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import neuron;
class Adaline(Neuron):
def __init__(self, n, r=0.8, inf=0):
super(Adaline, self).__init__(n,r,inf);
# > Delta-Rule weights adjustment
# > > l = input label (expected output)
# > > g = sum (given output)
# > > returns 'true' if any adjustment was needed, 'false' o... | cabraile/RNA-Modules | adaline.py | Python | mit | 1,614 | [
"NEURON"
] | 40e16eae8b045d2e0cfc9282e3aaac52fe22b79e773c89869c645a85281c3baf |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | casawa/mdtraj | mdtraj/tests/test_mdconvert.py | Python | lgpl-2.1 | 9,653 | [
"MDTraj",
"NetCDF"
] | c2b59d8d174fbe41ec9937974e7a23ee718f387fa24ffcd4a8942174d3ad3500 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def drawPoints(myscreen, clpoints, ccpoints):
c=camvtk.PointCloud( pointlist=clpoints, collist=ccpoints)
c.SetPoints()
myscreen.addActor(c )
def drawFiber(myscreen, f):
#myscreen.addActor( camvtk.Line(p1=(f.p1.x,f.p1.y,f.p1.... | AlanZatarain/opencamlib | scripts/fiber_01.py | Python | gpl-3.0 | 2,888 | [
"VTK"
] | 4c627a393b0edf924aacf187329f2b18e4bacc825e4bdb819393ab37751448b6 |
# 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 ... | to266/hyperspy | hyperspy/tests/signal/test_eds_sem.py | Python | gpl-3.0 | 13,035 | [
"Gaussian"
] | aec3a418c47423c033a5f129bf01f78ca905dca1d9c58ca85c5631cc81460021 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
3D visualization of activation maps using Mayavi
"""
# Author: Gael Varoquaux <gael dot varoquaux at normalesup dot org>
# License: BSD
import os
import tempfile
# Standard scientific libraries impo... | bthirion/nipy | nipy/labs/viz_tools/maps_3d.py | Python | bsd-3-clause | 14,510 | [
"Mayavi",
"VTK"
] | 2102a809ffe6dbc8885eb24b9874d93a41b9983c5f2695d35d61783b7c1512d9 |
# Author: Eli Draizen
# Date 5-1-14
# File: BlastXMLParser.py
#Standard libraries
import sys
import xml.etree.cElementTree as ET
import re
from math import exp
#Custom libraries
from Parser import Parser, Match, Matches
class HSP(Match):
"""Holds information about a given High-scoring Sequence Pair (HSP)
re... | edraizen/hsp_tiler | hsp_tiler/BlastXMLParser.py | Python | bsd-3-clause | 6,374 | [
"BLAST",
"Biopython"
] | 1135acddc02f49be95686cc228a1754ea037a913e5faaa2edc6d6bcc34593f4e |
import numpy as np
import math as mt
from stimulus import *
from myintegrator import *
import scipy.integrate as integrate
class Network:
''' Network class for homeostatic plasticity'''
def __init__(self):#Global parameters needed
# single neuron
self.n=10 #n pop
self.tau=10. #timescale of populations
self... | ulisespereira/PereiraBrunel2016 | figure10/functions.py | Python | gpl-2.0 | 5,552 | [
"NEURON"
] | 277d6a7407485d67f224ce23ee7d397c6667d3fb36c7fbd0685ca114aba07995 |
#! /usr/bin/env python
# -*- coding: UTF8 -*-
# Este arquivo é parte do programa Activlets
# Copyright 2013-2015 Carlo Oliveira <carlo@nce.ufrj.br>,
# `Labase <http://labase.selfip.org/>`__; `GPL <http://is.gd/3Udt>`__.
#
# Activlets é um software livre; você pode redistribuí-lo e/ou
# modificá-lo dentro dos termos da ... | carlotolla/activlets | src/test/test_model.py | Python | gpl-2.0 | 6,927 | [
"VisIt"
] | 88893ab1baf17cfc8a46abb0938e6d6c9462c0d1e7109e8d5512db0fec70490e |
#!/usr/bin/env python
"""Example code of DDPG on OpenAI Gym environments.
For DDPG, see: https://arxiv.org/abs/1509.02971
"""
from __future__ import print_function
from __future__ import division
import argparse
import collections
import copy
import random
import gym
import numpy as np
import chainer
from chainer im... | aonotas/chainer | examples/reinforcement_learning/ddpg_pendulum.py | Python | mit | 9,228 | [
"Gaussian"
] | ff49017da1f1cc4fcd487f145436844852ac28cc4f951946f2e5327c6220e728 |
# -*- coding: utf-8 -*-
"""
This module provides the AST. Subclass :py:class:`Context` and override the
various methods to allow minivect visitors over the AST, to promote and map types,
etc. Subclass and override :py:class:`ASTBuilder`'s methods to provide alternative
AST nodes or different implementations.
"""
from _... | shiquanwang/numba | numba/minivect/miniast.py | Python | bsd-2-clause | 50,407 | [
"VisIt"
] | 08bd60318a542bda9a286d3c75ce138ee1cffe8dc577361f5ad8ba3ad8327ba9 |
# coding=utf-8
import logging
import etcd
import gevent
from octopus import err
from octopus import constant
from octopus.service.octp_server import OctpServer
from octopus.proto import service_proto
log = logging.getLogger(constant.LOGGER_NAME)
class Election(object):
def __init__(self, os):
"""
... | ideascf/octopus | election/election.py | Python | mit | 2,701 | [
"Octopus"
] | d92f76580843561eb3db75ad29daa4e89f3e323dd81dc8f82c1497e76660a7cc |
langversion = 1
langname = "Français"
##updater
# text construct: "Version "+version+available+changelog
#example: Version 3 available, click here to download, or for changelog click here
available = "disponibles, cliquez pour télécharger"
changelog = ", ou pour la liste des changements cliquez ici"
##world gen
world... | Berserker66/omnitool | omnitool/Language/french.py | Python | mit | 3,555 | [
"VisIt"
] | dce4e0199fd0afbe1184bdb7749cb351b789f6b15a72175e04664635cdf7bb9c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Jerome Rapinat, B. Malengier
# Copyright (C) 2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public ... | beernarrd/gramps | gramps/plugins/quickview/lineage.py | Python | gpl-2.0 | 8,432 | [
"Brian"
] | 8c270219c34cd026e80ec9f9bc997d252389dbe74ad4ad39d3915b2f227ad107 |
#!/usr/bin/python
# coding: utf-8
# #################################################################################
# Copyright (C) 2014 Francesco Giovannini, Neurosys - INRIA CR Nancy - Grand Est
# Authors: Francesco Giovannini
# email: francesco.giovannini@inria.fr
# website: http://neurosys.loria.fr/
# Permission... | JoErNanO/brianmodel | brianmodel/neuron/ioniccurrent/ioniccurrentfactory.py | Python | gpl-3.0 | 4,164 | [
"NEURON"
] | 5f5a53dc746c9751668c294c873642a53891b731d5fad86aa4c193e11a5b3f44 |
"""
EvMenu
This implements a full menu system for Evennia. It is considerably
more flexible than the older contrib/menusystem.py and also uses
menu plugin modules.
To start the menu, just import the EvMenu class from this module,
```python
from evennia.utils.evmenu import EvMenu
EvMenu(caller, menu_module_... | shollen/evennia | evennia/utils/evmenu.py | Python | bsd-3-clause | 31,081 | [
"VisIt"
] | 4a20621a7882281178f967ab4a158c0b045028cf18d354a85619feb5d4033881 |
# encoding: utf-8
"""
Tests for IPConfigurable.loader
Authors:
* Brian Granger
* Fernando Perez (design help)
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is... | Carreau/IPConfigurable | IPConfigurable/test/test_loader.py | Python | bsd-3-clause | 5,056 | [
"Brian"
] | 5b3ca14c58e2f96023a0e97542cd6ba7e1885c308dca2406374ad7905445a7c9 |
#!/usr/bin/python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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 redistribute... | amjames/psi4 | doc/sphinxman/document_efpfrag.py | Python | lgpl-3.0 | 5,033 | [
"Psi4"
] | d1a11b7b31ad49e5c6ea0e8112e0b6c3a919920ccbc76e1d2ff308cb144671d0 |
"""
A script that takes the compliance dataset (the released version
of which is at https://github.com/ga4gh/compliance/tree/master/test-data)
and turns it into a directory bundle of binary and JSON files suitable
for use by the reference server.
"""
from __future__ import division
from __future__ import print_function... | ohsu-computational-biology/server | scripts/prepare_compliance_data.py | Python | apache-2.0 | 13,493 | [
"pysam"
] | 8dfb3e8cbd4e06e9d9b2521a1d93f4f1950a9688b400c5deff3ba7ee3173779d |
from __future__ import division
from .PolyIon import PolyIon
from ..Ion import fixed_state
from ..constants import boltzmann, kelvin, reference_temperature, \
elementary_charge, avogadro, lpm3, gpkg
from math import pi, exp
import numpy as np
from Bio import SeqUtils
from Bio.SeqUtils.ProtParam import ProteinAna... | lewisamarshall/ionize | ionize/PolyIon/Peptide.py | Python | gpl-2.0 | 3,691 | [
"Avogadro"
] | 3424a3fbd0ffaa670658764711efb62de51ae63a13e8a2dfc706f84093062024 |
from tabular import Tabular
from galaxy.datatypes import metadata
from galaxy.datatypes.metadata import MetadataElement
class ChromInfo( Tabular ):
file_ext = "len"
MetadataElement( name="chrom", default=1, desc="Chrom column", param=metadata.ColumnParameter )
MetadataElement( name="length", default=2, de... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/datatypes/chrominfo.py | Python | gpl-3.0 | 374 | [
"Galaxy"
] | ea69311d1d753d1c262887ad02b2cd1af214cd4d1a874d03038276268be444d9 |
#!/usr/bin/env python
import argparse
import contextlib
import collections
import csv
import itertools
import logging
import os.path
import operator
import shutil
import subprocess
import sys
import tempfile
from concurrent import futures
import pysam
log = logging.getLogger('prep_drm.contam')
@contextlib.contextman... | fhcrc/prepdrm | bin/blast_against_refs.py | Python | gpl-3.0 | 6,689 | [
"BLAST",
"pysam"
] | cd0c45f99e2f6299ce1fdab6b1e4f1da34d9d82a693b8979d45b87c8fe45fd46 |
import py
from rpython.rlib.parsing.ebnfparse import parse_ebnf
from rpython.rlib.parsing.regexparse import parse_regex
from rpython.rlib.parsing.lexer import Lexer, DummyLexer
from rpython.rlib.parsing.deterministic import DFA, LexerError
from rpython.rlib.parsing.tree import Nonterminal, Symbol, RPythonVisitor
from r... | cosmoharrigan/pyrolog | prolog/interpreter/parsing.py | Python | mit | 141,254 | [
"VisIt"
] | 095560ef5c3746c8ec69f5a2ca97c257ba54432aba91cf59ec2c10d31698ed92 |
import unittest
from test import support
from itertools import *
import weakref
from decimal import Decimal
from fractions import Fraction
import sys
import operator
import random
import copy
import pickle
from functools import reduce
import sys
import struct
maxsize = support.MAX_Py_ssize_t
minsize = -maxsize-1
def l... | technologiescollege/Blockly-rduino-communication | scripts_XP/Lib/test/test_itertools.py | Python | gpl-3.0 | 89,911 | [
"GULP"
] | dfc42707159d87eca02b4f898a8a29615c2549ff93024d7e068a070f82300b30 |
import client_conn
import filelist
import rsa
import hashlib
import getpass
import log
import os
import signal
import sys
# filename of list
mylist = "list"
password = None
def print_help():
"""
Print the available command list.
"""
print()
print()
if client_conn.is_login():
print("Lo... | oneonestar/CloudStorage | src/client/client.py | Python | gpl-3.0 | 7,136 | [
"MOE"
] | 0e43779208f929fe169b63bcc3fc2345809787f28b35926b9c40e850b299e46e |
#!/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... | gkc1000/pyscf | pyscf/mcscf/casci.py | Python | apache-2.0 | 44,351 | [
"PySCF"
] | 558023f1c283091fc4f43d706092e35f501e2078074a6ba64eff04bb1f051581 |
"""
Demo Application for Gaussian process latent variable models
====================================
"""
import logging as LG
import numpy.random as random
from pygp.gp import gplvm,gplvm_ard
from pygp.covar import linear,se, noise, combinators
import pygp.optimize as opt
import pygp.plot.gpr_plot as gpr_plot
impo... | PMBio/pygp | pygp/demo/demo_gplvm.py | Python | gpl-2.0 | 1,774 | [
"Gaussian"
] | 04cb1be718752a562e72178deb8e4759bc4cc4d57bb7cdd647c55a6e259e8efe |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008-2010, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License ... | NetNow/wmi-samba | pysamba/rpc/credentials.py | Python | gpl-2.0 | 770 | [
"VisIt"
] | fac2df877210031c333945a90c4dba3d8452f5efccc0532bcad9c94d8acac6ff |
#!/usr/bin/env python
# THIS FILE IS PART OF THE CYLC SUITE ENGINE.
# Copyright (C) 2008-2018 NIWA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at yo... | jonnyhtw/cylc | lib/cylc/network/httpserver.py | Python | gpl-3.0 | 33,530 | [
"VisIt"
] | 0d4f1bff1e9e8246a29dedf14613b10f73d8f07aa480b2983c6c60f85dfedf11 |
import scipy.ndimage as sp
import maya.cmds as cmds
import maya.OpenMaya as om
import maya.OpenMayaAnim as oma
import numpy as np
import scipy.interpolate as si
def bspline(cv, n=100, degree=3, periodic=False):
""" Calculate n samples on a bspline
cv : Array ov control vertices
n... | AndreySibiryakov/tools | smooth_curve_gaussian_class_api_2_w_smooth.py | Python | mit | 7,752 | [
"Gaussian"
] | 033ebf9e713c0dda358256855089279900b4bc0a4b5125fbcc30154203b2d62e |
'''
MFEM example 5p
See c++ version in the MFEM library for more detail
'''
import time
from numpy import sin, cos, exp
import numpy as np
from mfem import path
import mfem.par as mfem
from mfem.par import intArray
from mfem.common.mpi_debug import nicePrint
from os.path import expanduser, join, dirname
from ... | mfem/PyMFEM | examples/ex5p.py | Python | bsd-3-clause | 11,627 | [
"ParaView",
"VisIt"
] | bcd82a87533a06dd8cabb2c8e3d4e0e525edda688234d01216e937dfd0417419 |
# -*- coding: utf-8 -*-
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright © 2014, 2019 Dave Hocker
#
# 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 Fou... | dhocker/athomepowerlineserver | database/AtHomePowerlineServerDb.py | Python | gpl-3.0 | 4,815 | [
"xTB"
] | 2e5f32cf5f257718ac9700084c7debf4a80e6a18061cd7fb5b42ccfa4c14fe79 |
from scipy import stats
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
import pickle
import scipy
from astropy.io import fits
from astropy.table import Table
from astropy.coordinates import SkyCoord
from astropy.time import Time
# read data:
pkl_file = open(
'/Users/caojunzhi/Desktop/NYU... | peraktong/Cannon-Experiment | 0516_0306_plot_look_deeper.py | Python | mit | 9,319 | [
"VisIt"
] | a079ecc422e4045167814f9fd680828f0975ec371f178a5585086f7186593cf7 |
"""
This code includes initialization classes for shared variables.
At this stage, theano shared variable is not related.
Only numpy value is created and returned.
"""
import numpy as np
import theano
class BaseInitializer(object):
"""
This class defines abstract base class for initializers.
"""
def ... | khshim/lemontree | lemontree/initializers.py | Python | mit | 11,194 | [
"Gaussian"
] | e95dc41c873a47211b6277d8aafd0c597a66b7259ba18e1a636c11bf5e22bdaa |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/r-summarizedexperiment/package.py | Python | lgpl-2.1 | 2,628 | [
"Bioconductor"
] | 976c284ed80f6343cfd7e1677ed2fce474c268b52e9016bca60af77924116f71 |
# -*- encoding:ascii -*-
from mako import runtime, filters, cache
UNDEFINED = runtime.UNDEFINED
__M_dict_builtin = dict
__M_locals_builtin = locals
_magic_number = 6
_modified_time = 1417441807.90797
_template_filename='templates/webapps/galaxy/workflow/list.mako'
_template_uri='workflow/list.mako'
_template_cache=cach... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/database/compiled_templates/workflow/list.mako.py | Python | gpl-3.0 | 13,045 | [
"Galaxy"
] | 01e7401a996a48e7b1f82e96a46bc765afe6dc2163bd2bbd5a2f687a5d5f4749 |
"""
DIRAC.ConfigurationSystem.Client package
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
| yujikato/DIRAC | src/DIRAC/ConfigurationSystem/Client/__init__.py | Python | gpl-3.0 | 181 | [
"DIRAC"
] | 32e84793939a68974847982623355e86bffee4372dc099dc5b63bf9081227fa3 |
#
# 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... | spark-test/spark | python/pyspark/ml/regression.py | Python | apache-2.0 | 88,597 | [
"Gaussian"
] | 0108bee9c1d1bda261b8e07721bc6af67c8c94f9fc5142d3a3910ad4cd7a267d |
"""
SeqProp
=======
"""
import os.path as op
import pandas as pd
import tempfile
import requests
import logging
from copy import copy, deepcopy
from slugify import Slugify
import os
import subprocess
from Bio import SeqIO
from BCBio import GFF
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqFea... | SBRG/ssbio | ssbio/protein/sequence/seqprop.py | Python | mit | 36,093 | [
"BLAST",
"Biopython"
] | c766e420f612e42266275ab73d19602c0872a5181978478b1f6d7fd318f0fddc |
"""Factor Analysis.
A latent linear variable model.
FactorAnalysis is similar to probabilistic PCA implemented by PCA.score
While PCA assumes Gaussian noise with the same variance for each
feature, the FactorAnalysis model assumes different variances for
each of them.
This implementation is based on David Barber's B... | zorroblue/scikit-learn | sklearn/decomposition/factor_analysis.py | Python | bsd-3-clause | 12,180 | [
"Gaussian"
] | e3605bb87110b24045a1a9ab8265b39f9aa280116dcf46f51347832b76858629 |
""" DIRAC Encoding utilities based on json
"""
import datetime
import json
# Describes the way date time will be transmetted
# We do not keep miliseconds
DATETIME_DEFAULT_FORMAT = '%Y-%m-%d %H:%M:%S'
class JSerializable(object):
"""
Base class to define a serializable object by DIRAC.
An object that... | fstagni/DIRAC | Core/Utilities/JEncode.py | Python | gpl-3.0 | 5,625 | [
"DIRAC"
] | 54ffffba4514aac76609a89814b9dbc1048259f22e2121f4c62b6dc65108c282 |
"""
.. currentmodule:: pylayers.antprop.coverage
.. autosummary::
:members:
"""
from pylayers.util.project import *
#from pylayers.measures.mesuwb import *
from pylayers.simul.radionode import *
import pylayers.util.pyutil as pyu
from pylayers.util.utilnet import str2bool
from pylayers.gis.layout import Layout
imp... | pylayers/pylayers | pylayers/antprop/coverage.py | Python | mit | 38,833 | [
"Mayavi"
] | c98587e7458e35a3aafaab91b7d941b7d6f19f739ace0b564b17787a24ddcf9b |
'''
This modules solves the mobility or the resistance problem for one
configuration of a multibody supensions and it can save some data like
the velocities or forces on the bodies, the mobility of a body or
the mobility of the blobs.
'''
import argparse
import numpy as np
import scipy.linalg as scla
import scipy.spar... | stochasticHydroTools/RotationalDiffusion | multi_bodies/multi_bodies_utilities.py | Python | gpl-3.0 | 19,589 | [
"VTK",
"VisIt"
] | a4d45a990a524db56ac1cdc29574e35303c241e9bc505667e80356dcea54c37d |
########################################################################
# File: StorageElementHandler.py
########################################################################
"""
:mod: StorageElementHandler
.. module: StorageElementHandler
:synopsis: StorageElementHandler is the implementation of a simple Storag... | Andrew-McNab-UK/DIRAC | DataManagementSystem/Service/StorageElementHandler.py | Python | gpl-3.0 | 16,621 | [
"DIRAC"
] | 07bdca223325474398aaf250fd4210f5e7b47e7a3a4c16a0352815c0546c8459 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
"""Fast atom neighbor lookup using a KD tree (implemented in C++)."""
from __future__ imp... | zjuchenyuan/BioWeb | Lib/Bio/PDB/NeighborSearch.py | Python | mit | 4,703 | [
"Biopython"
] | 6dd9fda8041d07d2ad33e48f288140b0293fa84d519f15299a8fb140371e4a7a |
# -*- coding: utf-8 -*-
'''
.. versionadded:: 2016.3.0.
Manage Telemetry alert configurations
=====================================
Create, Update and destroy Mongo Telemetry alert configurations.
This module uses requests, which can be installed via package, or pip.
This module accepts explicit credential (telemet... | stephane-martin/salt-debian-packaging | salt-2016.3.3/salt/states/telemetry_alert.py | Python | apache-2.0 | 7,000 | [
"ORCA"
] | 947c4814429fe37eefce529cb9a8dd59beadcccf29728fa12ee73edd20133806 |
#! /usr/bin/env python
import cynest as nest
import cynest.voltage_trace
nest.ResetKernel()
neuron = nest.Create("iaf_neuron")
noise = nest.Create("poisson_generator", 2)
nest.SetStatus(noise, [{"rate": 80000.0}, {"rate": 15000.0}])
voltmeter = nest.Create("voltmeter")
nest.SetStatus(voltmeter, {"withgid": True, "... | QJonny/CyNest | cynest/examples/one-neuron-with-noise.py | Python | gpl-2.0 | 519 | [
"NEURON"
] | ddf53bfa2c790b3474988f0c2566ea9d73d2cb3b0010a9a36c0829a2fe421fb2 |
"""
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"
import numpy as np
from scipy import sparse as SP
import scipy.optimi... | chhao91/pysal | pysal/spreg/utils.py | Python | bsd-3-clause | 24,433 | [
"COLUMBUS"
] | 95c922c22cc02d7fefb79c83d41784fb8c36b2d1a66f64400f783059679a8296 |
import re, string
#####################################
# last update 11/16/2012 by J. Mass #
# version = 0.03 #
#####################################
class FastaHelper(object):
def remove_newlines(self, string):
yield string.replace("\n","")
def insert_newlines(self, string, e... | janinamass/gardening | Scythe/tmp/gffFastaTools.py | Python | gpl-3.0 | 13,317 | [
"BLAST"
] | 5a67f9fe089586f3bdcab0d662cc62fcac61880a001ecd8395edd22d76169990 |
# -*- coding: UTF-8 -*-
"""
Classes defining the likelihood and the posterior probability of the model
given the data
"""
from __future__ import absolute_import
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
from celerite.modeling import Model
from scipy.stats import n... | gnarayan/WDmodel | WDmodel/likelihood.py | Python | gpl-3.0 | 16,705 | [
"Gaussian"
] | 2884a4d99132d4e5bfb0cf9596376793481c6e295539830fb4851725894a4b75 |
"""
Methods for aligning raw fastq reads to a reference genome.
"""
from collections import defaultdict
import copy
from datetime import datetime
import os
import re
import shutil
import string
import subprocess
from subprocess import PIPE
from subprocess import Popen
import sys
from celery import task
from main.mod... | woodymit/millstone_accidental_source | genome_designer/pipeline/read_alignment.py | Python | mit | 31,675 | [
"BWA"
] | 8d93b838fc8372bd878778efca5d66e2e76c88fbd30c81b02f1afb7f046ebcb8 |
#!/usr/bin/env python2
import sys
sys.path.append('../../../src/')
import cgmap as cg
import mdtraj as md
import md_check as check
input_traj = "dppc_1_molecule.trr"
input_top = "dppc_1_molecule.pdb"
output_traj = "dppc_1_molecule.trr"
output_top = "dppc_1_molecule.pdb"
reference_traj = "dppc_1_molecule.trr"
refe... | uchicago-voth/cgmap | test/molecular_map_test/single_molecule_com/test_single_molecule_com.py | Python | apache-2.0 | 1,004 | [
"MDTraj"
] | bbcabca731aade7e4418a2085ec005435aeebe1f4f8408c7342f30f945121f68 |
# -*- 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 django.views import defaults as default_views
urlpat... | pikamar/scoop | config/urls.py | Python | bsd-3-clause | 1,275 | [
"VisIt"
] | 2cffa05912dbc223324e123d311c825d28498b667d0fdc6248003d2f038eb164 |
# 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... | alsrgv/tensorflow | tensorflow/python/autograph/pyct/cfg.py | Python | apache-2.0 | 29,003 | [
"VisIt"
] | 131a8811ed3ed8159ffc3a54905c8bb1c913c1a4999115cbe2f4f4934551f4ee |
import itertools
import os
import warnings
from intermol.forces import *
from intermol.gromacs.gromacs_parser import GromacsParser, default_gromacs_include_dir
from foyer.orderedset import OrderedSet
from foyer.atomtyper import find_atomtypes
def apply_forcefield(intermol_system, forcefield, debug=True):
"""App... | Jonestj1/foyer | foyer/forcefield.py | Python | mit | 12,884 | [
"Gromacs"
] | 5fff53ad35c3f28069e21f01046d5f3207bf8d86de09dba8299a7974d0c19633 |
description = """
analyse_reti is an analysis app that has been designed to analyse the replica exchange trajectory of all RETI
simulations in Sire. analyse_reti reads in a Sire Saved Stream (.s3) file that contains a Sire simulation restart file
(typically called ???_restart.s3). analyse_reti will extract the replica ... | michellab/Sire | wrapper/python/scripts/analyse_reti.py | Python | gpl-2.0 | 6,246 | [
"VisIt"
] | d5f3740d8242414869f8f19da4153628e772726c678de9e4d7f6a3654bb49a61 |
from django.db import models
from django.contrib.auth.models import User, Group
from django.conf import settings
from django.contrib.sites.models import Site
from django.template.defaultfilters import slugify
from django.db.models.signals import post_save
from django.template.defaultfilters import truncatewords
from dj... | agiliq/Dinette | dinette/models.py | Python | bsd-3-clause | 13,928 | [
"VisIt"
] | 6524d44f410c6a305ed1eb3dbdb41a8718e28a94e879ff0f8e900ca358db8447 |
""" DIRAC Graphs package provides tools for creation of various plots to provide
graphical representation of the DIRAC Monitoring and Accounting data
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/Phedex Project by ... <to be added>
"""
__RCSID__ = "$Id$"
# Make su... | andresailer/DIRAC | Core/Utilities/Graphs/__init__.py | Python | gpl-3.0 | 4,866 | [
"DIRAC"
] | bbdc2191ad95c351f427e85e81a79eba4f6379c26b8955fe1e542e638acaaf74 |
import os
import numpy as np
import logging
from scipy.stats import beta
from scipy.stats import binom
from scipy.stats import bernoulli
from app_globals import *
from r_support import matrix, cbind
"""
Support for Gaussian Processes
"""
# Define the kernel
def kernel(a, b, length_scale=1.):
""" GP squared expon... | shubhomoydas/pyaad | pyalad/gp_support.py | Python | mit | 13,644 | [
"Gaussian"
] | 721d676e829eb30397b55fe60bb5cbbaca22a2a04b841bb02e25e8dbf29181b3 |
#!/usr/bin/env python
#test exists to verify that structured grid blanking works as expected
import vtk
from vtk.test import Testing
#make up a toy structured grid with known characteristics
xlim=10
ylim=10
zlim=3
sg = vtk.vtkStructuredGrid()
sg.SetExtent(0,xlim,0,ylim,0,zlim)
#a handy point iterato... | timkrentz/SunTracker | IMU/VTK-6.2.0/Filters/Geometry/Testing/Python/structuredGridBlanking.py | Python | mit | 2,200 | [
"VTK"
] | 2bac79653cf1d3be1be57262eacdb28a8c5029479d999b17140b48fb5089a80a |
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #
# (c) 2010... | backmari/moose | python/chigger/exodus/ExodusReader.py | Python | lgpl-2.1 | 19,780 | [
"MOOSE",
"VTK"
] | 9f8724f922e0334d7d7259d48db3fbbaaadb097d2e995ec713c5ec2a3b4c9a92 |
"""Type annotations that are widely used in DeepChem"""
from typing import Any, Callable, List, Sequence, Tuple, TypeVar, Union
import numpy as np
T = TypeVar("T")
# An activation function for a layer: either a function or the name of a standard activation
ActivationFn = Union[Callable, str]
# A loss function for u... | deepchem/deepchem | deepchem/utils/typing.py | Python | mit | 919 | [
"RDKit",
"pymatgen"
] | 7399d98307a25bc84e3b7522122ed3363c5303e599623034b461dd169feff782 |
# -*- coding: utf-8 -*-
# Arco (c) Brian Lusina
import re
import os
import codecs
from setuptools import setup, find_packages
from distutils.dir_util import copy_tree
def read(*rnames):
return codecs.open(os.path.join(os.path.dirname(__file__), *rnames), 'r', 'utf-8').read()
def grep(attrname):
pattern = r... | BrianLusina/Arco | server/setup.py | Python | mit | 1,080 | [
"Brian"
] | ec6cb5b69b35ab63356fea6006f39582d52cf04b13b9961c36000dceede12d6a |
"""
Define common steps for instructor dashboard acceptance tests.
"""
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from __future__ import absolute_import
from lettuce import world, step
from mock import patch
from nose.tools import assert_in
from courseware.tests.factories import Staf... | louyihua/edx-platform | lms/djangoapps/instructor/features/common.py | Python | agpl-3.0 | 4,560 | [
"VisIt"
] | bfefb2ac8a07271bb9e3d69fb6444163df093cc588d92e4bbd3b57a051a54ff1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import collections
from pycparser import CParser
from pycparser import c_ast
def extractTypeAndName(n, defaultName=None):... | disconnect3d/pwndbg | pwndbg/funcparser.py | Python | mit | 2,567 | [
"VisIt"
] | f2c4f47a671280628b00ff0d88a0d38a3d1c22be14a2c3fcb32500903dd3c237 |
from __future__ import print_function
import sys
sys.path.insert(1,"../../../")
from tests import pyunit_utils
import h2o
import random
from h2o.utils.typechecks import assert_is_type
from h2o.frame import H2OFrame
def h2ocreate_frame():
"""
Python API test: h2o.create_frame(frame_id=None, rows=10000, cols=10,... | spennihana/h2o-3 | h2o-py/tests/testdir_apis/H2O_Module/pyunit_h2ocreate_frame.py | Python | apache-2.0 | 2,695 | [
"Gaussian"
] | 8a8890d1236791c587de779c8fc7efd47a7f10dda56ef20d184e9eb55ba08454 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Setup script for cxio-python library
To install, run:
python setup.py install
"""
from setuptools import setup, find_packages
setup(
name='cxio',
version='0.1.0',
description='Utility to parse CX JSON streams',
long_description='Utility cllection ... | keiono/cxio_python | setup.py | Python | mit | 1,331 | [
"Cytoscape"
] | 7088dd34dfd228f070968e1d19c845c3eeb77ba7945e7dc66a45056cb766e7bc |
# -*- coding: utf-8 -*-
import ast
from ast import NodeVisitor
class CodeGen(NodeVisitor):
def __init__(self, stream, show_comments = True):
# The current label number we're on, for generating
# jump labels in the assembly code (e.g., 'LO', 'L1', etc).
self.__label = 0
# Current ... | zeaphoo/mo | mocc/codegen.py | Python | mit | 6,207 | [
"VisIt"
] | f62c88fa4b6bc8b45fe6f245f9f3efb212ba6fc26800796d1bfe1ccb61e14000 |
""" The TimeLeft utility allows to calculate the amount of CPU time
left for a given batch system slot. This is essential for the 'Filling
Mode' where several VO jobs may be executed in the same allocated slot.
The prerequisites for the utility to run are:
- Plugin for extracting information from lo... | DIRACGrid/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/TimeLeft/TimeLeft.py | Python | gpl-3.0 | 8,194 | [
"DIRAC"
] | 8a2ce226431bae08c3fc532e90e22d28b804178b2095ee4ae584cd410a7142d2 |
"""
.. module:: Serotype_determiner_functions.py
.. moduleauthor:: Ali Al-Shahib, Georgia Kapatai
"""
import os, os.path, sys, subprocess, inspect
module_folder_paths = ["modules"]
for module_folder_path in module_folder_paths:
module_folder = os.path.realpath(os.path.abspath(os.path.join(os.path.split(inspect.g... | phe-bioinformatics/PneumoCaT | modules/Serotype_determiner_functions.py | Python | gpl-3.0 | 15,036 | [
"Bowtie",
"pysam"
] | c019a1d3f122cca44c3091771933b3270b79e5397dc4b764aebcb2dfeaf420ef |
"""
# Majic
# Copyright (C) 2014 CEH
#
# 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
# (at your option) any later version.
#
# This pr... | NERC-CEH/jules-jasmin | job_runner/job_runner/post_processing_scripts/postProcessBNG.py | Python | gpl-2.0 | 18,675 | [
"NetCDF"
] | a9e36caf87d7f65c448ad1cffd26ec0cf45b651224c565c252518df6e2ba2b0b |
from pymol import cmd
from pymol.cgo import *
from pymol.vfont import plain
cgo = []
axes = [[2.0,0.0,0.0],[0.0,2.0,0.0],[0.0,0.0,2.0]]
pos = [0.0,0.0,0.0]
wire_text(cgo,plain,pos,'Hello World',axes)
pos = [0.0,-3.0,0.0]
cyl_text(cgo,plain,pos,'Hello Universe',0.10,axes=axes)
cmd.set("cgo_line_radius",0.03)
cmd.l... | gratefulfrog/lib | python/pymol/pymol_path/examples/devel/cgo_3Dtext01.py | Python | gpl-2.0 | 371 | [
"PyMOL"
] | 1081cc113684552bd6d7b093507d6922ba7b909c3ad2c6fd06337af74cba8e28 |
#!/usr/bin/env python3
"""
Apply binary classification to cross-identify radio emission with
the associated host galaxy in ATLAS-EMU.
Input files:
- one-table-to-rule-them-all.tbl - contains Norris et al. (2006) table 6,
Franzen et al. (2015) 11JAN14 prerelease DR3, and Wong et al. (2017)
prerelease DR1.
- cro... | chengsoonong/crowdastro-projects | ATLAS-CDFS/scripts/pipeline.py | Python | mit | 69,403 | [
"Galaxy",
"Gaussian"
] | bc7bcb0542905d05c3dfa6711b17422c041d8253336538cb528b7d8c303b668e |
#!/usr/bin/env python3
import argparse
import math
import os
import re
import sqlite3
import sys
from collections import defaultdict
from biocode import annotation, gff, things, utils
## constants
DEFAULT_PRODUCT_NAME = "hypothetical protein"
## example invocation:
# parse_ergatis_euk_functional_pipeline.py -f HUZ2... | jorvis/biocode | sandbox/jorvis/parse_ergatis_euk_functional_pipeline.py | Python | mit | 40,819 | [
"BLAST"
] | 3d9613f8226bde32f11ad3879593a921a04bc758dd6fd6e0cf57e31e05cdd718 |
"""
Filename: config.py
Author: Brian Soe
Description: Configuration setting for Flask application.
"""
import os
basedir = os.path.abspath(os.path.dirname(__file__))
try:
SQLALCHEMY_DATABASE_URI = os.environ['DATABASE_URL']
except:
SQLALCHEMY_DATABASE_URI = 'sqlite:///' + os.path.join(basedir, 'database/tabl... | bsoe003/MWCH_Website | config.py | Python | mit | 549 | [
"Brian"
] | 77648b84c99f71a63eb4d9859f16e875f869f072a1986306f3a58c3a3ecfe406 |
""" The Notification service provides a toolkit to contact people via email
(eventually SMS etc.) to trigger some actions.
The original motivation for this is due to some sites restricting the
sending of email but it is useful for e.g. crash reports to get to their
destination.
Another use-case is... | fstagni/DIRAC | FrameworkSystem/Service/NotificationHandler.py | Python | gpl-3.0 | 10,700 | [
"DIRAC"
] | a20011cf41afcbd337f823fb915cf82987a7de4fcb315b2bdbc5d22f915e9502 |
#!/usr/bin/env python
'''
Monitor the aosn web site for new realtime data from Tethys and use
DAPloaders.py to load new data into the stoqs_realtime database.
Mike McCann
MBARI 17 May 2011
'''
import os
import sys
sys.path.insert(0, os.path.join(os.path.dirname(__file__), "../../"))
os.environ['DJANGO_SETTINGS_MODULE... | danellecline/stoqs | stoqs/loaders/CANON/realtime/monitorTethys.py | Python | gpl-3.0 | 10,672 | [
"VisIt"
] | 7d71e4634200ad2c7d52538e5884b2c8ee270509f428121b8c70580b18eb03f0 |
#!/usr/bin/env python3
# encoding: utf-8
from __future__ import unicode_literals
import collections
from molbiox.io import tabular
from molbiox.frame import interactive
# blast6m / blast7m
fieldlist_mini = [
('query.id', None),
('query.length', int),
('subject.length', int),
(... | frozflame/molbiox | molbiox/io/blast.py | Python | gpl-2.0 | 3,519 | [
"BLAST"
] | 71e0d38b23e17e43a6d97a9957de8a80cda86716431a189a79049c705715f9f8 |
"""Acceptance tests for LMS-hosted Programs pages"""
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.catalog import CatalogFixture, CatalogIntegrationMixin
from common.test.acceptance.fixtures.course import CourseFixture
from common.test.acceptance.fixtures.programs import ProgramsConfigMixin... | fintech-circle/edx-platform | common/test/acceptance/tests/lms/test_programs.py | Python | agpl-3.0 | 5,560 | [
"VisIt"
] | 7f714709666d8695f257cff5dfd7bb3e52242efedf3ec9d1def31db633baf97e |
#-*- coding: utf-8 -*-
###########################################################################
## ##
## Copyrights Frédéric Rodrigo 2012 ##
## ... | tyndare/osmose-backend | plugins/disabled/TagFix_Brand.py | Python | gpl-3.0 | 4,552 | [
"CASINO",
"Jaguar"
] | 429dd2d22c9b6f1334ebf0e2334f7be702e494bff00a8b9616a5235c704c8fbf |
#
# Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
# 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 copyrigh... | rdkit/rdkit | rdkit/Chem/SimpleEnum/Enumerator.py | Python | bsd-3-clause | 8,943 | [
"RDKit"
] | ec751af704cd77ff9cf3fdd0b70af2200d258a76750c689261dc4d2c7d54a011 |
"""
Converting the 'parse-tree' output of pyparsing to a SPARQL Algebra expression
http://www.w3.org/TR/sparql11-query/#sparqlQuery
"""
import functools
import operator
import collections
from rdflib import Literal, Variable, URIRef, BNode
from rdflib.plugins.sparql.sparql import Prologue, Query
from rdflib.plugi... | marma/rdflib | rdflib/plugins/sparql/algebra.py | Python | bsd-3-clause | 20,944 | [
"VisIt"
] | 2024e45f6c9bee5c4d616a8b8b5c4cebc334d204311f059faca63422f99cf59c |
import vtk
def main():
colors = vtk.vtkNamedColors()
textSource = vtk.vtkVectorText()
textSource.SetText("Hello")
textSource.Update()
# Create a mapper and actor
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(textSource.GetOutputPort())
actor = vtk.vtkActor()
actor.S... | lorensen/VTKExamples | src/Python/Visualization/VectorText.py | Python | apache-2.0 | 940 | [
"VTK"
] | 5b6606ff047cab946f7f4ece5e9a6df11740a8183c7295c1f53f1472560f09b9 |
import core.factory as default
from neuron.entities import Command
factory = default.DefaultFactory()
nlp, neuron = factory.cerebro()
def run(txt):
label = nlp.predict(txt)
return neuron.process(Command(label[0])) | Le-Bot/cerebro | cerebro/cerebro.py | Python | mit | 224 | [
"NEURON"
] | 2d7e41b2a5f36b62d371e0a102436fe7349ec497a11b7f43540c17176dba6cef |
# 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.
UA_TYPE_MAPPING = {
'desktop':
'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_3) '
'AppleWebKit/537.22 (KHTML, like Gecko) '
'Chrome/27... | androidarmv6/android_external_chromium_org | tools/telemetry/telemetry/core/user_agent.py | Python | bsd-3-clause | 1,021 | [
"Galaxy"
] | c5200b284c5362a632d46d6d056074be2619092715a8c5b29691d006aa3af8ac |
from ase import Atoms
from gpaw import GPAW
# Beryllium atom
atoms = Atoms(symbols='Be',
positions=[(0, 0, 0)],
pbc=False)
# Add 4.0 ang vacuum around the atom
atoms.center(vacuum=4.0)
# Create GPAW calculator
calc = GPAW(nbands=10, h=0.3)
# Attach calculator to atoms
atoms.set_calcu... | robwarm/gpaw-symm | doc/documentation/tddft/Be_gs_8bands.py | Python | gpl-3.0 | 639 | [
"ASE",
"GPAW"
] | 85750f97b2b7a8030e58be4b42f23a45f0c4d03b50db0eddeeaf04cff3590195 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import re
import math
import subprocess
import itertools
import logging
import glob
import warnings
import numpy as np
from monty.fractions import lcm
import ... | johnson1228/pymatgen | pymatgen/command_line/enumlib_caller.py | Python | mit | 16,097 | [
"VASP",
"pymatgen"
] | f4ce3e118f65ff05daefbfc6b4976c3c9024b92db3e3e3602e02722917826a42 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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 redistribute it and/or modify
#... | jgonthier/psi4 | psi4/driver/driver_findif.py | Python | lgpl-3.0 | 38,143 | [
"Psi4"
] | 20278889fcc8f024ff66e9c731565ac8798b0ee9baf64e05ddbbfb26d763bc7c |
import numpy as np
import os
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import matplotlib.pyplot as plt
import time
from datetime import datetime
from matplotlib.dates import date2num, num2date
import pyroms
import pyroms_toolbox
import _remapping
class nctime(object):
pass
def remap_bdry... | kshedstrom/pyroms | examples/Palau_HYCOM/remap_bdry_uv.py | Python | bsd-3-clause | 16,801 | [
"NetCDF"
] | 7bf6ee9c270f1ef59a7204aa941149ce0508f2f246bed3ec80c7dbdd2a936792 |
#!/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.
""" Generator for C style prototypes and definitions """
import glob
import os
import re
import sys
from idl_log import ErrOut, I... | GeyerA/android_external_chromium_org | ppapi/generators/idl_c_header.py | Python | bsd-3-clause | 11,840 | [
"VisIt"
] | 68e37e28c1c2ee5a73ec3d4401339fab039b4e0957335216e9675dccd410a882 |
"""
HTML Pages
"""
from support.VISinstrumentModel import VISinformation
from ETC import ETC
def front():
print "<html>"
print "<head><center><b>VIS Exposure Time Calculator</b></center></head>"
print "<body style='background-color:Moccasin;''>"
print "<p> A simple Exposure Time Calculator for Euclid ... | sniemi/EuclidVisibleInstrument | ETC/web/cgi-bin/pages.py | Python | bsd-2-clause | 3,027 | [
"Galaxy"
] | 5af809de146a24cb1869b5b68d9c9b17be5d0b0eee9d21852a972cec7770c871 |
"""Utility funcitons"""
import traceback
import time
import os
import numpy as np
from itertools import chain, combinations
def powerset(iterable):
"powerset([1,2,3]) --> () (1,) (2,) (3,) (1,2) (1,3) (2,3) (1,2,3)"
s = list(iterable)
return chain.from_iterable(combinations(s, r) for r in range(len(s)+1))... | brian-team/brian2cuda | brian2cuda/tools/test_suite/utils.py | Python | gpl-2.0 | 11,473 | [
"NEURON"
] | 66269385fb8244ce8c86ff982e2b603d02584e39388ca94254b30d83eeac8e8c |
from django.conf.urls import url
from crystal_dashboard.dashboards.crystal.zones.views import IndexView
from crystal_dashboard.dashboards.crystal.zones import views
urlpatterns = [
url(r'^$', IndexView.as_view(), name='index'),
url(r'^create/', views.CreateZone.as_view(), name='create'),
url(r'^update/(?P... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/zones/urls.py | Python | gpl-3.0 | 386 | [
"CRYSTAL"
] | 91b89272a2f98416fb4539bc90c2e785acc4b9ca756cb9238f2d54b4a06ef349 |
###########################################################################################
# $HeadURL$
###########################################################################################
"""Collection of DIRAC useful list related modules.
By default on Error they return None.
"""
__RCSID__ = "$Id$"
from t... | avedaee/DIRAC | Core/Utilities/List.py | Python | gpl-3.0 | 3,869 | [
"DIRAC"
] | ceada03ecd3a32e2e2a662b856bb15c3fdef129264aedf3e3e464fb68789f0f3 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.2
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | hryamzik/ansible | lib/ansible/modules/network/avi/avi_controllerproperties.py | Python | gpl-3.0 | 16,485 | [
"VisIt"
] | a1795d2b295cd94e8f5c3169e32247e3361418a207759e2c7f50d7eb9226acbc |
# 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.
"""Biopython interface for sequence search program outputs.
The SearchIO submodule provid... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/SearchIO/__init__.py | Python | gpl-2.0 | 29,001 | [
"BLAST",
"Biopython"
] | 513cbcc6b2986e5f32b3d35f9ab310da40bbe8ba0e82182331c8bababe4bc72a |
try:
import Tkinter as tk
from Tkinter import *
except:
import tkinter as tk
from tkinter import *
from math import atan2
from copy import deepcopy
import pygame
import time
pygame.init()
DIRECTIONS = [(1, 0), (1, 1), (0, 1), (-1, 1), # straight lines
(-1, 0), (-1, -1), (0, -1), (1, -1... | Orangeplumber/Chess-AI | chess_game.py | Python | mit | 14,583 | [
"FLEUR"
] | ee37bf92f103df574bdbd887cbcab821e4f257ad6c6448722cddb4e5c23f1fcb |
from module_base import ModuleBase
from module_mixins import IntrospectModuleMixin
import module_utils
import operator
HTML_START = '<html><body>'
HTML_END = '</body></html>'
def render_actions(lines):
ms = '<p><b><ul>%s</ul></b></p>'
# this should yield: <li>thing 1\n<li>thing 2\n<li>thing 3 etc
bullets ... | nagyistoce/devide | modules/viewers/QuickInfo.py | Python | bsd-3-clause | 8,108 | [
"VTK"
] | 946bfe593bc81025376d89f0379d1d3ea41e2278e44022c563cf61956d0a8006 |
import unittest, time, sys
sys.path.extend(['.','..','py'])
import h2o, h2o_cmd, h2o_hosts, h2o_import as h2i, h2o_print as h2p, h2o_glm
# Test of glm comparing result against R-implementation
# Tested on prostate.csv short (< 1M) and long (multiple chunks)
# kbn. just updated the parseFile and runGLMonly to match the... | janezhango/BigDataMachineLearning | py/testdir_multi_jvm/test_GLM2.py | Python | apache-2.0 | 5,955 | [
"Gaussian"
] | d8e2c533d967dcded769bfae3f436939ed482892c07ebb8fe08f5c863859aef3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Run on configured Raspberry Pi to test DoseNet server.
Have an Injector instance test-listening on TCP port 5101 (TESTING_TCP_PORT)
at dosenet.dhcp.lbl.gov
Authors:
Brian Plimley
Affiliation:
DoseNet
Applied Nuclear Physics Division
Lawrence Berkeley ... | tybtab/dosenet-raspberrypi | server_test.py | Python | mit | 3,914 | [
"Brian"
] | 26d8738c9a88c9510e5d0a9661ebbadbdb52f27addce8801fefae9f5e7fb3114 |
# Copyright 2007-2012 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... | pburdet/hyperspy | hyperspy/tests/model/test_set_parameter_state.py | Python | gpl-3.0 | 4,342 | [
"Gaussian"
] | 246b0f3c1c4d69bf94135d5042d711499c134e6fa6b56ff9e565d600a322109e |
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