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from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import random
from hashlib import md5
from DIRAC.Core.Utilities.ThreadSafe import Synchronizer
from DIRAC.Core.DISET.private.BaseClient import BaseClient
from DIRAC.Core.DISET.private.Messag... | yujikato/DIRAC | src/DIRAC/Core/DISET/MessageClient.py | Python | gpl-3.0 | 5,197 | [
"DIRAC"
] | 1c1569d1ba082387d96c433949911be857c52869ab08954d2da545f709a3417d |
# -*- coding: utf-8 -*-
"""
Sub-package with code handling netcdf datasets.
"""
import dataset
from operations import *
from dataset import *
from date_time import *
| jfrygeo/solutions-geoprocessing-toolbox | suitability/toolboxes/scripts/MultidimensionSupplementalTools/MultidimensionSupplementalTools/Scripts/mds/netcdf/__init__.py | Python | apache-2.0 | 166 | [
"NetCDF"
] | 5e495fbcd7dc4dcb84b522d0add4ebaaa743f343fa134f6d7470ce1af876f908 |
import numpy as np
import os, time
#Gaussian function
def gaussian(A,tauGaussian) :
return np.exp(-tauGaussian*A)
#Remove matrices for saving space
def removeOldMatrices() :
dirpath = "./Matrices"
filelist = [ f for f in os.listdir(dirpath)]
for f in filelist:
os.remove(dirpath+"/"+f)
#Initi... | bernardgut/MLTools | SMO/KernelComputation.py | Python | gpl-2.0 | 1,363 | [
"Gaussian"
] | 69c6a1078531ebee42655c330bb7a5d83a92bc9822108efb4f24be381a9939c9 |
#!/usr/bin/env python
""" This script is used to submit the jobs on the grid.
It uses an executable (first argument), creates
a directory in which it will store all the job ids (<jobName> args),
and submit a configurable amount of jobs.
"""
from __future__ import print_function
from DIRAC.Core.Base.Scri... | fstagni/DIRAC | tests/Performance/DFCPerformance/submitJobs.py | Python | gpl-3.0 | 1,214 | [
"DIRAC"
] | 940e2aba70b541045cc020d64993e72f469e57d45cd0a05598567b4ac7051e9a |
# Copyright 2012 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of ngs_crumbs.
# ngs_crumbs 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, ... | JoseBlanca/ngs_crumbs | test/seq/test_mate_chimeras.py | Python | gpl-3.0 | 8,781 | [
"BWA"
] | 5047edf860bb9a68df930dce0443e8906c3c80ef7fc9f1c84d5cff83056c88d0 |
import discord
from discord.ext import commands
import os
from .utils.dataIO import dataIO, fileIO
from __main__ import send_cmd_help
import asyncio
import random
from random import choice as rand_choice
import string
import datetime
import time
from collections import OrderedDict
import clashroyale
import requests
cr... | Gr8z/Legend-Cogs | legend/legend.py | Python | mit | 66,830 | [
"VisIt"
] | ec4d11acd2fcdb1929f4e3245b8d8676be895df4a2aa97f4668d2b5480f49ffc |
import numpy as np
from astropy.table import Table
from astropy.io import fits
import matplotlib.pyplot as plt
import matplotlib
import pickle
from TheCannon_2 import dataset,apogee
from TheCannon_2 import model
pkl_file = open('wl.pkl', 'rb')
wl = pickle.load(pkl_file)
pkl_file.close()
# load path
pkl_file = op... | peraktong/Cannon-Experiment | 0218_plot_three_suspect_star.py | Python | mit | 56,764 | [
"VisIt"
] | 3f28bca25a62fac1600bc57d11107b957619f02d5e046a9599e5fcaa10132c06 |
#
# Copyright (C) 2001-2004 greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
""" The "parser" for compound descriptors.
I almost hesitate to document this, because it's not the prettiest
thing the world has ever seen... but it does work (for at least some
definitions of the word).
Rather than gettin... | ptosco/rdkit | rdkit/ML/Descriptors/Parser.py | Python | bsd-3-clause | 12,437 | [
"RDKit"
] | d940433a8b23295bae9ec24ce7b8ace9368cd682ea553ce9e2fca3129441cc52 |
import numpy as _np
from scipy import ndimage as _nd
from . import norm as _norm
from ndarray.openalea import aleanode as _aleanode # decorator to declare openalea nodes
@_aleanode({'name':'kernel'})
def coordinates(shape):
"""
Compute an array containing for each axis the coordinates arrays of given s... | julien-diener/ndarray | src/ndarray/kernel.py | Python | bsd-3-clause | 4,556 | [
"Gaussian"
] | 0ee50a46198ecca51b229f4cb75070b805c671865931436a72fc06ba0ad5658f |
"""Analyze python import statements."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import ast
import os
import re
from . import types as t
from .io import (
read_binary_file,
)
from .util import (
display,
ApplicationError,
is_subdir,
)
from .data import... | j-carl/ansible | test/lib/ansible_test/_internal/import_analysis.py | Python | gpl-3.0 | 14,066 | [
"VisIt"
] | c5573d612fe504dd7d6c46b27d6d10c0e8a2b14bb8f5e20c46b2badffb3d33f6 |
def installed():
import os
from ase.test import NotAvailable
try:
fleur = os.getenv('FLEUR')
if fleur == None:
raise NotAvailable('FLEUR not defined')
except NotAvailable:
raise NotAvailable('Fleur required')
return True
| conwayje/ase-python | ase/test/fleur/__init__.py | Python | gpl-2.0 | 277 | [
"ASE",
"FLEUR"
] | dc956ff5fb6ef19a03a8d9e06f9380d13ba84863e6aef0f012c2fa53b892cf45 |
""" A computing element class using singularity containers.
This computing element will start the job in the container set by
the "ContainerRoot" config option.
DIRAC will the re-installed within the container, extra flags can
be given to the dirac-install command with the "ContainerExtraOpts"
opt... | arrabito/DIRAC | Resources/Computing/SingularityComputingElement.py | Python | gpl-3.0 | 11,803 | [
"DIRAC"
] | 6b3e9674a169b8370a12f59ede31eb01b375e795ced741f3673b08f2ad946a84 |
########################################################################
# $HeadURL$
########################################################################
""" This is the StorageElement class.
"""
__RCSID__ = "$Id$"
# # custom duty
import re
from types import ListType, StringType, StringTypes, DictType
# # from DI... | sposs/DIRAC | Resources/Storage/StorageElement.py | Python | gpl-3.0 | 36,591 | [
"DIRAC"
] | dd4762d05db804cc9e0e7efb682e514ddd5c30edd04620e7464ca003944d98ce |
# -*- coding: utf-8 -*-
__author__ = 'Vojtech Vozab'
import bigaussian
import argparse
import glob
import numpy as np
import os
from skimage import io
def process_16bit_folder(path, kernel_function, vesselness_function, sigma_foreground, sigma_background, step_size, number_steps, zratio):
suffix = 'tif'
image... | V17/bigaussian | main.py | Python | gpl-3.0 | 5,708 | [
"Gaussian"
] | e23d3e9b51de10f510e75e3db3fec486725c40a022577b75d726867a426ee7d1 |
'''
PathwayGenie (c) University of Manchester 2017
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
| synbiochem/PathwayGenie | plasmid_genie/__init__.py | Python | mit | 207 | [
"VisIt"
] | 541a7945b7483a40a830dca97094a29f756cc11ccf22ecdaa6b19d52843640e5 |
from __future__ import division
import numpy as np
import pyhsmm
from internals.states import FactorialStates,\
FactorialComponentHSMMStates,\
FactorialComponentHSMMStatesPossibleChangepoints
###################################
# overall problem wrapper class #
###################################
... | fivejjs/pyhsmm-factorial | models.py | Python | mit | 6,665 | [
"Gaussian"
] | a8a8210c8fff7ae6fab04657bbaf484058700e9b4ce0450e76b2aa3ec1b94150 |
""" Base class for all services
"""
import os
import types
import time
import DIRAC
from DIRAC.Core.DISET.private.FileHelper import FileHelper
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR, isReturnStructure
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.ConfigurationSystem.Client.C... | arrabito/DIRAC | Core/DISET/RequestHandler.py | Python | gpl-3.0 | 19,987 | [
"DIRAC"
] | 86c1a87e4d200ec88cf94088daba957bec801d7f994c584b292b975955c5a408 |
# Copyright 2018 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.
"""Implements commands for running and interacting with Fuchsia on devices."""
import boot_data
import logging
import os
import pkg_repo
import re
import su... | chromium/chromium | build/fuchsia/device_target.py | Python | bsd-3-clause | 15,282 | [
"Amber"
] | 626165b2f2a0a2548f7b32f0a83c6d449fb08e5c085ffbfbe9318ae542c07484 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2009 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Vlada Perić <vlada.peric@gmail.com>
# Copyright (C) 2011 Matt Keenan <matt.keenan@gmail.com>
# Copyright (C) 2011 Tim G L Lyo... | Forage/Gramps | gramps/plugins/lib/libnarrate.py | Python | gpl-2.0 | 92,851 | [
"Brian"
] | 752bef4a6abe7aaf8e65cf341e71917cad06464c5e5bacd4fe1b8f21df50ea08 |
"""
Copyright (c) 2015 Andreea Georgescu
Created on Wed Nov 19 00:18:55 2014
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any later version.
... | SamWitte/Codds_DarkMatter | src/Data/SuperCDMSLessT5.py | Python | gpl-2.0 | 3,116 | [
"DIRAC"
] | 084a41409f4f0e7e8fa44dbeb1dc010bef7b43a73536241abbfb2ffcd0dd5d10 |
from dateutil.relativedelta import relativedelta
from django.core.exceptions import ImproperlyConfigured
from django.test import TestCase, tag
from edc_appointment.models import Appointment
from edc_base import get_utcnow
from edc_facility.import_holidays import import_holidays
from edc_visit_schedule.site_visit_schedu... | botswana-harvard/edc-visit-tracking | edc_visit_tracking/tests/test_visit.py | Python | gpl-2.0 | 4,695 | [
"VisIt"
] | ae7aafb578f76c3ac7a300e22a8a1afba36177fdcf2da24b5be08611441a7f6e |
##############################################################################
# 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... | mfherbst/spack | var/spack/repos/builtin/packages/r-affy/package.py | Python | lgpl-2.1 | 2,060 | [
"Bioconductor"
] | a22a16c436729fcf1cc1866fb35de042926d3824d43d76c0041433ff05ae9354 |
##############################################################################
# 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-deseq/package.py | Python | lgpl-2.1 | 2,110 | [
"Bioconductor"
] | 05abda210518ec4f32ad2676f1f405eb3df1390f7b8b8405ef877cdc2057c28f |
import os
import pytest
from sphinx.errors import ConfigError, ExtensionError
import sphinx_gallery
from sphinx_gallery.gen_gallery import _complete_gallery_conf
from sphinx_gallery.scrapers import (figure_rst, mayavi_scraper, SG_IMAGE,
matplotlib_scraper, ImagePathIterator,
... | sphinx-gallery/sphinx-gallery | sphinx_gallery/tests/test_scrapers.py | Python | bsd-3-clause | 11,618 | [
"Mayavi"
] | 4d8beca938276b4f956843fa3697901e666a1036d59d993e02832cb06d5da917 |
from pvlib.iotools.tmy import read_tmy2, read_tmy3 # noqa: F401
from pvlib.iotools.epw import read_epw, parse_epw # noqa: F401
from pvlib.iotools.srml import read_srml # noqa: F401
from pvlib.iotools.srml import read_srml_month_from_solardat # noqa: F401
from pvlib.iotools.surfrad import read_surfrad # noqa: F401
... | anomam/pvlib-python | pvlib/iotools/__init__.py | Python | bsd-3-clause | 935 | [
"EPW"
] | 90e17f8a1353c7b80cd4ce05446c5fdbd4071a8577d83d0bb0939c9cff6cf507 |
'''
This file in tracpy is an example init file.
Functions to initialize various numerical experiments.
Contains:
test1
test2
galveston
hab1b
Make a new init_* for your application.
loc Path to directory of grid and output files
nsteps Number of steps to do between model outputs (iter in tracmass)
ndays numbe... | dcherian/tracpy | tests/init.py | Python | mit | 12,965 | [
"NetCDF"
] | 83adcce25ec37f484836a38ae67fc683827f03ec8b50df959765df084f74fb8d |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | pie/authentication/tests.py | Python | gpl-3.0 | 2,908 | [
"Brian"
] | 85ac72f67264691a1016c35e517674deb9b3a091b69f4e0fa740653951e4d960 |
"""
Test functions for models.GLM
"""
from statsmodels.compat import range
import os
import numpy as np
from numpy.testing import (assert_almost_equal, assert_equal, assert_raises,
assert_allclose, assert_, assert_array_less, dec)
from scipy import stats
import statsmodels.api as sm
from st... | DonBeo/statsmodels | statsmodels/genmod/tests/test_glm.py | Python | bsd-3-clause | 37,718 | [
"Gaussian"
] | ac3262475ffb23ff71d02277932505630edf3ab171eaa7ce90c1f8a5a6446d5f |
import vtk
from vmtk import vmtkscripts
from vmtk import pypes
########################################################
# #
# Author: Noel Conlisk #
# Email: noecon@gmail.com #
# Script function... | nconlisk/python | VTK/vol_from_images.py | Python | gpl-3.0 | 919 | [
"VTK"
] | 2a33b5303b8c0804ee19695e43d10e23c7a1b7f982861805f5c2339031616628 |
#!/usr/bin/env python
'''
NN modules
Based on the paper:
2012 Nov IEEE Signal Processing Magazine
"Deep Neural Networks for Acoustic Modeling in Speech Recognition
-The shared views of four research groups"
'''
class layer():
kind = 'layer' # property shared by all instances of this class
def __init__(self, dept... | yunque/PyML | pynn.py | Python | gpl-2.0 | 1,960 | [
"NEURON"
] | 2227ada9aef7784cb1fe858f5af39671c0c24bdbd8273a4cc157ea879bdd5aae |
import sys
import os
import copy
from subprocess import call
from rdkit import Chem
from rdkit.Chem import AllChem
import coot_git
import pyrogen_swig as pysw
import pyrogen_boost
import atom_types
from optparse import OptionParser
import tautomer
import urllib
from jay_util import *
global pyrogen_version
pyrog... | jlec/coot | pyrogen/pyrogen.py | Python | gpl-3.0 | 32,455 | [
"RDKit"
] | a2fc23d3105214ac3eb0fdcc5e4f44b2080d82244616ae876f973ae431edc1fe |
################################################################################
# The Neural Network (NN) based Speech Synthesis System
# https://svn.ecdf.ed.ac.uk/repo/inf/dnn_tts/
#
# Centre for Speech Technology Research
# University of Edinburgh, UK
# ... | ashmanmode/TTSDNNRepo | src/configuration/configuration.py | Python | apache-2.0 | 45,317 | [
"Gaussian"
] | fbab3f5873e246926585aefc57802c8d5f78ec4348c5b51e3ba865bf4a9077d3 |
# ===============================================================================
# Copyright (C) 2010 Diego Duclos
#
# This file is part of eos.
#
# eos is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, ... | DarkFenX/Pyfa | eos/saveddata/fit.py | Python | gpl-3.0 | 75,739 | [
"CRYSTAL"
] | d5e3af61cdfbee8f3cfb5f3c13c0b4f717a9ca51cecf8894bde729f892a1573f |
"""
Generalized Linear Models with Exponential Dispersion Family
"""
# Author: Christian Lorentzen <lorentzen.ch@googlemail.com>
# some parts and tricks stolen from other sklearn files.
# License: BSD 3 clause
import numbers
import numpy as np
import scipy.optimize
from ...base import BaseEstimator, RegressorMixin
... | glemaitre/scikit-learn | sklearn/linear_model/_glm/glm.py | Python | bsd-3-clause | 25,041 | [
"Gaussian"
] | b9cf81cda51274bd26c6f1469e5f0f402c3bd8b2980673f1233e707f03ae9740 |
#!/usr/bin/env python
import os
import sys
from glob import glob
sys.path.insert(0, os.path.abspath('lib'))
from ansible import __version__, __author__
from distutils.core import setup
# find library modules
from ansible.constants import DEFAULT_MODULE_PATH
dirs=os.listdir("./library/")
data_files = []
for i in dirs... | bezhermoso/home | setup.py | Python | gpl-3.0 | 1,396 | [
"Galaxy"
] | a3fcbdfe6713d425761f345e22fdf2546e02f33f47e8b8659d9421e336e7b12d |
#!/usr/bin/env python2
# coding:utf-8
# Based on GAppProxy 2.0.0 by Du XiaoGang <dugang.2008@gmail.com>
# Based on WallProxy 0.4.0 by Hust Moon <www.ehust@gmail.com>
# Contributor:
# Phus Lu <phus.lu@gmail.com>
# Hewig Xu <hewigovens@gmail.com>
# Ayanamist Yang <ayanamist@gmail.com>... | viger/docker | proxy/proxy/code/default/gae_proxy/local/proxy.py | Python | mit | 6,968 | [
"VisIt"
] | 72653eeb5f074bd94cd83b0db26a6b6c8d78cf11e702bcfb6403cde3e04d826a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import unittest
import os
import numpy as np
from rmgpy import getPath
from rmgpy.qm.main import QMCalculator
from rmgpy.molecule import Molecule
from rmgpy.qm.gaussian import GaussianMolPM3, GaussianMolPM6
gaussEnv = os.getenv('GAUSS_EXEDIR') or os.getenv('g09root') or os... | faribas/RMG-Py | rmgpy/qm/gaussianTest.py | Python | mit | 5,473 | [
"Gaussian"
] | 8bbc3dd84a21449c9deb42ad119dd08ff87eda281a83dae1d366df437287674f |
#
# Copyright 2014 CIRAD
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distribut... | guiguimartin/scaffremodler | bin/1_create_conf.py | Python | gpl-3.0 | 9,324 | [
"BWA",
"Bowtie"
] | 958cc2a1e5072ea50cf6eb4295c92f75d01cfa4811de8c79ff991b886fde86e9 |
import sys
from argparse import ArgumentParser, RawTextHelpFormatter
from typing import Any
from django.core.management.base import BaseCommand
from django.db import ProgrammingError
from confirmation.models import generate_realm_creation_url
from zerver.models import Realm
class Command(BaseCommand):
help = ""... | jackrzhang/zulip | zerver/management/commands/generate_realm_creation_link.py | Python | apache-2.0 | 1,697 | [
"VisIt"
] | 42ebedad890cf82ea7023439f28223f802171733ca4924ec4801556e89855073 |
'''
Inspired in part by http://code.alcidesfonseca.com/docs/rdflib/graph_merging.html
'''
import sys
from rdflib.graph import Graph
def main(argv):
# inputFileName1 = '/home/mikel/UPV-EHU/Eclipse_Workspace/MergeRDFGraphs-Galaxy/data/vc-db-3.rdf'
# inputFileName2 = '/home/mikel/UPV-EHU/Eclipse_Workspace/Merg... | mikel-egana-aranguren/MergeRDFGraphs-Galaxy | src/mergerdfgraphs/MergeRDFGraphs.py | Python | gpl-3.0 | 526 | [
"Galaxy"
] | eb6f9c081af11dcb3cbe92fc339f410d14714600cc25bc80bdb3fff9dc710f36 |
import os
import sys
from tarfile import is_tarfile
from zipfile import is_zipfile
from ase.atoms import Atoms
from ase.units import Bohr, Hartree
from ase.io.trajectory import PickleTrajectory
from ase.io.bundletrajectory import BundleTrajectory
from ase.io.netcdftrajectory import NetCDFTrajectory
from ase.calculator... | PHOTOX/fuase | ase/ase/io/__init__.py | Python | gpl-2.0 | 24,476 | [
"ABINIT",
"ASE",
"CASTEP",
"CRYSTAL",
"ESPResSo",
"FHI-aims",
"GPAW",
"GROMOS",
"Gaussian",
"Gromacs",
"LAMMPS",
"Mayavi",
"NWChem",
"NetCDF",
"Quantum ESPRESSO",
"SIESTA",
"TURBOMOLE",
"VASP",
"VTK",
"WIEN2k",
"exciting"
] | 147bc14f1d9f22da4186b5cac4c3b89debc158bdfd8996be7a3af7235d1c33c5 |
#
# ast_input_line.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) a... | kperun/nestml | pynestml/meta_model/ast_input_line.py | Python | gpl-2.0 | 8,453 | [
"NEURON"
] | 66c1996925c9687c94b9cdad875ce08ddcb45bc8d13959352bac83b56d0abce0 |
#!/usr/bin/python
#
# Open SoundControl for Python
# Copyright (C) 2002 Daniel Holth, Clinton McChesney
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the Licen... | avroshk/VRDAW | VRDAW_working/OSC.py | Python | gpl-3.0 | 11,400 | [
"VisIt"
] | 1c5fca6b363f6322f9c4e815485888db3b1d72f6f151a5d739a22f01d4eeda1e |
##############################################################################
# Copyright (c) 2013-2017, 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... | skosukhin/spack | var/spack/repos/builtin/packages/py-espressopp/package.py | Python | lgpl-2.1 | 3,452 | [
"ESPResSo"
] | 01ea6339a0b46d0aa88e469ddac707d9d530a2e3eaa56001e500844c5d052e0a |
""" Test case for DIRAC.Core.Utilities.File module
"""
##
# @author Krzysztof.Ciba@NOSPAMgmail.com
# @date 2011/01/17 14:01:18
# @brief Definition of FileTestCase class.
# imports
import os
from os.path import abspath
import re
import sys
from hypothesis import given
from hypothesis.strategies import floats
from pyt... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/test/Test_File.py | Python | gpl-3.0 | 4,498 | [
"DIRAC"
] | 6ee0eb61402f177e37231a9781644e6cebfee22240b7d5e3a854834d7776cd6c |
#! /usr/bin/env python
from MDAnalysis import *
import numpy
import math
import sys
my_traj = sys.argv[1]
my_struc = sys.argv[2]
u = Universe(my_struc,my_traj)
end = my_traj.find('.pdb')
fout_angle = my_traj[0:end] + '_angle.dat'
#a = u.selectAtoms("segid A and resid 78:182")
#b = u.selectAtoms("segid B and resid ... | demharters/git_scripts | angle_glob_mhcii.py | Python | apache-2.0 | 942 | [
"MDAnalysis"
] | be57022aad82f8c473159e0bf9edce21e7d26bc6014fe719a65be46f3c763139 |
#!/usr/bin/env python3
import sys
import time
import random
import os
import subprocess
import gzip
import io
import pickle
import argparse
import itertools
from distutils.version import LooseVersion
from distutils.spawn import find_executable
sys.path.insert(1,sys.path[0]+'/..')
try:
from .version import SeqSero... | denglab/SeqSero2 | bin/SeqSero2_package.py | Python | gpl-2.0 | 86,947 | [
"BLAST",
"BWA"
] | 78dc120e80303b50960b362803abe96b77e6212368caa6a901a94ea30830f400 |
#!/usr/bin/env python2
import sys
#sys.path.append('/data/antares/aux')
import os
import glob
import json
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.mlab import rec2csv, rec2txt
from astropy.visualization import hist
from collections import Counter, OrderedDict
from ANTARES_object import Touchst... | tayebzaidi/HonorsThesisTZ | ThesisCode/DES_Pipeline/gen_lightcurves/parse_des.py | Python | gpl-3.0 | 7,003 | [
"Gaussian"
] | 59e5586bec408b02d5526fb18520706409d134bc7e9988ab8d4388f2b2c5f8ba |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | KaiSzuttor/espresso | testsuite/scripts/samples/test_wang_landau_reaction_ensemble.py | Python | gpl-3.0 | 1,250 | [
"ESPResSo"
] | 620ca951fe4cf612762995a57500cdb9995bd7c78bb97c950eeea0ba92663afe |
"""
Testing code.
Updated BSM August 2015
"""
import unittest
import os
import numpy as np
import kriging_tools as kt
import core
import variogram_models
from ok import OrdinaryKriging
from uk import UniversalKriging
from ok3d import OrdinaryKriging3D
from uk3d import UniversalKriging3D
class TestPyKrige(unittest.Te... | yejingxin/PyKrige | pykrige/test.py | Python | bsd-3-clause | 82,157 | [
"Gaussian"
] | 11ea5ef4795a75c0f2de45cefaa92b21f611d1d2e23d07ab11f3c1a378a63c5a |
#! usr/bin/env python
import optparse, os, csv, glob, sys
import MySQLdb
import PEATSA.Core as Core
import PEATSA.Core.Matrix
import matplotlib.pyplot as plt
import numpy as np
import pypar
import Environment
class ProteinComplexTool:
def __init__(self):
self.proc = pypar.size()
self.myid = pypa... | dmnfarrell/peat | sandbox/ProteinComplexTool_parallel.py | Python | mit | 15,027 | [
"MDAnalysis"
] | d5e9f083db211f90bc32d98908b65484578d16d83a1c283f6acd0ec73cd1ea84 |
# A Python implementation of Ailey's matlab tensor code.
import os
import numpy as np
import math
import SimpleITK as sitk
from scipy import ndimage
import nibabel as nib
from PIL import Image
import scipy.misc
from scipy import signal
import warnings
#warnings.filterwarnings("ignore")
def doggen(sigma):
"""
... | NeuroDataDesign/seelviz | jon/algorithms/tractography.py | Python | apache-2.0 | 13,942 | [
"Gaussian"
] | 793aa78b126847a4af1d3f4f83cdc56a49a3d91ba4d52a9560be104834f55838 |
#! /usr/bin/env python
# coding:utf-8
#########################################
# Anomaly Detection #
#########################################
from numpy import *
import numpy as np
from random import random
from matplotlib.pyplot import *
from pylab import *
from scipy.optimize import fmin_bfgs
f... | Urinx/Machine_Learning | Anomaly-Detection/anomaly_detection.py | Python | gpl-2.0 | 4,101 | [
"Gaussian"
] | 7e567f1689e2198ddda3488e575575ba07b65407b9b8d64d47595dba6b6103cb |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jgonthier/psi4 | psi4/driver/__init__.py | Python | lgpl-3.0 | 1,918 | [
"Psi4"
] | da1cd11ffa4402a5c1c43263a381571f6a1b0de0c8585ea767ebfc4cd7a7cee7 |
import json
import os
import shutil
from click.testing import CliRunner, Result
from freezegun import freeze_time
from moto import mock_s3
import great_expectations
from great_expectations import DataContext
from great_expectations.cli import cli
from great_expectations.data_context.util import file_relative_path
fro... | great-expectations/great_expectations | tests/cli/upgrade_helpers/test_upgrade_helper.py | Python | apache-2.0 | 25,748 | [
"VisIt"
] | 8ffe58c5a9c824920b7fc8b1c46580c39d8caefe6d9a3453e6b93f415609912b |
# Standard lib imports
from sys import argv
import os
from time import sleep
import re
import pdb
import logging
import datetime
import csv
import json
from collections import defaultdict
# Third-party imports
import pandas as pd
import requests
from selenium import webdriver
from selenium.webdriver.support.ui import ... | NewsappAJC/precinct-election-map | data_cleaning/2016/clarity_live.py | Python | mit | 17,373 | [
"VisIt"
] | 369d063e2fc25e1fbb9c610758f427e01dd651e594a328a25b9c93190c7e6553 |
#!/usr/bin/env python
# MIDAS: Metagenomic Intra-species Diversity Analysis System
# Copyright (C) 2015 Stephen Nayfach
# Freely distributed under the GNU General Public License (GPLv3)
import sys, os, subprocess, Bio.SeqIO
from time import time
from midas import utility
from operator import itemgetter
def read_anno... | snayfach/MIDAS | midas/run/species.py | Python | gpl-3.0 | 10,659 | [
"BLAST"
] | 927cd9d6443e2572d5a5dd0aa19e6d153d983536a26ca36864708ebefc3c3d73 |
"""
Model grism spectra in individual FLTs
"""
import os
from collections import OrderedDict
import copy
import numpy as np
import scipy.ndimage as nd
import matplotlib.pyplot as plt
import astropy.io.fits as pyfits
from astropy.table import Table
import astropy.wcs as pywcs
import astropy.units as u
#import stwc... | albertfxwang/grizli | grizli/model.py | Python | mit | 186,462 | [
"Galaxy",
"Gaussian",
"VisIt"
] | 9de6b570ae3e0c6979ffec586d079132ce7d53f2c66876d39d549efbae974c3a |
"""
Base model of MindboggleDB
Base is a generic set of classes that model the vertices (nodes) and
edges (arcs) in the Mindboggle graph database implementation.
Domain Objects
Database -
Project - a collection of subjects
Person - an individual with a roll
Subject - a participant in a project -
... | binarybottle/mindboggle_sidelined | database/base.py | Python | apache-2.0 | 5,624 | [
"VisIt"
] | 5d286a8cc70c37c5c25036937feb9358d84a013bc3712ff0ebbe7d08407d030a |
# coding=utf-8
import gettext
import gtk
import misc, ui
translators = '''\
ar - Ahmad Farghal <ahmad.farghal@gmail.com>
be@latin - Ihar Hrachyshka <ihar.hrachyshka@gmail.com>
ca - Franc Rodriguez <franc.rodriguez@tecob.com>
cs - Jakub Adler <jakubadler@gmail.com>
da - Martin Dybdal <dybber@dybber.dk>
de - Paul Joh... | tuukka/sonata-svn-test | sonata/about.py | Python | gpl-3.0 | 8,442 | [
"Desmond"
] | a622ae81af95e797117593ff006b484c053619c39a922a127c627cd6721f5697 |
class Languages:
English = 'english'
Spanish = 'spanish'
CurrentLanguage = Languages.Spanish
def set_language(lang):
global CurrentLanguage
CurrentLanguage = lang
EnglishDictionary = {
'About...': 'About...',
'About this program:': 'About this program:',
'ABOUT_DIALOG': 'This program w... | Myoldmopar/EPLaunchLight | EPLaunchLite/International.py | Python | bsd-3-clause | 5,461 | [
"EPW"
] | 975a78ba31ec8e6c74379cfb925e0031a87d6dd4d6bbcb06a7d4b790566426d7 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# ... | andreaso/ansible | lib/ansible/modules/network/lenovo/cnos_command.py | Python | gpl-3.0 | 5,666 | [
"VisIt"
] | 6721eb5e50637baf9a66e7e03e4d39d04050a52857d322cbb66c6fa93dacfc48 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-affxparser/package.py | Python | lgpl-2.1 | 2,177 | [
"Bioconductor"
] | 2bec788c94c4e746f70af595c9e6bb1be357b25a18beee6de86cf976f5425bcf |
"""
Utilities for scripts
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import argparse
import functools
import os
import shlex
import subprocess
import sys
import time
import humanize
import requests
import yaml
import pysam
import requests.package... | macieksmuga/server | scripts/utils.py | Python | apache-2.0 | 8,309 | [
"pysam"
] | 81182b43118056b9b41413080a606a34ecc7ba53ddcedfa636abdf8d23cb7357 |
#!/usr/bin/env python
"""
Copyright (c) 2006-2017 sqlmap developers (http://sqlmap.org/)
See the file 'doc/COPYING' for copying permission
"""
import os
import re
import shlex
import sys
from optparse import OptionError
from optparse import OptionGroup
from optparse import OptionParser
from optparse import SUPPRESS_... | zhinaonet/sqlmap-z | lib/parse/cmdline.py | Python | gpl-3.0 | 45,290 | [
"VisIt"
] | 9fed3d5e70d19a48754cf5517fb8f281f51f2d9477ac2f42cc233e57f267b357 |
#!/usr/bin/env python
import vtk
import numpy as np
from vmtk import vmtkscripts
import argparse
import copy
# creates lines normal to surface for evaluation in the probe image with surface
def warp_surface(args):
print("warp the surface ")
reader = vmtkscripts.vmtkSurfaceReader()
reader.InputFileNa... | kayarre/Tools | vmtk/fuzzypsurface.py | Python | bsd-2-clause | 2,767 | [
"VTK"
] | 6c406b6dfae85a106e44bbd1b02d0cba7fe1168899caa77b4bff8cce5028b4c0 |
#
# The Python Imaging Library.
# $Id$
#
# the Image class wrapper
#
# partial release history:
# 1995-09-09 fl Created
# 1996-03-11 fl PIL release 0.0 (proof of concept)
# 1996-04-30 fl PIL release 0.1b1
# 1999-07-28 fl PIL release 1.0 final
# 2000-06-07 fl PIL release 1.1
# 2000-10-20 fl PIL release 1.1.1... | sumedh123/debatify | venv/lib/python2.7/site-packages/PIL/Image.py | Python | mit | 82,447 | [
"Gaussian"
] | 795411b9479d434b97ea09ca0b26d789aa9bf718785efe37e19b1cae0e307ce4 |
#
# Copyright (C) 2011 by Brian Weck
# Licensed under the MIT license: http://www.opensource.org/licenses/mit-license.php
#
import time
from . import log, reddit, queue
class Stylesheet:
#
CSSBOT_PAUSE = "/* --- cssbot action PAUSE --- */"
CSSBOT_BEGIN = "/* --- cssbot BEGIN --- */"
CSSBOT_END = "/* -... | bweck/cssbot | cssbot/style.py | Python | mit | 3,103 | [
"Brian"
] | 5990f1a8931700d25451572af8bb6b7327e98ad08f464d0bebcc5af80c95bbde |
#!/usr/bin/env python
########################################################################
# File : dirac-externals-requirements
# Author : Adri/Federico/Andrei
########################################################################
""" If RequiredExternals section is found in releases.cfg of any extension,
... | andresailer/DIRAC | Core/scripts/dirac-externals-requirements.py | Python | gpl-3.0 | 2,702 | [
"DIRAC"
] | 41558a11a0ec96976978466378db907336dc33fe36a7180f7c4cc8fc9af10464 |
from test import test_support
import unittest
import codecs
import StringIO
class UTF16Test(unittest.TestCase):
spamle = '\xff\xfes\x00p\x00a\x00m\x00s\x00p\x00a\x00m\x00'
spambe = '\xfe\xff\x00s\x00p\x00a\x00m\x00s\x00p\x00a\x00m'
def test_only_one_bom(self):
_,_,reader,writer = codecs.lookup("u... | trivoldus28/pulsarch-verilog | tools/local/bas-release/bas,3.9/lib/python/lib/python2.3/test/test_codecs.py | Python | gpl-2.0 | 11,956 | [
"FEFF"
] | 0142424d68f315bccfb3e8f53bc13b01010296cc50d35c02d90ec887f53bea65 |
from moose import Annotator
from PyQt4.QtGui import QColor
import numpy as np
import os
import config
import pickle
import random
import matplotlib
colormap_file = open(os.path.join(config.settings[config.KEY_COLORMAP_DIR], 'rainbow2.pkl'),'rb')
colorMap = pickle.load(colormap_file)
colormap_file.close()
ignoreColor=... | dilawar/moose-full | moose-gui/plugins/kkitUtil.py | Python | gpl-2.0 | 5,378 | [
"MOOSE"
] | 7e3ef2b858a8eaac0c81474ed95750036e5b25bbe8af8d560b91e9929dbeb0a7 |
#################################################
## PTDNN - Python Toolkit for Deep Neural Network
## Author: Yajie Miao
#################################################
import os
import sys
from utils.learn_rates import LearningRateExpDecay
class BnfExpConfig(object):
def __init__(self):
# working ... | irrawaddy28/babel | s5c/conf/bnf/config_limited.py | Python | apache-2.0 | 3,287 | [
"Gaussian"
] | ed8ee2a66aaa89481b72ffa26161eb5b22af7a7e874345249803373cb3cea334 |
# FermiLib plugin to interface with Psi4
#
# Copyright (C) 2017 ProjectQ-Framework (www.projectq.ch)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
... | ProjectQ-Framework/FermiLib-Plugin-Psi4 | examples/generate_diatomic.py | Python | lgpl-3.0 | 2,889 | [
"Psi4"
] | f2f95bb08f4f9ee2a5bde4d111ac8652a1b42d456ad41dc55aa2765cee8208f2 |
#!/usr/bin/env python3
import sys
from gaussian import GaussianCom, GaussianLog
import math
import sys
CUTOFF = 2.5
try:
atom_number = int(sys.argv[1])
distances_filename = sys.argv[2]
gaussian_file = GaussianCom(sys.argv[3])
except:
print("Usage: create_distances_file <atom_number> <distances_files>... | eduardoftoliveira/qt_scripts | scripts/create_distances_file.py | Python | gpl-3.0 | 1,141 | [
"Gaussian"
] | 3f526c1043aa18286771b3b48ab83d7fcd0a80d873c492ca24a561f80d2b6981 |
from collections import OrderedDict
import numpy as np
import tensorflow as tf
from tensorflow.contrib.staging import StagingArea
from baselines import logger
from baselines.her.util import (
import_function, store_args, flatten_grads, transitions_in_episode_batch, convert_episode_to_batch_major)
from baselines.h... | dsbrown1331/CoRL2019-DREX | drex-mujoco/learner/baselines/baselines/her/ddpg.py | Python | mit | 21,742 | [
"Gaussian"
] | 7a80586d94d76a846e3fae382bfc499b87f609a5db58dc5532728f3b0d785bf2 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | nburn42/tensorflow | tensorflow/contrib/autograph/pyct/static_analysis/live_values.py | Python | apache-2.0 | 5,123 | [
"VisIt"
] | 8e89896cbe987995c2868f087b24b21db8875c7258ac7d14faa1c0334aa6c66b |
# -*- coding: utf-8 -*-
import os
import sys
def check_cclib(cclib):
"""Make sure we are importing code from a subdirectory, which should exist
and should have been updated just before running this script. Note that
this script does not assume any version in the module and just takes
what it finds...... | hainm/cclib.github.io | sphinx/attributes.py | Python | lgpl-2.1 | 2,546 | [
"cclib"
] | d29e9adc5435ebe9a76ca256a1d2e58896c36cd31929c230d16e150e07e9a547 |
"""Support for the Amazon Polly text to speech service."""
import logging
import voluptuous as vol
from homeassistant.components.tts import PLATFORM_SCHEMA, Provider
import homeassistant.helpers.config_validation as cv
_LOGGER = logging.getLogger(__name__)
CONF_REGION = 'region_name'
CONF_ACCESS_KEY_ID = 'aws_acces... | MartinHjelmare/home-assistant | homeassistant/components/amazon_polly/tts.py | Python | apache-2.0 | 6,590 | [
"Brian"
] | bc39c0243108764e5840712b33e47d3100bbb26534f6d3c8f92a6a1d8ef9caf0 |
# Copyright (C) 2012 Alex Nitz
#
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in t... | cmbiwer/pycbc | pycbc/noise/gaussian.py | Python | gpl-3.0 | 5,087 | [
"Gaussian"
] | 71e0ca8449a9ee277bf4f00d3366f85c492e9d126eb1b89ee489b121659e54fb |
# Copyright (C) 2014 Sereina Riniker
#
# 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, found at the root
# of the RDKit source tree.
#
""" Torsion Fingerprints (Deviation) (TFD)
According to a paper from Schulz-Gasch et a... | adalke/rdkit | rdkit/Chem/TorsionFingerprints.py | Python | bsd-3-clause | 23,970 | [
"RDKit"
] | 07fae897fef175f8a4a857a05cff5421465eff36138f7d5ec33d27fe0302c837 |
from builtins import range
import numpy as np
def affine_forward(x, w, b):
"""
Computes the forward pass for an affine (fully-connected) layer.
The input x has shape (N, d_1, ..., d_k) and contains a minibatch of N
examples, where each example x[i] has shape (d_1, ..., d_k). We will
reshape each ... | gutouyu/cs231n | cs231n/assignment/assignment2/cs231n/layers.py | Python | mit | 32,482 | [
"NEURON"
] | 2e9a98b625f1f01e020e768c47f3aa276f9fcebfde924e910a3360d02d7ba173 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | strint/tensorflow | tensorflow/contrib/linalg/python/ops/linear_operator_test_util.py | Python | apache-2.0 | 24,190 | [
"Gaussian"
] | 096d939dda47ac0d87bc84031493e095729ed14a30babe5c8fb73462b505a683 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-get-proxy
# Author : Stuart Paterson
########################################################################
"""
Retrieve a delegated proxy for the given user and group
"""
from __future__ import p... | chaen/DIRAC | FrameworkSystem/scripts/dirac-admin-get-proxy.py | Python | gpl-3.0 | 4,434 | [
"DIRAC"
] | eb89167f0a9cf503bcdb00f54f5b603a1173473081d55d754691b0514169dc01 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | av8ramit/tensorflow | tensorflow/contrib/py2tf/pyct/static_analysis/activity.py | Python | apache-2.0 | 8,821 | [
"VisIt"
] | 0b1733e258aabd240fa0fe040a9f22a57073347a444f7606467c568208550cda |
from django.utils.translation import ugettext as _
from django.db import models
from django.conf import settings
from django.contrib.auth.models import User
from djangoedu.ldap.fields import LdapObjectField
try:
import mptt
except ImportError:
raise ImproperlyConfigured, "You're missing django-mptt, go get it... | tjnapster555/django-edu | djangoedu/core/models.py | Python | mit | 8,493 | [
"VisIt"
] | 12503da7a9802a674e451c4ffebc9d16db91264ff75af62c436e355670bbee5d |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | kobejean/tensorflow | tensorflow/python/autograph/converters/name_scopes.py | Python | apache-2.0 | 2,471 | [
"VisIt"
] | 59f38289e7219b071bb947822e427547d157ed353835197c06b8e20ee8591654 |
import csv
import numpy as np
import random
import Network as net
import ActivationFunctions as af
X = np.empty(shape=(4000,401), dtype=np.int8)
Y = np.zeros(shape=(4000,10), dtype=np.int8)
X_test = np.empty(shape=(200,401), dtype=np.int8)
Y_test = np.empty(shape=(200,401), dtype=np.int8)
def loadData():
random.s... | evalkaz94/neural_network_py | Example.py | Python | mit | 2,611 | [
"NEURON"
] | abccaaf10a688f26a990cb188ac6da0094e244fff603a702b055a4cc6ebea328 |
# 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... | indashnet/InDashNet.Open.UN2000 | android/external/chromium_org/PRESUBMIT.py | Python | apache-2.0 | 37,746 | [
"VisIt"
] | ac0f8d4e47f44650559157b4127f8fbc3605208f3b5110c1ad4abfe32d484dd6 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/analysis/test_distances.py | Python | gpl-2.0 | 9,822 | [
"MDAnalysis"
] | 18c8625479df2586eafa067da163b44354c0c0da7e1c483129f1245cd4944f5d |
import vtk
def setup():
# create a rendering window and renderer
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
# create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
return ren,renWin,iren
def create... | martindurant/misc | vtk_simple.py | Python | mit | 772 | [
"VTK"
] | 08e0f636954a1399fc45eae00dc89e85c9dc34241deaac9ae678615ee89b51cb |
# -*- coding: utf-8 -*-
"""
Created on Mon Jun 8 15:37:51 2015
@author: Anton O Lindahl
"""
import h5py
import argparse
import matplotlib.pyplot as plt
import numpy as np
import time
import os
import sys
import lmfit
import warnings
from aolPyModules import wiener, wavelet_filter
import time_to_energy_conversion as ... | aolindahl/streaking | process_hdf5.py | Python | gpl-2.0 | 46,151 | [
"Gaussian"
] | 6512bab1ab20d638fc5708b11ef844c7a0bc01614e6d062d94904deae0c22aca |
"""
Python implementation of the fast ICA algorithms.
Reference: Tables 8.3 and 8.4 page 196 in the book:
Independent Component Analysis, by Hyvarinen et al.
"""
# Authors: Pierre Lafaye de Micheaux, Stefan van der Walt, Gael Varoquaux,
# Bertrand Thirion, Alexandre Gramfort, Denis A. Engemann
# License: BS... | vortex-ape/scikit-learn | sklearn/decomposition/fastica_.py | Python | bsd-3-clause | 19,834 | [
"Gaussian"
] | 76a0f5876ea09c1882ac8000050c4d7cc885a5aa659e6b8cf5ed647a54b24694 |
#Standard imports
import os
import inspect
#Non-standard imports
import catmap
from catmap import ReactionModelWrapper
from catmap.model import ReactionModel
from ase.atoms import string2symbols
class ParserBase(ReactionModelWrapper):
def __init__(self,reaction_model=ReactionModel()):
"""Class for `parsi... | starry99/catmap | catmap/parsers/parser_base.py | Python | gpl-3.0 | 5,798 | [
"ASE"
] | 09f34aea03ffc285f34cd5624e7ae5badaf6dbdd834d3588cad0cd1adcf0f1b5 |
"""
A first test for the ELBO on the catalysis problem.
The target is consisted of an uninformative prior and a Gaussian likelihood.
The approximating mixture has two components.
Author:
Panagiotis Tsilifis
Date:
6/6/2014
"""
import numpy as np
import matplotlib.pyplot as plt
import os
import cPickle as p... | ebilionis/variational-reformulation-of-inverse-problems | unittests/test_up_0.py | Python | gpl-2.0 | 4,715 | [
"Gaussian"
] | e9507deb223c14b868f907bccfcc0525eabf8d569daf1df1499f2681a870c7ad |
## Program to simulate short-tE event observing sequence.
from astropy.time import Time, TimeDelta
import mulens_class
from astropy import constants
import matplotlib.pyplot as plt
from sys import argv, exit
from os import path
import numpy as np
import copy
def sim_short_te( params ):
"""Main driver function to ... | rachel3834/mulens_modeler | trunk/scripts/observe_shortte.py | Python | gpl-2.0 | 7,738 | [
"VisIt"
] | 6306e66fa9f2987b7a8087430f85293f2e3854dfeb0bcac491decb901f6b7245 |
from __future__ import division
import numpy as np
from numpy import dot
from dipy.core.geometry import sphere2cart
from dipy.core.geometry import vec2vec_rotmat
from dipy.reconst.utils import dki_design_matrix
# Diffusion coefficients for white matter tracts, in mm^2/s
#
# Based roughly on values from:
#
# Pierpao... | oesteban/dipy | dipy/sims/voxel.py | Python | bsd-3-clause | 26,641 | [
"Gaussian"
] | ff796a9ad41d97c7b5bb9b312f9a3404349011a5df9a39524c5015068dd84676 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/test_streamio.py | Python | gpl-2.0 | 16,041 | [
"CHARMM",
"MDAnalysis"
] | 49957ce8080bd032a4f4a08036a56c47c3e5e5cdde7cf0f0ff113028fa1f7878 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
import time
m = 2000
n = 4000
lambda1 = 3
lam... | sg0/Elemental | examples/interface/EN.py | Python | bsd-3-clause | 2,102 | [
"Gaussian"
] | 95e7dd2bfe1fcd39b1af98d03b7f89a1fadbec7112a4bf93cad791b2556f26c7 |
"""Data structure for genomic intervals and their annotation."""
import pandas as pd
import numpy as np
from natsort import natsorted
import pyranges as pr
from pyranges.tostring2 import tostring
from pyranges.methods.intersection import _intersection, _overlap
from pyranges.multithreaded import pyrange_apply, pyr... | biocore-ntnu/pyranges | pyranges/pyranges.py | Python | mit | 254,818 | [
"pysam"
] | b34f235cb1cc8b0e1f529c58c85d3f77269ff6066a441187c23386a12d8f7260 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | testsuite/python/stress.py | Python | gpl-3.0 | 13,812 | [
"ESPResSo"
] | 4c710a6a8fff63a24a6181856f676bb1cd21b4f2f97a47c28b42aa053ae1259f |
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