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import npc, random
from neuron import network
#CONSTANTS
POPSIZE = 100
NUM_GENERATIONS = 100
NUM_BEST_PARENTS = 5
LOCAL_OPT = 20
bestArr=[]
stuckCount=0
#init empty population list
pop = []
#for range popsize create random individual
for x in range(POPSIZE):
pop.append(network())
#initialize best to empty
be... | Josh-C-Montgomery/Evolving-Boss-Battles | GA.py | Python | apache-2.0 | 2,294 | [
"NEURON"
] | 273cde59bd7010b34c6f837a11321057ea39f9adf0096e52433a9769776f7c1d |
# -*- coding: utf-8 -*-
u"""PyTest for :mod:`sirepo.template.srw.py`
:copyright: Copyright (c) 2016 RadiaSoft LLC. All Rights Reserved.
:license: http://www.apache.org/licenses/LICENSE-2.0.html
"""
from __future__ import absolute_import, division, print_function
import pytest
import requests
import sirepo.crystal
de... | radiasoft/sirepo | tests/crystal_test.py | Python | apache-2.0 | 3,031 | [
"CRYSTAL"
] | 166d7a08e4916c1fcce9917720ed54e6dd56f7d1dd761698c40b6f458cb2df33 |
from ovito import *
from ovito.io import *
from ovito.modifiers import *
import numpy
node = import_file("../../files/LAMMPS/bonds.data.gz", atom_style = 'bond')
node.modifiers.append(WrapPeriodicImagesModifier())
print(node.compute().bonds.pbc_vectors)
| srinath-chakravarthy/ovito | tests/scripts/test_suite/bonds_pbc_vectors.py | Python | gpl-3.0 | 255 | [
"LAMMPS",
"OVITO"
] | e9244c6c4c02b079d4d53e592b66d3a8d8da95b0333c4141f5d0b5081c1eb9c3 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Auxiliary Functions and resources to PSF0X.
Created on Tue Jan 30 16:31:00 2018
:author: Ruyman Azzollini
"""
# IMPORT STUFF
from pdb import set_trace as stop
import numpy as np
import os
from collections import OrderedDict
import string as st
import copy
from mat... | ruymanengithub/vison | vison/point/PSF0Xaux.py | Python | gpl-3.0 | 10,426 | [
"Gaussian"
] | 31dd76fd5f03168fbc69312e79dbf4e4c26b025fe5c6f2043ef3ed60c9462f75 |
# -*- coding: utf-8 -*-
# This file is part of MOOSE simulator: http://moose.ncbs.res.in.
# MOOSE 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 lat... | dharmasam9/moose-core | python/moose/moose_constants.py | Python | gpl-3.0 | 2,148 | [
"MOOSE"
] | 7001b6785acac3571825b419e99bb290478449877e07bc9a44d108e74b98798d |
"""
Tools for different procedure estimations
"""
__author__ = "Luc Anselin luc.anselin@asu.edu, \
Pedro V. Amaral pedro.amaral@asu.edu, \
David C. Folch david.folch@asu.edu, \
Daniel Arribas-Bel darribas@asu.edu,\
Levi Wolf levi.john.wolf@gmail.com"
import numpy as np
from ... | ljwolf/pysal | pysal/spreg/utils.py | Python | bsd-3-clause | 20,482 | [
"COLUMBUS"
] | 91a402273d71a4f12451b117c6492dd6104564bfb4184c43aff15d3793c3c1b5 |
import logging
from subprocess import CalledProcessError
from django.contrib.auth.decorators import login_required
from django.http import HttpRequest, HttpResponse
from django.shortcuts import render
from core.utils import BLAST, get_context
log = logging.getLogger(__name__)
@login_required
def index(request: Ht... | carlosp420/VoSeq | blast_local/views.py | Python | bsd-3-clause | 1,206 | [
"BLAST"
] | 635f2d5be7b159b5852c226427ea25e6d909c79d71b819bfd5dc243940145e27 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from filebrowser.sites import site
urlpatterns = [
u... | wldcordeiro/cookiecutter-django-essentials | {{cookiecutter.repo_name}}/config/urls.py | Python | bsd-3-clause | 1,636 | [
"VisIt"
] | 10d76602a3c32f1f03c3606e270951e780c67e1bb71ec9e39363bb87b505d560 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure that all files contain proper licensing information."""
import json
import optparse
import os.path
import subproces... | highweb-project/highweb-webcl-html5spec | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 23,436 | [
"Galaxy"
] | 53bd60a698e8c93931c9d7e359cdccf19f8d87e4b80636f096d6a0f06cff140f |
"""
The B{0install remove-feed} command-line interface.
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
syntax = "[INTERFACE] FEED"
from zeroinstall import SafeException, _
from zeroinstall.injector import model, writer
from zeroinstall.cmd import add_feed, U... | timdiels/zeroinstall | zeroinstall/cmd/remove_feed.py | Python | lgpl-2.1 | 925 | [
"VisIt"
] | 359d4c43124f8df8695d4297bcd2b5d84752eb024649ad9b040b76aeca1cc794 |
"""
Methods for calculating Mutual Information in an embarrassingly parallel way.
Author: Daniel Homola <dani.homola@gmail.com>
License: BSD 3 clause
"""
import numpy as np
from scipy.special import gamma, psi
from sklearn.neighbors import NearestNeighbors
from sklearn.externals.joblib import Parallel, delayed
def g... | xrafael/readmission | src/mifs/mi.py | Python | gpl-3.0 | 5,353 | [
"Brian"
] | 596a39510da0b0934969b1cded68c3791ea4e211bf7f1cb7d44a591efc463470 |
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# Copyright 2013 IBM Corp.
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# ... | srajag/nova | nova/tests/network/test_manager.py | Python | apache-2.0 | 143,411 | [
"FEFF"
] | 807e7161a92ae80f9f507b0f8d4c08980f77c335f2086cbc46c8992e4847f2c4 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import datetime
import os
from django.contrib.auth.models import Permission
from django.conf import settings
from django.core import mail
from django.core.cache import cache
from django.core.urlresolvers import reverse
from django.core.exceptions import V... | webu/pybbm | pybb/tests.py | Python | bsd-2-clause | 121,776 | [
"VisIt"
] | 6abb2f289ef25bda4b4ec57a5c86b966091be54c39640e30a5b93c7767e19b73 |
"""
homeassistant.components.isy994
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Connects to an ISY-994 controller and loads relevant components to control its
devices. Also contains the base classes for ISY Sensors, Lights, and Switches.
For configuration details please visit the documentation for this component at
https://home-a... | alexkolar/home-assistant | homeassistant/components/isy994.py | Python | mit | 7,199 | [
"VisIt"
] | 90afccd63114b811d23643e39a9f079ca3bdcfec98a0ad28663a4586cc3be0c4 |
""" The Job Scheduling Executor takes the information gained from all previous
optimizers and makes a scheduling decision for the jobs.
Subsequent to this jobs are added into a Task Queue and pilot agents can be submitted.
All issues preventing the successful resolution of a site candidate are dis... | chaen/DIRAC | WorkloadManagementSystem/Executor/JobScheduling.py | Python | gpl-3.0 | 25,924 | [
"DIRAC"
] | ae4d34652f5ef797830e21bcee976cd5330d1bded783f5ed2caff36d9fae73f1 |
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ve... | magnunor/hyperspy | hyperspy/tests/samfire/test_samfire.py | Python | gpl-3.0 | 18,333 | [
"Gaussian"
] | e490ccebb25b2202b91e227b80ae5dbd9bf3b3d1c63fd63ae09bb0a24d956c5e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import os
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.structure import Structure
from pymatgen.core.units import Ha_to_e... | sonium0/pymatgen | pymatgen/io/abinitio/tests/test_abiobjects.py | Python | mit | 4,167 | [
"pymatgen"
] | f43ea2e90bb69f6695a4d54190c91b446c37c61f073062af052158460ee9f756 |
"""Comparator objects relevant to particles with adsorbates."""
from ase import Atoms
def count_ads(atoms, adsorbate):
"""Very naive implementation only taking into account
the symbols. atoms and adsorbate should both be supplied
as Atoms objects."""
syms = atoms.get_chemical_symbols()
tr... | suttond/MODOI | ase/ga/adsorbate_comparators.py | Python | lgpl-3.0 | 4,037 | [
"ASE"
] | a422aef1a3229673f73a7c45ab093ecb163f7217745480cf8c1b36f86ab57e4c |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC import gLogger
from DIRAC.Core.Tornado.Server.TornadoService import TornadoService
from DIRAC.DataManagementSystem.Service.FTS3ManagerHandler import FTS3ManagerHandlerMixin
sLog ... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/Service/TornadoFTS3ManagerHandler.py | Python | gpl-3.0 | 491 | [
"DIRAC"
] | a4f394681a0124edc1a24c851054d87d07174d2280cbb48dc538bad3d5db2463 |
#encoding=utf-8
############################################
# [config.py]
# CONFIGURATION SETTINGS FOR PROSODIC
#
# Here you may change the runtime settings for prosodic.
# For more help on this file, please see the README in this folder,
# or visit it online: <https://github.com/quadrismegistus/prosodic>.
# If you ha... | quadrismegistus/prosodic | prosodic/config.py | Python | gpl-3.0 | 7,803 | [
"VisIt"
] | 2f2f295f0294ac41248ba3d870fa43bfca5c880a3b9a23725a8d66b3db8a1023 |
#!/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... | fxfitz/ansible | lib/ansible/modules/network/cnos/cnos_vlan.py | Python | gpl-3.0 | 11,596 | [
"VisIt"
] | 42be4786e8a78f1ceee9fcda721b3d9d3116a7824b1340c903fd67415be0c36a |
#!/usr/bin/python
# Copyright (C) 2012 Sibi <sibi@psibi.in>
#
# This file is part of Neuron.
#
# Neuron 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) an... | psibi/Neuron | train.py | Python | gpl-3.0 | 15,183 | [
"Gaussian",
"NEURON"
] | ad4a0e97578192d619a137acc4c0d6953c81be1abdfd7bb3700da0bd9c04f1a1 |
#!/usr/bin/env python
# encoding: utf-8
"""
plot_hs.py - Plot the half-sarcomere with mayavi
Created by Dave Williams on 2010-10-4
"""
import numpy as np
from enthought.mayavi import mlab
# Configure the graph
fig = mlab.figure(1, bgcolor=(0, 0, 0), size=(350, 350))
mlab.clf()
fig.scene.parallel_projection = True
ml... | cdw/multifil | multifil/plot_hs.py | Python | mit | 7,128 | [
"Mayavi"
] | 02bd85a5b81112442a945a992fd0f9b8feea5b10e99ffd3ea851ce2207e0405b |
# mako/pyparser.py
# Copyright (C) 2006-2012 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Handles parsing of Python code.
Parsing to AST is done via _ast on Python > 2.5, otherwise th... | alanjw/GreenOpenERP-Win-X86 | python/Lib/site-packages/mako/pyparser.py | Python | agpl-3.0 | 18,596 | [
"VisIt"
] | 7aecb8487b6b01b4abc0f156cb97dd9af2fcc3840d3c89fc0d7d432d63e1fd5a |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | mkuron/espresso | testsuite/scripts/importlib_wrapper.py | Python | gpl-3.0 | 12,576 | [
"ESPResSo",
"Mayavi"
] | 48faad193edb4b24d355e97e812f379e58b98cd386643cff691f0562fbecd005 |
# ----------------------------------------------------------------------------
# Copyright (c) 2016--, Calour development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# -----------------------------------------------... | RNAer/Calour | calour/tests/test_io.py | Python | bsd-3-clause | 15,777 | [
"OpenMS"
] | 6154720206c19e67a728f16e679be95f1cc66f80d5b53e8b3285168355b9da3b |
# (c) 2014, Brian Coca, Josh Drake, et al
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
... | kaarolch/ansible | lib/ansible/plugins/cache/base.py | Python | gpl-3.0 | 1,564 | [
"Brian"
] | 0321d5f34ed5f740c8ba6aa333264bbfade497bba7dd6ceafd3e785551e556bb |
# -*- coding: utf-8 -*-
import logging
import os
import subprocess
from galaxy.datatypes.data import get_file_peek, Text
from galaxy.datatypes.metadata import MetadataElement
log = logging.getLogger(__name__)
def count_special_lines(word, filename, invert=False):
"""
searching for special 'words' using... | SANBI-SA/tools-iuc | datatypes/msa/stockholm_1_0/stockholm_1_0.py | Python | mit | 4,052 | [
"Galaxy"
] | ded758045a42c9e59c8758124540444a6bf46c307832a757dec3c76eee34f5a8 |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2011 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Fre... | andrebellafronte/stoq | stoq/gui/pos.py | Python | gpl-2.0 | 54,235 | [
"VisIt"
] | 9201a1280a9c804dbfb7ca153f1a3147a676dad93976bc00c1dcb8c5bf84fc4a |
# 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... | npuichigo/ttsflow | third_party/tensorflow/tensorflow/contrib/timeseries/python/timeseries/state_space_models/state_space_model.py | Python | apache-2.0 | 56,990 | [
"Gaussian"
] | 59c6ee729f438b8528788edb722f6da821ce8be7aef7747b3235ddc990c3268d |
from nose.tools import assert_equal #@UnresolvedImport
from whoosh import analysis, fields, qparser
from whoosh.compat import u, unichr
from whoosh.filedb.filestore import RamStorage
def test_regextokenizer():
value = u("AAAaaaBBBbbbCCCcccDDDddd")
rex = analysis.RegexTokenizer("[A-Z]+")
assert_equa... | waseem18/oh-mainline | vendor/packages/whoosh/tests/test_analysis.py | Python | agpl-3.0 | 12,325 | [
"VisIt"
] | d25a53f3b2687086de3aada4fa89db1b31f0f4d28b8cc3b3c6e1d361ad86cbf5 |
# -*- coding: utf-8 -*-
from __future__ import print_function
"""
functions.py - Miscellaneous homeless functions
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more infomation.
Most Interesting Contents:
siFormat / siEval - functions for dealing with numbers in SI notation
do... | meganbkratz/acq4 | acq4/util/functions.py | Python | mit | 83,674 | [
"Gaussian"
] | 346bae5a2f00426c184c3ebbad38a074fb8badd432f3180a450e8088b59b2e80 |
""" Used by the executors for dispatching events (IIUC)
"""
import threading, time, types
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.ReturnValues import isReturnStructure
from DIRAC.Core.Utilities.ThreadScheduler import gThreadScheduler
class ExecutorState( object ):
def __init__( self, log... | Andrew-McNab-UK/DIRAC | Core/Utilities/ExecutorDispatcher.py | Python | gpl-3.0 | 29,006 | [
"DIRAC"
] | f00439c3792b4002055fc33a1fcb6a607d95aa2add6ca1a0b9a612381463c0dd |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | matthiasdiener/spack | var/spack/repos/builtin/packages/parallel-netcdf/package.py | Python | lgpl-2.1 | 3,279 | [
"NetCDF"
] | 2f004c936d05575d85b3bfde788f6485374534f0157415b824dc8cf214b2497b |
#!/usr/bin/env python
"""
Command-line tool to convert a binary map output to netcdf.
"""
from __future__ import print_function
import argparse
import sys,os
import numpy as np
import stompy.model.delft.io as dio
parser = argparse.ArgumentParser(description='Convert D-WAQ binary map output to NetCDF.')
parser.add_a... | rustychris/stompy | examples/dwaq_map_to_nc.py | Python | mit | 1,704 | [
"NetCDF"
] | 2a5151b9c89878ba0278511c22bec3198d92dd6468078b6d4f3563e32d4f25d7 |
# Copyright (C) 2014 Olaf Lenz
#
# 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 version.
#
# ESPR... | sehrhardt/espresso | src/python/espressomd/gen_pxiconfig.py | Python | gpl-3.0 | 1,826 | [
"ESPResSo"
] | ba1b3b577c6fd6a50c13413a63490c598da0c7a50733a2ec208b4e157888d054 |
# Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO fasta-m10 indexing."""
import os
import unittest
from search_tests... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_SearchIO_fasta_m10_index.py | Python | gpl-2.0 | 2,166 | [
"Biopython"
] | a71f9d125106ff400f0208723590f59b4214bac18e3b263490bae2513c3b04ed |
#!/usr/bin/env python
#
# @Xiaming Chen
import sys
import numpy as np
import time
import math
from datetime import datetime, date
class CellMap(object):
def __init__(self, data):
self._map = {}
print("loading data ...")
for line in open(data, 'rb'):
parts = line.strip('\r\n ').s... | caesar0301/paper-flowmap-code | src/040.flow-miner.py | Python | gpl-3.0 | 9,135 | [
"VisIt"
] | 48770336fa4a4d1f07a60a2afa61dcbbe56da8981effe8603e260c9bb7139d3f |
"""
PyXNAT
======
pyxnat provides an API to access data on XNAT (see http://xnat.org)
servers.
Visit http://packages.python.org/pyxnat for more information.
"""
from .version import __version__
from .core import Interface
from .core import SearchManager
from .core import CacheManager
from .core import Select
from .... | BrainIntensive/OnlineBrainIntensive | resources/HCP/pyxnat/pyxnat/__init__.py | Python | mit | 707 | [
"VisIt"
] | 550707408f2638a70c2ca304503d973abae0dbb789435800cf527551bb2204ec |
# Import the old tracking id from the RCM file for period 19660101-19701231,
# as it is the first used file to create historical indices:
# (e.g. tas_EUR-44_IPSL-IPSL-CM5A-MR_historical_r1i1p1_SMHI-RCA4_v1_day_19660101-19701231.nc)
#track_GCM_indice=$(
import netCDF4
from netCDF4 import Dataset
import ctypes
impor... | igryski/Indices_icclim_ClipC | src/TMEAN/get_put_invar_tracking_id_python_TAS.py | Python | gpl-3.0 | 11,493 | [
"NetCDF"
] | 4d0e42db6b66a77184df536972b4530b2761c03d5b9476182490cc8d4ebd8c4e |
import os, sys
import csv
import unittest
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
from types import *
import math
import shutil
class DiagnosticIndex(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/b... | laurapascal/DiagnosticIndexExtension | src/DiagnosticIndex/DiagnosticIndex.py | Python | apache-2.0 | 76,598 | [
"VTK"
] | 5d833e12d4531d3be0856b083679a8c8598b0bfdd9d876daa36153c5628cf97a |
from lettuce import step, world
# Browse from page to page
@step(r'(?:visit|access|open) the url "(.*)"')
def go_to_the_url(step, url):
world.response = world.browser.visit(url)
@step(r'go back(?: a page)?')
def go_back(step):
world.browser.back()
@step(r'go forward(?: a page)?')
def go_forward(step):
... | adw0rd/salad-py3 | salad/steps/browser/navigation.py | Python | bsd-3-clause | 436 | [
"VisIt"
] | 82372633afbecd1c5031e6fc628aa664a7528d7d1f1a3f209756da222fd4d168 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | realfake/kubernetes | cluster/juju/layers/kubernetes-worker/reactive/kubernetes_worker.py | Python | apache-2.0 | 29,377 | [
"CDK"
] | 4da21d95270ba427f8c673641a9a6ba3c93ccef5cdfeaa4410625c3cb96c1644 |
import argparse
import numpy as np
import os
from LigParGenTools import *
if __name__ == "__main__":
parser = argparse.ArgumentParser(
prog='Converter.py',
formatter_class=argparse.RawDescriptionHelpFormatter,
description="""
SCRIPT TO CREATE CUSTOM SOLVENT BOXES FOR
OPENMM AND NAMD FR... | leelasd/LigParGenTools | CustomSolBox.py | Python | mit | 1,333 | [
"NAMD",
"OpenMM"
] | 3731e856e9980cca46c5b0ab446b61bd7ad86ab35d63b4231c526af63cbb2652 |
import numpy as np
import matplotlib.pyplot as plt
class ChainBundle():
def __init__(self):
self.data = None
def compute(self, n_chains, persistence_length, contour_length, n_segments=100):
"""
:param n_chains: How many chains to include in the bundle
:param persistence_length... | stefanhuber1993/worm_like_chain | WLC.py | Python | gpl-3.0 | 3,436 | [
"MDAnalysis"
] | 13d372997b0196456fb589f7918de747e9b3e6f4c04883be5c2b702efbb488ad |
"""Handle disambiguation of reads from a chimeric input, splitting by organism.
Given specification of mixed input samples, splits a sample into multiple
sub-samples for alignment to individual genomes, then runs third-party disambiguation
scripts to reconcile.
Uses disambiguation scripts contributed by AstraZeneca, ... | guillermo-carrasco/bcbio-nextgen | bcbio/pipeline/disambiguate/__init__.py | Python | mit | 8,391 | [
"BWA"
] | cc4d9c7cc849b638cb9b80ddb5cf5524b7f07eae9146775bf3897a98c22a898a |
# -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# ... | vlegoff/tsunami | src/secondaires/familier/constantes.py | Python | bsd-3-clause | 4,223 | [
"FLEUR"
] | 430b938433140bd70fd267d80772dcac3bb5f8f1b6b61d2855702ef10464a8e6 |
#!/usr/bin/env python
"""Search for non-ASCII characters in the ABINIT src files"""
import os
import re
import sys
__author__ = "M. Giantomassi"
def isascii(string, verbose=False):
"""False if string cointains non-ASCII characters."""
try:
string.decode('ascii')
return True
except UnicodeDecodeError:
... | SamKChang/abinit-7.10.5_multipole | special/scripts/check_ascii.py | Python | gpl-3.0 | 1,758 | [
"ABINIT"
] | 2abfa29d2fe4f9672b008cd8c8dd03602a4afc81e5333785c792391f3c1f9a32 |
import librosa
from scipy.signal import lfilter
from functools import partial
import numpy as np
from scipy.signal import gaussian
from librosa.core.spectrum import stft
PADDING = 0.1
def load_waveform(file_path):
signal, sr = librosa.load(file_path, sr=None)
signal = lfilter([1., -0.95], 1, signal, axis=0... | samihuc/PolyglotDB | polyglotdb/acoustics/utils.py | Python | mit | 1,440 | [
"Gaussian"
] | 6b00216e2323d4f183b36082310bf607051ab8689af19384641171a58c601f23 |
import numpy as np
import theano
from theano import tensor as T
from theano.tensor.shared_randomstreams import RandomStreams
import scipy.misc
from src.utils import load_MNIST
from src.utils import display_weigths
from src.utils import display_samples
from src.utils import normalize_img
class GRBM(object):
# Imple... | glgerard/MDBN | src/archived/grbm_grad.py | Python | apache-2.0 | 6,281 | [
"Gaussian"
] | 1a09f71c313bec4210ad99d4de3f4b89ff2f9c03f140bc9fa20fee3032a29472 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkCellDataToPointData(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkCellDataToPointData.py | Python | bsd-3-clause | 497 | [
"VTK"
] | e5603d900d185f09984a5fa4623705a1ba8b039ed88117316d878f5d39005f0d |
# (c) 2014, Brian Coca, Josh Drake, et al
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
... | scottcunningham/ansible | lib/ansible/plugins/cache/jsonfile.py | Python | gpl-3.0 | 4,628 | [
"Brian"
] | e231d3326bf2da8d9211c24d7849d9bd551b04c1386ba49e8fb3fc8db26e79b7 |
### https://hg.python.org/cpython/file/3.6/Lib/html/entities.py
"""HTML character entity references."""
# maps the HTML5 named character references to the equivalent Unicode character(s)
html5 = {
'Aacute': '\xc1',
'aacute': '\xe1',
'Aacute;': '\xc1',
'aacute;': '\xe1',
'Abreve;': '\u0102',
'a... | neno1978/pelisalacarta | python/main-classic/core/entities.py | Python | gpl-3.0 | 57,381 | [
"Bowtie"
] | 96c63fa11c1b93400146d69d92e20ff5d5c7607e5cd6b8a8ce152f0667fc9966 |
#!/usr/local/bin/env python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Analyze YANK output file.
"""
#============================================... | jchodera/yank | Yank/commands/analyze.py | Python | lgpl-3.0 | 1,754 | [
"NetCDF"
] | 47016022d1ce5598337215c5ceecbd24586ccf2af43f70a3ae2d9db63b849cc5 |
""" core implementation of testing process: init, session, runtest loop. """
from __future__ import absolute_import, division, print_function
import functools
import os
import sys
import _pytest
import _pytest._code
import py
try:
from collections import MutableMapping as MappingMixin
except ImportError:
from... | hoehnp/navit_test | lib/python2.7/site-packages/_pytest/main.py | Python | gpl-2.0 | 29,707 | [
"VisIt"
] | 805fc5b74c317f9c536097074fe55b469f5df77084275aebabd2700dee454b70 |
"""
@name: PyHouse/src/Modules/Computer/Web/_test/test_web_utils.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com>
@copyright: (c) 2014-2017 by D. Brian Kimmel
@license: MIT License
@note: Created on Jun 29, 2013
@Summary: Test web utilities module
Passed all 7 tests - DBK - 2017-01-12
... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/Web/test/test_web_utils.py | Python | mit | 3,750 | [
"Brian"
] | b251bfd49949009a1fc4d6d414c165bd2f4029cc265cf9d2165c013628e58226 |
"""
Recode homopolymer regions, adding/subtracting bases if the difference is
within some threshold
"""
import argparse
from contextlib import closing
import itertools
import logging
import operator
import pysam
from .. import gff3, pwalign, rle, samutil
from ..util import isolate_region
log = logging.getLogger(__na... | fhcrc/prepdrm | python/prep_drm/scripts/recode_homopolymer_regions.py | Python | gpl-3.0 | 4,593 | [
"pysam"
] | 702a2b59f8dad6fd055decf045a84e15c227e52b8526b2d5370b6f6df5fbd438 |
# !/usr/bin/env python
# -*- coding: UTF-8 -*-
# Copyright (c) 2012-2015 Christian Schwarz
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitat... | T-002/pycast | pycast/tests/profilemetest.py | Python | mit | 3,823 | [
"Gaussian"
] | f5ed12abaeeaefa3410be6213b0d115ec7f38062c7b2387caf4fb77cf4abdc98 |
import json
from base64 import b64decode
from urllib.parse import urlencode, quote_plus
from urllib.request import urlopen, Request
from urllib.error import HTTPError
from .objects import *
from .util import parse_bugzilla_datetime
class BugzillaException(Exception):
def __init__(self, code, *args, **kw):
... | DenSA-Inc/bugzilla-python | bugzilla/__init__.py | Python | gpl-3.0 | 36,709 | [
"VisIt"
] | ccf1415a5593d668ae016119af725ce139a0f2961fcbf41a249aa7a711ab03f6 |
from __future__ import division
from statsmodels.compat.python import iteritems, range, string_types, lmap, long
import numpy as np
from numpy import dot, identity
from numpy.linalg import inv, slogdet
from scipy.stats import norm
from statsmodels.regression.linear_model import OLS
from statsmodels.tsa.tsatools import... | yl565/statsmodels | statsmodels/tsa/ar_model.py | Python | bsd-3-clause | 33,978 | [
"Gaussian"
] | 6d4730507514f7b4605e9740e8fab9a647db2e358ef74f4ede504a02c39e2d80 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
import os
import sys
from multiprocessing import Pool
def bam(args):
(inpath, bed, exonbed, t, ref, R1, R2, sampleID, outpath) = (args[0],
args[1], args[2], args[3], args[4], args[5], args[6], args[7], args[8])
sam = "%s/%s.sam" % (inpath,sampleID)
ba... | longrw/mypython | bamQC.py | Python | gpl-3.0 | 8,267 | [
"BWA"
] | 24e4bbd8d304b6434f9570f76ea9085798de3811a5ab86d7c4c9aa433ac9d7cb |
import numpy
import warnings
from simphony.core.keywords import KEYWORDS
from simphony.core.cuba import CUBA
def supported_cuba():
""" Return the list of CUBA keys that can be supported by vtk.
"""
return {
cuba for cuba in CUBA
if default_cuba_value(cuba) is not None}
def default_cub... | simphony/simphony-mayavi | simphony_mayavi/core/cuba_utils.py | Python | bsd-2-clause | 2,376 | [
"VTK"
] | 4ad7651bb0c1b2d8f881add513bb1ad0c0322aa79af8ed2d9d1925a21594742f |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/analysis/rdf.py | Python | gpl-2.0 | 21,430 | [
"MDAnalysis"
] | 2b2290c0c9e2427a1fff4b682cdb7d1544114351eed65a0ab431514437982ec1 |
#! /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-asset | scripts/fixup_asset_v1p4beta1_keywords.py | Python | apache-2.0 | 6,046 | [
"VisIt"
] | b9bb8d971d65eecb20902b9113f3fc02371dfcd4a83849dca8faa9064cee71d8 |
import pathlib
import os
import weakref
import numpy as np
import pytest
import vtk
import pyvista
from pyvista import examples
from pyvista.plotting import system_supports_plotting
test_path = os.path.dirname(os.path.abspath(__file__))
VTK9 = vtk.vtkVersion().GetVTKMajorVersion() >= 9
# must be manually set until... | akaszynski/vtkInterface | tests/test_grid.py | Python | mit | 38,339 | [
"VTK"
] | 942873ab382b417bce8a49a1b9d3ce37db7212f88e3c35f59b28f5497696ec50 |
#!/usr/bin/env python3
from ..distributions import MultivariateNormal
from ..likelihoods import _GaussianLikelihoodBase
from .marginal_log_likelihood import MarginalLogLikelihood
class ExactMarginalLogLikelihood(MarginalLogLikelihood):
"""
The exact marginal log likelihood (MLL) for an exact Gaussian process... | jrg365/gpytorch | gpytorch/mlls/exact_marginal_log_likelihood.py | Python | mit | 2,895 | [
"Gaussian"
] | fdb9dcb3e7e377fc19bc8e57fa1c3cb9e09c24d44f67803c8c62dfdccd5b881c |
"""
Tests for analysis.
"""
import VMD
from pyvmd.analysis import hydrogen_bonds, HydrogenBond
from pyvmd.atoms import Atom, Selection
from .utils import data, PyvmdTestCase
class TestAnalysis(PyvmdTestCase):
"""
Test analysis utilities.
"""
def setUp(self):
molid = VMD.molecule.load('psf', ... | ziima/pyvmd | pyvmd/tests/test_analysis.py | Python | gpl-3.0 | 1,500 | [
"VMD"
] | 696fe63df47ae9877be44b83df8494cd0cb89f91c6652b0a50ddc3356f38e28b |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# ... | SKIRT/PTS | dustpedia/config/get_sed.py | Python | agpl-3.0 | 899 | [
"Galaxy"
] | 7db53cf321b4f51bd627ddf5492702b7c60bef9d5f22a81a75d7d3287cd4fcba |
########################################################################
# $HeadURL$
########################################################################
""" X509Request is a class for managing X509 requests with their Pkeys
"""
__RCSID__ = "$Id$"
import GSI
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Security.... | coberger/DIRAC | Core/Security/X509Request.py | Python | gpl-3.0 | 4,610 | [
"DIRAC"
] | 868968b2f648ebdb6b1f1f3aeb1cb6b4e49664f76e4f1e30104210e9d61c7522 |
import unittest
import os
from collections import defaultdict
from mpinterfaces.utils import *
from pymatgen import Structure
from pymatgen.io.vasp.inputs import Kpoints
from pymatgen.symmetry.bandstructure import HighSymmKpath
__author__ = "Michael Ashton"
__copyright__ = "Copyright 2017, Henniggroup"
__maintainer_... | henniggroup/MPInterfaces | mpinterfaces/tests/test_utils.py | Python | mit | 5,130 | [
"VASP",
"pymatgen"
] | f3cd9d0a786fafcf6e4d458a68b2025cb64482dbbece08a3c9fbcb951b8b1794 |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# generate_ufuncs.py to generate the docstrings for the ufuncs in
# scipy.special at the C lev... | Newman101/scipy | scipy/special/add_newdocs.py | Python | bsd-3-clause | 137,537 | [
"Gaussian"
] | 7f350a55004c900411fd76ce837d318c80e8383d6b651cf2b087ade763709284 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the Opera browser history parsers."""
import unittest
from plaso.parsers import opera
from tests.parsers import test_lib
class OperaTypedParserTest(test_lib.ParserTestCase):
"""Tests for the Opera Typed History parser."""
def testParse(self):
"""... | Onager/plaso | tests/parsers/opera.py | Python | apache-2.0 | 2,745 | [
"VisIt"
] | 4151e7ca3beb4f97ec1881484dc540c065a9ab511f329ce54fc7bc621dd2ae6a |
from __future__ import print_function
import numpy as np
np.seterr(divide='ignore', invalid='ignore')
from orphics import maps
from pixell import enmap, utils
from scipy.special import factorial
try:
from pixell import lensing as enlensing
except:
print("WARNING: Couldn't load pixell lensing. Some features will... | msyriac/orphics | orphics/lensing.py | Python | bsd-2-clause | 104,980 | [
"Gaussian",
"TINKER"
] | fe8c0e6ea5256934736081563845d0a05e7de718878c11223b6a3dce22c4ff2e |
# coding: utf-8
import sublime
import re
st_version = int(sublime.version())
if st_version > 3000:
from JoomlaPack.lib.inflector.base import Base
else:
from lib.inflector.base import Base
class English(Base):
'''
Inflector for pluralize and singularize English nouns.
This is the default Inflect... | renebentes/JoomlaPack | lib/inflector/english.py | Python | mit | 8,988 | [
"Elk",
"MOOSE"
] | 7cdcc17d1017586d5a414457388c3ccbd19ab72c0694b936c7d95b23f9e87b78 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RAffxparser(RPackage):
"""Affymetrix File Parsing SDK.
Package for parsing Affymet... | iulian787/spack | var/spack/repos/builtin/packages/r-affxparser/package.py | Python | lgpl-2.1 | 1,412 | [
"Bioconductor"
] | 54fa85642e8180e5d51a79f509fd7c0465f3f32a120f6c39d0df8ca08938e179 |
import numpy as np
from ase import Atoms, units
from ase.data import chemical_symbols, atomic_numbers
from ase.io import PickleTrajectory
from ase.md import VelocityVerlet
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.lattice.cubic import SimpleCubic
from asap3 import Morse
from asap3.t... | auag92/n2dm | Asap-3.8.4/Test/Morse.py | Python | mit | 2,979 | [
"ASE"
] | 5967e71abd33bae9bec456adea08c790974d16481eec1a53ebda30b13894c4b5 |
from gpaw.transport.analysor import Transport_Plotter
import numpy as np
import sys
from pylab import *
if '*' in sys.argv[1]:
fd=0
bias_step = int(sys.argv[1].split('*')[0])
else:
fd=1
bias_step = int(sys.argv[1])
plotter=Transport_Plotter(fd)
plotter.plot_setup()
tc = plotter.tc(bias_step)
ee=np.lins... | qsnake/gpaw | doc/documentation/transport/transport_analysis_scripts/tc.py | Python | gpl-3.0 | 914 | [
"GPAW"
] | 843b48b6079788fc1aac4911ad81429c9b65078d93f8b131ac16c03960dd3547 |
""" The Bdii2CSAgent performs checking BDII for availability of CE
resources for a given or any configured VO. It detects resources not yet
present in the CS and notifies the administrators.
For the CEs already present in the CS, the agent is updating
if necessary settings which were changed in the BDII recently
The f... | ic-hep/DIRAC | src/DIRAC/ConfigurationSystem/Agent/Bdii2CSAgent.py | Python | gpl-3.0 | 13,380 | [
"DIRAC"
] | 975bf488349d6c7e41643a54dac727fe38ca2c8433550d4f6e6fa583a1c8de41 |
#!/usr/bin/env python3
#Copyright 2018 OSIsoft, 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 required by applicable law or agree... | osisoft/OMF-Samples | Community Samples/Python3/SendOMFDataToPISystemFromBeagleBoneBlue.py | Python | apache-2.0 | 23,066 | [
"VisIt"
] | c556c70d974aa74dee0940121d2827a6e6ccce37013fb357b802be3da21304f9 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, division, absolute_import, print_function
from builtins import * # noqa pylint: disable=unused-import, redefined-builtin
from past.builtins import basestring
import logging
import re
import time
from datetime import datetime, timedelta
from dateutil.pa... | qk4l/Flexget | flexget/plugins/internal/api_trakt.py | Python | mit | 53,240 | [
"VisIt"
] | ff9fc1551a88d7ee772ec86eefc82f5fbb428db3617b0e918e89d0641e4d28ea |
"""
Views for user API
"""
import six
from django.contrib.auth.signals import user_logged_in
from django.shortcuts import redirect
from django.utils import dateparse
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import UsageKey
from rest_framework import generics, views
from rest_framework.decorat... | cpennington/edx-platform | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 13,824 | [
"VisIt"
] | ed0ccbfe35bedf7051a9812e3f79d3ff1fd61dc60059bb9196e6e8a1756512d2 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import warnings
import subprocess
import numpy as np
import os.path
import copy
from pymatgen.core import Structure, Lattice, PeriodicSite, Molecule
from pyma... | nisse3000/pymatgen | pymatgen/analysis/graphs.py | Python | mit | 80,226 | [
"CRYSTAL",
"Jmol",
"pymatgen"
] | aa6440ab1cc66e9de923df8cd42145d78440e4f651d5240b8fd0feb00e363083 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio-Query-Parser.
# Copyright (C) 2014, 2015, 2016 CERN.
#
# Invenio-Query-Parser 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
# ... | Panos512/invenio-query-parser | invenio_query_parser/contrib/spires/walkers/spires_to_invenio.py | Python | gpl-2.0 | 3,179 | [
"VisIt"
] | d43c5be14676deafeac9c35ab01d676a4c9498e91fd1affd213942f8bb12e833 |
#!/usr/bin/env python
#------------------------------------------------------------
# Script compares efficiency of automatic derivatives vs
# analytical in mpfit.py
# Vog, 31 okt 2011
#------------------------------------------------------------
import numpy
from matplotlib.pyplot import figure, show, rc
from kapteyn... | kapteyn-astro/kapteyn | doc/source/EXAMPLES/kmpfit_example_partialdervs_confidence.py | Python | bsd-3-clause | 10,832 | [
"Gaussian"
] | fa85bad58fec9071023a19ac4abbb7302fa312c6c2204c2942bb83298a63240c |
"""
Lift ckernels to their appropriate rank so they always consume the full array
arguments.
"""
from __future__ import absolute_import, division, print_function
from dynd import nd, ndt, _lowlevel
from ..traversal import visit
class CKernelLifter(object):
"""
Lift ckernels to their appropriate rank so the... | talumbau/blaze | blaze/compute/air/frontend/ckernel_lift.py | Python | bsd-3-clause | 2,666 | [
"VisIt"
] | 4ebbf89603261e9493040628f9a0c0118454265c88eeff93c9624175f8e6d998 |
"""Next gen sequence alignments with Bowtie2.
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
"""
import os
from bcbio.pipeline import config_utils
from bcbio.distributed.transaction import file_transaction
from bcbio.provenance import do
from bcbio import bam, utils
from bcbio.pipeline import datadict as dd
fr... | vladsaveliev/bcbio-nextgen | bcbio/ngsalign/bowtie2.py | Python | mit | 6,941 | [
"Bowtie",
"Galaxy"
] | a9f611abfe175c844e7fd59dc794c21de8f45c416b47bb3a3ab15a199ab577f1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module defines some useful design patterns.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = ... | sonium0/pymatgen | pymatgen/core/design_patterns.py | Python | mit | 624 | [
"pymatgen"
] | b65caf48e34e6b730b9d5a2dce120dd57a76f2bba1c02c894eb0f2f7fc92d25a |
import os
import glob
import mdtraj as md
from fahmunge import fah
target_id_map = {"NSD1_HUMAN_D0":"91f51e8a-7b40-4adc-8ca9-38786a9fe654", "SETD2_HUMAN_D0":"aa5325a2-2fec-46ac-a14a-ce1d46328a4c", "NSD2_HUMAN_D0":"23166b8f-dd82-408f-b1e8-b5657c67141c"}
for target, target_id in target_id_map.iteritems():
storage_p... | kyleabeauchamp/fah-projects | code/analysis/concat_siegetank_trajectories.py | Python | gpl-2.0 | 811 | [
"MDTraj"
] | ccfa56ccca826c0b5f10f63aa11c0b87f59302a2778d0985395a77f86513778c |
#!/usr/bin/env python
'A model of the earth and its magnetic field, with earth center as origin.'
from __future__ import division # avoid integer division
import numpy as np
import mayavi
from mayavi.mlab import *
def makeRcoordinates(x,y,z):
'''Makes r length and r^hat from coordinates'''
r = np.sqrt(x**2 + ... | arve0/TFY4240-Semester-project | src/solar_wind.py | Python | mit | 7,906 | [
"Mayavi"
] | b3330096f54d6cefa5459690b996aff6844c438aca8650ae66fd5fbb88c0473b |
#!/usr/bin/env python
# Contact: Jacob Schreiber
# jacobtribe@soe.ucsc.com
# parsers.py
#
# This program will read in an abf file using read_abf.py and
# pull out the events, saving them as text files.
from __future__ import division, print_function
import sys
from itertools import tee,izip,chain
import re
... | jmschrei/PyPore | PyPore/parsers.py | Python | mit | 29,489 | [
"Gaussian"
] | 79df1da2139ed790db957c7e11650dd7e38e8e65e0590ce80abb8270f7f15c0c |
# Authors: CommPy contributors
# License: BSD 3-Clause
"""
=============================================
Pulse Shaping Filters (:mod:`commpy.filters`)
=============================================
.. autosummary::
:toctree: generated/
rcosfilter -- Raised Cosine (RC) Filter.
rrcosfilter -- ... | veeresht/CommPy | commpy/filters.py | Python | bsd-3-clause | 4,711 | [
"Gaussian"
] | a88e43d1a050590400f352f75478676477c2acb6714a4d5d85ba3e2d9603ba50 |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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... | ashutoshvt/psi4 | psi4/share/psi4/fsapt/copy_pymol2.py | Python | lgpl-3.0 | 1,339 | [
"Psi4",
"PyMOL"
] | 6e6954fafb70e315f3f5fd1e968190ff850e2da1a0542a0b98e101fff220cfc2 |
# -*- coding: utf-8 -*-
#
# hl_api_models.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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, ... | terhorstd/nest-simulator | pynest/nest/lib/hl_api_models.py | Python | gpl-2.0 | 5,656 | [
"NEURON"
] | 074c06c8b7d6c31a67b3e73fe3d1f17ec29b5dea26da182fc3d61f0bd48c7b16 |
# coding=utf-8
# Copyright 2018 The Tensor2Tensor 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... | mlperf/training_results_v0.5 | v0.5.0/google/research_v3.32/gnmt-tpuv3-32/code/gnmt/model/t2t/tensor2tensor/models/research/moe_experiments.py | Python | apache-2.0 | 13,050 | [
"MOE"
] | 8349d6dcd19dc0beb27cbdf0e4ec736d775b473a1a6610b92f8c80acd8f4916e |
from __future__ import division, print_function, absolute_import
import numpy as np
from numpy import array
from numpy.testing import (assert_array_almost_equal, assert_array_equal,
assert_allclose,
assert_equal, assert_, assert_array_less)
from pytest import raise... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/scipy/signal/tests/test_windows.py | Python | mit | 23,428 | [
"Gaussian"
] | 3eb89047f6e0f6802b30760d82d01ab85d0e39332d791aa346ef4b289a59d72b |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements input and output processing from Nwchem.
2015/09/21 - Xin Chen (chenxin13@mails.tsinghua.edu.cn):
NwOutput will read new kinds of data:
1. normal hessian matrix. ["hessian"]
... | materialsproject/pymatgen | pymatgen/io/nwchem.py | Python | mit | 35,100 | [
"Gaussian",
"NWChem",
"pymatgen"
] | 1ecd5815e8ec68d22de2915c7fda9794307d9f5481bdc6dafdfd16bddbf41347 |
#!/usr/bin/env python
"""Convert a BLAST XML file to tabular output.
Takes three command line options, input BLAST XML filename, output tabular
BLAST filename, output format (std for standard 12 columns, or ext for the
extended 24 columns offered in the BLAST+ wrappers).
The 12 columns output are 'qseqid sseqid piden... | naumenko-sa/bioscripts | blast/blast.xml2flat1.py | Python | mit | 15,755 | [
"BLAST",
"Galaxy"
] | 4e6d47d9a0b3293f9e239cba6e758d3287ce9990a15164592a1a18b2e2a4f176 |
from sympy import *
import sympy.polynomials
import random
class NonSquareMatrixException(Exception):
pass
class ShapeError(ValueError):
"""Wrong matrix shape"""
pass
class Matrix(object):
def __init__(self, *args):
"""
Matrix can be constructed with values or a rule.
>>> ... | certik/sympy-oldcore | sympy/matrices/matrices.py | Python | bsd-3-clause | 40,228 | [
"DIRAC",
"Gaussian"
] | 9274fa63bf0f2b26ce49da22a41f12c8bee8ae647ce1d543aa518ba4da7989c0 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-get-pilot-output
# Author : Stuart Paterson
########################################################################
"""
Retrieve output of a Grid pilot
Example:
$ dirac-admin-get-pilot-output http... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_get_pilot_output.py | Python | gpl-3.0 | 1,226 | [
"DIRAC"
] | 8192fa3d5ea78a8d388dafac7c2ad2e78b882c20e641d21953d9e3728f5fdae3 |
import os
import unittest
from __main__ import vtk, qt, ctk, slicer
import urllib
#
# SlicerTestRecentFilesTests
#
class SlicerTestRecentFilesTests:
def __init__(self, parent):
parent.title = "SlicerTestRecentFilesTests"
parent.categories = ["Testing.TestCases"]
parent.dependencies = []
parent.contr... | agirault/VesselView | Applications/App/Testing/Python/SlicerTestRecentFilesTests.py | Python | apache-2.0 | 6,572 | [
"VTK"
] | cb2fde71518325cb02446cbe98a4d1371b6df8012a252d845c59bc9377b17486 |
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