text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
# flake8: noqa
import sys
import subprocess
from .exceptions import PyperclipException
EXCEPT_MSG = """
Pyperclip could not find a copy/paste mechanism for your system.
For more information, please visit https://pyperclip.readthedocs.org """
PY2 = sys.version_info[0] == 2
text_type = unicode if PY2 else str
... | andyraib/data-storage | python_scripts/env/lib/python3.6/site-packages/pandas/util/clipboard/clipboards.py | Python | apache-2.0 | 3,984 | [
"VisIt"
] | 935b334b814d5d12906dce55a00da748fe6b40b51f283c2f3c10e7b0c0322ab1 |
"""
The recovery operators used for lowest-order advection schemes.
"""
from enum import Enum
import ufl
from firedrake import (BrokenElement, Constant, DirichletBC, FiniteElement,
Function, FunctionSpace, Interpolator, Projector,
SpatialCoordinate, TensorProductElement,
... | firedrakeproject/gusto | gusto/recovery.py | Python | mit | 19,027 | [
"Gaussian"
] | 80622bc72f768050071e2f850b64f24443a9323b71918afcfdb5baef75b78a83 |
# Copyright 2015 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... | jiaphuan/models | tutorials/image/cifar10/cifar10.py | Python | apache-2.0 | 14,665 | [
"Gaussian"
] | e273876b2a9a5d1f93768c531c28a0660b01b461495b594a81b9118342c41663 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkXMLPImageDataWriter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkXMLPImageDataWriter.py | Python | bsd-3-clause | 504 | [
"VTK"
] | 8af5db4e66a0717a1745a4bde930dc92f884e274774214e7193594647f5f555f |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | examples/demo2.py | Python | gpl-3.0 | 6,455 | [
"Galaxy"
] | 7ae8fcefb4f6e64d5ae785b8908a48f6e3d8d51e1cd81b9c75d4f120f192d37f |
""" A computing element class that attempts to use glexec if available then
defaults to the standard InProcess Computing Element behaviour.
"""
__RCSID__ = "$Id$"
from DIRAC.Resources.Computing.ComputingElement import ComputingElement
from DIRAC.Core.Utilities.ThreadScheduler import ... | calancha/DIRAC | Resources/Computing/glexecComputingElement.py | Python | gpl-3.0 | 13,436 | [
"DIRAC"
] | 168885c6fcbd97f06f42fa144a449c9e9e93c5c789814c6762d7afbdb568d667 |
#!/usr/bin/python
import sys, pylab, scipy.stats.mstats, scipy.optimize
import numpy as np
import src.lib.utils as fn
import src.lib.wsutils as ws
out = fn.Verbose()
def get_sky_val(data, show=False, range=None, nbins=None, save=None):
#TODO: prendre la median a partir d'un certain point
if range is None: ra... | COSMOGRAIL/COSMOULINE | pipe/modules/src/_1_get_sky.py | Python | gpl-3.0 | 3,705 | [
"Gaussian"
] | 3f68f2085dacf8626509849796192d47269c7bd68496a099992ce05da6a0ab2e |
import string
import random
import json
from collections import defaultdict
from django.http import HttpResponse
from django.shortcuts import render_to_response
from django.template.context import RequestContext
from catmaid.fields import Double3D
from catmaid.models import Log, NeuronSearch, CELL_BODY_CHOICES, \
... | fzadow/CATMAID | django/applications/catmaid/control/common.py | Python | agpl-3.0 | 8,080 | [
"NEURON"
] | 668efdca3132a9613a0ea59d3c5db0594334ee109b7763a76b1fb2dbef94ac74 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2009 Prof. William H. Green (whgreen@mit.edu) and the
# RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free ... | faribas/RMG-Py | rmgpy/cantherm/qchem.py | Python | mit | 16,767 | [
"Q-Chem"
] | bf15303c47b06748cad5a2e2ad750684da14e96b4b5447171e3382183d441caa |
#! /usr/bin/env python2
# -*- coding: utf-8 -*-
#
# This file is part of the Bacterial and Archaeal Genome Analyser
# Copyright (C) 2015-16 David Williams
# david.williams.at.liv.d-dub.org.uk
# License GPLv3+: GNU GPL version 3 or later
# This is free software: you are free to change and redistribute it
# There is NO W... | daveuu/baga | baga_cli.py | Python | gpl-3.0 | 167,531 | [
"BWA",
"pysam"
] | 721ba3dc265c99cb6a15a8f242fa01d65d2d0711a2b0f8e134644b1c54bd58a6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import unittest
import subprocess
import os
import shutil
from rmgpy import getPath
from rmgpy.qm.main import QMSettings, QMCalculator
from rmgpy.molecule import Molecule
from rmgpy.qm.gaussian import Gaussian
from rmgpy.qm.mopac import Mopac
class TestQMSettings(unittest.T... | nyee/RMG-Py | rmgpy/qm/mainTest.py | Python | mit | 9,396 | [
"Gaussian",
"MOPAC",
"Molpro"
] | aeed0a6bdb350d299708dd787ef8e3c6b6e69c79d372b74a91b36e887b2f9778 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyBrian(PythonPackage):
"""A clock-driven simulator for spiking neural networks"""
ho... | LLNL/spack | var/spack/repos/builtin/packages/py-brian/package.py | Python | lgpl-2.1 | 687 | [
"Brian"
] | 322a7fcba447f96a7b6bef9608505844d3cecdbca598b8dd703283aad573db55 |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | espressomd/espresso | testsuite/scripts/samples/test_visualization_cellsystem.py | Python | gpl-3.0 | 1,263 | [
"ESPResSo"
] | e7d65457b3a28587a39b18fa00c584b9d06105b3632f908fedcec6d7b4009277 |
#!/usr/bin/env python
#
# This program straightens the spinal cord of an anatomic image, apply a smoothing in the z dimension and apply
# the inverse warping field to get back the curved spinal cord but smoothed.
#
# ---------------------------------------------------------------------------------------
# Copyright (c)... | benjamindeleener/scad | scripts/sct_smooth_spinalcord.py | Python | mit | 10,698 | [
"Gaussian"
] | a4b534094c973033f23675863b2a467b394dce7bd0af0396a638892bcf9ff0df |
"""
SIRV_Generate_heatmap.py
This script generates a heatmap of the estimated mean abundance compared to the expected abundance in all SIRVs.
see python path/to/SIRV_Generate_boxplot.py -h
updated: 25 Oct 2016 Patrick Schagerl
(c)2016 Lexogen GmbH
Examples:
python package_SIRVs/V4_final_testing_C_I_O/SIRV_Generat... | sirvsuite-support/sirvsuite | tools/SIRV_Generate_heatmap.py | Python | gpl-3.0 | 16,115 | [
"Galaxy"
] | a1e9f4a6f56c1187120648d2d07e9d397369a12e29e41399609bc62596f74794 |
# We only import librairies needed for plotting
# Other librairies are imported in the class definition file, G3D_class.py,
# which contains all process and variables function definition.
import matplotlib
matplotlib.use('pdf')
import matplotlib.pyplot as plt
import matplotlib.dates as mdates
import datetime as dt
im... | acapet/GHER-POSTPROC | Examples/EasyExample.py | Python | gpl-3.0 | 2,826 | [
"NetCDF"
] | cc6f31258ba4f6560cc76c6e3144bb1c689a031b1c81aaaeba513233acf85f66 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2021, 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... | numenta/nupic.research | projects/dendrites/gaussian_classification/run_dendritic_network.py | Python | agpl-3.0 | 7,724 | [
"Gaussian"
] | 609db8a3d3f9a5fab63ae65fde847d5ffeb67ef4cac6b6dce87d4b60cb790a2c |
# coding: utf-8
"""0MQ Socket pure Python methods."""
#-----------------------------------------------------------------------------
# Copyright (C) 2013 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING... | skycucumber/Messaging-Gateway | webapp/venv/lib/python2.7/site-packages/zmq/sugar/socket.py | Python | gpl-2.0 | 14,978 | [
"Brian"
] | 3719db0a732f12534f95f5612f434b72b648af3a281db890936d39b20b149a80 |
# -*- coding: utf-8 -*-
"""This module contains helper functions for other IO functions."""
from .exc import ImportVersionWarning
from ..config import PYBEL_MINIMUM_IMPORT_VERSION
from ..struct import BELGraph
from ..utils import tokenize_version
def raise_for_old_graph(graph):
"""Raise an ImportVersionWarning ... | pybel/pybel | src/pybel/io/utils.py | Python | mit | 1,585 | [
"Pybel"
] | 9d2255790d9ab3b98395ca0a681eeccabb229d6f00f2cbba64c503efba6f70fc |
"""
==========================================
Affine Registration in 3D
==========================================
This example explains how to compute an affine transformation to register two
3D volumes by maximization of their Mutual Information [Mattes03]_. The
optimization strategy is similar to that implemented i... | StongeEtienne/dipy | doc/examples/affine_registration_3d.py | Python | bsd-3-clause | 10,585 | [
"Gaussian"
] | e8932a2aad821a823ace2548b56666cff73a1aecf05f3ae0610524daa7a70de6 |
# vi:sts=4:sw=4:et
"""Code for parsing OpenEmbedded license strings"""
import ast
import re
from fnmatch import fnmatchcase as fnmatch
class LicenseError(StandardError):
pass
class LicenseSyntaxError(LicenseError):
def __init__(self, licensestr, exc):
self.licensestr = licensestr
self.exc = e... | PhiInnovations/mdp28-linux-bsp | openembedded-core/meta/lib/oe/license.py | Python | mit | 3,982 | [
"VisIt"
] | 6087b0d3160598305d153cf8f2534a61a7959f636858bb480cefad9a689204b4 |
import discord
import asyncio
import wolframalpha
import brainfuck
import youtube_dl
import subprocess
import os
import urbandict
import xmltodict
import urllib.request
from ctypes.util import find_library
from discord.ext import commands
from discord.ext.commands import formatter
from unidecode import unidecode
import... | TesseractCat/TesseractBot | bot.py | Python | mit | 12,941 | [
"VisIt"
] | f303f3bf7c02b132dbaeb8d21b790feed74f67f568fadd175528c846040ec8b8 |
import numpy as np
def create_perturb_params(countsmat, transmat=None):
'''
Computes transition probabilities and standard errors of the transition probabilities due to
finite sampling using the MSM counts matrix. First, the transition probabilities are computed
by dividing the each element c_ij by ... | msmbuilder/msmbuilder | msmbuilder/msm/validation/transmat_errorbar.py | Python | lgpl-2.1 | 2,619 | [
"Gaussian"
] | 0926f9554a41947069213cb0601a799fb5c8c873f1e24a8182ac78935fe0fd7f |
""" This is the RFIO StorageClass
"""
__RCSID__ = "$Id$"
import types
import re
import os
import time
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Resources.Storage.Utilities import checkArgumentFormat
from DIRAC.Resources.Storage.StorageBase import Storage... | vmendez/DIRAC | Resources/Storage/RFIOStorage.py | Python | gpl-3.0 | 38,359 | [
"DIRAC"
] | 72f91ba78caa4b8b88e431b67722fa7418f0d561732f655696640642dbe85de7 |
#-------------------------------------------------------------------------------
# Core routines for computing properties of symmetric random matrices.
#-------------------------------------------------------------------------------
import numpy
ra = numpy.random
la = numpy.linalg
def GOE(N):
"""Creates an NxN el... | mastizada/kuma | vendor/packages/ipython/docs/examples/kernel/rmtkernel.py | Python | mpl-2.0 | 1,221 | [
"Gaussian"
] | cc35922bccf2a12e39c7039edf3707db232552152ef0a90b261ff303e9a2efdd |
"""
Bok choy acceptance and a11y tests for problem types in the LMS
See also lettuce tests in lms/djangoapps/courseware/features/problems.feature
"""
import random
import textwrap
import unittest
from abc import ABCMeta, abstractmethod
from nose.plugins.attrib import attr
from selenium.webdriver import ActionChains
... | nttks/edx-platform | common/test/acceptance/tests/lms/test_problem_types.py | Python | agpl-3.0 | 26,501 | [
"VisIt"
] | 402650e760803a93de3cbe3c607ab2a108f62d2e083e3db06e833913d18b8e9f |
"""
desisim.scripts.quickgalaxies
=============================
"""
from __future__ import absolute_import, division, print_function
import healpy as hp
import numpy as np
import os
from datetime import datetime
from abc import abstractmethod, ABCMeta
from argparse import Action, ArgumentParser
from astropy.table i... | desihub/desisim | py/desisim/scripts/quickgalaxies.py | Python | bsd-3-clause | 13,799 | [
"Galaxy"
] | 43e7e082e66f2ab29c291c994ab23a552809afeb34393ab19b1f18b7a941edc4 |
#!/usr/bin/env python
# File: mk_ds9_rgb.py
# Created on: Mon 18 Jun 2012 11:20:57 AM CDT
# Last Change: Tue Mar 5 11:46:25 2013
# Purpose of script: <+INSERT+>
# Author: Steven Boada
import numpy as np
import sys
import os
import stat
# read info files from comamnd line
#data = np.loadtxt(sys.argv[1])
#Does the s... | boada/ICD | sandbox/legacy_plot_code/mk_ds9_rgb.py | Python | mit | 4,819 | [
"Galaxy"
] | 8301bc8a33ea62604c5d400ae5d466772c01da906358230b0f668e9a25b1b264 |
"""
System class for biomolecules using AMBER ff.
Set up using prmtop and inpcrd files used in Amber GMIN and Optim.
Potential parameters (e.g. non-bonded cut-offs are set in
TODO:
Parameters
----------
prmtopFname : str
prmtop file name
inpcrdFname : str
inpcrd file name
... | js850/pele | pele/amber/amberSystem.py | Python | gpl-3.0 | 28,485 | [
"Amber",
"OpenMM",
"PyMOL"
] | afeb5bcb5815645a8a283fe19bc0fd798d6e330c1e16622f82ccc6bb5505575a |
from ase.atoms import Atoms
def read_dftb(filename='dftb_in.hsd'):
"""Method to read coordinates form DFTB+ input file dftb_in.hsd
additionally read information about fixed atoms
and periodic boundary condition
"""
from ase import Atoms
if isinstance(filename, str):
myfile = open(filen... | suttond/MODOI | ase/io/dftb.py | Python | lgpl-3.0 | 5,488 | [
"ASE"
] | 28263ea6ab37013efe6268045d5351b77505ba46985c802972b25761a71a392b |
#!/usr/bin/env python
import numpy as np
import tables as tb
import sys,os
import cPickle
three_letter_aa = dict(
A='ALA', C='CYS', D='ASP', E='GLU',
F='PHE', G='GLY', H='HIS', I='ILE',
K='LYS', L='LEU', M='MET', N='ASN',
P='PRO', Q='GLN', R='ARG', S='SER',
T='THR', V='VAL', W=... | John-Jumper/Upside-MD | py/upside_config.py | Python | gpl-2.0 | 78,297 | [
"CRYSTAL"
] | aec557f35629630267062a9b30d7d2932b0bcf8f4801cd125373210c25e4d8b2 |
# Copyright 2014 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# pylint: disable=W0401,W0614
from telemetry.page.actions.all_page_actions import *
from telemetry.page.page_set import PageSet
from telemetry.page.page impor... | chromium2014/src | tools/perf/page_sets/alexa1-10000.py | Python | bsd-3-clause | 666,348 | [
"ADF",
"CASINO",
"MOE"
] | 5539744288798ad940b017d7b8065616e43a3a6174ee310070d12953614c2786 |
# coding=utf-8
"""Base class for Ladybug Data Collections."""
from __future__ import division
from .header import Header
from .datatype.base import DataTypeBase
from .datatype import TYPESDICT, BASETYPES
try:
from collections.abc import Iterable # python < 3.7
except ImportError:
from collections import Ite... | ladybug-analysis-tools/ladybug-core | ladybug/_datacollectionbase.py | Python | gpl-3.0 | 45,622 | [
"EPW"
] | b0c4dfc01a6fa9d7cda198a1eb8558b370c52db9237f2a893678aa7bc86f684f |
#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# ChemPy - A chemistry toolkit for Python
#
# Copyright (c) 2012 by Joshua W. Allen (jwallen@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of... | enochd/RMG-Py | rmgpy/molecule/adjlist.py | Python | mit | 44,800 | [
"ChemPy"
] | 9488885a65094fd8875e8d456766d75a77dd23fe5102949c1ec2d889a717dca4 |
# Copyright 2016 Mingbo Cai, Princeton Neuroscience Instititute,
# Princeton University
#
# 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... | lcnature/brainiak | tests/reprsimil/test_brsa.py | Python | apache-2.0 | 29,837 | [
"Gaussian"
] | 3598455d051875cc9e19c650027991f110d22081060cef2e71384cc42be50609 |
# -*- coding: utf-8 -*-
"""Plist parser plugin for Safari history plist files."""
from dfdatetime import cocoa_time as dfdatetime_cocoa_time
from plaso.containers import events
from plaso.containers import time_events
from plaso.lib import definitions
from plaso.parsers import plist
from plaso.parsers.plist_plugins i... | kiddinn/plaso | plaso/parsers/plist_plugins/safari.py | Python | apache-2.0 | 3,591 | [
"VisIt"
] | 3c184c0785e56de3fada2baf27cc293b97e57475cffebc3a756d9af44d445f39 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Build and Launch iPhone Application in Simulator or install
# the application on the device via iTunes
#
import os, sys, uuid, subprocess, shutil, signal, string, traceback, imp, filecmp, inspect
import platform, time, re, run, glob, codecs, hashlib, datetime, plistli... | xissy/titanium-mobile-sdk | iphone/builder.py | Python | apache-2.0 | 58,468 | [
"VisIt"
] | aade8b76cfd17cbc5ca12997019238a469aae88b93ca7faeeeb1b9abc9ed6344 |
#!/usr/bin/env python
'''
written by Rose A. Finn on 2/3/2013
GOAL:
- create a mastertable for each LCS cluster that uses the NASA-Sloan atlas as the parent sample
METHOD:
- match NSA to 24-micron apex catalog
- pull AGC data (NSA contains AGC number)
- match with galaxy zoo info
- append ne... | rfinn/LCS | paper1code/LCSwritemasterNSA.py | Python | gpl-3.0 | 10,228 | [
"Galaxy"
] | 8b657d369460d528d1075dc7acc608a8e11513457155ba9c0a024fbc0d54ad12 |
"""
Interactivity functions and classes using matplotlib and IPython widgets
**Gravity forward modeling**
* :class:`~fatiando.gravmag.interactive.Moulder`: a matplitlib GUI for 2D
forward modeling using polygons
----
"""
from __future__ import division, absolute_import
from future.builtins import zip
try:
im... | rafaelmds/fatiando | fatiando/gravmag/interactive.py | Python | bsd-3-clause | 24,042 | [
"Gaussian"
] | a2d0fd9ae082520ec0999d382a96071a9415a11c15858eef76629e36f1509f1a |
# Standard libraries
from collections import deque
from urlparse import urlsplit
import datetime
import re
import socket
import types
import urllib
import urllib2
# Third-party libraries
from BeautifulSoup import BeautifulSoup
from BeautifulSoup import BeautifulStoneSoup
import openanything
import simple... | pbarton666/buzz_bot | bot_project/buzzbot/searcher.py | Python | mit | 29,230 | [
"VisIt"
] | 76cb74d254dd4c358ae346c55dff29ed3b7b3fee31e817e60f2716152a8209c6 |
#!/usr/bin/env python3
# Copyright (C) 2021
# Sebastian Eibl, Max Planck Computing & Data Facility
#
# 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,... | espressopp/espressopp | testsuite/io/test_h5md_parallel.py | Python | gpl-3.0 | 3,193 | [
"ESPResSo",
"VisIt"
] | a9a6a929d02ea8cb93f5c976e1b53179c88dd942c6fe78cec7102566f88b977c |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/__init__.py | Python | bsd-3-clause | 2,365 | [
"scikit-bio"
] | aef6afcad5207a1f71d0b2362c135ca69c464e05fe9ba383f1cbd6ffe58b75e4 |
#
# Copyright 2018 Analytics Zoo 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... | intel-analytics/analytics-zoo | pyzoo/zoo/examples/orca/learn/pytorch/cifar10/cifar10.py | Python | apache-2.0 | 6,360 | [
"ORCA"
] | 78cce4d3557fd78f0ef736638bde70c8e0e21bec55f6cf0db7fac9a1dc61c018 |
#-----------------------------------------------------------------------------
# Copyright (c) 2010-2012 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING.BSD, distributed as part of this software.
#-----... | ellisonbg/pyzmq | zmq/tests/test_context.py | Python | lgpl-3.0 | 8,546 | [
"Brian"
] | f29f6c6ece1c200356d067e908f35690a1fe48cb6225e6707f6925deb9fe94e2 |
"""Display the contents of the implementation cache."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
import os
import gtk
from zeroinstall.injector import namespaces, model
from zeroinstall.zerostore import BadDigest, manifest
from zer... | pombredanne/zero-install | zeroinstall/gtkui/cache.py | Python | lgpl-2.1 | 14,749 | [
"VisIt"
] | f13077065c62ea2cfb73a42cb3a29ecc74731fd0a51547162f0b60cfbef52f1c |
from matplotlib import pyplot
from math import cos, sin, atan
import matplotlib
matplotlib.style.use('ggplot')
matplotlib.pyplot.rcParams['figure.figsize'] = (15, 3)
matplotlib.pyplot.rcParams['font.family'] = 'sans-serif'
class Neuron():
def __init__(self, x, y):
self.x = x
self.y = y
def dra... | evelkey/vahun | vahun/neuroplot.py | Python | apache-2.0 | 4,110 | [
"NEURON"
] | fcc3c8abd1c2fdb16ae890d0bc5863ddb82149c698e56cfb8b9e553c4a739c7f |
import json
import time, os, fnmatch
import re
import textwrap
def make_date_string(t):
lt=time.localtime(t)
return '%(y)04d-%(m)02d-%(d)02d' % { 'y' : lt.tm_year, 'm' : lt.tm_mon,
'd' : lt.tm_mday }
def replace_path_bits(path,user,maxlen):
res=re.sub('/work/[0-9]+/'+user,r... | ubccr/tacc_stats | analyze/process_pickles/lariat_utils.py | Python | lgpl-2.1 | 4,195 | [
"Amber",
"CHARMM",
"DL_POLY",
"Gromacs",
"LAMMPS",
"NAMD",
"VASP"
] | 3125c8c621f8850cce9e84282e539aeb6dad9377089ede0fb0725cd033b359fb |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2011 OpenStack LLC.
# 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/... | tucbill/manila | manila/tests/api/test_xmlutil.py | Python | apache-2.0 | 25,565 | [
"VisIt"
] | 2d1e17b45f3a94df70c1b0a596b667b62082fcd7a2115aa1a6d84f09f4a6c6ec |
import numpy as np
import scipy.linalg as slg
from frankenstein import scf, mp
from frankenstein.tools.io_utils import dumpMat
from frankenstein.tools.tensor_utils import ao2mo_xform_nosymm
def get_Vovov(V, C, nocc):
# Vovov = np.einsum("pqrs,pi,qa,rj,sb->iajb", V, \
# C[:,:nocc],C[:,nocc:],C[:,:nocc],C[... | hongzhouye/frankenstein | tools/mp2_utils.py | Python | bsd-3-clause | 26,754 | [
"MOE"
] | fc6d649b1af9e43ccc456fdacd26cf9713996e9fc5f7a0b8cbe0c55f1227612b |
#!/bin/env python
""" create and put 'PutAndRegister' request with a single local file
warning: make sure the file you want to put is accessible from DIRAC production hosts,
i.e. put file on network fs (AFS or NFS), otherwise operation will fail!!!
"""
__RCSID__ = "$Id: $"
import os
from DIRAC.Core.Base... | Sbalbp/DIRAC | DataManagementSystem/scripts/dirac-dms-put-and-register-request.py | Python | gpl-3.0 | 2,952 | [
"DIRAC"
] | 0a1c17f1b2748207868dde5f087e301dd3c8f88f6a171744cdfff780705218e4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module contains classes to wrap Python VTK to make nice molecular plots.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Mate... | migueldiascosta/pymatgen | pymatgen/vis/structure_vtk.py | Python | mit | 34,037 | [
"Jmol",
"VTK",
"pymatgen"
] | d181b4c5ecf805161a03a80672fc90afdda6f385b4b463503d06c7d0de47603c |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/io/_iosources.py | Python | bsd-3-clause | 6,117 | [
"scikit-bio"
] | c70819950a84bfd9e2f45c5820c596e167f13aa3058f49c9328bd50f7fd5ca86 |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import glob
import itertools
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import time
import urllib2
import xmlrpclib
import zlib
from xml.etree import ElementTree
from cStringIO import StringIO
import b... | iw3hxn/LibrERP | web_client/ea_web-github/addons/web/controllers/main.py | Python | agpl-3.0 | 81,900 | [
"VisIt"
] | acbfcc0b1f15d65bc53d6a200573d0b0a2239addc28e045ecb2ebc1a16f83f14 |
from __future__ import division, print_function
from __future__ import absolute_import
from __future__ import unicode_literals
from os import path
from collections import OrderedDict
from IPython.display import display, clear_output
from matplotlib import pyplot as plt
from matplotlib import transforms
from matplotli... | PySCeS/PyscesToolbox | psctb/utils/plotting/_plotting.py | Python | bsd-3-clause | 45,441 | [
"PySCeS"
] | a118ac5e63bd420e4d4b2d26abbe63e06913ba61a67c28cb6297d751ac3d8f1d |
#!/usr/bin/env python
# Copyright (C) 2017,2018
# Max Planck Institute for Polymer Research
#
# 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 ... | espressopp/espressopp | examples/adress/piadress_water/AdaptivePIwater.py | Python | gpl-3.0 | 21,464 | [
"ESPResSo"
] | 90ee1482de389c15a690ff9518a201347ed9a920b4345bc157fabacaaf7d0326 |
##########################################################################################################
#Visualization of RNA ensembles
#getMap
#getMapDB
#getRef
#getRefDB
#main
##########################################################################################################
import sys
i... | cbtolson/ensemblerna_package | ensemblerna/main.py | Python | gpl-3.0 | 13,070 | [
"VisIt"
] | 9d7ca5beb1755ca28ef041bd83d8353390ca2ada42062a430ad253d38a49d004 |
import os
import re
import logging
import urllib2
import requests
import pandas as pd
import pydap.client
import pydap.exceptions
import xray
from bs4 import BeautifulSoup
from collections import namedtuple
from contextlib import closing
from datetime import datetime
from requests.exceptions import ConnectionError
fro... | biofloat/biofloat | biofloat/ArgoData.py | Python | mit | 31,176 | [
"NetCDF"
] | 64e0f56463e23df0b93aaf55d00ed86a57e49a256bd114d78b0c482b981534c0 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Stephane Charette
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the ter... | arunkgupta/gramps | gramps/plugins/tool/removeunused.py | Python | gpl-2.0 | 18,389 | [
"Brian"
] | 2522da598729f59467b9ecfd7489ba3e8ecee08080b11090f98d554ebec06a34 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpatt... | stepanovsh/project_template | {{cookiecutter.repo_name}}/config/urls.py | Python | bsd-3-clause | 1,464 | [
"VisIt"
] | 70b656926ab43b7eea63efd53d3a3f0639e113605fa4ec14d9983e05f53e559b |
#!/usr/bin/env python
from numpy import *
import numpy as np
from scipy import interpolate
from matplotlib.pyplot import *
import os
def finddt(epmin, mumin, dx, dy, dz):
epmin = epmin*ep0
mumin = mumin*mu0
dtmax = 6.0/7.0*sqrt(epmin*mumin/(1.0/dx**2 + 1.0/dy**2 + 1.0/dz**2))
print "dt max = ", dtmax
... | IFDYS/IO_MPI | mkmodel.py | Python | gpl-2.0 | 16,270 | [
"Gaussian"
] | 90bcafe60af24e0484dfc326c261c493ff55f42e2e31463d17893c396dd2049c |
import os
import re
import ssl
import sys
import tempfile
from doctest import testfile
from io import StringIO, TextIOWrapper
from unittest import TestCase
from unittest.mock import DEFAULT, Mock, patch
from urllib3.exceptions import LocationParseError
from crate.client.exceptions import ProgrammingError
from crate.c... | crate/crash | tests/test_integration.py | Python | apache-2.0 | 34,483 | [
"Galaxy"
] | 73a396cbf3abbd2630879884e36da0bd17877a0d3daab55f4a46d9c3b40bbe17 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 ... | sam-m888/gprime | gprime/plug/menu/_person.py | Python | gpl-2.0 | 1,774 | [
"Brian"
] | 3ee744a13ff8860e4295bbb05afc1ae18772d117424365b932b355a4be167a18 |
# coding: utf-8
# Copyright 2013 Google Inc. 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 ap... | haoyuchen1992/CourseBuilder | tests/functional/test_classes.py | Python | apache-2.0 | 168,170 | [
"VisIt"
] | 85834ca083aae40e30598f3f1b46231a0e26836b375bac1fd889b9f714378361 |
# 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... | nburn42/tensorflow | tensorflow/contrib/learn/python/learn/estimators/__init__.py | Python | apache-2.0 | 12,688 | [
"Gaussian"
] | ead03684a3468a7bca35bcb25ebc4d0d52c355e33f534741e3f36f235be20617 |
# Copyright 2018 Google Inc. 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 applicable law or... | googlegenomics/gcp-variant-transforms | gcp_variant_transforms/libs/processed_variant.py | Python | apache-2.0 | 22,796 | [
"pysam"
] | 577787c68ef17e4332d48c388d3a1ded96c73124e758e73e86da010ae4368670 |
# TODO check num_threads before testing / 8 for Cisco Server
# TODO ATTTENTION! Maybe there are some mistakes in neuron parameters! Write to alexey.panzer@gmail.com.
from func import *
logger = logging.getLogger('neuromodulation')
startbuild = datetime.datetime.now()
nest.ResetKernel()
nest.SetKernelStatus({'overwri... | research-team/NEUCOGAR | NEST/cube/noradrenaline/scripts/neuromodulation.py | Python | gpl-2.0 | 6,161 | [
"NEURON"
] | 89d116676ecc9f7ef366d1569a6e735bc445a2b93904f25ad4e1bbdd98ca4d2e |
# -*- coding: utf-8 -*-
"""
Created on Fri Mar 29 10:34:10 2019
@author: cwhanse
"""
import numpy as np
def fit_sdm_cec_sam(celltype, v_mp, i_mp, v_oc, i_sc, alpha_sc, beta_voc,
gamma_pmp, cells_in_series, temp_ref=25):
"""
Estimates parameters for the CEC single diode model (SDM) using ... | anomam/pvlib-python | pvlib/ivtools.py | Python | bsd-3-clause | 19,237 | [
"pysam"
] | d5296d39da0a9a5efc8f27d3b2abb339fe0467e99f6ed002341a6d7dd3e24447 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/drug_coverage.py | Python | apache-2.0 | 16,284 | [
"VisIt"
] | 78ac3e87656bccf7e157097ff9798553f1b154ea996308dccb973458a2baccad |
# A Python port of the C++ port of the NTIA ITS ITM FORTRAN code.
#
# Original FORTRAN code documentation is at:
# http://www.its.bldrdoc.gov/media/50674/itm.pdf
#
# Section numbers referenced here correspond to the FORTRAN code document.
#
# Andrew Clegg
# October 2016
# Last update: Nov 5, 2016
import math
# Static... | krlinus/Spectrum-Access-System | src/prop_current/itm.py | Python | apache-2.0 | 49,748 | [
"CRYSTAL",
"VMD"
] | 86130ed8d93d64e3ff6e9bc3ca9c98ec827af547c3af18facf55379185cdb0e6 |
# Copyright (c) 2007 The Regents of The University of Michigan
# Copyright (c) 2010 The Hewlett-Packard Development Company
# 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 sou... | andrewfu0325/gem5-aladdin | src/python/m5/stats/__init__.py | Python | bsd-3-clause | 7,968 | [
"VisIt"
] | 841842fdc9a17b554c86b65981cbc76bb0da0fecd74e33a308732c6c73e3885c |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
class RegionGrowing(ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
... | nagyistoce/devide | modules/filters/RegionGrowing.py | Python | bsd-3-clause | 4,889 | [
"VTK"
] | 05f024983e88ea17bf8b44adcb94c574d6d60b741848872ce56fb883381f963b |
"""
<description>
"""
import numpy as np
import pytest as pt
import teetool as tt
def test_basis():
"""
testing basis class
"""
mpoints = 10
x_test = np.linspace(0, 1, mpoints)
mbasis = 5
mdim = 3
# test exception
with pt.raises(NotImplementedError) as testException:
_ ... | WillemEerland/teetool | test/test_basis.py | Python | mit | 1,365 | [
"Gaussian"
] | 67423dbf250ad3046609ce5a6428c41f63ec883a2b813803e21b58ca708d7eb9 |
'''
Created on 2013-05-29
@author: brian
'''
from src.util import Vector2
class Fallback(object):
def __init__(self, actor):
self.actor = actor
self.target = None
def condition(self):
self.target = None
for entity in self.actor.getEnemies():
if self.actor.distance(entity.position) < 3:
se... | Greymerk/python-rpg | src/ai/task/fallback.py | Python | gpl-3.0 | 1,079 | [
"Brian"
] | d46f08a1f156df2c116d11a4e25404cf2cec22f727dc35b0cbb9a65c210329e5 |
#
# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" a module for interacting... | strets123/rdkit | rdkit/Dbase/__init__.py | Python | bsd-3-clause | 340 | [
"RDKit"
] | e3ceda22e8ab851899c9459a2a6b9b902ac4e9d171c6f0612f37b35b319948f7 |
"""
N-ary Tree implementations.
@author: Lia Nemeth
"""
import weakref
class NaryTree(object):
"""
A generic N-ary tree implementation, that uses a list to store
its children.
"""
def __init__(self, key=None, item=None, children=None, parent=None):
self.key = key
self.item = item
... | lucasnemeth/forest | forest/NaryTree.py | Python | bsd-3-clause | 1,678 | [
"VisIt"
] | 148c6765e83269a6bfb53cd08a7d144aa598d5b5fcf88078448f7168e7a099f9 |
import cgi
import os
import datetime
import HTMLParser
import json
import logging
import re
import ushlex as shlex
import urllib
from bson.objectid import ObjectId
from django.conf import settings
from django.contrib.auth import authenticate, login as user_login
from django.core.urlresolvers import reverse, resolve, g... | jhuapl-marti/marti | crits/core/handlers.py | Python | mit | 182,605 | [
"Amber"
] | 8bff9b4018943185096345b9e447d864017cf22d3a3a1d9845cec7267bb29ea0 |
# sybase/base.py
# Copyright (C) 2010-2015 the SQLAlchemy authors and contributors
# <see AUTHORS file>
# get_select_precolumns(), limit_clause() implementation
# copyright (C) 2007 Fisch Asset Management
# AG http://www.fam.ch, with coding by Alexander Houben
# alexander.houben@thor-solutions.ch
#
# This module is par... | sunze/py_flask | venv/lib/python3.4/site-packages/sqlalchemy/dialects/sybase/base.py | Python | mit | 28,775 | [
"ASE"
] | fecf2d7fa2d981e48e258fc8492a431e2e8928f2b8c27ac9fb9180c30e043cda |
#interfacing with SVU class and forming core data structures
import glob
import os
import csv
import re
import datetime
#pip installed libs
import numpy as np
#local libs
import fusion_utils as fu
import read_utils as ru
import structural_variant_unit
def get_sv_types():
return structural_variant_unit.SVU().get_sv... | timothyjamesbecker/FusorSV | fusorsv/svu_utils.py | Python | gpl-3.0 | 50,453 | [
"BWA",
"HTSeq"
] | ecd33e9218cb2f2dd5dc77f8bcd4472abfdf01e43eaf0dda8f6a669c96b62236 |
# encoding: utf-8
"""
An object for managing IPython profile directories.
Authors:
* Brian Granger
* Fernando Perez
* Min RK
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License... | cloud9ers/gurumate | environment/lib/python2.7/site-packages/IPython/core/profiledir.py | Python | lgpl-3.0 | 8,011 | [
"Brian"
] | 81a640d12c8e7c39e7598a797ee3bebd66847039663eb059474d6e3776dc1611 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""fitting.py -- Default posterior probability function and high-level fitting
methods for prospector
"""
import time
from functools import partial as argfix
import numpy as np
from scipy.optimize import minimize, least_squares
from .minimizer import minimize_wrapper,... | jrleja/bsfh | prospect/fitting/fitting.py | Python | mit | 19,143 | [
"Gaussian"
] | 3c975cce9225876baf30d2fff77bb461077513913b503e99f330b67373e6c8cb |
# Copyright 2008-2011 Nokia Networks
# Copyright 2011-2016 Ryan Tomac, Ed Manlove and contributors
# Copyright 2016- Robot Framework Foundation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the Licens... | rtomac/robotframework-selenium2library | src/SeleniumLibrary/__init__.py | Python | apache-2.0 | 32,904 | [
"VisIt"
] | 4e163efe9e40e15ec18c867bee62f370f24d90d1c6030fbdb2f244d35f60eb34 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides
"""
from collections import OrderedDict, namedtuple
from monty.functools import lazy_property
from monty.json import MSONable # , MontyEncoder
from monty.string import is_string
from pymatgen.core.l... | vorwerkc/pymatgen | pymatgen/core/xcfunc.py | Python | mit | 10,413 | [
"ABINIT",
"GPAW",
"pymatgen"
] | 39a6073e1f9b744a95d58f30934870687d71b0b0f2b69c92e3fd44ea17bc03ae |
"""
DIRAC.WorkloadManagementSystem.private package
"""
| DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/private/__init__.py | Python | gpl-3.0 | 58 | [
"DIRAC"
] | ce7c40c9670722eadb7b9b6feab65293a6c297f7113032d8a3dcde7b81aa5cce |
from __future__ import print_function
import os
import unittest
from rdkit.six.moves import cStringIO as StringIO
from rdkit import RDConfig
from rdkit.Chem import PandasTools
gotPandas = PandasTools.pd is not None
import numpy
import tempfile, shutil
import gzip
methane = """\
Methane
RDKit
1 0 0 0 0 ... | adalke/rdkit | rdkit/Chem/UnitTestPandasTools.py | Python | bsd-3-clause | 6,573 | [
"RDKit"
] | 80751b52326370c6bd76da4b4c79a627fc5424d0feb2a612423f8f2c0e83974f |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkOBJReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkO... | nagyistoce/devide | modules/vtk_basic/vtkOBJReader.py | Python | bsd-3-clause | 464 | [
"VTK"
] | 3a607c04eade7e95edf9d0137e9360a31196fa6547b74bad61372be909a77cea |
""" Useful physical and mathematical values. Physical constants in
Gaussian cgs units when not indicated otherwise. From 2010 CODATA
recommended values where available (see
http://physics.nist.gov/cuu/Constants/index.html).
>>> import constants as c
>>> from math import sqrt
>>> Planck_length = sqrt(c.hbar * c.G / c.... | nhmc/LAE | python_modules/barak/constants.py | Python | mit | 6,258 | [
"Gaussian"
] | 654eaea6140e78fb30cfbf19848a991419e72b8f70652dfa32f7706e8c4150cc |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-genomicalignments/package.py | Python | lgpl-2.1 | 2,795 | [
"Bioconductor"
] | 5367886d4b33160c687992b7329d4eef83b9d73e191e5c5209d2060296721dad |
import calendar
import json
import re
import uuid
import mock
from nose.tools import eq_, ok_
from django.core.cache import cache
from django.contrib.auth.models import User
from django.core import mail
from django.core.urlresolvers import reverse
from airmozilla.main.models import Event
from airmozilla.base.tests.t... | mozilla/airmozilla | airmozilla/comments/tests/test_views.py | Python | bsd-3-clause | 23,872 | [
"VisIt"
] | 738261c90eb95bbd5b95c8f3da992e12ab51361c973c1444f3f5156aebf36e78 |
# 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... | apark263/tensorflow | tensorflow/tools/compatibility/ast_edits.py | Python | apache-2.0 | 22,130 | [
"VisIt"
] | 051969d0aae4b5a4c9b785d2469454df8ddb1206d282f564fc79bc13226d251a |
import sys
import os, os.path
import string
import traceback
import antlr
version = sys.version.split()[0]
if version < '2.2.1':
False = 0
if version < '2.3':
True = not False
import LinkExtractor
class LinkListener:
def hrefReference(self, target, line):
raise NotImplementedError
def imag... | rmartinho/boo | lib/antlr-2.7.5/examples/python/linkChecker/LinkChecker.py | Python | bsd-3-clause | 7,759 | [
"VisIt"
] | d9d710a9268dbba51d3f454a9be7babb2cb58bf014b6b7c4d572de7d50550d6e |
from ase.data.molecules import molecule
from gpaw import GPAW
from gpaw import dscf
from gpaw.test import equal
# Ground state calculation
#------------------------------------------------------------------
calc_mol = GPAW(nbands=8, h=0.2, xc='PBE', spinpol=True,
convergence={'energy': 100,
... | qsnake/gpaw | gpaw/test/big/miscellaneous/dscf_CO.py | Python | gpl-3.0 | 2,347 | [
"ASE",
"GPAW"
] | 9b2d18ad7ac0ca8d7c37c8d0618b8d988b87fd623c6c065447c8eb9c368437bf |
# -*- coding: utf-8 -*-
#
# evaluate_quantal_stp_synapse.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 o... | hakonsbm/nest-simulator | pynest/examples/evaluate_quantal_stp_synapse.py | Python | gpl-2.0 | 7,597 | [
"NEURON"
] | fed9f303357aef89c11fb8cc27ea56aedadb426cfc0cefc8e3e43273f395a35e |
# coding=utf-8
from __future__ import absolute_import
from flask import url_for
from flask_login import current_user
import pytest
from firefly.app import create_app
from firefly.ext import db
from firefly.models.user import User
@pytest.fixture
def app(request):
app = create_app('tests/settings.py')
db_nam... | thcode/firefly | conftest.py | Python | mit | 1,201 | [
"Firefly"
] | 49941a3523530953ac453e930434106ea3d34de2d11138ab5b5c6a4dc4eeecf7 |
try:
import xml.etree.cElementTree as et
except:
import xml.etree.ElementTree as et
try:
from galaxy.model import Job
job_states = Job.states
except ImportError:
# Not in Galaxy, map Galaxy job states to Pulsar ones.
from galaxy.util import enum
job_states = enum(RUNNING='running', OK='comp... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/jobs/runners/util/cli/job/torque.py | Python | gpl-3.0 | 3,726 | [
"Galaxy"
] | 5d3476b438d37e60a21e60a2ad61a9708da32c00cbbf87405dd4f3f3c2e23200 |
#adam-use# I THINK: you run redsequence.py before plot_rederr.py. This code identifies red-sequence galaxies!
# usage: python redsequence [options]
# Identifies and fits the red sequence using apparent magnitude and one color.
# Option of identifying star column and only using objects larger.
import pylab
params_pyl... | deapplegate/wtgpipeline | redsequence.py | Python | mit | 24,118 | [
"Galaxy"
] | 09ab1400a77e5ca045e83558ae914e0fe3aedec3fa3068b3e14f1d17c4c56475 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your optio... | pmghalvorsen/gramps_branch | gramps/gen/filters/rules/person/_hasgallery.py | Python | gpl-2.0 | 2,046 | [
"Brian"
] | 9704091e48f5298a37f724a736bdc7c36b3b63b6fc774af730adaae4b8de1336 |
"""
hull_cost_model.py
Matthew Woodruff (mjw5407@arl.psu.edu)
The Pennsylvania State University
Applied Research Laboratory
2013
Compute the cost and lead time for the hull based on physical
description
"""
import copy
import argparse
import math
import json
import StringIO
from collections import nam... | pombredanne/metamorphosys-desktop | metamorphosys/META/analysis_tools/iFAB/psu_python_library/hull_cost_model.py | Python | mit | 14,518 | [
"BLAST"
] | 12688fa9b7f38765cd7ea7b392f87b73eb33166e6a2385ff2ca844dcf507beb0 |
"""
`quadrature_tables` are organized as follows::
quadrature_tables = {
'<geometry1>' : {
order1 : QuadraturePoints(args1),
order2 : QuadraturePoints(args2),
...
},
'<geometry2>' : {
order1 : QuadraturePoints(args1),
order2 : Quad... | sfepy/sfepy | sfepy/discrete/quadratures.py | Python | bsd-3-clause | 53,551 | [
"Gaussian"
] | 78cc3e653ef7f1904075982a5317075fb5fb026f766549ea01c9e0d9010245c6 |
# Copyright 2014 Douglas RAILLARD
#
# This file is part of BrownBat.
#
# BrownBat is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | DouglasRaillard/BrownBat | brownbat/C.py | Python | lgpl-3.0 | 58,225 | [
"VisIt"
] | d56a480023064fde52311a6802f084a7ff61d9b4f7beea6e3b6afdc1423ede22 |
"""
Generalized linear models currently supports estimation using the one-parameter
exponential families
References
----------
Gill, Jeff. 2000. Generalized Linear Models: A Unified Approach.
SAGE QASS Series.
Green, PJ. 1984. "Iteratively reweighted least squares for maximum
likelihood estimation, and some ... | phobson/statsmodels | statsmodels/genmod/generalized_linear_model.py | Python | bsd-3-clause | 64,398 | [
"Gaussian"
] | 034486a64296d502c189b36d416a31c4d83a5b66c061c7d641e953128619d297 |
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