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""" This object is a wrapper for setting and getting jobs states
"""
from __future__ import print_function, absolute_import
__RCSID__ = "$Id"
import datetime
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.WorkloadManagementSystem.Client.JobState.JobManifest import JobManifest
from DIRAC.WorkloadManagementSyste... | fstagni/DIRAC | WorkloadManagementSystem/Client/JobState/JobState.py | Python | gpl-3.0 | 14,396 | [
"DIRAC"
] | 8392db0c5282d49c7f218f089857ca0bd4e02a789fde62abcc12b406fdc239b6 |
"""add distinct visit counts
Revision ID: 3513057132ca
Revises: ed28b84f061e
Create Date: 2019-03-01 16:36:41.722682
"""
import sqlalchemy as sa
from alembic import op
# revision identifiers, used by Alembic.
revision = "3513057132ca"
down_revision = "ed28b84f061e"
branch_labels = None
depends_on = None
def upgrad... | all-of-us/raw-data-repository | rdr_service/alembic/versions/3513057132ca_add_distinct_visit_counts.py | Python | bsd-3-clause | 1,149 | [
"VisIt"
] | e01d42d6156bdf295493b2b2546f5bbd59a5443d675bfb34fa7de1c36d9e1611 |
# -*- 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
urlpatterns = [
# Django Admin
url(r'^admin/', include(admin.site.urls)),
# User managemen... | goldhand/link-shortener | config/urls.py | Python | bsd-3-clause | 1,068 | [
"VisIt"
] | 22cb7ab9a12c678398edd54d2919245ca1dc5e87f66370017463e19e553b309d |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# This example shows how to visualise the variation in shape in a set of objects using
# vtkPCAAnalysisFilter.
#
# We make three ellipsoids by distorting and translating a sphere and ... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Hybrid/Testing/Python/TestPCA.py | Python | gpl-3.0 | 8,348 | [
"VTK"
] | f3a403b1524854268ff83f1ef05840f96944526d9c89acb08c324190eeb8bae2 |
# -*- coding: utf-8 -*-
"""
(c) 2019 - Copyright Red Hat Inc
Authors:
Pierre-Yves Chibon <pingou@pingoured.fr>
"""
from __future__ import unicode_literals, absolute_import
import arrow
import copy
import datetime
import unittest
import shutil
import sys
import time
import os
import flask
import json
import m... | pypingou/pagure | tests/test_pagure_flask_api_fork_update.py | Python | gpl-2.0 | 26,863 | [
"VisIt"
] | ef9db5067d91953424d2da5beee46394fffbd72b6accf587fc4871da047e4703 |
"""
This sample illustrates how particles of interest can be accessed via slicing.
"""
#
# Copyright (C) 2013-2018 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 Fr... | hmenke/espresso | samples/slice_input.py | Python | gpl-3.0 | 2,975 | [
"ESPResSo"
] | 70422cc2c081fae20aa5b872a79d78473c86861002896f0a947ad5c7a3243ad1 |
# proxy module
from __future__ import absolute_import
from mayavi.filters.extract_unstructured_grid import *
| enthought/etsproxy | enthought/mayavi/filters/extract_unstructured_grid.py | Python | bsd-3-clause | 109 | [
"Mayavi"
] | 36cc5f765ea43df68b6fdfe423ae78be8ed0aee17023f63a1bf5f2e17f14f658 |
../../../../../../../share/pyshared/orca/scripts/apps/planner/speech_generator.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/planner/speech_generator.py | Python | gpl-3.0 | 81 | [
"ORCA"
] | 4e30b0dc7cdbaa5a4ae2487caf04295647abba9164a07d22912d8b4c721235e7 |
from __future__ import print_function
from builtins import zip
from builtins import range
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
import random
def random_attack():
def attack(family, train, valid, x, y):
... | YzPaul3/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_NOPASS_random_attack_medium.py | Python | apache-2.0 | 5,702 | [
"Gaussian"
] | 4c2567c666227ee6c3d80d80ead4af99b11993bcafcea78cc71108fa89bcf61e |
# Hidden Markov Model Implementation
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 roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/force_codes/true_false_cases/continuous_hmm_final_true_prediction2.py | Python | mit | 9,391 | [
"Gaussian",
"Mayavi"
] | efd2387d75fec96fc4a671c43e6074b3f3d5bfb0b3129838554f693ca846be33 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to store, generate, and manipulate material interfaces.
"""
from itertools import product
from typing import Iterator, Optional, Tuple, Union
import numpy as np
from scipy.linalg import polar
... | vorwerkc/pymatgen | pymatgen/analysis/interfaces/coherent_interfaces.py | Python | mit | 10,512 | [
"pymatgen"
] | 1554af97c7562f51b969d1889359319b947592bdac7b5332c0e8f1a1bfff635a |
import re
import models.job_keyword_type as keyword_type
keywords = {
# Keywords with spaces are prioritized
'A-0 System': {
'keyword': 'A-0 System',
'type': keyword_type.types['PROGRAMMING_LANG']
},
'ABC ALGOL': {
'keyword': 'ABC ALGOL',
'type': keyword_type.types['PR... | Mo-Talha/Nomad | data/analysis/corpus/computerscience/keywords.py | Python | mit | 171,855 | [
"GULP",
"ORCA",
"Octopus"
] | 1911255a21c7cd497f27a550b954fbaab29eba29ab5d8adcaf8a767bb843f509 |
import numpy as np
import numpy.ma as ma
import pylab as plt
import cmocean as cm
from scipy import linalg
from scipy.interpolate import interp2d,interp1d
from scipy.optimize import curve_fit,leastsq,least_squares
from scipy.optimize import minimize
from scipy import ndimage
from scipy.stats import pearsonr
from scip... | Josue-Martinez-Moreno/trackeddy | trackeddy/geometryfunc.py | Python | mit | 36,023 | [
"Gaussian"
] | e97843d3d754ac83bd30ef3676a4454d6afb5373340016ee61dbdb9347084ec7 |
#!/usr/bin/python
#//Library/Frameworks/Python.framework/Versions/Current/bin/python
from __future__ import division
from sys import *
import math
import string
import numpy as np
from scipy import linalg
import random
import time
import copy
#import matplotlib.pyplot as plt
#import ManyBodyHilbert as mbh
# MIRMOD B... | kingfisher1337/tns | ising_entanglement_spectrum_laeuchli/IsingPEPS_optimized.py | Python | gpl-3.0 | 5,443 | [
"Mayavi"
] | ee65205dfd83a245160fb0ecfb67038908e5f69d9bc3f2ae8d2c3cbfbbbefc0c |
#!/usr/bin/env python
from __future__ import division, print_function
from bisect import bisect
from collections import defaultdict
import csv
from functools import partial
from itertools import imap, islice, takewhile
import os
import random
import warnings
import numpy as np
from vlfeat.phow import (vl_phow, DEFAU... | dougalsutherland/py-sdm | sdm/extract_image_features.py | Python | bsd-3-clause | 17,660 | [
"Gaussian"
] | 9bd8bf7a042fa9788881ee100d2cb12eaa760ad01b73161658c35fe1ee5b1c1c |
from dict_utils import deep_merge
from yaml_util import explain
from sync import sync_is_enabled, sync
from config import settings
import commands
import environment
import extension_manager
import logger
import paths
import config
def run():
cli_args = commands.parse_allay_args()
deep_merge(settings, paths.l... | orionnetworksolutions/Allay | allay/__init__.py | Python | mit | 1,566 | [
"Brian"
] | ae102ea2bab62026e8e75d89797fdc403d8781107df5fa40512ea7fce4f280cf |
import os
import unittest
import mock
from kalliope.core.NeuronModule import MissingParameterException
from kalliope.neurons.say.say import Say
class TestSay(unittest.TestCase):
def setUp(self):
self.message = "message"
self.random = "random"
self.pico_say_method_path = "kalliope.tts.pi... | kalliope-project/kalliope | kalliope/neurons/say/tests/test_say.py | Python | gpl-3.0 | 3,491 | [
"NEURON"
] | 09a9b453936f64837d2923ba45db1ce46874617e8102cf30a775e62d90e07144 |
# 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.
#
"""Dynamic Programming algorithms for general usage.
This module contains classes which implement Dynamic Programming
algorithms that can be used ge... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/HMM/DynamicProgramming.py | Python | gpl-2.0 | 12,772 | [
"Biopython"
] | dea29d9d3f43999480fb740bf31221c421cb4f55873e92ba5a6e781ac4856278 |
"""
@name: Modules/House/Lighting/_test/test_utility.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2019-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Jan 20, 2019
@summary: Test
"""
__updated__ = '2020-02-17'
# Import system type stuff
from twisted... | DBrianKimmel/PyHouse | Project/src/Modules/House/Lighting/_test/test_utility.py | Python | mit | 5,647 | [
"Brian"
] | 33f6ae77f7948b606f6f65d75d6c2c88659ef9e2a29d70a36667fdfed6e306c1 |
# 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... | capoe/espressopp.soap | src/integrator/StochasticVelocityRescaling.py | Python | gpl-3.0 | 1,924 | [
"ESPResSo"
] | ddfb3d27b88830aa1afc9c8d1aaffa976ff3a2ac521a286e0e9ffad620e3fa26 |
from setuptools import setup, find_packages
def readme():
with open("README.md", 'r') as f:
return f.read()
setup(
name="idnest",
description="A RESTful API for nested identifier association",
version="0.0.1",
long_description=readme(),
author="Brian Balsamo",
author_email="balsa... | uchicago-library/idnest | setup.py | Python | gpl-3.0 | 685 | [
"Brian"
] | ed0a81e11643d96e6d984f2dbda881f5e6c9e4836c2bc3901bf72afbc746dbfd |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/utils/Platform/generic/generic_GetIPAddressV6.py | Python | gpl-3.0 | 2,158 | [
"ORCA"
] | 037268c00b83fccf1babb66508207c014e05c67f6510cc339251885f5c132710 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-configure
# Author : Ricardo Graciani
########################################################################
"""
Main script to write dirac.cfg for a new DIRAC installation and initial downl... | avedaee/DIRAC | Core/scripts/dirac-configure.py | Python | gpl-3.0 | 17,643 | [
"DIRAC"
] | 6763c628d270a01dfeadac9065aba290c30fd33ef156e314917ec0bbe2ab53a3 |
#* 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 os, ... | nuclear-wizard/moose | python/TestHarness/XMLDiffer.py | Python | lgpl-2.1 | 12,190 | [
"MOOSE",
"VTK"
] | 5aef00e7ac9df1baf0977d2e03c83ce8f73d849bf7676b32b5a6ee274fe3d549 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Final/results/objects/6/test10_cross_validate_objects_6_1200ms.py | Python | mit | 4,252 | [
"Mayavi"
] | efd3772ba4648595084d8fd06495267292d524982b4e5eed3aea28659f8470d5 |
# Lint as: python3
# Copyright 2018 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 ... | tensorflow/lingvo | lingvo/core/layers_with_attention.py | Python | apache-2.0 | 113,676 | [
"Gaussian",
"MOE"
] | 2fdfd6cd6e2d4d4ccf91f1fccc2c3f128121d7e8c666cdcf16734bf889d88ccb |
#
# Copyright (C) 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 vers... | mkuron/espresso | doc/tutorials/04-lattice_boltzmann/scripts/part4_plot.py | Python | gpl-3.0 | 1,625 | [
"ESPResSo"
] | 4c3b68c1eaa26f49d8d6ed6be2d7a79186c567141fd7a6d8239c6a6a412cd916 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | vinodpanicker/scancode-toolkit | src/textcode/strings.py | Python | apache-2.0 | 9,392 | [
"VisIt"
] | 7862e7f6cead6962e576cf956af72ffa99c77a538e0ad04acd2a86d163f2133a |
# -*- coding: utf-8 -*-
import numpy as np
from scipy.stats import multivariate_normal
from pgmpy.factors.distributions import BaseDistribution
class GaussianDistribution(BaseDistribution):
"""
In its most common representation, a multivariate Gaussian distribution
over X1, X2, ..., Xn is characterized b... | pgmpy/pgmpy | pgmpy/factors/distributions/GaussianDistribution.py | Python | mit | 19,796 | [
"Gaussian"
] | a486d08cf00e654dcfde6a1fe7251e3979b7f7d27e822bb98ab43304cf8b83e3 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""The 'grit android2grd' tool."""
import getopt
import os.path
import StringIO
from xml.dom import Node
import xml.dom.minidom
... | hujiajie/chromium-crosswalk | tools/grit/grit/tool/android2grd.py | Python | bsd-3-clause | 19,036 | [
"xTB"
] | 8727579d9eb8ec8e6efcb5b3e0cece5b09c5f23911e871aab564655640cdd663 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
###########################################################################
# ESPResSo++ #
# Test script for Tabulated potentials (LJ, FENE, Cosine) #
# ... | acfogarty/espressopp | testsuite/tabulated/polymer_melt_tabulated.py | Python | gpl-3.0 | 7,649 | [
"ESPResSo",
"Gromacs",
"LAMMPS"
] | 307e3f63281336b1268def00f8c90e086c3c40b027706399fb1e49b813417d7b |
#!/usr/bin/env python
"""Description:
Setup script for CRISPResso -- Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from deep sequencing data
@status: beta
@version: $Revision$
@author: Luca Pinello
@contact: lpinello@jimmy.harvard.edu
"""
import os
import sys
import re
from setuptools imp... | lucapinello/CRISPResso | setup.py | Python | agpl-3.0 | 7,878 | [
"Biopython"
] | 525767d47f8080f6d76169f0956b6519810515e1ad1ee40e8d81c72cdfbf68e3 |
import pytest
from stellar_sdk import (
Asset,
MuxedAccount,
Network,
RequestsClient,
Server,
TransactionEnvelope,
)
from stellar_sdk.account import Thresholds
from stellar_sdk.call_builder.call_builder_sync import *
@pytest.mark.slow
class TestServerSync:
def test_load_acount(self):
... | StellarCN/py-stellar-base | tests/test_server_sync.py | Python | apache-2.0 | 6,890 | [
"MOE"
] | 62f999a2578de19ba3eb1faf17e87174664b59304464aea48283b62db788468f |
"""Contains the drivers and interface code for pinball machines which
use the Multimorphic P3-ROC hardware controllers.
Much of this code is from the P-ROC drivers section of the pyprocgame project,
written by Adam Preble and Gerry Stellenberg. It was originally released under
the MIT license and is released here unde... | qcapen/mpf | mpf/platform/p3_roc.py | Python | mit | 52,637 | [
"Brian"
] | c5e556ba4a7b057a72212835dbceeb6e4650b0ce061a5ea44563c9fbf450857e |
# Copyright (C) 2010-2018 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 v... | hmenke/espresso | testsuite/python/observable_cylindrical.py | Python | gpl-3.0 | 8,897 | [
"ESPResSo"
] | 1e127c3fbd9eaeee4f27795f50bc1541044622666350108434f5a40c2dccc22b |
#!/usr/bin/python
#
# Author: Rajesh Sinha, Karan Narain
# from altmetric
import logging
import sys
from bs4 import BeautifulSoup
import urllib2
import re
import config
from apiclient import discovery
import json
import pandas as pd
## Some Important constants
_parser = "lxml" ## remember to pip install... | sinharrajesh/dbtools | google-plus-analysis/dump2.py | Python | apache-2.0 | 2,803 | [
"ADF"
] | 5d1072cb0d107394dcbb93798aa3568cb60d72ae3d64b45799b10d1f1557bbfe |
import numpy as np
from numpy import linalg
from ase.transport.selfenergy import LeadSelfEnergy, BoxProbe
from ase.transport.greenfunction import GreenFunction
from ase.transport.tools import subdiagonalize, cutcoupling, tri2full, dagger
class TransportCalculator:
"""Determine transport properties of device sand... | freephys/python_ase | ase/transport/calculators.py | Python | gpl-3.0 | 11,688 | [
"ASE"
] | 8d37a83252e63cee6459e721681b981b24aaaad1b4c2517a0b61b04fe360c8a5 |
#!/usr/bin/env python
# Copyright (C) 2014 Swift Navigation Inc.
# Contact: Colin Beighley <colin@swift-nav.com>
#
# This source is subject to the license found in the file 'LICENSE' which must
# be be distributed together with this source. All other rights reserved.
#
# THIS CODE AND INFORMATION IS PROVIDED "AS... | gsmcmullin/piksi_firmware | scripts/one_click_update.py | Python | gpl-3.0 | 11,162 | [
"VisIt"
] | 30f622c96f8e2b77825ad1fe6f5c5fafc24484234ea750bb7b766a6086e93513 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2013 The Plaso Project Authors.
# Please see the AUTHORS file for details on individual 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 L... | iwm911/plaso | plaso/parsers/winjob.py | Python | apache-2.0 | 8,761 | [
"Brian"
] | a63edf3001338d57973802bd981f9ecfccae03e4c148456f8166cfd6563f8654 |
# GromacsWrapper: run.py
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
:mod:`gromacs.run` -- Running simulations
=========================================
Helper functions and classes around :class:... | jandom/GromacsWrapper | gromacs/run.py | Python | gpl-3.0 | 12,589 | [
"Gromacs"
] | 4c5d58846437a2abb3e13cf428037e95f24219b501066b921d4b78c678dbcafa |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# This example converts data to a field and then displays it using
# parallel coordinates,
# Create a reader and write out the field
reader = vtk.vtkUnstructuredGridReader()
reader.S... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Rendering/Core/Testing/Python/TestParallelCoordinates.py | Python | gpl-3.0 | 1,467 | [
"VTK"
] | bf54233e2a8609046434d3d661fd1c0a7cab41bf6a35b1e27a50ce8be2da8c2b |
#
# 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... | tgroh/beam | sdks/python/apache_beam/runners/portability/fn_api_runner.py | Python | apache-2.0 | 54,155 | [
"VisIt"
] | c47c7fbed96e83715008ade828c7629d1ea1a94f5f8968096a6af4931591648d |
# -*- coding: utf-8 -*-
"""Functions to make 3D plots with M/EEG data."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Mainak Jas <maina... | bloyl/mne-python | mne/viz/_3d.py | Python | bsd-3-clause | 139,640 | [
"Mayavi"
] | 822acc7b7824c92c6bec0a60ef18e961ab834b2ea001d0e905b3cabd5410ba4b |
#!/usr/bin/env python3
########################################################################
# Solves problem 27 from projectEuler.net.
# Finds the 2 coeficients of a quadratic function that generates the
# longest sequence of primes and return the product.
# Copyright (C) 2010 Santiago Alessandri
#
# Th... | sanSS/programming-contests | project-euler/problem027.py | Python | gpl-3.0 | 1,626 | [
"VisIt"
] | 1612138ff7f09bfd00edfcbb7719d52c63e5cbe33be3354fdccddf4d371953c3 |
import os
import unittest
import vtk, qt, ctk, slicer
import math
import sys
#
# AstroModelingSelfTest
#
class AstroModelingSelfTest:
def __init__(self, parent):
parent.title = "Astro Modeling SelfTest"
parent.categories = ["Testing.TestCases"]
parent.dependencies = ["AstroVolume"]
parent.contributo... | Punzo/SlicerAstro | AstroModeling/Testing/Python/AstroModelingSelfTest.py | Python | bsd-3-clause | 6,102 | [
"VTK"
] | 8001760f6ec3ea9be0fd32af3cbcacbe30529744c050492c8738b7b78870f2f3 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | ravibhure/ansible | lib/ansible/modules/network/avi/avi_applicationpersistenceprofile.py | Python | gpl-3.0 | 6,681 | [
"VisIt"
] | 1b83f4cf44f3ad0145bb3ee23e6532955e0e6fe82da5353775f62a6cb32af7c1 |
from ase.structure import bulk
from gpaw import GPAW, FermiDirac
def groundstate(a, k):
si = bulk('Si', 'diamond', a)
si.calc = GPAW(kpts=(k, k, k),
xc='PBE',
gpts=(20, 20, 20),
occupations=FermiDirac(0.01),
parallel={'domain': 1},
... | ajylee/gpaw-rtxs | doc/tutorials/pbe0/si_pbe.py | Python | gpl-3.0 | 414 | [
"ASE",
"GPAW"
] | a8a98402aab1763e6417f97f3b438396534d56ccbb724ae0de0917e7fad1e23a |
import re
from .. import factories as f
def test_regional_lead_flow(base_url, browser, outbox):
f.create_usertype(slug='tutor', display_name='tutor')
user = f.create_user(is_staff=True)
user.set_password('123123')
user.save()
user2 = f.create_user()
user2.set_password('123123')
user2.save... | shankisg/wye | tests/functional/test_regional_lead_flow.py | Python | mit | 1,922 | [
"VisIt"
] | e653ba581878c041ab3100895fe1883db3f0eefea3eafb8ddc86c12df77c522e |
# -*- coding: utf-8 -*-
from nose import SkipTest
from nose.tools import eq_, ok_, assert_raises
from parsimonious import Grammar, NodeVisitor, VisitationError, rule
from parsimonious.nodes import Node
class HtmlFormatter(NodeVisitor):
"""Visitor that turns a parse tree into HTML fragments"""
grammar = Gram... | lucaswiman/parsimonious | parsimonious/tests/test_nodes.py | Python | mit | 4,296 | [
"VisIt"
] | 3a9bc759347a07ebcd53170669d7c72bda51c05b956db605cba58badae03008e |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# ... | SKIRT/PTS | evolve/tests/Rastrigin/test.py | Python | agpl-3.0 | 7,146 | [
"Gaussian"
] | 58e5bc040f840625c561ff9e46d663218944d32127fa29714f7b7e950c94bf15 |
#
# Copyright (C) 2000 greg Landrum
#
""" unit testing code for trees and decision trees (not learning/xvalidation) """
from __future__ import print_function
import unittest
import copy
from rdkit import RDConfig
from rdkit.ML.DecTree import Tree,DecTree
from rdkit.six.moves import cPickle
class TreeTestCase(unitt... | adalke/rdkit | rdkit/ML/DecTree/UnitTestTree.py | Python | bsd-3-clause | 2,989 | [
"RDKit"
] | 9e32de61ad2ff0116f082c09f30ce27c1c98f2b1a338795553b5274ed9688176 |
"""Reads quantum espresso files. Tested for output on PWSCF v.5.0.2, only
for typical output of input files made with ASE -- that is, ibrav=0."""
import numpy as np
from ase.atoms import Atoms, Atom
from ase import units
from ase.calculators.singlepoint import SinglePointDFTCalculator
def read_espresso_out(fileobj, ... | alexei-matveev/ase-local | ase/io/espresso.py | Python | gpl-2.0 | 8,173 | [
"ASE",
"CRYSTAL",
"ESPResSo",
"Quantum ESPRESSO"
] | 5d05434fcc597bd50226a0e54262ceb32a6da41d3fc50c8f7e544931bf99e81a |
#!/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/ajax/bouquets.py | Python | gpl-2.0 | 6,416 | [
"VisIt"
] | face163cd434641dee323102254ae99638063e2c0ae96ea6186c5f596c6e6fd4 |
import numpy as np
from ase.atoms import Atoms
from ase.units import Bohr
def read_turbomole(filename='coord'):
"""Method to read turbomole coord file
coords in bohr, atom types in lowercase, format:
$coord
x y z atomtype
x y z atomtype f
$end
Above 'f' means a fixed atom.
"""
... | suttond/MODOI | ase/io/turbomole.py | Python | lgpl-3.0 | 5,839 | [
"ASE",
"TURBOMOLE"
] | b09ff2a323abd26868ab4c37c5db58f5577cd339445d9d3885484e16922e075c |
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | daafgo/CourseBuilder-Xapi | modules/analytics/clustering.py | Python | apache-2.0 | 47,170 | [
"VisIt"
] | bd634a2dc86c5dbdbcd57456a07874e7f4f0d9c77599e1a3dd2c9d6e5207b8ec |
import numpy as np
from .output import error
class Body:
"""Parent class for all geometrical bodies.
Attributes:
shift_vector: Origin of the body.
"""
# (type, shape, optional, has_coordsys_version)
arguments = {
"shift_vector": ( "floatarray", (3,), True, Tru... | aradi/nanocut | src/nanocut/body.py | Python | bsd-2-clause | 5,991 | [
"CRYSTAL"
] | 8dc0799354115de450b7ab981701b079a1aebd40a7085377738cc78382d244d2 |
# Copyright (C) 2010-2019 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 v... | pkreissl/espresso | testsuite/python/lb_buoyancy_force.py | Python | gpl-3.0 | 4,021 | [
"ESPResSo"
] | fbf0c2e48db960c75fdcd40c470da3d83a2c819a290d2069ad6bee1aa1b810b6 |
#!/bin/env python2
# -*- mode: Python; tab-width: 4; indent-tabs-mode: nil; -*-
# ex: set tabstop=4 :
"""
Generate logstash config to categorize expenses.
Likely to require customization.
"""
TEMPLATE = """
grok {{
match => {{ "{}" => "{}" }}
add_field => {{
category => "{}"
}... | atorok/elk-save-money | gen_category_filters.py | Python | gpl-3.0 | 8,556 | [
"CRYSTAL"
] | 7514388b4fafb1169bf4d7cdcd58af883e48d80157fddfcaed204316f02ab814 |
"""
ast
~~~
The `ast` module helps Python applications to process trees of the Python
abstract syntax grammar. The abstract syntax itself might change with
each Python release; this module helps to find out programmatically what
the current grammar looks like and allows modifications of... | prefetchnta/questlab | bin/x64bin/python/37/Lib/ast.py | Python | lgpl-2.1 | 13,182 | [
"VisIt"
] | 28c0f7374f4e307584e7299900ab4a48c5ba71296f9b1d3ec55a8e36ee7f455d |
import smtplib
server = smtplib.SMTP('smtp.sparkpostmail.com', 587)
server.set_debuglevel(1)
server.starttls()
# You will need an API Key with 'Send via SMTP' permissions.
# Create one here: https://app.sparkpost.com/account/credentials
server.login('SMTP_Injection', '<YOUR API KEY>')
# sparkpostbox.com is a sending... | SparkPost/code-snippets | snippets/SMTP/smtp_example.py | Python | apache-2.0 | 819 | [
"VisIt"
] | 6ecdc550c77f2dc666a78475befc73deaec0e5001e0bd270da291010a528d23d |
# -*- 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 ... | francbartoli/geonode | geonode/security/tests.py | Python | gpl-3.0 | 67,309 | [
"VisIt"
] | 45883bae495d75ed17735e6367167f0b40eef3454eacb81defb409ad9b4c5563 |
#########################################################################
## rdesigneur0_4.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 the
## GNU General Public ... | rahulgayatri23/moose-core | python/rdesigneur/rmoogli.py | Python | gpl-3.0 | 5,808 | [
"MOOSE"
] | 5cac2f256f8ae1f927d58ed12c45fd891072007eca445795174d95d0be4cd15e |
import decimal
import json
import networkx as nx
import re
from operator import itemgetter
from datetime import datetime, timedelta
from collections import defaultdict
from itertools import chain
from functools import partial
from django.core.serializers.json import DjangoJSONEncoder
from django.http import HttpRespon... | AdaEne/CATMAID | django/applications/catmaid/control/skeleton.py | Python | gpl-3.0 | 55,707 | [
"NEURON"
] | 6ff45c1e3feb9f6a5efa843eb5516cb9d1bc69b861da2694c886386ac1e0553c |
''' file name : modify_image.py
Description : This sample shows how to convert a color image to grayscale and save it into disk
This is Python version of this tutorial : http://opencv.itseez.com/doc/tutorials/introduction/load_save_image/load_save_image.html
Level : Beginner
Benefits : Learn 1) to convert RGB image... | asrob-uc3m/rpc_rpi | src/python/opencv_python_tutorials/Official_Tutorial_Python_Codes/1_introduction/modify_image.py | Python | gpl-3.0 | 902 | [
"VisIt"
] | 64ce397a682160a4c86e6dd4a449081c19c53dcdbc97ce49074cf37cffd3c8a8 |
"""
Copyright (c) 2010 Patrick Wagstrom
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 the rights
to use, copy, modify, merge, publish, distribut... | pridkett/TSASimulation | tsa.py | Python | mit | 11,694 | [
"TINKER"
] | cdeddb71c2a9b67209b5f98c9b6c3488bd501bf847fe10acdf42f28deeeece85 |
"""
:Author: Pierre Barbier de Reuille <pierre.barbierdereuille@gmail.com>
Module implementing non-parametric regressions using kernel smoothing methods.
"""
from __future__ import division, absolute_import, print_function
from scipy import stats
from scipy.linalg import sqrtm, solve
import scipy
import numpy as np
f... | sergeyfarin/pyqt-fit | pyqt_fit/kernel_smoothing.py | Python | gpl-3.0 | 20,695 | [
"Gaussian"
] | 3e1b74f3541241d648d0d42648be1fb6664e9205c82c2cfcddbbfe2b849f931d |
import os
import cv2
import numpy as np
from scipy.ndimage.morphology import binary_dilation
from flask import Flask, request, redirect, url_for, send_from_directory
from werkzeug import secure_filename
UPLOAD_FOLDER = '/Users/charleslai/Documents/Programming/other-projects/waldoBot/server/imgs'
UPLOAD_FOLDER = '/User... | Shikkic/waldoBot | server/hello.py | Python | mit | 2,875 | [
"Gaussian"
] | a459fdbd91b436ef5dd2b6eb1dc3ae9c37f699d131b4271db181d19f8cab8bcd |
import numpy
import numpy.linalg
def training(inputs, minvar=0.1):
"""Trains a naive-bayes classifier using inputs
Returns means and variances of the classifiers
"""
return numpy.mean(inputs, axis=0), numpy.maximum(minvar, numpy.var(inputs, axis=0))
def gaussian(input, mu, sigma2):
"""Calculates ... | pymir3/pymir3 | mir3/lib/naive_bayes.py | Python | mit | 1,643 | [
"Gaussian"
] | 9c6014d5d12bcb32503f3cd436e2b1cae50efafdc1e09aa39027b2d1d10aaf06 |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathem... | sknepneklab/SAMoS | analysis/batch_nematic/batch_analyze_nematic_R16b.py | Python | gpl-3.0 | 2,381 | [
"VTK"
] | bcfb782cc3becf09e40d4a2a0cc1695c22da0265e86d3e6ee8b0a31dbf0a9400 |
import os
import logging
import numpy as np
from sklearn.externals import joblib
from sklearn.metrics import confusion_matrix
from sklearn.cross_validation import train_test_split
from midi_ml.pipelines.midi_reads import LabeledCorpusSet
from midi_ml.models.decomposition import PrincipalComponents
from midi_ml.tools.ut... | flylo/midi-ml | midi_ml/pipelines/train_and_evaluate.py | Python | mit | 2,899 | [
"Gaussian"
] | 16c0dd359a214861aef1d842e52f183209463caaeb8481c84156d00ccf69afec |
import copy
import os
from visitor import *
from stringstream import *
class Rewriter(NodeVisitor):
""" Class for rewriting of the original AST. Includes:
1. the initial small rewritings,
2. transformation into our representation,
3. transforming from our representation to C-executable code,
4. cre... | dikujepsen/OpenTran | v1.0/src/framework/rewriter.py | Python | mit | 39,294 | [
"VisIt"
] | 12d47e4304b275b3853fa4eb9f673ff0057e7157924fa2cbb677a5bd99814017 |
# PART 1 - INITIALIZATION
actual_ranking = [1,6,7,5,9,10,4,8,2,3] # actual_ranking[i] = patient.number of rank
actual_ranking1 = [1,9,10,7,4,2,3,8,5,6] # actual_ranking1[i] = rank of patient[i]
exercises = [1,2,3,4,5,6,7,8,9,10,12]
patients = [1,2,3,4,5,6,7,8,9,10]
class patients(object):
def __init__(self,number,sc... | easyCZ/SLIP-A-2015 | respiratory/Processed Datasets/Processed Datasets/week9.py | Python | mit | 11,955 | [
"Gaussian"
] | 9241fe8f008351f92c403ff5fa00fc44ae0673729b80fb04254cbbb7e8f439b9 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import re
import time
import gzip
from six.moves import queue as Queue
import threading
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.ThreadScheduler import gThreadScheduler
from ... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/private/SecurityFileLog.py | Python | gpl-3.0 | 4,336 | [
"DIRAC"
] | c13784b5ac735de3cec816d4a3df93899cf5580a2cbedfa75a59bdab6c202247 |
#!/usr/bin/python
from selenium import webdriver
from selenium.webdriver.firefox.firefox_binary import FirefoxBinary
from shutil import unpack_archive
import utils
if __name__ == "__main__":
from sys import platform
# Get nightly URL
nightly_url = utils.make_nightly_link("firefox", utils.parse_nightly_ver... | MDTsai/webcompat-system-addon-autotest | Bug_1337726.py | Python | mpl-2.0 | 987 | [
"VisIt"
] | 5cbb868c7a1a58055a8979183228600f0dd51f70efbf0d6ba404937ed1ff5962 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
import collections
import logging
import threading
import itertools
import time
import types
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
FIRST_COMPLETED = 'FIRST_COMPLETED'
FIRST_EXCEPTION = 'FIRST_EXCEPTION'
... | listyque/TACTIC-Handler | thlib/side/concurrent/futures/_base.py | Python | epl-1.0 | 23,813 | [
"Brian"
] | 39f8e88c3576c70f14616f4cd01e36902bd49e39bc4eb0a50b03dbf909c42c5a |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | lidakanari/NeuroM | neurom/fst/_core.py | Python | bsd-3-clause | 6,276 | [
"NEURON"
] | 7428f2c259556bceeeecc6856a25f0be76790e7304825513e3f4e1b999ae3cb5 |
# -*- coding: utf-8 -*-
# test ASE3 eos vs ASE2' on EMT Al bulk
import numpy as np
from ase.test import NotAvailable
try:
import scipy
except ImportError:
raise NotAvailable('This needs scipy module.')
from ase.structure import bulk
from ase.io.trajectory import PickleTrajectory
from ase.calculators.emt i... | conwayje/ase-python | ase/test/eos.py | Python | gpl-2.0 | 6,196 | [
"ASE"
] | 10fe05e2b7c284739c1f353081bd0e62645fb56675cb4c284d59d9fa716c4ed4 |
'''
Created on Jun 30, 2015
I'm thinking evenutally we'll start reusing our lists,
and the functions we're using to create lists of things.
So, I figure, let's start sticking them all in a "lists" module.
@author: Leiran Biton, John O'Brien
'''
from solver.word import strip_accents
import requests
import re
def g... | johnobrien/pyshortz | solver/lists.py | Python | mit | 27,260 | [
"Elk",
"Jaguar",
"MOOSE",
"ORCA"
] | 26d70c4147bc053aec73dd632bc81636ade0ae51e552d078e7ad19c9939066fc |
import abc
import datetime
import enum
import typing
import jsii
import jsii.compat
import publication
from jsii.python import classproperty
import aws_cdk.aws_cloudwatch
import aws_cdk.aws_iam
import aws_cdk.core
__jsii_assembly__ = jsii.JSIIAssembly.load("@aws-cdk/aws-logs", "1.15.0", __name__, "aws-logs@1.15.0.js... | randyzingle/tools | kub/services/archive/cdk/python/sample-app/.env/lib/python3.6/site-packages/aws_cdk/aws_logs/__init__.py | Python | apache-2.0 | 94,375 | [
"CDK"
] | 694b62a0e9ecb9e776b811f814f18b9930c84dcd4a16f80581a4c33b18c2c011 |
#pylint: disable=C0111
from lettuce import world, step
from xmodule.modulestore import Location
from contentstore.utils import get_modulestore
from selenium.webdriver.common.keys import Keys
VIDEO_BUTTONS = {
'CC': '.hide-subtitles',
'volume': '.volume',
'Play': '.video_control.play',
}
# We should wait ... | abo-abo/edx-platform | cms/djangoapps/contentstore/features/video.py | Python | agpl-3.0 | 6,672 | [
"VisIt"
] | 2ac2ef4cf845a2d11d71d860ed4a36a0c8a7a7d20eccbd1de14d0ff3dc5fc7de |
# coding=utf-8
"""
Application terminology
For any given application, there are a number of different documents.
The primary application document is an instance of Application. This
document id is what you'll see in the URL on most app manager pages. Primary
application documents should have `copy_of == None` and `i... | qedsoftware/commcare-hq | corehq/apps/app_manager/models.py | Python | bsd-3-clause | 221,033 | [
"VisIt"
] | 526630b3f63b1b9d2bb3b42f34b52fcd558c5bc0f3eac0a00a24cfe869398490 |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | toastedcornflakes/scikit-learn | sklearn/cluster/k_means_.py | Python | bsd-3-clause | 59,017 | [
"Gaussian"
] | 16e2f6f6827f933750b2428fc0ebf9cb87dc635af1d12da54d2002a63510db15 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | pvagner/orca | src/orca/braille_generator.py | Python | lgpl-2.1 | 18,994 | [
"ORCA"
] | 268b6e12d628f32d6c9499c9aa572b82b5ec4a62daec8afd2c8cbf85abf7348d |
from __future__ import absolute_import, division, print_function
import sys
import string
import llvm.core as lc
from llvm import LLVMException
from .. import llvm_array as lla
from .blaze_kernels import BlazeElementKernel, refresh_name
from . import blaze_kernels
from blaze.py2help import _strtypes
def letters(sour... | xsixing/blaze | blaze/compute/bkernel/kernel_tree.py | Python | bsd-3-clause | 10,324 | [
"VisIt"
] | 5b824becbe28a72bfbda05f6be18d55d26207e8379f267756cb65af32e23cc7f |
import numpy as np
import tensorflow as tf
from tensorflow.contrib import rnn
def _print_success_message():
print('Tests Passed')
def test_create_lookup_tables(create_lookup_tables):
with tf.Graph().as_default():
test_text = '''
Moe_Szyslak Moe's Tavern Where the elite meet to drink
... | udacity/deep-learning | tv-script-generation/problem_unittests.py | Python | mit | 13,052 | [
"MOE"
] | b2434e6bdbbe59071710a581d1250753fd74d248bf86274d5d868dc9c11d6ce8 |
# // license
# Copyright 2016, Free Software Foundation.
#
# This file is part of Solent.
#
# Solent is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option)
... | solent-eng/solent | solent/console/pygame/pygame_console.py | Python | lgpl-3.0 | 10,557 | [
"Amber"
] | 2bf6f47ba7f991c00f0dc61de4cc2742e3b4954a01e31089b7e8d44bfc6c6567 |
# Author: Idan Gutman
# Modified by jkaberg, https://github.com/jkaberg for SceneAccess
# URL: http://code.google.com/p/sickbeard/
#
# This file is part of SickGear.
#
# SickGear is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Sof... | ressu/SickGear | sickbeard/providers/hdtorrents.py | Python | gpl-3.0 | 13,424 | [
"VisIt"
] | 5b0eb4447dfacce393f4bb4eaac4fde8c32609cfa8f28804521ada032fdcb48b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Regression tests for PBxplore.
This script run the various PBxplore programs with various argument, and makes
sure the output is the expected one. The aim is to check that the programs are
not broken during development.
Be careful this script does not test that the o... | jbarnoud/PBxplore | pbxplore/test/test_regression.py | Python | mit | 24,350 | [
"MDAnalysis"
] | 878d178cfb5cb6af2316de50841ab952e9709075c83315093873c33f17689fe9 |
#
# The OpenDiamond Platform for Interactive Search
#
# Copyright (c) 2018 Carnegie Mellon University
# All rights reserved.
#
# This software is distributed under the terms of the Eclipse Public
# License, Version 1.0 which can be found in the file named LICENSE.
# ANY USE, REPRODUCTION OR DISTRIBUTION OF THIS S... | cmusatyalab/opendiamond | tests/test_client.py | Python | epl-1.0 | 2,688 | [
"BLAST"
] | a8fca0c556b8b43080b671d37a95a6d459cb36827707e2dbe93e9bc140ccbe8b |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation... | aperigault/ansible | lib/ansible/galaxy/__init__.py | Python | gpl-3.0 | 2,348 | [
"Brian",
"Galaxy"
] | c89417ed01ad6b3383ba1771ce0893bbc023b3cbc1b21a6d8325ad736bcddfbb |
"""This directory is setup with configurations to run the main functional test.
It exercises a full analysis pipeline on a smaller subset of data.
"""
import os
import subprocess
import unittest
import shutil
import contextlib
import collections
import functools
from nose import SkipTest
from nose.plugins.attrib impo... | SciLifeLab/bcbio-nextgen | tests/test_automated_analysis.py | Python | mit | 14,159 | [
"Galaxy"
] | 355300b8a52ae3253cf837ede9f904be4a20805b231abc8c31d6013e70c1e2b1 |
# (C) 2013, James Cammarata <jcammarata@ansible.com>
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import json
import os
import tarfile
import u... | anryko/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 25,126 | [
"Galaxy"
] | facbab2803a0f460cd810debf7b5f802f1b3584acf6f8fa772c102ce3ab12879 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
'''
Description: ARP poisons a LAN victim and prints all the interesting unencrypted info like usernames, passwords and messages. Asynchronous multithreaded arp spoofing packet parser.
Prerequisites: Linux
nmap (optional)
nbtscan (optional)
... | pdellaert/LANs.py | LANs.py | Python | gpl-3.0 | 54,471 | [
"VisIt"
] | 0c0146c20a95850b9c8775516dbc1d2cdaa63f12e8dcf25c079d91eecd907a28 |
#!/usr/bin/python
# Copyright: Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
'status': ['stableinterf... | rmfitzpatrick/ansible | lib/ansible/modules/cloud/amazon/elb_classic_lb.py | Python | gpl-3.0 | 54,010 | [
"Dalton"
] | 03ca81f67fb02df4866c9f6a1faa397e7b4d86c32bee1be3e85154b1b9b0b0d5 |
from HappyTools.util.fitting import gauss_function
#from HappyTools.util.functions import determine_breakpoints, subset_data
from HappyTools.bin.peak import Peak
import logging
import tkinter.filedialog as filedialog
from math import sqrt, log
from numpy import linspace
from pathlib import Path
from bisect import bisec... | Tarskin/HappyTools | HappyTools/util/peak_detection.py | Python | apache-2.0 | 5,108 | [
"Gaussian"
] | 0a6075cdbf5cae0d16b3961a081312a527ee52614c4ceb2086d82254f079e824 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import numpy as np
import scipy.constants as const
from pymatgen.core.structure import Structure
from pymatgen.util.coord import get_linear_interpolated_value
... | gpetretto/pymatgen | pymatgen/phonon/dos.py | Python | mit | 13,569 | [
"Avogadro",
"Gaussian",
"pymatgen"
] | e90cd3593be8ba7395339708a5561d14de802710e0a85dab1b73c7d3db2b7b1e |
# Copyright iris-grib contributors
#
# This file is part of iris-grib and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Module to support the loading and convertion of a GRIB2 message into
cube metadata.
"""
from argparse import Na... | SciTools/iris-grib | iris_grib/_load_convert.py | Python | lgpl-3.0 | 98,655 | [
"Gaussian"
] | 4c371494f3d81a66302dca117b62a9d8ebedd824dff7ec2f6d4eb08ea9a78b65 |
# Copyright 1999 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from __future__ import print_function
import string
from Bio._py3k import StringIO
from Bio i... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_ParserSupport.py | Python | gpl-2.0 | 4,703 | [
"Biopython"
] | 4944c8871546e9c25ba6cbc954dc8e8a823ff45590b31d98ea62167b39ddfc92 |
#!/usr/bin/env python
#ryan g. coleman ryan.g.coleman ATSYMBOL gmail.com ryangc ATSYMBOL mail.med.upenn.edu
#kim sharp lab http://crystal.med.upenn.edu
import string
import sys
import pdb
def calcRMSDprintTable(pdbFileNames):
pdbDatas = []
for pdbFileName in pdbFileNames:
pdbDatas.append(pdb.pdbData(pdbFileN... | ryancoleman/traveldistance | src/rmsdTable.py | Python | gpl-2.0 | 1,238 | [
"CRYSTAL"
] | 9c3c85131b60770018f17faeac4704e2ae7e0289d9c1f40311c6a5110ae628aa |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2006, 2007, 2008, 2009, 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,... | zenodo/invenio | invenio/legacy/websubmit/admin_engine.py | Python | gpl-2.0 | 241,978 | [
"VisIt"
] | 393611e35d784ff0a9019dd6c844ca221ae639ebeead412334a472936badc6f8 |
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