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# -*- coding: utf-8 -*-
##############################################################################
#
# Copyright (C) 2012-2013 Daniel Reis
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Sof... | acsone/project | service_desk/__openerp__.py | Python | agpl-3.0 | 2,193 | [
"CRYSTAL"
] | 5fe48f1e00293d6c0fddb5fc478f5ae1107e091f9977701a912ac760d99ec78c |
#!/usr/bin/env python
"""
================================================
ABElectronics ServoPi 16-Channel PWM Servo Driver
Requires smbus2 or python smbus to be installed
================================================
"""
try:
from smbus2 import SMBus
except ImportError:
try:
from smbus import SMB... | abelectronicsuk/ABElectronics_Python_Libraries | ServoPi/ServoPi.py | Python | gpl-2.0 | 25,007 | [
"TINKER"
] | 2ff45d5b246d42a156f9640bd88d2704ec77201a1227d92adf47303ab0f484b8 |
from collections import defaultdict
import logging
import pickle
import json
from typing import Dict, List, Optional, Tuple, Any
from ray.tune import ExperimentAnalysis
from ray.tune.result import DEFAULT_METRIC
from ray.tune.sample import Domain, Float, Quantized
from ray.tune.suggest.suggestion import (
UNRESOLV... | ray-project/ray | python/ray/tune/suggest/bayesopt.py | Python | apache-2.0 | 15,763 | [
"Gaussian"
] | 112bdbed367184201bd29bae94e963e6f5998ae431f14ed3c793d95da07b8ef0 |
import numpy as np
from scipy.optimize import leastsq
import pylab as pl
def check_degenerate_bands(filename, etol):
from gpaw import GPAW
calc = GPAW(filename,txt=None)
print 'Number of Electrons :', calc.get_number_of_electrons()
nibzkpt = calc.get_ibz_k_points().shape[0]
nbands = calc.get_num... | robwarm/gpaw-symm | gpaw/response/tool.py | Python | gpl-3.0 | 5,300 | [
"GPAW"
] | 483f0b9451bcb323742e8d20c203b1a38b8fc0773dc87b2786219453198b410b |
import datetime
from nose.tools import (
assert_raises,
eq_,
set_trace,
)
from . import DatabaseTest
from bot import Bot
from model import (
InvalidPost,
Post,
_now,
)
class TestBot(DatabaseTest):
def test_publishable_posts(self):
bot = self._bot(config=dict(
state_... | leonardr/botfriend | botfriend/tests/test_bot.py | Python | mit | 6,911 | [
"Gaussian"
] | 4285e62606ea9a9e7caccb34f2f440a198af2c02e5227ffee10e1be56dbd4134 |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/dbShared.py | Python | gpl-3.0 | 21,346 | [
"Galaxy"
] | 9ee56ef003ffde8e87675c9fc4710a7ba370b2574e767664823a0fa4808c7886 |
# FIXME: should be rewritten as real unittest
# import DIRAC
# from DIRAC.Core.Utilities.CFG import CFG
#
# DIRAC.gLogger.initialize('test_gConfig','/testSectionDebug')
#
# testconfig = '%s/DIRAC/ConfigurationSystem/test/test.cfg' % DIRAC.rootPath
# dumpconfig = '%s/DIRAC/ConfigurationSystem/test/dump.cfg' % DIRAC.root... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/test/Test_gCFG.py | Python | gpl-3.0 | 1,827 | [
"DIRAC"
] | 99a8dbc0234725c0844a7181995c23eb6a5f7a6bf88c1345f15c279085025180 |
#!/usr/bin/python
# COMPONENT SCRIPT FOR ITERATIVE RESP CHARGE GENERATION (WRITE GAMESS INPUT FILE)
# Original script by Kyle Sutherland-Cash, modified by Chris Whittleston (csw34)
# CHECK: Make sure ~csw34/gamess/rungms exists on the machine you are running this on!
# If not - modify the line near the bottom o... | marktoakley/LamarckiAnt | SCRIPTS/AMBER/iterative_resp/write_gamess_input.py | Python | gpl-3.0 | 2,865 | [
"GAMESS"
] | 8017d5527568ebe27b179150cf60e701226172f6fa57716df9c0fd719a777440 |
# -*- coding: utf-8 -*-
import math
from .line import Line
from .point import Point
from .vector import Vector
def draw_parallels(renderer, box, start, count, direction, delta,
color=(0.7, 0.7, 0.7), opacity=0.5):
"""Draw count parallel lines, pointing in direction, starting at
start and cha... | Kingdread/sgl | sgl/draw.py | Python | gpl-3.0 | 4,550 | [
"VTK"
] | e4beafc8e9b972399139bd09786058bba1b56db8f5ca4bae0fae5502984b6d10 |
""" This module loads all the classes from the VTK GenericFiltering
library into its namespace. This is an optional module."""
from vtkGenericFilteringPython import *
| b3c/VTK-5.8 | Wrapping/Python/vtk/genericfiltering.py | Python | bsd-3-clause | 169 | [
"VTK"
] | 2474cde22449494f1447dba5ba231bf2387295e5d6dbbc33290b1da7d534efad |
##
# Copyright 2009-2018 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | bartoldeman/easybuild-easyblocks | easybuild/easyblocks/n/netcdf_fortran.py | Python | gpl-2.0 | 2,773 | [
"NetCDF"
] | f63b32b033813f423d8ee5861874251721ccbaa5fe7d34eadde59ce07de97a88 |
__author__ = 'amandeep'
import re
country_codes_2 = [
"AF", "AL", "DZ", "AS", "AD", "AO", "AI", "AQ", "AG", "AR", "AM", "AW", "AU", "AT", "AZ", "BS", "BH", "BD", "BB",
"BY", "BE", "BZ", "BJ", "BM", "BT", "BO", "BA", "BA", "BA", "BW", "BV", "BV", "BR", "IO", "BN", "BG", "BF", "BI",
"KH", "CM", "CA", "CV", ... | usc-isi-i2/dig-alignment | versions/3.0/karma/python/location_manipulation.py | Python | apache-2.0 | 18,663 | [
"BWA"
] | bc6e5089d6c056fd7548dbe4ded0aa807d846c4eb0c8197229542e6c0aedf303 |
#!/usr/bin/env python
""" A set of tools for modelling the antenna reponse and for callibrating the amplitude vs frequency of the antennas
based on pyCRtools. see Schellart et al. Detecting cosmic rays with the LOFAR radio telescope, and Nelles et al. Calibrating the absolute amplitude scale for air showers measured ... | Bhare8972/LOFAR-LIM | LIM_scripts/antenna_response.py | Python | mit | 37,390 | [
"Brian"
] | 6afccc07687e25e32f6bdac06283830e3aeee89f60577e9c469a561d0c362d88 |
r"""
Uncertainty propagation class for arithmetic, log and exp.
Based on scalars or numpy vectors, this class allows you to store and
manipulate values+uncertainties, with propagation of gaussian error for
addition, subtraction, multiplication, division, power, exp and log.
Storage properties are determined by the nu... | SasView/sasview | src/sas/sascalc/data_util/uncertainty.py | Python | bsd-3-clause | 11,407 | [
"Gaussian"
] | 10b5189aee9665f872ba4d29414ea4483e98f5d4f4716a12dd8d31f35d3ac3d1 |
# copyright 1997-2001 Just van Rossum, Letterror. just@letterror.com
import Splash
import FrameWork
import Wapplication
import W
import os
import sys
import MacOS
import EasyDialogs
from Carbon import File
from Carbon import Files
if MacOS.runtimemodel == 'macho':
ELLIPSIS = '...'
else:
ELLIPSIS = '\xc9'
de... | xbmc/atv2 | xbmc/lib/libPython/Python/Mac/Tools/IDE/PythonIDEMain.py | Python | gpl-2.0 | 19,929 | [
"Jaguar"
] | 2b26e7479194476b2955d8cc9657ec09bd9f5d7b2883259d7539865839ce765b |
import os, sys, glob, csv, itertools
import networkx as nx
from argparse import ArgumentParser
__author__ = "Anthony Gitter"
def Main(argList):
"""Parse the arguments, which either come from the command line or a list
provided by the Python code calling this function
"""
parser = CreateParser()
op... | mmacgilvray18/Phospho_Network | pcsf/cluster/summarize_sif.py | Python | gpl-3.0 | 10,961 | [
"Cytoscape"
] | 218253e4f79ea3a352598d0af565e25ba135ab7a6bb773685974590f05e4ea79 |
"""
===========
Shape Index
===========
The shape index is a single valued measure of local curvature,
derived from the eigen values of the Hessian,
defined by Koenderink & van Doorn [1]_.
It can be used to find structures based on their apparent local shape.
The shape index maps to values from -1 to 1,
representing... | paalge/scikit-image | doc/examples/features_detection/plot_shape_index.py | Python | bsd-3-clause | 4,382 | [
"Gaussian"
] | 65f8a5517a5a605c6c47f16c2d5ba1f6ca9c3184e58b7deb9b8dff31140008b9 |
"""Machine learning using crowdsourced labels on the Radio Galaxy Zoo.
MIT-licensed. See license.txt.
Matthew Alger & Cheng Soon Ong
The Australian National University
2016
"""
__version__ = '0.1.1'
__description__ = 'Automated cross-identification of radio objects and host ' \
'galaxies using crow... | chengsoonong/crowdastro | crowdastro/__init__.py | Python | mit | 387 | [
"Galaxy"
] | 2559ff17826897ca1b4a9e0ac1ee731ff13356839d1ae04c3ea25cd97e57b837 |
#!/usr/bin/python
import cv
import datetime
SAMPLE_PERIOD = 100 #ms (time between individual samples)
SAMPLING_TIME = 1.0 # sec (time to collect samples before analysing)
IMG_STACK_LEN = int(SAMPLING_TIME/(SAMPLE_PERIOD/1000.))
ANALYSIS_LAYER = 6
FFT_CHAN_MIN = 2
FFT_CHAN_MAX = 20
window1 = "Current"
window2 = "Olde... | OpenSeizureDetector/OpenSeizureDetector | video_version/Seizure_Detector_lowCPU.py | Python | gpl-3.0 | 6,061 | [
"Gaussian"
] | cee18c907da31915e5dedcea2cb1f74682fdf5a73d974f7121f6dae47024df01 |
##############################################################################
# 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/formats/netcdf.py | Python | lgpl-2.1 | 22,883 | [
"Amber",
"MDTraj",
"NetCDF"
] | 66966287223ac8aa739ca68464448929536f730c30fb12d818faad7e8bf48afa |
#!/usr/bin/env python
# -*- coding: utf8 -*-
"""
This script checks that all the external archive included in the repository are
as small as they can be.
"""
from __future__ import print_function
import os
import sys
import glob
ROOT = os.path.join(os.path.dirname(__file__), "..", "..")
ERRORS = 0
# when adding new ... | Luthaf/Chemharp | tests/lints/check-external-size.py | Python | mpl-2.0 | 1,428 | [
"NetCDF"
] | 1b3ba9aaae1543caccae8742d415eea5b606fa50f4a78dc48ebca68010d14622 |
import numpy as np
import scipy.sparse as sp
import scipy.sparse.linalg as linalg
import matplotlib.pyplot as plt
import matplotlib.animation as animation
import time
from anim import animate_wavefunction
class CrankNicolson:
def __init__(self,a,L,waveform="gaussian",*args):
self.waveform = waveform
self... | dbouman1/iccp-assignment-3 | QD/dynamics.py | Python | mit | 3,530 | [
"Gaussian"
] | b2a35f8abbc3a00b8e5ddcaa379d149438d4f745da7c246ea620ca6649b3bd30 |
"""
Class to process emsao output and combine information to generate a velocity field.
Parses the input data and outputs reformatted data to a file.
Combines velocity information with the coordinate information
to generate a velocity field and outputs this information to
a comma separated ascii file.
Will also gener... | sniemi/SamPy | resolve/kinematics/processVelocities.py | Python | bsd-2-clause | 7,905 | [
"Galaxy"
] | cfeb88494fd88ac5d07856e0c60c42547a0b617dcd93ace9a696d13768caf56c |
# -*- coding: utf-8 -*-
"""
werkzeug.contrib.fixers
~~~~~~~~~~~~~~~~~~~~~~~
.. versionadded:: 0.5
This module includes various helpers that fix bugs in web servers. They may
be necessary for some versions of a buggy web server but not others. We try
to stay updated with the status of the bug... | wildchildyn/autism-website | yanni_env/lib/python3.6/site-packages/werkzeug/contrib/fixers.py | Python | gpl-3.0 | 10,179 | [
"VisIt"
] | 811d3a4fec3bd6eafeb4743fdf590fff88e93a770f27859cd5d3aa4ef62eb2bf |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/dictdb.py | Python | gpl-2.0 | 25,285 | [
"PyMOL"
] | a337f199db6eaa85f5a90cb4980f2deb059fc69e4d5b79d8bd6dc066b448afbb |
"""
Add color cycling fun to your i3bar.
This is the most pointless yet most exciting module you can imagine.
It allows color cycling of modules. Imagine the joy of having the current time
change through the colors of the rainbow.
If you were completely insane you could also use it to implement the i3bar
equivalent ... | valdur55/py3status | py3status/modules/rainbow.py | Python | bsd-3-clause | 6,252 | [
"exciting"
] | ad8cfb0ba50d0e2253f1698eb6dcc889f15614ce683edd09092777cec8059b42 |
# coding: utf-8
# ### Functions for mapping paired end reads to reference fasta using bwa-mem
# * map_bwa_mem - maps reads using bwa mem algorithm
# * bwa_index_ref - indexing reference genome
# * bam_sort - sorting bam file
# * bam_index - indexing bam
# * sam_to_bam - converting alignment format
#
# In[13]:
impo... | nate-d-olson/micro_rm_dev | dev/bwa_mem_pe.py | Python | gpl-2.0 | 2,725 | [
"BWA"
] | e5089aaccc9e9cc5995c69aa37c6ea8db789228bb8f12527393c14ee97658c69 |
##############################################################################
# Copyright 2016-2018 Rigetti Computing
#
# 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... | rigetticomputing/pyquil | pyquil/api/_config.py | Python | apache-2.0 | 12,232 | [
"VisIt"
] | 369b4cd7434bbb4baec96c6a55d46d31c6b92d2b68108a20e8a97887a9f504a3 |
#pylint: disable=C0111
from lettuce import world, step
from xmodule.modulestore import Location
from contentstore.utils import get_modulestore
from selenium.webdriver.common.keys import Keys
VIDEO_BUTTONS = {
'CC': '.hide-subtitles',
'volume': '.volume',
'play': '.video_control.play',
'pause': '.video... | TangXT/GreatCatMOOC | cms/djangoapps/contentstore/features/video.py | Python | agpl-3.0 | 6,384 | [
"VisIt"
] | 595d70b221bce262373e139df7cea4d68dd1edf95e9f2e7eb0e967b6cc897d49 |
#!/usr/bin/env python
# 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 for doing logistic regressions.
Classes:
LogisticRegression Holds information for a LogisticReg... | bryback/quickseq | genescript/Bio/LogisticRegression.py | Python | mit | 4,455 | [
"Biopython"
] | ce8e8682a5504259e85c3f415fb88677fd966bce36df381637f079732c469ba3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
########################################################################
# File : dirac-create-distribution-tarball
# Author : Adria Casajus
########################################################################
"""
Create tarballs for a given DIRAC release
"""
impo... | petricm/DIRAC | Core/scripts/dirac-create-distribution-tarball.py | Python | gpl-3.0 | 23,939 | [
"DIRAC"
] | 33d0adc113249a7859ee131f207d2f8d81b0e623d29cbc11c47290f2b94c0bd6 |
#!/usr/bin/env python3
from netcdfTools import *
import sys
import argparse
import numpy as np
'''
Description:
Author: Mikko Auvinen
Finnish Meteorological Institute
'''
#==========================================================#
def idBounds( cmin, cmaxL, cminL, dc, nc ):
ic1 = np.round((cminL-cmin)/dc ... | mjsauvinen/P4UL | pyNetCDF/concatNetcdfFiles.py | Python | mit | 7,244 | [
"NetCDF"
] | 1e1c3432fc70d14684fe323d8630d7a6d8c031891cc12af6ebc013cef266dec8 |
#!/usr/bin/python
"""
This program makes a new copy of a BEAST XML config file and changes the name of the log and tree files.
The names have to be changed since Galaxy does not support dynamic output file names.
The new XML file name must not be the same as the original!!!
Script prints unique filename.
Usage: pytho... | xibalbanus/PIA2 | osiris_phylogenetics/phylogenies/beast.py | Python | mit | 935 | [
"Galaxy"
] | 3af07cffa6d5dd3c6baa8f60d83917311ef7775a9d2e71de082f37f024bf6371 |
import sys
from ase import Atoms
from gpaw import GPAW
from gpaw import KohnShamConvergenceError
from gpaw.utilities import devnull, compiled_with_sl
from ase.data.molecules import molecule
# Calculates energy and forces for various parallelizations
tolerance = 4e-5
parallel = dict()
basekwargs = dict(mode='lcao'... | qsnake/gpaw | gpaw/test/parallel/lcao_parallel_kpt.py | Python | gpl-3.0 | 3,991 | [
"ASE",
"GPAW"
] | ff0cf05efa22dae4642ee9f58158065f047d9fae6c78e308acb88c76e486bae5 |
#!/usr/bin/env python2.7
# -*- coding:utf-8 -*-
# Copyright (c) 2015, Galaxy Authors. All Rights Reserved
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
#
# Author: wangtaize@baidu.com
# Date: 2015-04-20
import argparse
import json
import sys
import os
import trace... | fxsjy/galaxy | deploy/deployer.py | Python | bsd-3-clause | 13,593 | [
"Galaxy"
] | 6a1a229403d9b6e8d65dee8eca183ca5931580090b22a6196b67fa2406b38f31 |
#!/usr/bin/python
"""
Copyright 2016 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | druss316/G-Harvestor | html/getRecipeList.py | Python | gpl-3.0 | 10,173 | [
"Galaxy"
] | 6ad3152a697bb91d3c6e94cd87a44dd16017edcb9f47141d9b81a2cc8789862c |
import matplotlib.pyplot as plt
from scipy.stats import norm
import powerlaw
import matplotlib.mlab as mlab
import numpy as np
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("numberBins", type=int,
help="Set number of bins for histogram")
args = parser.parse_args()
numBins =... | WillArmentrout/galSims | plotting/RadialLogHistGC.py | Python | gpl-2.0 | 1,329 | [
"Galaxy"
] | 6e4cf9493cd71a49254afd4e0a28aabd5d3aede3c0b035ad9f04c511e04ff4f6 |
import vtk as v
def save_lesion(output_file, input_file, field, limits):
reader = v.vtkXMLUnstructuredGridReader()
reader.SetFileName(input_file)
reader.Update()
threshold = v.vtkThreshold()
threshold.SetInput(reader.GetOutput())
if limits[0] is None:
threshold.ThresholdByLower(limit... | go-smart/glossia-quickstart | code/vtk_tools.py | Python | mit | 848 | [
"VTK"
] | 0617998a0ecb3f543ea0407cd1076ba9526c7a76440cdeb524139c5024d86cb2 |
# coding=utf-8
'''Define Schema'''
from __future__ import absolute_import
from datetime import datetime
from flask import url_for, g
from firefly.ext import db
from firefly.views.utils import timesince
from firefly.models.consts import CATEGORY_COLORS
from .user import User
__all__ = ["Category", "Post", "Video", "... | dongweiming/firefly | firefly/models/topic.py | Python | mit | 3,007 | [
"Firefly"
] | 8df086e88a9a473ed71e9dd7d85111eb18cbff4ce6985c29049bebdf836480b9 |
test = "tes's is \" adf \""
print "orig is " + test
test = test.replace("'", "\"")
print "after is " + test
| saikatgomes/recsys | data/db/test.py | Python | apache-2.0 | 108 | [
"ADF"
] | 105385450dd9327820358362aefec373aeca299e9d41e6f200116a19a7365656 |
import random
import time
import datetime
#saveFile = open('importdata.json', 'a')
# creating timestamp for file names
timestr = time.strftime("%Y%m%d-%H%M%S")
# creating output files one for phone, Active Directory (events), and NMA
saveFileNMA = open('testDataNMA' + timestr + '.txt', 'a')
saveFilePBX = open('test... | DavidNovo/ExplorationsWithPython | createimportfiles.py | Python | mit | 18,035 | [
"Amber",
"Brian",
"CRYSTAL"
] | 39cbae4f225a08ff2d4b81f0d37cc06d2bff8deb1feed2f8aa48ffd67559a836 |
##############################################################################
# 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... | swails/mdtraj | mdtraj/reporters/basereporter.py | Python | lgpl-2.1 | 10,852 | [
"Dalton",
"MDTraj",
"OpenMM"
] | 6fa1feb719aaa1a8bad84e13bd716d7cbb21a18e0b8e95f22d464905000610d6 |
"""Workflow to run an optical-response calculation."""
from __future__ import print_function
#from os.path import join as pjoin
#from os.path import dirname
#from os import getcwd
import os
from ..external import Structure
from ..core import Workflow
from ..Abinit import AbinitScfTask, AbinitWfnTask
__all__ = ['OPTfl... | trangel/OPTpy | OPTpy/flows/optflow.py | Python | gpl-3.0 | 8,259 | [
"ABINIT",
"pymatgen"
] | eb18cf43d3e3026696e75ae7641666b7f3026a2d724b725da65760994322d97b |
# -*- coding: utf-8 -*-
"""Perses: Tools for expanded-ensemble simulations with OpenMM
"""
from __future__ import absolute_import, print_function
DOCLINES = __doc__.split("\n")
import os
import sys
from os.path import join as pjoin
from os.path import relpath
from setuptools import setup
import versioneer
try:
... | choderalab/perses | setup.py | Python | mit | 2,587 | [
"OpenMM"
] | fd469535b8c98b6a15e27274cf699c1c71bd345dd145de51fdb49bf41d61e8c1 |
"""
.. versionadded:: 0.4
This function generates Brownian noise series. The noise is produced by
integration of white noise (gaussian or uniform).
This function uses
`numpy.random.normal` and `numpy.random.uniform`
Example Usage
==================
The following example produce 1000 samples of brownian noise starti... | matousc89/signalz | signalz/generators/brownian_noise.py | Python | mit | 2,325 | [
"Gaussian"
] | 46292400b996223b11fdb9dca80a50cee424a513ae372692ba3088c831fd9576 |
import os.path as op
import numpy as np
import pandas as pd
import numpy.testing as npt
import shablona as sb
data_path = op.join(sb.__path__[0], 'data')
def test_transform_data():
"""
Testing the transformation of the data from raw data to functions
used for fitting a function.
"""
# We start w... | katiehamren/splash | splash/tests/test_shablona.py | Python | mit | 3,917 | [
"Gaussian"
] | 6c8a2c1750d2c05378349602947bde2ca4e6573acfd4ccf472d247a671a52330 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2020 Satpy developers
#
# This file is part of satpy.
#
# satpy 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... | pytroll/satpy | satpy/modifiers/_crefl.py | Python | gpl-3.0 | 6,694 | [
"NetCDF"
] | a7702dca9341d85592478694f40a7f6a23d372c131143f5d8a7ec6ae9e55d901 |
#!/usr/bin/env python
from __future__ import print_function
import dist2, spacetime
import numpy as np
import scipy.io
import os, sys, itertools
EPS = np.finfo( float ).eps
def __rebuild( data_file, bin_file, num_vols, dtype, binary ):
'''
parse the raw data in data_file and
store the co-authorship m... | sunk/spacetime | nips_exp.py | Python | bsd-2-clause | 11,758 | [
"Gaussian"
] | 94fcd08e621d36819a89293ed87e43511e063cb7f962e9dd6047411de9397f96 |
"""
Views for user API
"""
from courseware.model_data import FieldDataCache
from courseware.module_render import get_module_for_descriptor
from django.shortcuts import redirect
from django.utils import dateparse
from rest_framework import generics, permissions, views
from rest_framework.authentication import OAuth2A... | peterm-itr/edx-platform | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 11,102 | [
"VisIt"
] | 7ed0d1e1071fafada34aea56c33fe0e639075ba71c7a4dc57c8aa185c37d896d |
import numpy as np
from ..misc.tools import normalize
from .head import head_direction
import scipy.signal as sig
def unit_vector(v):
""" Return unit vector of v
modified from David Wolever,
https://stackoverflow.com/questions/2827393/angles
-between-two-n-dimensional-vectors-in-python
"""
ret... | CINPLA/exana | exana/tracking/tools.py | Python | gpl-3.0 | 10,765 | [
"Gaussian"
] | b9ab0985fb1678650c5d65ed76ade001ca8e1036890664ea8ab66a84d40b6e7e |
import random
import numpy
from rdkit.ML.DecTree import ID3
def GenRandomExamples(nVars=10, randScale=0.3, bitProb=0.5, nExamples=500, seed=(0, 0),
addResults=1):
random.seed(seed[0])
varWeights = numpy.array([random.random() for _ in range(nVars)]) * randScale
examples = [None] * nExamp... | ptosco/rdkit | rdkit/ML/DecTree/randomtest.py | Python | bsd-3-clause | 1,003 | [
"RDKit"
] | 1f3e1c486dc01acf5361f929c383eae0b1e39f3813bc4f0349a099a2408d028e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
__author__ = 'Brian Hicks'
__email__ = 'brian@brianthicks.com'
__version__ = '0.0.2'
| BrianHicks/probe | probe/__init__.py | Python | bsd-3-clause | 132 | [
"Brian"
] | 7a7b3ece734e779b9a31fedd57bce2020eedc0014a213ce236552d3a11296994 |
# This file is part of MOOSE simulator: http://moose.ncbs.res.in.
# MOOSE is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# MOOSE is ... | rahulgayatri23/moose-core | python/libmumbl/utility/nml.py | Python | gpl-3.0 | 1,363 | [
"MOOSE"
] | 58f5083bd6373844369b3f7691649f1e236676111fd7bfe6f9021682d32a72b0 |
#!/usr/bin/env python
import sys,os
import numpy as np
from PyQt5.QtWidgets import (QApplication, QWidget, QMainWindow, QTabWidget,
QTabBar,QHBoxLayout, QVBoxLayout, QSizePolicy,
QStatusBar, QSplitter, QToolBar, QAction,
QFileDial... | darioflute/sospex | sospex/mainwindow.py | Python | gpl-3.0 | 309,523 | [
"Gaussian"
] | 2dce80b8a8564e2b7addf6b51aa8d7394fa6c2369054afc7c48125039a1cd79d |
"""Calculate quality control metrics for UMI tags and consensus generation.
"""
import collections
import math
import os
import numpy as np
import pysam
import yaml
from bcbio import bam, utils
from bcbio.pipeline import datadict as dd
def run(_, data, out_dir):
stats_file = os.path.join(utils.safe_makedir(out_d... | brainstorm/bcbio-nextgen | bcbio/qc/umi.py | Python | mit | 2,886 | [
"pysam"
] | b8ad62abceaa1345eec7db074b177e55cdacc948f4653514856e254282898dd0 |
"""
Execute an external process to set_meta() on a provided list of pickled datasets.
This should not be called directly! Use the set_metadata.sh script in Galaxy's
top level directly.
"""
import logging
logging.basicConfig()
log = logging.getLogger( __name__ )
import os, sys, cPickle
assert sys.version_info[:2] >... | volpino/Yeps-EURAC | scripts/set_metadata.py | Python | mit | 4,385 | [
"Galaxy"
] | 21d4c1cf52a510d76753ca159376f221058b4cb9b8f2e8efd3bebaec13809fcf |
#!/usr/bin/env python3
import sys
from vaspirin import outcar,graceIO,datIO
import argparse
################################
## PARSING AND HELLO MESSAGES ##
################################
def positive_int (value):
'''
Type for allowing only positive int values for argparser
taken from http://stackoverflow.com/... | gmsn-ita/vaspirin | scripts/plot_compared_bands.py | Python | gpl-3.0 | 6,165 | [
"VASP"
] | 39dbfdd27865a587e03a6f1e9371f7f4dc7c60e6bf197983dfc520058aa80699 |
# -*- 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 rest_framework.routers import DefaultRouter
from tas... | chedv13/taskist | config/urls.py | Python | bsd-3-clause | 1,815 | [
"VisIt"
] | c2790279759d9d2852b37ff3bd264906f9ad43426a21f07b03ac7ca1b48ef942 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, division, absolute_import
from builtins import * # pylint: disable=unused-import, redefined-builtin
import pytest
from flexget.manager import Session
from flexget.plugins.api_trakt import ApiTrakt, TraktActor, TraktMovieSearchResult, TraktShowSearchRes... | qvazzler/Flexget | tests/test_trakt.py | Python | mit | 18,570 | [
"CRYSTAL"
] | e0db86c65f707f011ad74c36cd322c8a9bfc130d7163d11589ca6ee16d1d6448 |
""" CacheFeederAgent
This agent feeds the Cache tables with the outputs of the cache commands.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN CacheFeederAgent
:end-before: ##END
:dedent: 2
:caption: CacheFeederAgent options
"""
from DIRAC import S_OK
from DIRAC.Core.Base.AgentModule import ... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Agent/CacheFeederAgent.py | Python | gpl-3.0 | 6,595 | [
"DIRAC"
] | 830b2bb0b781d9d8ff98f3f646167170fad6455ad933b5f15a092f0811be0c61 |
# This file defines custom jobs for AuroraWatchNet plotting.
'''
This module defines custom jobs for AuroraWatchNet plotting. It can be
used to send emails, tweets or Facebook posts in response to important
events.
The events which can cause actions are:
* geomagnetic activity
* low battery
* missing data... | stevemarple/AuroraWatchNet | software/server/awnetd/aurorawatch_jobs.py | Python | gpl-2.0 | 28,203 | [
"Amber"
] | 7435e284c226b6ceaa78e90a25a0683786eeaa28957498f2156ac95704d572fb |
import re,os,subprocess,csv
from rjv.fasta import *
from rjv.fileio import *
source_file = '/home/rov/rjv_files/seq_data/database/source_list'
database_file = '/home/rov/rjv_files/seq_data/database/db.pickle'
blastnbin = '/usr/bin/blastn'
blastdbcmdbin = '/usr/bin/blastdbcmd'
newline = '\n'
#list of all available bla... | robertvi/rjv | blast_old.py | Python | gpl-2.0 | 10,571 | [
"BLAST"
] | 1e518740f966b7239b7a2ed6ad87ed586a5bcadd9f0d9ca15bf35c801cac7bf7 |
from galaxy_analysis.plot.plot_styles import *
import matplotlib.pyplot as plt
import glob
import deepdish as dd
import yt
from galaxy_analysis.utilities import utilities
import numpy as np
from matplotlib.ticker import NullFormatter
from galaxy_analysis.particle_analysis.abundances import single_MDF
#
from galaxy_anal... | aemerick/galaxy_analysis | method_paper_plots/star_abundances.py | Python | mit | 26,128 | [
"Galaxy"
] | ef2dbbeed5f97e3acad7c75ff937d32241282f19588d5a265326200c759f944e |
# Dataset created from this:
# Elements of Statistical Learning 2nd Ed.; Hastie, Tibshirani, Friedman; Feb 2011
# example 10.2 page 357
# Ten features, standard independent Gaussian. Target y is:
# y[i] = 1 if sum(X[i]) > .34 else -1
# 9.34 is the median of a chi-squared random variable with 10 degrees of freedom
# ... | rowhit/h2o-2 | py/testdir_single_jvm/test_KMeans_hastie_shuffle_fvec.py | Python | apache-2.0 | 5,295 | [
"Gaussian"
] | ecec50b709d18f6c4f9a0a7cc239f45f8f2e0a799c620e069111dc6a2ae0bac5 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <headingcell level=1>
# New Cannabinoid Analysis
# <markdowncell>
# Here I am looking for the effect of Cannabinoid use on the progression of HIV related dementia. This is currently being measured by the Total Modified Hopkins Dementia Score (HIVD-score). This is... | JudoWill/ResearchNotebooks | NewCannabAnalysis.py | Python | mit | 41,519 | [
"VisIt"
] | e0cb9519f87869221afed8f48d069c9df4190e68f3bdd2e6b59a4766ffd8e97e |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | vinodpanicker/scancode-toolkit | src/scancode/cli.py | Python | apache-2.0 | 14,023 | [
"VisIt"
] | a1cbff96d5b4fde90150098b0cc7749b286084731678a86d5f2a1196381fae6a |
import numpy
from chainer.functions.connection import linear
from chainer import link
class Linear(link.Link):
"""Linear layer (a.k.a. fully-connected layer).
This is a link that wraps the :func:`~chainer.functions.linear` function,
and holds a weight matrix ``W`` and optionally a bias vector ``b`` as
... | sinhrks/chainer | chainer/links/connection/linear.py | Python | mit | 2,272 | [
"Gaussian"
] | 3f4f221b119731af70aeedb6870c55213773818ddc28bdab519553553ff242b1 |
"""
Module to set up run time parameters for Clawpack -- classic code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#------------------------------
def setrun(claw_pkg='classic'):
#---------------------------... | amath574w2015/am574-class | labs/lab4/chap6/compareadv/setrun.py | Python | bsd-3-clause | 7,172 | [
"Gaussian",
"NetCDF"
] | 7a8f64220c249ca13ef32b0d1999e20f309c380d15639f2b4a31ca66d7deba16 |
#!/usr/bin/env python
from datamanagerpkg import ProtonCommunication_data_manager
import requests
import json
import pprint
import os
import paramiko
from scp import SCPClient
import subprocess
import time
from shutil import copyfile
##########################
#URL PROTON
##########################
from GlobalVaria... | CARPEM/GalaxyDocker | data-manager-hegp/analysisManager/analysismanager/sequencer/Prod_performRunProtonBackup.py | Python | mit | 24,552 | [
"Galaxy"
] | fd6c5d7cf0c2f6f2a34b80a61fd83876a8bbf967f3e616086c9868eef0a8c856 |
import StringIO
import os
import sys
import componentinfo
import configutil
from util import *
###
def cmake_quote_string(value):
"""
cmake_quote_string(value) -> str
Return a quoted form of the given value that is suitable for use in CMake
language files.
"""
# Currently, we only handle e... | hoangt/ScaffCC | llvm/utils/llvm-build/llvmbuild/main.py | Python | bsd-2-clause | 35,060 | [
"VisIt"
] | 489584bf5a154ab32481afc32cc8335ef8f7022818c08c9fd506f444c22f3187 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/io/_iosources.py | Python | bsd-3-clause | 6,993 | [
"scikit-bio"
] | 94677e44daaf7a886f520e6252d48eb93aa42d5eeabfdeac85218410c25ccbdf |
from jaspyx.visitor import BaseVisitor
class Return(BaseVisitor):
def visit_Return(self, node):
self.indent()
if node.value is not None:
self.output('return ')
self.visit(node.value)
else:
self.output('return')
self.finish()
| iksteen/jaspyx | jaspyx/visitor/return_.py | Python | mit | 299 | [
"VisIt"
] | 82b1d9db0035c0cc131406770b5fad6b6c7a33cfd98a711e7981f795300f5187 |
import cPickle as pkl
import numpy
import copy
import theano
from collections import OrderedDict
import sys
sys.path.insert(0,'data/')
def ortho_weight(ndim):
"""
Random orthogonal weights
Used by norm_weights(below), in which case, we
are ensuring that the rows are orthogonal
(i.e W = U \Sigma ... | aayushP/IM2TXT | utils.py | Python | mit | 6,252 | [
"Gaussian"
] | eb2870c7ee148180b389559fe4fe5e66b781b698e072935e5080fc861b5a5f30 |
# -*- coding: utf-8 -*-
def VtkDibujaKPts(nmbActor):
# Define el actor a emplear para dibujar kpoints.
sphereKPts= vtk.vtkSphereSource()
sphereKPts.SetRadius(0.03)
sphereKPts.SetThetaResolution(5)
sphereKPts.SetPhiResolution(5)
markKPts= vtk.vtkGlyph3D()
markKPts.SetInput(ugrid)
markKPts.SetSo... | lcpt/xc | python_modules/postprocess/xcVtk/CAD_model/vtk_plot_kpoints.py | Python | gpl-3.0 | 603 | [
"VTK"
] | ad7c0833fc5e8f14ca518059407f28b39d14418ff78bc571efd9f1069f1c67a3 |
__RCSID__ = "$Id $"
import datetime
# Requires at least version 3.3.3
import fts3.rest.client.easy as fts3
from fts3.rest.client.exceptions import FTS3ClientException
from fts3.rest.client.request import Request as ftsSSLRequest
from DIRAC.Resources.Storage.StorageElement import StorageElement
from DIRAC.Framework... | arrabito/DIRAC | DataManagementSystem/Client/FTS3Job.py | Python | gpl-3.0 | 19,587 | [
"DIRAC"
] | 814cbcf6fc3e2b81cce0f74bc78888ebc4890746640499518104858a740a6aeb |
'''
preprocessing.py
Preprocess locations by clustering them
Ankur Goswami, agoswam3@ucsc.edu
'''
from sklearn.cluster import KMeans
from sklearn import mixture
import numpy as n
import itertools
from os import remove
import numpy as np
from scipy import linalg
import matplotlib.pyplot as plt
import matplo... | ankur-gos/PSL-Bipedal | preprocessing/preprocessing.py | Python | mit | 10,004 | [
"Gaussian"
] | bd8d38aeb1418090458d61b3f9c46f734d9ff66af4244bad6079f74c04c5c283 |
# -*- coding: utf-8 -*-
"""
Auto-aligning spectrometer: centres in on a nanoparticle after a short scan
"""
#import traits
#from traits.api import HasTraits, Property, Instance, Float, Range, Array, Int, String, Button, Bool, on_trait_change
##import traitsui
#from traitsui.api import View, Item, HGroup, VGroup, Tabbe... | nanophotonics/nplab | nplab/instrument/spectrometer/spectrometer_aligner_Andorfeedback.py | Python | gpl-3.0 | 17,307 | [
"Gaussian",
"VisIt"
] | 3354755990f954259dc24160854ac931cea2c38ddf9708267f5b3bfb906f29ca |
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/Yellow_Sea/Inputs/Boundary/remap_bdry_uv.py | Python | bsd-3-clause | 16,831 | [
"NetCDF"
] | cf1395953cf4c627b6c412bbad8c98d9c74cfa315a32baae913f9ec39a6f5bba |
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/cryptanalytic-model-extraction | src/hyperplane_normal.py | Python | apache-2.0 | 8,310 | [
"NEURON"
] | 229635b8834ef44d7760a32cd8d05651bd7e1327f8173f9109796218adea95a6 |
#!/usr/bin/env python
from __future__ import division,print_function,unicode_literals,absolute_import
from hollow import *
from geode import *
from geode.geometry.platonic import *
import subprocess
import sys
def test_neo_hookean():
props = 1e6,.4 # E,nu
random = Random(1311)
neo_hookean_test(props,random,100)... | otherlab/hollow | hollow/elastic/test_elastic.py | Python | bsd-2-clause | 6,869 | [
"VTK"
] | 7ba3b86b2822d941ac1943f5cecc14777f69b0edc0a28064cf463ea999df0db5 |
from os.path import dirname, join
import numpy as np
import pandas as pd
import pytest
from bambi.models import Model
@pytest.fixture(scope="module")
def data_numeric_xy():
x = np.random.uniform(size=100)
y = x + np.random.normal(scale=0.5, size=100)
data = pd.DataFrame({"y": y, "x": x})
return data... | bambinos/bambi | bambi/tests/test_predict.py | Python | mit | 7,778 | [
"Gaussian"
] | 3a91e9500dbd13f8fd1e33f8f70b2864366a9af1a5d6728f702729cdc17b241d |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall.injector.namespaces import XMLNS_IFACE
from xml.dom import Node, XMLNS_NAMESPACE
class Namespace(object):
def __init__(self):
self.namespace_prefixes = {} # Namespace -> prefix
def register_name... | gfxmonk/0repo | repo/namespace.py | Python | lgpl-2.1 | 2,538 | [
"VisIt"
] | 5cf2a2aeeff403e5a2f96a87c3a4c7634c91b80c069ad414f8e9d8d6a6805b48 |
#
# Copyright (C) 2001,2002 greg Landrum and Rational Discovery LLC
#
""" descriptor calculator for compounds defined by a composition alone
(only the composition is required)
"""
from __future__ import print_function
from rdkit import RDConfig
from rdkit.utils import chemutils
import os
from rdkit.Dbase.DbConnect... | adalke/rdkit | rdkit/ML/Descriptors/CompoundDescriptors.py | Python | bsd-3-clause | 14,700 | [
"RDKit"
] | 0ef061cb985a53a603d60e4c2da8f0184f6fdf0f19094b797058961e27a6dd8e |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS Instructor Dashboard.
"""
import time
from flaky import flaky
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from ..helpers import UniqueCourseTest, get_modal_alert, EventsTestMixin
from ...pages.common.logout import LogoutPage
... | jbzdak/edx-platform | common/test/acceptance/tests/lms/test_lms_instructor_dashboard.py | Python | agpl-3.0 | 39,417 | [
"VisIt"
] | 754a37e82e239bb3406dde0ea78062fcda9a60fa8e08c2c27ead113d31c2060a |
# -*- 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_sellablepriceeditor.py | Python | gpl-2.0 | 2,656 | [
"VisIt"
] | e18716c8d65fe400dbaf2aeb09e43e602fcc8deb07a52f946bc21ca0bc058760 |
#! /usr/bin/env python
"""
Retrieve status of DIRAC jobs
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from signal import signal, SIGPIPE, SIG_DFL
import six
from COMDIRAC.Interfaces import ConfigCache
from DIRAC.Core.Utilities.... | DIRACGrid/COMDIRAC | src/COMDIRAC/Interfaces/scripts/dstat.py | Python | gpl-3.0 | 7,988 | [
"DIRAC"
] | cc2de886013c0ad230203306c0b210cb9dfd18f1ecf3935c8a16134a61607be3 |
# encoding: utf-8
"""
Common implementation of ID, Population, PopulationView and Assembly classes.
These base classes should be sub-classed by the backend-specific classes.
:copyright: Copyright 2006-2016 by the PyNN team, see AUTHORS.
:license: CeCILL, see LICENSE for details.
"""
import numpy
import logging
impor... | anupkdas-nus/global_synapses | pyNN-dispackgaes/common/populations.py | Python | gpl-3.0 | 59,451 | [
"NEURON"
] | 754b219dcc5e1f0540a371c93608c4144c94e5b9f9993f923ebe3128f8684cf6 |
import numpy as np
import matplotlib.pyplot as plt
from grid_world import standard_grid, negative_grid
from iterative_policy_evaluation import print_values, print_policy
from monte_carlo_es import max_dict
GAMMA = 0.9
ALL_POSSIBLE_ACTIONS = ('U', 'D', 'L', 'R')
# NOTE: find optimal policy and value function
# u... | balazssimon/ml-playground | udemy/lazyprogrammer/reinforcement-learning-python/monte_carlo_no_es.py | Python | apache-2.0 | 4,200 | [
"VisIt"
] | b20d1f10a3376e582fe1ce5f4df2b2e2781f06ebe1c22c444b99207bca54647e |
#!/usr/bin/env python
# encoding: utf-8
'''
Created by Brian Cherinka on 2016-03-28 23:30:14
Licensed under a 3-clause BSD license.
Revision History:
Initial Version: 2016-03-28 23:30:14 by Brian Cherinka
Last Modified On: 2016-03-28 23:30:14 by Brian
'''
from __future__ import print_function
from __future__... | albireox/marvin | python/marvin/db/marvindb.py | Python | bsd-3-clause | 7,086 | [
"Brian"
] | 9e383c9ef03cd68568cbcabfcb1e29e149d40bc8ed24fcadccbe0ffbfce0dc17 |
######################################################################
# Copyright (C) 2013 Jaakko Luttinen
#
# This file is licensed under Version 3.0 of the GNU General Public
# License. See LICENSE for a text of the license.
######################################################################
####################... | nipunreddevil/bayespy | bayespy/inference/vmp/nodes/tests/test_gaussian.py | Python | gpl-3.0 | 29,154 | [
"Gaussian"
] | 1c597c101880408b5815160aba430e8fc6529cc4a7bb90f2fc9d0cdf66cce702 |
"""Build a PDB structure from sequence.
"""
from __future__ import print_function
DOCLINES = __doc__.split("\n")
import os
import sys
import shutil
import tempfile
import subprocess
from distutils.ccompiler import new_compiler
from setuptools import setup, Extension
import numpy
try:
from Cython.Distutils impor... | kyleabeauchamp/PDBBuilder | setup.py | Python | gpl-2.0 | 1,664 | [
"MDTraj"
] | 73a7842c58a7665e74cc5f9540aaf0c48d516b44161200b8f6f3e535643f3ce2 |
# Copyright (C) 2013,2014 The ESPResSo project
# Copyright (C) 2012 Olaf Lenz
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or... | Marcello-Sega/espresso | config/gen_sampleconfig.py | Python | gpl-3.0 | 1,894 | [
"ESPResSo"
] | 4dd14fceffae3b14c81a11c0bd77286235a3ad02ba3206156212b6a00888061a |
#
# 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... | ConeyLiu/spark | python/pyspark/ml/regression.py | Python | apache-2.0 | 88,419 | [
"Gaussian"
] | 340b32b3f0e0ebe70724f79c35e0eda9f85d23d6decd6a9820b97e6fa64a993b |
import ast
from . import astlib as _a
from .library import Library
from .parser import visitor
register = Library()
@register.tag
def load(parser, token):
args, kwargs = parser.parse_args(token)
assert len(args) == 1, '"load" tag takes only one argument.'
assert isinstance(args[0], ast.Str), \
... | funkybob/knights-templater | knights/tags.py | Python | mit | 5,904 | [
"VisIt"
] | 1354fbc91ad22c526217aab584bef7da4cf1f41adc54aba897fdd072fa012e8a |
# Copyright (C) 2007-2014 CEA/DEN, EDF R&D, OPEN CASCADE
#
# Copyright (C) 2003-2007 OPEN CASCADE, EADS/CCR, LIP6, CEA/DEN,
# CEDRAT, EDF R&D, LEG, PRINCIPIA R&D, BUREAU VERITAS
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as ... | FedoraScientific/salome-paravis | src/ENGINE/no_wrap/PVSERVER.py | Python | lgpl-2.1 | 10,037 | [
"ParaView"
] | 938dba467ef83d4b6d11b8da37d5fa30a39fa5ab26a60890a61807856498d7ac |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# Copyright: (c) 2015, Brian Coca <bcoca@ansible.com>
# Copyright: (c) 2016-2017, Konstantin Shalygin <k0ste@k0ste.ru>
# Copyright: (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING... | thnee/ansible | lib/ansible/modules/find.py | Python | gpl-3.0 | 18,786 | [
"Brian"
] | 1b34744d8602a1af15747f43dbea603c9f7f2a75ae69d810a0cab24908ea5ea3 |
'''
Created on 2010 aza 30
@author: peio
It test the mapping module of franklin
'''
import unittest, os, StringIO
from os.path import join, exists
from tempfile import NamedTemporaryFile
from franklin.utils.misc_utils import TEST_DATA_DIR, NamedTemporaryDir
from franklin.mapping import map_reads_with_gmap, map_read... | JoseBlanca/franklin | test/mapping_test.py | Python | agpl-3.0 | 6,577 | [
"BLAST",
"BWA"
] | ee6ad132c2ac3dd933cbc0ea379e40b0411bcc93efd57e431b16ef432219fcdf |
# -*- coding: utf_8 -*-
###
#
# Thanks to Knirch/wanders for the iso88591 function
# and
# thanks to http://submarinemovies.com, http://imdb.com, http://wikipedia.org
# for the movies.
#
###
from supybot.commands import *
import supybot.log as log
import supybot.callbacks as callbacks
import sqlite3
mynick = 'jolt'
... | joltcan/supybot-plugin-dvd | DVD/plugin.py | Python | mit | 7,660 | [
"Octopus"
] | 28f8de22a18266fc97fa126acb0c8df2b38c719ee55052bd6d78157a9e6a36f8 |
from netpyne import specs
###############################################################################
# NETWORK PARAMETERS
###############################################################################
netParams = specs.NetParams() # object of class NetParams to store the network parameters
# Cell parameters
... | Neurosim-lab/netpyne | doc/source/code/tut7.py | Python | mit | 5,073 | [
"NEURON"
] | 77a8b98e24e7c2f40afc52773167e261a4d9c60de09a441d84f591aaefe5dae8 |
# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. 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 modules allows for asynchronous execution of Fdist and
spliti... | bryback/quickseq | genescript/Bio/PopGen/FDist/Async.py | Python | mit | 6,819 | [
"Biopython"
] | ad72b42af0b900e6bc7f2bd074817485480fcfe86100aa955696615290b5dc49 |
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