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|---|---|---|---|---|---|---|---|
import os
import unittest
import pysal
import numpy as np
class Testuser(unittest.TestCase):
def setUp(self):
self.wq = pysal.queen_from_shapefile(
pysal.examples.get_path("columbus.shp"))
self.wr = pysal.rook_from_shapefile(
pysal.examples.get_path("columbus.shp"))
de... | chhao91/pysal | pysal/weights/tests/test_user.py | Python | bsd-3-clause | 7,673 | [
"COLUMBUS",
"Gaussian"
] | 00d4ef9f7933f0c64a06199e96d4ae634eab7597038a7c6283db90bc3e2fd13f |
#!/usr/bin/env python
# encoding: utf-8
'''
Created by Brian Cherinka on 2016-04-08 14:31:34
Licensed under a 3-clause BSD license.
Revision History:
Initial Version: 2016-04-08 14:31:34 by Brian Cherinka
Last Modified On: 2016-04-08 14:31:34 by Brian
'''
from __future__ import print_function
from __future__... | bretthandrews/marvin | python/marvin/web/controllers/galaxy.py | Python | bsd-3-clause | 22,585 | [
"Brian",
"Galaxy"
] | f9b8894eb291f75ce700b276826841f4ac6726cd5a2fe527d90c3c844bb82e8b |
from unittest.mock import MagicMock
import numpy as np
import pytest
from emukit.bayesian_optimization.acquisitions.expected_improvement import (
ExpectedImprovement,
MeanPluginExpectedImprovement,
)
from emukit.core.interfaces import IModel, IModelWithNoise
from emukit.model_wrappers import GPyModelWrapper
... | EmuKit/emukit | tests/emukit/bayesian_optimization/test_mean_plugin_expected_improvement.py | Python | apache-2.0 | 2,899 | [
"Gaussian"
] | 412e22909bc73673bc1b8f0baaaca82ad4aa8d15e29154bbdfe70b3e65b4d5f2 |
# -*- coding: utf-8 -*-
#
# Copyright 2008 - 2019 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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, e... | dursobr/Pythics | pythics/settings.py | Python | gpl-3.0 | 812 | [
"Brian"
] | cc4afec76adaa5da802c917f890b3946b99a8efefeb67fb83dddb2a58928e60d |
import ispyb.model.__future__
import ispyb.model.datacollection
import ispyb.model.sample
def test_dc_no_sample(testdb, testconfig):
ispyb.model.__future__.enable(testconfig)
dc = testdb.get_data_collection(1002287)
assert dc.sample is None
def test_dc_sample_groups(testdb, testconfig):
ispyb.model.... | DiamondLightSource/ispyb-api | tests/model/test_sample.py | Python | apache-2.0 | 1,526 | [
"CRYSTAL"
] | ab5762df093c907d5d41130dc83e626b15b1893c2a9b6eb584f82a845764d584 |
# -*- coding: utf-8 -*-
#
# Pyplis is a Python library for the analysis of UV SO2 camera data
# Copyright (C) 2017 Jonas Gliss (jonasgliss@gmail.com)
#
# This program is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License a
# published by the Free Software Foundat... | jgliss/pyplis | pyplis/processing.py | Python | gpl-3.0 | 48,843 | [
"Gaussian"
] | b0d958c871ecaf4f762e13b3753291c7f787422efd9cf5e55a49fde68db5dda0 |
from func import *
# ATTTENTION! Maybe there are some mistakes in neuron parameters!
logger = logging.getLogger('neuromodulation')
startbuild = datetime.datetime.now()
nest.ResetKernel()
nest.SetKernelStatus({'overwrite_files': True,
'local_num_threads': 8,
'resolution': 0... | research-team/NEUCOGAR | NEST/cube/integration/integration-10/run8.py | Python | gpl-2.0 | 32,025 | [
"NEURON"
] | d98169e880541652e3edd278a03c6aa02ca4b2cefac441e55ea1c6eb3f71dcda |
# -*- coding: utf-8 -*-
"""
Some helpful tools
"""
import numpy as np
def minmax(input):
"""
Calculate min, max for each row
"""
input = np.asfarray(input)
assert input.ndim == 2
min = input.min(axis=0)
max = input.max(axis=0)
out = [x for x in zip(min, max)]
return tuple(out)
... | blagasz/python-ann | neurolab/tool.py | Python | gpl-2.0 | 7,250 | [
"NEURON"
] | 88c7e583aad0d4531f7502039d6a546ce7d7f39fafe2b5a1985e0c6fd031ee27 |
#!/usr/bin/env python
'''
uframe endpoints
'''
__author__ = 'Andy Bird'
#base
from flask import (jsonify, request, current_app, url_for, Flask, make_response,
url_for, Response)
from ooiservices.app import db, cache, celery
from ooiservices.app.uframe import uframe as api
from ooiservices.app.models... | birdage/ooi-ui-services | ooiservices/app/uframe/controller.py | Python | apache-2.0 | 44,986 | [
"NetCDF"
] | 87c7e98db2a2e2e576f6fdbb5de19c142159b9de6296f31c9fb73e3681cc1736 |
# -*- coding: utf-8 -*-
#########################################################################
## rdesigneur0_5.py ---
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of th... | dharmasam9/moose-core | python/rdesigneur/rdesigneur.py | Python | gpl-3.0 | 57,169 | [
"MOOSE",
"NEURON"
] | 469d6ceccb96205e84fac36c09d6aafe480546f094f03c2bcff8cb1c017415cf |
#
# This file is part of Sequana software
#
# Copyright (c) 2016-2021 - Sequana Development Team
#
# Distributed under the terms of the 3-clause BSD license.
# The full license is in the LICENSE file, distributed with this software.
#
# website: https://github.com/sequana/sequana
# documentation: http://sequana.r... | sequana/sequana | sequana/fasta.py | Python | bsd-3-clause | 12,901 | [
"pysam"
] | 230e5f37299629c18626a33d2d167563dadae79080843fab810827cad2371786 |
# Copyright (C) 2012-2018
# Max Planck Institute for Polymer Research
# Copyright (C) 2008-2011
# 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 the GNU General... | govarguz/espressopp | src/interaction/Interaction.py | Python | gpl-3.0 | 3,721 | [
"ESPResSo"
] | c50a8c7c597fb91c41f0689f81d7da6f82748d187b98b9ec7e9a54e4d0670016 |
# Copyright 2009-2011 by Eric Talevich. All rights reserved.
# Revisions copyright 2009-2013 by Peter Cock. All rights reserved.
# Revisions copyright 2013 Lenna X. Peterson. All rights reserved.
#
# Converted by Eric Talevich from an older unit test copyright 2002
# by Thomas Hamelryck.
#
# This code is part of the ... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_PDB.py | Python | gpl-2.0 | 52,905 | [
"Biopython"
] | 563eecee1794e1413b7f906250171a1b8c814f7e18c2580a5d5f67379e950125 |
#!/usr/bin/env python
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# MSMTools is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software... | markovmodel/PyEMMA | setup.py | Python | lgpl-3.0 | 12,936 | [
"MDTraj"
] | cdf2e3db831ca89786616fa02647ce087355b7e0d4a7552f1921b57267d6f678 |
from __future__ import division
import numpy as np
import netCDF4 as nc
import sys
import os
import fnmatch
sys.path.append('/home/wesley/github/UTide/')
from utide import ut_solv, ut_reconstr
from shortest_element_path import shortest_element_path
import matplotlib.pyplot as plt
import matplotlib.tri as Tri
import mat... | wesleybowman/karsten | project/fvcomClass.py | Python | mit | 13,827 | [
"NetCDF"
] | 79762dc2e1d14cbb3617949eefb7eabb5ff469b8a20ce7d4936e352a5320c42c |
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches
def new_pulse_fig(figsize):
'''
Open a new figure and configure it to plot pulse schemes.
'''
fig, ax = plt.subplots(1, 1, figsize=figsize, frameon=False)
ax.axis('off')
fig.subplots_adjust(bottom=0, top=1, left=0, ri... | QudevETH/PycQED_py3 | pycqed/utilities/pulse_scheme.py | Python | mit | 3,498 | [
"DIRAC",
"Gaussian"
] | cb42f7add22583573b5e8fa0499909914fad93fb4dc73f97303679ce57dae385 |
#
# 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 | testsuite/python/observables.py | Python | gpl-3.0 | 8,599 | [
"ESPResSo"
] | cf6e476ed40509272e858cd6c1d1e7372012c6fd13e4d88e122b1166b449a3aa |
"""Plotting functions for visualizing distributions."""
from numbers import Number
from functools import partial
import math
import warnings
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.transforms as tx
from matplotlib.colors import to_rgba
from matp... | mwaskom/seaborn | seaborn/distributions.py | Python | bsd-3-clause | 90,480 | [
"Gaussian"
] | 6d424ae334daf106edd754589eefb645125da3d8d2a5cf62d0fd8f35e624e557 |
from datetime import datetime, timedelta
from copy import copy
import re
import os
import pylab
from util.config import Config
from util.units import Units
import util.derived as derived
from util.util import uniquify, any, fatalError, warning
#from util.callCount import FunctionCallCount
class HootPy(object):
... | pulsatrixwx/PulsatrixWx | base/hootpy.py | Python | mit | 23,563 | [
"NetCDF"
] | 3436d663162655647a2c15220d1982104ceb49698159c98ada6a8be92782b603 |
# -*- coding: utf-8 -*-
#
# Instant Press. Instant sites. CMS developed in Web2py Framework
# Site: http://www.instant2press.com
#
# Copyright (c) 2010 Mulone, Pablo Martín
#
# License Code: GPL, General Public License v. 2.0
# License Content: Creative Commons Attribution 3.0
#
# Also visit: www.web2py.com
# ... | syed/instatnt-press | modules/widgets.py | Python | gpl-2.0 | 28,880 | [
"VisIt"
] | 3a9721949ba35d411a4b61acd54f57f0701806cd0c36514a4e26abb9755c40fb |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | arunkgupta/gramps | gramps/plugins/textreport/familygroup.py | Python | gpl-2.0 | 32,883 | [
"Brian"
] | e75c2f47a34e32aabb4d11149047ef0d5d900c14b641f0b317a3cee69f3f7c93 |
from __future__ import absolute_import
import MDAnalysis
from MDAnalysis.tests.datafiles import GRO, XTC
universe = MDAnalysis.Universe(GRO, XTC)
#old selection
all_selection = universe.selectAtoms('all')
#additional old selectAtoms selection (this comment shouldn't be modified despite containing the method name)
all... | kain88-de/mdanalysis | package/MDAnalysis/migration/test_dummy_old_MDA_code.py | Python | gpl-2.0 | 6,373 | [
"MDAnalysis"
] | b6098570e5e0491e3ebbac860ac30b4507069180b2e77008bf4c4641a915f0ea |
import logging
from .frame import Frame
from .mapping import Mapping
from .bondset import BondSet
from .forcefield import ForceField
from .interface import Progress
logger = logging.getLogger(__name__)
def main(args, config):
"""
Main function of the program PyCGTOOL.
Performs the complete AA->CG mappi... | jag1g13/pycgtool | pycgtool/pycgtool.py | Python | gpl-3.0 | 3,645 | [
"Gromacs"
] | 6d5085d72f4a03dc34de7afa7dd56a415a5225efea19ac12f0e55d587c6b6d89 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
This package contains various command line wrappers to programs used in
pymatgen that do not have Python equivalents.
"""
| xhqu1981/pymatgen | pymatgen/command_line/__init__.py | Python | mit | 277 | [
"pymatgen"
] | d4908798b821104e96efbafea072577a24270dbb2c5b6368ccf3dfd8a1e78663 |
""" JobWrapper test
"""
import unittest
import os
import sys
from DIRAC import gLogger
from DIRAC.Resources.Computing.ComputingElementFactory import ComputingElementFactory
from DIRAC.WorkloadManagementSystem.Utilities.Utils import createJobWrapper
from DIRAC.Core.Security.ProxyInfo import getProxyInfo
class JobWra... | DIRACGrid/DIRAC | tests/Integration/WorkloadManagementSystem/Test_JobWrapper.py | Python | gpl-3.0 | 2,686 | [
"DIRAC"
] | 5f8eaa8736ab4c5508e760b6b620fca608a62d6d5b5090723ca52a657c791710 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2007-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. ... | Clyde-fare/cclib | test/testTD.py | Python | lgpl-2.1 | 4,216 | [
"ADF",
"cclib"
] | 14eb62d612c39700d24dd7e8df0c5cc1a65b9c03872285aa914621d9526ddb5e |
from __future__ import print_function
from builtins import range
import sys
sys.path.insert(1,"../../")
import h2o
from tests import pyunit_utils
import random
import os
def javapredict_dynamic_data():
# Generate random dataset
dataset_params = {}
dataset_params['rows'] = random.sample(list(range(5000,150... | YzPaul3/h2o-3 | h2o-py/tests/testdir_javapredict/pyunit_javapredict_dynamic_data_paramsGLM.py | Python | apache-2.0 | 3,164 | [
"Gaussian"
] | ca39333cefafad5e2b5d88c238e9685702dad64f793a21b404f1fcf3adeb7974 |
'''
Created on Mar 23, 2015
@author: venkatesan
'''
#import sys
#sys.path.append("/home/venkatesan/Downloads/biopython-1.65/Bio")
from Bio import SwissProt
from riceKB.globalVars import *
import pprint
import re
import os
from _collections import defaultdict
def upToRDF(up_files, rdf_out_dir): #, output_file
... | aravindvenkatesan/AgroLD-scripts | AgroLD_ETL/riceKB/uniprotToRDF.py | Python | cc0-1.0 | 7,725 | [
"Biopython"
] | d8c14428e48035ef70a928a1c790ae8ea0ea4818367bdfdc635a34d1eea0baa1 |
import json
import colorsys
from random import random
from string import upper
from django.http import HttpResponse
from django.contrib.auth.decorators import user_passes_test
from django.contrib.auth.models import User
def access_check(user):
""" Returns true if users are logged in or if they have the general
... | fzadow/CATMAID | django/applications/catmaid/control/user.py | Python | agpl-3.0 | 6,114 | [
"NEURON"
] | d0c06d6a44c4a7eb94613c3a337a5b90dcc694dd4ed863865155dce9d9ba96b9 |
'''
This script gets barcode data from a barcode scanner using serial communication
and sends the state representated by the barcode scanner & the barcode string
to the Galaxy LIMS RabbitMQ server. The message is sent in XML which has 2 tags,
barcode & state. The state of the scanner should be set in the galaxy_amq.i... | volpino/Yeps-EURAC | scripts/galaxy_messaging/client/amqp_publisher.py | Python | mit | 2,944 | [
"Galaxy"
] | 7e7d92cf093a73a358dab1d49ba0f07754ffb77626cade0f7a68d27255b31f89 |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import ddt
import functools
import random
import pytz
import io
import json
import shutil
import tempfile
from urllib import quote
from django.conf import settings
from django.contrib.auth.models import User
from django.core import ... | IndonesiaX/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 212,156 | [
"VisIt"
] | 60f5d7799dc274bc5a5a57b0baade9779467a678743d9cfd967a35ea73182ddb |
# Copyright (c) 2012 Spotify AB
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not
# use this file except in compliance with the License. You may obtain a copy of
# the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, s... | h3biomed/luigi | setup.py | Python | apache-2.0 | 3,094 | [
"VisIt"
] | 33b20a24b125724918e3223ad979c679ecc4be3eea61179b339e4a9ebf682b91 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Written by Lucas Sinclair.
MIT Licensed.
Contact at www.sinclair.bio
"""
# Built-in modules #
# Internal modules #
from seqsearch.databases import Database
from seqsearch.search import SeqSearch
# First party modules #
from autopaths.tmp_path import new_temp_dir... | xapple/seqsearch | seqsearch/databases/nt.py | Python | mit | 2,601 | [
"BLAST"
] | a888a0111cc61ac18db074ea6b5c007eba05e02a487a217f6b35cb8fc8c8fcc6 |
#
# The Python Imaging Library.
# $Id$
#
# the Image class wrapper
#
# partial release history:
# 1995-09-09 fl Created
# 1996-03-11 fl PIL release 0.0 (proof of concept)
# 1996-04-30 fl PIL release 0.1b1
# 1999-07-28 fl PIL release 1.0 final
# 2000-06-07 fl PIL release 1.1
# 2000-10-20 fl PIL release 1.1.1... | FreddieShoreditch/image_folder_organiser | venv/lib/python2.7/site-packages/PIL/Image.py | Python | mit | 81,182 | [
"Gaussian"
] | 541c6ecd6eb97264efcbd69b3534a09e1b0201dd77286e46d67be6cd59665981 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008-2011 Kees Bakker
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2013-2017 Alois Poettker
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Publi... | gramps-project/gramps | gramps/plugins/lib/libprogen.py | Python | gpl-2.0 | 84,341 | [
"Brian"
] | c384ace8ffbefbde19493cf64b4c3592f84b59aef2f9e50506da4618dda2af90 |
from octopus.sequence.runtime import *
from octopus.sequence.util import Trigger
from twisted.internet import reactor
def fn ():
print ("fn called")
return sequence(
log("fn called"),
set(v, False)
)
v = variable(False, "v", "v")
v2 = variable(False, "v", "v")
o1 = Trigger(v == True, fn)
o2 = Trigger(v2 == T... | richardingham/octopus | examples/test_on.py | Python | mit | 593 | [
"Octopus"
] | a5cf9a553da1598a03b2e79bf6a8f04525241739ac25364b8cacb637801c2f47 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from .mooseu... | harterj/moose | python/mooseutils/__init__.py | Python | lgpl-2.1 | 1,976 | [
"MOOSE"
] | 0c7823ee3efa897be7090b1c84d348d2c2c878860124a9a45d1cb0492edabc5d |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
#This file is part of pyAlienFX.
#
# pyAlienFX 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 ... | Findarato/pyalienfx | pyAlienFX_daemon.py | Python | gpl-3.0 | 9,699 | [
"VisIt"
] | c17b7a0d5cde68afcd4a1a2fbeb7e1164f9f61ae87eec2ffebfb643b15b5ae18 |
#!/usr/bin/env python
from __future__ import division
from optparse import OptionParser
import roslib
import rospy
import rosparam
import copy
# import cv: open cv 1 not used
import cv2
import numpy as np
import threading
import dynamic_reconfigure.server
from cv_bridge import CvBridge, CvBridgeError
from sensor_msgs.m... | florisvb/multi_tracker | nodes/liveviewer.py | Python | mit | 10,903 | [
"Firefly"
] | bfcad77327dd06d4f7aa66de7d5c517ed5aab1d3cb79e1f64b548370b49eb9b6 |
#!/usr/bin/python2
import httplib2
import os
import sys
import json
from apiclient.discovery import build
from oauth2client.client import flow_from_clientsecrets
from oauth2client.file import Storage
from oauth2client.tools import argparser, run_flow
# The CLIENT_SECRETS_FILE variable specifies the name of a file t... | SimplifyData/pypu | scripts/build_json_from_youtube.py | Python | gpl-2.0 | 4,612 | [
"VisIt"
] | 87a9c6481f51f7bcc9fcd5b8bcf502aa86490e4198e36b5669912b327c03b7d6 |
## This file is part of Invenio.
## Copyright (C) 2006, 2007, 2008, 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 option) any ... | MSusik/invenio | invenio/legacy/elmsubmit/config.py | Python | gpl-2.0 | 4,355 | [
"VisIt"
] | 43dce4850a02ec614084847d613195cda9c278a3e9898ad8d56a7c14ec79b8a5 |
'''
libChEBIpy (c) University of Manchester 2015
libChEBIpy is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=too-many-arguments
from ._base_object import BaseObject
class Name(BaseObject):
'''Class repr... | libChEBI/libChEBIpy | libchebipy/_name.py | Python | mit | 981 | [
"VisIt"
] | ffd446e1d0d19b16001380b2b5c5e04117fb662c0dcc6af0a3c835b1e380a5ea |
import pycparser.c_ast as c_ast
from pycparserext.ext_c_generator import GnuCGenerator
class CodeGenerator(GnuCGenerator):
def __init__(self, emit_line_numbers=True):
super(CodeGenerator, self).__init__()
self.cur_filename = None
self.cur_line_number = 0
self.emit_line_numbers = em... | KivApple/c_ext | c_ext/codegen.py | Python | mit | 4,860 | [
"VisIt"
] | 635a1b5929e9272fa9325511a37c7815f09900f90b0da45f6b7486457565008e |
"""
nflgame is an API to retrieve and read NFL Game Center JSON data.
It can work with real-time data, which can be used for fantasy football.
nflgame works by parsing the same JSON data that powers NFL.com's live
GameCenter. Therefore, nflgame can be used to report game statistics while
a game is being played.
The p... | icebluesun/nflgame | nflgame/__init__.py | Python | unlicense | 19,483 | [
"VisIt"
] | c09f626c711c6a6039a96968c9f50469c812a35e274422d35eff869182ac79f5 |
from __future__ import absolute_import, division, print_function
from jaspyx.context.block import BlockContext
from jaspyx.visitor import BaseVisitor
class While(BaseVisitor):
def visit_While(self, node):
self.indent()
self.output('while(')
self.visit(node.test)
self.output(') ')
... | ztane/jaspyx | jaspyx/visitor/while_.py | Python | mit | 413 | [
"VisIt"
] | 6a859037328dd5be92b0b5edee0ef0ed3394611da0f255643cacf8f9177c1f40 |
import ast
import optparse
import sys
import typing
from core.cfg import *
from core.expressions import *
from core.statements import *
from visualization.graph_renderer import CfgRenderer
def main(args):
optparser = optparse.OptionParser(usage="python3.6 -m frontend.cfg_generator [options] [string]")
optpar... | gitsimon/spadup-lyra | frontend/cfg_generator.py | Python | mpl-2.0 | 23,329 | [
"VisIt"
] | 7de862e1fd265a7f3b83d8f5aafb923a438083bee4cc7802673740c5896e6486 |
from enum import Enum
import arrow
class Region(Enum):
brazil = "BR"
europe_north_east = "EUNE"
europe_west = "EUW"
japan = "JP"
korea = "KR"
latin_america_north = "LAN"
latin_america_south = "LAS"
north_america = "NA"
oceania = "OCE"
turkey = "TR"
russia = "RU"
@prope... | meraki-analytics/cassiopeia | cassiopeia/data.py | Python | mit | 27,636 | [
"CRYSTAL"
] | 0f79cb9190cebe06ed7c1f660181dc1fe4ee753dba35211dc9a0c4eef23903dc |
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# Copyright 2013 IBM Corp.
# 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
#
# ... | devendermishrajio/nova | nova/tests/unit/network/test_manager.py | Python | apache-2.0 | 167,357 | [
"FEFF"
] | 07f4e358306ed2f770cc70f91b626e8708f4fcee3513f7faca754a02a5cdb394 |
import importlib as il
import os.path
import inspect
import re
import logging
import json
from .ParserData import Struct
from .ParserData import ParseContainer
from .ParserData import StructEncoder
from .QCBase import GenFormatter, VarNames as V
class Parser(object):
FIND_MAX_LINES = 100
def __init__(self, o... | spectre007/CCParser | Parser.py | Python | mit | 11,057 | [
"Gaussian",
"MOLCAS",
"Psi4",
"Q-Chem",
"TURBOMOLE"
] | da74ca20de29cc28dbfb82d708cbb073785e57f02b5a4bddb4267f57e2812331 |
"""Example to solve 3D aqueous foam pipe flow using rheological
Herschel-Bulkley power law for bulk and wall shear stress dependent
slip velocity law for wall layer
"""
import numpy as np
import foam_controlwrapper
from simphony.core.cuba import CUBA
from simphony.api import CUDS, Simulation
from simphony.cuds.meta i... | simphony/simphony-openfoam | foam_internalwrapper/examples/aqueous_foam_slit_flow_steady_state_meso_coupling.py | Python | gpl-2.0 | 6,010 | [
"Mayavi"
] | 5af93565b20ee8f3e498415a1b28dc42ff95bbece44f174c11097e6caab53f86 |
# Copyright 2018 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... | google/differentiable-atomistic-potentials | dap/py/xsf.py | Python | apache-2.0 | 2,354 | [
"ASE",
"CRYSTAL"
] | 461c785ced069e7d1858fbe69dc6e280c821e77ec76dcf9cf55949d4e74171e2 |
#!/usr/bin/env python
import unittest
from decimal import Decimal
from traversal import Node, visit, avg
def d(float_value):
assert float_value is not None
return Decimal(str(float_value))
class NodeTest(unittest.TestCase):
def test_init_node(self):
node = Node(43)
self.assertEqual(node.... | satyrius/traversal | test.py | Python | mit | 1,389 | [
"VisIt"
] | 33f64c750937cddff0c7859568997b6541dfd13e9f3eab12fe42846982fb0228 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 16.3.8
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | adityacs/ansible | lib/ansible/modules/network/avi/avi_pkiprofile.py | Python | gpl-3.0 | 4,715 | [
"VisIt"
] | c9e454da626d90b7d4ae84c69e66bf9b41a8a7830b69dfb233da608c89c58c9a |
#!/usr/bin/env python3
"""
Start the atram preprocessor.
This wrapper module parses the input arguments and passes them to the module
that does the actual preprocessing (core_preprocessor.py).
"""
import argparse
import os
import textwrap
from datetime import date
from glob import glob
from itertools import chain
fro... | juliema/aTRAM | atram_preprocessor.py | Python | bsd-3-clause | 6,668 | [
"BLAST"
] | 3086528a707dbfe8cd6038a457c88d8a31e875975b336e6dc5dc75c43f475252 |
"""
"""
import pickle
import numpy as np
from mayavi import mlab
def plot_catalogue(ax, pickle_fname, vsc):
cat = pickle.load(open(pickle_fname, 'rb'))
ax.scatter(cat.data['longitude'], cat.data['latitude'],
cat.data['depth']*vsc,
s=cat.data['magnitude'], c=cat.data['depth'])
d... | GEMScienceTools/oq-subduction | openquake/sub/plotting/tools.py | Python | agpl-3.0 | 1,766 | [
"Mayavi"
] | 3fe4c3f5cf416b49633e35a60a820ff21a710f0c6ba8b968761dd1102981c606 |
#!/usr/bin/python
#
# Copyright 2017 "OVS Performance" 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 ... | chaudron/ovs_perf | ovs_performance.py | Python | apache-2.0 | 172,751 | [
"TINKER"
] | 5b8b579828433756d9b5b8559f50cd668b72797b54b7152e9f786a8933e47d2f |
"""
vtkImageExportToArray - a NumPy front-end to vtkImageExport
This class converts a VTK image to a Numeric Python array.
To use this class, you must have the LLNL Numeric Python distribution
(http://numpy.sf.net)
Methods
SetInput(input) -- connect to VTK image pipeline
GetArray() -- execute pipeline and ... | sgh/vtk | Wrapping/Python/vtk/util/vtkImageExportToArray.py | Python | bsd-3-clause | 3,919 | [
"VTK"
] | 23e5c73f274c1e1b59760c5353327a807899431b59305b146a9ff9c8292af705 |
import vtk
from vtk.util.vtkAlgorithm import VTKPythonAlgorithmBase
from vtk.numpy_interface import dataset_adapter as dsa
import numpy as np
import matplotlib.pyplot as plt
from itertools import cycle
from timeit import default_timer as timer
import logging
class FilterWorldMesh(VTKPythonAlgorithmBase):
"""
... | lucasplus/MABDI | mabdi/FilterWorldMesh.py | Python | bsd-3-clause | 2,462 | [
"VTK"
] | 36636356632668e4e2467629fdd556a903acb404a82875c8fcd3dffd1edb1258 |
#! /usr/bin/env python
#
# jaxml
# (C) Jerome Alet <alet@librelogiciel.com> 2000-2001
# You're welcome to redistribute this software under the
# terms of the GNU General Public Licence version 2.0
# or, at your option, any higher version.
#
# You can read the complete GNU GPL in the file COPYING
# which should come alo... | denys-duchier/Scolar | config/softs/jaxml-3.01/setup.py | Python | gpl-2.0 | 823 | [
"VisIt"
] | c59b92547235fc448019d121a12f942ff38429ec134038b73b11fa8b57b2d54c |
import urllib.request
import json
data = {
"Inputs": {
"input1":
[
{
'idx': "1",
'age': "1",
'promotion_num': "1",
'identity': "1",
... | cse-ml-project/cse-ml-basic | code/python/churn.py | Python | mit | 1,814 | [
"CRYSTAL"
] | a6329022cd714baab64709a52fa1f06e62d1c0dbb6a9755cc0e55509059d1886 |
"""Tests for items views."""
import os
import json
import tempfile
from uuid import uuid4
import copy
import textwrap
from pymongo import MongoClient
from django.core.urlresolvers import reverse
from django.test.utils import override_settings
from django.conf import settings
from contentstore.tests.utils import Cour... | mtlchun/edx | cms/djangoapps/contentstore/views/tests/test_transcripts.py | Python | agpl-3.0 | 27,376 | [
"FEFF"
] | 0b235c6f8d009b0a4c776ef4b63d6eb3151e6c2d6f6bcabc7cfe05b0a2be845b |
# -*- coding: utf-8 -*-
"""pybooru.resources
This module contains all resources for Pybooru.
SITE_LIST (dict):
Contains various Moebooru and Danbooru-based default sites.
HTTP_STATUS_CODE (dict):
Contains http status codes for Moebooru and Danbooru API.
"""
# Default SITE_LIST
SITE_LIST = {
'konachan':... | LuqueDaniel/pybooru | pybooru/resources.py | Python | mit | 2,102 | [
"MOE"
] | 89d9121d5a998367f8f6ca138f7ba7d061b303733f9bbc120d139aea58b1e877 |
'''
Created on Jan. 8, 2020
A module to load different datasets obtained from the Canadian Surface Prediction Archive (CaSPAr).
@author: Andre R. Erler, GPL v3
'''
## some CDO commands to process CaSPAr data
#
# # get timing of commands (with loops)
# time bash -c 'command' # single quotes; execute in same folder
#... | aerler/GeoPy | src/datasets/CaSPAr.py | Python | gpl-3.0 | 40,304 | [
"NetCDF"
] | 4f63191d4ca0107f100de3079d1dcb1dc44c491cf657d82627fdffb8dd8079e6 |
# for python 3
# You'll need to customize this according to your needs. Proper orientation of
# the kinect is vital; if participants are able to maintain their head or wrists
# continuously inside the word rects, they will repeatedly trigger the collision
# detection
from pykinect2 import PyKinectV2
from pykinect2.PyKi... | jgerschler/ESL-Games | Kinect/Sentence Builder/Deprecated/SentenceBuilderOriginal.py | Python | mit | 10,661 | [
"VisIt"
] | 5aeacf10ad723598cdfda9f536b6989c25386faa00203d002fcc519412c508ab |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/web/epgsearchrss.py | Python | gpl-2.0 | 8,144 | [
"VisIt"
] | 32a4c5723d3ad854493a29147c7023648b3df8d6c8be65301423047bb2c89622 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Version: Sat 27 Apr 2013
# Initial build.
#
"""
Scripts for dealing with the SDSS
Catalogue Archive Server (CAS) and
the results obtained herefrom.
"""
import os
import sys
import time
# Will mechanize work with proxies?
# Maybe I should create a wrapper or use sock... | xidus/ted | ted/sdss/cas.py | Python | bsd-3-clause | 34,382 | [
"Galaxy"
] | 746d9829a180582f73ffd02cf45862181ca2a08a12c99a0ad32efbdebf816397 |
import sys
import urllib.parse
import pycurl
from io import StringIO,BytesIO
import re
import subprocess
from subprocess import check_output
import random
from bs4 import BeautifulSoup
import os
import os.path
import base64
try:
from headlessBrowser import BrowseUrl
except:
from headlessBrowser_webkit import BrowseUr... | kanishka-linux/AnimeWatch | Python-SETUP/AnimeWatch_PyQt5/Plugins/SubbedAnime.py | Python | gpl-3.0 | 82,738 | [
"ADF"
] | e882ec5bc144155ff9083e894b3ef478695df33e3eeed50587810634cbbdf35d |
#! /usr/bin/env python
"""
This script performs event averaging for particle
spectra and anisotropic flow coefficients calculated
from event-by-event simulations
v_n is analyzed up to n = 6
Format for particle_XXX_vndata.dat file:
n_order real_part real_part_err imag_part imag_part... | chunshen1987/HBTcorrelation_MCafterburner | ebe_scripts/average_event_spvn_unitweight.py | Python | mit | 78,494 | [
"Psi4"
] | e151fc03acb9bcb8f7698da9070818f190ef92fcdf8cf2293838ab4f5b8d5ebe |
"""
JupyterHub Spawner to spawn user notebooks on a Kubernetes cluster.
This module exports `KubeSpawner` class, which is the actual spawner
implementation that should be used by JupyterHub.
"""
import asyncio
import os
import signal
import string
import sys
import warnings
from functools import partial
from functools... | jupyterhub/kubespawner | kubespawner/spawner.py | Python | bsd-3-clause | 109,371 | [
"VisIt"
] | 8e8db3c6563e59c514ccc77f0b9c95bc2914412526cbd218ec94c5389396d105 |
# -*- coding: utf-8 -*-
"""
Unitary Event (UE) analysis is a statistical method that
enables to analyze in a time resolved manner excess spike correlation
between simultaneously recorded neurons by comparing the empirical
spike coincidences (precision of a few ms) to the expected number
based on the firing rates of... | pietroquaglio/elephant | elephant/unitary_event_analysis.py | Python | bsd-3-clause | 27,650 | [
"NEURON"
] | f0b9e4df0ac9e044386c539826ed5a8773b727292b0b7784c32f382e17f2d803 |
import threading
#Because eval(valenc) might require it
import datetime
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import DEncode, List
from DIRAC.Core.Base.ExecutorModule import ExecutorModule
from DIRAC.WorkloadManagementSystem.Client.JobState.CachedJobState import CachedJobState
class Optimi... | vmendez/DIRAC | WorkloadManagementSystem/Executor/Base/OptimizerExecutor.py | Python | gpl-3.0 | 6,380 | [
"DIRAC"
] | 6fc0da56a3d7aba1b2f359816823cf86573e009e7bad1be1d80dd3d7b836a356 |
''' PolicyCaller
Module used for calling policies. Its class is used for invoking
real policies, based on the policy name.
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import S_ERROR
from DIRAC.ResourceStatusSystem.Utilities import Ut... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/PolicySystem/PolicyCaller.py | Python | gpl-3.0 | 2,830 | [
"DIRAC"
] | a5884f9d852fc29a69f370afa84070b258ed7d4d635fd9ac37e13f7940e7979e |
#!/usr/bin/env python
"""Tests for alignedsignal.py"""
########################################################################
# File: alignedsignal_test.py
# executable: alignedsignal_test.py
#
# Author: Andrew Bailey
# History: Created 03/09/18
#######################################################################... | UCSC-nanopore-cgl/nanopore-RNN | nanotensor/tests/alignedsignal_test.py | Python | mit | 12,508 | [
"BWA"
] | a54adb1f42be194734277aa804c3a7901bd311b39650b372df60e00f56885724 |
import os
import sys
import numpy
import platform
import sysconfig
try:
from setuptools import setup, Extension
use_setuptools = True
print("setuptools is used.")
except ImportError:
from distutils.core import setup, Extension
use_setuptools = False
print("distutils is used.")
try:
from se... | atztogo/phono3py | setup.py | Python | bsd-3-clause | 12,839 | [
"phonopy"
] | a362bb50fe860755488efb5129ed917d12c6dbbc54b979d1d32dc04972a9416e |
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 06 14:25:40 2017
@author: Zhenqin Wu
"""
import os
import time
import csv
import numpy as np
import tensorflow as tf
import deepchem
import pickle
from deepchem.molnet.run_benchmark_models import benchmark_classification, benchmark_regression
from deepchem.molnet.check_av... | lilleswing/deepchem | deepchem/molnet/run_benchmark.py | Python | mit | 12,434 | [
"Gaussian"
] | 779917c312042b146eb7b1f8905d57a8eff7d9004d778888369d09539799712f |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011, 2012, 2013 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 ... | jmartinm/invenio | modules/bibupload/lib/batchuploader_engine.py | Python | gpl-2.0 | 29,348 | [
"VisIt"
] | 0b1366c20019258c32dbd5bc381e8ce99c1c94c5451e6eb2730dfc8a4b05016a |
#!/usr/bin/env python
# errors.py
#
# Copyright (C) 2014 Kano Computing Ltd.
# License: http://www.gnu.org/licenses/gpl-2.0.txt GNU General Public License v2
#
#
# Standard Errors
#
# This file only contains typical errors to be reported on the UI.
INTERNET_ERROR = {
'title': 'No internet connection..',
'des... | KanoComputing/kano-burners | src/common/errors.py | Python | gpl-2.0 | 1,964 | [
"VisIt"
] | a8ebbf6ed8aa4fd209fb6ce641dc46ef98576a9ccf7deb78641e72a76f857c1b |
'''
This function loads one random recording from CinC Challenge and use pre-trained model in predicting what it is using Residual Networks
For more information visit: https://github.com/fernandoandreotti/cinc-challenge2017
Referencing this work
Andreotti, F., Carr, O., Pimentel, M.A.F., Mahdi, A., & De Vos, M. ... | fernandoandreotti/cinc-challenge2017 | deeplearn-approach/predict.py | Python | gpl-3.0 | 3,999 | [
"VisIt"
] | f1f29a1259d59a50048c3557148b32225d544bd24bb7ec2511adaf52b2cfeda2 |
"""
[2017-09-20] Challenge #332 [Intermediate] Training for Summiting Everest
https://www.reddit.com/r/dailyprogrammer/comments/71gbqj/20170920_challenge_332_intermediate_training_for/
# Description
You and your friend wish to summit Mount Everest the highest peak in the world. One problem: you live at sea level and
... | DayGitH/Python-Challenges | DailyProgrammer/DP20170920B.py | Python | mit | 2,176 | [
"VisIt"
] | c909181a0e124d6456b79112b77bfa98ec17ea8a55b02e777f857b3301129c03 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import sys
i... | harterj/moose | python/TestHarness/__init__.py | Python | lgpl-2.1 | 637 | [
"MOOSE"
] | f86c20595dd02d056c9a096781b2a40757d1df496ebef4afc863277d382c2dc2 |
# HF XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
# HF X
# HF X f90wrap: F90 to Python interface generator with derived type support
# HF X
# HF X Copyright James Kermode 2011
# HF X
# HF X These portions of the source code are released under the GNU General
# HF X Public License, ve... | davidovitch/f90wrap | f90wrap/transform.py | Python | gpl-2.0 | 42,373 | [
"VisIt"
] | 6d8a31ae7d43abc3dfe60811a8493edfa9e59816c58bca0d33259b0632635db8 |
"""
Traits View definition file.
The view trait of the parent class has been extracted from the model
definition file. This file can either be exec()ed or imported. See
core/base.py:Base.trait_view() for what is currently used. Using exec()
allows view changes without needing to restart Mayavi, but is slower than
i... | dmsurti/mayavi | mayavi/components/ui/contour.py | Python | bsd-3-clause | 1,652 | [
"Mayavi"
] | b8ca25daa4e087a96decb2c8d2842bd90108db097bcafeaf5e8bcb781f8c4292 |
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from datetime import date, timedelta
from workalendar.core import WesternCalendar, ChristianMixin
from workalendar.core import SUN, MON, TUE, WED, THU, FRI, SAT
class UnitedStates(West... | ChrisStevens/workalendar | workalendar/america.py | Python | mit | 6,675 | [
"COLUMBUS"
] | 705c1067928c83223faa4d3482cf1c1be47b4df68ef603a3d622691c7288043a |
import sys
import mechanize
import re
import json
import time
import urllib
import dogcatcher
import HTMLParser
import os
h = HTMLParser.HTMLParser()
cdir = os.path.dirname(os.path.abspath(__file__)) + "/"
tmpdir = cdir + "tmp/"
voter_state = "MI"
source = "State"
result = [("authority_name", "first_name", "last_na... | democracyworks/dog-catcher | michigan.py | Python | mit | 14,550 | [
"CRYSTAL"
] | 4b98324201c8ec758b0c77c2e6046e430e84b301a8dc089367ddb1fd6aed5faa |
# TODO: Determine which tests are valid for GLSAR, and under what conditions
# TODO: Fix issue with constant and GLS
# TODO: GLS: add options Iterative GLS, for iterative fgls if sigma is None
# TODO: GLS: default if sigma is none should be two-step GLS
# TODO: Check nesting when performing model based tests, lr, wald,... | bert9bert/statsmodels | statsmodels/regression/linear_model.py | Python | bsd-3-clause | 103,184 | [
"Gaussian"
] | 63fee05f3692770b52f13c423920014e061b0b73ce198172c4b14d5835483d28 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
""" Script to test the precise aeif behaviours """
import argparse
from itertools import chain
import time
import numpy as np
import matplotlib
import matplotlib.cm as cm
import matplotlib.pyplot as plt
from matplotlib import rcParams
import nest
from nest.raster_plot imp... | Silmathoron/nest-models | test/compare_aeif_gp.py | Python | gpl-2.0 | 7,109 | [
"NEURON"
] | 727654dbe75b0a63f4959f45dcb904ee3f2722a2a413e8bcb7acfd3c0b2d21d4 |
#!/usr/bin/env python
"""
Install.py tool to download, unpack, build, and link to the plumed2 library
used to automate the steps described in the README file in this dir
"""
from __future__ import print_function
import sys, os, subprocess, shutil
from argparse import ArgumentParser
sys.path.append('..')
from install... | timattox/lammps_USER-DPD | lib/plumed/Install.py | Python | gpl-2.0 | 5,096 | [
"LAMMPS"
] | b6883fbd256404857836e9550346ad45f112c4c205444c16b4337c0e2524acd5 |
import numpy as np
from traits.api import HasTraits, Instance, Button, \
on_trait_change
from traitsui.api import View, Item, HSplit, Group
from mayavi import mlab
from mayavi.core.ui.api import MlabSceneModel, SceneEditor
class MyDialog(HasTraits):
scene1 = Instance(MlabSceneModel, ())
scene2 = Instan... | HPCGISLab/STDataViz | WorkingVersion/LibTry/MayaviGUI/mlabMultiScene.py | Python | bsd-3-clause | 1,603 | [
"Mayavi"
] | 7a5f7ec42a74654abac515d9376116ad75240bc4633b65383c5ea86dc6026438 |
#!/usr/bin/env python
#
# Copyright 2007 Google 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 o... | octavioturra/aritial | google_appengine/google/appengine/ext/bulkload/transform.py | Python | apache-2.0 | 14,943 | [
"VisIt"
] | ead9098c59b0bfb436163e231e3feb2b388c71004ba9dbbfb2aef6a6c2ccfe8b |
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
import sys
# Add path to Bio
sys.path.append('../../..')
"""Perform two-point crossovers between the genomes of two organisms.
This module performs... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/GA/Crossover/Point.py | Python | gpl-2.0 | 1,060 | [
"Biopython"
] | 1ad64c7da8f2565bd0f6661a8e7c4e7a5348ea7116728c4c155616c38185a5a8 |
# -*- 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
from photologue.views import PhotoListView, GalleryListVi... | javierwilson/forocacao | config/urls.py | Python | bsd-3-clause | 1,579 | [
"VisIt"
] | 31e692104d8de59370c6f8c2d93f3544654632c3d83f83e14448748e6e5a7f90 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
import time
import threading
import urllib.parse
import re
import datetime
from bs4 import BeautifulSoup
import pymongo.... | geezhawk/palantiri | src/core/crawler.py | Python | mpl-2.0 | 6,339 | [
"VisIt"
] | 5188c1aa2292a9acb6cbc501b28667980bc56ebed9fac21f9ad7d39622d017e8 |
""" ProxyRepository class is a front-end to the proxy repository Database
"""
__RCSID__ = "$Id$"
import time
import random
import types
import hashlib
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Base.DB import DB
from DIRAC.Core.Security.X509Request import X509Request
from DIRAC.Core.Security.... | marcelovilaca/DIRAC | FrameworkSystem/DB/ProxyDB.py | Python | gpl-3.0 | 43,566 | [
"DIRAC"
] | 82ca59a49bc1c6c10fecc5bae82dda166baebcc5f845db76a04fab018eb68c3c |
# -*- coding: utf-8 -*-
#########################################################################
#
# Copyright (C) 2016 OSGeo
#
# 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 ... | ppasq/geonode | geonode/security/tests.py | Python | gpl-3.0 | 57,433 | [
"VisIt"
] | 2d24670fa908089867012730ad55b1d65e248b01b2f3886ab9a1abf6a42fefd0 |
'''
user interface for viewing genesis simulation results
'''
import sys
import os
import csv
import time
import matplotlib
# check if Xserver is connected
# havedisplay = "DISPLAY" in os.environ
# if not havedisplay:
# # re-check
# exitval = os.system('python -c "import matplotlib.pyplot as plt; plt.figure()"')
# ha... | sserkez/ocelot | gui/genesis_plot.py | Python | gpl-3.0 | 99,812 | [
"Gaussian"
] | fbc78a2d6e38e2d408caddd8eeddc80dfbdbc8da02858e3b03d17a563916ac9f |
""" This contains unit tests to make sure that the migration between PyGSI and M2Crypto is as smooth as possible
The test covers only the method exposed by the PyGSI version for the time being.
We are not testing:
* generateProxyRequest with bitStrengsh -> I should...
* getIssuerDN: does not make any ... | yujikato/DIRAC | src/DIRAC/Core/Security/test/Test_X509Request.py | Python | gpl-3.0 | 3,251 | [
"DIRAC"
] | 4de2d203b9b082bdc46e15b6d83207878818812fbc9a623e569f463fd7c4ca53 |
# -*- coding: utf-8 -*-
""" Sahana Eden Climate Model
@copyright: 2011-2014 (c) Sahana Software Foundation
@license: MIT
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 witho... | julianprabhakar/eden_car | modules/s3db/climate.py | Python | mit | 27,377 | [
"NetCDF"
] | a00cb021d4d4e613de5f02532f63485bbe0ebb342a874381def0494bcef9e7bc |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Interface to ASE Atoms, and Calculators.
"""
import logging
import qmpy
from qmpy.materials.structure import Structure
from qmpy.materials.atom import Atom
logger = logging.getLogger(__name__)
if qmpy.FOUND_ASE:
import ase
import ase.io
def structure_to_at... | wolverton-research-group/qmpy | qmpy/io/ase_mapper.py | Python | mit | 2,038 | [
"ASE"
] | 7c10b758666611462830e0b7009f7aa4e92d35d68952f3d160b1101d9b72375c |
#! /usr/bin/env python
__author__ = 'Chengwei Luo (luo.chengwei@gatech.edu)'
__version__ = '0.0.1'
__date__ = 'November 2013'
"""
metaHGT (meta-community Horizontal Gene Transfer tracker):
in-situ and real time HGT tracker for series metagenomes
Copyright(c) 2013 Chengwei Luo (luo.chengwei@gatech.edu)
This prog... | fw1121/metaHGT | src/metaHGT.py | Python | gpl-3.0 | 15,284 | [
"BWA"
] | feca812ff95cb5851451a5c6f46b71be7158ba21bf8fb76f195d4108fdb27511 |
import re
def find_n_elect(file_name):
log_file = open('%s' % file_name)
for line in log_file:
if 'alpha electrons' in line:
alpha = int(line.split()[0])
beta = int(line.split()[3])
n_ele = alpha + beta
break
return n_ele, alpha, beta
def find_homo(... | Wo0o0o0ble/stags | g09_grab_numbers.py | Python | gpl-3.0 | 6,321 | [
"Gaussian"
] | 7c8e9384cdba57fec0a1a8872c8657ec7f31ef8edb9cfe6814fee8d82f947f15 |
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