text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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"""
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.
Written (W) 2013 Heiko Strathmann
Written (W) 2013 Dino Sejdinovic
"""
fro... | karlnapf/kameleon-mcmc | kameleon_mcmc/tools/Visualise.py | Python | bsd-2-clause | 5,656 | [
"Gaussian"
] | 09cb5762af93ecab661fa1394be17970d170336e0ce96f52275349e1a942ef2b |
from octopus.sequence.runtime import *
from octopus.sequence.control import Bind
from twisted.internet import defer
defer.Deferred.debug = True
v = variable(0, "i", "i")
d = variable(False, "b", "b")
d_ctrl = Bind(d, v, lambda x: x > 5)
s = sequence(
log("Running"),
loop_while(v < 10, [
increment(v),
log("v =... | richardingham/octopus | examples/test_bind.py | Python | mit | 425 | [
"Octopus"
] | bcd6b996a939b057a7ab12fd8cb531c5f9b2c6ce69e84fa1c896c3c184f0e06a |
# -*- coding: utf-8 -*-
"""
The module provides visualization routines for displaying spatial and
energy distributions of synchrotron sources in 2D and 3D."""
__author__ = "Konstantin Klementiev"
__date__ = "12 Mar 2014"
#import cmath
import time
import copy
import numpy as np
#import matplotlib as mpl
import matplo... | kklmn/xrt | tests/raycing/test_sources.py | Python | mit | 14,626 | [
"Mayavi"
] | 50d9536d9c83f8d76774c77f87ab35729575eec97ea569155415812ec2d50ff9 |
# coding=utf-8
from __future__ import unicode_literals
from .. import Provider as PersonProvider
class Provider(PersonProvider):
formats = (
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_n... | ericchaves/faker | faker/providers/person/de_DE/__init__.py | Python | mit | 33,335 | [
"Brian",
"FLEUR"
] | c0d4f0b97129d30ec33e0a9d565ed473cb1614686045278d6ec03d566ab98b80 |
"""
Created on 16.05.2010
@author: RevEn
This module defines common training methods for neural networks.
Example:
Assume we have a simple neural network with two inputs and one output
and we'd like to train it XOR function.
Initialize neural network with 2 inputs, one hidden layers with 2 neurons
and one o... | reven86/gpgpu-neuralnet | nn/training.py | Python | gpl-3.0 | 34,249 | [
"NEURON"
] | 70e1eca929fc9df9296e6901d01effa51c59727d91ae05a126da2134124e5ad9 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# License: BSD style
import numpy as np
from scipy import linalg, optimize, rand
from ..base import BaseEstimator, RegressorMixin
from ..metrics.pairwise import m... | sgenoud/scikit-learn | sklearn/gaussian_process/gaussian_process.py | Python | bsd-3-clause | 34,381 | [
"Gaussian"
] | d8db0a18200d798bf8484da9da3ccd7301766b8defc6c6e84d30331f008fe366 |
import sys
from pymol import cmd
def save_surface(arg1):
cmd.disable()
cmd.enable(arg1)
cmd.hide("everything", arg1)
cmd.show("surface", arg1)
cmd.save("%s.obj" % arg1, arg1)
cmd.enable()
def prepare_data(arg1):
cmd.load("%s_r_b.pdb" % arg1, zoom=0)
cmd.load("%s_l_b.pdb" % arg1, zoo... | icekeeper/docking | benchmark/scripts/prepare_data.py | Python | mit | 817 | [
"PyMOL"
] | 804521e0afe5795a35be70f37e5e8dc5100b7f5aaaf5f514480989c31ba32ec8 |
# coding: utf-8
#
# Detection of extreme intervals in multivariate time-series
# Author: Erik Rodner (2015-) & Björn Barz (2016)
# Novelty detection by minimizing the KL divergence
# In the following, we will derive a similar algorithm based on Kullback-Leibler (KL) divergence
# between the distribution $p_I$ of data ... | cvjena/libmaxdiv | maxdiv/maxdiv.py | Python | lgpl-3.0 | 12,655 | [
"Gaussian"
] | d572d20b1ee2d5a450200a30a5daaf169bb446342d2fddd6ae4142287c935078 |
#!/usr/bin/env python 2.7.5
# -*- coding: utf-8 -*-
# @name: nessus.py
# @author: Brian Warehime
# @date: 2014/03/07
# @copyright: <https://www.gnu.org/licenses/gpl-3.0.html>
#############
# LIBRARIES #
#############
import urllib2
import argparse
import os
import xml.etree.cElementTree as ET
... | brianwarehime/nessus-api | nessus.py | Python | gpl-2.0 | 9,442 | [
"Brian"
] | ee33cb66e7b4852a08035c9198dae00f1b3edb7422e81f8de57aa05a3ee241c3 |
"""
Class for reading output files from NEST simulations
( http://www.nest-simulator.org/ ).
Tested with NEST2.10.0
Depends on: numpy, quantities
Supported: Read
Authors: Julia Sprenger, Maximilian Schmidt, Johanna Senk
"""
# needed for Python3 compatibility
import os.path
import warnings
from datetime import dat... | samuelgarcia/python-neo | neo/io/nestio.py | Python | bsd-3-clause | 31,935 | [
"NEURON"
] | 30afafa754ee41d7050d4c43035a0b398d045bc97ef1d67aa6040191b22515cb |
#
# Author: Henrique Pereira Coutada Miranda
# Tests for yambopy
# Si
#
import matplotlib
import unittest
import sys
import os
import shutil
import argparse
import subprocess
import filecmp
from yambopy import *
from qepy import *
class TestPW_Si(unittest.TestCase):
""" This class creates the input files for Si an... | henriquemiranda/yambopy | tests/test_si.py | Python | bsd-3-clause | 10,900 | [
"Yambo"
] | 27cd3a811aec1c03da37eab0e229d30e8b1e8ccfe869e72232a9a0fb95a4bac1 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
#!/usr/bin/python
import sys, getopt, scipy, os, h5py, matplotlib
import numpy as np, pylab as pl
from sklearn.utils.arpack import eigsh
from sklearn.cluster import KMeans
from mayavi.mlab import *
import nibabel.gifti.giftiio as gio
from IPython.core... | margulies/topography | utils_py/embedding.py | Python | mit | 4,389 | [
"Mayavi"
] | 9d25d2b9728f768ccbd83bdb0aa19d79b3075fdbeab074b6ec605b040c25978d |
# Copyright (C) 2013 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
# (a... | roehm/espresso | config/gen_featureconfig.py | Python | gpl-3.0 | 3,624 | [
"ESPResSo"
] | d71ba6fb70271bd15ef30e5143ba0537b891c2ae8baf7e7ea728831e5026f546 |
#! /usr/bin/env python
# Stewart Jamieson (Stewart.Jamieson@ed.ac.uk) and Magnus Hagdorn, 2005 - University of Edinburgh.
# This script reads ascii spatial data files (e.g. created in ArcGIS) and outputs a netCDF file.
import sys, getopt,numpy, PyCF, datetime, string, PyCF.CF_proj
def usage():
"print short help ... | glimmer-cism/PyCF | progs/a2c.py | Python | gpl-2.0 | 16,119 | [
"NetCDF"
] | 966bf0c75aa5bafad0ca44dce2e08ca0084a1f18e6bb8e023779127dc6dd20fc |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import itertools
import os
from spack import *
class Paraview(CMakePackage, CudaPackage):
"""ParaView is an open-so... | LLNL/spack | var/spack/repos/builtin/packages/paraview/package.py | Python | lgpl-2.1 | 21,875 | [
"NetCDF",
"ParaView",
"VTK"
] | aac2e8715774ef35e3765cca044a738b0e888c2a3e07f0ff8d5cf05397d21ef2 |
########################################################################
# $HeadURL$
# File : ServerUtils.py
# Author : Ricardo Graciani
########################################################################
"""
Provide uniform interface to backend for local and remote clients (ie Director Agents)
"""
__RCSID__ ... | myco/VMDIRAC | WorkloadManagementSystem/Client/ServerUtils.py | Python | gpl-3.0 | 809 | [
"DIRAC"
] | 1b5df5445ce63fbb34f6c7998cddba289a417987633dd2715eca0decf75ee358 |
import numpy as np
from netCDF4 import Dataset
import os
import sys
from ._threedcube import _LogStart
_lg=_LogStart().setup()
#needed to add this for python 3 support...
from .scf import call_ffmpeg,axisEqual3D
"""
MkMov: sub-command "3dcube" workhorse file.
"""
def dispay_passed_args_threedcube(arguments,working... | chrisb13/mkmov | commands/threedcube.py | Python | gpl-3.0 | 19,134 | [
"NetCDF"
] | becc9cd9bc171f44a27ee0947bab0011383103acfb42589d326b41e0ad2d62d2 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, absolute_import
"""
This module provides conversion between the Atomic Simulation Environment
Atoms object and pymatgen Structure objects.
"""
__author__ = ... | sonium0/pymatgen | pymatgen/io/ase.py | Python | mit | 1,853 | [
"ASE",
"pymatgen"
] | 93b2a06bebbdadd9b699e4acfae6708b2f53b3465cf600448a3d8e0ab24fdfee |
#!/usr/bin/env python
"""Utility script to convert an old VTK file format to the new VTK XML
file format (serial format). The output XML file will contain *all*
the existing scalars, vectors and tensors in the input file.
This requires VTK 4.x or above.
Created May 2003, Prabhu Ramachandran <prabhu@aero.iitm.ernet.... | sgh/vtk | Utilities/vtk2xml.py | Python | bsd-3-clause | 5,255 | [
"VTK"
] | fe928dfb29b8401fd99a9ccb425a25adec2d9dbd4b07e6ef8634d2a7e77d10ef |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2019 Jonathan Dent, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# ... | dictoon/blenderseed | translators/objects/__init__.py | Python | mit | 1,419 | [
"VisIt"
] | 2d2e5c539707325ec8d0c5031cfa46e88818030fcde07638875fb0534bc3704f |
from __future__ import absolute_import, division, print_function
# ----------------------------------------------------------------------------
# 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 ... | JWDebelius/scikit-bio | skbio/io/_exception.py | Python | bsd-3-clause | 1,381 | [
"scikit-bio"
] | 43208065e49292d5427b26fe1e46ceda3e05f81d4f9471389df898711ecfd564 |
import ocpaccess.download
"""
Two sets of tokens are supplied below -- `common` and `full`.
common The most common data download.)
full LARGE FILE WARNING
For the compressed data, visit [our website].
"""
# Common
common = ['kasthuri11',
'kat11vesicles',
'kat11segments',
'k... | openconnectome/Kasthuri-et-al-2014 | ramonify/old/download_data.py | Python | apache-2.0 | 1,868 | [
"VisIt"
] | 0b2339a9808ac2ec74ec40213b5b0ef646517073c13306a429f747286d868102 |
""" Operation handler to set the status for transformation files
TODO: Is there any good reason why this is just not using a forwardDISET instead?
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities ... | ic-hep/DIRAC | src/DIRAC/TransformationSystem/Agent/RequestOperations/SetFileStatus.py | Python | gpl-3.0 | 1,991 | [
"DIRAC"
] | 4288468cb6298b1ef844fd347b09b7e2264d9fd7df2b34b03f20a20b99b18b6f |
#!/usr/bin/env python
#
# Gaze tracking calibration
# - use calibration video heatmap and priors
#
# AUTHOR : Mike Tyszka
# PLACE : Caltech
# DATES : 2014-05-15 JMT From scratch
#
# This file is part of mrgaze.
#
# mrgaze is free software: you can redistribute it and/or modify
# it under the terms of the GNU Ge... | jmtyszka/mrgaze | build/lib/mrgaze/calibrate.py | Python | mit | 16,096 | [
"Gaussian"
] | 004d1b48753bb96c7abc844b8eeddd46dd73afdb74261d26a6e53b9f93c147cb |
from collections import defaultdict
from nodes import GraphNode as Node
from queue import Queue
from stack import Stack
class Edge(object):
weight = None
src = None
dst = None
def __init__(self, n1, n2, weight=0):
self.weight = weight
self.src = n1
self.dst = n2
# def con... | mr-uuid/datastructs | datastructs/directedgraphs.py | Python | gpl-2.0 | 7,428 | [
"VisIt"
] | d055629fe903b645370cc9f4e08d6fddfd8348345f039102c022b38d05af9305 |
#Copyright ReportLab Europe Ltd. 2000-2016
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/platypus/paraparser.py
__version__='3.3.0'
__doc__='''The parser used to process markup within paragraphs'''
import string
import re
import sys
... | EduPepperPDTesting/pepper2013-testing | lms/djangoapps/reportlab/platypus/paraparser.py | Python | agpl-3.0 | 49,348 | [
"VisIt"
] | 3e99dd8e67f51af777e8b908e7c8f3b8eedcfd80383199b2af864253dacdcdcc |
#============================================================================
#
# Copyright (c) Kitware Inc.
#
# 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... | KitwareMedical/VesselView | Modules/Scripted/InteractiveSegmentTubes/InteractiveSegmentTubesLogic/InteractiveSegmentTubesLogic.py | Python | apache-2.0 | 8,954 | [
"VTK"
] | 23c4c4e0fc62d563fea105e72ced8c5a3b8f9f7a3f2edcc2e8df73955d89043b |
# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from .. import kern
from ..likelihoods import Gaussian
from ..core.parameterization.variational import NormalPosterior, NormalPrior
from ..inference.latent_function_inference.var_dtc... | ptonner/GPy | GPy/models/bayesian_gplvm_minibatch.py | Python | bsd-3-clause | 10,878 | [
"Gaussian"
] | 2fff4d3f600ebfd5828352ff3f91d34dab762bd889312650ea91b153774a87c4 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Provides the capability to load netCDF files and interpret them
according to the 'NetCDF Climate and Forecast (CF) Metadata... | SciTools/iris | lib/iris/fileformats/cf.py | Python | lgpl-3.0 | 46,634 | [
"NetCDF"
] | 85a973a4ebb975573f1376bc2b4ce1d3459a36e91b778b0988c6b3a7ca069a3d |
"""
Basic enumeration, providing ordered types for collections. These can be
constructed as simple type listings...
::
>>> from stem.util import enum
>>> insects = enum.Enum("ANT", "WASP", "LADYBUG", "FIREFLY")
>>> insects.ANT
'Ant'
>>> tuple(insects)
('Ant', 'Wasp', 'Ladybug', 'Firefly')
... or with ove... | abcdef123/stem | stem/util/enum.py | Python | lgpl-3.0 | 4,576 | [
"Firefly"
] | b49636feb299e697438910856d4108dbc9e8ef35c441c678e36f02d8ad9759ad |
########################################################################
# $HeadURL $
# File: DataLoggingClient.py
########################################################################
""" :mod: DataLoggingClient
=======================
.. module: DataLoggingClient
:synopsis: client for DataLoggingDB
... | avedaee/DIRAC | DataManagementSystem/Client/DataLoggingClient.py | Python | gpl-3.0 | 760 | [
"DIRAC"
] | 63bc1a0a51235165b239e71b12e1ac6580e7d8fb38f512ba104cf95a19863c5c |
confirmation = "".join(['<!doctype html>','<html>','<head>','<title>MINC Community Signup Confirmation</title>','<meta name="viewport" content="width=device-width, initial-scale=1">',
'<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">','<link rel="stylesheet" href="https://app.divshot.com/themes/f... | nicodee/minc | mailContent.py | Python | mit | 4,135 | [
"VisIt"
] | 89705d36f2088b8183fed13aec5fe25cd82c44f6e4c8c91fc8bd0229700ba286 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/sources/finder.py | Python | agpl-3.0 | 71,362 | [
"Galaxy",
"Gaussian"
] | 5db63865127633f8e524e82172d6582706be19e96e1ca3033ac1ae0fc7cc50eb |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'VisitRegistrationError'
db.create_table(u'clinics_visitre... | myvoice-nigeria/myvoice | myvoice/clinics/migrations/0012_auto__add_visitregistrationerror__add_visitregistrationerrorlog.py | Python | bsd-2-clause | 14,195 | [
"VisIt"
] | 4a8518bb17fd3c4b923f6d3fc3ca5b08152e15ddabfc47be92187853ef6d7da6 |
#!/usr/bin/env python2
if __name__ == "__main__":
import argparse
from libs.IO import is_folder
from plugins.importer import import_history
from plugins.images import IO as ImageIO
from os import listdir
from os.path import isfile, join
from sys import exit
from plugins.analysis import... | nico202/pyNeMo | MakeImageFromHash.py | Python | gpl-2.0 | 6,394 | [
"NEURON"
] | 25411ec21125f7ddf098d0275ac0e2c3f060055b3cf66685653f0a186617bc1a |
# Copyright 2014-2017 Insight Software Consortium.
# Copyright 2004-2009 Roman Yakovenko.
# Distributed under the Boost Software License, Version 1.0.
# See http://www.boost.org/LICENSE_1_0.txt
class declaration_not_found_t(RuntimeError):
"""Exception raised when the declaration could not be found"""
def __i... | thewtex/ITK | Modules/ThirdParty/pygccxml/src/pygccxml/declarations/runtime_errors.py | Python | apache-2.0 | 1,492 | [
"VisIt"
] | 4893723a537dc8bbbea3fad5aa0422391a5bb5fcf0520d9af0b8c95155ab44b1 |
from WebAppDIRAC.Lib.WebHandler import WebHandler, WErr, WOK, asyncGen
from WebAppDIRAC.Lib.SessionData import SessionData
from DIRAC import gConfig, S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import Time
from DIRAC.Core.Utilities.List import uniqueElements
from DIRAC.ConfigurationSystem.Client.Helpers.Operation... | atsareg/WebAppDIRAC | WebApp/handler/JobLaunchpadHandler.py | Python | gpl-3.0 | 9,222 | [
"DIRAC"
] | 654def81fb877737ca962f61bb5141aefd0a052b9dcbf2f26b83fb66fdf5e59b |
# encoding: utf-8
from woo.dem import *
from woo.fem import *
import woo.core
import woo.dem
import woo.pyderived
import woo.models
import math
from minieigen import *
class FallingHorse(woo.core.Preprocessor,woo.pyderived.PyWooObject):
'''Preprocessor for the falling horse simulation. The falling horse is historica... | tarthy6/dozer-thesis | py/pre/horse.py | Python | gpl-2.0 | 11,731 | [
"ParaView",
"VTK"
] | 3abb28e6efaf4e33427344ab81da0068b117e71c236a4f95434cba0a5cd0c054 |
import ROOT
#get other things from ROOT
from ROOT import TH1F, TH2F, Math
from math import tanh, floor, sqrt, cos
import numpy as np
from numpy import random as rng
#load library with dictionaries for objects in tree
ROOT.gSystem.Load("libFWCoreFWLite.so")
ROOT.AutoLibraryLoader.enable()
#open ROOT file
fIn=ROOT.T... | lgray/HGCanalysis | test/playingWithPions.py | Python | gpl-3.0 | 13,139 | [
"Gaussian"
] | 7ae7e192369c900d88086c648713c215c87d3e9272efe2d63e2c584a73493455 |
# -*- coding: utf-8 -*-
#
# grid_to_gssha.py
# GSSHApy
#
# Created by Alan D Snow, 2016.
# License BSD 3-Clause
from builtins import range
from datetime import datetime
from io import open as io_open
import logging
import numpy as np
from os import mkdir, path, remove, rename
import pangaea as pa
import pandas as ... | CI-WATER/gsshapy | gsshapy/grid/grid_to_gssha.py | Python | bsd-3-clause | 55,286 | [
"NetCDF"
] | f948112709daef7672716da445be0fe4259e1e95dd1dee12954c5b701fb6685f |
#! /usr/bin/env python
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
from DIRAC.Resources.Catalog.FileCatalog import FileCatalog
from DIRAC.Core.Utilities.File import makeGuid
from DIRAC.Core.Utilities.Adler ... | Sbalbp/DIRAC | Resources/Catalog/test/TestCatalogPlugin.py | Python | gpl-3.0 | 18,043 | [
"DIRAC"
] | b55cbcc19409169944b750efb51465d52e498f590be643790c6435ca756f664e |
""" Unit tests for pipelines expressed via dask.delayed
"""
import functools
import logging
import sys
import unittest
import numpy
from astropy import units as u
from astropy.coordinates import SkyCoord
from data_models.polarisation import PolarisationFrame
from processing_components.image.operations import export... | SKA-ScienceDataProcessor/algorithm-reference-library | tests/processing_components/test_imaging.py | Python | apache-2.0 | 8,060 | [
"Gaussian"
] | ad713f819ed0e6f2b06fbbe0ca5d92b9a5e7b82015118c446f12e8f510e22e8c |
#! /usr/bin/env python
# A script to test triplet STDP (stdp_triplet_synapse)
# Presently, both potentiation and depression are additive
# Author: Eilif Muller
# try:
# $ ipython -pylab
# >>> execfile('test_triplet_stdp.py')
# produces nice plot, hopefully!
import numpy
import numpy.random as nr
import time
dt =... | QJonny/CyNest | developer/unittests/test_triplet_stdp.py | Python | gpl-2.0 | 9,889 | [
"NEURON"
] | e0bf5483a41ad642023317dfbec746b7e0465f38480b2a480dea40ff8d07a2c5 |
# $Id$
#
# importsym.py: Import C symbol decls (structs, enums, etc) and write them
# to another file
#
# Copyright (C)2013 Teluu Inc. (http://www.teluu.com)
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# t... | VoIPGRID/PJSIP | pjsip-apps/src/swig/importsym.py | Python | gpl-2.0 | 5,063 | [
"VisIt"
] | cd1f4b13f169ab65605798d3eb4b42a905bf4d860a47485ef2d1f76745d2e6a4 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
"""Installed collections management package."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import errno
import fnmatc... | j-carl/ansible | lib/ansible/galaxy/collection/__init__.py | Python | gpl-3.0 | 70,137 | [
"Galaxy"
] | e5fe624484d20c443f9ba3105f324f9fa7d833637b54f3185a16aad0c4d38b25 |
'''
Created on Nov 13, 2012
@author: Shunping Huang
'''
__all__ = ['fixmate']
import gc
import pysam
import logging
logger = logging.getLogger()
MAX_SEGMENTS_PER_HIT = 2
def process(reads, rname):
'''Process a set of reads with the same read name'''
nReads = len(reads)
assert nReads > 0
... | andrewparkermorgan/lapels | lapels/matefixer.py | Python | mit | 5,855 | [
"pysam"
] | 3fd33ca8e27e31fbf6af40c995496405c59f81b49528e51a5ac192540a8fdb85 |
../../../../../../../share/pyshared/orca/scripts/apps/planner/braille_generator.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/planner/braille_generator.py | Python | gpl-3.0 | 82 | [
"ORCA"
] | 0391681080c005a1cf19065bb9065a541ae0072d4a54c7fff47393b8592877c8 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed May 24 15:40:25 2017
@author: Gerardo A. Rivera Tello
"""
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
from scipy.io import netcdf
from osgeo import gdal,osr
import numpy as np
import os
#%%
if 'GDAL_DATA' not in os.environ:
... | DangoMelon0701/PyRemote-Sensing | NETCDF scripts/SODA3/anomalies.py | Python | mit | 5,546 | [
"NetCDF"
] | c3664e16bc740648134510108a5c0960320a589bc6dc213a1098f390e3e037b9 |
########################################
# Read TRMM netcdf files.py
#
# Created by: Peter Willetts
# Created on: 12/11/2013
#
########################################
#
#
###################################################
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import numpy as np
from... | peterwilletts24/Python-Scripts | era_interim/netcdf_fileread_one_file.py | Python | mit | 3,089 | [
"NetCDF"
] | 5d5bc05457799bfd7478d87f6162cf4ffb7157b5c5ba4fa55a01576412ded299 |
import os
from shutil import rmtree
from string import Template
from tempfile import mkdtemp
try:
from galaxy import objectstore
except ImportError:
from lwr import objectstore
from contextlib import contextmanager
DISK_TEST_CONFIG = """<?xml version="1.0"?>
<object_store type="disk">
<files_dir path="${te... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/unit/test_objectstore.py | Python | gpl-3.0 | 7,833 | [
"Galaxy"
] | 2da78da692341299e6791edd2587346a9f5dab2d1a383f7b018d4c30117dfaba |
# -*- coding: utf-8 -*-
{
"'Cancel' will indicate an asset log entry did not occur": "'Abbrechen' wird angeben, dass ein Asset Log Eintrag nicht eingetreten ist",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that... | collective/eden | languages/de.py | Python | mit | 255,558 | [
"VisIt"
] | dbad583e3dc52ab04a005eaf6522a7c70ec14a98de9ded1822baf9002bdbc3ab |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-setup-site
# Author : Ricardo Graciani
########################################################################
"""
Initial installation and configuration of a new DIRAC server (DBs, Services, A... | Sbalbp/DIRAC | Core/scripts/dirac-setup-site.py | Python | gpl-3.0 | 1,587 | [
"DIRAC"
] | 4b05be6a65ec7e5fe25ab9c8ab1290b71eb983e10e5c991552cfca6c4dc8f0cd |
"""
Diff collections, as sets
"""
__author__ = "Dan Gunter <dkgunter@lbl.gov>"
__date__ = "3/29/13"
# System
import logging
import re
import time
# Package
from pymatgen.db import util
from pymatgen.db.query_engine import QueryEngine
from pymatgen.db.dbconfig import normalize_auth
_log = logging.getLogger("mg.vv.dif... | materialsproject/pymatgen-db | pymatgen/db/vv/diff.py | Python | mit | 15,009 | [
"pymatgen"
] | 9912cb56e47c808ea5f9732e013013a18e3e2fb2e478fdce06551e46596026d3 |
##############################################################################
# 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/mefit/package.py | Python | lgpl-2.1 | 1,877 | [
"HTSeq"
] | 7a84f8066bba162b72e2d78bbb32e7f8dd9464d8eccd489ad49fc49b9bed06c8 |
import pygame
def test_fun():
print "test_fun called!"
menu = { "Menu1" : ("Header 1", { "Menu item 1" : None,
"Menu item 2" : test_fun,
}),
"Menu2" : ("Header 2", { "Menu 2 item 1" : None,
"Menu 2 item ... | jakbob/guitarlegend | gui/menu.py | Python | gpl-3.0 | 964 | [
"MOE"
] | cf89bd887b85c01b00ce672e28db0519ef7a2eba2d882ce4f81b92a89a58a6e6 |
from aces.materials import Material
from aces.modify import get_unique_atoms
from ase import Atoms,Atom
from math import pi,sqrt
from ase.dft.kpoints import ibz_points
from ase.lattice import bulk
from aces import config
class structure(Material):
def set_parameters(self):
self.enforceThick=False
self.latx=1
se... | vanceeasleaf/aces | aces/materials/Sii.py | Python | gpl-2.0 | 1,250 | [
"ASE"
] | 5749e21ba4d42c244e9ddc0a0e3afef4a5d4ee5ba9b50bd76ba4a6fbe99af098 |
# -*- coding: utf-8 -*-
"""
Models used to implement SAML SSO support in third_party_auth
(inlcuding Shibboleth support)
"""
from __future__ import absolute_import
import json
import logging
from config_models.models import ConfigurationModel, cache
from django.conf import settings
from django.contrib.sites.models im... | fintech-circle/edx-platform | common/djangoapps/third_party_auth/models.py | Python | agpl-3.0 | 30,925 | [
"VisIt"
] | 787ee609e465b94e3890aa77232a22a8e915c24aa8e5393784df9c0fcc461880 |
#------------------------------------------------------------------------------
# Copyright (c) 2007, Enthought, Inc.
# All rights reserved.
#
# This software is provided without warranty under the terms of the BSD
# license included in enthought/LICENSE.txt and may be redistributed only
# under the conditions describe... | enthought/etsproxy | enthought/util/distribution/api.py | Python | bsd-3-clause | 895 | [
"Gaussian"
] | 916956db2b61352b1b9c4ef890d6618f059dc5a92fae686ff6ac31cee770322b |
# Author: Yang Long <longyang_123@yeah.net>
#
# License: LGPL-2.1
import numpy as np
def Uniform(chromes,LB,UB,mutationrate,IntCon,args):
'''
Uniform random mutation (Default)
'''
preal = 0.1
pint = 0.2
if 'preal' in args:
preal = args['preal']
if 'pint' in args:
pint = arg... | longyangking/Husky | Husky/GA/Mutation.py | Python | lgpl-2.1 | 2,717 | [
"Gaussian"
] | 10835cf61e000ec8793a3a09c27455388a768d3268df7ba526863d8785394ddd |
# -*- coding: utf-8 -*-
"""Tests for data integration tools."""
import unittest
from pybel import BELGraph
from pybel.constants import GENE
from pybel.dsl import Gene, Protein, Rna
from pybel_tools.integration import overlay_type_data
HGNC = 'hgnc'
class TestIntegrate(unittest.TestCase):
"""Tests for data int... | pybel/pybel-tools | tests/test_integrate.py | Python | mit | 1,343 | [
"Pybel"
] | 3d497eeac34d8012d60ad6ce1f2f89642b44eb5d87f5c3fe2de5b762dd331a48 |
#
# Copyright (C) 2000-2008 greg Landrum
#
""" handles doing cross validation with k-nearest neighbors model
and evaluation of individual models
"""
from rdkit.ML.Data import SplitData
from rdkit.ML.KNN import DistFunctions
from rdkit.ML.KNN.KNNClassificationModel import KNNClassificationModel
from rdkit.ML.KNN.K... | bp-kelley/rdkit | rdkit/ML/KNN/CrossValidate.py | Python | bsd-3-clause | 3,874 | [
"RDKit"
] | 95aee27b79b7ea920d7076a0c7f01453d61c19a1e4095f81de445165e4b44f98 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | eickenberg/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 25,192 | [
"Gaussian"
] | 4b8a02ea82ce10b727eb9165bfd8799871fe64703832dae68a404ca96a21b94d |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'openWECv2.ui'
#
# Created: Wed May 06 10:39:04 2015
# by: PyQt4 UI code generator 4.9.6
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
from matplotlib.backends import qt_compat
from matplotlib... | tverbrug/openWEC | Run/openWEC_OY.py | Python | gpl-3.0 | 78,747 | [
"exciting"
] | 17a7b1884e06dea4a8f752ab6ee0b217b244ac738a6f6fb3cead1654cc54ada5 |
#!/usr/bin/env python
"""Example code of DDPG on OpenAI Gym environments.
For DDPG, see: https://arxiv.org/abs/1509.02971
"""
from __future__ import division
import argparse
import collections
import copy
import random
import gym
import numpy as np
import chainer
from chainer import functions as F
from chainer impor... | rezoo/chainer | examples/reinforcement_learning/ddpg_pendulum.py | Python | mit | 9,188 | [
"Gaussian"
] | 37cd3601aaa84c525758fe151ec5d003e35ca748533d01316978e830b797c692 |
from itertools import groupby
import json
import logging
from operator import itemgetter
import os
import shutil
import tempfile
import numpy as np
import scipy.sparse
from scipy.sparse import coo_matrix
import bcolz
from pybedtools import BedTool
from pysam import FastaFile
from tqdm import tqdm
import wWigIO
from ... | ueser/FIDDLE | _deprecated/shm.py | Python | gpl-3.0 | 3,111 | [
"pysam"
] | c0797d5245143a251cf8073e2493b67a85c633de7812a908e6a19a23ab4d7c30 |
"""
This sample sets up a diamond-structured polymer network.
"""
#
# Copyright (C) 2013-2018 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 Foundatio... | hmenke/espresso | samples/minimal-diamond.py | Python | gpl-3.0 | 4,489 | [
"ESPResSo"
] | b1f9ed7b1352c0b8dc72d08e9fd616bfef94226dc811befcfc6a3ac243ee573b |
""" This is a test of the creation of the pilot wrapper
"""
# pylint: disable=protected-access, invalid-name, no-self-use
import os
import base64
import bz2
import unittest
from DIRAC.WorkloadManagementSystem.Utilities.PilotWrapper import pilotWrapperScript
class PilotWrapperTestCase(unittest.TestCase):
""" Bas... | petricm/DIRAC | WorkloadManagementSystem/Utilities/test/Test_PilotWrapper.py | Python | gpl-3.0 | 3,835 | [
"DIRAC"
] | 29f85fbf26a1f8b09948f5782413b5ec995ffd1f3f0510358580d306bdd8c155 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2012, Regents of the University of California
# All rights reserved.
"""
ltemplify.py
The "ltemplify.py" script... | crtrott/lammps | tools/moltemplate/src/ltemplify.py | Python | gpl-2.0 | 156,244 | [
"LAMMPS"
] | 3509cdc7f5eb1bb16611f8cf50ea99f0bea680d9a2dd975dab33b64087e9f2a0 |
import unittest
from mock import patch
from ncclient.transport.session import *
from ncclient.devices.junos import JunosDeviceHandler
try:
from Queue import Queue, Empty
except ImportError:
from queue import Queue, Empty
import logging
rpc_reply = """<rpc-reply xmlns:junos="http://xml.juniper.net/junos/12.1X... | einarnn/ncclient | test/unit/transport/test_session.py | Python | apache-2.0 | 8,582 | [
"Firefly"
] | 3014f9e81cedeeb4f62ba7f5703958793620f81425050455314bd08da2423eb7 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Tim G L Lyons
#
# 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 Fr... | pmghalvorsen/gramps_branch | gramps/gen/plug/__init__.py | Python | gpl-2.0 | 2,677 | [
"Brian"
] | c9099709602bf64d75a3d01b7d160e2e9d59976f012e35e692beb0d489da7a84 |
# -*- coding: utf-8 -*-
'''
Some of the utils used by salt
'''
# Import python libs
from __future__ import absolute_import, division, print_function
import contextlib
import copy
import collections
import datetime
import distutils.version # pylint: disable=import-error,no-name-in-module
import errno
import fnmatch
im... | stephane-martin/salt-debian-packaging | salt-2016.3.3/salt/utils/__init__.py | Python | apache-2.0 | 93,916 | [
"VisIt"
] | d094d3de3c1e695dc26ea01c1f6d0e34c909198718e1e604ef48956a44e7dfff |
from collections import OrderedDict
expected = OrderedDict(
[
("type", "figure"),
(
"assets",
[
OrderedDict(
[
("type", "image"),
("doi", u"10.7554/eLife.27041.006"),
... | elifesciences/elife-tools | tests/fixtures/test_body_block_content/content_16_expected.py | Python | mit | 3,071 | [
"Gaussian"
] | 98e09344ec5c7742c19f6922db4e295fe6fbf797062d8227346ab407a0f94260 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2016, Brian Coca <bcoca@ansible.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1... | h3biomed/ansible | lib/ansible/modules/system/systemd.py | Python | gpl-3.0 | 21,150 | [
"Brian"
] | ff10733e4d3f4c05a24a221cc1f55295a4f34921364e0d0917a58d2efad5a274 |
# Copyright 2008-2015 Nokia Networks
# Copyright 2016- Robot Framework Foundation
#
# 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
... | alexandrul-ci/robotframework | src/robot/model/visitor.py | Python | apache-2.0 | 6,509 | [
"VisIt"
] | 086aab1001c97ea20d672c7f5cc7c69597caa14de2cdfa35ad82ea1810bdda29 |
# -*- 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_noteeditor.py | Python | gpl-2.0 | 2,731 | [
"VisIt"
] | 96cf5da9d3abc2fe06dd3ca0446c163734bb744a1c1b6608c8416cf9a3873bf3 |
import vtk
import sys
# Author: Rashed Karim, 2018
# Hello world of vtk visualisation for lassy shells
# On Windows, use Anaconda to install vtk
# On MacOS, use pip install vtk
# Usage: python vtkTest.py lahsell.vtk
# Generate polygon data for a cube
reader = vtk.vtkPolyDataReader()
reader.SetFileName(sys.argv[1... | drkarim/lassy | pyLibs/lesion/viz/vtkTest.py | Python | apache-2.0 | 1,460 | [
"VTK"
] | 5cf1d3473c3fa8f9b73981b805b7c58862bc2cc3feaea5ede7aa5d73e8e78bf7 |
# 4455770 Dennis Verheijden KI
# 4474139 Remco van der Heijden KI
# multiAgents.py
# --------------
# Licensing Information: Please do not distribute or publish solutions to this
# project. You are free to use and extend these projects for educational
# purposes. The Pacman AI projects were develop... | ScaleRunner/PacmanAI | 6 - Contest/competitionAgents-Uni-PC.py | Python | mit | 11,612 | [
"VisIt"
] | 4764409e0bfb92e1ff89b2db4c62a3e40d1ebd7182b5a9b3c5be2950d5fb1837 |
import os
from datetime import datetime, timedelta
from django.conf import settings
from django.contrib.auth.models import User
from django.contrib.sites.models import Site
from django.core import mail
from django.test.utils import override_settings
import mock
from nose.tools import eq_
from pyquery import PyQuery a... | dbbhattacharya/kitsune | kitsune/users/tests/test_views.py | Python | bsd-3-clause | 21,880 | [
"VisIt"
] | 3a07c3e5eef1dc736116d05737843855f721b8080570c686cc3f61ad22a5a2e6 |
#
# Copyright (C) 2013-2019 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... | psci2195/espresso-ffans | testsuite/python/interactions_bond_angle.py | Python | gpl-3.0 | 9,036 | [
"ESPResSo"
] | 72c505eb442de65f85bb501043de255a446a67f4a8487ce9dc9c394373696b24 |
import vtk
from glob import glob
import os
file_path = "/raid/home/ksansom/caseFiles/mri/PAD_proj/case1/fluent3/ensight"
out_dir = "/raid/home/ksansom/caseFiles/mri/PAD_proj/case1/fluent3/vtk_out"
wall = False
surface = True
inlet = True
file_pattern = "TH_0_PATIENT7100_M-3-?.????.dat.encas"
filelist = sorted(glob(... | kayarre/Tools | vtk/ensight2vtk_test.py | Python | bsd-2-clause | 4,270 | [
"VTK"
] | 649530a443bb48d2f47d17d47eb02c139bb88eee518c21f8f5d2be6116ecb5bd |
#!/usr/bin/env python
import argparse
import os
from pipelines_utils import parameter_utils, utils
from pipelines_utils_rdkit import rdkit_utils
### start main execution #########################################
def main():
### command line args defintions #########################################
### Def... | InformaticsMatters/pipelines | src/python/pipelines/rdkit/rxn_selector.py | Python | apache-2.0 | 2,599 | [
"RDKit"
] | d641f7bf463187d6586bf0ba8372683e40f0ea684983ff9729963265291886e4 |
# ======================================================================
# USER-GFMD - Elastic half-space methods for LAMMPS
# https://github.com/Atomistica/user-gfmd
#
# Copyright (2011-2016,2021)
# Lars Pastewka <lars.pastewka@imtek.uni-freiburg>,
# Tristan A. Sharp and others.
# See the AUTHORS file in the top... | Atomistica/user-gfmd | tests/force_analysis.py | Python | gpl-2.0 | 7,578 | [
"LAMMPS"
] | 2899a9cc28554e432ec155210be6e9e937f0af2bfd3606ba3a181bbf943eee8a |
"""
Miscellaneous utility functions.
"""
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__license__ = "BSD 3-clause"
import gzip
import numpy as np
import os
import pandas as pd
import sys
import tempfile
import tarfile
import zipfile
from urllib.request import urlretrieve
def ... | miaecle/deepchem | deepchem/utils/__init__.py | Python | mit | 5,298 | [
"RDKit"
] | f015f77da18244820943027ff5b142e8738ee902156b113355387970cbeadfc9 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | anksp21/Community-Zenpacks | ZenPacks.AndreaConsadori.LenovoRDThinkServer/ZenPacks/AndreaConsadori/LenovoRDThinkServer/modeler/plugins/Ibm_LenovoDeviceMap.py | Python | gpl-2.0 | 1,303 | [
"VisIt"
] | 73f6a3b80f0f6df3766418b53c68acd3911514ed083ab9bb714984e26ab0dc23 |
"""
Generate allele sequences for pan-class I models.
Additional dependency: biopython
"""
from __future__ import print_function
import sys
import argparse
import numpy
import pandas
import Bio.SeqIO # pylint: disable=import-error
from mhcflurry.common import normalize_allele_name
parser = argparse.ArgumentParse... | hammerlab/mhcflurry | downloads-generation/allele_sequences/make_allele_sequences.py | Python | apache-2.0 | 8,863 | [
"Biopython"
] | 0548c245dcb1134dad42a599fe6833de2587afd39c1b9652a527536461ed2dd5 |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import math
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_etree_fromstring,
compat_getpass,
compat_http_client,
... | codesparkle/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 102,347 | [
"VisIt"
] | 69edecf0924d4ac5ddee2c76c0202eaca5070d7ea131c0a85bc7aea9503f097a |
from django.test import TransactionTestCase
from django.contrib.auth.models import Group
from django.conf import settings
from hs_core import hydroshare
from hs_core.hydroshare import utils
from hs_core.models import CoreMetaData
from hs_core.testing import TestCaseCommonUtilities
class TestNetcdfMetaData(TestCaseCo... | ResearchSoftwareInstitute/MyHPOM | hs_app_netCDF/tests/test_netcdf_metadata_user_zone.py | Python | bsd-3-clause | 6,564 | [
"NetCDF"
] | a60e3a92b36e93370dc4b79ec138bfed5b5d1f2d685caec8d0f21b81846fbb63 |
# -*- coding: utf-8 -*-
# Copyright (C) 2009 Canonical
#
# Authors:
# Michael Vogt
#
# 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; version 3.
#
# This program is distributed in the hope that... | armikhael/software-center | softwarecenter/backend/reviews/__init__.py | Python | gpl-3.0 | 28,963 | [
"exciting"
] | 2abad39184ea2772860f07349d6da41c32f26759d2470feca07fff2384dbeb12 |
"""
=============================
Ledoit-Wolf vs OAS estimation
=============================
The usual covariance maximum likelihood estimate can be regularized
using shrinkage. Ledoit and Wolf proposed a close formula to compute
the asymptotically optimal shrinkage parameter (minimizing a MSE
criterion), yielding th... | depet/scikit-learn | examples/covariance/plot_lw_vs_oas.py | Python | bsd-3-clause | 2,867 | [
"Gaussian"
] | 2e712ffe3d83d9c8170e2d710c69ccde0180f4d2abb41eb9dad0fa30397510b4 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012-2013 Paul Franklin
#
# 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
# t... | jralls/gramps | gramps/gui/plug/report/_docreportdialog.py | Python | gpl-2.0 | 12,658 | [
"Brian"
] | 5f5992b40a51254a3031cd3b6ffc766b8d4329c601af763cb8499103927dd1c5 |
"""
The Job Agent class instantiates a CE that acts as a client to a
compute resource and also to the WMS.
The Job Agent constructs a classAd based on the local resource description in the CS
and the current resource status that is used for matching.
"""
from __future__ import absolute_import
from __future__ i... | petricm/DIRAC | WorkloadManagementSystem/Agent/JobAgent.py | Python | gpl-3.0 | 26,267 | [
"DIRAC"
] | 1e9940547943773c35e199f26f687e02836bddae7412ec28739a3b403d2b7de1 |
# find the inverse of a matrix using Gaussian elimination
import numpy
def inverse(AInput):
""" return the inverse of AInput """
A = AInput.copy()
N = len(A[:,0])
# A is square, with each dimension of length N
if not (A.shape[0] == A.shape[1]):
print "ERROR: A should be square"
... | bt3gl/Numerical-Methods-for-Physics | others/lin_algebra/inverse.py | Python | apache-2.0 | 2,859 | [
"Gaussian"
] | 0fddd1bce11c3c40e09fa1fef49f0d061d02f2a72ccbe7fff24190354851820e |
# The minimal basis sets used by Molpro.
#
# Comments from Molpro
#
# ! These are minimal basis sets created by taking the first
# ! nOcc contracted functions out of the cc-pVTZ or cc-pVTZ-PP
# ! basis sets. They are intended as auxiliary sets for SCF
# ! convergence experiments and atomic density guess purposes.
# ! S... | sunqm/pyscf | pyscf/gto/basis/minao.py | Python | apache-2.0 | 117,876 | [
"Molpro"
] | 83bf3f1bdcafb85b62b22be17b9be19a89d485161af37a040ffb23e2883b7f69 |
##
# Copyright 2009-2015 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://vscentrum.be/nl/en),
# the Hercules foundation (htt... | valtandor/easybuild-easyblocks | easybuild/easyblocks/n/netcdf.py | Python | gpl-2.0 | 6,473 | [
"NetCDF"
] | 796118155dce8caee3368425766ea4d906b600e48b12313536bb26d8a886056d |
# it.po
val = {"" : "Project-Id-Version: sheltermanager\nReport-Msgid-Bugs-To: FULL NAME <EMAIL@ADDRESS>\nPOT-Creation-Date: 2013-01-24 10:55+0000\nPO-Revision-Date: 2013-12-29 19:15+0000\nLast-Translator: Katpurrr <Unknown>\nLanguage-Team: Italian <it@li.org>\nMIME-Version: 1.0\nContent-Type: text/plain; charset=UTF-... | aubzen/sheltermanager | src/locale/locale_it.py | Python | gpl-3.0 | 134,475 | [
"Amber",
"VisIt"
] | ddd389075c7c9cf6c1dfc9e9d3e16ea048d62d1ee648a7d41927e87ffc288b09 |
"""
WSGI config for amber project.
It exposes the WSGI callable as a module-level variable named ``application``.
For more information on this file, see
https://docs.djangoproject.com/en/1.11/howto/deployment/wsgi/
"""
from __future__ import absolute_import, unicode_literals
import os
from django.core.wsgi import ... | Taywee/amberherbert.com | amber/wsgi.py | Python | mit | 457 | [
"Amber"
] | eedb1786f584a98d1736f797e3f1cad0d671309eb1861f4d2eafa06815139b6f |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | erh3cq/hyperspy | hyperspy/tests/component/test_gaussian.py | Python | gpl-3.0 | 4,488 | [
"Gaussian"
] | e8d19cc9d39667509de73007d860db1196d57012f490de89cf5ea23d08344977 |
# Copyright (c) 2021, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and t... | google/deepconsensus | deepconsensus/inference/quick_inference_test.py | Python | bsd-3-clause | 4,842 | [
"pysam"
] | 3871b68731ef63eaaed2ce6c0d4c2996d98e8b789cbff4af4ea778d4e6407186 |
# Copyright 2020 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... | annarev/tensorflow | tensorflow/compiler/mlir/tfr/python/op_reg_gen.py | Python | apache-2.0 | 5,092 | [
"VisIt"
] | 727d80766c4862017cd380eb22e7fe869c890bf85475458c621a2b3255319335 |
import os
import webbrowser
import logging
import logging.config
import sys
from oauth2client.client import flow_from_clientsecrets
from oauth2client.file import CredentialsFileSymbolicLinkError, Storage
from oauth2client.tools import ClientRedirectServer, ClientRedirectHandler
from backupme.settings_parser import Se... | BackupMe/BackupMe | google_api_driver/authorization.py | Python | mit | 5,758 | [
"VisIt"
] | b836168e33bea9d27648966d56c8c4ffd5b2a9d9d1e74ec3ab661cb77bdad650 |
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