTestCase):
def test_update_security_group_rules_author... | signal/dalton | dalton/tests/test_updater.py | Python | apache-2.0 | 4,698 | [
"Dalton"
] | 1178793905c58bdeed5f670cde07f1c124b47d4954979797dd29a206c8afecdf |
#
# @BEGIN LICENSE
#
# QCDB: quantum chemistry common driver and databases
#
# Copyright (c) 2011-2017 The QCDB Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of QCDB.
#
# QCDB is free software; you can redistribute it and/or modify
# it ... | loriab/qcdb | qcdb/qchem.py | Python | lgpl-3.0 | 18,471 | [
"CFOUR",
"Psi4",
"Q-Chem"
] | 9516613e2923270ac9a1977f49fc8de93426c47b7584e14c8eb317d826cbdaff |
import argparse
import json
import os
import re
import sys
from pycparser import c_ast, parse_file
from typing import Any, Dict, List, Set, Tuple, Union
def strip_quotes(arg: str) -> str:
if arg[0] != '"' or arg[-1:] != '"':
raise Exception(arg)
return arg[1:-1]
def find_function_calls(file: s... | apache/qpid-proton | c/tools/codec-generator/find_specs.py | Python | apache-2.0 | 3,924 | [
"VisIt"
] | ced6a667c3d0b711396efda13b4db1e25acba7c5dd3f853d2af298000fcf18c8 |
#!/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/tools/chkfile_util.py | Python | apache-2.0 | 2,342 | [
"PySCF"
] | ed98e84c75a5e2fe0c1c714eaba81af5b4cc6543972ee60b4217c8c62c6415ec |
# Software selection spoke classes
#
# Copyright (C) 2011-2013 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is... | projectatomic/anaconda | pyanaconda/ui/gui/spokes/software.py | Python | gpl-2.0 | 17,228 | [
"VisIt"
] | de6aa3481c9865dcd6b197c2b1255bc116a26ef9334b5199cc8860a73103dc53 |
"""
cats
"""
__version__ = 0.4
import cats.styles
import cats.data
import cats.formatters
def format(input_, *args, **kwargs):
"""Formats bioinformatics related data for display on the console."""
import os
import sys
from io import BufferedReader
from Bio import SeqIO
from Bio import Seq, Seq... | khughitt/cats | cats/__init__.py | Python | bsd-2-clause | 7,712 | [
"Biopython"
] | cbae99aa0a585adf50970d4e079765f403943beb9158a123aa17f9872aaaf3b8 |
# -*- coding: utf-8 -*-
"""Copyright 2015 Roger R Labbe Jr.
Code supporting the book
Kalman and Bayesian Filters in Python
https://github.com/rlabbe/Kalman-and-Bayesian-Filters-in-Python
This is licensed under an MIT license. See the LICENSE.txt file
for more information.
"""
from __future__ import (absolute_imp... | zaqwes8811/micro-apps | self_driving/deps/Kalman_and_Bayesian_Filters_in_Python_master/kf_book/ukf_internal.py | Python | mit | 13,135 | [
"Gaussian"
] | 32bf2cf413a7b605446b6c91e5a58d3610cb472d34103e229f59a9e5c513403b |
from vj4.model import builtin
class Error(Exception):
pass
class HashError(Error):
pass
class InvalidStateError(Error):
pass
class UserFacingError(Error):
"""Error which faces end user."""
def to_dict(self):
return {'name': self.__class__.__name__, 'args': self.args}
@property
def http_statu... | vijos/vj4 | vj4/error.py | Python | agpl-3.0 | 8,627 | [
"VisIt"
] | eea9fa1a6d6277e2b4eff36d239822066ad3ec5293dfccf5f22a98cf06e21c81 |
from hubspace.model import *
from datetime import datetime
import popen2
class Population (object):
pass
def populate ():
objs = Population()
classes = ['Visit','VisitIdentity','Group','User','Permission','Location',
'Resource','RUsage','Pricing','Todo','Invoice','Note']
for c in classes:
... | thehub/hubspace | populate_real.py | Python | gpl-2.0 | 4,995 | [
"VisIt"
] | 780fd1bdc0a1c1dc9f7c84e9ba7bba008f9bed4c6c02daa199422dddaef2b361 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project Compiler
#
import os, sys, re, shutil, time, run, sgmllib, codecs, tempfile
this_dir = os.path.dirname(__file__)
root_scripts_dir = os.path.dirname(this_dir)
common_scripts_dir = os.path.join(root_scripts_dir, "common")
module_scripts_dir = os.path.join(root_s... | appcelerator/titanium_mobile_tooling | scripts/iphone/compiler.py | Python | apache-2.0 | 23,391 | [
"VisIt"
] | 9a31d573faff0b9795873fbedce8ed1176a718f3bbb967f02e6358b7fb277767 |
from __future__ import absolute_import, print_function
import os
import re
import shelve
import shutil
import posixpath
import json
from xml.etree.ElementTree import ElementTree
from collections import defaultdict
from functools import partial
from contextlib import closing
from contextlib import contextmanager
try:... | tomazc/orange-bio | orangecontrib/bio/arrayexpress.py | Python | gpl-3.0 | 41,127 | [
"ADF"
] | e50963d6e604d0d7d952a51517a756dbb3e15877dd8416cdb9b29ab219525d29 |
from .r_dependencies import *
from .r_base import r_base
from math import sqrt
class r_pls(r_base):
def calculate_plsda_mixomics(self,data_I,factor_I= "sample_name_abbreviation",
ncomp=5,max_iter=500,
tol = 1e-3, near_zero_var = "TRUE",
method_... | dmccloskey/r_statistics | r_statistics/r_pls.py | Python | mit | 56,346 | [
"Bioconductor"
] | 4c06998b5d9590286cb011cf83ae690e8d47bdbd73c19e52fdf49791dbeb1394 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Licensed to Cloudera, Inc. under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. Cloudera, Inc. licenses this file
# to you under the Apache License, Version 2.0 (... | jayceyxc/hue | apps/useradmin/src/useradmin/tests.py | Python | apache-2.0 | 44,411 | [
"MOE"
] | 79f801c7b9a4d7e77706248f4f4d61e156cd96438ebcd6b784947f58eba59236 |
#!/usr/bin/env python
# CREATED:2013-03-08 15:25:18 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa core (__init__.py)
#
from __future__ import print_function
# Disable cache
import os
try:
os.environ.pop("LIBROSA_CACHE_DIR")
except:
pass
import librosa
import glob
import numpy as np
import ... | bmcfee/librosa | tests/test_core.py | Python | isc | 61,375 | [
"Brian"
] | 57ab6a41ff05329feb0287a6d945887fa50715bb4c042a535802c8bad30b9d62 |
input_names = {'TL': '../examples/large_deformation/hyperelastic.py',
'UL': '../examples/large_deformation/hyperelastic_ul.py',
'ULM': '../examples/large_deformation/hyperelastic_ul_up.py'}
output_name_trunk = 'test_hyperelastic_'
from sfepy.base.testing import TestCommon
from tests_basic... | RexFuzzle/sfepy | tests/test_hyperelastic_tlul.py | Python | bsd-3-clause | 3,003 | [
"VTK"
] | 33add098022aa0854bede3e92914747079f6653798ae3a2c83d0eeb22ccbe2db |
""" The Site Director is an agent performing pilot job submission to particular sites/Computing Elements.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN SiteDirector
:end-before: ##END
:dedent: 2
:caption: SiteDirector options
"""
import os
import sys
import random
import socket
from collect... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Agent/SiteDirector.py | Python | gpl-3.0 | 60,165 | [
"DIRAC"
] | 5162026e5d7936f398d66c4649c0fd6ecf1edc547872abb7408b5cd6e6d01892 |
import functools
import pytest
from django import forms
from testapp.models import Team, Player
from testapp.forms import PlayerForm
def test_import():
import django_addanother.widgets
import django_addanother.views
import django_addanother.contrib
@pytest.mark.django_db
def test_widget_deepcopy():
... | jonashaag/django-addanother | test_project/testapp/tests.py | Python | isc | 4,572 | [
"VisIt"
] | 5e399476521ad34f58cdc6cba51355f29ae6f5f0b4c0a054f3f2425acf4bfc72 |
# 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/integrator/BerendsenBarostat.py | Python | gpl-3.0 | 4,224 | [
"ESPResSo"
] | 92953c46eaf50647c4a28ef7881478859a27e44e19be147cc3751bebafe75494 |
import openvoronoi as ovd
import ovdvtk
import time
import vtk
import math
import offset2vtk
import sys
import os
sys.path.append( os.path.join(os.path.dirname(__file__), "../"))
from SvgReader import SvgReader
def insert_polygon_points(vd, poly):
pts=[]
for p in poly:
offsetx = center[0]
... | aewallin/openvoronoi | python_examples/ma-offset/svg_offset.py | Python | lgpl-2.1 | 3,841 | [
"VTK"
] | c7c04b966d364df35da11730c957f3b2eea9866c8de7060bbd9054caa30a6c53 |
import sys
from framework.plumbing import *
from framework.node import *
from framework.value_types import *
from framework.data_model import *
from framework.encoders import *
import framework.dmhelpers.xml as xml
from framework.dmhelpers.json import *
from framework.dmhelpers.xml import tag_builder as xtb
from fram... | k0retux/fuddly | data_models/tutorial/tuto.py | Python | gpl-3.0 | 21,047 | [
"xTB"
] | 1081d45d3a199952333b774548268c1a6b4558c13bda52db58e68fc102931743 |
"""
Filter VCF and output only SNP calls in a sequence context where there
is a different homopolymer either side of the site, one of which is the same base as the ALT
allele, and one is the ref e.g. ref sequence is AAAAATTTTT and SNP is T-->A or A --> A.
"""
import sys
import pysam
a = pysam.Fastafile(sys.argv[1])
t... | andyrimmer/Platypus | scripts/filterReadThrough.py | Python | gpl-3.0 | 2,444 | [
"pysam"
] | 33fa8ee21d72045c0c968eee89a4e0eec6388307df07727478b5991ac7a7d829 |
__author__ = "Xiang-Guo Li"
__copyright__ = "Copyright 2018, The Materials Virtual Lab"
__email__ = "xil110@eng.ucsd.edu"
__date__ = "07/30/18"
import os
import unittest
import warnings
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.analysis.gb.grain import GrainBoundary, GrainBoundar... | vorwerkc/pymatgen | pymatgen/analysis/gb/tests/test_grain.py | Python | mit | 16,955 | [
"pymatgen"
] | 696e9d42e03da1d6bab6fa1bd162e7166304ce9c5b370c4c48d9d98748196e0f |
# pylint: disable=too-many-ancestors, invalid-name, no-self-use
""" View Set for personalised GymItem api """
from django.shortcuts import get_object_or_404
from rest_framework.response import Response
from rest_framework import viewsets, status
from app.models.profile import Profile
from app.models.gym_item import Gym... | Gimpneek/exclusive-raid-gym-tracker | app/views/view_sets/personalised_gym_item_view_set.py | Python | gpl-3.0 | 3,546 | [
"VisIt"
] | 126eeefd28620ee72a747fed9bd5b911137650a579172de458082e92f95d0921 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
import pyscf
'''
A simple example to run DFT calculation.
See also pyscf/dft/libxc.py and pyscf/dft/xcfun.py for the complete list of
available XC functionals.
'''
mol = pyscf.M(
atom = 'H 0 0 0; F 0 0 1.1', # in Angstrom
basis = '631g',... | gkc1000/pyscf | examples/dft/00-simple_dft.py | Python | apache-2.0 | 767 | [
"PySCF"
] | af3079efb12a2e0495e63401f532760ca47287568e6f3b992fbb8eadf6a87451 |
"""A dialog box for displaying help text."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import gtk
import sys
class HelpBox:
"""A dialog for showing longish help texts.
The GTK widget is not created until L{display} is called.
"""
box = None
title = None... | timdiels/0install | zeroinstall/gtkui/help_box.py | Python | lgpl-2.1 | 2,097 | [
"VisIt"
] | fdab99fec6356f609295dc7b03fc9f34c57c0a0803bfea5b8f286dee16eb15a7 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | MartialD/hyperspy | hyperspy/tests/component/test_components.py | Python | gpl-3.0 | 20,329 | [
"Gaussian"
] | 1fbb248b19bb8c6f0522a4df1c41d10f9b0493fb49f3a2305eeebaf2638f5b07 |
"""
Courseware page.
"""
import re
from bok_choy.page_object import PageObject, unguarded
from bok_choy.promise import EmptyPromise
from selenium.webdriver.common.action_chains import ActionChains
from common.test.acceptance.pages.lms.bookmarks import BookmarksPage
from common.test.acceptance.pages.lms.course_page i... | angelapper/edx-platform | common/test/acceptance/pages/lms/courseware.py | Python | agpl-3.0 | 22,691 | [
"VisIt"
] | 2ca81c32784b27f034b8edaac02c617a6cb9991c97894d49048f224900446b47 |
'''
Created on 9 Oct. 2018
@author: Alex Ip
Utility to read metadata from CSW query and/or netCDF file into dataset metadata cache
'''
import sys
import re
from geophys_utils.dataset_metadata_cache import get_dataset_metadata_cache, Dataset, Distribution
import logging
import netCDF4
import numpy as np
from datetime ... | alex-ip/geophys_utils | geophys_utils/dataset_metadata_cache/csw2dataset_metadata_cache.py | Python | apache-2.0 | 9,816 | [
"NetCDF"
] | 5504588fa3db9bb52a41093ae20b73eb854f7a32eab0e3361a4a410f79ab7c40 |
# Read .Mat Files
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import scipy.io
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz as ... | tapomayukh/projects_in_python | rapid_categorization/cross-validation check/sample_length_effect/resulting_graph.py | Python | mit | 1,136 | [
"Mayavi"
] | a0775ab0bb50ddb9e21c8bffac24ac980644afc591569396040d6b32b2093cef |
from __future__ import print_function
from six import iteritems
from six.moves import range
import os
from numpy import arange, mean, amax, amin, array
import vtk
from vtk import vtkHexahedron, vtkQuad, vtkTriangle, vtkTetra
from pyNastran.converters.tecplot.tecplot import Tecplot
from pyNastran.converters.tecplot.u... | saullocastro/pyNastran | pyNastran/converters/tecplot/tecplot_io.py | Python | lgpl-3.0 | 10,639 | [
"VTK"
] | 488acf61721b547b7a8e22c827c6c256fd67618c0cd7eba2768179f2994b23f2 |
from common import Modules, data_strings, load_yara_rules, PEParseModule, ModuleMetadata, is_ip_or_domain
class easterjackpos(PEParseModule):
def __init__(self):
md = ModuleMetadata(
module_name="easterjackpos",
bot_name="Easter JackPOS",
description="Point of sale malw... | bwall/bamfdetect | BAMF_Detect/modules/easterjackpos.py | Python | mit | 1,531 | [
"Brian"
] | 1517284ea820210bb125a8cb6ca04ac9cff589ee4d9ce9bcdc582c9adeadc8d3 |
from __future__ import unicode_literals
import six
from six.moves import xrange
from scrapi.base import XMLHarvester
from scrapi.base.schemas import DOESCHEMA
from scrapi.linter.document import RawDocument
from scrapi.base.helpers import updated_schema, build_properties, single_result
RAW_DOC = {
'doc': b'{}',
... | alexgarciac/scrapi | tests/utils.py | Python | apache-2.0 | 7,872 | [
"Brian"
] | 60a907054bec958738a4be7c4b4b1b580d745f546b73507c60a04eee6e20b639 |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'abinit'
tab.settings['Output file name'] = 'AlAs.out'
#
# SettingsTab
#
tab = self.notebook.settingsTab
tab.settings['Eckart flag'] = False
tab.settings['Neutral Born charges'] = False
tab.settings['Sigma value'] = 5
tab.settings['Mass definition'] = ... | JohnKendrick/PDielec | Examples/ATR/AlAs/script.py | Python | mit | 1,740 | [
"ABINIT"
] | 7ce90421f23dae39f42c5290a7af9b5e0ae7854ac6d23c39fc85af1c3a30881c |
#!/usr/bin/python
import numpy as np
import sys
# === setup
k0 = 50.0 # this converge with time_step 0.01
#k0 = 5.0 # this converge with time_step 0.05
l0 = 1.94
dlmax = 0.5
imol = 0
jatom = 0
pos0 = np.array([0.0,0.0,0.0])
fligands = sys.argv[1]
fsubstrate = sys.argv[2]
# === Functions
def findNea... | ProkopHapala/SimpleSimulationEngine | cpp/apps/MolecularEditor/py/gen_bonds.py | Python | mit | 1,074 | [
"Jmol"
] | a6a31acae88c20a13653ba4b5bb1d900cd841773295203c113f459f762e13380 |
#!/usr/bin/env python
__author__ = "waroquiers"
import json
import os
import unittest
from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
AngleNbSetWeight,
CNBiasNbSetWeight,
DeltaCSMNbSetWeight,
DeltaDistanceNbSetWeight,
DistanceAngleAreaNbSetWeight,
Distanc... | gmatteo/pymatgen | pymatgen/analysis/chemenv/coordination_environments/tests/test_weights.py | Python | mit | 33,223 | [
"pymatgen"
] | 0423b8228630bcada043baf1a94c3a80b757adcc0c4f1deaf92c75bb374a6cbe |
from __future__ import print_function, division
from sympy.core import Mul
from sympy.functions import DiracDelta, Heaviside
from sympy.core.compatibility import default_sort_key
from sympy.core.singleton import S
def change_mul(node, x):
"""change_mul(node, x)
Rearranges the operands of a product, bring... | Titan-C/sympy | sympy/integrals/deltafunctions.py | Python | bsd-3-clause | 7,296 | [
"DIRAC"
] | 395fe7e8be366b64069c47410359e159890025b6d122e2e28273ac04e794080a |
# encoding: UTF-8
#
# The MIT License (MIT)
#
# Copyright (c) 2016-2021 yutiansut/QUANTAXIS
#
# 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... | yutiansut/QUANTAXIS | QUANTAXIS/QACmd/__init__.py | Python | mit | 35,142 | [
"VisIt"
] | 1647091267c62c2e47e5eff265e61033d20911978c97fdbafcf5694bea00f078 |
#------------------------------------------------------------------------------
# setlx2py: setlx_codegen.py
#
# Code generator for the setlx2py AST
#
# Copyright (C) 2014, Jan-Christoph Klie
# License: Apache v2
#------------------------------------------------------------------------------
import re
from setlx2py.s... | Rentier/setlx2py | setlx2py/setlx_codegen.py | Python | apache-2.0 | 14,026 | [
"VisIt"
] | f831d411d284e31b1ca3a64a6fafa30378380d69c7588ad051604d29298e9b35 |
from ANNarchy.core.Population import Population
from ANNarchy.core.Neuron import Neuron
import ANNarchy.core.Global as Global
from ANNarchy.generator.Compiler import extra_libs
try:
from PIL import Image
except:
Global._warning('The Python Image Library (pillow) is not installed on your system, unable to crea... | vitay/ANNarchy | ANNarchy/extensions/image/ImagePopulation.py | Python | gpl-2.0 | 9,944 | [
"NEURON",
"VTK"
] | eba59e58caf7c414dc5e3e17209643aaa98140922989155e94c4959fbf201b4a |
###############################################################################
##
## Copyright (C) 2014-2016, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | VisTrails/VisTrails | scripts/gen_vtk_examples/vtk_to_vt.py | Python | bsd-3-clause | 55,962 | [
"VTK"
] | 4c5d49f4b474b6e03b011743b513db88d92ae47411fd8209f2b0cf5452092a3b |
"""
Module to set up run time parameters for Clawpack -- classic code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#import clawpack.geoclaw.shallow_1d.data as geoclaw1d
import geoclaw1d # in this directory for n... | clawpack/seismic | tsunami/1d/pwlinear1/setrun.py | Python | bsd-2-clause | 8,386 | [
"NetCDF"
] | 18ae92b3bf74b17086366792ba0b71b01e2b7199dbedca40cf4a9095ed102715 |
#!/usr/bin/python
####
# http://peerit.blogspot.com/2007/07/multipartposthandler-doesnt-work-for.html
# http://code.activestate.com/recipes/146306/
#
# 02/2006 Will Holcomb <wholcomb@gmail.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Publ... | uogbuji/akara | lib/util/multipart_post_handler.py | Python | apache-2.0 | 5,174 | [
"Brian"
] | f3933bb997cc9370b0750f5c620535c2bd14a363be178d8ae12a73377a630f96 |
""" Schemas for structural stacks. """
import datajoint as dj
from datajoint.jobs import key_hash
import matplotlib.pyplot as plt
import numpy as np
import scanreader
from scipy import signal
from scipy import ndimage
from scipy import optimize
import itertools
from . import experiment, notify, shared, reso, meso
anat... | dimitri-yatsenko/pipeline | python/pipeline/stack.py | Python | lgpl-3.0 | 135,783 | [
"Gaussian"
] | 321b6bf6f6a5b80ae5a3874e8463f544845793e4713e556696baf950987d776d |
'''
SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
... | madscatt/zazzie_1.5 | trunk/sassie/analyze/density_plot/density_plot.py | Python | gpl-3.0 | 28,955 | [
"Gaussian"
] | a3068eceef1eb510f131ed5b0eb45740c31061ae7c54a98803401b2eefac7d9a |
# Copyright 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.
UA_TYPE_MAPPING = {
'desktop':
'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_3) '
'AppleWebKit/537.36 (KHTML, like Gecko) '
'Chrome/40.0.2... | sahiljain/catapult | telemetry/telemetry/internal/browser/user_agent.py | Python | bsd-3-clause | 1,342 | [
"Galaxy"
] | b10cfc5a3c44f2dc316ea17053952b259accee6c5afde22d568add1176da27aa |
import configparser
from time import sleep
import requests
import aiohttp
from Firefly import logging, scheduler
from Firefly.const import COMMAND_UPDATE, SERVICE_CONFIG_FILE
from Firefly.helpers.events import Command
from Firefly.helpers.service import Service
from Firefly.core.service_handler import ServicePackage... | Firefly-Automation/Firefly | Firefly/components/hue/hue_service.py | Python | apache-2.0 | 8,525 | [
"Firefly"
] | b996ba797715034db57e855aa1db1fe329e52a35645f5356c95d7a94a73f8999 |
#!/usr/bin/env python
# encoding: utf-8
"""
elastics.py
Part of the MaterialsGrid project
Copyright (c) 2007-2008 Dan Wilson. All rights reserved.
"""
import sys
import os
import re
import optparse
import scipy as S
import CijUtil
import castep
version = 1
def main(input_options, libmode=False):
def analyse... | duyuan11/elastic-constants | elastics.py | Python | bsd-3-clause | 25,847 | [
"CASTEP"
] | d7245006f254a58bfc92e54aa024c47f09ad07990abdf0866931676ec5027d9b |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import DataMigration
from django.db import models
from django.template.defaultfilters import slugify
class Migration(DataMigration):
def forwards(self, orm):
for record in orm.GeoRecord.objects.all():
record.slug = slugif... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0009_recreate_georecord_slug.py | Python | mit | 9,740 | [
"MOE"
] | d7c5a4980936dd2696ff1dd77e6aa53a1b5fef5429bf05ea2e4fbac230e2a993 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright (C) 2013-2018 Florian Festi
#
# Based on pipecalc by Christian F. Coors
# https://github.com/ccoors/pipecalc
#
# 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
# ... | florianfesti/boxes | boxes/generators/organpipe.py | Python | gpl-3.0 | 6,777 | [
"FEFF"
] | 1f82e2931cc10f51855a34bb7c1d918ffb50ead1ed9e4c5f3c63e3c644cc95f5 |
"""
Workflow class is the main container of Steps and Modules
"""
import os
import re
import types
import xml.sax
from DIRAC.Core.Workflow.Parameter import *
from DIRAC.Core.Workflow.Module import *
from DIRAC.Core.Workflow.Step import *
from DIRAC.Core.Workflow.Utility import *
from DIRAC import S_OK, S_ERROR
_... | andresailer/DIRAC | Core/Workflow/Workflow.py | Python | gpl-3.0 | 15,047 | [
"DIRAC"
] | b673765725ee0495de093bff177bc90a96e6530abba3b4c0818bb90f7c12745c |
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