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# 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.
#
"""Provide Tournament style selection.
This implements selection based on a tournament style. In this model of
selection, two individuals are random... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/GA/Selection/Tournament.py | Python | gpl-2.0 | 2,889 | [
"Biopython"
] | b2e9af9987c0e0cb7de716deaec2ebdf5e16e1ce82d58ed8d37891b0b69c4f97 |
'''
Written by J Meza, updates by J Fuchs. UNC - Chapel Hill
:INPUTS:
listZero: string, file containing bias images
listFlat: string, file containing flat images
listSpec: string, file containing spectral images
listFe: string, file containing Fe lamp spectra
ReduceSpec.py w... | joshfuchs/ZZCeti_pipeline | ReduceSpec.py | Python | mit | 9,754 | [
"Gaussian"
] | 6affb436272186a722794a341162d2693c6de8ef142f03d8fe3b8026fc1ce6d7 |
#!/usr/bin/env python
from distutils.core import setup
from glob import glob
scripts = glob('bin/*')
setup(name='turbocontrol',
version='2.0',
description='Job Submitter and manager for TurboMole',
long_description=open('README.md').read(),
author='Philip Bulsink',
author_email='philip.... | pbulsink/turbocontrol | setup.py | Python | mit | 998 | [
"TURBOMOLE"
] | b1747bebd450c69bc927cbf4b3c00542262f2ec0c768768e077d594e8eb54e97 |
import sys
from math import sqrt
import numpy as np
import gpaw.mpi as mpi
MASTER = mpi.MASTER
from ase.parallel import paropen
from ase.units import Hartree
from gpaw import debug
import gpaw.mpi as mpi
from gpaw.poisson import PoissonSolver
from gpaw.output import initialize_text_stream
from gpaw.lrtddft.excitation... | ajylee/gpaw-rtxs | gpaw/lrtddft/omega_matrix.py | Python | gpl-3.0 | 24,000 | [
"ASE",
"GPAW"
] | 7a85cd99e6c8fceac9e227bc8581985f4f50991ba9724f36ec7d7f59766f14a2 |
#!/usr/bin/python
# Copyright (C) 2011 Zhang Initative Research Unit
# potential_region.py -description
# system
import sys, os
# biopython
# user-defined modules
import fileio
def potintial_wrong_region( model_pdb, out_dir, avg_rms, mutual_rmsds):
line_to_be_printed = ""
print model_pdb + " " + str(avg_rms... | chhattu/apmds | potential_region.py | Python | gpl-2.0 | 1,097 | [
"Biopython"
] | 200e2161b827708760afd860023ebaba95e0be076ca3509cd21c97ede0ec9015 |
r"""
Vibro-acoustic problem
3D acoustic domain with 2D perforated deforming interface.
*Master problem*: defined in 3D acoustic domain (``vibro_acoustic3d.py``)
*Slave subproblem*: 2D perforated interface (``vibro_acoustic3d_mid.py``)
Master 3D problem - find :math:`p` (acoustic pressure)
and :math:`g` (transversal... | RexFuzzle/sfepy | examples/acoustics/vibro_acoustic3d.py | Python | bsd-3-clause | 4,245 | [
"VTK"
] | cbb56bced3daa78f7b5f892ffa13c7711b4f5911ab2624a773415dec55d6eb3b |
"""
This is the Data Integrity Client which allows the simple reporting of
problematic file and replicas to the IntegrityDB and their status
correctly updated in the FileCatalog.
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gLogger, gConfig
from DIRAC.DataM... | sposs/DIRAC | DataManagementSystem/Client/DataIntegrityClient.py | Python | gpl-3.0 | 41,159 | [
"DIRAC"
] | 50540b5fdf38dbed7645fd78e3a528ddff4427488c8d71854e5bd83a85f8f5e9 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2016, SylvainCecchetto
# GNU General Public License v2.0+ (see LICENSE.txt or https://www.gnu.org/licenses/gpl-2.0.txt)
# This file is part of Catch-up TV & More
from __future__ import unicode_literals
# The following dictionaries describe
# the addon's tree architecture.
# *... | Catch-up-TV-and-More/plugin.video.catchuptvandmore | resources/lib/skeletons/et_live.py | Python | gpl-2.0 | 9,066 | [
"MOE"
] | f540bf026fe00d4ac59b1e5ec6b9164433cd2551722eb70b668ccaed43bb81c4 |
# Copyright 2008-2013 Nokia Siemens Networks Oyj
#
# 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... | ktan2020/legacy-automation | win/Lib/site-packages/robot/result/executionerrors.py | Python | mit | 1,541 | [
"VisIt"
] | 0c79a50fe05971eff75ed3791b75567386a76e2a66119987d9ccd525aceb2951 |
"""
alignReads
"""
import subprocess
import os
import logging
logger = logging.getLogger('root')
logger.propagate = False
def alignReads(BWA_path, HG19_path, read1, read2, outfile):
sample_name = os.path.basename(outfile).split('.')[0]
output_folder = os.path.dirname(outfile)
if not os.path.exists(outp... | aryeelab/guideseq | guideseq/alignReads.py | Python | agpl-3.0 | 1,840 | [
"BWA"
] | 2253127b76727c911be761e6ff2f21a500276e9b0f631105d8b9dc9d5e250d87 |
from geneutils import *
DB_DIR = '../Proteomes/Candida_proteomes/'
BLASTN_RESULTS_DIR = 'resultsn/'
#MAIN_SPECIES = 'S288C'
#SUBJECT_DBS = ['AWRI1631_ABSV01000000', 'AWRI796_ADVS01000000', 'CBS7960_AEWL01000000', \
#'CLIB215_AEWP01000000', 'CLIB324_AEWM01000000', 'CLIB382_AFDG01000000', 'EC1118_PRJEA37863', \
#'EC9-8... | q10/gene | align.py | Python | bsd-3-clause | 3,687 | [
"BLAST"
] | 329ea2a958eff5a03aeea7d4fad83fc47d3852b12d2745bfc02f23e19a1d5f9f |
#
# Parse tree nodes for expressions
#
from __future__ import absolute_import
import cython
cython.declare(error=object, warning=object, warn_once=object, InternalError=object,
CompileError=object, UtilityCode=object, TempitaUtilityCode=object,
StringEncoding=object, operator=object,
... | c-blake/cython | Cython/Compiler/ExprNodes.py | Python | apache-2.0 | 505,775 | [
"VisIt"
] | 37aeb1e2b9965c8f6a89f7505dede856a784f61889d9a2545fdcef60142b5472 |
import os
try:
import cPickle as pickle
except:
import pickle
from PIL import Image
from subprocess import Popen
import numpy as np
from numpy.lib.stride_tricks import as_strided
import os
import gzip
from random import shuffle
from collections import OrderedDict
import inspect
import h5py
import sys
from skima... | bittlingmayer/Theano-Lights | toolbox.py | Python | mit | 26,468 | [
"Gaussian"
] | 59a47cee4ddbbeb08f4b6c557e15d9b84b269e79054ea626ad5d86ab724b47d0 |
# This file is part of OpenHatch.
# Copyright (C) 2010 Parker Phinney
# Copyright (C) 2010 Jack Grigg
# Copyright (C) 2009, 2010 OpenHatch, Inc.
# Copyright (C) 2010 Jessica McKellar
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as... | mzdaniel/oh-mainline | mysite/search/tests.py | Python | agpl-3.0 | 62,680 | [
"VisIt"
] | 59c4475507ade00a7de51906cc347b796a93c13b820ddd2c0a15199e665d0117 |
"""
Tests the converters
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import tempfile
import unittest
import pysam
import ga4gh.protocol as protocol
import ga4gh.converters as converters
class TestSamConverter(unittest.TestCase):
"""
Base... | ekalosak/server | tests/unit/test_converters.py | Python | apache-2.0 | 1,536 | [
"pysam"
] | 47c29b1207cef0ab0b393ef6c0d983829c5efb628608f487c310d55faffa9c3f |
#!/usr/bin/python
# script for computing z10 signature from a bowtie genomic output
# version 1 8-5-2012 using SmRNAtools class imported from smRtools
# Usage z10_genome.py <bowtie input> <windowsize> <outputpipi> <outputpisi> <outputsisi> <bowtie index>
import sys, subprocess
from smRtools import get_fasta, antipara,... | mvdbeek/tools-artbio | unstable/local_tools/z10_genome.py | Python | mit | 2,499 | [
"Bowtie"
] | ecae10243a52c64cc5d786073efa11276e369d3d49bfa6a88555cc2a9ea651ad |
from os import path
from random import choice
import re
import plugin
class Plugin(plugin.Plugin):
def register_commands(self):
self.commands = [
('hhg <character>', self.quote),
('hhg', self.quote_anyone)
]
def quote_anyone(self, message, args):
args['charact... | colons/pyfoot-plugins | hhg.py | Python | bsd-3-clause | 1,121 | [
"Galaxy"
] | 8a3de2636e894a613c9f4ee0b3abc4d9a221f0c71853cc93069509523cfbccb1 |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | harterj/moose | python/chigger/exodus/ExodusResult.py | Python | lgpl-2.1 | 4,019 | [
"MOOSE"
] | eaced7ff63251a82ad984d310317c77d27b152e7a21a747669d292805789656b |
import tensorflow as tf # neural network for function approximation
import gym # environment
import numpy as np # matrix operation and math functions
from gym import wrappers
import gym_morph # customized environment for cart-pole
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import time
star... | GitYiheng/reinforcement_learning_test | test03_monte_carlo/t30_rlvps06_hn6_clr0p003.py | Python | mit | 7,659 | [
"NEURON"
] | d1094e33fcf0f08dad53e418209fa1d850c3b8f8566f929b6019ac36d6e0bb99 |
"""
Tests for Coulomb matrix calculation.
"""
import numpy as np
import unittest
from rdkit import Chem
from deepchem.feat import coulomb_matrices as cm
from deepchem.utils import conformers
class TestCoulombMatrix(unittest.TestCase):
"""
Tests for CoulombMatrix.
"""
def setUp(self):
"""
... | Agent007/deepchem | deepchem/feat/tests/test_coulomb_matrices.py | Python | mit | 3,826 | [
"RDKit"
] | 784c11bd96c5a84a6b95e14b02094c3bdf027d2d6b8fd2052627840b5fa94933 |
class constraints:
constraints = {
#http://wiki.secondlife.com/wiki/SimStats
#Ratio of time passage in region to real time passage.
"LL_SIM_STAT_TIME_DILATION": 0,
#Number of timesteps taken per second, rolling scale. Perfect is 45.0
"LL_SIM_STAT_FPS": 1,
#Number of t... | FelixWolf/pyverse | pyverse/constraints.py | Python | mit | 25,492 | [
"VisIt"
] | 538cc4cb784893e2cde32c8697a526fe81833a56834f7c8fb6c60d15b09ae547 |
#
# Copyright 2009 Mathieu Leocmach
#
# This file is part of Colloids.
#
# Colloids 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 ... | MathieuLeocmach/colloids | python/colloids/lif.py | Python | gpl-3.0 | 25,018 | [
"VTK"
] | e0ba798264ca68032995fe6644d06cf58acf6531fd1cdbeaf9096def59bb89db |
# Copyright 2014 Joe Cora.
# 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.
"""Provides objects to represent NEXUS standard data type matrix coding.
"""
from __future__ import pr... | zjuchenyuan/BioWeb | Lib/Bio/Nexus/StandardData.py | Python | mit | 3,711 | [
"Biopython"
] | 269a703b5ea1b5ea62bd9236753f44917a1f065934664aaa50fb2e6f5749d1a2 |
import random
from googleimages import GoogleImagesSearch
words = ["ability","able","aboard","about","above","accept","accident","according",
"account","accurate","acres","across","act","action","active","activity",
"actual","actually","add","addition","additional","adjective","adult","adventure",
"advice","affect","a... | ugosan/passwordgen | app/xkcd.py | Python | bsd-3-clause | 17,445 | [
"VisIt",
"exciting"
] | 292cfe4bd140ed7cc60433c8461c97d80715e334a4b94b24edcf2a1b3dcf228a |
# Copyright 2015 Adriana Supady
#
# This file is part of fafoom.
#
# Fafoom is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | FHIBioGroup/fafoom-dev | fafoom/pynwchem.py | Python | gpl-3.0 | 4,662 | [
"NWChem"
] | 748dac3cdeb345f405924165a415b9dbc7583401d2a6135e0ab81a0ba30f2c72 |
# 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... | kkreis/espressopp | src/tools/lammps.py | Python | gpl-3.0 | 16,178 | [
"ESPResSo",
"LAMMPS"
] | aca0f074e7e3bbe4f86457da4b45c06174e69aae7974d4166ba0821f8520babb |
"""Build instructions associated with CloudMan.
http://wiki.g2.bx.psu.edu/Admin/Cloud
Adapted from Enis Afgan's code: https://bitbucket.org/afgane/mi-deployment
"""
cm_upstart = """
description "Start CloudMan contextualization script"
start on runlevel [2345]
task
exec python %s 2> %s.log
"""
import os
from ... | heuermh/cloudbiolinux | cloudbio/cloudman.py | Python | mit | 16,113 | [
"Galaxy"
] | e5c4b5f99d662052a8b3e42699e9d8872265862c3146dcb54eec95e79e6dc4b1 |
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
import numpy as np
# The offset values in Az given to the telescope. Note that
# This does not necesarily mean that the telescope was pointing in this
# direction, since it might not move if the difference is too small.
xdata = [
-20,
-19,
-18,
-17,... | varenius/salsa | Developer_notes/Beam_measurements/Beam_2014-10-03/single.py | Python | mit | 2,675 | [
"Gaussian"
] | 7e67c8d0f2f9d5123e7df358f735b78ef579d1957a657048ececaaa0e3c9fbb2 |
from util import utils
import sys,os
import tables
import numpy as np
import matplotlib.pyplot as plt
from util.ObsFile import ObsFile
from util import MKIDStd
from util.rebin import rebin
import matplotlib
from scipy import interpolate
from scipy import integrate
from scipy.optimize.minpack import curve_fit
from math ... | bmazin/ARCONS-pipeline | examples/Pal2012_landoltPhot/landoltMagComparison.py | Python | gpl-2.0 | 10,423 | [
"Gaussian"
] | c0a080427dddde644f1929d102ff550427fa10a5b0de27974c93ee47d198c6b3 |
# Name: mapper_globcolour_l3b
# Purpose: Mapping for GLOBCOLOUR L3B data
# Authors: Anton Korosov
# Licence: This file is part of NANSAT. You can redistribute it or modify
# under the terms of GNU General Public License, v.3
# http://www.gnu.org/licenses/gpl-3.0.html
import ... | yuxiaobu/nansat | mappers/mapper_globcolour_l3b.py | Python | gpl-3.0 | 5,989 | [
"NetCDF"
] | 6e9d3d6331f9c146449e3c97230855d7047bd3ebe9e9a85084e4495ae56c8607 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
# -*- coding: utf-8 -*-
r"""Regression detection in ASV is based on detecting stepwise changes
in the graphs. The assumptions on the data are as follows: the curves
are piecewise constant plus random noise. We don't know the scaling of
the data or the ampl... | qwhelan/asv | asv/step_detect.py | Python | bsd-3-clause | 31,538 | [
"Gaussian"
] | 23c0d816a9fda8afcc242fd00da60321f43bc2cdd2d4912a7d78bf3c2124bbe8 |
"""
Computational Neurodynamics
Coursework
Simulates two layers of Izhikevich neurons. Layer 0 consists of 8 modules
of 100 neurons stimulated with a constant base current ? ? ? and layer 1
consists of 200 inhibitory neurons. Connections are described in the code
"""
from BuildModularNetwork import BuildModularNetwo... | JackThorp/ComputationalNeurodynamics | Exercise_4/Run2L.py | Python | gpl-3.0 | 4,185 | [
"NEURON"
] | 4ce30dd1bda8955b08ce7a73b1e123fa50efeb80320131c06e34280ee347e669 |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
# Disable the "wildcard import" warning so we can bring in all methods from
# course helpers and ui helpers
# pylint: disable=wildcard-import
# Disable the "Unused import %s from wildcard import" warning
# pylint: disable=unused-wildcard-impor... | ahmedaljazzar/edx-platform | common/djangoapps/terrain/steps.py | Python | agpl-3.0 | 7,397 | [
"VisIt"
] | 1349318eed5917eddf9379356d439fba50d5d9956652a2b86ed7bfc0496c2bcc |
#!/usr/bin/env python3
#
# Copyright (c) 2014, Scott Silver Labs, LLC.
#
import os
from setuptools import setup, find_packages
from setuptools.command.install import install as _install
# Utility function to read the README file.
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
... | scottsilverlabs/raspberrystem-projects | setup.py | Python | apache-2.0 | 1,536 | [
"Brian"
] | 09c7e37c31261849dcb485f0c84a931e107b39aa1466117e6d50d2b82c90b3cd |
#!/usr/bin/python
import sys, string
if len(sys.argv)<2 or len(sys.argv)>11:
print ('Usage: python comp_band_abinit2elk.py [abinit _EIG file] ...')
print (' ... [elk BAND.OUT file] [align #kpt #band] ...')
print (' ... [nbdbuf #] [Fermi #abinit #elk]')
print (' ... | abinit/abinit | doc/tutorial/paw3_assets/scripts/comp_bands_abinit2elk.py | Python | gpl-3.0 | 8,881 | [
"ABINIT",
"Elk"
] | bbcec0c6440d1dfba89cddf404f3a6fd710a05131e91cab1e8b7b1b23660f2d6 |
"""creates: bigpicture.svg bigpicture.png"""
import os
from math import pi, cos, sin
import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.patches as mpatches
import matplotlib.pyplot as plt
class Box:
def __init__(self, name, description=(), attributes=(), color='grey'):
self.nam... | ajylee/gpaw-rtxs | doc/devel/bigpicture.py | Python | gpl-3.0 | 9,151 | [
"ASE"
] | 60f794a7c2dd3a69836f0a2fbbea8c49abb4fbfdb87cf05a36b84630cd3c4c81 |
from past.types import basestring
from builtins import * # noqa: F403, F401
import os
import shutil
import pprint
import requests
import time
from io import BytesIO
from xml.etree import ElementTree
from zipfile import ZipFile, is_zipfile
from requests.auth import HTTPBasicAuth
import geoserver
from geoserver.catalo... | CI-WATER/tethys_dataset_services | tethys_dataset_services/engines/geoserver_engine.py | Python | bsd-2-clause | 99,564 | [
"NetCDF"
] | 7798d372dc3fa8903960ca6419d9e7100d016ed7ab41e42a5f30969b65bdb567 |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import os
import itertools
from django.core.urlresolvers import reverse, NoReverseMatch
from django.template import (TemplateSyntaxError,
Context, Template, loader)
i... | Bashar/django | tests/test_client_regress/tests.py | Python | bsd-3-clause | 64,590 | [
"VisIt"
] | ed33867518abeda7b2c2e91e666b718e899dfa17294e22e064e486f1ea503a88 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | mhlechner/psi4 | psi4/driver/inputparser.py | Python | gpl-2.0 | 30,572 | [
"CFOUR",
"Psi4"
] | fc3e8fdba6baeb2f3cd1876a27d9fcf3b3bcd3826000c5dd6da6f628c71864da |
# Default Django settings. Override these with settings in the module
# pointed-to by the DJANGO_SETTINGS_MODULE environment variable.
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
gettext_noop = lambda s: s
#################... | rogerhu/django | django/conf/global_settings.py | Python | bsd-3-clause | 22,613 | [
"VisIt"
] | 72668b228e77c9e70cf1e6bfd85c88f2d6c31496a81d6bcd3090664a2de6032f |
# -*- coding: utf-8 -*-
# Section class for flux calculations
from __future__ import division, absolute_import
import numpy as np
from roppy.depth import sdepth
class FluxSection(object):
"""Class for flux calculations across sections
A FluxSection object is defined by a sequence of psi-points
followi... | bjornaa/roppy | roppy/fluxsec.py | Python | mit | 6,958 | [
"NetCDF"
] | e305c2c57106a55ff478864ffa8746d73e1b9b02491dd2b17b730c42e628df20 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import sys
import os.path
from glob import glob
from math import exp, log
import numpy as np
from scipy.special import gammaln
from scipy.linalg... | PyAbel/PyAbel | abel/basex.py | Python | mit | 22,774 | [
"Gaussian"
] | 58fe3f4f2c9bf988864eee88366d20a51580a74579bb382ac5e27f1d864734fc |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | kain88-de/mdanalysis | package/MDAnalysis/topology/tpr/obj.py | Python | gpl-2.0 | 4,963 | [
"MDAnalysis"
] | f26e0f3b43d0bcd5ac025f8c5c6ec0be7f6bd96780ae6704d60ec44e4d036219 |
from __future__ import print_function
from builtins import range
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
import random
def cars_checkpoint():
cars = h2o.upload_file(pyunit_utils.locate("smalldata/junit/cars_20mpg.csv"))
s = cars.runif()
train = cars[s > .2]
... | nilbody/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_DEPRECATED_NOPASS_cars_checkoutGBM.py | Python | apache-2.0 | 7,887 | [
"Gaussian"
] | 867a6e18041d68025cc7d8090d09a795b2fa15f82fcec3d0d97324aa1047eb61 |
# -*- coding: utf-8 -*-
# Krzysztof Joachimiak 2017
# sciquence: Time series & sequences in Python
#
# Statistic utils
# Author: Krzysztof Joachimiak
#
# License: MIT
import scipy.stats
def gaussian_breakpoints(n_ranges):
'''
Get quantiles of Gaussian distribution.
Parameters
----------
n_range... | krzjoa/sciquence | sciquence/utils/statistics.py | Python | mit | 646 | [
"Gaussian"
] | 83a62819968a2cbe0b1e8799e7d81afa0507d7fc739ce9bd218b30aedabc530e |
#!/usr/bin/env python
#from sumatra.projects import load_project
#from sumatra.parameters import build_parameters
#from sumatra.decorators import capture
from ruffus import *
import sys
import os
import time
import datetime
import drmaa
from omics_pipe.utils import *
from omics_pipe.modules.fastqc import fastqc
from... | adammaikai/OmicsPipe2.0 | tests/custom_TCGA_counts.py | Python | mit | 3,124 | [
"HTSeq"
] | a1dbd2db485d68bafcfb9cb13d3ef93c463e919a7b52fb3e93ae9ed732778245 |
""" Utilities for WMS
"""
import io
import os
import sys
import json
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.File import mkDir
from DIRAC.ConfigurationSystem.Client.Helpers import Registry
from DIRAC.FrameworkSystem.Client.ProxyManagerClient import gProxyManager
from DIRAC.Configura... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Utilities/Utils.py | Python | gpl-3.0 | 6,567 | [
"DIRAC"
] | 9e5f034efbfa32c64a050cfdabbec36f100bb8e0aeebc45d408e8661bc227672 |
"""
Copyright (C) 2004-2015 Pivotal Software, Inc. All rights reserved.
This program and the accompanying materials are made available under
the terms of the 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
... | CraigHarris/gpdb | src/test/tinc/tincrepo/mpp/gpdb/tests/storage/uao/uao_heap_compaction/test_uao_heap_compaction.py | Python | apache-2.0 | 1,054 | [
"ORCA"
] | 547a11ef58aa550519b28467d8b127fbdad7f85887b8b13badf10d41de4727ae |
# -*- coding: utf-8 -*-
#pylint:disable=too-many-lines
"""
This database should really be a database...
Also - needs updating.
Also - needs to move to Eva.
"""
from __future__ import unicode_literals, division, print_function
AIRPORTS_ICAO_TO_IATA = {
"YMOR" : "MRZ",
"USRN" : "NFG",
"USRO" :... | evature/flightstats | flightstats/airports_icao_to_iata.py | Python | mit | 172,363 | [
"ADF",
"ASE",
"BWA",
"CDK",
"FEFF"
] | 19d54993c98a9605611445d7eb312437c0fbca0f4a9cec7251f87cccfede106d |
# Dataset created from this:
# Elements of Statistical Learning 2nd Ed.; Hastie, Tibshirani, Friedman; Feb 2011
# example 10.2 page 357
# Ten features, standard independent Gaussian. Target y is:
# y[i] = 1 if sum(X[i]) > .34 else -1
# 9.34 is the median of a chi-squared random variable with 10 degrees of freedom
# ... | woobe/h2o | py/testdir_single_jvm/test_GLM2_hastie_shuffle.py | Python | apache-2.0 | 4,276 | [
"Gaussian"
] | dfd480d15e3c54a92965c79222878bd2c1da169205122e73550fbc2bd87c27b2 |
""" Job accounting type.
Filled by the JobWrapper (by the jobs) and by the agent "WorloadManagement/StalledJobAgent"
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import DIRAC
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import Bas... | yujikato/DIRAC | src/DIRAC/AccountingSystem/Client/Types/Job.py | Python | gpl-3.0 | 2,771 | [
"DIRAC"
] | 6ec15c18936cbda7791a29e6fff7777b05dff2db89b99bc0c7359f3fb1dc6594 |
#!/usr/bin/env python2
import espressopp
from espressopp.tools import replicate, readxyz
from espressopp import Real3D
import time, sys
import numpy as np
def bench_lj(xyz_file):
# read from xyz file
print "reading from: ", xyz_file
pid, type, xpos, ypos, zpos, xvel, yvel, zvel, Lx, Ly, Lz = readxyz(xyz... | govarguz/espressopp | testsuite/potential_array/potential_array_test.py | Python | gpl-3.0 | 6,079 | [
"ESPResSo"
] | 31b761337c93f686b39d3a6a1331178dbf0b2bd1c11b5c407d5b934728bf79fe |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0136_h2o_rks_rpa_pb.py | Python | apache-2.0 | 1,546 | [
"PySCF"
] | 17c465ed62ea9d2c728d78aa040a8bccf549990c5a6d348b2e568affdb0613ec |
"""
==============================================
Use different base estimators for optimization
==============================================
Sigurd Carlen, September 2019.
Reformatted by Holger Nahrstaedt 2020
.. currentmodule:: skopt
To use different base_estimator or create a regressor with different paramete... | scikit-optimize/scikit-optimize.github.io | 0.7/_downloads/0e6508d1c491f60b6990c6fb16ba7bad/optimizer-with-different-base-estimator.py | Python | bsd-3-clause | 5,943 | [
"Gaussian"
] | 4515f5c3f6d750e1a1e815661caa3cefc7cbe9d8415ae620261480773f694441 |
#!/usr/bin/env python
import pysam
import argparse, sys
import math, time, re
from collections import Counter
from argparse import RawTextHelpFormatter
__author__ = "Colby Chiang (cc2qe@virginia.edu)"
__version__ = "$Revision: 0.0.1 $"
__date__ = "$Date: 2015-09-27 09:31 $"
# --------------------------------------
#... | abelhj/svtools | svtools/bin/svtyper/scripts/update_info.py | Python | mit | 13,626 | [
"pysam"
] | b0d5b4c30448b4906993d3025ffe624c8472d7eab5d11b1afa325df29fce296e |
import os
import json
import urllib.request
import redis
# set configs
redis_host = '<redis host>'
auth_key = '<redis auth key>'
redis_db = redis.StrictRedis(host=redis_host, port=6379, db=0, password=auth_key)
url = '<azure ml endpoint>'
api_key = '<azure ml api key>'
headers = {'Content-Type':'application/json', 'A... | ds-project/ds-realtime-cache | code/real-time.py | Python | mit | 2,391 | [
"CRYSTAL"
] | f943c5047d4bf044c08afc1922047e049be6fcb1431be88933e9fdbebf993164 |
'''
Key plots to illustrate results
'''
import numpy as np
import pickle
import catalog as Cat
import evolver as Evol
import observables as Obvs
import util as UT
import matplotlib.pyplot as plt
import bovy_plot as bovy
from ChangTools.plotting import prettyplot
from ChangTools.plotting import prettycolors
de... | changhoonhahn/centralMS | centralms/plots.py | Python | mit | 3,844 | [
"Galaxy"
] | 1ce1bf91645e110724f9c00f2aab6be0a5e9aaa12b79f5b035a50ae8e50d6e7a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#/**********************************************************************
#** This program is part of 'MOOSE', the
#** Messaging Object Oriented Simulation Environment.
#** Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS
#** It is made available under the terms... | dilawar/moose-full | moose-examples/snippets/IntegrateFireZoo.py | Python | gpl-2.0 | 9,349 | [
"MOOSE",
"NEURON"
] | c63e9a860ea927080931de5cd83be7bc4fb9ff60ad9e92616697946ddbacbfa4 |
# Copyright 2013 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.
import atexit
import logging
import re
from devil.android import device_errors
logger = logging.getLogger(__name__)
class PerfControl(object):
"""Provi... | mrtnrdl/.macdots | scripts/bin/platform-tools/systrace/catapult/devil/devil/android/perf/perf_control.py | Python | unlicense | 7,854 | [
"Galaxy"
] | 96e01b7d231d85a6557f26b67d037b7ea557ba9fc520e009fc7d613dad500a40 |
# Copyright (C) 2016 Barry Warsaw
#
# This project is licensed under the terms of the Apache 2.0 License.
"""Flake8 extensions for Barry's PEP 8 derived coding style."""
from ast import NodeVisitor
from collections import namedtuple
from enum import Enum
class ImportType(Enum):
non_from = 0
from_import = 1... | CanonicalLtd/ubuntu-image | ubuntu_image/testing/flake8.py | Python | gpl-3.0 | 5,319 | [
"VisIt"
] | 209ff5dbf7d1736102d646491a3710b91f12eda031dba5604d0fbe64bba16d55 |
# Orca
#
# Copyright 2012 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# 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 o... | GNOME/orca | src/orca/orca_gui_navlist.py | Python | lgpl-2.1 | 6,822 | [
"ORCA"
] | 41ae55b82f986c010f0fb2675e56cab225e5e781c860406875389ee5cbefd149 |
#!/usr/bin/env python
"""
Ben Payne
ben.is.located@gmail.com
Yoga graph
This file contains two functions called by the main YogaGraph program:
-pose_properties: contains information about the pose
-pose_transitions: set of edges on the graph
This work is licensed under the Creative Commons Attribution-ShareAlike 4.0... | bhpayne/yoga_graph | src/yoga_db.py | Python | gpl-2.0 | 159,863 | [
"Firefly",
"VisIt"
] | 0055456eebf72e2b7ddf2e6d6a3cee18bd067b5ab70c30c9a2d9f6cbd00eaac0 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
#
# Copyright 2010 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... | nearlyfreeapps/python-googleadwords | tests/adspygoogle/adwords/ad_group_ad_service_unittest.py | Python | apache-2.0 | 5,066 | [
"VisIt"
] | a4a3c14a618bd8d3b77f034a36e6203a1ef80f9bd885905f8901a0c7fdbfc90f |
# -*- coding: utf-8 -*-
"""
Массив данных для моделирования нейронов (представляет из себя объект, который
содержит по одному вектору на каждый из параметров нейрона)
"""
from openre.metadata import MultiFieldMetadata, MultiFieldExtendableMetadata
from openre.vector import MultiFieldVector
from openre.data_types import... | openre/openre | openre/neurons.py | Python | mit | 4,771 | [
"NEURON"
] | 8b2b0268f1907cc215e32c138d16b0e46d414ce4cc2915a8d4c8d201be3b7233 |
#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# ChemPy - A chemistry toolkit for Python
#
# Copyright (c) 2012 by Joshua W. Allen (jwallen@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of... | chatelak/RMG-Py | rmgpy/molecule/adjlist.py | Python | mit | 44,826 | [
"ChemPy"
] | dd09c81b19ea6925ce1f1831faa3a103b77b3c6644d52c1d1fb0f7362151ad62 |
# Copyright (C) 2015 Henrique Pereira Coutada Miranda, Alejandro Molina Sanchez
# All rights reserved.
#
# This file is part of yambopy
#
#
import os
import re
from math import sqrt
import numpy as np
from qepy.auxiliary import *
eVtocm1 = 8065.54429
cm1toeV = 1.0/eVtocm1
ha2ev = 27.211396132
ev2ha = 1.0/ha2ev
Thz2c... | palful/yambopy | qepy/dynmat.py | Python | bsd-3-clause | 11,565 | [
"Quantum ESPRESSO"
] | fd159e3bc909315687cff434da47861c7f1b5900c1386e114a6ffb3bcca7c547 |
"""
NH3 fitter wrapper
==================
Wrapper to fit ammonia spectra. Generates a reasonable guess at the position
and velocity using a gaussian fit
Example use:
.. code:: python
import pyspeckit
sp11 = pyspeckit.Spectrum('spec.nh3_11.dat', errorcol=999)
sp22 = pyspeckit.Spectrum('spec.nh3_22.dat',... | allisony/pyspeckit | pyspeckit/wrappers/fitnh3.py | Python | mit | 14,053 | [
"Gaussian"
] | f1162fe03a087ca735622ae3b06296db5e993a2e6955a845542f1c3c22ca39bf |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <headingcell level=2>
# ROMS Glider
# <markdowncell>
# Virtual glider extraction: (lon,lat,time) interpolation from ROMS files
# <codecell>
%matplotlib inline
from okean.roms import glider
from okean import netcdf
import numpy as np
import matplotlib.pyplot as ... | rsignell-usgs/notebook | ROMS/roms_glider-Copy0.py | Python | mit | 2,028 | [
"ESPResSo",
"NetCDF"
] | 77cdc511528fe8753b5ea8985a31f4fd27acc32b862d0ad7657c9acac9b0b46c |
#!/usr/bin/env python
import os, sys, copy, numpy as np
DelTempFiles = True
# constants
N_A = 6.023e23
Mass_B = 78.11 #g/mol
Mass_W = 18.0 #g/mol
rho_B = 0.874 #g/cc
rho_W = 1.00 #g/cc
# system parameters
NB = 20
NW = 50
TempSet = 300
Packmol_tol = 4.0
# iteration steps
# (dummy values and must be set by ca... | tanmoy7989/benwat | makeGromacs.py | Python | gpl-2.0 | 18,327 | [
"Gromacs"
] | e3c2a4c80beb5aa75d1f7e4c06e13950a34b4e019eccb52ead9793294413f781 |
from threading import Lock
class ResponsibleGenerator(object):
"""A generator that will help clean up when it is done being used."""
__slots__ = ['cleanup', 'gen']
def __init__(self, gen, cleanup):
self.cleanup = cleanup
self.gen = gen
def __del__(self):
self.cleanup()
... | hwroitzsch/DayLikeTodayClone | venv/lib/python3.5/site-packages/rdflib/plugins/stores/concurrent.py | Python | mit | 2,690 | [
"VisIt"
] | 77127b146076716ad037247e1326257c874eb1e91d99351733b61e35b9a4d934 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/core/threaded_logging.py | Python | gpl-2.0 | 8,012 | [
"VisIt"
] | 7ab1cb831c7f21b55948fa5cc5fd2c70961a65f64552130d170aa85baad3c041 |
from sys import exit, version_info
from os import environ
import logging
logging.basicConfig(level=environ.get("LOGLEVEL", "INFO"))
if version_info <= (3, 0):
logging.fatal("Sorry, requires Python 3.x, not Python 2.x\n")
exit(1)
from setuptools import setup
import pincer
with open("README.md", ... | Andre-Tan/Pincer | setup.py | Python | gpl-3.0 | 1,285 | [
"Biopython"
] | af7aaa1a8df49b8c5c9c334a789e950d7c4ea5e84bd0c2fe3ad3e21f36dd32fc |
from __future__ import print_function, division, absolute_import #, unicode_literals
import os
import sys
import shutil
import tempfile
import warnings
from subprocess import Popen, PIPE, call
__version__ = "0.1"
__author__ = "Matteo Giantomassi"
__all__ = [
"RestrictedShell",
"StringColorizer",
"Edito... | jmbeuken/abinit | tests/pymods/tools.py | Python | gpl-3.0 | 21,205 | [
"NetCDF"
] | d039a3cde88ad68c715192cc85fcc143af949b0cf0d00cc03d1165e276aef1c4 |
"""Implementation of magic functions for interaction with the OS.
Note: this module is named 'osm' instead of 'os' to avoid a collision with the
builtin.
"""
from __future__ import print_function
#-----------------------------------------------------------------------------
# Copyright (c) 2012 The IPython Developmen... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/IPython/core/magics/osm.py | Python | bsd-3-clause | 26,559 | [
"VisIt"
] | 68cbf2aec724b374f484e2ca98f0b5da74223b81821426227530fe300fb46954 |
# $Id$
#
# Copyright (C) 2005-2006 greg landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from __future__ import... | adalke/rdkit | rdkit/DataStructs/VectCollection.py | Python | bsd-3-clause | 6,312 | [
"RDKit"
] | 81d5ba01738b163aa98ace0ca48e7072c813208432d48029d3ee7b11eb62e2ca |
#
# Copyright 2001 - 2016 Ludek Smid [http://www.ospace.net/]
#
# This file is part of Outer Space.
#
# Outer Space 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
# (... | dahaic/outerspace | server/lib/ige/ospace/ISystem.py | Python | gpl-2.0 | 42,195 | [
"Galaxy"
] | d54f8e3d203e2153bfbd4d17a00f14a6af873043a8642a928e88a280e815bf4c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 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... | Forage/Gramps | gramps/plugins/tool/reorderids.py | Python | gpl-2.0 | 9,524 | [
"Brian"
] | 88712cdcb171f41790fd7e0ea4599282434aace87b290b16049ee3cc32945e2c |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
import os
import sys
import time
import atexit
import pickle
import numpy as np
from gpaw import debug
from gpaw import dry_run as dry_run_size
from gpaw.utilities import is_contiguous
from gpaw.utilities import gcd
from gp... | ajylee/gpaw-rtxs | gpaw/mpi/__init__.py | Python | gpl-3.0 | 27,596 | [
"GPAW"
] | 81c379003ec62faf1675d45996ca280360ecd86b9afa1413fd9f81f0f204081e |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2017, California Institute of Technology
# All rights reserved.
g_program_name = __file__.split('/')[-1] # = 'charge_by_bond.py'
g_date_str = '2017-10-03'
g_version_str = '0.14.0'
... | quang-ha/lammps | tools/moltemplate/moltemplate/charge_by_bond.py | Python | gpl-2.0 | 17,911 | [
"LAMMPS"
] | 4dd733398f8df2a8365f37088f2f78b4877dff6de2716ab810ca82b84bc51311 |
import base64
import json
import re
from abc import ABC, abstractmethod
from dataclasses import asdict, dataclass, field
from enum import Enum
from pathlib import PureWindowsPath
from typing import Any, Dict, Iterator, List, Optional, Tuple, Union
from pymisp import MISPAttribute, MISPEvent, MISPObject
from .rest_ap... | VirusTotal/misp-modules | misp_modules/lib/_vmray/parser.py | Python | agpl-3.0 | 46,502 | [
"Galaxy"
] | 9cc679f00c1e9101c0195531e6ab5f0e63dbb181747feff43f7bf408a43901b1 |
# 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/FreeEnergyCompensation.py | Python | gpl-3.0 | 2,994 | [
"ESPResSo"
] | df0b7afab98cc4c07b39b5526b1abf2954a2c788c79befe280b5c66791f891c6 |
from __future__ import division
from flask import render_template, redirect
from weblog import app, bots
from weblog.auth import requires_auth
from datetime import datetime, timedelta
from weblog.models import Visit
import json
@app.route("/dashboard/")
@requires_auth
def dashboard_default():
return redirect("/das... | Tethik/apache-web-log | weblog/routes/dashboard.py | Python | gpl-3.0 | 4,239 | [
"VisIt"
] | 3d6c79292c38d869c1103e74fae6e2442015dae27dbf9f730a45ded8173f1957 |
# coding: utf-8
"""
This modules defines an SQLAlchemy ORM model for a flat.
"""
# pylint: disable=locally-disabled,invalid-name,too-few-public-methods
from __future__ import absolute_import, print_function, unicode_literals
import logging
import enum
import arrow
from sqlalchemy import (
Boolean,
Column,
... | Phyks/Flatisfy | flatisfy/models/flat.py | Python | mit | 5,969 | [
"VisIt"
] | 31ac4e9cec91f4402439eecff8dc869bf943083b779f84ae547af9ec9283d83f |
#!/usr/bin/env python
""" Toma un complejo proteina-DNA en formato PDB y pone los H faltantes con open babel."""
__author__ = 'Bruno Contreras-Moreira'
import os,sys,getopt,subprocess
BABELEXE = '/usr/bin/babel' # get it from http://openbabel.org
# edit according to your settings
#########################... | eead-csic-compbio/bioinformatica_estructural | code/files/add_hydrogens.py | Python | cc0-1.0 | 4,558 | [
"Open Babel"
] | 7d7a9e61de626f4293566354e4c3640d38694b4730638025ddde6c71e3d4da76 |
#!/usr/local/bin/env python
#
#=============================================================================================
# FILE DOCSTRING
#=============================================================================================
"""
Automated selection and imposition of receptor-ligand restraints for absolute... | jchodera/yank | Yank/restraints.py | Python | lgpl-3.0 | 21,659 | [
"OpenMM"
] | 72ebd162a66530e6985ac33bfe40ed58f32830ae50cffc060c24f5d658285361 |
#!/usr/bin/env python
#
# Copyright 2012 Google Inc. All Rights Reserved.
"""Python script for interacting with BigQuery."""
import cmd
import codecs
import datetime
import httplib
import json
import os
import pdb
import pipes
import platform
import shlex
import sys
import time
import traceback
import types
impor... | osmanpub/google-samples | data/bigquery-2.0.17/bq.py | Python | apache-2.0 | 78,673 | [
"VisIt"
] | fe86ddc017eafea18cca8f8f1059ea888291eb2bdddd2bdada0e7e906493308c |
"""Bayesian Gaussian Mixture Models and
Dirichlet Process Gaussian Mixture Models"""
from __future__ import print_function
# Author: Alexandre Passos (alexandre.tp@gmail.com)
# Bertrand Thirion <bertrand.thirion@inria.fr>
#
# Based on mixture.py by:
# Ron Weiss <ronweiss@gmail.com>
# Fabian Ped... | florian-f/sklearn | sklearn/mixture/dpgmm.py | Python | bsd-3-clause | 30,576 | [
"Gaussian"
] | ad13a96d1c28f869e0d4c2e2ba3c2d2f6767c7d57886d8adb78dd88b2cce4003 |
# -*- coding: utf8 -*-
"""
This file contains configuration for Cexio stock.
"""
__author__ = "Jan Seda"
__copyright__ = "Copyright (C) Jan Seda"
__credits__ = []
__license__ = ""
__version__ = "0.1"
__maintainer__ = "Jan Seda"
__email__ = ""
__status__ = "Production"
import urllib.parse
import sys
import datetime
... | Honzin/ccs | ccs/cexio/public/__init__.py | Python | agpl-3.0 | 35,036 | [
"VisIt"
] | c72e590a0e3a87e5012eead6223df1b30913359ae9a6d4abe161d489e581ef86 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import json
import os
import re
import pyte... | s-hertel/ansible | test/units/galaxy/test_api.py | Python | gpl-3.0 | 46,719 | [
"Galaxy"
] | 3b6d0a9f5f799d4c4e54a7227fe9eaf84b426bc218ea0787623e9f4339387ed0 |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Danelle Cline'
__copyright__ = '2018'
__license__ = 'GPL v3'
__contact__ = 'duane at mbari.org'
__doc__ = '''
Master loader for all CANON off season activities in 2018
Mike McCann, Duane Edgington, Danelle Cline
MBARI 17 January 2018
@var __date__: Dat... | danellecline/stoqs | stoqs/loaders/CANON/loadCANON_os2018.py | Python | gpl-3.0 | 12,619 | [
"NetCDF"
] | 74fcca127793dc70f2655839ee7079840124f27ea1733867fe07c928b42957cf |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | tqchen/tvm | tests/python/contrib/test_arm_compute_lib/infrastructure.py | Python | apache-2.0 | 12,238 | [
"VisIt"
] | dd81c8a9b16a0afc3068b40131b707d795df81121bee2f043300f44b29820906 |
#!/usr/bin/env python3
"""Cheap and simple API helper
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.3 $"
__date__ = "$Date: 2004... | jtraver/dev | python3/env/apihelper.py | Python | mit | 1,811 | [
"VisIt"
] | 0d1dee623edc560c4bd0b1a662c2370cd53f051ec8e0b36d54be41ebd88a7e82 |
#!/usr/local/bin/python -i
# preceeding line should have path for Python on your machine
# gui.py
# Purpose: control a continuously running LAMMPS simulation via a Tkinter GUI
# Syntax: gui.py in.lammps Nfreq
# in.lammps = LAMMPS input script
# Nfreq = query GUI every this many steps
# IMPORTANT: t... | val-github/lammps-dev | python/examples/gui.py | Python | gpl-2.0 | 2,807 | [
"LAMMPS"
] | 8706ef9128b05a207d11fe95be29e6e98a6775a118743c3112f421beacdf0479 |
# -*- coding: utf-8 -*-
import os
import re
import uuid
import urllib
import logging
import datetime
import urlparse
from collections import OrderedDict
import warnings
import pytz
import blinker
from flask import request
from HTMLParser import HTMLParser
from modularodm import Q
from modularodm import fields
from mo... | revanthkolli/osf.io | website/project/model.py | Python | apache-2.0 | 89,092 | [
"VisIt"
] | 2d8eb13608dd8d0adfe6b2111c5a3384cfaca31efa977b63134fa65b4fb01ac8 |
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
The maths module provides higher-level interfaces to some of the operations
that can be performed with the fslmaths command-line program.
Change directory to provide... | carolFrohlich/nipype | nipype/interfaces/fsl/maths.py | Python | bsd-3-clause | 12,876 | [
"Gaussian"
] | b1a4dcef5213d520f80db39a9ffdeeccbb41a0f0514f4f32e237648be0395a9d |
webs = [ # FROM https://theuselessweb.com/
"http://heeeeeeeey.com/",
"http://tinytuba.com/",
"http://corndog.io/",
"http://thatsthefinger.com/",
"http://cant-not-tweet-this.com/",
"http://weirdorconfusing.com/",
"http://eelslap.com/",
"http://www.staggeringbeauty.com/",
"http://burymewithmymoney.com... | berbus/proyectoIV | aleatoriedad/web_list.py | Python | mit | 2,504 | [
"MOE"
] | 14e3645e4df65694b08071d6450395f8633bc1832409a3cc450aad872c633576 |
# Project Name: SleekWebBot
# Author: Kevin Bazira
# Descripttion: SleekWebBot is an internet robot that visits a website and clicks on a specified web element.
# How it works: Requests User Input,
# Function visit_web(): Opens Browser, Loads URL, Waits for some time, Finds Element, Clicks Element, Waits for some time... | kevinbazira/sleek-web-bot | SleekWebBot.py | Python | mit | 3,072 | [
"VisIt"
] | 29f0da03ae28a73daa19f1bdd39a56dd1a1cbe3b5cfd855dec5e63311dd47de5 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | alshedivat/tensorflow | tensorflow/python/autograph/pyct/cfg.py | Python | apache-2.0 | 27,459 | [
"VisIt"
] | cfe183d295739b8d9aa6cc565c98851a18e16f21d6b95ed3e15877383ee30411 |
"""
An estimator to model data using a fixed number of multivariate Gaussian
distributions with a single multivariate latent factor, using maximum
likelihood as the objective function.
"""
__all__ = ["MLMixtureModel"]
import logging
import numpy as np
import scipy
from sklearn import (cluster, decomposition)
from ... | andycasey/snob | snob/slf_mixture/ml.py | Python | mit | 8,307 | [
"Gaussian"
] | a592fc5f8ceb68335c96242041ad194262915280eae891d1143b3132120774df |
"""The test module for the Octojobs project."""
import faker
from octojobs.models import Job
from octojobs.models import get_tm_session
from octojobs.models.meta import Base
from pyramid import testing
from pyramid.httpexceptions import HTTPFound
import pytest
import transaction
fake = faker.Faker()
DUMMY_JOBS = [J... | OctoJobs/Octojobs | octojobs/tests.py | Python | mit | 21,846 | [
"Octopus"
] | 12f6577af9c32cbf313c1ba8ec57ccf032f78fa8de2d9bc43c8cfc87a444d2c4 |
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