text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
import argparse
import numpy as np
from datetime import datetime
import sklearn.gaussian_process as gp
import matplotlib.pyplot as plot
import parser as gcparser
import os
import os.path
import running
def main(indir, outdir):
"""
Main driver method.
"""
# Generate a list of all the files.
listing ... | magsol/garmin | gp.py | Python | mit | 3,648 | [
"Gaussian"
] | 93fc88e11f23e3fd3d181a407bf98196987a67aac37ef4d3f7b7252dbd1f4439 |
import sugartensor as tf
__author__ = 'namju.kim@kakaobrain.com'
# set log level to debug
tf.sg_verbosity(10)
#
# hyper parameters
#
batch_size = 32 # batch size
num_dim = 50 # latent dimension
#
# inputs
#
# MNIST input tensor ( with QueueRunner )
data = tf.sg_data.Mnist(batch_size=32)
# input images
... | buriburisuri/sugartensor | sugartensor/example/mnist_vae.py | Python | mit | 1,452 | [
"Gaussian"
] | ba37f6de33b52faa962d6c161edfcb290484597d0873f71a96ac2c6cc06c5e91 |
# Copyright 2016 James Hensman
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, so... | jameshensman/VFF | experiments/mcmc_pines/plot_pines.py | Python | apache-2.0 | 2,449 | [
"Gaussian"
] | 3c09735a3438cb7246beeebc75c3d238cbea7e14fddcc17f9b2a93acb67fa22e |
import os
import parabem
import numpy
class CaseToVTK():
def __init__(self, case, _dir, suffix=None):
"""automatic export of a case"""
self.case = case
self.make_sure_path_exists(_dir)
self._dir = _dir
self.suffix = ""
if suffix:
self.suffix = "_" + suff... | looooo/panel-method | parabem/vtk_export/__init__.py | Python | gpl-3.0 | 9,746 | [
"VTK"
] | 2275c0a3c90e37ecb244f60f728d397452e2b93b37e9a01c18c95e23c716ea7b |
from math import pi
import numpy as np
from ase.atoms import Atoms
def make_test_dft_calculation():
a = b = 2.0
c = 6.0
atoms = Atoms(positions=[(0, 0, c / 2)],
symbols='H',
pbc=(1, 1, 0),
cell=(a, b, c),
calculator=TestCalculator()... | slabanja/ase | ase/calculators/test.py | Python | gpl-2.0 | 4,190 | [
"ASE"
] | 0784632f64b657d175ff1cdc6e2135613abdf5aa5529cb4f11a8eb0e043e48b6 |
"""Collection of :class:`~chainer.Function` implementations."""
from chainer.functions.activation import clipped_relu
from chainer.functions.activation import elu
from chainer.functions.activation import leaky_relu
from chainer.functions.activation import log_softmax
from chainer.functions.activation import lstm
from ... | cemoody/chainer | chainer/functions/__init__.py | Python | mit | 8,284 | [
"Gaussian"
] | d2fca82b8a45673d8d23335be4fe6e2ebb3b0212edb968e1adbc314914ebfdd0 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""This is a demonstration of a small domain-specific language for building
strings up out of other strings.
You can define variables that are equal to literal strings or built up out of
other variables.
Evaluating a program will return a dictionary of all the variables ... | codeyash/plugins | PyPlugins/PhpParser/py/string_expression_language.py | Python | apache-2.0 | 4,427 | [
"VisIt"
] | 33a22bfd4de3b17bed14536e5a14194ed95457e8357abd5ae206d62e9c47668f |
"""Metrics to assess performance on classification task given class prediction.
Functions named as ``*_score`` return a scalar value to maximize: the higher
the better.
Function named as ``*_error`` or ``*_loss`` return a scalar value to minimize:
the lower the better.
"""
# Authors: Alexandre Gramfort <alexandre.gr... | anntzer/scikit-learn | sklearn/metrics/_classification.py | Python | bsd-3-clause | 97,201 | [
"Brian"
] | 0c6248cd4e072eeaea7a933ee870985f89f1d407967760792e313f38b5da6538 |
from mumax2 import *
# Standard Problem 4
# define geometry
# number of cells
Nx = 32
Ny = 32
Nz = 32
setgridsize(Nx, Ny, Nz)
# physical size in meters
sizeX = 160e-9
sizeY = 160e-9
sizeZ = 160e-9
setcellsize(sizeX/Nx, sizeY/Ny, sizeZ/Nz)
# load modules
load('exchange6')
load('demag')
load('zeeman')
load('llg')
... | mumax/2 | tests/exch-bench.py | Python | gpl-3.0 | 1,501 | [
"VTK"
] | 491642f12e1b08d3f7cbd3085cb37bdc08e5f0ffbe615c18c79d1af3b9396ea7 |
import random
from bot import Command, utils, categories
url_settings = {
'cat': ['http://aws.random.cat/meow', ['gato', 'gatito', 'neko'], 'file'],
'dog': ['https://dog.ceo/api/breeds/image/random', ['perro', 'perrito', 'doggo'], 'message'],
'shiba': ['http://shibe.online/api/shibes', ['shibe', 'shibainu... | jvicu2001/alexis-bot | modules/animals.py | Python | mit | 2,408 | [
"MOE"
] | 0fb0a4166779abcf09115e259199474abd5dcc5e36ea0ba76d8fd454b4ce7c77 |
"""
VolumeVisualizationRamp
:Authors:
Berend Klein Haneveld
"""
from VolumeVisualization import VolumeVisualization
from VolumeVisualization import VisualizationTypeRamp
from vtk import vtkVolumeProperty
from vtk import vtkColorTransferFunction
from vtk import vtkPiecewiseFunction
from PySide.QtGui import QWidget
fro... | berendkleinhaneveld/Registrationshop | ui/visualizations/VolumeVisualizationRamp.py | Python | mit | 2,500 | [
"VTK"
] | 544c81bd10e39fee3c44e9bb6e6e2b06da1e0ef31ec92304037e1659eb6e43d3 |
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from .core import UnitedStates
# FIXME: According to wikipedia, Kansas only has all federal holidays, except
# the Columbus Day and Washington's Birthday.
# Unfortunately, other sources... | sayoun/workalendar | workalendar/usa/kansas.py | Python | mit | 882 | [
"COLUMBUS"
] | ddbc456cafd778b8a37f79bf8d72084caf835b1f322f5675573946f0617daf74 |
# Prepare a cut-down version of the World Ocean Atlas 2018 salinity
# data to use with the AddSalinityPreprocessor.
# Input files are 0.25° seasonal files for the years 2005-2017,
# available from https://www.nodc.noaa.gov/cgi-bin/OC5/woa18/woa18.pl
# Files are:
#
# woa18_A5B7_s13_04.nc - Winter (DJF) = Season 1
# wo... | BjerknesClimateDataCentre/QuinCe | external_scripts/NRT/salinity_data/prepare_salinity.py | Python | gpl-3.0 | 2,813 | [
"NetCDF"
] | 5135effb96c9ff74bcf8d6c448fea2f303af7ed05cc613542a8f2668f880f2a3 |
from __future__ import print_function
import os
import sys
import numpy as np
from distutils.core import setup, Extension, setup_keywords
from distutils.sysconfig import get_config_var
sys.path += [ "." ]
from config import get_system_config
data_files = []
# data files & folders (folders nest only two levels down... | pekkosk/hotbit | setup.py | Python | gpl-2.0 | 3,232 | [
"ASE"
] | c49b1bbd15cc02d242fe13e368a0cc5d1302c673c646ad5b3cded0078d824b14 |
# Lint as: python2, python3
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
... | davidzchen/tensorflow | tensorflow/tools/compatibility/tf_upgrade_v2_test.py | Python | apache-2.0 | 101,974 | [
"Gaussian"
] | 989eb0d149db9847a0395b0ba9a03041d42693061d66ed31cc2d171e7876cc06 |
# -*- coding: utf-8 -*-
import os
import tempfile
import types
import json
from mock import patch
from nose.tools import eq_
from helper import TestCase
import appvalidator.constants
from appvalidator.errorbundle import ErrorBundle
from appvalidator.specs.webapps import WebappSpec
import appvalidator.webapp
class T... | mozilla/app-validator | tests/test_webapp.py | Python | bsd-3-clause | 55,619 | [
"exciting"
] | 7d2070c4d405e7a6766aef617491988fe6f5dad5661939f00a5e958a53924910 |
# Copyright (C) 2010, Jesper Friis
# (see accompanying license files for details).
"""Definition of the Spacegroup class.
This module only depends on NumPy and the space group database.
"""
import os
import warnings
import numpy as np
__all__ = ['Spacegroup']
class SpacegroupError(Exception):
"""Base excepti... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/lattice/spacegroup/spacegroup.py | Python | gpl-2.0 | 25,861 | [
"ASE",
"CRYSTAL"
] | 68dc83fa27ab74c42aa105cc22f572d655ee798a924632bf2f0738f2f49ea0ba |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse, sys, fnmatch, os, dma_resolver, shlex, pickle, re
import shutil
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help='Output directory')
parser.add_argument(
'--bootloade... | night-ghost/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 49,714 | [
"CRYSTAL"
] | 3a76977591b8cafbd8e732d0fded15d62a23dae460295c39fa7fe3b767e5e2c6 |
##############################################################################
# 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... | krafczyk/spack | var/spack/repos/builtin/packages/r-mzid/package.py | Python | lgpl-2.1 | 2,214 | [
"Bioconductor"
] | f8025f3c36e34a63817c8182d3ac06ed3c464a24c5087f9dad9c4638a3c032e0 |
#!/usr/bin/env python
# Family size distribution of tags which were aligned to the reference genome
#
# Author: Monika Heinzl & Gundula Povysil, Johannes-Kepler University Linz (Austria)
# Contact: monika.heinzl@edumail.at
#
# Takes at least one TABULAR file with tags before the alignment to the SSCS,
# a BAM file wit... | natefoo/tools-iuc | tools/fsd/fsd_regions.py | Python | mit | 12,083 | [
"pysam"
] | 2e8677f8adbc78dc9e33e82cb911926c30f0b74fd2b429110abde99938ce5a9d |
# Authors : Denis A. Engemann <denis.engemann@gmail.com>
# Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License : BSD-3-Clause
from copy import deepcopy
import numpy as np
from ..io.pick import _pick_data_channels, pick_info
from ..utils import verbose, warn, fill_doc, _validate_type
from ..paralle... | wmvanvliet/mne-python | mne/time_frequency/_stockwell.py | Python | bsd-3-clause | 9,627 | [
"Gaussian"
] | 4e88170cf41662924346ba324832cff4a4a0ea3533d6dfdbece22c8548328fc9 |
#!/usr/bin/env pythonfx
#
# This file is part of FIREwork
#
# FIREwork 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.
#
# FIREwork is... | hksonngan/astir.firework | utils/filter.py | Python | gpl-3.0 | 13,249 | [
"Gaussian"
] | 1ab2cd640096c7e8bb44d607b5024a31bb8f436a807549f39d46dbee1e3a924f |
#!/usr/bin/env python2
import os.path
import subprocess
import sys
import urllib
KEY_FILE = "submit.token"
def main(filename):
# Prompt for key if missing
if not os.path.exists(KEY_FILE):
print "Please visit http://css.csail.mit.edu/6.858/2015/labs/handin.html"
print "and enter your API key."
... | rychipman/858-labs | submit.py | Python | mit | 1,317 | [
"VisIt"
] | 0018111be1e24044bffe32e80ec751d41128c8e77ad5488fcdb8847ea3541680 |
#!/usr/bin/env python
# test --create
command += oiiotool ("--create 320x240 3 -d uint8 -o black.tif")
command += oiiotool ("--stats black.tif")
# test --pattern constant
command += oiiotool ("--pattern constant:color=.1,.2,.3,1 320x240 4 -o constant.tif")
command += oiiotool ("--stats constant.tif")
# test --patte... | OpenImageIO/oiio | testsuite/oiiotool-pattern/run.py | Python | bsd-3-clause | 3,464 | [
"Gaussian"
] | 925daec2b1d2cc6d6865efde7bae479518f8453fbf998ca9db15ce98a0974c32 |
# coding: utf-8
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause License.
R"""Simulate rounded, faceted shapes in molecular dynamics.
The DEM component provides forces which apply short-range, purely
repulsive interacti... | joaander/hoomd-blue | hoomd/dem/__init__.py | Python | bsd-3-clause | 2,758 | [
"HOOMD-blue"
] | 5ad9b68e90c3b78546c96e3bb55613b5ad453974d162c68a75f9e52b2f71b16b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# infile_maker.py
#
# Copyright 2016 Carlos Eduardo Sequeiros Borja <casebor@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation;... | casebor/labioscripts | python/infile_maker.py | Python | gpl-3.0 | 12,974 | [
"Amber"
] | 8875e2ad3b1e15abeb7633bfd510ce78a07b552e0b0d917eab5d2cec5892fcf4 |
import unittest
import numpy as np
import pysal
from pysal.spreg.twosls import TSLS, BaseTSLS
from scipy import sparse as SP
class TestBaseTSLS(unittest.TestCase):
def setUp(self):
db = pysal.open(pysal.examples.get_path("columbus.dbf"),'r')
self.y = np.array(db.by_col("CRIME"))
self.y = n... | spreg-git/pysal | pysal/spreg/tests/test_twosls_sparse.py | Python | bsd-3-clause | 14,544 | [
"COLUMBUS"
] | bf472607afd7bd65e0c0bc91c3f1d7c4f1cd7665c49c5de5c6088dfe7afb0991 |
#!/usr/bin/env python
"""Catalysis Micro-kinetic Analysis Package (CatMAP)"""
import os
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
from catmap import __version__ as version
maintainer = 'Andrew J. Medford'
maintainer_email = 'ajmedfor@slac.stanford.edu'
author = mai... | chuanshi/catmap | setup.py | Python | gpl-3.0 | 2,231 | [
"ASE"
] | ef4ef5159c351add65821baa9adbb6837d203848da3f907ccbac5c136154b554 |
"""
atsp.py: solve the asymmetric traveling salesman problem
formulations implemented:
- mtz -- Miller-Tucker-Zemlin's potential formulation
- mtz_strong -- Miller-Tucker-Zemlin's potential formulation with stronger constraint
- scf -- single-commodity flow formulation
- mcf -- multi-commodity flow fo... | mattmilten/PySCIPOpt | examples/finished/atsp.py | Python | mit | 8,748 | [
"VisIt"
] | 8d0cc889cfdcaead83151a36a3c325ee8ae601e8a24cff751e20f206903a2918 |
# Copyright 2013 by Leighton Pritchard. 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.
"""
This module provides code to work with data from the KEGG database.
References:
Kan... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/KEGG/KGML/__init__.py | Python | gpl-2.0 | 468 | [
"Biopython"
] | 681ddaeec7cad6b94204316a0ae6a01a763bb2887fc3d1ac45ec205a28843633 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/bibles/lib/versereferencelist.py | Python | gpl-2.0 | 5,402 | [
"Brian"
] | 8eb6c7194d03198067b0d1eeaf0e591aa65547dcbf750f811dcb453fe85d7af2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
background:
- Pictures exported from iPhoto do not have their original date in the finder.
- This info is hidden in exif
- this has to do with the daily photo app on iOS
This script
- loops over images in a folder (exported from iPhoto)
- extracts date-time-stamp fro... | clausTue/stamp_daily_images | process_iPhone_exports.py | Python | gpl-2.0 | 4,124 | [
"Mayavi"
] | 9603ad2d12801545e3c79bec0b1097122dfed20afc9f97b77585ddbb0de1f553 |
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Ralph Hempel <rhempel@hempeldesigngroup.com>
# Copyright (c) 2015 Anton Vanhoucke <antonvh@gmail.com>
# Copyright (c) 2015 Denis Demidov <dennis.demidov@gmail.com>
# Copyright (c) 2015 Eric Pascual <eric@pobot.org>
#
# ... | dwalton76/ev3dev-lang-python | ev3dev2/led.py | Python | mit | 20,477 | [
"Amber"
] | e80ffc1dc9f956c6d923ef7d234d14c8831ad4187398ced87b159f0da128ba34 |
"""
Fit redshifts and classifications on DESI bricks
"""
import sys
import os
import numpy as np
import multiprocessing
import traceback
from desispec import io
from desispec.interpolation import resample_flux
from desispec.log import get_logger, WARNING
from desispec.zfind.redmonster import RedMonsterZfind
from des... | timahutchinson/desispec | py/desispec/scripts/zfind.py | Python | bsd-3-clause | 14,535 | [
"Galaxy"
] | 6f031aa1b389662e731fcac7f6e1e3f9d23342447f264578f578f21e061fbfbc |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""This module defines an interface to CASTEP for
use by the ASE (Webpage: http://wiki.fysik.dtu.dk/ase)
Authors:
Max Hoffmann, max.hoffmann@ch.tum.de
Jörg Meyer, joerg.meyer@ch.tum.de
"""
__all__ = [
'Castep',
'CastepCell',
'CastepParam',
'create_... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/calculators/castep.py | Python | gpl-2.0 | 76,859 | [
"ASE",
"CASTEP"
] | 73270e3d993fc5e618acceb640202e4cedca9defc9233ac1a99fc62fe2c9cfb9 |
"""Migration script to add status and error_message columns to the tool_shed_repository table."""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
import datetime
now = datetime.datetime.utcnow
# Need our custom types, but don't import anything else from mode... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py | Python | gpl-3.0 | 2,843 | [
"Galaxy"
] | 29da31a94acc0aa91f95545495e86de7417a2b42ed652f70d77826ef91954801 |
##############################################################################
# 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... | krafczyk/spack | var/spack/repos/builtin/packages/r-iranges/package.py | Python | lgpl-2.1 | 2,378 | [
"Bioconductor"
] | 7afea282c4717802d0cf183a36ee64417b8f2e59460f1d0b2e937fde72e03f84 |
# 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.
"""Some Bio.PDB-specific exceptions."""
# General error
class PDBException(Exception):
... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/PDB/PDBExceptions.py | Python | gpl-2.0 | 513 | [
"Biopython"
] | 30ea8fed8beafe36eb21d7b7cb649683864ef99f880a9ad3727717f27495dde1 |
# -*- coding: utf-8 -*-
import sys
reload(sys)
sys.setdefaultencoding('utf-8')
from BrowserFactory import BrowserFactory
if __name__ == '__main__':
# 1 new factory object
factory = BrowserFactory()
# 2 create object
browser = factory.create('BrowserUrllib2')
# browser = factory.create('BrowserP... | xtuyaowu/jtyd_python_spider | browser_interface/browser/demo.py | Python | mit | 510 | [
"VisIt"
] | d86731234255bf37473cdc89087409164657e3fef6dd1b21eab51ddcda3561c8 |
# proxy module
from __future__ import absolute_import
from mayavi.modules.text3d import *
| enthought/etsproxy | enthought/mayavi/modules/text3d.py | Python | bsd-3-clause | 90 | [
"Mayavi"
] | 34a7f41e76d3d4ccbc3fa37b2712087e86281dae1edc2d46a3de102db3a22ee4 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 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 Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_purchase_wizard.py | Python | gpl-2.0 | 7,958 | [
"VisIt"
] | 3739cd7b718c4ac78f91fd652b9cfdb5fb74392cdc2f88001e3d38500e102b96 |
import gflags
import httplib2
import re, sys, datetime
days = ["Mon", "Tue","Wed","Thu","Fri"]
## GCAL SETUP ##
from apiclient.discovery import build
from oauth2client.file import Storage
from oauth2client.client import OAuth2WebServerFlow
from oauth2client.tools import run
from dateutil.relativedelta import relativ... | FloatingGhost/GCalTimetable | Scanner.py | Python | gpl-2.0 | 5,203 | [
"VisIt"
] | b4f635c6fc6ebfcdfbdae7692f7d96987c7d7505e6cf67e5118cdcdc31fc5d7a |
class Neuron:
outSynapse = list()
| Nakou/MARVIN | neuronal/Neuron.py | Python | mit | 43 | [
"NEURON"
] | ec67291c131593d15f911259969b98162021616cba636543904c57a985bed852 |
import os
import os.path
import sys
sys.path.insert(0, os.path.abspath('lib'))
from ansible.release import __version__, __author__
try:
from setuptools import setup, find_packages
except ImportError:
print("Ansible now needs setuptools in order to build. Install it using"
" your package manager (usua... | tux-00/ansible | setup.py | Python | gpl-3.0 | 3,659 | [
"Galaxy"
] | c5651fc3d5a9a8eb5d7a430e04f88c8d61b479411f6378534bffa5de2289df60 |
"""
Description:
Provides a pyGtk vtkRenderWindowInteractor widget. This embeds a
vtkRenderWindow inside a GTK widget and uses the
vtkGenericRenderWindowInteractor for the event handling. This is
based on vtkTkRenderWindow.py.
The class uses the gtkgl.GtkGLArea widget (gtkglarea). This avoids
... | timkrentz/SunTracker | IMU/VTK-6.2.0/Wrapping/Python/vtk/gtk/GtkVTKRenderWindowInteractor.py | Python | mit | 10,171 | [
"VTK"
] | d75b508588bf8460f82582c8e69b05ed1fb5c9e30f50b2ff459b88692d161e53 |
"""A module that contains a base class that has helper methods for testing PyT."""
import unittest
from pyt.cfg import make_cfg
from pyt.core.ast_helper import generate_ast
from pyt.core.module_definitions import project_definitions
from pyt.core.transformer import PytTransformer
class BaseTestCase(unittest.TestCase... | python-security/pyt | tests/base_test_case.py | Python | gpl-2.0 | 1,226 | [
"VisIt"
] | e99870b74e5e627a2189777e3a7d6a1691842f8e73ec924d0be986df2a84f5cc |
# -*- coding: utf-8 -*-
"""
@file bible/api.py
@author Brian Kim
@brief the definition of routes for the api
"""
from flask import Blueprint, request, abort
import controller, methods, model
from util import *
import traceback as tb
api = Blueprint('api',__name__)
parse_dispatch = {
'lang' : controller.p... | briansan/bible | bible/api.py | Python | bsd-2-clause | 4,238 | [
"Brian"
] | 0936bbf8da571de22b7f47310602cb120ead47b33ead77a76569c11eed2b5bba |
import numpy as np
import ctypes as ct
import ast
from ctree.jit import LazySpecializedFunction, ConcreteSpecializedFunction
from ctree.transformations import PyBasicConversions
from ctree.transforms.declaration_filler import DeclarationFiller
from ctree.c.nodes import CFile
import ctree.c.nodes as C
from ctree.nodes ... | ucb-sejits/ctree | examples/hwacha.py | Python | bsd-2-clause | 13,736 | [
"VisIt"
] | d35b82e4cdf80764171dad80a699fb435ec1b1f28ec94e32c93429fc400545eb |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'castep'
tab.settings['Output file name'] = 'phonon.castep'
#
# SettingsTab
#
tab = self.notebook.settingsTab
tab.settings['Eckart flag'] = False
tab.settings['Neutral Born charges'] = False
tab.settings['Sigma value'] = 10
tab.settings['Mass definitio... | JohnKendrick/PDielec | Examples/Castep/MgO/script.py | Python | mit | 2,364 | [
"CASTEP"
] | 57947a1a5d9381f0f8d2e1e2815b3fc83fc28e99c02a609b28c21571238f100d |
from Sire.Tools import Nautilus
from Sire.Tools import readParams
import Sire.Config
import argparse
import os
import sys
parser = argparse.ArgumentParser(description="Subgrids, subtracts grids in dx format to get differences where gridf.dx-"
"gridl.dx=diff.dx. Grids mus... | michellab/Sire | wrapper/python/scripts/nautilus-subgrids.py | Python | gpl-2.0 | 3,048 | [
"MDTraj",
"VisIt"
] | 89d9bf770dde947aaf1b14cc8f9be13f0e91b410224ee13ad6556abd935f5084 |
from director import objectmodel as om
from director import visualization as vis
from director import vtkAll as vtk
from director import transformUtils
from director import filterUtils
from director.timercallback import TimerCallback
class AffordanceGraspUpdater(object):
def __init__(self, robotModel, ikPlanner, ... | patmarion/director | src/python/director/affordanceupdater.py | Python | bsd-3-clause | 7,248 | [
"VTK"
] | 95959fb18370be93b9d9908ce73f8508d49b33ad9eb5decf4e89d94394aa45b1 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# read data
#
reader = vtk.vtkStr... | ashray/VTK-EVM | Filters/Geometry/Testing/Python/officeStreamPoints.py | Python | bsd-3-clause | 10,816 | [
"VTK"
] | a29fb65c7e070c46dfd8a722c86a0cfc9f165ab0e3f3f312a55bf69becfc1c61 |
import pybel
from datanator_query_python.util import mongo_util
import pymongo
import numpy as np
import multiprocessing as mp
import datanator.config.core
from datanator.util import chem_util
class CalcTanimoto(mongo_util.MongoUtil):
'''Calculating the Tanimoto similarity matrix
given two compound co... | KarrLab/kinetic_datanator | datanator/util/calc_tanimoto.py | Python | mit | 9,777 | [
"Pybel"
] | 9b31c3a5d86538b79eafd6fc1edec61eadc46b04e2f9a8d7e9d46bcf38e923bc |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageEuclideanDistance(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkImageEuclideanDistance.py | Python | bsd-3-clause | 507 | [
"VTK"
] | b8c70f2a9a0ae9d20c605f5f92537c030cec40a4565ccd92482102e8c6b38575 |
# -*- coding: utf-8 -*-
# Copyright 2012 Jerry Peng
#
# Tomate is a time management tool inspired by the
# pomodoro technique(http://www.pomodorotechnique.com/).
#
# Tomate 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... | moonranger/tomate | tomate/timequotes.py | Python | gpl-3.0 | 7,739 | [
"Brian"
] | e170e08e63a02a94d9699b18d959ed0517cd52c8a91012d99e05a45735f83711 |
#!/usr/bin/env python
"""
An animated image
"""
from __future__ import (absolute_import, division, print_function)
import netCDF4 as nc4
import numpy as np
import pysgrid
from datetime import timedelta
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.animation import FFMpegWri... | NOAA-ORR-ERD/pysgrid | demos/matlabanim.py | Python | bsd-3-clause | 7,903 | [
"NetCDF"
] | e82e65ec067b287f33ad759d79af1d5bdd69ae422054629661c41cc6cdea969a |
#===============================================================================
# LICENSE XOT-Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported Lic... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/net.rieter.xot.smallplayer/resources/libs/settings.py | Python | gpl-2.0 | 4,602 | [
"VisIt"
] | df7cf8b18fa6d7223929e8f4529d86f8064d6db59c9d593029e1a0d98688a9ce |
"""
:mod: Pfn
.. module: Pfn
:synopsis: pfn URI (un)parsing
.. moduleauthor:: Krzysztof.Ciba@NOSPAMgmail.com
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
# # imports
import os
from urllib import parse
# # from DIRAC
from DIRAC... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/Pfn.py | Python | gpl-3.0 | 7,782 | [
"DIRAC"
] | cfb7d31058a385e14b30ebadaea79d740e12fa78b4f1b17dcd017785e32640b8 |
# $HeadURL$
__RCSID__ = "$Id$"
from DIRAC.FrameworkSystem.Client.Logger import Logger
class SubSystemLogger( Logger ):
def __init__( self, subName, masterLogger, child = True ):
Logger.__init__( self )
self.__child = child
self._minLevel = masterLogger._minLevel
for attrName in dir( masterLogger ):... | Andrew-McNab-UK/DIRAC | FrameworkSystem/private/logging/SubSystemLogger.py | Python | gpl-3.0 | 872 | [
"DIRAC"
] | 51a2a2dbd5b9a9f392b519b5645e3673e9a0ce280d7248a6a249f5ba18806dd3 |
#%% DEMO 03: Generate sample data and add realistic CT noise to it.
#
# This demo will show how to generate sample data for image reconstruction
#
#
# --------------------------------------------------------------------------
# --------------------------------------------------------------------------
# This file is pa... | CERN/TIGRE | Python/demos/d03_generateData.py | Python | bsd-3-clause | 2,012 | [
"Gaussian"
] | be23e811720fbc937937cea7179de54749bd09033d7f923af614a3ee9317fab0 |
#
# Copyright (c) Brian C. Welch. www.brianwelch.se
# All rights reserved.
# Licensed under the MIT License.
# Persons are free to reproduce this code provided
# they do not removed this header
# + + + + + + + + + + + + + + + +
def binary_calc(digit_in):
'''converting an integer into a binary'''
binary_di... | brian-welch/Code-Snippets | binary_number_convertor.py | Python | mit | 739 | [
"Brian"
] | cb73206dfce5a18d9789c9c65ca77d0f96157d9487c58d1e4379a550a9a7c2cc |
from __future__ import absolute_import
import numpy as nm
import sfepy.discrete.fem.periodic as per
from sfepy.discrete.fem.mesh import Mesh
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
from sfepy.homogenization.utils import define_box_regions
import sfepy.homogenization.coefs_base as cb
from sfepy... | sfepy/sfepy | examples/homogenization/homogenization_opt.py | Python | bsd-3-clause | 5,071 | [
"VTK"
] | 48888d9e981a943b1db547c983150d377065bb08aa62a6aeb69d00075e6c9d29 |
#!/usr/bin/env python3
###########
#
# Created by Bruno Costa @ITQB
# 24/04/2017
# This allows the extraction of specific coordinates from a fasta file
#
############
import argparse
import re
parser = argparse.ArgumentParser(description='This allows the extraction of specific coordinates from a fasta file')
## bla... | netbofia/Fasta_extractor | splice_fasta.py | Python | mit | 2,195 | [
"BLAST"
] | cf54e41f06b8b3c89add9ca05b333b110fd279c457ec66e20c677e92bfed7739 |
""" codecs -- Python Codec Registry, API and helpers.
Written by Marc-Andre Lemburg (mal@lemburg.com).
(c) Copyright CNRI, All Rights Reserved. NO WARRANTY.
""" # "
import __builtin__, sys
# ## Registry and builtin stateless codec functions
try:
from _codecs import *
except ImportError, why:
raise Syste... | ppyordanov/HCI_4_Future_Cities | Server/src/virtualenv/Lib/codecs.py | Python | mit | 35,196 | [
"FEFF"
] | ef6c908e742337b8bfd224f397fafd2e11e929df6a7a8f9b68ace8f13525180c |
from ob_pipelines import s3
import pysam
import sys
@s3.s3args()
def dedupe_by_pos_strand(infile, outfile):
infile = pysam.AlignmentFile(infile, 'rb')
outfile = pysam.AlignmentFile(outfile, 'wb', template=infile)
pos_list = set()
for aln in infile:
pos_strand = (aln.reference_start, aln.... | outlierbio/ob-pipelines | ob_pipelines/apps/pysam/dedupe.py | Python | apache-2.0 | 721 | [
"pysam"
] | 5bbb87827a63c959f81537891006c64a342827a58ef7ab3a2b0f90a2b54e5d4f |
# 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.
"""Top-level presubmit script for Chromium.
See http://dev.chromium.org/developers/how-tos/depottools/presubmit-scripts
for more details about the presu... | loopCM/chromium | PRESUBMIT.py | Python | bsd-3-clause | 36,636 | [
"VisIt"
] | 153987a4065ddebfc8fb74d7b15359e199b3b8474e711a72eed12b4b61cc92cf |
##############################################################################
# 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... | tcmoore3/mdtraj | mdtraj/reporters/dcdreporter.py | Python | lgpl-2.1 | 2,912 | [
"Amber",
"CHARMM",
"MDTraj",
"NAMD",
"NetCDF",
"OpenMM"
] | 097e7ed8201c197fc5d191871690265790a0af1607488a2886a4493012dc0052 |
'''
An implementation of the Fully Adapted Auxiliary Particle Filter as described by Whiteley and Johansen
Chapter 3 Algorithm 2 on page 5 of Recent Developments in Auxiliary Particle Filtering:
http://www.maths.bris.ac.uk/~manpw/apf_chapter.pdf
The algorithm is taylored to perform inference in nonlinear dynamical sys... | amoretti86/auxiliary-particle-filter | apf_fhn.py | Python | mit | 6,209 | [
"Gaussian"
] | 9613590e4ccedc1cbe3ad7178fa98650834af7396725b04c4d62cc47fb5f053a |
import numpy as np
class QIFNetwork:
"""
Network of quadratic integrate-and-fire neurons.
"""
def __init__(self, _neuronsPerLayer, _Dmax):
"""
Initialise network with given number of neurons
Inputs:
_neuronsPerLayer -- List with the number of neurons in each layer. A list
... | pmediano/ComputationalNeurodynamics | Fall2015/Exercise_2/Solutions/QIFNetwork.py | Python | gpl-3.0 | 3,697 | [
"NEURON"
] | b75faa17f5106034f8f55d9cb4ae730ba49964229c0019514e123e68a5674d1f |
import gtk
import goocanvas
import cairo
LEFT = 50.0
RIGHT = 350.0
MIDDLE = 150.0
DEFAULT_WIDTH = 2
DEFAULT_SHAPE_A = 4
DEFAULT_SHAPE_B = 5
DEFAULT_SHAPE_C = 4
def set_dimension (canvas, arrow_name, text_name, x1, y1, x2, y2, tx, ty, dim):
points = goocanvas.Points([(x1, y1), (x2, y2)])
item = canvas.get... | GNOME/pygoocanvas | demo/simple_demo/arrowhead_demo.py | Python | lgpl-2.1 | 10,540 | [
"FLEUR"
] | e562335206283defbb48659cbf11fa06248d15f99a28060f4e3bb2300b1b3533 |
"""
# ==============================================================================
Plots data vs model response computed by an Inversion Method
# ==============================================================================
"""
import matplotlib.gridspec as gridspec
import matplotlib.pyplot as plt
import numpy as n... | MTgeophysics/mtpy | legacy/plot_response.py | Python | gpl-3.0 | 114,878 | [
"VTK"
] | e4e26504fb5b3c69bf2d6c76fc86102d10ab5e4ff80696edf8ba92d7d702324f |
from __future__ import division
import warnings
import os, sys
import numpy as np
import scipy.spatial
import scipy.weave
import scipy.stats.kde
import matplotlib.pyplot as pp
import bisect
# apparently scipy.weave is depricated. I really shouldn't have used it.
# the best thing would probably be to port entropy_nn()... | rampasek/seizure-prediction | features/entropy.py | Python | gpl-2.0 | 10,855 | [
"Gaussian"
] | 86e9a9f8405d4c86ba975e7ceeb20b149f43057af067150b30097cebbffabb66 |
# -*- coding: utf-8 -*-
"""
@author: nicholas
"""
import sys
import logging
import shutil
import os
import unittest
import time
from unittest.mock import Mock
from riboSeed.shared_methods import md5
from riboSeed.riboScore import getSnagCmd, getSelectCmd, getScanCmd, \
parseDirContents, make_nuc_nuc_recip_blas... | nickp60/riboSeed | tests/test_riboScore.py | Python | mit | 7,679 | [
"BLAST"
] | f680bc9f556fe4df9e8c0726b9153447d327b3ab06390806c3adf074bd814f62 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Denis Engemann <denis.engemann@gmail.com>
# Andrew Dykstra <andrew.r.dykstra@gmail.com>
# Teon Brooks <teon.brooks@gmail.c... | bloyl/mne-python | mne/channels/channels.py | Python | bsd-3-clause | 75,094 | [
"Mayavi"
] | 57201032fc8ad8c42ed0e5ccbad623ae42e8df19ab15b6c364d4eab27917d367 |
import unittest
import numpy as np
import pysal
from pysal.spreg.twosls import TSLS, BaseTSLS
from scipy import sparse as SP
from pysal.common import RTOL
class TestBaseTSLS(unittest.TestCase):
def setUp(self):
db = pysal.open(pysal.examples.get_path("columbus.dbf"),'r')
self.y = np.array(db.by_col... | ljwolf/pysal | pysal/spreg/tests/test_twosls_sparse.py | Python | bsd-3-clause | 14,413 | [
"COLUMBUS"
] | 927b164819dcb4fac349ae474fcbac16c05f96cf4736e4e939979de99a3a042b |
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
AUTHORS
The original version of this software, called LMFIT, was written in FORTRAN
as part of the MINPACK-1 package by XXX.
Craig Markwardt converted the FORTRAN code to IDL. The information for ... | shfengcj/pydm | pydm/mpfit/mpfit.py | Python | gpl-2.0 | 93,480 | [
"Gaussian"
] | c9e8e00197e35a0f1be5bf0b931f36c8b15fb4e41561fc0c37257dedfdc6154b |
# encoding: utf-8
"""
A base class for a configurable application.
Authors:
* Brian Granger
* Min RK
"""
from __future__ import print_function
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of th... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/IPython/config/application.py | Python | bsd-3-clause | 21,855 | [
"Brian"
] | 238213c07fbc5dd169c7bda8331dfa07389b9f908bbe3f0b1850ff69252b3beb |
#The DF of a tidal stream
import copy
import numpy
import multiprocessing
import scipy
from scipy import special, interpolate, integrate
if int(scipy.__version__.split('.')[1]) < 10: #pragma: no cover
from scipy.maxentropy import logsumexp
else:
from scipy.misc import logsumexp
from galpy.orbit import Orbit
fro... | followthesheep/galpy | galpy/df_src/streamdf.py | Python | bsd-3-clause | 117,381 | [
"Gaussian"
] | b420806e285f6c3cd071744aecf57f020d46e4cfb4703fb37ccc48867799f233 |
""" TokenAgent
This agent inspect all elements, and resets their tokens if necessary.
The following options can be set for the TokenAgent.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN TokenAgent
:end-before: ##END
:dedent: 2
:caption: TokenAgent options
"""
from __future__ import absolut... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Agent/TokenAgent.py | Python | gpl-3.0 | 6,701 | [
"DIRAC"
] | 5cc6fbd3f405a349f9e226a2c7cfaa625a7527d58de0e8830efdd0c7c68a1688 |
#process all record
#for each record find template for spike in each channel
#then compute signal to noise ratio (snr) for each cluster
import pickle
import signal_processing as sig_proc
import numpy as np
import copy
import matplotlib.pyplot as plt
dir_name = '../data/r415/'
img_ext = '.eps'
save_img = True
show = F... | scauglog/brain_record_toolbox | script_r415_snr_evo_with_new_pattern.py | Python | mit | 4,035 | [
"NEURON"
] | 4698af917abf929b963d64981f1a620b92a7d6618409f6df2deabb72391751fa |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | nuclear-wizard/moose | python/chigger/misc/AxisSource.py | Python | lgpl-2.1 | 1,445 | [
"MOOSE",
"VTK"
] | 9ed3d59fd3814c132ef500fbdee5c0dd805eca4a9992d7ed59762c040593d7a4 |
# physcon Physical constants
# Note: type physcon.help() (after import physcon)
from math import pi
# define light velocity, because we need it in calculations
cloc =299792458.
# dictionary of physical constants in SI units. Values CODATA 2010 http://www.physics.nist.gov/cuu/Constants/
# each item: [description (str... | trigfa/notebooks | physcon.py | Python | mit | 7,418 | [
"Avogadro",
"DIRAC"
] | e0396dac9ba317a20d8608ac492e17aa82406def8f2670a6a3d98e53846ac7d4 |
r"""
File I/O (:mod:`skbio.io`)
==========================
.. currentmodule:: skbio.io
This package provides I/O functionality for skbio.
Supported file formats
----------------------
For details on what objects are supported by each format,
see the associated documentation.
.. currentmodule:: skbio.io.format
.. au... | gregcaporaso/scikit-bio | skbio/io/__init__.py | Python | bsd-3-clause | 8,073 | [
"scikit-bio"
] | e42662bf8d04fab7bc1471a2247dc7afa0c88d5573b90ae349b4c64e82a68470 |
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
# $Id$
#
# Copyright (C) 2000-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, foun... | rdkit/rdkit-orig | rdkit/Chem/__init__.py | Python | bsd-3-clause | 3,165 | [
"RDKit"
] | cff4fa9d286b1ccec015d9fc4c3825c37358caceaed3b0aa29a07f8092a9a626 |
""" SiteStatus helper
Module that acts as a helper for knowing the status of a site.
It takes care of switching between the CS and the RSS.
The status is kept in the RSSCache object, which is a small wrapper on top of DictCache
"""
from __future__ import absolute_import
from __future__ import division
from __future__... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Client/SiteStatus.py | Python | gpl-3.0 | 10,057 | [
"DIRAC"
] | 2151be4728a1523d0bd19a7af800c6e2d00596071441ac8ac1577d14c586b701 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
reload(sys)
sys.setdefaultencoding('utf-8')
import os, csv
COV = None
if os.environ.get('FLASK_COVERAGE'):
import coverage
COV = coverage.coverage(branch=True, include='app/*')
COV.start()
if os.path.exists('.env'):
print('Importing environment ... | Spandex-at-Exeter/demography_database | manage.py | Python | mit | 43,949 | [
"Amber"
] | bec16371db65d2b4a3880d360d4117d0997987c743cda5b69ca320b408d01805 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | alejob/mdanalysis | package/MDAnalysis/analysis/encore/clustering/__init__.py | Python | gpl-2.0 | 1,294 | [
"MDAnalysis"
] | 1d40f140821af6774d09d500f59e664032048fb49643e3600dbb2bbdb37da0b4 |
# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Scientific Package. This package holds all simulators, and
# analysers necessary to run brain-simulations. You can use it stand alone or
# in conjunction with TheVirtualBrain-Framework Package. See content of the
# documentation-folder for more details. See also http://www... | stuart-knock/tvb-library | tvb/simulator/models/jansen_rit.py | Python | gpl-2.0 | 25,472 | [
"NEURON"
] | f5fd48ea59de2efedd3557e42082c64aded95bb1026fa1b4e3c95a2592978c9f |
#-*- coding: utf-8 -*-
'''
Created on 25 mars. 2014
Toolbox for downloading era_interim Parameters
depending to the code EMCWF a shapefile or an extend for the area,
the period needed and an optional outputFile for downloaded raster
@author: yoann Moreau
@author: benjamin tardy
'''
import sys
import getopt
impor... | yoannMoreau/gfsDownload | python/eraInterimDownload.py | Python | cc0-1.0 | 8,200 | [
"NetCDF"
] | 4ebc38cbade34b1d1fbaadb618f4ac16cbf4854b3270592b161a824c084fa13c |
from typing import Sequence, Union, Any
from collections import OrderedDict
from numpy import Inf, exp
import pandas as pd
from hbayesdm.base import TaskModel
from hbayesdm.preprocess_funcs import prl_preprocess_func
__all__ = ['prl_rp']
class PrlRp(TaskModel):
def __init__(self, **kwargs):
super().__i... | CCS-Lab/hBayesDM | Python/hbayesdm/models/_prl_rp.py | Python | gpl-3.0 | 9,952 | [
"NEURON"
] | 2e0382bc1b93a3fc2d0a8dac50a98276e4d2dfc4a915688e44f7d49774161f7f |
import os
import re
import sys
import six
import json
import shutil
from nose.tools import raises
from rabix.tests import mock_app_bad_repo, mock_app_good_repo, \
result_parallel_workflow, result_nested_workflow
from rabix.main import main
from rabix.docker import docker_client, get_image
__test__ = False
@rai... | lowks/rabix | rabix/tests/integration_test.py | Python | agpl-3.0 | 5,350 | [
"BWA"
] | 1e8605f04247b7c5980b671562179d8ed42f7602f937bc53c174faf2fc282a5f |
"""
DIRAC.DataManagementSystem.Client test package
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
| yujikato/DIRAC | src/DIRAC/DataManagementSystem/Client/test/__init__.py | Python | gpl-3.0 | 167 | [
"DIRAC"
] | 63585c9c2453881141f3fe3fae1b04931c057b01960633876057e93601fb18bb |
# The MIT License
#
# Copyright (c) 2008 James Piechota
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify... | redpawfx/massiveImporter | python/ns/evolve/Mutate.py | Python | mit | 15,629 | [
"Gaussian"
] | 42692675d67243dd4aa25dc6de4f77c802d083222288d4f11403ca9685a7a0ba |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/gto/ft_ao.py | Python | apache-2.0 | 7,194 | [
"PySCF"
] | e10789114becaa5311c01e49ae3019a16183b78a37e53ef0271cb2ead20981f4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides utility classes for string operations.
"""
import re
from fractions import Fraction
def str_delimited(results, header=None, delimiter="\t"):
"""
Given a tuple of tuples, genera... | fraricci/pymatgen | pymatgen/util/string.py | Python | mit | 11,931 | [
"pymatgen"
] | a39e56a4a14787fc819cdbb1baf2679606f5b15674fc1e7bd2ae29a251fa7025 |
"""
Unit tests for HDF5 parsing; runs tests in multiple libraries
"""
__author__ = 'Dallas R. Trinkle'
import unittest
import numpy as np
import h5py
import onsager.crystal as crystal
import onsager.PowerExpansion as PE
import onsager.GFcalc as GFcalc
import onsager.crystalStars as stars
import onsager.OnsagerCalc as... | DallasTrinkle/Onsager | test/test_HDF5.py | Python | mit | 11,073 | [
"CRYSTAL",
"VTK"
] | 3546b466d8480f7ad2fedb4368651d09e3fc16442f73ce972370b5ddcdac45bb |
# -*- coding: utf-8 -*-
"""A plugin to generate a list of domains visited."""
from urllib import parse as urlparse
from plaso.analysis import interface
from plaso.analysis import manager
class UniqueDomainsVisitedPlugin(interface.AnalysisPlugin):
"""A plugin to generate a list all domains visited.
This plugin ... | kiddinn/plaso | plaso/analysis/unique_domains_visited.py | Python | apache-2.0 | 1,934 | [
"VisIt"
] | 8877eb7e3738139e2d7eb943c21e7b010bb49b5eed2866a871474cc1d8686745 |
# -*- coding: utf-8 -*-
import fauxfactory
import pytest
import cfme.configure.access_control as ac
from cfme import test_requirements
from cfme.configure.access_control import Tenant
from cfme.fixtures import pytest_selenium as sel
from cfme.automate import explorer as automate
from cfme.provisioning import provision... | kzvyahin/cfme_tests | cfme/tests/infrastructure/test_infra_quota.py | Python | gpl-2.0 | 9,036 | [
"VisIt"
] | 958ff4452040f4e30e42ce0ef447db32822e44f462166e59e771eff3bae2adf6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import division, print_function
import numpy as np
import warnings
try:
import horton
except:
warnings.warn("Running without support for horton", RuntimeWarning)
import h5py
from .utilities import load_qmfiles, number2name, name2number, angstrom2bo... | peter-reinholdt/propertyfit | propertyfit/structures.py | Python | gpl-3.0 | 16,394 | [
"TeraChem"
] | 2ef82abf60e59a8ac5627cc5a4dac9f0b8bd418938f3f9e020cc42d69517d1cf |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
r'''
Applying creation or annihilation operators on FCI wavefunction
a |0>
Compute density matrices by
gamma_{ij} = <0| i^+ j |0>
Gamma_{ij,kl} = <0| i^+ j^+ l k |0>
'''
import numpy
from pyscf import gto, scf, fci
mol = ... | gkc1000/pyscf | examples/fci/31-apply_2nd_quantized_op.py | Python | apache-2.0 | 2,959 | [
"PySCF"
] | 879600639ce2e08ef0778d0797d27f86acfca088e973e895831c8a981327e2e3 |
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