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#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2011 ~ 2012 Deepin, Inc.
# 2011 ~ 2012 Hou Shaohui
#
# Author: Hou Shaohui <houshao55@gmail.com>
# Maintainer: Hou Shaohui <houshao55@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the ter... | dragondjf/QMusic | src/dwidgets/coverlrc/mycurl.py | Python | lgpl-2.1 | 7,129 | [
"VisIt"
] | 5d0fea59d15dabd1bc2d9f035fbebf7bb079e7c5fe422c462f2d7ea0db16e2f7 |
from __future__ import print_function, division
from sympy.core import Mul
from sympy.functions import DiracDelta, Heaviside
from sympy.core.compatibility import default_sort_key
from sympy.core.singleton import S
def change_mul(node, x):
"""change_mul(node, x)
Rearranges the operands of a product, bring... | drufat/sympy | sympy/integrals/deltafunctions.py | Python | bsd-3-clause | 7,395 | [
"DIRAC"
] | 7481a8e42aed80170c86234105a20faf28ce1cb1d80d5dee91da8d7f17b98db6 |
import tempfile
from pele.systems import AtomicCluster
from pele.potentials import LJ
from pele.utils.xyz import write_xyz
__all__ = ["LJCluster"]
class LJCluster(AtomicCluster):
"""
define the System class for a Lennard-Jones cluster
Parameters
----------
natoms : int
See Also
... | smcantab/pele | pele/systems/ljcluster.py | Python | gpl-3.0 | 4,106 | [
"PyMOL"
] | 2b65038e1b177efcadc7a7df9b30f335d56b08a7b26b7a0b71d405a7467a9aca |
#!/usr/bin/python
# 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) any later version.
#
# Ansible is distributed... | tonyyarusso/ansible-modules-core | cloud/amazon/elasticache.py | Python | gpl-3.0 | 21,321 | [
"Dalton"
] | 31f375c0241c6d389e44a1ed5f3cb20b9363c1a3c8645600111bd201c67edb6c |
#!/usr/bin/env python
'''unit testing code for pysam.
Execute in the :file:`tests` directory as it requires the Makefile
and data files located there.
'''
import pysam
import unittest
import os
import re
import sys
import subprocess
import shutil
from TestUtils import checkBinaryEqual
IS_PYTHON3 = sys.version_info[0... | brendanofallon/pysam | tests/samtools_test.py | Python | mit | 12,544 | [
"pysam"
] | 5fbc8d7b2cad448aa34f6fbfaa8990261c022d5760d1370c4310d9bfe6efd7c1 |
import numpy as nm
from sfepy.base.base import output, OneTypeList, Struct
from sfepy.discrete.fem.mesh import Mesh
from sfepy.discrete.fem.meshio import MeshIO
from sfepy.solvers.ts import TimeStepper
from sfepy.base.ioutils import get_trunk, write_dict_hdf5
def _linearize(out, fields, linearization):
new = {}
... | RexFuzzle/sfepy | sfepy/postprocess/time_history.py | Python | bsd-3-clause | 7,496 | [
"VTK"
] | 640904df029f15c3896cbadd5088f36963569c8831b9930339f1c85990c378eb |
import types
from DIRAC.Core.Utilities import Time
class DBUtils:
def __init__( self, db, setup ):
self._acDB = db
self._setup = setup
def _retrieveBucketedData( self,
typeName,
startTime,
endTime,
... | vmendez/DIRAC | AccountingSystem/private/DBUtils.py | Python | gpl-3.0 | 11,695 | [
"DIRAC"
] | 97ace447fceddfc81a0928145d15e3f00025a49675b742d16f918abedf12b529 |
#########################################################################################
# LSF.py
# 10.11.2014
# Author: A.T.
#########################################################################################
""" LSF.py is a DIRAC independent class representing LSF batch system.
LSF objects are used as bac... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/LSF.py | Python | gpl-3.0 | 7,238 | [
"DIRAC"
] | d4a46abd4524c59f96d1cdd59274fd8ef1787bd86d9b3f1ebddf4c9b752b4b00 |
# -*- coding: utf-8 -*-
""":mod:`itertools` is full of great examples of Python generator
usage. However, there are still some critical gaps. ``iterutils``
fills many of those gaps with featureful, tested, and Pythonic
solutions.
Many of the functions below have two versions, one which
returns an iterator (denoted by ... | suranap/boltons | boltons/iterutils.py | Python | bsd-3-clause | 30,327 | [
"VisIt"
] | 540328c64406f3601c411c223b2db2a3a4e28721e1e3ec3504a431e330c646b4 |
import _ast
import ast
from jaspyx.context.block import BlockContext
from jaspyx.visitor import BaseVisitor
class For(BaseVisitor):
def visit_For(self, node):
if node.orelse:
raise Exception('for-else is not supported.')
if isinstance(node.iter, _ast.Call) and isinstance(node.iter.fun... | iksteen/jaspyx | jaspyx/visitor/for_.py | Python | mit | 2,102 | [
"VisIt"
] | b94473a2b076fd77f7c7fe058f34d12f6cc6c4966c029bff5f460dc2112c67c9 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2013 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/remindor-qt | remindor_qt/DateDialog.py | Python | gpl-3.0 | 8,672 | [
"Brian"
] | f7a1272f2a1891c6516a5fbe7bb0a90339dd77a228d9a2cf4329a309944ca788 |
# -*- coding: utf-8 -*-
"""
Calculates rho(z) to maintain hydrostatic equilibrium in a thin disc.
Assumes uniform temperature in the disc, and an infinite disc where
rho can be treated (at least locally) as only a function of z.
Created on Mon Jan 20 12:30:06 2014
@author: ibackus
"""
# ICgen packages
import isaac... | dflemin3/ICgen | backup03/calc_rho.py | Python | mit | 11,325 | [
"Gaussian"
] | 25ad8a39401d7912f5fecaadbcd7a3d12350f88aaff7283ee8a8dd2e953158a8 |
##############################################################################
# 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: ... | thempel/adaptivemd | adaptivemd/project.py | Python | lgpl-2.1 | 24,986 | [
"MDTraj"
] | 7457a93b5751980f63d212073a4c8d541f2dfca154c1315b1c580023a9feafb2 |
from __future__ import with_statement
# ==============================================================================
# GGisy (python v2.7)
#
# Author: Sandro Valenzuela (sandrolvalenzuead@gmail.com)
# Bugs and errors: https://github.com/Sanrrone/GGisy/issues
#
# Please type "python GGisy.py -h" for usage help... | Sanrrone/GGisy | GGisy.py | Python | apache-2.0 | 14,845 | [
"BLAST"
] | 8abc26b836a94471da7c9efe104d88ea6ff2050d6863c60feb6c4bcaf872b924 |
#!/usr/bin/env python
"""VisualizeTestTimes.py
Visualize CTest test times with VTK.
Run from the top of the build tree after the ctest has been run at least once.
Pass the --modular-grouping flag to group by module."""
from __future__ import print_function
import os
import pprint
import subprocess
... | RayRuizhiLiao/ITK_4D | Utilities/Maintenance/VisualizeTestTimes.py | Python | apache-2.0 | 5,456 | [
"VTK"
] | 8904403f507256aa83b54d3e12a11ec194d6058aafa2894682fa26fcdb11d6f6 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.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... | tchernomax/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 40,953 | [
"VisIt"
] | 09fc5889c0d48eb9e1e91309d60c90abcdfd610abbaefc01efcbe4a4309d3dc0 |
import random
import unittest
from hearthbreaker.agents.basic_agents import PredictableAgent, DoNothingAgent
from tests.agents.testing_agents import OneCardPlayingAgent, EnemySpellTestingAgent, \
CardTestingAgent, EnemyMinionSpellTestingAgent, PlayAndAttackAgent, HeroPowerAndCardPlayingAgent
from hearthbreaker.con... | jomyhuang/sdwle | testsHB/card_tests/warlock_tests.py | Python | mit | 35,057 | [
"BLAST",
"CRYSTAL"
] | c7cd6929eb98eba186672c4497425e9bd2635fb331054e29e6988aa5adca71f6 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/ao2mo/eris.py | Python | apache-2.0 | 8,686 | [
"PySCF"
] | d0a125bb931454254d54c62583cc2ad86be3437f7429c18c6786cdf69afa0f04 |
#!/usr/bin/env python
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg & Johan Leckner
##
## 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 Softwar... | ostrokach/biskit | scripts/Biskit/amber_pdb2parm.py | Python | gpl-3.0 | 5,523 | [
"Amber"
] | b5343cbb5dbee2835a4815add838ed44e1365c54dc1091b5b02b9c6202a57a42 |
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpatterns = [
url(r'^$', TemplateView.as_view(template_name='page... | brayan15/Events | config/urls.py | Python | mit | 1,546 | [
"VisIt"
] | 272145e725853e4dab501d225ede3f658c974ce4dceae8bc89807adc94292db4 |
from __future__ import absolute_import
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
from . import utils
import scipy as sp
from scipy import ndimage
from six.moves import zip
def plot_stars(p, x, y, size='large', horizontalalignment='center', **kwargs):
''' Plots si... | gentnerlab/behav-analysis | behav/plotting.py | Python | bsd-3-clause | 12,668 | [
"Gaussian"
] | 216d0b69b8cc1647d5e61b1a762fdb8dcbd9822e3372002ccf1b36d7dcb4a8bc |
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division,
print_function, unicode_literals)
from future.builtins import *
import time
import numpy as np
from scipy import signal
import audiolazy
class Simulation(object):
"""The Simulation object can be used if a real exp... | p3trus/heatcapacity | heatcapacity/simulation.py | Python | bsd-3-clause | 2,158 | [
"Gaussian"
] | 9fd8f4be8de21cd3281037e35637c9231d6cd1d4261f54517e601de16b9f337b |
# -*- coding: utf-8 -*-
u"""
==================================
Input and output (:mod:`scipy.io`)
==================================
.. currentmodule:: scipy.io
SciPy has many modules, classes, and functions available to read data
from and write data to a variety of file formats.
.. seealso:: `NumPy IO routines <ht... | lhilt/scipy | scipy/io/__init__.py | Python | bsd-3-clause | 2,453 | [
"NetCDF"
] | 1ebc76aea26241cd7ac1bd1dca1dbe87ef8317a1ca02d15e6ecffcc357c81a8b |
from unittest import skipIf
from openmoltools import utils, amber, packmol, gromacs
from distutils.spawn import find_executable
import os
def test_gromacs_merge():
etoh_filename = utils.get_data_filename("chemicals/etoh/etoh.mol2")
benzene_filename = utils.get_data_filename("chemicals/benzene/benzene.mol2")
... | jchodera/openmoltools | openmoltools/tests/test_gromacs.py | Python | gpl-2.0 | 2,794 | [
"Amber",
"Gromacs"
] | f195e6738ca3a6d8b6f933c55423df6b8287c3aedca23dbad728eafa583ad858 |
"""
Custom nodes for a Tree Editor that provide views for adding various nodes
to the tree.
"""
# Authors: Judah De Paula <judah@enthought.com>
# Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import (HasTrai... | liulion/mayavi | mayavi/core/adder_node.py | Python | bsd-3-clause | 13,368 | [
"Mayavi"
] | 059890a44c8d27506d787f7410c2fd0bbd79f418b71d11eae17167a22f540c04 |
# Copyright (C) 2008-2009 Open Society Institute
# Thomas Moroz: tmoroz@sorosny.org
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License Version 2 as published
# by the Free Software Foundation. You may not use, modify or distribu... | boothead/karl | karl/models/subscribers.py | Python | gpl-2.0 | 9,622 | [
"VisIt"
] | 9d563b9cdaa3e4d706d983139412f59f6e12b551d02f69a92fc79851a7194b31 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | retrography/scancode-toolkit | tests/commoncode/test_codec.py | Python | apache-2.0 | 4,920 | [
"VisIt"
] | 82d73c037003f6a132c1c62665316510921620c931aa55faeac62abc88738e7b |
""" VOMSService class encapsulates connection to the VOMS service for a given VO
"""
import requests
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Security.Locations import getProxyLocation, getCAsLocation
from DIRAC.ConfigurationSystem.Client.Helpers.Registr... | DIRACGrid/DIRAC | src/DIRAC/Core/Security/VOMSService.py | Python | gpl-3.0 | 4,693 | [
"DIRAC"
] | f75197066ed8705bf36bb03b210c0cb78bfca636087fd6e0a5c58d65167c79a2 |
# -*- coding: utf-8 -*-
###############################################################################
#
# This source file is part of the tomviz project.
#
# Copyright Kitware, Inc.
#
# This source code is released under the New BSD License, (the "License").
#
# Unless required by applicable law or agreed to in ... | mathturtle/tomviz | tomviz/python/tomviz/io/formats/matlab.py | Python | bsd-3-clause | 1,632 | [
"VTK"
] | c4b351a0149130cc3ec20b622c9d3ecdf7a71504b84552355329fb8f5e83c2fc |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright 2011 Sebastian Pölsterl
#
# Permission is granted to copy, distribute and/or modify this document
# under the terms of the GNU Free Documentation License, Version 1.3
# or any later version published by the Free Software Foundation;
# with no Invariant Sections, no ... | pwaller/pgi | examples/gtk/linkbutton_example.py | Python | lgpl-2.1 | 820 | [
"VisIt"
] | 6ecc6b47ee22d643f0867e89e9398cc1394be8b3796cf2a69504073f31710b85 |
#-------------------------------------------------------------------------------
# Copyright (c) 2011 Anton Golubkov.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Lesser Public License v2.1
# which accompanies this distribution, and is available at
#... | anton-golubkov/Garland | src/ipf/ipftype/ipfadaptivethresholdmethod.py | Python | lgpl-2.1 | 1,073 | [
"Gaussian"
] | 44dbc30df7441a11c64c77679698d8bd80b1114fabf41017f5d5310d140b90f8 |
# -*- coding: utf-8 -*-
"""This file contains a plugin for parsing Google Analytics cookies."""
from urllib import parse as urlparse
from dfdatetime import posix_time as dfdatetime_posix_time
from dfdatetime import semantic_time as dfdatetime_semantic_time
from plaso.containers import events
from plaso.containers im... | joachimmetz/plaso | plaso/parsers/cookie_plugins/ganalytics.py | Python | apache-2.0 | 12,786 | [
"VisIt"
] | 9cf0df7fd4d2f7fc8acd0a2415068312aaaaf93c5b751f02e2e4cb258c9917e5 |
#!/usr/bin/python2.4
# encoding: utf-8
"""
ppi.py
High-level functions for interacting with the protein-protein interaction sections of the ddG database.
Classes:
BindingAffinityDDGInterface - an class used to interface with the database. Call get_interface to get a user API based on this class.
Created by Shane O'Co... | Kortemme-Lab/kddg | kddg/api/ppi.py | Python | mit | 189,894 | [
"PyMOL"
] | 6dc727c32171db6915abfe738876e387a2b77bc227492542ecd237ee5270af7e |
# -*- test-case-name: twisted.web.test.test_util -*-
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
"""
An assortment of web server-related utilities.
"""
from __future__ import division, absolute_import
import linecache
from twisted.python import urlpath
from twisted.python.compat import _... | bdh1011/wau | venv/lib/python2.7/site-packages/twisted/web/util.py | Python | mit | 10,875 | [
"VisIt"
] | f4b9cf9120c14099dc7eb914713683fa7eb534eab96da95ce0cd3ce2dd16e3e6 |
# Copyright (c) 2004 Canonical Limited
# Author: Robert Collins <robert.collins@canonical.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at y... | freyes/percona-xtradb-cluster-5.5 | python-for-subunit2junitxml/subunit/tests/TestUtil.py | Python | gpl-2.0 | 2,794 | [
"VisIt"
] | d1859917be893690f041103fbe320f6064164b2a23bfb6504d6adda6c6a55cae |
__author__ = 'Tom Schaul, tom@idsia.ch'
from pybrain.structure.modules.module import Module
class NeuronLayer(Module):
"""Module conceptually representing a layer of units """
# Number of neurons
dim = 0
def __init__(self, dim, name=None):
"""Create a layer with dim number of units."""
... | pybrain/pybrain | pybrain/structure/modules/neuronlayer.py | Python | bsd-3-clause | 691 | [
"NEURON"
] | 41eb31d74316fa33c2319f5218c771aceb38e78375ed3620cd66f87cba72c652 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/topology/test_pdb.py | Python | gpl-2.0 | 10,944 | [
"MDAnalysis"
] | 7ace0710386345f0464e9ee66c45b21194cf6f8db228f4bb2199004a1e1a8149 |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2009-2013 CRS4.
#
# This file is part of biodoop-blast.
#
# biodoop-blast 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 opt... | crs4/biodoop-blast | bl/blast/mr/blastall/reducer.py | Python | gpl-3.0 | 914 | [
"BLAST"
] | df6363839dc192dea9d2d285d15472507c8d2d2ab71b4a40cdbcdf36f49d2f28 |
#Copywrite (c) Paul & John Ashby 2014
#Weight Effect
#This game is an RPG that is designed by my brother (John) and myself (Paul).
#We built this to explore python programing, open source github, and to have some fun.
#
print("\\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\")
print("\\ \\ \\ \\ \\Weight Ef... | bedevere/FailHub | weighteffect.py | Python | mit | 23,719 | [
"TINKER"
] | 3b68711ab085c96e12eb70c283121c64f02b9cbabb8e862d48e1ddfb04cd17f4 |
# Copyright (C) 2014 Brian Marshall
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in... | bmars/sisko | sisko/__init__.py | Python | gpl-3.0 | 713 | [
"Brian"
] | 4c46d25b1ae2b7fec9dbb59911c6965fc6d92ff0de8d8d216579e3325a4d363f |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.import string
"""
function for calculating the convergence of an x, y data set
main api:
test_conv(xs, ys, name, tol)
tries to fit multiple functions to the x, y data
calculates which function fits best
for tol < 0
returns ... | vorwerkc/pymatgen | pymatgen/util/convergence.py | Python | mit | 15,849 | [
"pymatgen"
] | 9a3fb6500171081914a1878bf6a0f5960989628ca4e26e83e7cc4518cc30803b |
#!/usr/bin/python
# Copyright: Ansible Project
# 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': '1.1',
'status': ['preview'],
... | Nicop06/ansible | lib/ansible/modules/cloud/amazon/cloudwatchevent_rule.py | Python | gpl-3.0 | 15,715 | [
"Dalton"
] | 899ee25687911805b4c4c689e4f3eccd5a816f24dcc1c8051e50901f07ec5ea8 |
import numpy as np
# import FitsUtils
import FittingUtilities
import HelperFunctions
import matplotlib.pyplot as plt
import sys
import os
from astropy import units
from astropy.io import fits, ascii
import DataStructures
from scipy.interpolate import InterpolatedUnivariateSpline as interp
import MakeModel
import Helper... | kgullikson88/HET-Scripts | Smooth.py | Python | gpl-3.0 | 6,217 | [
"Gaussian"
] | 9bca67d3cef137aec3176935bc1efb3802bd09bcd0d14970e99a76d6ccb00bf0 |
#!/usr/bin/env Python
##########################################################################
#
# Copyright (C) 2015-2017 Sam Westreich
#
# 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;
#
# T... | transcript/samsa2 | python_scripts/standardized_DIAMOND_analysis_counter.py | Python | gpl-3.0 | 8,256 | [
"BLAST"
] | b378c33b03c37929f957cd60356d0f0d949c3aca2316cbd32994d2921ab63d7f |
# -*- coding: utf-8 -*-
# -*- coding: utf-8 -*-
import os
#from numpy import *
import numpy as np
import numpy.matlib
from numpy.matlib import repmat
from scipy.integrate import trapz
import copy as copyModule
#from libc.stdio import printf
from pyhrf import xmlio
from pyhrf.tools import resampleToGrid, get_2Dtable... | philouc/pyhrf | python/pyhrf/jde/nrl/bigaussian.py | Python | gpl-3.0 | 196,426 | [
"Gaussian"
] | 5cd1bb532d58dd82f5c71ddb801716572565b16742d485338c2edfc791aca276 |
"""Shared functionality for interacting with Galaxy.
"""
| lpantano/bcbio-nextgen | bcbio/galaxy/__init__.py | Python | mit | 57 | [
"Galaxy"
] | f758cbe85bcd4b79197060c229afc94861b3772bdfabdc14ce41a7937891bb95 |
"""Hilbert spaces for quantum mechanics.
Authors:
* Brian Granger
* Matt Curry
"""
from __future__ import print_function, division
from sympy import Basic, Interval, oo, sympify
from sympy.core.compatibility import u, range
from sympy.printing.pretty.stringpict import prettyForm
from sympy.physics.quantum.qexpr imp... | kaichogami/sympy | sympy/physics/quantum/hilbert.py | Python | bsd-3-clause | 19,528 | [
"Brian"
] | e847ddf095871b51d249a2c09625b7355d449ce72c1a05956a4a2a308a91617b |
import os
import sys
from time import ctime, time
import numpy as np
from ase.units import Hartree, Bohr
from ase.utils import prnt
from scipy.special.orthogonal import p_roots
from scipy.special import sici
from gpaw import GPAW
from gpaw.blacs import BlacsGrid, Redistributor
from gpaw.utilities.blas import gemmdot,... | robwarm/gpaw-symm | gpaw/xc/fxc.py | Python | gpl-3.0 | 24,057 | [
"ASE",
"GPAW"
] | e23130d1f3a624c32a10887b34eda93278a6ff3fff65b9e546a9146becd36fbb |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/presentations/presentationplugin.py | Python | gpl-2.0 | 8,434 | [
"Brian"
] | 15c6bb09fc1252cc569f2ac9a42cdb86590743c353bdb0850b504ef88af406b6 |
"""
Test refinement of beam, detector and crystal orientation parameters
using generated reflection positions from ideal geometry.
Control of the experimental model and choice of minimiser is done via
PHIL, which means we can do, for example:
cctbx.python tst_orientation_refinement.py \
"random_seed=3; engine=LBFGScu... | dials/dials | tests/algorithms/refinement/test_orientation_refinement.py | Python | bsd-3-clause | 9,452 | [
"CRYSTAL"
] | 6b9f12889383f2aee1ac151b709500f8ba4a303d46d1387292cf3848edef7071 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | modeling/build/suite.py | Python | agpl-3.0 | 42,102 | [
"Galaxy"
] | d36267e0b44b709ad4050cd3d41ae2aced1270fd13d93750c21e13acd6c2c325 |
# Copyright Yair Benita Y.Benita@pharm.uu.nl
# Biopython (http://biopython.org) license applies
"""Calculate isoelectric points of polypeptides using methods of Bjellqvist.
pK values and the methos are taken from::
* Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez,
J.-Ch., Frutige... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/SeqUtils/IsoelectricPoint.py | Python | apache-2.0 | 4,328 | [
"Biopython"
] | 2f3052427889d261dd2eb5af0e60258e6efe324f52608639cdf0fe3aa8eb9a16 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
from openbci.offline_analysis.obci_signal_processing import read_manager
import analysis_offline
class ReadSignal(object):
def __init__(self, files):
self.files = files
def process(self, files=None):
if not self.files is None:
files = s... | BrainTech/openbci | obci/analysis/p300/chain_analysis_offline.py | Python | gpl-3.0 | 7,721 | [
"Gaussian"
] | 426ca6a79b1749bcfce96d7a52e39af7215fc00ca0707c093c80fd97a24af963 |
# -*- coding: utf-8 -*-
"""OpenERP community addons standard plugin for flake8"""
from __future__ import absolute_import
import common_checker
from common_checker.base_checker import BaseChecker
# When OpenERP version 8 API will be frozen
# We will be able to do version toggle here
import v7
__version__ = '0.0.1'
... | nbessi/openerp-conventions | openerp_conventions.py | Python | mit | 1,370 | [
"VisIt"
] | 0283b5c0cbc78a66f82b6342c63cc72c3c0cd3b0b69b7595aaff2bb02cfed375 |
#
#-*- coding:utf-8 -*-
"""
Gentoo-keys - actions.py
Primary api interface module
@copyright: 2012 by Brian Dolbec <dol-sen@gentoo.org>
@license: GNU GPL2, see COPYING for details.
"""
from __future__ import print_function
import os
from gkeys.seedhandler import SeedHandler
from gkeys.lib import ... | dol-sen/gentoo-keys | gkeys/actions.py | Python | gpl-2.0 | 11,653 | [
"Brian"
] | 6eea7d507fb25a9538978b03b8171bd7d78e8a47bc6a6021c4577e910a3b8d68 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | testsuite/python/analyze_distribution.py | Python | gpl-3.0 | 3,526 | [
"ESPResSo"
] | d34688696f748af7c39c460db054cd7d715d17641cd9c74848deab267f4842d4 |
"""User-friendly public interface to polynomial functions. """
from __future__ import print_function, division
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple
)
from sympy.core.mul import _keep_coeff
from sympy.core.symbol import Symbol
from sympy.core.basic import preorder_traversal
... | wolfram74/numerical_methods_iserles_notes | venv/lib/python2.7/site-packages/sympy/polys/polytools.py | Python | mit | 171,109 | [
"Gaussian"
] | 6b26dd59225c93802a32ac952799ed45b737bb78a53c0652bb657ded355be75b |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | samples/chamber_game.py | Python | gpl-3.0 | 17,946 | [
"ESPResSo"
] | f117e5eb7a9ec85e5373ff11fdba989b6257cd86c04437b3acaa48e067f5f39f |
# ******************************************************************************
# pysimm.apps.random_walk module
# ******************************************************************************
#
# psuedo random walk algorithm written using pysimm tools
#
# *************************************************************... | plin1112/pysimm | pysimm/apps/random_walk.py | Python | mit | 13,307 | [
"LAMMPS"
] | 2802887d3f7a64df06c08165590853303b366879a3978b47fda3660932365698 |
#!/usr/bin/env python2
# Copyright (C) 2020
# Max Planck Institute for Polymer Research & JGU Mainz
#
# 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,... | govarguz/espressopp | testsuite/vectorization/test_vectorization.py | Python | gpl-3.0 | 4,384 | [
"ESPResSo"
] | c22c12b216a18c65a77e653aedf5c51ae4d0c111b9020c9bbe8098602c624622 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# showvgridprivatefile - View VGrid private files for owners and members
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms... | heromod/migrid | mig/shared/functionality/showvgridprivatefile.py | Python | gpl-2.0 | 4,210 | [
"Brian"
] | 9c59246136423bae4ebf17c009cfaf4ddb821bcd1b85dcbc5f9d9923cb0631f2 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 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/dialogs/tillhistory.py | Python | gpl-2.0 | 4,857 | [
"VisIt"
] | 1fa1d043702f257825a27cc9522097351a67fb86b1abc96ba9722fdab43e6102 |
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
import sys
sys.path.append("../")
from functions import *
from pylab import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import matplotlib.cm as cm
import os
#####################################... | gviejo/ThalamusPhysio | python/figure_article_v4/main_article_v4_fig_4.py | Python | gpl-3.0 | 26,031 | [
"Gaussian"
] | 9b4be43838ce34a50430a045ce9be157afb3bb66f773a780802226ff0c009e62 |
#! /usr/bin/env python
"""A module for authenticating against and communicating with selected
parts of the Garmin Connect REST API.
"""
import json
import logging
import os
import re
import requests
from StringIO import StringIO
import sys
import zipfile
import dateutil.parser
import os.path
from functools import wrap... | dlenski/garminexport | garminexport/garminclient.py | Python | apache-2.0 | 18,466 | [
"VisIt"
] | 99e82cfbb49fbca7740bb1f199dcd69b55b2f4911c5ef022b27d778b721d3f6d |
# -*- coding: utf-8 -*-
"""
Main FISSA user interface.
Authors:
- Sander W Keemink <swkeemink@scimail.eu>
- Scott C Lowe <scott.code.lowe@gmail.com>
"""
from __future__ import print_function
import collections
import datetime
import functools
import glob
import itertools
import os.path
import sys
import time... | rochefort-lab/fissa | fissa/core.py | Python | gpl-3.0 | 74,650 | [
"NEURON"
] | 56231f38a0a3ada54b51d15ddd2c1fa98e0be44813ec1f58b4c29e8c4f972cf9 |
from galaxy.jobs import JobDestination
import os
import sys
import json
import cStringIO
import logging
log = logging.getLogger( __name__ )
def dump(obj, nested_level=0, output=sys.stdout):
spacing = ' '
if type(obj) == dict:
print >> output, '%s{' % ((nested_level) * spacing)
for k, v in o... | kaktus42/galaxytools | tools/gatk/tool-data/destinations.py | Python | gpl-2.0 | 2,338 | [
"Galaxy"
] | aa2ce769c1aebfbcfb036a8185683c522dad3abea69ac3c99ade9a6e065285e9 |
"""
Copyright 2014, Roberto Paleari (@rpaleari)
Abstract class for QTrace output modules.
"""
import abc
import trace.reader
import trace.syscall
class OutputGenerator(object):
__metaclass__ = abc.ABCMeta
def __init__(self, stream):
self.__stream = stream
self.__stream.write(self._prologue(... | rpaleari/qtrace | tools/output/output.py | Python | gpl-2.0 | 1,867 | [
"VisIt"
] | d886698ce459141243ae6e80e81f286b9313ae84c83f943a249c3b6ea806653d |
# Copyright 2014 NeuroData (http://neurodata.io)
#
#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 ... | neurodata/ndstore | webservices/ndwsrest.py | Python | apache-2.0 | 83,674 | [
"NEURON"
] | 17830706453c43f9b94c81c54ec13b8a19172d657f99501c2b83329bb0391926 |
#!/usr/bin/env python
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##... | aewebb80/VESPA | vespa.py | Python | gpl-3.0 | 163,608 | [
"BLAST"
] | a9f5b8619f2aaa8b2350f4c7044882e7c3502fc5f1de5fb0fa6653449d559a0b |
from math import pi
import numpy as np
from pysisyphus.calculators.Calculator import Calculator
from pysisyphus.constants import KB, AU2J
from pysisyphus.intcoords.PrimTypes import prims_from_prim_inputs
from pysisyphus.intcoords.update import correct_dihedrals
from pysisyphus.intcoords import Torsion
class LogFermi... | eljost/pysisyphus | pysisyphus/calculators/ExternalPotential.py | Python | gpl-3.0 | 6,354 | [
"xTB"
] | 321f4ec291aeb219d90793252d1ae1a08f84e7ac7863682827673dff6a066772 |
#! /usr/bin/env python
## Copyright (c) 1999 - 2003 L. C. Rees. All rights reserved.
## See COPYRIGHT file for license terms.
from __future__ import generators
__name__ = 'spider'
__version__ = '0.5'
__author__ = 'L.C. Rees (xanimal@users.sf.net)'
__all__ = ['ftpurls', 'ftppaths', 'weburls', 'ftpmirror', 'ftpspider',... | heitara/webfetcher | spider.py | Python | apache-2.0 | 42,576 | [
"VisIt"
] | a924a47d9f6a5f1f51c83f41354761a5e049b939dd71cf9a16c38cee839f9aee |
{
"name" : "Unified Chart of Accounts for US Non-Profits",
"version" : "2.6.0",
"author" : "Free Geek Twin Cities",
'email': 'brian@freegeektwincities.org',
'website': 'http://tryton-ucoa.googlecode.com/',
"category" : "Accounting",
"description": "Defines an account template for US non-prof... | FreeGeekTwinCities/tryton-ucoa | __tryton__.py | Python | gpl-3.0 | 447 | [
"Brian"
] | 5825421bdc413fdd62f8b2a9d21c36c40e234cfe601805f37be6e35d7b6ba1fd |
""" This file contains different utility functions that are not connected
in anyway to the networks presented in the tutorials, but rather help in
processing the outputs into a more understandable way.
For example ``tile_raster_images`` helps in generating a easy to grasp
image from a set of samples or weights.
... | Philip-Bachman/ICML-2015 | utils.py | Python | mit | 11,903 | [
"Gaussian"
] | 444ff2f8e4b563f6de70ac5c1b970fb4b692c74eff718f83f63452c73d7747dd |
# -*- coding: utf-8 -*-
"""
Created on Thu Sep 1 11:23:01 2016
@author: camacho
"""
#Exemplo da pagina do george
########## GERAR DADOS INICIAIS ALEATORIOS ##########
import numpy as np
import matplotlib.pyplot as pl
pl.close("all") #fecha todas as figuras anteriores
#Generate some fake noisy data.
x = 10 * np... | jdavidrcamacho/Tests_GP | 00 - Other examples/George_0.2.1 examples/01_Exemplo_simples.py | Python | mit | 1,565 | [
"Gaussian"
] | 27efaf054651a6bb8395899c731657d75e2fbead50772740240350c36505be3a |
from django.contrib.auth.models import User
from django.utils.timezone import utc, make_aware
from django.core.mail import send_mass_mail
from django.core.management.base import BaseCommand
from django.template import Context, loader
from optparse import make_option
from datetime import datetime, timedelta
import log... | shashi792/courtlistener | alert/userHandling/management/commands/cl_welcome_new_users.py | Python | agpl-3.0 | 2,495 | [
"Brian"
] | b5a122f4df4edf2aaeaadc8df174d044e840305029e2a43901b53e70186d9fcf |
import sys
from classFinder import *
from classHTMLRenderer import *
# The purpose this this code is to generate documentation for the
# text interface of Magpie. It will parse the Javadoc from Magpie
# to identify all implemented classes. Then, it assembles a website
# that tells users the name of each class, how ... | amarkrishna/demo1 | doc/generate-command-autodoc.py | Python | mit | 5,845 | [
"CRYSTAL"
] | c4cbff85f4ee1ed349d4658380fcd7278aab45b69361c9ce778c493aa6ea1ba1 |
#!/usr/bin/env python
"""Copyright 2008 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.4'
__date__ = 'May 02 2008'
#Basi... | jantman/tuxostat | fs_backup/home/tuxostat/devel/Python/Accelerometer-simple.py | Python | gpl-3.0 | 3,507 | [
"VisIt"
] | 2e8aeee4ed99a3c31594aebaa2abd5747e6795121f70302a8dcd42c74ec8b926 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements various equation of states.
Note: Most of the code were initially adapted from ASE and deltafactor by
@gmatteo but has since undergone major refactoring.
"""
import logging
import warnings
from abc... | materialsproject/pymatgen | pymatgen/analysis/eos.py | Python | mit | 19,614 | [
"ASE",
"pymatgen"
] | 2706c42d1ab4279d115c1b377913221f7cc919ab974d72b0e48b635d20fa3ab9 |
# -*- coding: utf-8 -*-
#
# rate_neuron_dm.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License,... | lekshmideepu/nest-simulator | pynest/examples/rate_neuron_dm.py | Python | gpl-2.0 | 5,947 | [
"NEURON"
] | 4fa3fef01071e39cf4cd0095d17e32a6ad497f5b15eecbbe927d43068e963851 |
from smashbox.utilities import *
# utilities to create and process self-describing hashfiles
# a hashfile encodes its content checksum in its name
# the name of a hashfile may be specified using a template string (filemask) where {md5} string represents the content checksum
# for example: "test_{md5}.dat"
# hashfi... | labkode/smashbox | python/smashbox/utilities/hash_files.py | Python | agpl-3.0 | 8,598 | [
"Gaussian"
] | 967c7028a16e26dc4d7526d9acc3df0d3fd08eb7bcda37bb51b3e8cb2ce3651d |
# -*- coding:utf-8 -*-
# Copyright (c) 2015, Galaxy Authors. All Rights Reserved
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import datetime
import time
import urllib
from common import util
from common import pb2dict
from bootstrap import settings
from trace i... | bluebore/galaxy | platform/src/trace/views.py | Python | bsd-3-clause | 19,257 | [
"Galaxy"
] | c2d2d02e749bacc25bcbcba31ea746b5f0c49ccd200727d18cf2401ad44b3838 |
import unittest
import time
import numpy as np
# Standard library imports...
from mock import patch, MagicMock, mock_open
import utils
from core.octopus.patterns.rpcTestPattern import RpcTestPattern
from core.tests.integrationTest import IntegrationTest
class TestIntegrationTest(unittest.TestCase):
# Mock OPC... | TheGentlemanOctopus/thegentlemanoctopus | octopus_code/core/tests/integrationTestTests.py | Python | gpl-3.0 | 1,546 | [
"Octopus"
] | dd47e2721cf8ef16fc7e785ceed8d13f6bb98512e8a1b073bbbebbcef24494ca |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2013, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | chetan51/nupic | nupic/swarming/permutationhelpers.py | Python | gpl-3.0 | 26,127 | [
"Gaussian"
] | 7fa1e2daeefe8cb7ea617129a65510e70fddece589404e5a5e407a8d2e215317 |
"""Install proteomics tools not currently packaged.
"""
import os
import re
from fabric.api import cd
from fabric.context_managers import prefix
from shared import (_if_not_installed, _make_tmp_dir,
_get_install, _make_copy,
_java_install, _symlinked_java_version_dir,
... | heuermh/cloudbiolinux | cloudbio/custom/bio_proteomics.py | Python | mit | 22,414 | [
"BLAST",
"Galaxy",
"OpenMS"
] | 73905bb5b9eada023546e8ac44a128e571c76dbb23d83c96472ed9894ec7bbcb |
#!/usr/bin/env python
"""
Kyle McChesney
Ruffus pipeline for simple bowtie alignment
"""
from ruffus import *
from big_wig_extras import BigWigExtras
import ruffus.cmdline as cmdline
import subprocess
import logging
import os
import pprint
import re
import time
parser = cmdline.get_argparse(description='Given a dire... | mbiokyle29/pipelines | wig/bigwig_pipeline.py | Python | mit | 5,414 | [
"Bowtie"
] | a2fb39bae67991d63adc7ee47567f3fdfb1e9bcef85ae1e71f758361c90ffc7f |
""" The SGE TimeLeft utility interrogates the SGE 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
__RCSID__ = "$Id$"
import os
import re
import time
import socket
from DIRAC import S_... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/TimeLeft/SGEResourceUsage.py | Python | gpl-3.0 | 4,887 | [
"DIRAC"
] | 65a4a69764303954e797182b57e6b6a8943a8f58db9325bf2840116998cf8e4d |
#
# File:
# TRANS_read_ASCII.py
#
# Synopsis:
# Illustrates how to read an ASCII file
#
# Categories:
# I/O
#
# Author:
# Karin Meier-Fleischer, based on NCL example
#
# Date of initial publication:
# September 2018
#
# Description:
# This example shows how to read an ASCII file.
#
# Effects ... | KMFleischer/PyEarthScience | Transition_examples_NCL_to_PyNGL/read_data/TRANS_read_ASCII.py | Python | mit | 1,300 | [
"NetCDF"
] | d21e6e691936d46538e5d8b363cb16fd8f3a4753de24134e8cc5e7fbbb3b0230 |
# A Python program to run speed and evaluate the performance of MPIR
# routines.
#
# Copyright (c) 2009, Brian Gladman, Worcester, UK.
#
# This file is part of the MPIR Library. The MPIR Library is free
# software; you can redistribute it and/or modify it under the terms
# of the GNU Lesser General Public License ve... | jpflori/mpir | build.vc15/run-speed.py | Python | gpl-3.0 | 10,546 | [
"Brian"
] | 562d6546b32c681e8a9fab17bab8474e72ac7d62d3ef9b283a54487c3fddf3f5 |
# Turta IoT HAT Helper for Raspbian
# Distributed under the terms of the MIT license.
# Python Driver for Relay Controller
# Version 1.01
# Updated: July 14th, 2018
# Visit https://docs.turta.io for documentation.
import RPi.GPIO as GPIO
class RelayController:
"""Relay Controller"""
#Variables
is_initi... | Turta-io/IoTHAT | DriverSource/Raspbian/Python/Turta_RelayController.py | Python | mit | 1,618 | [
"VisIt"
] | 60d6c2b50fe5e654fe9788fbce367548a29bcf96734845d15b1eac64b2619f32 |
""" Proxy Renewal agent is the key element of the Proxy Repository
which maintains the user proxies alive
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK
from DIRAC.Core.Base.AgentModule import A... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/Agent/MyProxyRenewalAgent.py | Python | gpl-3.0 | 2,776 | [
"DIRAC"
] | 7074acd1f48d02f445144fdeb25f35b7016d3864d081bbd3f779ff8847f95d58 |
# $HeadURL: $
''' VOBOXAvailabilityCommand module
'''
import urlparse
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.ResourceStatusSystem.Client.ResourceManagementClient import ResourceM... | sposs/DIRAC | ResourceStatusSystem/Command/VOBOXAvailabilityCommand.py | Python | gpl-3.0 | 2,271 | [
"DIRAC"
] | a7d373dd52a1b97312707c99a93eb73995fde616cd2af2c3c9447a37d87abf41 |
import pandas as pd
import neuroelectro.models as m
__author__ = 'shreejoy'
def assign_error_type_to_data_tables():
'''uses computational method to assign standard deviation error types to each data table and user submission object'''
# for articles with some nedms and has a data table
data_tables = m.D... | neuroelectro/neuroelectro_org | db_functions/identify_error_type.py | Python | gpl-2.0 | 2,519 | [
"NEURON"
] | 79539852a31b47995ecedaf08c1c17dbd3c4dd19605462cca64c3bc573ef0aef |
from lightify import Luminary
from Firefly import logging
from Firefly.const import ACTION_LEVEL, AUTHOR, COMMAND_SET_LIGHT, COMMAND_UPDATE, EVENT_ACTION_OFF, EVENT_ACTION_ON, LEVEL, SWITCH, ACTION_ON, ACTION_OFF
from Firefly.helpers.device import COLOR, COLOR_TEMPERATURE
from Firefly.helpers.device_types.light import... | Firefly-Automation/Firefly | Firefly/components/lightify/lightify_device.py | Python | apache-2.0 | 2,437 | [
"Firefly"
] | 847414490e3a1a686b6ea13e69ed3a73a5630e2f8c53f089292f7460eea2ff52 |
from basics import BubbleFinder2D
from basics.utils import sig_clip
from spectral_cube import SpectralCube
import astropy.units as u
import matplotlib.pyplot as p
import scipy.ndimage as nd
from scipy.stats import binned_statistic
import numpy as np
from skimage.segmentation import find_boundaries
from skimage.morpholo... | e-koch/VLA_Lband | 14B-088/HI/analysis/co_comparison/co_vs_hi_boundaries.py | Python | mit | 28,598 | [
"Gaussian"
] | 4116dacdc6ea09b41d55847ace5eabc414eb3c8d182798bd5d02297a0604a2f2 |
########################################################################
# $Id$
########################################################################
""" A set of common tools to be used in pilot commands
"""
import sys
import time
import os
import pickle
import getopt
import imp
import types
import urllib2
import... | vmendez/DIRAC | WorkloadManagementSystem/PilotAgent/pilotTools.py | Python | gpl-3.0 | 17,650 | [
"DIRAC"
] | 34a442dcb4c37a8ad60506d3c7f11118f3b8af8b533f85aa9fbea32eac9c3023 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# This file is part of pyunicorn.
# Copyright (C) 2008--2015 Jonathan F. Donges and pyunicorn authors
# URL: <http://www.pik-potsdam.de/members/donges/software>
# License: BSD (3-clause)
"""
Provides classes for analyzing spatially embedded complex networks, handling
multiva... | wbarfuss/pyunicorn | pyunicorn/timeseries/surrogates.py | Python | bsd-3-clause | 43,471 | [
"Gaussian"
] | e69799395d9efee23bcd459d291fbbe1077be6f64c022c57f20d1c38a1d02141 |
import numpy as np
from sklearn.metrics.pairwise import pairwise_distances
import matplotlib.pyplot as plt
from sklearn.neighbors import KernelDensity
from dpp import sample_dpp
def select_diverse(X, k):
m = X.shape[0]
sigma = 0.1*np.mean(pairwise_distances(X)+np.identity(m))
sample = [np.random... | IDEALLab/domain_expansion_jmd_2017 | diverse_selection.py | Python | mit | 2,406 | [
"Gaussian"
] | 82cace507860b9bcbee9265d877df72cc0708154f3e4996de8a1a9b21ffa74d7 |
from math import pi
import numpy as np
from ase.atoms import Atoms
from ase.calculators.calculator import Calculator
def make_test_dft_calculation():
a = b = 2.0
c = 6.0
atoms = Atoms(positions=[(0, 0, c / 2)],
symbols='H',
pbc=(1, 1, 0),
cell=(a, b,... | suttond/MODOI | ase/calculators/test.py | Python | lgpl-3.0 | 3,985 | [
"ASE"
] | b2e9b0c024dd4ddce2f871591d1d9af149a539c9236989f591c1ce16521a1eae |
# Copyright 2000 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Collection of modules for dealing with biological data in Python.
The Biopython Project is ... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/__init__.py | Python | apache-2.0 | 2,429 | [
"Biopython"
] | 54c0052e040c42e51276314076b3885ff22faac4fc27fe6b1747ff26a822d34c |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import webnotes
from webnotes import session, msgprint
from webnotes.utils import today
from utilities.transaction_base import TransactionBase
... | saurabh6790/test-med-app | support/doctype/customer_issue/customer_issue.py | Python | agpl-3.0 | 2,037 | [
"VisIt"
] | 4bd4447c06af664513aa4935162f597e253a025c70177cd173ebbb16aeeec34e |
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