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"""Module collecting functions dealing with the GLUE2 information schema
:author: A.Sailer
Known problems:
* ARC CEs do not seem to publish wall or CPU time per queue anywhere
* There is no consistency between which memory information is provided where,
execution environment vs. information for a share
* Some ... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/Glue2.py | Python | gpl-3.0 | 16,119 | [
"DIRAC"
] | 60af180f62d952e94a7bbbff320aade90e748d6e7c0b60b6b44a64a4c80d865f |
# -*- coding: utf-8 -*-
#
# MNE documentation build configuration file, created by
# sphinx-quickstart on Fri Jun 11 10:45:48 2010.
#
# This file is execfile()d with the current directory set to its containing
# dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... | rajegannathan/grasp-lift-eeg-cat-dog-solution-updated | python-packages/mne-python-0.10/doc/conf.py | Python | bsd-3-clause | 9,408 | [
"Mayavi"
] | dfcedb18eb4b690cbb8d30957a8ff6b48b0beb8ee5f0851b6ca99acf786eb823 |
# wxapp.py
#
# Copyright 2009 dan collins <quaninux@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
#... | badbytes/pymeg | gui/wx/PyMEG.py | Python | gpl-3.0 | 150,866 | [
"VTK"
] | 0472c48e61ea04f49de83e84068a0f49d58c80f8d2edb1104c057a0569869c40 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/topology/test_tprparser.py | Python | gpl-2.0 | 6,550 | [
"Gromacs",
"MDAnalysis"
] | 5ec39900b18981f5c82f557d19fbfb33bd50cc9e08c19c982dfc2fe65271be98 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | tests/functional/openlp_plugins/songs/test_foilpresenterimport.py | Python | gpl-2.0 | 9,878 | [
"Brian"
] | 1a1b36c85bc2dc4d65d156c1c673cbacd652348ace998aeaebc29550a1c4e423 |
########################################################################
# $HeadURL$
########################################################################
""" DIRAC FileCatalog plugin class to manage file metadata. This contains only
non-indexed metadata for the moment.
"""
__RCSID__ = "$Id$"
# import time
i... | Sbalbp/DIRAC | DataManagementSystem/DB/FileCatalogComponents/FileMetadata.py | Python | gpl-3.0 | 23,429 | [
"DIRAC"
] | af8557e41155b513f4bae1a58555fbfcb273141b042185344f68d22e9a2b9cb4 |
#! /usr/bin/env python
# This script reproduces the spike synchronization
# behavior of integrate-and-fire neurons in response to a subthreshold
# oscillation. This phenomenon is shown in Fig. 1 of
# C.D. Brody and J.J. Hopfield
# Simple Networks for Spike-Timing-Based Computation,
# with Application to Olfacto... | magnastrazh/NEUCOGAR | nest/dopamine/test_files/Brody_and_Hopfield_model.py | Python | gpl-2.0 | 1,958 | [
"Gaussian",
"NEURON"
] | 0af47a4285e724b407bd5cfbec46b8b68b4cfe388682fb015c23d2dff1e4a0f3 |
MAX_COORD_INTEGER = 16384
def basenpc_coords(ent):
"""basenpc_coords returns the game coordinates of the given tarrasque BaseNPC-derived entity"""
cellwidth = 1 << ent.properties[(u'DT_BaseEntity', u'm_cellbits')]
x = ((ent.properties[(u'DT_DOTA_BaseNPC', u'm_cellX')] * cellwidth) - MAX_COORD_INTEGER)\
... | grschafer/alacrity | alacrity/parsers/utils.py | Python | mit | 18,327 | [
"CRYSTAL",
"TINKER"
] | 99ba176dd812becb0e5909188864db030c8104380797f314f0585172e0f03a16 |
#!/usr/bin/env python
import unittest
from ct.crypto import error
from ct.crypto.asn1 import tag
from ct.crypto.asn1 import types
from ct.crypto.asn1 import type_test_base
class TagDecoratorTest(unittest.TestCase):
"""Test the automatic creation of tags."""
def test_universal_tag(self):
class Test(... | rep/certificate-transparency | python/ct/crypto/asn1/types_test.py | Python | apache-2.0 | 28,141 | [
"exciting"
] | 046f0c5e6aac00bed9da73476966ce7e0ee49a8a5849ce997df6dad175bb0996 |
import time
from org.gumtree.gumnix.sics.control.events import DynamicControllerListenerAdapter
from org.gumtree.gumnix.sics.control import IStateMonitorListener
from org.gumtree.gumnix.sics.io import SicsProxyListenerAdapter
from org.eclipse.swt.events import DisposeListener
from org.eclipse.swt.widgets import Ty... | Gumtree/Kookaburra_scripts | Internal/Initialise_scan.py | Python | epl-1.0 | 11,345 | [
"Gaussian"
] | b3d8edd6695991a242315810b15d6495a79478879ead764e7ce6eef2b47515ae |
#!/usr/bin/env python3
from olctools.accessoryFunctions.accessoryFunctions import MetadataObject
from genemethods.geneseekr.geneseekr import GeneSeekr
from genemethods.geneseekr.blast import BLAST
import multiprocessing
from glob import glob
from time import time
import os
test_path = os.path.abspath(os.path.dirname(_... | OLC-Bioinformatics/GeneSeekr | tests/test_blastx.py | Python | mit | 8,006 | [
"BLAST"
] | 71f9a5fab138a54afba9aa10516ffbd9f015c024be25ea028057ea4b456d1ddf |
from __future__ import print_function, division
import math
import numpy as np
from sklearn.cluster import MiniBatchKMeans
class hard_EM_GMM(object):
""" A class for performing hard-EM clustering into a Gaussian
mixture model.
Hard-EM clustering is like 'normal' EM clustering, but each
ob... | stuartsale/pyBHC | pyBHC/hardEM.py | Python | bsd-3-clause | 10,575 | [
"Gaussian"
] | 597824fab2d7482707e530718f567ffee888f8f064a56209a7e003a913d9f0af |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
Defines an abstract base class contract for Transformation object.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__versi... | migueldiascosta/pymatgen | pymatgen/transformations/transformation_abc.py | Python | mit | 2,801 | [
"pymatgen"
] | 6f8879435dc80d16647d90108624f36bb18ab8786c56bb43157df9c0ebf1ef11 |
#!/usr/bin/env python3
'''Manual DDNS testing'''
from dnstest.utils import *
from dnstest.test import Test
import random
t = Test()
def check_soa(master, prev_soa):
soa_resp = master.dig("ddns.", "SOA")
compare(prev_soa, soa_resp.resp.answer, "SOA changed when it shouldn't")
def verify(master, zone, dnssec... | CZ-NIC/knot | tests-extra/tests/ddns/basic/test.py | Python | gpl-3.0 | 27,901 | [
"Elk"
] | 927930d0e63c36598e77bff8a1718f540e52ffe9bfd014691cca00e2b795c72e |
# tests for openbabel in python
# A test of some smiple SMILES manipulation
# by Richard West <r.west@neu.edu>
# Three SMILES, first two obviously the same, third one a resonance isomer.
smis=['[CH2]C=CCO', 'C([CH2])=CCO','C=C[CH]CO']
import pybel
canonicals = [pybel.readstring("smi", smile).write("can").strip() for ... | dmaticzka/bioconda-recipes | recipes/openbabel/2.4.1/run_test.py | Python | mit | 646 | [
"Pybel"
] | 994ba4ea83090bde6bdacc345d32a5d1e0f6da06b650294ba0d815e95d2b585f |
#
# 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... | rikima/spark | python/pyspark/ml/regression.py | Python | apache-2.0 | 66,566 | [
"Gaussian"
] | 04df7ef02cc1b609bb6b57eef9abbe9e6265bbe8e3aee875c662ca43d69d7732 |
# 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 ag... | flgiordano/netcash | +/google-cloud-sdk/lib/surface/feedback.py | Python | bsd-3-clause | 5,403 | [
"VisIt"
] | 78e6b6904eb6c64fed59384732a9efe84b332ae4ca83b4074a561eaea3b61920 |
#!/usr/bin/env python
#
# Urwid Palette Test. Showing off highcolor support
# Copyright (C) 2004-2009 Ian Ward
#
# 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
# ... | rndusr/urwid | examples/palette_test.py | Python | lgpl-2.1 | 9,400 | [
"ADF"
] | f7e299a941e5dd4d133c368c976346b1e80f3a0dbc13d30e565a1e35d9176e6e |
# 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... | psci2195/espresso-ffans | testsuite/python/elc_vs_mmm2d_nonneutral.py | Python | gpl-3.0 | 5,864 | [
"ESPResSo"
] | 5ea5582fe6b30dd7f57836617653f94312dd38497cefc2235767fc21b127d686 |
import time
import numpy as np
import matplotlib.pyplot as plt
import h5py
from ..doublyPeriodic import doublyPeriodicModel
from numpy import pi
class model(doublyPeriodicModel):
def __init__(self, name = None,
# Grid parameters
nx = 256, ny = None, Lx = 1e6, Ly = None,
# So... | glwagner/py2Periodic | py2Periodic/physics/hydrostaticWaveEqn_xy.py | Python | mit | 12,965 | [
"Gaussian"
] | bee5d3f580852fffa3c8ba8ae7ee48a55338fb8e469a4fca2e06cb21c077ac0e |
#!/usr/bin/python
import os
import sys
import Bio
from Bio import AlignIO
"""Functions for parsing and manipulating sequence alignment files
Functions by Zach Zbinden and Tyler Chafin"""
#Function to parse a PHYLIP formatted file of SNPs
#Function returns a BioALign object
def read_phylip(infile):
for aln in AlignI... | tkchafin/fst_filter.py | aln_file_tools.py | Python | gpl-3.0 | 4,867 | [
"Biopython"
] | e16e3d29ba3aa16d3cd819e2f58e5cb52c63b2b0f4a41a7a912f8fbb07b3264e |
# coding: utf-8
import constance
from django.conf import settings
from hub.models import ConfigurationFile, PerUserSetting
from hub.utils.i18n import I18nUtils
def external_service_tokens(request):
out = {}
if settings.GOOGLE_ANALYTICS_TOKEN:
out['google_analytics_token'] = settings.GOOGLE_ANALYTICS_... | kobotoolbox/kpi | kpi/context_processors.py | Python | agpl-3.0 | 2,236 | [
"VisIt"
] | 017e9a5200411d06a9aaf91c0287d3c2e7ec5dee75b671a49be86a3ac4604b0a |
# coding: utf-8
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import random
import re
import socket
import ssl
import sys
import time
import math
from ..compat import (
compat_cookiejar_Cookie,
compat_cookies,
compat_etree_Element,
... | spvkgn/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 143,174 | [
"VisIt"
] | a948277513fbf7c34a9be0d156d137630433f1b849caef8bc75dab80b90ace00 |
# -*- coding: utf-8 -*-
################################
######## Red - Discord bot #####
################################
# made by Twentysix
#
#
import discord
import logging
import time
import datetime
import requests
import aiohttp
import traceback
import re
import youtube_dl
import os
import... | AnsonRS/HAL-9000 | hal.py | Python | gpl-3.0 | 81,472 | [
"Brian"
] | de58cce232282129e9447bd8a944e443ca1fb270c4869dbec2da87ca1214c572 |
# _ __
# | |/ /___ ___ _ __ ___ _ _ ®
# | ' </ -_) -_) '_ \/ -_) '_|
# |_|\_\___\___| .__/\___|_|
# |_|
#
# Keeper Commander
# Copyright 2021 Keeper Security Inc.
# Contact: ops@keepersecurity.com
#
import argparse
import base64
import getpass
import logging
from typing import Optional
from .. import ... | Keeper-Security/Commander | keepercommander/commands/breachwatch.py | Python | mit | 11,030 | [
"VisIt"
] | 5eccdebceb1fe76902f7c9892f4ab4c130cad46bd63f1bccbe8cd12fff28ad74 |
# Copyright (C) 2012,2013,2015
# 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... | capoe/espressopp.soap | src/VerletList.py | Python | gpl-3.0 | 3,547 | [
"ESPResSo"
] | 89b1e790be51eb31cccce4ca97b68299a2214b67ebc640aea1ac46dd43d5eaed |
import numpy as np
import itertools
import scipy.ndimage
from scipy.ndimage.filters import gaussian_filter
def smoothvoxels(data_4d, fwhm, time):
"""
Return a 'smoothed' version of data_4d.
Parameters
----------
data_4d : numpy array of 4 dimensions
The image data of one subject
fwhm : width of... | reychil/project-alpha-1 | code/utils/functions/smooth.py | Python | bsd-3-clause | 707 | [
"Gaussian"
] | a8a0bece4ce37fd5a64fabcda55f772cb2db67f0827b3403c0a0c2cfda3c6937 |
import math
from ..libmp.backend import xrange
class QuadratureRule(object):
"""
Quadrature rules are implemented using this class, in order to
simplify the code and provide a common infrastructure
for tasks such as error estimation and node caching.
You can implement a custom quadrature rule by ... | JensGrabner/mpmath | mpmath/calculus/quadrature.py | Python | bsd-3-clause | 38,312 | [
"Gaussian"
] | 30e971b37565594a2c27a7d0ea8d6866c37864de844b6345f3352c9a3965384c |
""" The CountryMapping module performs the necessary CS gymnastics to resolve country codes """
__RCSID__ = "$Id$"
from DIRAC import gConfig, S_OK, S_ERROR
def getCountryMapping(country):
""" Determines the associated country from the country code"""
mappedCountries = [country]
while True:
mappedCountry... | fstagni/DIRAC | Core/Utilities/CountryMapping.py | Python | gpl-3.0 | 1,042 | [
"DIRAC"
] | 375dd289e353ac1b69ed7d6aa869df9e0869727251b3c596dd27b00e5282024d |
# Copyright 2015 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... | dyoung418/tensorflow | tensorflow/python/ops/template.py | Python | apache-2.0 | 14,441 | [
"VisIt"
] | c282ad847120309f5fe3d063708ade118245f729a7e887d8f4e7d1c2cab1c84c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Module is used for converting data from pkl format to raw.
"""
import argparse
import numpy as np
import misc
import qmisc
def main():
parser = argparse.ArgumentParser(description=__doc__) # 'Simple VTK Viewer')
parser.add_argument('-i','--inputfile', defaul... | mjirik/lisa | lisa/convert_pkl.py | Python | bsd-3-clause | 1,231 | [
"VTK"
] | 4563b77e05fc263b343085acbcde9d198a4cdc0d9eb56337c1cdcccb37e9df12 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | liuwenf/moose | python/chigger/tests/range/none.py | Python | lgpl-2.1 | 1,336 | [
"MOOSE"
] | 88f93906a6386166a7cbf702acfbcaf0d239801ea4616a2acff29cd281efdb6e |
# 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... | sunqm/pyscf | pyscf/pbc/geomopt/__init__.py | Python | apache-2.0 | 871 | [
"PySCF"
] | c93200da92497eeb6d017fac3bc398a4acbbf9f742882ea90e7bf40fb2ff9566 |
"""
The B{0install show} command-line interface.
"""
# Copyright (C) 2012, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import _
from zeroinstall.cmd import select, UsageError
from zeroinstall.injector import qdom, selections
... | dsqmoore/0install | zeroinstall/cmd/show.py | Python | lgpl-2.1 | 1,362 | [
"VisIt"
] | 41ae820b59c25f933a5af3197a274bbba48000a451abb59b52165f5621187b64 |
# $HeadURL$
"""
SystemLoggingHandler is the implementation of the Logging service
in the DISET framework
The following methods are available in the Service interface
addMessages()
"""
__RCSID__ = "$Id$"
from types import ListType, StringTypes, StringTypes
from DIRAC ... | avedaee/DIRAC | FrameworkSystem/Service/SystemLoggingHandler.py | Python | gpl-3.0 | 2,500 | [
"DIRAC"
] | 50123aecf9929570c5b3ca2074930ed88bc5fab46bb90aff30c366d269fb2553 |
#* 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 subp... | nuclear-wizard/moose | python/TestHarness/tests/test_MissingGold.py | Python | lgpl-2.1 | 997 | [
"MOOSE"
] | 92639b0657f54fc60541329006186b5f5989ffcc65366e07cd8239c88e44f942 |
"""Minimal Python 2 & 3 shim around all Qt bindings
DOCUMENTATION
Qt.py was born in the film and visual effects industry to address
the growing need for the development of software capable of running
with more than one flavour of the Qt bindings for Python - PySide,
PySide2, PyQt4 and PyQt5.
1. Bu... | bohdon/maya-pulse | src/pulse/scripts/pulse/vendor/Qt/__init__.py | Python | mit | 66,075 | [
"VisIt"
] | 23844db5bb99e6265c91aa4951a95eb24021ee576fe806912c032b84cf1bc4f9 |
from PyOpenWorm.neuron import Neuron
from PyOpenWorm.data import DataUser
import neuroml as N
class NeuroML(DataUser):
@classmethod
def generate(cls, o, t=2):
"""
Get a NeuroML object that represents the given object. The ``type``
determines what content is included in the NeuroML obj... | gsarma/PyOpenWorm | PyOpenWorm/my_neuroml.py | Python | mit | 1,377 | [
"NEURON"
] | 626036e29a8987e66a8393c3c0c9015286c5332639a550334f3cf34eef13f72e |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/pbc/df/incore.py | Python | apache-2.0 | 8,293 | [
"PySCF"
] | 71b169a413ba38823afdeda367322b37fef3a94805c4716cfe3019424d33e954 |
# encoding: utf-8
"""
An application for IPython.
All top-level applications should use the classes in this module for
handling configuration and creating componenets.
The job of an :class:`Application` is to create the master configuration
object and then create the configurable objects, passing the config to them.
... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/core/application.py | Python | apache-2.0 | 15,149 | [
"Brian"
] | b3b5cc9502b0922f13cf95d33b4b9ffb9b98b5f04335ab29f87fb2eca272d6f3 |
# 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/Time_Window/test10_cross_validate_objects_400ms.py | Python | mit | 4,258 | [
"Mayavi"
] | c237c591be793cf87aab14899ae87c6f21f78d5e0cd80cc55fe7229ad7468a16 |
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from builtins import zip
from builtins import range
from builtins import object
import itertools as it
import warnings
import numpy as np
from scipy.special import gammaln
try:
from bottleneck import nansu... | vjlbym/sima | sima/motion/hmm.py | Python | gpl-2.0 | 35,739 | [
"Gaussian",
"NEURON"
] | 305fc0b149d64c327cbc144697f5434161295bf2cda0fc3fce96a150b2509286 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Renaming column for 'DenominatorPart.data' to match new field type.
db.rename_column(u'profiles_denomina... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0005_auto__chg_field_denominatorpart_data__chg_field_indicatorpart_data.py | Python | mit | 28,575 | [
"MOE"
] | 3df81f605bd62bedb4ce63e398d174df64f830072ea5c7dc1213e0eef1e537d1 |
"""
There are ways to measure the quality of a separated source without
requiring ground truth. These functions operate on the output of
clustering-based separation algorithms and work by analyzing
the clusterability of the feature space used to generate the
separated sources.
"""
from sklearn.metrics import silhouett... | interactiveaudiolab/nussl | nussl/ml/confidence.py | Python | mit | 14,980 | [
"Gaussian"
] | ceaf26e00d0b23cb7b0e7b0739b57b625dd9d315cbe45f83eafa09ef2832e6d8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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 Licens... | caphrim007/ansible | lib/ansible/modules/network/cnos/cnos_vlan.py | Python | gpl-3.0 | 22,092 | [
"VisIt"
] | 2ac98161acf88de3448f908ae12505d6ec624bdbd64b67c4153a3e12efe9539e |
"""Implements API endpoints under ``/api/org``"""
from typing import Any, Dict
from flask import Blueprint, jsonify
from werkzeug.exceptions import abort
from bson import ObjectId
from shrunk.client import ShrunkClient
from shrunk.util.ldap import is_valid_netid
from shrunk.util.decorators import require_login, requ... | oss/shrunk | backend/shrunk/api/org.py | Python | mit | 9,690 | [
"VisIt"
] | 975353fc882b70afa5917a98b15e4534c8b95c6604b622c1f11dd46bff4fd27d |
from dateutil import parser as datetime_parser
from colander import (
Invalid,
Mapping,
SchemaNode,
null,
)
from deform.compat import (
string_types,
text_,
)
from deform.widget import (
Widget,
)
from deform.widget import _StrippedString
import logging
import json
LOGGER = logging.get... | bird-house/pyramid-phoenix | phoenix/geoform/widget.py | Python | apache-2.0 | 4,428 | [
"NetCDF"
] | dd237870f6dfd40fe4ce4e8231f2c13ee7d552f7bea30ca82e5cf62636d527ac |
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/main/utils/__init__.py | Python | apache-2.0 | 899 | [
"Galaxy"
] | c3a37e46e83236f11504134e1f9bd26a5e7f3c2bd52a54ea425c4ae8652cf29f |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting model 'DataDisplayTemplate'
db.delete_table('profiles_datadisplaytemplate')
# Removing... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0036_auto__del_datadisplaytemplate__del_datadisplay__chg_field_indicator_da.py | Python | mit | 18,644 | [
"MOE"
] | 2d1a140164baf3546f311f7f59122d54f1be21f19882c23e1489488331fad00d |
# coding: utf-8
"""0MQ Socket pure Python methods."""
#-----------------------------------------------------------------------------
# Copyright (C) 2013 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING... | IsCoolEntertainment/debpkg_python-pyzmq | zmq/sugar/socket.py | Python | lgpl-3.0 | 13,277 | [
"Brian"
] | fc698f9157d0cd247ead697301237c74a1a23468f88145a460545b17cc45902d |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import argparse
import sys
import tempfile
import os
import tensorflow as tf
from tensorflow.examples.tutorials.mnist import input_data
from scipy.constants import Boltzmann
import random
from numpy import exp... | HPCC-Cloud-Computing/press | prediction/Simulated-Annealing/sacnn.py | Python | mit | 8,943 | [
"NEURON"
] | ed890a34d7a20d08e678dfdcb09284cd9e6b458f62bba59c40ec73b74f0955c4 |
from __future__ import print_function, division
from sympy.core import S, C, sympify
from sympy.core.function import Function, ArgumentIndexError
from sympy.core.logic import fuzzy_and
from sympy.ntheory import sieve
from math import sqrt as _sqrt
from sympy.core.compatibility import reduce, as_int, xrange
from sympy... | Cuuuurzel/KiPyCalc | sympy/functions/combinatorial/factorials.py | Python | mit | 18,067 | [
"VisIt"
] | 0ac7e8f9a20e27b1278ed4344f355cfab01c9387e7ae17b1645555f8d7cb43f8 |
import os.path
import time
from remsci.lib.utility import path
from libpipe.cmds.base import BaseCmd
import logging
log = logging.getLogger(__name__)
class HisatCmd(BaseCmd):
'''HISAT command setup
Command usage:
hisat [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} -S <sam>
'''
NAM... | muppetjones/rempipe | libpipe/cmds/align.py | Python | gpl-3.0 | 6,515 | [
"Bowtie"
] | 3d15c62f58fef34d37e0d6e35b7119aa7c9e2cc2a0002488a0f2634f2f2c7878 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor(... | hlzz/dotfiles | graphics/VTK-7.0.0/Common/Transforms/Testing/Python/spherical.py | Python | bsd-3-clause | 1,983 | [
"VTK"
] | 5b717beea36cc74a2828f87a43b83b2394a5123c9c69cd5bac92bd4bf9ed13ba |
#! /usr/bin/python
"""Copyright 2011 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__="Adam Stelmack"
__version__="2.1.8"
__date__ ="14-Jan-2011 2:29:14 PM"
#Basic imports... | danielsuo/mobot | src/move/Python/Bridge-simple.py | Python | mit | 4,555 | [
"VisIt"
] | 990a4a5bd3f957a265f68f8dfeddb68cc9565394ccc18d889f3fba059736e814 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#-------------------------------------------------------------------------------
'''
This software has been developed by:
GI Genética, Fisiología e Historia Forestal
Dpto. Sistemas y Recursos Naturales
ETSI Montes, Forestal y del Medio Natural
Universida... | GGFHF/NGScloud | Package/xlib.py | Python | gpl-3.0 | 50,618 | [
"BLAST",
"Bioconda"
] | 87ca2a464697049f94c87d71157834b8639a0437be9b88bd40e50715eee850bc |
from modal_noise_script import (save_new_object, set_new_data,
save_baseline_object, save_fft_plot,
save_modal_noise_data)
import numpy as np
import os
import csv
from copy import deepcopy
NEW_DATA = True
NEW_OBJECTS = False
NEW_BASELINE = False... | rpetersburg/FiberProperties | scripts/modal_noise_600um.py | Python | mit | 5,353 | [
"Gaussian"
] | f035823e755db7448802aaaba7fde41ecb0a16b6d6c013534abd821aa7c48cb8 |
import unittest
from os import path
import pysam
from cigar import Cigar
from mock import Mock
from pyfasta import Fasta
from clrsvsim.simulator import (
make_split_read,
modify_read,
modify_read_for_insertion,
invert_read,
unpack_cigar,
get_max_clip_len,
get_inverse_sequence,
overlap
... | color/clrsvsim | clrsvsim/test_simulator.py | Python | apache-2.0 | 10,536 | [
"pysam"
] | c20d2d19a5c3717b108f1ee6c0146c8c688f3a8990242c4b31a62c8093f2ee06 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
n0 = 50
n1 = 50
display = True
worldSize = El... | birm/Elemental | examples/interface/RemoteUpdate.py | Python | bsd-3-clause | 3,212 | [
"Gaussian"
] | ab6f49f8d27aed2d95255b8f84e063be45264c426b93bbd937b7703e36fd9aba |
from __future__ import print_function
import os, sys, inspect
import h5py
import numpy as np
import matplotlib
import random
import math
import multiprocessing
from PIL import Image
from Crypto.Random.random import randint
from functools import partial
# Load the configuration file
import config
cmd_folder = os.path.... | srinituraga/caffe_neural_models | dataset_08/network_generator.py | Python | bsd-2-clause | 16,036 | [
"Gaussian"
] | 6adb8bf8a8216b48dbdc87f16b082253c518a9cd601e9209846c8887feaa85eb |
import py
import os
import execnet
from xdist.slavemanage import HostRSync, NodeManager
pytest_plugins = "pytester",
def pytest_funcarg__hookrecorder(request):
_pytest = request.getfuncargvalue('_pytest')
config = request.getfuncargvalue('config')
return _pytest.gethookrecorder(config.hook)
def pytest_fu... | curzona/pytest-xdist | testing/test_slavemanage.py | Python | mit | 9,121 | [
"VisIt"
] | b22edb8de3b3c110eb3073e7a3ff99e13f6c222c308d4559c3b2c9ed5e92d1d3 |
from __future__ import absolute_import
from builtins import object
import argparse
import textwrap
from .utils import load_json
class CommandLineParser(object):
def __init__(self):
self._instantiate_parser()
self._add_arguments()
def _instantiate_parser(self):
self._parser = argparse.... | mdiener/grace | grace/cmdparse.py | Python | gpl-3.0 | 4,036 | [
"VisIt"
] | 52fec7db18596334c591acb9ed21ab1be80126360d13b2f3ae2c46bf5b071d24 |
# coding=utf-8
"""**Utilities for storage module**
"""
import os
import re
import copy
import numpy
import math
from ast import literal_eval
from osgeo import ogr
from geometry import Polygon
from safe.common.numerics import ensure_numeric
from safe.common.utilities import verify
from safe.common.exceptions import B... | danylaksono/inasafe | safe/storage/utilities.py | Python | gpl-3.0 | 35,117 | [
"NetCDF"
] | fb16cde37570cdaf9ca9f4b92b47fdb18c99b69b00a2a457337e9c96811a084f |
#!/usr/bin/env python
# module implementing Felix's artefact removal method, based on the earlier R version
import sys, os, os.path
import numpy as np
import scipy as sp
import numpy.random as rng
import scipy.interpolate as spi
import scipy.stats as sst
import scipy.signal as sig
# for the moment, we keep these loc... | bcmd/BCMD | batch/felix.py | Python | gpl-2.0 | 10,844 | [
"Gaussian"
] | e11a655c5c6add1e511fcc6170f4565f950aef6ffe0d5bd9c8eff2117b9aa47c |
import getpass
import sys
from splinter import Browser
with Browser() as browser:
# Visit URL
url = 'https://www.sasktel.com/iam/SasktelLogin.jsp'
browser.visit(url)
username = browser.find_by_xpath('//input[contains(@name, "username")]')[0]
username.fill(sys.argv[1])
password = browser.find_... | ezralalonde/water-bill-summary | sasktel.py | Python | bsd-3-clause | 619 | [
"VisIt"
] | dfbb6efb151064c2d4ccd340af66a7099babb3911f3351f4b1634ae72adab889 |
"""
Physical units and dimensions.
The base class is Unit, where all here defined units (~200) inherit from.
The find_unit function can help you find units for a given quantity:
>>> import sympy.physics.units as u
>>> u.find_unit('coul')
['coulomb', 'coulombs']
>>> u.find_unit(u.charge)
['C', 'ch... | wdv4758h/ZipPy | edu.uci.python.benchmark/src/benchmarks/sympy/sympy/physics/units.py | Python | bsd-3-clause | 8,212 | [
"Avogadro"
] | a64aaedddf8cf06d62899a930b78170550c81da7306a8e154e6e4c27b35de0ac |
"""
@name: Modules/Core/__init__.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2014-2020 by D. Brian Kimmel
@note: Created on Mar 1, 2014
@license: MIT License
Core is the main portion of every PyHouse node.
It is always present.
"""
__updated__ = '2020-02-13'
__versio... | DBrianKimmel/PyHouse | Project/src/Modules/Core/Config/__init__.py | Python | mit | 1,588 | [
"Brian"
] | 590689b30acad114bc423c38fe7d302d418479dfadf352871a4946e5fbadb4ac |
'''
Determine optimum aperture and use Source Extractor to get photometry
'''
import sys
import os
from subprocess import call, Popen, PIPE
import glob
import math
import numpy as np
import Sources
import Quadtree
import createSexConfig
import createSexParam
import findBestAperture
import calcZeropoint
import makeRegi... | SAGES-UCSC/Photometry | Examples/UCD_Photometry.py | Python | mit | 10,373 | [
"Galaxy"
] | 346e295a0e8e7463276522bd711208d66cbeda313d8d8eb43c85748e00a1f900 |
import director.applogic as app
from director import lcmUtils
from director import transformUtils
from director import visualization as vis
from director import filterUtils
from director import drcargs
from director.shallowCopy import shallowCopy
from director.timercallback import TimerCallback
from director import vtk... | RobotLocomotion/director | src/python/director/kinectlcm.py | Python | bsd-3-clause | 5,859 | [
"VTK"
] | 60b71b5c917d834d5d8db71a7272566a67ee43f69c9f04acffa0a496d728086d |
"""This file contains code for use with "Think Bayes",
by Allen B. Downey, available from greenteapress.com
Copyright 2012 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
import math
import numpy
import random
import sys
import correlation
import thinkplot
import matplotlib.pyplot as pypl... | jtrussell/think-bayes-workspace | src/vendor/AllenDowney/kidney.py | Python | mit | 21,021 | [
"Gaussian"
] | ccf7c66a7e7ca759f8d0bb1a7abbc6d0a76fda2d6dabf5d67d0e23809233645e |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Calculate BOLD confounds
^^^^^^^^^^^^^^^^^^^^^^^^
.. autofunction:: init_bold_confs_wf
.. autofunction:: init_ica_aroma_wf
"""
from os import getenv
from nipype.algorithms import confounds as nac
fro... | poldracklab/fmriprep | fmriprep/workflows/bold/confounds.py | Python | bsd-3-clause | 33,266 | [
"Gaussian"
] | bf7fc098b94c5735f1c987fdf6c8d79259e4ada25ea9f74c8fcdac0dfc2e2db1 |
# ============================================================================
#
# 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/view/export/outlook.py | Python | gpl-2.0 | 1,770 | [
"VisIt"
] | e87acb7eac3fe2b1a5402a38ef82730425aae5d0658363f0f744db92581d71e1 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import unittest
import distutils.spawn
import itertools
import logging
import numpy as np
import os
from rmgpy import getPath
from rmgpy.qm.main import QMCalculator
from rmgpy.molecule import Molecule
from rmgpy.qm.gaussian import Gaussian, GaussianMolPM3, GaussianMolPM6
e... | pierrelb/RMG-Py | rmgpy/qm/gaussianTest.py | Python | mit | 5,432 | [
"Gaussian"
] | 25be911f95f6ea91432414d89ba9599b08d334b111f101fbdb5e8c825b94b18f |
# Copyright (C) 2015-2020 The Software Heritage developers
# See the AUTHORS file at the top-level directory of this distribution
# License: GNU Affero General Public License version 3, or any later version
# See top-level LICENSE file for more information
from distutils.util import strtobool
from functools import pa... | SoftwareHeritage/swh-web-ui | swh/web/api/views/origin.py | Python | agpl-3.0 | 14,799 | [
"VisIt"
] | b85bb22f5b960e562d637da8ca827dc8ea3aaccce7b18a30edfbf86ab01479f5 |
import os
import xarray.tests.test_dataset as td
from pywps import Process
from pywps import ComplexOutput, FORMATS
from pywps.ext_autodoc import MetadataUrl
import logging
LOGGER = logging.getLogger("PYWPS")
class NcMLAgg(Process):
def __init__(self):
inputs = []
outputs = [
Complex... | bird-house/emu | emu/processes/wps_ncml.py | Python | apache-2.0 | 2,245 | [
"NetCDF"
] | 2162b4a71476f7d3fe660675bd22acd0b1c003c16de34c1694ed8237769dfb5a |
# Standard library imports
import string, pkgutil
from xceptions import *
# Third party imports
#### netcdf --- currently support cdms2, python-netCDF4 and Scientific
l = pkgutil.iter_modules()
ll = map( lambda x: x[1], l )
supportedNetcdf = ['cdms2','netCDF4','Scientific','ncq3']
installedSupportedNetcdf = []
#... | martinjuckes/ceda_cc | ceda_cc/file_utils.py | Python | bsd-3-clause | 12,507 | [
"NetCDF"
] | f48596912c63f5e233746f53094d1b43638c6b8208af3cc611e626466602d703 |
import numpy as np
"""
Read AMBER topology file
"""
class AMBERFILES_TOP:
def __init__(self, top=''):
self.topology_file = top
flag_atom_name = flag_charge = flag_mass = flag_atom_type = flag_num_excl = flag_nonbonded_parm_index = flag_residue_label = flag_residue_pointer = flag_bond_const = \... | CTEricLai/amberfiles | MD_IO.py | Python | gpl-3.0 | 21,744 | [
"Amber"
] | 651159d6e3afe9e407087cef59d23b40643f8f0ea3e813a494a8b3c5eb9cd381 |
import tomviz.operators
from vtk import vtkImageData, VTK_DOUBLE
class TestOperator(tomviz.operators.Operator):
def transform_scalars(self, data):
image_data = vtkImageData()
image_data.SetDimensions(3, 4, 5)
image_data.AllocateScalars(VTK_DOUBLE, 1)
dims = image_data.GetDimension... | mathturtle/tomviz | tests/cxx/fixtures/update_data.py | Python | bsd-3-clause | 553 | [
"VTK"
] | 99c33b4f34baf2d8f0c5307568c81ac1d6039a3bb6b15801862f02e423860573 |
import math
from chainer.functions.activation import softplus
from chainer.functions.math import exponential
from chainer.functions.math import sum
from chainer import variable
def gaussian_kl_divergence(mean, ln_var):
"""Computes the KL-divergence of Gaussian variables from the standard one.
Given two vari... | AlpacaDB/chainer | chainer/functions/loss/vae.py | Python | mit | 3,825 | [
"Gaussian"
] | 18c1f38edb66ef5e79b1c69281f48c9237ad354eac6f7726c5a2675fbc01f88b |
#* 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 subp... | nuclear-wizard/moose | python/peacock/ExodusViewer/plugins/GoldDiffPlugin.py | Python | lgpl-2.1 | 12,189 | [
"MOOSE",
"VTK"
] | 1c82b21ca059c2554fdb0c91c04ef3063d3f58816d9dd1daed38adfc6e223d9e |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/chronos/src/bigdl/chronos/forecaster/utils.py | Python | apache-2.0 | 3,604 | [
"ORCA"
] | e596070464bcba6815c555ee26b2c7e14d88f120e98e3e507afe90b0f72e6c79 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# 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 requi... | googleapis/python-service-control | scripts/fixup_servicecontrol_v1_keywords.py | Python | apache-2.0 | 6,155 | [
"VisIt"
] | 60d40f2d852da890de34a202482029e83ccdbeda70ef4faa2d69b2dc539e167e |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistri... | psi4/psi4 | psi4/share/psi4/fsapt/copy_pymol.py | Python | lgpl-3.0 | 1,344 | [
"Psi4",
"PyMOL"
] | abf472fcec50500824b33e323e53debe10c90c8d24d5b8a961a3123eeacd3650 |
"Yang/Wu's OEP implementation, in PyQuante."
from math import sqrt
from PyQuante.NumWrap import zeros,matrixmultiply,transpose,dot,identity,\
array,solve
from PyQuante.Ints import getbasis, getints, getJ,get2JmK,getK
from PyQuante.LA2 import geigh,mkdens,trace2,simx
from PyQuante.hartree_fock import get_fock
from... | gabrielelanaro/pyquante | PyQuante/OEP.py | Python | bsd-3-clause | 25,758 | [
"Gaussian"
] | 20bac74ef41451d292aea47ac1f5c936f5812ac07e6c7713d28d86e0aa55b43e |
"""
Purpose: To snag which residues need to be converted to DNA from RNA
Syntax: python R2Dparser.py ~/Location/outputFileName
*Replace Location with location of the output file from charmm that lists the residues needing to be converted
Output: a file named patch.out with the patch expressions for in xrange(1,1... | cfourt/R2DParser | R2Dparser.py | Python | mit | 2,816 | [
"CHARMM"
] | d48ad072984ff4ccb6f4f13cc058cce65bfb9395d786ef85f2118eb43e5b5c33 |
#!/usr/bin/env python
#
'''
Perform analysis on whole 2D data sets.
'''
import time
import matplotlib
matplotlib.use('agg')
import grid_cell_model.visitors as vis
import grid_cell_model.visitors.spikes
import grid_cell_model.visitors.bumps
import grid_cell_model.visitors.signals
import grid_cell_model.visitors.plottin... | MattNolanLab/ei-attractor | grid_cell_model/simulations/007_noise/analysis_EI.py | Python | gpl-3.0 | 6,633 | [
"VisIt"
] | 6ca2cb0bd9bdddd6111074929cc0b64d4f27003d84bf9278567a031cbaf47158 |
"""0MQ Error classes and functions."""
#-----------------------------------------------------------------------------
# Copyright (C) 2013 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING.BSD, distribut... | ellisonbg/pyzmq | zmq/error.py | Python | lgpl-3.0 | 4,885 | [
"Brian"
] | 0619ba7be8c53172d88a870168209db8c98ae9235f6e585ab7ec5705d01bce68 |
from ase import Atom, Atoms
from gpaw import GPAW
L = 6
name='N2'
a = Atoms([Atom('N', (L/2.+1.098/2.,L/2.,L/2.)),
Atom('N', (L/2.-1.098/2.,L/2.,L/2.))], cell=(L, L, L), pbc=False)
calc=GPAW(h=0.22, xc='PBE',convergence={'eigenstates':1.0e-7}, stencils=(3,3), txt = name+'.txt',
eigensolver='rmm-d... | robwarm/gpaw-symm | gpaw/test/big/miscellaneous/revtpss_tpss_scf.py | Python | gpl-3.0 | 1,567 | [
"ASE",
"GPAW"
] | 543caf77697aa7c6d47201c4f359dc89421c1c2cd16305cb7d6a4c35880a018f |
"""
10 nov. 2014
iterative mapping copied from hiclib
"""
import os
import tempfile
import gzip
import pysam
import gem
from warnings import warn
N_WINDOWS = 0
def get_intersection(fname1, fname2, out_path, verbose=False):
"""
Merges the two files corresponding to each reads sides. Reads found in both
... | yuanbaowen521/tadbit | _pytadbit/mapping/mapper.py | Python | gpl-3.0 | 12,840 | [
"pysam"
] | 7e62fc19d819e7a6fcd8a56faa149f4fd6ab00a5b2df7bc4eee077b77ec7ab36 |
"""
Courseware views functions
"""
import logging
import urllib
import json
import cgi
from datetime import datetime
from django.utils import translation
from django.utils.translation import ugettext as _
from django.utils.translation import ungettext
from django.conf import settings
from django.core.context_process... | jazztpt/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 61,937 | [
"VisIt"
] | 80e1932cce279ba4e24f5fb4a79c177d6de5cf19737305c501da8c89dfd76718 |
from __future__ import division, absolute_import, print_function
import numpy as np
from numpy.testing import (
TestCase, run_module_suite, assert_, assert_raises, assert_equal,
assert_warns)
from numpy import random
from numpy.compat import asbytes
import sys
class TestSeed(TestCase):
def test_sc... | ViralLeadership/numpy | numpy/random/tests/test_random.py | Python | bsd-3-clause | 32,289 | [
"Gaussian"
] | cbbbedcef5557e284b16c58b96216d8deba0cbb40a1e274378dfbd36c4ba499c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# managejobs - simple job management interface
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public... | heromod/migrid | mig/shared/functionality/managejobs.py | Python | gpl-2.0 | 5,682 | [
"Brian"
] | 5750eebfa90e8df250ebd120cf069620f0dc5dc5bbf81364a3e1ccd13f1cf5a8 |
from __future__ import division, absolute_import, print_function
import warnings
import sys
import collections
import operator
import numpy as np
import numpy.core.numeric as _nx
from numpy.core import linspace, atleast_1d, atleast_2d
from numpy.core.numeric import (
ones, zeros, arange, concatenate, array, asarr... | saquiba2/numpy2 | numpy/lib/function_base.py | Python | bsd-3-clause | 143,343 | [
"Gaussian"
] | 9ee8721281153a1dc5a20f8bd8f0e0e56c2d30b2c76fdf9785e70c9c2de4dece |
import os
import unittest
import netCDF4
from lxml import etree
from petulantbear.netcdf_etree import parse_nc_dataset_as_etree, dataset2ncml
namespaces = {
'x': 'http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2'
}
class TestPb(unittest.TestCase):
def setUp(self):
self.file = os.path.abspath(... | ioos/petulant-bear | petulantbear/test_pb.py | Python | gpl-3.0 | 1,718 | [
"NetCDF"
] | 89f07c5fb6286bfb8f090ea4e65be4b42b88955c4b3b37e064e052216007a0e7 |
from __future__ import division
import imgaug as ia
from scipy.misc import imsave
from imgaug import augmenters as iaa
import numpy as np
import glob
import matplotlib.image as img
import matplotlib.pyplot as plt
import cv2
images = img.imread('/home/ahmed/Pictures/cogedis/cogedis_words_3/0d167103-1b66-4373-9a78-5b21... | ahmedmazari-dhatim/CRNN-for-sequence-recognition- | data_aug_2.py | Python | mit | 3,073 | [
"Gaussian"
] | e968fd0d05b894e40871636233f07a4119a01c3422bf52625d3e502cc1032fc0 |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
###########################################################################
# ESPResSo++ #
# Test script for Converting GROMACS tabulated file #
# ... | BackupTheBerlios/espressopp | examples/convert_gromacs_tables/convert_gromacs_table.py | Python | gpl-3.0 | 6,132 | [
"ESPResSo",
"Gromacs"
] | 1a0c42e3a52bf92f71c4fa3d145d70a1e04459450b9f0167ebb30c1fe933d78b |
import types
import time
import random
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import DEncode
from DIRAC.Core.Base.ExecutorMindHandler import ExecutorMindHandler
random.seed()
class PingPongMindHandler( ExecutorMindHandler ):
MSG_DEFINITIONS = { 'StartReaction' : { 'numBounces' : ( types... | chaen/DIRACDocs | source/DeveloperGuide/AddingNewComponents/DevelopingExecutors/PingPongMindHandler.py | Python | gpl-3.0 | 2,911 | [
"DIRAC"
] | 7f5e409acfaab5d8d25bfca0a17abae440bcfdf1aee9bbe1768d00dacd932e44 |
####
# This sample is published as part of the blog article at www.toptal.com/blog
# Visit www.toptal.com/blog and subscribe to our newsletter to read great posts
####
import logging
from pathlib import Path
from time import time
from functools import partial
from concurrent.futures import ProcessPoolExecutor
from PI... | volker48/python-concurrency | processpool_thumbnails.py | Python | mit | 1,589 | [
"VisIt"
] | 65ff044506a7534458bfcb9251ec2dd186ad6d0f556e5965aa95d081680c87b0 |
# Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
# Copyright (c) 2006, The Regents of the University of California, through
# Lawrence Berkeley National Laboratory (subject to receipt of any required
# approvals from the U.S. Dept. of Energy). All rights reserved.
# This software is distributed unde... | NarlikarLab/DIVERSITY | weblogoMod/corebio/seq_io/__init__.py | Python | gpl-3.0 | 6,149 | [
"BioPerl"
] | 23b0c49167146c0fb0f72649d432785ecd7e4b9ac56fdd5953d9c3cf0c8b78d1 |
"""
This is a simple script that verifies several ways of accessing numpy arrays
and ensures that their memory is properly cleaned.
"""
from addons import *
import psi4
import numpy as np
# If it's too small, something odd happens with the memory manager
mat_size = 10000
def snapshot_memory():
import memory_pr... | amjames/psi4 | tests/pytest/test_np_views.py | Python | lgpl-3.0 | 2,399 | [
"Psi4"
] | 3c499b2b45ee81881646c7201d3bedfd9bfd97332d03d5ce12f65a8907ce0ecd |
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