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#!/usr/bin/env python
##########################################################################
#
# Copyright 2012 Jose Fonseca
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in th... | PeterLValve/apitrace | scripts/unpickle.py | Python | mit | 7,712 | [
"VisIt"
] | 3a27dae1fc6678a6e3d2f6c7023213e017717c3456e32202adf264a422acfa16 |
from sfepy.base.base import *
from sfepy.postprocess.utils import mlab
from sfepy.fem import Mesh
from sfepy.fem.meshio import MeshIO, vtk_cell_types, supported_formats
from sfepy.solvers.ts import TimeStepper
from dataset_manager import DatasetManager
from enthought.tvtk.api import tvtk
from enthought.mayavi.sources.... | olivierverdier/sfepy | sfepy/postprocess/sources.py | Python | bsd-3-clause | 10,261 | [
"Mayavi",
"VTK"
] | 460f1d7bb8440f0380df4e4c4495d5d2a232102c1e444fe77b92a9a70c25cadd |
# -*- coding: utf-8 -*-
#/**********************************************************************
#** This program is part of 'MOOSE', the
#** Messaging Object Oriented Simulation Environment.
#** Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS
#** It is made available under the terms of the
#** GNU Lesse... | BhallaLab/moose-examples | snippets/recurrentIntFire.py | Python | gpl-2.0 | 4,293 | [
"MOOSE"
] | bfb09c3a40f5d7de658f80c772fc5773172b7e6827ad410644f01ba3b83a742e |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008-2011 Daniel Moisset, Ricardo Quesada, Rayentray Tappa,
# Lucio Torre
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the... | eevee/cocos2d-mirror | cocos/skeleton.py | Python | bsd-3-clause | 14,706 | [
"VisIt"
] | 61a97ee9c4a71cf4c4a401621b2f8957c6b99f6ff69a3b560598070752c749ba |
#!/usr/bin/env python
# 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.
"""
Unit tests for the contents of device_utils.py (mostly DeviceUtils).
"""
# pylint: disable=protected-access
# pylint: disable=unus... | mrtnrdl/.macdots | scripts/bin/platform-tools/systrace/catapult/devil/devil/android/device_utils_test.py | Python | unlicense | 120,907 | [
"MOE"
] | 6db6bfb9bca0d116891e3b50320e156a7b7ec7d3b8565bb2532d57a5ea5e9c88 |
import numpy as np
import matplotlib.pyplot as plt
import uncertainties
from scipy.signal import find_peaks
from scipy.optimize import curve_fit
import scipy.constants as sc
import scipy.integrate as integrate
from uncertainties import ufloat
from uncertainties import unumpy as unp
from uncertainties.unumpy import nomi... | smjhnits/Praktikum_TU_D_16-17 | Fortgeschrittenenpraktikum/Protokolle/V18_Germaniumdetektor/Python/unbekannt1.py | Python | mit | 5,412 | [
"Gaussian"
] | 655e7c008b2e1e3d5560bf2712bf68e5455ab655d519e20564e5cc34a0745b8e |
from uaperrors import StepError
import sys
import os
from logging import getLogger
from abstract_step import AbstractStep
logger = getLogger('uap_logger')
class HtSeqCount(AbstractStep):
'''
The htseq-count script counts the number of reads overlapping a feature.
Input needs to be a file with aligned seq... | kmpf/uap | include/steps/htseq_count.py | Python | gpl-3.0 | 6,953 | [
"HTSeq"
] | b7d74e58b17ff81e42e92d311e97ec18beb840caad04d40f7dca6121b2b76267 |
from __future__ import print_function
import re
splitExpr = re.compile('[\t\ ]')
from rdkit import Chem
def runit(fName):
inLines = open(fName, 'r').readlines()
nFailed = 0
nPassed = 0
nTried = 0
for line in inLines:
if len(line):
smi = splitExpr.split(line)[1]
if smi[-1] == '\n':
s... | jandom/rdkit | Code/GraphMol/Wrap/test_data/do_smiles.py | Python | bsd-3-clause | 780 | [
"RDKit"
] | c84f6a890b3dd1613cca1a558892d8385540b644c1e8cbc69b16b9d2a28a9daa |
import numpy as np
import os
def XMLtoCSV(XMLinput):
"""
This function takes as an input the XML file that comes out of the electronic structure calculations and transforms
it into 2 CSV files. The first one is the 'X part' of the data. It contains a sample per line. Each line has a format:
atom label ... | RobertArbon/YAMLP | SciFlow/ImportData.py | Python | mit | 16,678 | [
"Molpro"
] | 6511fc1f78e24d5f7ad2eb767f857e568c7eac5e7ad140b5277655a188905a84 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2016 Loreto Parisi <loretoparisi@gmail.com>
# Copyright (C) 2016 Silvio Olivastri <silvio.olivastri@gmail.com>
# Copyright (C) 2016 Radim Rehurek <radim@rare-technologies.com>
"""This script allows converting word-vectors from word2vec format into Tensor... | mattilyra/gensim | gensim/scripts/word2vec2tensor.py | Python | lgpl-2.1 | 3,735 | [
"VisIt"
] | 00d40be0011033ef921bd8331594750922156a7ce4ea7c01f79fbf7c972f30f7 |
#!/usr/bin/env python
"""
A linting tool to check for xss vulnerabilities.
"""
from __future__ import print_function
import argparse
import ast
import os
import re
import sys
import textwrap
from enum import Enum
class StringLines(object):
"""
StringLines provides utility methods to work with a string in te... | Lektorium-LLC/edx-platform | scripts/xss_linter.py | Python | agpl-3.0 | 101,168 | [
"VisIt"
] | a4131fc4c6e135a5092eb9749c7a18142959c49e9ca7e87c4bd7a5b7f8356611 |
#!/usr/bin/env python
# Mesa 3-D graphics library
#
# Copyright (C) 1999-2001 Brian Paul All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, inc... | execunix/vinos | xsrc/external/mit/MesaLib/dist/src/mapi/glapi/gen/mesadef.py | Python | apache-2.0 | 7,558 | [
"Brian"
] | ef3874cb1180faf7b56a096cb27c4c65ff05886d3841e807054390346747df75 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Tests that relate to evaluating models with quantity parameters
"""
import numpy as np
import pytest
from numpy.testing import assert_allclose
from ..core import Model
from ..models import Gaussian1D, Shift, Scale, Pix2Sky_TAN
from ... import unit... | DougBurke/astropy | astropy/modeling/tests/test_quantities_evaluation.py | Python | bsd-3-clause | 13,490 | [
"Gaussian"
] | 3e7e6ed9490ca8754e76d7fded5f5aa069cb392d13ee88d07474bf007e30ebe2 |
# Copyright (C) 2018 Henrique Pereira Coutada Miranda
# All rights reserved.
#
# This file is part of yambopy
#
#
import unittest
import os
import shutil as sh
from yambopy.analyse import YamboAnalyser
from yambopy.io.outputfile import YamboOut
from qepy.lattice import Path
test_path = os.path.join(os.path.dirname(__f... | alexmoratalla/yambopy | yambopy/tests/test_yamboanalyse.py | Python | bsd-3-clause | 2,195 | [
"Yambo"
] | ded2440000d929307cb04bfd43ec23b572fa63914b88cfd6ca348cb86d0fa492 |
# -*- coding: utf-8 -*-
from parse import clauses
def parse_clause(text):
parsed = clauses.grammar.parse(text)
return clauses.ClauseVisitor().visit(parsed)
| uclmr/inferbeddings | notebooks/simple/parse/base.py | Python | mit | 167 | [
"VisIt"
] | 18069be83cd2a9fabc94b0dedda066c9dfc9fd29691795a4a97c5255effce8ec |
import networkx
from claripy.utils.orderedset import OrderedSet
from ..misc.ux import deprecated
# errors
from ..errors import AngrForwardAnalysisError
# notices
from ..errors import AngrSkipJobNotice, AngrDelayJobNotice, AngrJobMergingFailureNotice, \
AngrJobWideningFailureNotice
from .cfg.cfg_utils import CFGUt... | tyb0807/angr | angr/analyses/forward_analysis.py | Python | bsd-2-clause | 23,692 | [
"VisIt"
] | 46a12b504e39fa9405334b094b1902462f9aac1f02ce366b0c1351d4a6cdba08 |
import gtk
from gettext import gettext as _
import gobject
from ase.gui.widgets import pack
class Movie(gtk.Window):
def __init__(self, gui):
gtk.Window.__init__(self)
self.set_position(gtk.WIN_POS_NONE)
self.connect('destroy', self.close)
#self.connect('delete_event', self.exit2)
... | grhawk/ASE | tools/ase/gui/movie.py | Python | gpl-2.0 | 4,556 | [
"ASE"
] | f8f88fe0e618251157f5b5bf25acef393a7d76d8b35513fc27645a756c1b7825 |
# -*- coding: utf-8 -*-
"""----------------------------------------------------------------------------
Author:
Huang Quanyong (wo1fSea)
quanyongh@foxmail.com
Date:
2017/6/29
Description:
test_neuron_network.py
----------------------------------------------------------------------------"""
import unitt... | wo1fsea/PyTWEANN | tests/test_neuron_network.py | Python | mit | 4,968 | [
"NEURON"
] | 2400529a24a15500974fb370bf4329046db83d091f566b691868e61d1493e3eb |
"""
Backend wrapper
"""
__RCSID__ = "$Id$"
class AbstractBackend(object):
"""
AbstractBackend is used to create an abstraction of handler and formatter concepts from 'logging'.
It corresponds to the backend concept of the old gLogger.
It is useful for different reasons:
- to gather handler and formatter,... | andresailer/DIRAC | Resources/LogBackends/AbstractBackend.py | Python | gpl-3.0 | 3,329 | [
"DIRAC"
] | e5591abba549177af9e9053153a20fc1ffc55a157eb3370f820b4f710624ddd0 |
"""
Simple ga server for the basicbot.
"""
import argparse
import json
import zmq
import random
import threading
from deap import base
from deap import creator
from deap import tools
############################################################################
###################################################... | jaredmoore/ros_gazebo_python | src/basicbot_ga/test/ga_server.py | Python | gpl-3.0 | 8,606 | [
"Gaussian"
] | 317ba8def43eb2ccc5024f528dce3416e49cf2cb940234b4d80ea2ceb2466678 |
"""
Course Outline page in Studio.
"""
import datetime
from bok_choy.javascript import js_defined, wait_for_js
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise
from selenium.webdriver import ActionChains
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.suppor... | Stanford-Online/edx-platform | common/test/acceptance/pages/studio/overview.py | Python | agpl-3.0 | 40,144 | [
"VisIt"
] | 82f95bc286eeacf76d8acd57fa35882472ec05a91709aec0445bca084f99a214 |
import json
from .visitor import Visitor, visit
__all__ = ['print_ast']
def print_ast(ast):
return visit(ast, PrintingVisitor())
class PrintingVisitor(Visitor):
def leave_Name(self, node, *args):
return node.value
def leave_Variable(self, node, *args):
return '$' + node.name
def l... | gabriel-laet/graphql-py | graphql/core/language/printer.py | Python | mit | 3,464 | [
"VisIt"
] | 1c1b274cf409f4172710afa218e9e07690e1ee4b13cc1b113b611c746e467b6a |
from setuptools import setup
from ircu.consts import version_str
setup(
name='ircu',
version=version_str,
author='Brian Cline',
author_email='brian.cline@gmail.com',
description=('An IRC network state machine for Undernet ircu-based '
'services using the P10 protocol.'),
long... | briancline/ircu-python | setup.py | Python | mit | 1,699 | [
"Brian"
] | cd9e3ee56e22bbc3efd1c7d20ed5f92872ad71b3db48dde106e4a21d71a8a7aa |
#!/usr/bin/env python
import sys
import os
import re
import gzip
from optparse import OptionParser
# biopython
from Bio import PDB
# TODO: normalize atom names, ie.
# O1P => OP1, O2P => OP2, itd.
# O3* => O3', itd.
def parse_args():
"""setup program options parsing"""
parser = OptionParser(description="normal... | mmagnus/rna-pdb-tools | rna_tools/tools/clarna_play/ClaRNAlib/normalize_pdb.py | Python | gpl-3.0 | 4,083 | [
"Biopython"
] | 6ef1e07b04b06beba320864a8341a8401b6dc4e959086e82af15d3cdf84319d0 |
import numpy as np
try:
# use scipy if available: it's faster
from scipy.fftpack import fft, ifft, fftshift, ifftshift
except:
from numpy.fft import fft, ifft, fftshift, ifftshift
def FT_continuous(t, h, axis=-1, method=1):
"""Approximate a continuous 1D Fourier Transform with sampled data.
This... | nhuntwalker/astroML | astroML/fourier.py | Python | bsd-2-clause | 6,982 | [
"Gaussian"
] | a6d50e5a942920098d298a8ccb6ea7c0038b3c6ad5aac6dbb74c3595cfcf28a6 |
intro = """
<br>
You have subscribed to receive alerts from <a href='http://www.globalforestwatch.org/'>Global Forest Watch</a>. This message reports new forest change alerts and user stories for the area of interest you selected. You will receive a separate email for each distinct area of interest you subscribe to.
<... | aagm/gfw-api | gfw/mailers/digest_mailer.py | Python | gpl-2.0 | 2,740 | [
"VisIt"
] | 699973391ec0fa76d4fefd665d99a4af0d16b9f95a61ada38e15b9f48693e6f0 |
# $HeadURL$
"""
Set of utilities to retrieve Information from proxy
"""
__RCSID__ = "$Id$"
import base64
import types
import inspect
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Security.X509Chain import X509Chain, g_X509ChainType
from DIRAC.Core.Security.VOMS import VOMS
from DIRAC.Core.Security import Locations
... | avedaee/DIRAC | Core/Security/Misc.py | Python | gpl-3.0 | 5,743 | [
"DIRAC"
] | e2e67a057570f444a8cdb6c1a25d91b3573280602f5c73e8c26c35a4de3d3cc7 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 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 | remindor/simple_dialog.py | Python | gpl-3.0 | 2,392 | [
"Brian"
] | 45e069a1fc6669cb77d710b9564f3c9517832aca50e17180bf54f565b236ae55 |
#!/usr/bin/env python
"""
Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy.
usage: %prog input output level sigma mode exclusion strand
"""
import sys
from galaxy import eggs
import pkg_resources
pkg_resources.require( "GeneTrack" )
from genetrack.scripts import peakpred
from genetrack impor... | volpino/Yeps-EURAC | tools/visualization/genetrack_peak_prediction.py | Python | mit | 1,016 | [
"Galaxy"
] | 258df0d7e2e7f3d17783f1606798a4dc7bca88ae060aa8491ce450bbca05e4e4 |
"""
Module with RecXElectrode from Allen Brain Institute
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
from __future__ import absolute_import
# Allen Institute Software License - This software license is the 2-clause BSD license plus clause a third
... | Neurosim-lab/netpyne | netpyne/support/recxelectrode.py | Python | mit | 5,581 | [
"NEURON"
] | e25a8e1b0990d0e32c334cecb2b0db7317cf8cbc14df3f59e1f46fcdbe5956e5 |
import numpy as np
import pytest
from pysisyphus.calculators.AFIR import AFIR
from pysisyphus.calculators.PySCF import PySCF
from pysisyphus.calculators import XTB
from pysisyphus.constants import AU2KJPERMOL
from pysisyphus.helpers import geom_loader
from pysisyphus.init_logging import init_logging
from pysisyphus.op... | eljost/pysisyphus | tests/test_afir/test_afir.py | Python | gpl-3.0 | 2,352 | [
"PySCF",
"xTB"
] | ab58b423e7bc135bce0241c75c4914ca992f1878921123828cb067ea652714ed |
# -*- coding: utf-8 -*-
#
# Copyright 2008 - 2013 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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... | LunarLanding/Pythics | pythics/libinstrument.py | Python | gpl-3.0 | 4,074 | [
"Brian"
] | 215c1c23e81740f38fb60addb7b8e3c554811052ab14871abb54531ca1e3cd26 |
#!/usr/bin/env python
"""
Script to build a "binary wheel" for the 'pip' Python package manager for
the LAMMPS python module which includes the shared library file. After a
successful build the script attempts to install the wheel into a system
specific site-packages folder or - failing that - into the corresponding
u... | akohlmey/lammps | python/install.py | Python | gpl-2.0 | 4,578 | [
"LAMMPS"
] | 2f11ede4f6e062b89cc65bfb72844b79dcc3d3105041ad297505f82bf4bbefd9 |
# commands.py - command processing for mercurial
#
# Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from node import hex, nullid, nullrev, short
from lock import release
from i18... | joewalnes/idea-community | plugins/hg4idea/testData/bin/mercurial/commands.py | Python | apache-2.0 | 143,852 | [
"VisIt"
] | 9fed6cf127ed48dd6d5f74da6a30d2a2fe80227f558cfce10c3e0456632cc8fe |
"""Core, non-language-specific features of DXR, implemented as a Plugin"""
from base64 import b64encode
from itertools import chain
from os.path import relpath, splitext, realpath, basename
import re
from flask import url_for
from funcy import identity
from jinja2 import Markup
from parsimonious import ParseError
fr... | pombredanne/dxr | dxr/plugins/core.py | Python | mit | 20,394 | [
"VisIt"
] | 162e7df37dc88d460744e8f44b1760bb8ae6e40afde6a880c5f70ccf6a739d63 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2011 L Fiaschi, T Kroeger, C Sommer, C Straehle, U Koethe, FA Hamprecht. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are
# permitted provided that the following conditions are met:
# ... | ilastik/ilastik-0.5 | setup_mac.py | Python | bsd-2-clause | 9,322 | [
"VTK"
] | 03452128d4b3763374e4d0b2728fd26c4bea62df1c690b053e2101b0451ee3e1 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 appl... | fingeronthebutton/RIDE | src/robotide/application/releasenotes.py | Python | apache-2.0 | 5,022 | [
"VisIt"
] | a711f5162eebd2b6f45ed343da092518298b04ba41dc852475f5d970bc6b7831 |
# -*- coding: utf-8 -*-
"""
flaskbb.utils.helpers
~~~~~~~~~~~~~~~~~~~~
A few helpers that are used by flaskbb
:copyright: (c) 2014 by the FlaskBB Team.
:license: BSD, see LICENSE for more details.
"""
import re
import time
import itertools
import operator
import struct
from io import BytesIO
from ... | SeanChen0617/flaskbb | flaskbb/utils/helpers.py | Python | bsd-3-clause | 14,644 | [
"VisIt"
] | 3aed9be4b153f4897da8544a170c144a0e56c6cf23017935158b23f3959c6b7a |
##
# title: Server.py
# by: Brian Kim
# description: the top-level script that
# executes RAMS and roams
#
| briansan/rams | RAMS/app/Server.py | Python | bsd-3-clause | 109 | [
"Brian"
] | 194e77b9cf80936e546c849655f07328ddcb831c0476ac8df7c2d2f3ee093e87 |
"""
Assesment of Generalized Estimating Equations using simulation.
Only Gaussian models are currently checked.
See the generated file "gee_simulation_check.txt" for results.
"""
from statsmodels.compat.python import range, lrange, zip
import scipy
import numpy as np
from itertools import product
from statsmodels.gen... | rgommers/statsmodels | statsmodels/genmod/tests/gee_simulation_check.py | Python | bsd-3-clause | 9,456 | [
"Gaussian"
] | 8156f7b06dab38edfc1927ade9566bf458d25b098faf97c9493efd217125ad2b |
# $Id$
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
""" Various bits and pieces for calculating Molecular descriptors
"""
import re
from rdkit.Chem import Descriptors as DescriptorsMod
from rdkit.ML.Descriptors import Descriptors
from rdkit.RDLogger import logger
import pickle
logger = lo... | bp-kelley/rdkit | rdkit/ML/Descriptors/MoleculeDescriptors.py | Python | bsd-3-clause | 3,244 | [
"RDKit"
] | e0c364a6f8aee2ddb6dab638232748c953226bd700d013468bccd3f93e304f8f |
#!/usr/bin/env python
from __future__ import print_function
import os
import sys
import requests
from openbabel import pybel
from openbabel import openbabel as ob
# TODO: process Open Babel resdata.txt
# if we can find certain non-standard residues
mdLigands = [
"ASH", # Neutral ASP
"CYX", # SS-bonded CYS
"CYM",... | OpenChemistry/avogadrolibs | scripts/getresdata.py | Python | bsd-3-clause | 5,683 | [
"Avogadro",
"Open Babel",
"Pybel"
] | a59d5f9fe0bf09daba9a35dc62498b796cb45a2880dd324a89be1e67badb164d |
"""
Created August 14 2014
James Houghton <james.p.houghton@gmail.com>
Changed May 03 2017
Alexey Prey Mulyukin <alexprey@yandex.ru> from sdCloud.io developement team
Changes:
[May 03 2017] Alexey Prey Mulyukin: Integrate support to
logical operators like 'AND', 'OR' and 'NOT'.
Fix support the... | JamesPHoughton/pysd | pysd/translation/xmile/SMILE2Py.py | Python | mit | 11,669 | [
"VisIt"
] | 668bd9329f5aae494d98f182e4cf072886f44871b6e61b2b2af6d94c6f354823 |
#!/usr/bin/env python
import unittest
import numpy as np
from pymatgen.core.lattice import Lattice
from pymatgen.symmetry.maggroups import MagneticSpaceGroup
from pymatgen.symmetry.groups import SpaceGroup
from pymatgen.util.testing import PymatgenTest
__author__ = "Matthew Horton"
__copyright__ = "Copyright 2017, Th... | tschaume/pymatgen | pymatgen/symmetry/tests/test_maggroups.py | Python | mit | 7,182 | [
"pymatgen"
] | 1a644aac36db8b74107348a68c7f5db349c83120fec12298ab33364385a7de8a |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008) - although it uses the... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_nosyn_0128/brian2_benchmark_COBAHH_nosyn_0128.py | Python | gpl-3.0 | 3,347 | [
"Brian"
] | c403baff7f3633de7b1d9d16d5b27eaf7ff124a07f73a5b93ee5e94fd172a7cb |
# SPDX-License-Identifier: Apache-2.0
#
# Copyright (C) 2015, ARM Limited and contributors.
#
# 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
#
# ... | credp/lisa | lisa/analysis/functions.py | Python | apache-2.0 | 32,267 | [
"VisIt"
] | 37ca2d096019a9aa1d7776b4990420996766ca5adc95f15c6dad72d5de9bb64f |
# -*- coding: utf-8 -*-
#------------------------------------------------------------
# pelisalacarta - XBMC Plugin
# Canal para unsoloclic
# http://blog.tvalacarta.info/plugin-xbmc/pelisalacarta/
#------------------------------------------------------------
import re
import urlparse
from core import config
from core ... | Hernanarce/pelisalacarta | python/main-classic/channels/unsoloclic.py | Python | gpl-3.0 | 7,369 | [
"ADF"
] | b131d864cebdc0529d22896931144ed7a2817ba1d25b24c6d1d7efd93071e666 |
# Copyright (c) 2014 Intel Corporation.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# * Redistributions of works must retain the original copyright notice, this list
# of conditions and the following disclaimer.... | YongseopKim/crosswalk-test-suite | tools/atip/atip/web/web.py | Python | bsd-3-clause | 18,181 | [
"VisIt"
] | 36df8a608d6f60af79c2c4c69a2158ff029afbad6ad2c7de53e6bb27d388766f |
import numpy as np
from def_get_mags import get_zdistmod, get_kcorrect2, aper_and_comov, abs2lum, lumdensity, abs_mag
import math
from defclump import meanlum2, medlum2, get_error
import matplotlib.pyplot as plt
from def_mymath import halflight
def get_ind_lums(newdata, bands, aperture, scale=''):
import numpy as np
... | anewmark/galaxy_dark_matter | def_clean.py | Python | mit | 8,425 | [
"Galaxy"
] | fd220559b97dad1fbc48ddac8d0455eea8ac52d0bf7ca37a73fbf6e22dcc22d9 |
#!/usr/bin/env python
#Dan Blankenberg
#%prog bounding_region_file mask_intervals_file intervals_to_mimic_file out_file mask_chr mask_start mask_end interval_chr interval_start interval_end interval_strand use_mask allow_strand_overlaps
import sys, random
from copy import deepcopy
from galaxy import eggs
import p... | volpino/Yeps-EURAC | tools/encode/random_intervals_no_bits.py | Python | mit | 10,644 | [
"Galaxy"
] | 243eb5cd34ff4fa884b8111b0c98e4457a846d6b799532e706a51ccf72a2ec5b |
import ast
from .base import BaseAnalyzer, Result
DESCRIPTION = """
``{name}`` function has been deprecated in Django 1.2 and removed in 1.4. Use
``{propose}`` class instead.
"""
class TemplateLoadersVisitor(ast.NodeVisitor):
def __init__(self):
self.found = []
removed_items = {
'django.t... | beni55/djangolint | project/lint/analyzers/template_loaders.py | Python | isc | 1,600 | [
"VisIt"
] | 25d915b031cadb47473b708e9035bfc4ce27080514d6f4b6f8e50a6921cd589d |
# coding: utf-8
"""
Acceptance tests for Studio's Setting pages
"""
from __future__ import unicode_literals
import os
from textwrap import dedent
from bok_choy.promise import EmptyPromise
from mock import patch
from nose.plugins.attrib import attr
from base_studio_test import StudioCourseTest
from common.test.accept... | fintech-circle/edx-platform | common/test/acceptance/tests/studio/test_studio_settings.py | Python | agpl-3.0 | 39,646 | [
"VisIt"
] | f994cc91725a39fb4d48f60ab3d53c28a361f07ad10d51c39a24450133d51488 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright 2013 The Plaso Project Authors.
# Please see the AUTHORS file for details on individual 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 Li... | iwm911/plaso | plaso/parsers/sqlite_plugins/firefox_test.py | Python | apache-2.0 | 10,639 | [
"VisIt"
] | d72f5ea44b9a51e2ac7de3e708e260cc4a25cd3a847321c3fd811b3f57038366 |
from __future__ import print_function
#import global_vars
import os
import exceptions
import smtplib
import email.mime.text
import copy
"""
class Classifier(object):
name = ""
l = [] #Classifier | ParamList
def __init__(self, label):
self.name = label
def prnt(self):
print("ClassifierName", self.name)
for el ... | Abi1ity/uniclust2.0 | old_uniclust_model/task1.py | Python | bsd-3-clause | 12,191 | [
"VisIt"
] | ba5d4e9e8736d3982127b843a998959bd3232a4267f3d5ba3e68df0a9f429562 |
"""
Represents a diffraction setup using a shadow3 preprocessor (bragg) file
Except for energy, all units are in SI.
"""
import numpy
import scipy.constants as codata
from crystalpy.diffraction.DiffractionSetupAbstract import DiffractionSetupAbstract
from shadow4.physical_models.bragg.bragg import Bragg
from crystalp... | srio/minishadow | shadow4/physical_models/bragg/s4_diffraction_setup.py | Python | mit | 4,753 | [
"CRYSTAL"
] | 115f49e39ed4bff558b0066ae012749e4c3235fc75481ff4843f86ac1dfc0104 |
# The MIT License
#
# Copyright 2014, 2015 Piotr Dabkowski
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the 'Software'),
# to deal in the Software without restriction, including without limitation the rights
# to use, copy, modif... | felipenaselva/felipe.repository | script.module.streamhublive/resources/modules/js2py/translators/pyjsparser.py | Python | gpl-2.0 | 103,330 | [
"VisIt"
] | c953a1ca2462327af61be0917c4fad8e05351a9d72a27872a72db6f04ca67e9a |
#!/usr/bin/python
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
""" Module: itim
============
"""
from __future__ import print_function
import platform
from multiprocessing import Process, Queue
import numpy as np
try:
from __bui... | Marcello-Sega/pytim | pytim/itim.py | Python | gpl-3.0 | 16,830 | [
"GROMOS",
"MDAnalysis",
"MDTraj",
"OpenMM"
] | ade4c26e25460b15dfa4088bb5f3f792f56283ef972076a63970accec9743bc4 |
import sys, config
from galaxy.web import security
import galaxy.webapps.demo_sequencer.registry
class UniverseApplication( object ):
"""Encapsulates the state of a Universe application"""
def __init__( self, **kwargs ):
print >> sys.stderr, "python path is: " + ", ".join( sys.path )
self.name ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/demo_sequencer/app.py | Python | gpl-3.0 | 858 | [
"Galaxy"
] | e6598fd1bc5ffef2200e8c60547808711a321549320ccdcdd2df0c9bdbf0e0bd |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Jakim Friant
#
# This program ... | Forage/Gramps | gramps/gen/plug/docgen/graphicstyle.py | Python | gpl-2.0 | 4,929 | [
"Brian"
] | 7fb26ded477bd8f49eb8f9093601070cd9e580ad332bc78f79c3350b8219999d |
r"""
Ordination results format (:mod:`skbio.io.format.ordination`)
=============================================================
.. currentmodule:: skbio.io.format.ordination
The ordination results file format (``ordination``) stores the results of an
ordination method in a human-readable, text-based format. The form... | anderspitman/scikit-bio | skbio/io/format/ordination.py | Python | bsd-3-clause | 14,413 | [
"scikit-bio"
] | 449648c2bb4cc83f4d11afedfdbf8da95423d14363de06a98bf3906440adebe1 |
r"""OS routines for NT or Posix depending on what system we're on.
This exports:
- all functions from posix or nt, e.g. unlink, stat, etc.
- os.path is either posixpath or ntpath
- os.name is either 'posix' or 'nt'
- os.curdir is a string representing the current directory (always '.')
- os.pardir is ... | prefetchnta/questlab | bin/x64bin/python/36/Lib/os.py | Python | lgpl-2.1 | 38,595 | [
"VisIt"
] | b5d3c4c0e5170a83a8800eb795a672287174fcf98c3f3a5e2aded97107b60ea5 |
import numpy as np
import pickle
from time import time, ctime
from datetime import timedelta
from ase.structure import bulk
from ase.units import Hartree
from gpaw import GPAW, FermiDirac
from gpaw.response.gw import GW
from gpaw.xc.hybridk import HybridXC
from gpaw.xc.tools import vxc
from gpaw.mpi import serial_comm,... | ajylee/gpaw-rtxs | gpaw/test/gw_test.py | Python | gpl-3.0 | 2,541 | [
"ASE",
"GPAW"
] | 7499d34495f155c9c99f749454cb251bbb86577a605b1d136587f5044d8728ea |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | KaiSzuttor/espresso | maintainer/benchmarks/lj.py | Python | gpl-3.0 | 7,805 | [
"ESPResSo"
] | d296d889f7b1a1319444ce40b7aec856654a5a59ce46776d9e12ce54cd3f0404 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# A script to test the stencil filter.
# removes all but a sphere.
reader = vtk.vtkPNGReader()
reader.SetDataSpacing(0.8,0.8,1.5)
reader.SetDataOrigin(0.0,0.0,0.0)
reader.S... | hlzz/dotfiles | graphics/VTK-7.0.0/Imaging/Core/Testing/Python/TestStencilWithFunction.py | Python | bsd-3-clause | 1,439 | [
"VTK"
] | 67c3879100433b268dd4b0e0b1e5e5cf040e1736f1af9b4145eb977cb897daf2 |
# -*- 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_hoomdxml.py | Python | gpl-2.0 | 3,324 | [
"MDAnalysis"
] | ac3ab9a4cd29595dd6339ef98e111f1c04ccf6c57acf42e8c9fbf92405c06525 |
# 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... | yanchen036/tensorflow | tensorflow/contrib/distributions/python/ops/mvn_diag.py | Python | apache-2.0 | 8,105 | [
"Gaussian"
] | 8b08c6c9b2c6b2ab054d27868bb0ecb30bcf239b4079a60489311b07fe479b47 |
#!/usr/bin/env python
from netCDF4 import Dataset
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
from matplotlib.colors import colorConverter
from ase.units import Bohr
import os.path
from ase_utils.kpoints import cubic_kpath
from collections import namedtuple
de... | mailhexu/pyDFTutils | pyDFTutils/perovskite/plotphon.py | Python | lgpl-3.0 | 14,848 | [
"ASE"
] | 7b6dab3253275aaf8d04e811c7c07e19465897e8893fcef0c1f224c18bc7b92b |
# tasks.py (contains classes for various playfield devices)
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
from copy import copy
import time
... | jabdoa2/mpf | mpf/system/tasks.py | Python | mit | 8,393 | [
"Brian"
] | bc734102cf9fc867bfb04c6297d45d24958829a97e58c3c431107d7ffe86acd3 |
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import json
import os
import os.path
import re
import sys
import warnings
from collections import defaultdict
try:
from setuptools import setup, find_packages
from setuptools.command.build_py import build_py as BuildPy
... | abadger/ansible | setup.py | Python | gpl-3.0 | 14,340 | [
"Galaxy"
] | b15f4a1620f20583460955d7a158029332cee914b1a7bb24024cdbd1284a73b7 |
# ***************************************************************************
# *
# * Copyright (C) 2013-2016 University of Dundee
# * All rights reserved.
# *
# * This file is part of SAMoS (Soft Active Matter on Surfaces) program.
# *
# * SAMoS is free software; you can redistribute it and/or modify
# * it unde... | sknepneklab/SAMoS | utils/Interaction.py | Python | gpl-3.0 | 8,546 | [
"Gaussian"
] | 743d54825cda22cc2b6d6f65e0e198c772c0dfa3881476de4d50ee41257c389f |
from __future__ import print_function, division
import os,os.path, glob
import logging
import re
import json
from configobj import ConfigObj
try:
import numpy as np
except ImportError:
np = None
try:
import pandas as pd
except ImportError:
pd = None
import numpy.random as rand
import scipy.optim... | styra/isochrones | isochrones/starmodel.py | Python | mit | 66,539 | [
"Gaussian"
] | 67645aeb6a1fd69246cae8d4d1d8261555f070fb2a513834846f1f1ab30e25a8 |
# -*- coding: utf-8 -*-
"""Volumes of raw image and labeled object data."""
from __future__ import division
from collections import namedtuple
import csv
import logging
import os
import re
import h5py
import math
import numpy as np
from PIL import Image
import pytoml as toml
import requests
from scipy import ndimag... | aschampion/diluvian | diluvian/volumes.py | Python | mit | 61,524 | [
"Gaussian"
] | eaf095a20b764c4a4ca39a7e191ccd6e98bfc1269b8b5c4e9bc25b75e9185f6e |
#!/usr/bin/env python
import __future__
import gtk
from gettext import gettext as _
import os.path
import numpy as np
import sys
from ase.gui.widgets import pack, Help
from ase.data.colors import jmol_colors
from ase.atoms import Atoms
class Execute(gtk.Window):
""" The Execute class provides an expert-user windo... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/gui/execute.py | Python | gpl-2.0 | 13,683 | [
"ASE"
] | 1cdb0a1b48221db79efc5553363447fb8bf8fffb907625b114c4b8f094faeceb |
inp=open('blastx_glimmer_ncbi_tce1_n3_b80.xls', 'r')
inp2=inp.read()
spl=inp2.split('# Query:')
headers=open('headers_ncbi_DB.txt','r').read()
intergenic=open('blastx_glimmer_annotated.xls','w') #no es intergenic, pero asi se llama la variable ;)
orfs=open('genes_glimmer_TCE1.fasta','r').read()
#######################... | elecabfer/BLAST- | blastx_ncbi2.py | Python | mit | 1,469 | [
"BLAST"
] | 68af1a0acaf465a98b6cda7865fd2a2375c57bb890f2458cdf4ad7e4c71b3fd2 |
"""
Functions used to save model data and to perform analysis
"""
import numpy as np
from parameters import *
from sklearn import svm
import time
import pickle
import stimulus
import os
import copy
import matplotlib.pyplot as plt
from itertools import product
from scipy import signal
from scipy.optimize import curve_f... | nmasse/Short-term-plasticity-RNN | analysis.py | Python | apache-2.0 | 49,221 | [
"NEURON"
] | 4c87ef0ad79a5554052800e412bd791659d5be4d85bb0f7741180aabec70bfcf |
"""Functions supports the creation of general 1 and n-dim profiles including
normal and sersic profiles
TODO:
Limitations:
1. The sersic profile assumes radial symmetry
"""
import numpy as np
class FunctionsError(Exception):
"""Exception Raised for Function errors"""
pass
def Normal(arr, mean, sigma, sc... | crawfordsm/pyspectrograph | PySpectrograph/Utilities/Functions.py | Python | bsd-3-clause | 1,782 | [
"Gaussian"
] | 4e4cd36252b57c9df0b3eca2c1d868a8fca72197df4d00cc1e0ad4793bc76421 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# grep - text search
# 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 of the GNU General Public License as published by
#... | heromod/migrid | mig/shared/functionality/grep.py | Python | gpl-2.0 | 5,569 | [
"Brian"
] | 77d9a0ecbabe243b68f23c370a8ee5b8fee02dc38d29c064576b86dadcb3d752 |
import oauth2 as oauth
import time
import json
import traceback
import config as cfg
consumer = oauth.Consumer(key=cfg.twitter['consumer_key'], secret=cfg.twitter['consumer_secret'])
access_token = oauth.Token(key=cfg.twitter['access_token'], secret=cfg.twitter['access_token_secret'])
client = oauth.Client(consumer, ... | mirkolai/twitter-experiment | python/rest API/friends-list.py | Python | gpl-2.0 | 1,819 | [
"CRYSTAL"
] | fdff25b6e916b5684da1097a686ce0336999e68f948101fef72809de0dd166fe |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import json
import numpy as np
import warnings
import xml.etree.cElementTree as ET
from pymatgen.core.periodic_table import Element... | gpetretto/pymatgen | pymatgen/io/vasp/tests/test_outputs.py | Python | mit | 56,558 | [
"VASP",
"pymatgen"
] | f1f862516992754fcff07d10a7d527782613a30c7e0d3a741f71c84473691b77 |
#!/bin/env python
#-------------------------------------------------------------------------------
#
# Filename : all_trunc_gaus.py
# Description : Matplotlib file for generating allthe various Truncated
# Gaussians determined describe in the article
# Author : Yi-Mu "Enoch" Chen [ ensc@hep1.p... | enochnotsocool/enochnotsocool.github.io | images/genimage/stat_infer/all_trunc_gaus.py | Python | mit | 2,776 | [
"Gaussian"
] | 2c4f8c7d8adbbd8fe7ed394252256f5a9b926c76f6d6c6341a10e9e878dad1da |
#!/usr/bin/env python
# Created: Wed May 29 08:07:18 2002
# thomas@cbs.dtu.dk, Cecilia.Alsmark@ebc.uu.se
# Copyright 2001 by Thomas Sicheritz-Ponten and Cecilia Alsmark.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have ... | bryback/quickseq | genescript/Bio/SeqUtils/__init__.py | Python | mit | 11,238 | [
"BioPerl",
"Biopython"
] | 0bd191912d36d7017a363cbe81926c9b496a634e0a737c7285b2b0fa042b175b |
"""
@name: PyHouse/src/Modules/_test/test_Computer.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2018 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 29, 2015
@Summary:
"""
__updated__ = '2018-02-12'
from twisted.trial import unittest, reporter, ru... | DBrianKimmel/PyHouse | Project/src/Modules/_test/test_Computer.py | Python | mit | 753 | [
"Brian"
] | 606566c65a1b16dbda295e4a45dc9a1c9e5a22197815cb8366276c906dc369a1 |
#! /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 | CallVariants.py | Python | gpl-3.0 | 181,875 | [
"BWA",
"pysam"
] | 50d04d94802b88193ab7e23a203726525e7bbe8e6bfbfb44d8cdbd2adb1100ed |
import numpy as np
from spherical_functions import LM_total_size
from .. import ModesTimeSeries
from .. import Inertial
class AsymptoticBondiData:
"""Class to store asymptotic Bondi data
This class stores time data, along with the corresponding values of psi0 through psi4 and sigma.
For simplicity, the d... | moble/scri | scri/asymptotic_bondi_data/__init__.py | Python | mit | 7,236 | [
"Psi4"
] | a00148456b2e220660b74f02c08f39a70d8b554b68efb1ae5ffbfe18676e4167 |
# 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... | AsimmHirani/ISpyPi | tensorflow/contrib/tensorflow-master/tensorflow/contrib/bayesflow/python/kernel_tests/monte_carlo_test.py | Python | apache-2.0 | 7,445 | [
"Gaussian"
] | e97320eaab9532adc78ea19919f65ceedfa582aa912375a3a0694cf8fbdf38f4 |
#!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# 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, eit... | govarguz/espressopp | examples/parallel_tempering/parallel_tempering.py | Python | gpl-3.0 | 4,272 | [
"ESPResSo"
] | 6b161dc89f56c3f8399664d9fa2ca2559c3da36405ceb9da900e5773a376fc9a |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | SamStudio8/scikit-bio | skbio/stats/tests/test_gradient.py | Python | bsd-3-clause | 54,863 | [
"scikit-bio"
] | f08330d34327deaab47c070293b7bac81d8f767eea6fd37528aef5d85707e508 |
LONG_HORN = 750
LONG_HORN_SPACE = LONG_HORN/2
SHORT_HORN = 400
SHORT_HORN_SPACE = SHORT_HORN/2
sequences = {
'CreekFleet': {
# Three long horns immediately (three minutes to start)
0: 'LLL',
# Two long horns a minute later (two minutes to start)
60000: 'LL',
# One... | agmlego/Creekfleet_Timer | firmware/horn_sequence.py | Python | mit | 2,928 | [
"BLAST"
] | c03825103194a28a92a092cc821739a10667c62bf207ff66b734021cf7482917 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | theflofly/tensorflow | tensorflow/python/autograph/pyct/transformer_test.py | Python | apache-2.0 | 11,209 | [
"VisIt"
] | 120c441558d1acd619f7d9d357554c2c04d1eaba30d9c2eab353f91230c0fc15 |
# -*- coding: utf-8 -*-
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
import warnings
from collections.abc import Iterable
from functools import wraps
import ctypes
import numpy as np
from scipy._lib.doccer import (extend_notes_in_docstring,
... | andyfaff/scipy | scipy/stats/_continuous_distns.py | Python | bsd-3-clause | 281,380 | [
"CRYSTAL",
"DIRAC",
"Gaussian"
] | 875c8a4212e8a331d2c256d97cd01fd42c2fa2765b04341a734d4390724e4987 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/Screen.py | Python | gpl-3.0 | 19,899 | [
"ORCA"
] | c1717db4971b1053d376aff3625800ea568f4a723ff327647f76573bb412c677 |
from asap3 import *
from ase.lattice.cubic import FaceCenteredCubic
pbc = False
atoms = FaceCenteredCubic(symbol='Cu', size=(10,10,10), pbc=pbc)
atoms.set_calculator(EMT())
paramfile = open("configuration.txt", "w")
print >>paramfile, int(pbc)
print >>paramfile, len(atoms)
z = atoms.get_atomic_numbers()
r = atoms.get... | auag92/n2dm | Asap-3.8.4/OpenKIMexport/test/makeinput.py | Python | mit | 482 | [
"ASE"
] | 6937acf0937df2ea3c4e051495cd60f601e33e90632bdd677a78fcfa20ac0fa5 |
# This file is part of Indico.
# Copyright (C) 2002 - 2022 CERN
#
# Indico is free software; you can redistribute it and/or
# modify it under the terms of the MIT License; see the
# LICENSE file for more details.
"""Extension to python-markdown to support LaTeX (rather than html) output.
Authored by Rufus Pollock: <h... | indico/indico | indico/util/mdx_latex.py | Python | mit | 19,890 | [
"Bowtie"
] | 4b6194ef809428a867a9092edd3ea659f9ffe263eaad812b594e3d0aae729182 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
@package Contavect
@brief **Main Class of Contavect program**. Contains The Main class and top level instructions
@copyright [GNU General Public License v2](http://www.gnu.org/licenses/gpl-2.0.html)
@author Adrien Leger - 2014
* <adrien.leger@gmail.com>
* ... | a-slide/ContaVect | ContaVect.py | Python | gpl-2.0 | 23,151 | [
"BLAST",
"BWA",
"pysam"
] | d5855a45a8d5e6f76bee430669031f255c8b997841985a651050ba47d32352a9 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/scripttemplates/Template_Tools.py | Python | gpl-3.0 | 2,165 | [
"ORCA"
] | 47c15d9ac9cd64aeef3dc036c3a83ded5899ce637e3e8b7c5287f0de536ccc68 |
from func import *
# ATTTENTION! Maybe there are some mistakes in neuron parameters!
logger = logging.getLogger('neuromodulation')
startbuild = datetime.datetime.now()
nest.ResetKernel()
nest.SetKernelStatus({'overwrite_files': True,
'local_num_threads': 8,
'resolution': 0... | research-team/NEUCOGAR | NEST/appraisal/scripts/neuromodulation.py | Python | gpl-2.0 | 24,062 | [
"NEURON"
] | aa7c6d8228d516d72198f10b203bcf1bb2de02553c93fb1da02765f77e832333 |
##############################################################################
# MSIBI: A package for optimizing coarse-grained force fields using multistate
# iterative Boltzmann inversion.
# Copyright (c) 2017 Vanderbilt University and the Authors
#
# Authors: Christoph Klein, Timothy C. Moore
#
# Permission is her... | mosdef-hub/msibi | msibi/utils/general.py | Python | mit | 3,629 | [
"MDTraj"
] | 6708fe37dca549133a661a16cd1f46c6c6db2d7ec3a250bc2a9424bd51222f12 |
#Brian Refsdal's parallel_map, from astropython.org
#Not sure what license this is released under, but until I know better:
#
#Copyright (c) 2010, Brian Refsdal
#All rights reserved.
#
#Redistribution and use in source and binary forms, with or without
#modification, are permitted provided that the following conditions... | jobovy/galpy | galpy/util/multi.py | Python | bsd-3-clause | 6,614 | [
"Brian"
] | 3ca2b89abaf6f50798b57f968fad082e6a3ca11d1f45bbd95e18b0390e34f44e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides classes for analyzing phase diagrams.
"""
from six.moves import zip
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, T... | aykol/pymatgen | pymatgen/phasediagram/analyzer.py | Python | mit | 19,145 | [
"pymatgen"
] | 6c244f9345575494969f5ebd9213983e44f02ef285a208f9d8a96e938d6213d6 |
import datetime
import difflib
from flask import redirect, render_template, render_template_string, Blueprint, flash
from flask import request, url_for, jsonify
from flask_user import current_user, login_required, roles_accepted
from flask_login.mixins import AnonymousUserMixin
from flask_mail import Mail, Message
fro... | piyushhari/nash | app/views.py | Python | bsd-2-clause | 14,015 | [
"VisIt"
] | fa1fcd5ba24bc752aab86fc19cad52cf7923791519f648dae44669b0ae95698d |
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