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# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import os
import unittest
from monty.serialization import loadfn, dumpfn
from pymatgen.io.qchem_io.outputs import QCOutput
from pymatgen.util.testing import PymatgenTes... | nisse3000/pymatgen | pymatgen/io/qchem_io/tests/test_outputs.py | Python | mit | 6,602 | [
"pymatgen"
] | 5f103165f591ac63268f2e436160004840fe837af8f1a0bd4be83f0a3e368d08 |
# step 1. imports
from sqlalchemy import (create_engine, MetaData, Table, Column, Integer,
String, ForeignKey, Float, DateTime, event)
from sqlalchemy.orm import sessionmaker, mapper, relationship
from sqlalchemy.ext.horizontal_shard import ShardedSession
from sqlalchemy.sql import operators, visitors
import date... | alex/sqlalchemy | examples/sharding/attribute_shard.py | Python | mit | 9,466 | [
"VisIt"
] | 03dec7b0f8b11abcafc65e6eade25f4db8897e9ff8ae7557301c71275abdd9a8 |
import sys
import functools
from types import MethodType
import gevent
import nose
import shorten
from shorten.lock import Lock
from shorten import UUIDTokenGenerator, KeyInsertError, TokenInsertError, RevokeError
def spawn_nicely(*args):
g = gevent.spawn(*args)
g.link_exception(die_nicely)
return g
def... | clibc/shorten | tests/common.py | Python | mit | 8,059 | [
"Elk"
] | 5ccb481cd013278e640f03a37943d9758be1cc93c13fe318959f86d376f857ec |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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, o... | wvangeit/python-mode | pymode/libs/pylama/lint/pylama_pylint/pylint/checkers/classes.py | Python | lgpl-3.0 | 30,490 | [
"VisIt"
] | dfcadc30c10f9f37425a7b5e6bdfc05040ee76df07ec0de427e7329780338922 |
from __future__ import print_function, division
import random
from sympy.core.basic import Basic
from sympy.core.compatibility import is_sequence, as_int, range
from sympy.core.function import count_ops
from sympy.core.decorators import call_highest_priority
from sympy.core.singleton import S
from sympy.core.symbol i... | toolforger/sympy | sympy/matrices/dense.py | Python | bsd-3-clause | 43,120 | [
"DIRAC"
] | 5fd3ecedeefd475caac4dd094e2698cad8eb8618b6534570c43c447e9d317112 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | Tong-Chen/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 29,287 | [
"Brian"
] | 6de42123c1e674c49a9651f9d36a54892b85c6d5bc4a6698bb5ad10e98ce3c37 |
# $Id$
#
# Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above c... | adalke/rdkit | rdkit/Chem/Draw/UnitTestSimilarityMaps.py | Python | bsd-3-clause | 6,949 | [
"RDKit"
] | 45c42c26afb7d58aff68e564093ea8d7e7ed12081f73f87b305e7b1a0997e4da |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
#
# 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 Licens... | tsdmgz/ansible | lib/ansible/modules/network/cnos/cnos_interface.py | Python | gpl-3.0 | 27,201 | [
"VisIt"
] | 6257856a531b9e7ae2bddf2aa8e8c3fec2baccf53a12a19de6f8204f4604b769 |
#
# This source file is part of appleseed.
# Visit https://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 | operators/texture_ops.py | Python | mit | 5,174 | [
"VisIt"
] | aaec28e4f71ca00ecd3b7a91b588d2c0fd417eba3a925ac904ed1fb163dc320f |
from DIRAC import S_OK
from DIRAC.Core.Utilities import DEncode
from DIRAC.Core.Base.ExecutorModule import ExecutorModule
class PingPongExecutor(ExecutorModule):
@classmethod
def initialize(cls):
"""
Executors need to know to which mind they have to connect.
"""
cls.ex_setMind(... | DIRACGrid/DIRAC | docs/source/DeveloperGuide/AddingNewComponents/DevelopingExecutors/PingPongExecutor.py | Python | gpl-3.0 | 1,060 | [
"DIRAC"
] | 8d97e71af099bf846605d471e6f4985663799738a2d2d704336c41166bdd9660 |
input_name = '../examples/linear_elasticity/elastic_contact_planes.py'
output_name = 'test_elastic_contact_planes.vtk'
from tests_basic import TestInput
class Test(TestInput):
pass
| RexFuzzle/sfepy | tests/test_input_elastic_contact_planes.py | Python | bsd-3-clause | 186 | [
"VTK"
] | 2476c589fa8b65b437d7ca95e40930040f42c3d56be1633ade521299d46ac431 |
import fresh_tomatoes
import media
# Create movie instances by calling init in Movie class in media.py
# Each movie's variables are passed when calling init
guardians_galaxy = media.Movie("Guardians of the Galaxy",
"Awesome space raccoon shooting stuff",
"... | omgapuppy/udacity | python_intro/entertainment_center.py | Python | mit | 2,208 | [
"Galaxy"
] | 43308bbe84e816bb521864b5efa95b9d96a03a1896b50d64234920efdd11cf0a |
# encoding:utf-8
"""
:synopsis: views diplaying and processing main content post forms
This module contains views that allow adding, editing, and deleting main textual content.
"""
import datetime
import logging
import os
import os.path
import random
import sys
import tempfile
import time
from django.shortcuts import ... | fitoria/askbot-devel | askbot/views/writers.py | Python | gpl-3.0 | 35,694 | [
"VisIt"
] | 65cc25207a9bd4b3e140b25778f42d0323ed2f35d85b531041d66bd481313ad8 |
# Copyright (c) 2010 OpenStack 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
#
# Unless required by applicable law or agreed to ... | wenhuizhang/swift | test/unit/common/middleware/test_staticweb.py | Python | apache-2.0 | 33,522 | [
"VisIt"
] | 63c5fa78461290196e7b838e1c7eb5cb62b93dd25b60fe2d50c434f15da74f38 |
"""
Simulation data for dark matter power spectra at 3 redshifts, z = 0, 0.509, 0.987
For more, see the detailed description of these simulations in Okumura et al. 2012.
"""
from .. import data_dir, numpy as np, os as _os
import pandas as pd
__all__ = ['load',
'P00_mu0_z_0_000',
'P00_mu0_z_0_509... | nickhand/pyRSD | pyRSD/data/__init__.py | Python | gpl-3.0 | 12,455 | [
"Galaxy",
"Gaussian"
] | 263b56f7e252bb182b4fa3a13b70d2df64e90174f60dfe1c59eae283654fe2bc |
from textwrap import dedent
import py, pytest
from _pytest.config import PytestPluginManager
@pytest.fixture(scope="module", params=["global", "inpackage"])
def basedir(request, tmpdir_factory):
from _pytest.tmpdir import tmpdir
tmpdir = tmpdir(request, tmpdir_factory)
tmpdir.ensure("adir/conftest.py").wr... | Akasurde/pytest | testing/test_conftest.py | Python | mit | 13,655 | [
"VisIt"
] | a54136ac193ef39f5ec146b4280a17d5656d1125811804297114770e23003cc5 |
'''
Created on Aug 3, 2009
@author: rb
'''
import os;
import os.path;
import tempfile;
def main(blastPath, qryPath, outPath, batchSize):
blastCmd = "{0}/bin/blastall -p blastx -d {0}/db/nr -i {1} -o {2} -e 1e-5 -m 8 -a 6"
fOut = open(outPath, 'w');
with open(qryPath, 'r') as fQry:
hdr = None;
cnt = 0;
while... | orionzhou/robin | old/BlastJobSplit.py | Python | gpl-2.0 | 1,276 | [
"BLAST"
] | 907ae436103ced9fbec06d4c13c313a570efa0f0a88e228169fedebef5542628 |
##############################################################################
# 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-tmixclust/package.py | Python | lgpl-2.1 | 2,323 | [
"Bioconductor",
"Gaussian"
] | fcfd5a2072e77f2c255679dd4b22473740cf35aa3c2b04e7a62a0214ed7d9a78 |
"""
this module contains a class that fits a gaussian model to the central
part of an histogram, following schwartzman et al, 2009. This is
typically necessary to estimate a fdr when one is not certain that the
data behaves as a standard normal under H_0.
Author : Bertrand Thirion, 2008-2009
"""
import numpy as np
fro... | yarikoptic/NiPy-OLD | nipy/neurospin/utils/emp_null.py | Python | bsd-3-clause | 17,408 | [
"Gaussian"
] | bac0010d707bedbf5f0617c05aaa40222a92dfdfb7446a1adf2d2366471f4fc9 |
import gettext
from gettext import gettext as _
import os
def C_(ctx, s):
"""Provide qualified translatable strings via context.
(copied from Orca)"""
translated = gettext.gettext('%s\x04%s' % (ctx, s))
if '\x04' in translated:
# no translation found, return input string
return s
re... | ruibarreira/linuxtrail | usr/lib/python2.7/dist-packages/caribou/i18n.py | Python | gpl-3.0 | 471 | [
"ORCA"
] | 960ef1b26284d82a9fe5015ce57f466ebfeec68ede1e3f59d1ec1799b99b79d5 |
"""
Handles URL downloads.
This is the low-level interface for downloading interfaces, implementations, icons, etc.
@see: L{fetch} higher-level API for downloads that uses this module
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import tempfile, os
from ... | dabrahams/zeroinstall | zeroinstall/injector/download.py | Python | lgpl-2.1 | 5,510 | [
"VisIt"
] | b22915fa40ec8bafcd06862005e011dedd2fa04a2478ec70a8211d000eca0376 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes used to define a non-periodic molecule and a
periodic structure.
"""
import math
import os
import json
import collections
import itertools
from abc import ABCMeta, abstractmeth... | mbkumar/pymatgen | pymatgen/core/structure.py | Python | mit | 163,442 | [
"ABINIT",
"CRYSTAL",
"Gaussian",
"NetCDF",
"VASP",
"exciting",
"pymatgen"
] | e3a448ad6860bde90f137e537b7da2dcf8447ad21f0326c6f4c35a0ee6ca4c38 |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
# Create the RenderWindow, Renderer and Interactor.
#
renderer = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(renderer)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWi... | lorensen/VTKExamples | src/Python/Modelling/Bottle.py | Python | apache-2.0 | 2,775 | [
"VTK"
] | 5500f730100cca186e2beee95e2be9c3cb95730e0867335a58ad5f53206d1e83 |
"""
Contains an abstract base class that supports chemically aware data splits.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar, Aneesh Pappu "
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "MIT"
im... | joegomes/deepchem | deepchem/splits/splitters.py | Python | mit | 23,865 | [
"RDKit"
] | 764ada16c90a1033adcf4239ac22c6e92228264555e06b9d732ace44f4be6885 |
# 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... | AndreasMadsen/tensorflow | tensorflow/contrib/factorization/python/ops/gmm.py | Python | apache-2.0 | 7,497 | [
"Gaussian"
] | 9647fdeaa7ac796f0fd07e774fbafcac2494ca7d4ab461e2f6195a96158bfe01 |
# -*- coding: utf-8 -*-
"""
ePSproc IO functions.
=====================
Module for file IO and data parsing.
Main function: :py:func:`epsproc.IO.readMatEle`:
readMatEle(fileIn = None, fileBase = None, fType = '.out'):
Read ePS file(s) and return results as Xarray data structures containing matrix elements.
... | phockett/ePSproc | epsproc/IO.py | Python | gpl-3.0 | 72,264 | [
"NetCDF",
"ParaView",
"VTK"
] | 7214373eb23e3409f054ccf841a6fcf3d0e1ba565ce5bea580d1886b0eb933e8 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageWeightedSum(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
v... | nagyistoce/devide | modules/vtk_basic/vtkImageWeightedSum.py | Python | bsd-3-clause | 495 | [
"VTK"
] | 134292e77cf34b4211e08fd8d17ccabd1b2f44c077b5da8f537185eb9980b55d |
''' CacheFeederAgent
This agent feeds the Cache tables with the outputs of the cache commands.
'''
from DIRAC import S_OK
from DIRAC.AccountingSystem.Client.ReportsClient import ReportsClient
from DIRAC.Core.Base.AgentModule ... | Andrew-McNab-UK/DIRAC | ResourceStatusSystem/Agent/CacheFeederAgent.py | Python | gpl-3.0 | 5,886 | [
"DIRAC"
] | 6ad1fa357da81de9aabf689ca5097af5759a7e92916a3dabdffb6bbf830a4f05 |
"""
dmath v0.9.1
Python math module for Decimal numbers. All functions should return Decimal
numbers. Probably only works with real numbers.
pi, exp, cos, sin from Decimal recipes:
http://docs.python.org/lib/decimal-recipes.html
float_to_decimal from Decimal FAQ:
http://docs.python.org/lib/decimal-faq.html... | SeanHayes/dmath | dmath/__init__.py | Python | mit | 15,535 | [
"Brian"
] | 4db90997563a11675ff24526f7ada5374e229558ab14b7257851ec059fd99ee2 |
"""
To know more or get code samples, please visit my website:
https://morvanzhou.github.io/tutorials/
Or search: 莫烦Python
Thank you for supporting!
"""
# please note, all tutorial code are running under python3.5.
# If you use the version like python2.7, please modify the code accordingly
# 8 - RNN Classifier exampl... | tencrance/cool-config | ml_keras_learn/tutorials/kerasTUT/7-RNN_Classifier_example.py | Python | mit | 2,500 | [
"VisIt"
] | 38aa284e061d884f2bd2070d23ae3f71597859dcac893d6f4c71170a729a4eb3 |
import filecmp
import logging
import os
import tempfile
from galaxy.tools import Tool
from galaxy.tools import parameters
from galaxy.tools.parameters import dynamic_options
from tool_shed.tools import data_table_manager
from tool_shed.util import basic_util
from tool_shed.util import hg_util
from tool_shed.util imp... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/tools/tool_validator.py | Python | gpl-3.0 | 19,484 | [
"Galaxy"
] | f0fedcb388ed8bca7915d49dba64a4b1a5cea36548e561b4acdeac715a761371 |
## twofish.py - pure Python implementation of the Twofish algorithm.
## Bjorn Edstrom <be@bjrn.se> 13 december 2007.
##
## Copyrights
## ==========
##
## This code is a derived from an implementation by Dr Brian Gladman
## (gladman@seven77.demon.co.uk) which is subject to the following license.
## This Python implemen... | hupf/passwordchest | src/loxodo/twofish/twofish.py | Python | gpl-2.0 | 15,604 | [
"Brian"
] | 492a062654877babce335af4703f272f14bb395bbf7f18135b252ad6773aed97 |
import networkx as nx
import numpy as np
import pandas as pd
import mdtraj as md
from mixtape.utils import iterobjects
input_filename = "./hmms.jsonlines"
models = list(iterobjects(input_filename))
df = pd.DataFrame(models)
x = df.ix[0]
T = np.array(x["transmat"])
p = np.array(x["populations"])
g = nx.from_numpy_... | choderalab/MSMs | attic/src/code/hmsm/plot_network.py | Python | gpl-2.0 | 573 | [
"MDTraj"
] | d6ca22483f8ca62bb48b41a1ec936562fee32f804b5f6f042bdbf73afb3f6e97 |
#!/usr/bin/python -u
import os, subprocess
from argparse import Namespace
from gmx_lib import run_setup, gro_and_top
from gmx_lib.run_setup import WorkdirStructure
from gmx_lib.gmx_engine import GmxEngine
from gmx_lib.gmx_params import GmxParameters
from gmx01_core import core
##################################... | ivanamihalek/smallmol | gmx07_protein_RNA_simple.py | Python | gpl-2.0 | 2,494 | [
"Gromacs"
] | 1d3c0011c36a788bee88cddf08d146d0063fc194bf40ba5839735390a227a001 |
exampleText_2D = """\
Example 2D data for testing
Paste your own 2D data here
X Y
5.357 10.376
5.457 10.489
5.936 11.049
6.161 11.327 ending text is ignored
6.697 12.054
8.442 14.744
9.769 17.068
9.861 17.104
"""
exampleText_3D = """\
Example 3D data for testing
Paste your own 3D da... | endolith/pyeq2 | Examples/GUI/guifiles/DataForControls.py | Python | bsd-2-clause | 1,856 | [
"Gaussian"
] | 66923614840bd603da9580c78ec7dcb7d8c8dc905b4613384aeea8c30390fef6 |
##################################################################
# Copyright 2018 Open Source Geospatial Foundation and others #
# licensed under MIT, Please consult LICENSE.txt for details #
##################################################################
"""Validating functions for various inputs
"""
im... | bird-house/PyWPS | pywps/validator/__init__.py | Python | mit | 1,971 | [
"NetCDF"
] | 3650dfcc3850e72aeade783f2aa16fdddb619f7693b153d631098f5c19eab330 |
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space 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 Lice... | OuterDeepSpace/OuterDeepSpace | libs/client/osci/dialog/MessagesDlg.py | Python | gpl-2.0 | 17,842 | [
"Galaxy"
] | cda10675d50fd3b13147955b40ba9dee3f849a6ccc263f1ad6d7b9fed44068ae |
from flask import url_for, request, current_app
from markupsafe import Markup
from . import get_renderer
class NavigationItem(object):
"""Base for all items in a Navigation.
Every item inside a navigational view should derive from this class.
"""
#: Indicates whether or not the item represents the ... | mbr/flask-nav | flask_nav/elements.py | Python | mit | 3,907 | [
"VisIt"
] | 2fa6574597d3f68ac853c31e7dc598e9e7364f2d03cc36affcb4ad6da685d08f |
"""Draws a simple axes using tvtk.CubeAxesActor2D.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2006, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Instance, Property, true
from traitsui.api import View, Group, HGroup, \
Item, Boolea... | dmsurti/mayavi | mayavi/modules/axes.py | Python | bsd-3-clause | 9,396 | [
"Mayavi",
"VTK"
] | edaeb28f31a004a97d58c9a400b4c7d493148506723f4d9c01e7727136745228 |
"""
Tests the representation of site pages.
"""
import logging
from unittest import TestCase
from unittest.mock import Mock
import pytest
from selenium.common.exceptions import WebDriverException
from bok_choy.page_object import (PageLoadError, PageObject, WrongPageError,
unguarded)... | edx/bok-choy | tests/test_page_object.py | Python | apache-2.0 | 5,641 | [
"VisIt"
] | aaf78cd9bbbfb359d72c99994224d49a43b4c1b1217c7405416ed52c2ddff6d9 |
from arrow.arrow import Arrow
from django import forms
from django.apps import apps as django_apps
from django.conf import settings
from django.utils import timezone
from edc_base.utils import convert_php_dateformat
from edc_constants.constants import YES, NO
from edc_form_validators import FormValidator
class Requis... | botswana-harvard/edc-lab | edc_lab/forms/modelform_mixins.py | Python | gpl-2.0 | 4,560 | [
"VisIt"
] | 9be4315da662722a12e718e2d6ed3690d577e5b7db25e659de7cafb5a8c9bdfd |
#!/usr/bin/env python
"""Processed version of the documentation.
The documentation from the objects of raw_doc is further processed into
objects from the module proc_doc. These objects can then be processed
into structured documents such as HTML more easily.
"""
# TODO(holtgrew): Location traceability for entries an... | weese/seqan | util/py_lib/seqan/dox/proc_doc.py | Python | bsd-3-clause | 55,324 | [
"VisIt"
] | f36a5941d486cc71fa38b8401970c26d73be8f8bb95be48eab7be5af61f9e004 |
from gandalf.analysis.facade import *
import numpy as np
from scipy.stats import powerlaw
#Usual stuff that we saw before
sim=newsim(ndim=3,sim='sph')
#Here a few parameters that you might want to set
#Of course you can set other ones if you want
sim.SetParam('ic','python')
Ngas=?
sim.SetParam('Nhydro',Ngas) #or wha... | gandalfcode/gandalfcode.github.io | gandalf-school/disc_stub.py | Python | gpl-2.0 | 1,902 | [
"Gaussian"
] | 8e683fceb61c9bdb170fe49e64309bb97400ecb485a31e74965dc8eb5e0c0df2 |
#!/usr/bin/env python
import sys
import requests
import requests_cache
from bs4 import BeautifulSoup
from pprint import pprint
from lib.csvtools import dict_to_csv
def main() :
requests_cache.install_cache('scraper_cache')
domain = "http://web.raleighchamber.org"
caturls = []
compur... | jctanner/scrapers | ralcham.py | Python | apache-2.0 | 2,524 | [
"VisIt"
] | 71f50bf54a8dc12d1dddab69d7a56b42e62c290b87955cc045ec089aff461c52 |
"""Script to install mooltool on developer and test machines. We use python
virtual environment based approach for setting up the development environment.
Required packages before the script can be used are:
* Java >= 1.7.0
* python >= 2.7.3
* g++
It is supposed to work on Mac OS, Ubuntu and Centos.
Please visit mool... | rocketfuel/mool | installer/install_mooltool.py | Python | bsd-3-clause | 32,679 | [
"VisIt"
] | 1b3e1c8e80a5207cf09b55317c3eea586c2558659b439006f93a14a04ece4a47 |
# -*- coding: utf-8 -*-
# imports here
from aiida.parsers.exceptions import OutputParsingError
#
from aiida.orm.data.folder import FolderData
from aiida.orm.data.parameter import ParameterData
from aiida.orm.data.structure import StructureData
from aiida.orm.data.array import ArrayData
#
from aiida.parsers.plugins.vas... | abelcarreras/aiida_extensions | plugins/parsers/vasp/instruction/data/output_parameters.py | Python | mit | 2,130 | [
"VASP",
"phonopy",
"pymatgen"
] | f1e8d5bc288ccccc254e1c0101d00593d586aa139d742929ecff6157474a383f |
"""Interfaces to different ASE compatible force-calculators."""
import numpy as np
from ase import _deprecate_things_from_ase_module
from ase.calculators.lj import LennardJones
from ase.calculators.emt import EMT
from ase.calculators.siesta import Siesta
from ase.calculators.dacapo import Dacapo
from ase.calculators.... | slabanja/ase | ase/calculators/__init__.py | Python | gpl-2.0 | 1,123 | [
"ASE",
"SIESTA",
"TURBOMOLE",
"VASP",
"exciting"
] | 7ff47aa5a6fccc1563e8e422612fab86249f53265679c32f16eb7a7510c4b80b |
# Copyright 2018 the GPflow authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writi... | GPflow/GPflow | tests/gpflow/test_logdensities.py | Python | apache-2.0 | 4,339 | [
"Gaussian"
] | 8d80d17ed4397174d53eba255d7a4c82d1d8a73d1bbd76388963a8d2dcd28da8 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/plugins/manytooneeditorplugin.py | Python | gpl-2.0 | 1,494 | [
"VisIt"
] | f27d7e1bb90122570662a1fb15a51c20ff9bd3c4813156cb773309203d3ce004 |
import copy
import numpy
import vigra
from functools import partial
from lazyflow.graph import Operator, InputSlot, OutputSlot
from lazyflow.operators.operators import OpSlicedBlockedArrayCache, OpUnblockedArrayCache
from lazyflow.roi import enlargeRoiForHalo, roiToSlice
from lazyflow.request import Request, RequestPo... | nielsbuwen/ilastik | ilastik/applets/iiboostFeatureSelection/opIIBoostFeatureSelection.py | Python | gpl-3.0 | 18,961 | [
"Gaussian"
] | 508a1da7971ad900853e42b278690b567b15d9a9677ba8a5e8530b3e28170763 |
"""
GWR is tested against results from GWR4
"""
import unittest
import pickle as pk
from crankshaft.regression.gwr.gwr import GWR, FBGWR
from crankshaft.regression.gwr.sel_bw import Sel_BW
from crankshaft.regression.gwr.diagnostics import get_AICc, get_AIC, get_BIC, get_CV
from crankshaft.regression.glm.family import ... | CartoDB/crankshaft | release/python/0.8.2/crankshaft/crankshaft/regression/gwr/base/tests/test_gwr.py | Python | bsd-3-clause | 45,423 | [
"Gaussian"
] | 12d5d29d68cba85e201ce68b21615e3b3e33173b634d2adc0258906ad7f38dc4 |
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2009 Peter Schmidtke, Raik Gruenberg
##
## 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 versi... | graik/biskit | biskit/edparser.py | Python | gpl-3.0 | 7,985 | [
"VMD"
] | 69c091cd66e41d1b1dd708273ed51dffde16eed4f1647635eb583ef1e4f32f21 |
import lb_loader
import simtk.openmm.app as app
import numpy as np
import pandas as pd
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
pd.set_option('display.width', 1000)
n_steps = 3000
temperature = 300. * u.kelvin
#testsystem = testsystems.LennardJonesFlui... | kyleabeauchamp/HMCNotes | code/old/test_xhmc.py | Python | gpl-2.0 | 2,490 | [
"OpenMM"
] | 366caf730427537222815573d0efbd537ddc3ea1701f1896f983c116243381fa |
#!/usr/bin/env python
import os, sys
import pickleTraj
import cgmodel as cg
# LDCuts:--
# BB: 1st shell or 2nd shell
# WW: 1st shell or 2nd shell (both must be same shell)
# BW and WB : (BB+WW)/2
NB = int(sys.argv[1])
NW = int(sys.argv[2])
LammpsTraj = '/home/cask0/home/tsanyal/benwat/data/gromacs/NB%dNW%d/NB%dNW%d_... | tanmoy7989/benwat | data/cgff/NB250NW250/control/main_cg.py | Python | gpl-2.0 | 2,047 | [
"Gromacs"
] | 259d8165744d24075b46d357e9fbeb1b9989ba2038cfc15fcc15f494c71df076 |
# -*- coding: utf-8 -*-
import os
import tempfile
import types
import json
from mock import patch
from nose.tools import eq_
from helper import TestCase
import appvalidator.constants
from appvalidator.errorbundle import ErrorBundle
from appvalidator.specs.webapps import WebappSpec
import appvalidator.webapp
class T... | diox/app-validator | tests/test_webapp.py | Python | bsd-3-clause | 55,192 | [
"exciting"
] | 412aab867863f9c405d6275db76131a3d0fbab5d2a1f3bca97a602dbacaab727 |
from math import sqrt
from ase import Atoms, Atom
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
from ase.io import read
from ase.vibrations import Vibrations
from ase.visualize import view
# Distance between Cu atoms on a (100) surface:
d = 3.6 / sqrt(2)
... | grhawk/ASE | tools/ase/test/replay.py | Python | gpl-2.0 | 965 | [
"ASE"
] | 8154aa84c92c006c3f6bf710f08d0756b96bd58f975fa61e4f8b5eff01103376 |
"""
================================
Time-related feature engineering
================================
This notebook introduces different strategies to leverage time-related features
for a bike sharing demand regression task that is highly dependent on business
cycles (days, weeks, months) and yearly season cycles.
I... | manhhomienbienthuy/scikit-learn | examples/applications/plot_cyclical_feature_engineering.py | Python | bsd-3-clause | 31,012 | [
"Gaussian"
] | 3b26a036a232455a7553c0e04f9291fa82723b9ba94562a1205083040fb91a0a |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# NACCESS interface adapted from Bio/PDB/DSSP.py
import os, sys, tempfile
from Bio.PDB.PD... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/PDB/NACCESS.py | Python | apache-2.0 | 6,798 | [
"Biopython"
] | d9ff05a604a648c7d37bd356afc7865094ac1e9eabc6f7f7e4d087bc54313bb5 |
#===============================================================================
# LICENSE XOT-Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported Lic... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/net.rieter.xot.smallplayer/resources/libs/helpers/database.py | Python | gpl-2.0 | 8,320 | [
"VisIt"
] | 871965be939d68fefe0b5651ac03e4f7cefad39c0337981f2c810dd01dbc8227 |
# pylint: disable=C0111
# pylint: disable=W0621
from lettuce import world, step
from common import *
from terrain.steps import reload_the_page
from selenium.common.exceptions import (
InvalidElementStateException, WebDriverException)
from nose.tools import assert_in, assert_not_in, assert_equal, assert_not_equal ... | hkawasaki/kawasaki-aio8-1 | cms/djangoapps/contentstore/features/grading.py | Python | agpl-3.0 | 7,108 | [
"VisIt"
] | eab2565999983410b9cb132a9f9953284f06a087e58e82dfdbd73d910c8435d6 |
"""Tests of tools for setting up interactive IPython sessions."""
import ast
import uuid
from diofant.interactive.session import (IntegerDivisionWrapper,
unicode_identifiers)
__all__ = ()
def test_IntegerDivisionWrapper():
tree = ast.parse('1/3')
tree2 = ast.parse(... | diofant/diofant | diofant/tests/interactive/test_ipython.py | Python | bsd-3-clause | 1,751 | [
"VisIt"
] | 3b4ea9d37b068e99b5638cabe4823b60fff6f671a764e95ef2b1c7ea8605ea04 |
""" The HTCondor TimeLeft utility interrogates the HTCondor batch system for the
current CPU consumed, as well as its limit.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.Resources.Computing.Batc... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/TimeLeft/HTCondorResourceUsage.py | Python | gpl-3.0 | 2,636 | [
"DIRAC"
] | a2e148da757cb2357cac802152d66e45441adae02708d884427f171f575380a5 |
""" Base classes for classification """
import numpy
# import matplotlib as mpl
# mpl.rcParams['text.usetex']=True
# mpl.rcParams['text.latex.unicode']=True
import matplotlib.pyplot as plt
import os
import cPickle
import logging
import math
import numpy
import os
import timeit
import warnings
# base class
from pyS... | MMKrell/pyspace | pySPACE/missions/nodes/classification/base.py | Python | gpl-3.0 | 89,554 | [
"Gaussian"
] | 212cbb05bb29aa308e135b8558bdf11fbc67d1d09f5b88500b031ad30dd11cdc |
"""Main entry point for distributed next-gen sequencing pipelines.
Handles running the full pipeline based on instructions
"""
from collections import defaultdict
import copy
import os
import sys
import resource
import tempfile
import yaml
from bcbio import log, heterogeneity, hla, structural, utils
from bcbio.cwl.i... | Cyberbio-Lab/bcbio-nextgen | bcbio/pipeline/main.py | Python | mit | 21,648 | [
"Bowtie"
] | 74a3ac676219d2ebf7575ad48375c679f82648f326bdf4a5a4c9f2086c56845c |
# -*- coding: utf-8 -*-
{
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '\\ " update\\ " è un\' espressione facoltativa come " field1=\'newvalue\'". Non è possibile aggiornare o eliminare i risultati di una JOIN',
'# of International Staff': '# di Pe... | flavour/eden | languages/it.py | Python | mit | 392,619 | [
"VisIt"
] | aa57801440c16a05e936aab38fff4e81aa37fefd71b094450239a0ca67cdcddb |
# peppy Copyright (c) 2006-2010 Rob McMullen
# Licenced under the GPLv2; see http://peppy.flipturn.org for more info
"""Hyperspectral image processing filters
This file is a repository of actions that operate on the HSI mode.
"""
import os, struct, mmap, math
from cStringIO import StringIO
import wx
from peppy.acti... | robmcmullen/peppy | peppy/hsi/filter_menu.py | Python | gpl-2.0 | 7,831 | [
"Gaussian"
] | d5b02c7d90111b142c3dc31964c510f18c1aaaaaf3c49455d1d70a0c2e070f4d |
"""
======================================================================
A demo of structured Ward hierarchical clustering on an image of coins
======================================================================
Compute the segmentation of a 2D image with Ward hierarchical
clustering. The clustering is spatially ... | scikit-learn/scikit-learn | examples/cluster/plot_coin_ward_segmentation.py | Python | bsd-3-clause | 2,386 | [
"Gaussian"
] | 6b66f7e3f037bb961e42a2e9eeec11c9983da72c670435f64d50d201c666c429 |
import six
from nn.layer import Layer
from theano import dot
from theano.tensor import tanh
class ContiguousLayer(Layer) :
'''This class describes a Contiguous Neural Layer.
layerID : unique name identifier for this layer
inputSize : number of elements in input buffer. This can al... | mbojrab/playbox | trunk/modules/python/nn/contiguousLayer.py | Python | mit | 4,593 | [
"NEURON"
] | 47f2cfd97922a929ea4cf23d19b6a33b447155ef1e3474592205a17c1790ca4b |
import PyQt5 # this force pyqtgraph to deal with Qt5
# For matplotlib to Qt5 :
# * this avoid tinker problem when not installed
# * work better with GUI
# * trigger a warning on notebook
import matplotlib
import warnings
with warnings.catch_warnings():
try: ... | tridesclous/tridesclous | tridesclous/gui/__init__.py | Python | mit | 2,001 | [
"TINKER"
] | 3798dda70a1a8da654efa5be7d26f5026e01c2d0c0120761abb254ef653f36d8 |
#!/bin/env python3
import sys
import os
import os.path
import traceback
from os.path import join, dirname, realpath
try:
sys.path.append(join(dirname(realpath(__file__)),
'..', '..', 'common', 'src'))
except NameError:
pass
from collections import defaultdict
from pysamimport import py... | HorvathLab/NGS | SCExecute/src/scBAMStats.py | Python | mit | 2,970 | [
"pysam"
] | 3321dc35fdc6faf8b9d5dd8bc960a646d43729d787bf28be37b3da2084f17061 |
#!env python
from __future__ import print_function, division
from collections import namedtuple
import unittest
import numpy as np
from numpy import array, concatenate, dot, eye, log, outer, zeros, \
r_, c_, pi, mean, cov
from numpy.random import rand, randn
from numpy.linalg import cholesky, det, inv
from scipy i... | mcobzarenco/nce-models | ncegauss.py | Python | gpl-2.0 | 8,158 | [
"Gaussian"
] | c6224e7522d22926ebc80f051dc0023cc4b279d62232f7e60c1fb694b7684e1d |
"""Build an index of top-level symbols from Python modules and packages."""
import os
import sys
import ast
import json
import logging
import re
from contextlib import contextmanager
from distutils import sysconfig
from importmagic.util import parse_ast
LIB_LOCATIONS = sorted(set((
(sysconfig.get_python_lib(st... | pombredanne/importmagic | importmagic/index.py | Python | bsd-2-clause | 14,475 | [
"VisIt"
] | b291aeeeb088b65e12f9be007d81c88489fc0d5bc1e8ebf2193b937c3610b50d |
from typing import Any
from sqlalchemy import select
from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession
from virtool.blast.models import NuVsBlast
from virtool.db.transforms import AbstractTransform
from virtool.types import Document
class AttachNuVsBLAST(AbstractTransform):
"""
Attach BLAST recor... | igboyes/virtool | virtool/blast/transform.py | Python | mit | 1,493 | [
"BLAST"
] | d1320d6334a9364736ee9f44c25f54adc9280b447489606539e9964674a99dd1 |
#!python
# ----------------------------------------
# scikit-ribo
# ----------------------------------------
# main wrapper
# ----------------------------------------
# author: Han Fang
# contact: hanfang.cshl@gmail.com
# website: hanfang.github.io
# date: 3/28/2017
# ----------------------------------------
from __f... | hanfang/scikit-ribo | build/scripts-3.4/scikit-ribo-run.py | Python | gpl-2.0 | 9,520 | [
"pysam"
] | 9cd86019490cd49c463739d8be064c7cb8d1140df2503e98a8ee053309b8c6bb |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# 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
# (at your option) an... | hfinucane/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 22,042 | [
"Galaxy",
"MOOSE"
] | d5eb1d0b6ee0a28320b5de4dfd623556178d10dc2a740bbb9de06a0df77055d0 |
from __future__ import with_statement
__license__ = 'GPL v3'
__copyright__ = '2008, Kovid Goyal <kovid at kovidgoyal.net>'
'''
Defines various abstract base classes that can be subclassed to create powerful news fetching recipes.
'''
__docformat__ = "restructuredtext en"
import os, time, traceback, re, urlparse, sy... | insomnia-lab/calibre | src/calibre/web/feeds/news.py | Python | gpl-3.0 | 73,428 | [
"VisIt"
] | 30e34da41b48b9f92f78e4f8876a86807481183358c1cc955f6c3530534cec3b |
# SVI for a GMM
# Modified from
# https://github.com/brendanhasz/svi-gaussian-mixture-model/blob/master/BayesianGaussianMixtureModel.ipynb
#pip install tf-nightly
#pip install --upgrade tfp-nightly -q
# Imports
import superimport
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import tensorf... | probml/pyprobml | scripts/svi_gmm_model_tfp.py | Python | mit | 4,690 | [
"Gaussian"
] | 508fe5beb528f576a99c53703cc19ba873040fceb7d9dd147c8993aab5ac2f27 |
## To Do:
## If a value outside of the original range is applied, the scalar bar range is not updated.
## Refers to TriangleWriter in _save_fired() - change to correct location
## More descriptive description
# Author: Daryl Harrison
# Enthought library imports
from enthought.traits.api import Instance, Range, Bool, ... | FluidityStokes/fluidity | mayavi/mayavi_amcg/filters/boundary_marker_editor.py | Python | lgpl-2.1 | 7,799 | [
"Mayavi"
] | 692c7ef00230ea8d9b18bf9636517cce358260bcb390de7087de4901f78a71f5 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# 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
# (at your option) an... | emersonsoftware/ansiblefork | lib/ansible/constants.py | Python | gpl-3.0 | 28,895 | [
"Galaxy",
"MOOSE"
] | 42547e9953ec2c26b4e18887f7e4aeaafd69fd909f63fa2fb7d11aac3a1c726d |
#!/cm/shared/apps/intelpython/intelpython3/bin/python
##!/Users/fujinobuaki/anaconda/bin/python
##!/tools/python
"""
This is a very simple plot script that reads a 3D DSM-Kernel sensitivity kernel
file and make a plot of it.
"""
import matplotlib.pyplot as plt
import numpy as np
import sys
from pyevtk.hl import gridTo... | IPGP/DSM-Kernel | examples/global_kernels/multiplekernel_write_vtk.py | Python | gpl-3.0 | 9,150 | [
"VTK"
] | e9c44116d4a2532aa9e50bc9e2f2674fe92bf4ab44bd516f0956a807ac23f578 |
#!/usr/bin/env python
import argparse
from pathlib import Path
from packaging.version import Version
import requests
def make_release(version, commit_hash, release_notes=""):
"""Create a new GitHub release using the given data
This function always makes a pre-release first to ensure the "latest" release nev... | DIRACGrid/DIRAC | .github/workflows/make_release.py | Python | gpl-3.0 | 2,264 | [
"DIRAC"
] | ac1e0f0c8ebe48ee6765945409d77af4329cb895b20eac289a56f5b608cc1b54 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | markovmodel/adaptivemd | adaptivemd/util.py | Python | lgpl-2.1 | 5,983 | [
"MDTraj"
] | e0927fb885a0190ecaea8d66f860a0883ed91d214bfc86ecf7feb6efe69a074b |
from flyingpigeon.visualisation import map_ensembleRobustness
from flyingpigeon.utils import get_variable
from flyingpigeon.utils import sort_by_filename
from flyingpigeon.utils import get_time
import logging
logger = logging.getLogger(__name__)
def worker(resource=[], start=None, end=None, timeslice=20,
vari... | sradanov/flyingpigeon | flyingpigeon/ensembleRobustness.py | Python | apache-2.0 | 6,739 | [
"NetCDF"
] | 1708418034408404f3e444af3922831f2085644ab545b8002c121693764d8b0d |
"""Tests for running lammps using CUDS and Simulation classes."""
import unittest
from simphony.api import CUDS, Simulation
from simphony.core.cuba import CUBA
from simphony.cuds.meta import api
from simphony.cuds.particles import Particles
from simphony.engine import EngineInterface
from simphony.testing.utils import... | simphony/simphony-lammps-md | simlammps/tests/test_cuds.py | Python | bsd-2-clause | 1,598 | [
"LAMMPS"
] | 7d15b23a5dae409a922729ffe7d6d309f3acae82eb0003d74e6fd9624f279194 |
# $HeadURL: $
""" ResourceStatus
Module use to switch between the CS and the RSS.
"""
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.DIRACSingleton import DIRACSingleton
from DIRAC.ConfigurationSystem.Client.Helpers import Re... | miloszz/DIRAC | ResourceStatusSystem/Client/ResourceStatus.py | Python | gpl-3.0 | 12,716 | [
"DIRAC"
] | 97491d9e5acc0ffafbae350700bfadd386b91ff173c8b98cef945b17728646d0 |
from numpy.testing import assert_equal, assert_array_equal, assert_allclose
from nose.tools import assert_true, assert_raises, assert_not_equal
from copy import deepcopy
import os.path as op
import numpy as np
from scipy import sparse
import os
import warnings
from mne import read_evokeds
from mne.datasets import test... | alexandrebarachant/mne-python | mne/tests/test_utils.py | Python | bsd-3-clause | 21,617 | [
"Mayavi"
] | 8eed469663e76bd3d720b685c0c2a5057db56eac2fa3485af5f794e0b6396b54 |
"""
Implementation of a language model class.
TODO: write more documentation
"""
__docformat__ = 'restructedtext en'
__authors__ = ("Razvan Pascanu "
"KyungHyun Cho "
"Caglar Gulcehre ")
__contact__ = "Razvan Pascanu <r.pascanu@gmail>"
import numpy
import itertools
import cPickle as p... | tomsbergmanis/gh_rnn_lm | groundhog/models/LM_model.py | Python | bsd-3-clause | 10,364 | [
"Gaussian"
] | b0e66be21809f7004a590e80fa07849f7c95dcf3fb0f0691bd22e6f3f6c77fed |
from pysamimport import pysam
import re, sys
from collections import defaultdict
class ChromLabels(object):
def __init__(self,labels=[]):
self.labels = list(labels)
self.label2chrom = {}
self.chrom2label = {}
self.labelorder = {}
self.scheme = None
if len(self.lab... | HorvathLab/NGS | attic/readCounts/src/chromreg.py | Python | mit | 7,413 | [
"pysam"
] | 1fca56ab08b8550cdd24ed066d52269f709d245408e1f2ebc75c160a25b00f40 |
# coding=utf-8
# Copyright 2020 The TF-Agents Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable la... | tensorflow/agents | tf_agents/agents/qtopt/qtopt_agent.py | Python | apache-2.0 | 28,159 | [
"Gaussian"
] | 004854f9fa2dead59f2cd3c2cdd6eb785499e4809a41a52c0ddfdfd301387690 |
# proxy module
from __future__ import absolute_import
from mayavi.modules.metadata import *
| enthought/etsproxy | enthought/mayavi/modules/metadata.py | Python | bsd-3-clause | 92 | [
"Mayavi"
] | 2615dbb41a42ba51221459d3cf74fb791136fd5e4f2630e4cdb26e39d80ebd4c |
"""
Filename: approximation.py
Authors: Thomas Sargent, John Stachurski
tauchen
-------
Discretizes Gaussian linear AR(1) processes via Tauchen's method
"""
import numpy as np
from scipy.stats import norm
def tauchen(rho, sigma_u, m=3, n=7):
"""
Computes the Markov matrix associated with a discretized ver... | agutieda/QuantEcon.py | quantecon/markov/approximation.py | Python | bsd-3-clause | 1,809 | [
"Gaussian"
] | 5958597605e97bca0a7f6906201b503b4ad5efeb67eae1a9cd37cd87fc720814 |
# -*- encoding:ascii -*-
from mako import runtime, filters, cache
UNDEFINED = runtime.UNDEFINED
__M_dict_builtin = dict
__M_locals_builtin = locals
_magic_number = 6
_modified_time = 1417014254.639858
_template_filename=u'templates/refresh_frames.mako'
_template_uri=u'/refresh_frames.mako'
_template_cache=cache.Cache(_... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/database/compiled_templates/refresh_frames.mako.py | Python | gpl-3.0 | 3,420 | [
"Galaxy"
] | 6b900742da19ff275bbb146ae6f6d9dc013ac00408ced3699ef888340abcd149 |
import os
import sys
import vtkAll as vtk
from ddapp import botpy
import math
import time
import types
import functools
import numpy as np
from collections import defaultdict
from ddapp import transformUtils
from ddapp import lcmUtils
from ddapp.timercallback import TimerCallback
from ddapp.asynctaskqueue import Async... | rdeits/director | src/python/ddapp/terraintask.py | Python | bsd-3-clause | 62,670 | [
"VTK"
] | 83b20bcb1dc8fce9d97ffb2ae56c703582acadaad5510f7fd815eb1f5e63dd31 |
import pytest
from tests.utils import resource_file
from owslib.wps import WebProcessingService, WPSExecution, Process, is_reference, Input
from owslib.etree import etree
@pytest.fixture
def wps():
'''Returns a WPS instance'''
# Initialize WPS client
wps = WebProcessingService('http://example.org/wps', ... | kalxas/OWSLib | tests/test_wps.py | Python | bsd-3-clause | 3,259 | [
"NetCDF"
] | b37ed8ce8a2bf956898f04d3fd8ca3f882635d8a1bd3e7d0bb94e37b7d143e18 |
import openpnm as op
import numpy as np
# work space and project
ws = op.Workspace()
proj = ws.new_project()
# network
np.random.seed(7)
net = op.network.Cubic(shape=[20, 1, 1], spacing=1e-4, project=proj)
# geometry
geo = op.geometry.StickAndBall(network=net,
pores=net.Ps,
... | TomTranter/OpenPNM | scripts/nonNewtonian_01.py | Python | mit | 2,009 | [
"VTK"
] | 76e499fc30c09b85490bbcd6ef154a15abcca5224d7abe289451a1d177545170 |
import numpy as np
import pandas as pd
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
opencl = mm.Platform_getPlatformByName("OpenCL")
cuda = mm.Platform_getPlatformByName("CUDA")
#platform = opencl
platform = cuda
n_steps = 5000
temperature = 300. * u.kelvi... | kyleabeauchamp/HMCNotes | code/old/test_hmc.py | Python | gpl-2.0 | 2,132 | [
"OpenMM"
] | 0b7b6e0b3a37f1b95bf0d49a779fa9827f894121d5170dd1d55a17cd251d403e |
#
# @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
#... | CDSherrill/psi4 | psi4/driver/p4util/util.py | Python | lgpl-3.0 | 12,333 | [
"Psi4"
] | 10e247ad99eb851c80c062accc129218aeda03ffd9e27761fe51c0b7dcfccdfb |
# Author: Robert McGibbon <rmcgibbo@gmail.com>
# Contributors:
# Copyright (c) 2014, Stanford University
# All rights reserved.
#-----------------------------------------------------------------------------
# Imports
#-----------------------------------------------------------------------------
from __future__ import... | dotsdl/msmbuilder | msmbuilder/cluster/__init__.py | Python | lgpl-2.1 | 3,143 | [
"MDTraj"
] | 715ba19351c0d48f27b9c60352e193eba0d97f44423d849bbfac605a9843771f |
# Copyright 2017 Google 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/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | hanmy75/voice-recognizer | src/action.py | Python | apache-2.0 | 11,287 | [
"Galaxy"
] | 4d5e5040dfc449b917fcc02c1a8e778472ee9d79e5eae4c1b463ad14f3253074 |
from __future__ import division
from __future__ import absolute_import
from __future__ import unicode_literals
from __future__ import print_function
# reinforcementTestClasses.py
# ---------------------------
# Licensing Information: Please do not distribute or publish solutions to this
# project. You are free to use a... | rlpy/rlpy | rlpy/Domains/PacmanPackage/reinforcementTestClasses.py | Python | bsd-3-clause | 48,402 | [
"VisIt"
] | a8a6d1d2c983253500d74fae166c640812ec1954782493f7a0ff411aa152b7c2 |
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