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# -*- coding: utf-8 -*-
#
# MySLLIS Core documentation build configuration file, created by
# sphinx-quickstart on Tue Aug 19 15:31:03 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
... | koebbe/django-core | docs/conf.py | Python | gpl-2.0 | 8,664 | [
"Brian"
] | cf48e0b16fafa1766fc0650f853beea067dd4536f3a0c61b56c41318a941b918 |
from __future__ import absolute_import
import os
import sys
import llvmbuild.componentinfo as componentinfo
import llvmbuild.configutil as configutil
from llvmbuild.util import *
###
def cmake_quote_string(value):
"""
cmake_quote_string(value) -> str
Return a quoted form of the given value that is suit... | lodyagin/bare_cxx | tests/utils/llvm-build/llvmbuild/main.py | Python | bsd-3-clause | 36,346 | [
"VisIt"
] | 537ea969f5c0541ddc8a9f913bbf71275434a1b276800cf98444900a78c9655e |
#!/usr/bin/env python
import theano
import theano.tensor as T
import numpy
import numpy as np
import pickle as pkl
from collections import OrderedDict
import cPickle as pickle
from theano import config
from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams
floatX = config.floatX
def shared_to_cpu(sha... | codedecde/ImageQA | Src/TheanoModel/Code/mlstm_theano.py | Python | mit | 19,880 | [
"Gaussian"
] | b0e4857bd57a1731a385fe0b761684fb319daec03a7bbb566c9c550ee3b0250e |
import json
import random
import typing
from pathlib import Path
from discord.ext import commands, vbu
import aiohttp
API_BASE_URL = 'https://secure.runescape.com/m=itemdb_oldschool/'
MEMBERS_MAPPING = {
'true': 'Yes',
'false': 'No',
}
class RunescapeCommands(vbu.Cog):
def __init__(self, bot):
... | 4Kaylum/SkyBot | cogs/runescape_commands.py | Python | gpl-3.0 | 4,116 | [
"BLAST"
] | 7cce350b4ad59ea659c4f3da91b00d5723fe0f9b38db1f1a6586992d82ba4545 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkHyperOctreeLimiter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkHyperOctreeLimiter.py | Python | bsd-3-clause | 491 | [
"VTK"
] | 3dcba2e96e5c401e4265c4f651754817d084abc991c68ada09865217b39b72ff |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Johann Rohwer (jrohwer@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permissi... | asttra/pysces | pysces/PyscesParScan.py | Python | bsd-3-clause | 12,745 | [
"PySCeS"
] | 10fae90784ac32f6c7333a3090bf6515fbc12d59acc75cb67bedc055dad087b1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This file is part of the web2py Web Framework
Copyrighted by Massimo Di Pierro <mdipierro@cs.depaul.edu>
License: LGPLv3 (http://www.gnu.org/licenses/lgpl.html)
The widget is called from web2py.
"""
import datetime
import sys
import cStringIO
import time
import threa... | montaggroup/montag-token-redeemer | web2py/gluon/widget.py | Python | gpl-3.0 | 44,651 | [
"VisIt"
] | 6bf103d946ccab9696d3fd5c7e74c20c709a3edd8551c866ec216ce9e5231649 |
from octopus.sequence.runtime import *
def fn ():
return sequence(
log("fn called")
)
run(sequence(
call(fn)
))
| richardingham/octopus | examples/test_call.py | Python | mit | 120 | [
"Octopus"
] | 367c6fdaec6963ea2fa1c5b9b102323bf9e1d6acf11b8aa54eb34b3e194aacc4 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Alexander Yang
#
# MDTraj is free software: you can redistribu... | dwhswenson/mdtraj | mdtraj/formats/gsd.py | Python | lgpl-2.1 | 11,154 | [
"MDTraj"
] | 5b8f97c625634b6c42258e9f7475caa7b30d0b083cd97c3bd5d0876c715b62dc |
# -*- coding: utf-8 -*-
from nose.tools import eq_
from ip2country import (
ipv4_to_bytes,
ipv6_to_bytes,
)
def test_ipv4_to_bytes():
eq_(ipv4_to_bytes('1.2.3.4'), b'\x01\x02\x03\x04')
def test_ipv6_to_bytes():
eq_(ipv6_to_bytes('::1'), b'\x00' * 14 + b'\x00\x01')
eq_(ipv6_to_bytes('1::'), b'\... | yosida95/ip2country | ip2country/tests/test_utils.py | Python | mit | 551 | [
"FEFF"
] | 5f2f70a363761ff4de7a875d60ab254e4f4dbc31c72834a10873b80c752efba0 |
from setuptools import setup
from simon import __version__
setup(
name='simon_mac',
version=__version__,
author='Ray Chen',
author_email='ray@half0wl.com',
packages=['simon'],
scripts=['bin/simon'],
url='http://pypi.python.org/pypi/simon_mac/',
license='MIT',
description='Simple m... | half0wl/simon | setup.py | Python | mit | 1,103 | [
"VisIt"
] | 6f6f3cee485c26e6324ef4ecb3e319972d7689088ee93ab8ec1848ab5286c9b9 |
from os import path
import shutil
from tempfile import mkdtemp
from GangaCore.GPIDev.Lib.File.FileBuffer import FileBuffer
from GangaCore.testlib.GangaUnitTest import GangaUnitTest
from GangaCore.testlib.mark import external
from GangaCore.testlib.monitoring import run_until_completed
from GangaCore.GPIDev.Base.Prox... | ganga-devs/ganga | ganga/GangaLHCb/test/GPI/TestExternalGaudiExec.py | Python | gpl-3.0 | 7,090 | [
"DIRAC"
] | 095c87bed09dc2abd193fd0213ce5112749e6315c4c058980d67c935046bdc91 |
"""
:mod: RssConfiguration
Module that collects utility functions.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id$'
from DIRAC import S_OK
from DIRAC.Core.Utilities import List
from DIRAC.ConfigurationSystem.Client.Helpers.Operations... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Utilities/RssConfiguration.py | Python | gpl-3.0 | 3,285 | [
"DIRAC"
] | be67c1adc10ed94b271e08bae9256b95565cdea01a42216da7514fed863079be |
#!/usr/bin/env python
"""
System administrator client.
Example:
$ dirac-admin-sysadmin-cli --host dirac.in2p3.fr
DIRAC Root Path = /afs/in2p3.fr/home/h/hamar/DIRAC-v5r12
dirac.in2p3.fr >
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = ... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_admin_sysadmin_cli.py | Python | gpl-3.0 | 898 | [
"DIRAC"
] | c9ad8e6686f841163b90191d536e8e0d794ceef339d410d5d980ece8e9a24bf3 |
from datetime import timedelta
from django.test import TestCase
from anagrafica.permessi.applicazioni import DELEGATO_CO
from anagrafica.permessi.costanti import GESTIONE_CENTRALE_OPERATIVA_SEDE
from attivita.models import Attivita
from django.utils import timezone
from autenticazione.utils_test import TestFunzionale... | CroceRossaItaliana/jorvik | centrale_operativa/tests.py | Python | gpl-3.0 | 6,527 | [
"VisIt"
] | e0aca38bacfd99e8fbcc8d69b6540ab40a7993ccc84edd0b3909bd501c9f88af |
################################################################################
# Copyright (C) 2013-2014 Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
import numpy as np
import warnings
import scipy
from bayespy.uti... | SalemAmeen/bayespy | bayespy/inference/vmp/transformations.py | Python | mit | 57,174 | [
"Gaussian"
] | e1423b1ae21932db775d65f483674bf986df272fc6503f96ca562ef779ebc2e3 |
import aug2cmds
import aug2cmds.outputs
from augeas import Augeas
import os.path
import shutil
import tempfile
import unittest
class FakeNode:
def setpath(self):
return "/files/foo[.='bar']"
def value(self):
return "bar"
def children(self):
return [FakeChild()]
class FakeChild:
... | domcleal/aug2cmds | unit_tests/test_OutputAugtool.py | Python | bsd-3-clause | 2,846 | [
"VisIt"
] | da6f67231ce847e110f6157228b222349c6ec2845e3e49a798c61eecf8b1061e |
'''
Unittests for spreg.error_sp_hom module
'''
import unittest
import pysal
#from pysal.spreg import error_sp_hom as HOM
import numpy as np
from pysal.contrib.handler import Model
from functools import partial
GM_Combo_Hom = partial(Model, mtype='GM_Combo_Hom')
GM_Error_Hom = partial(Model, mtype='GM_Error_Hom')
GM_... | schmidtc/pysal | pysal/contrib/handler/tests/test_error_spom.py | Python | bsd-3-clause | 17,886 | [
"COLUMBUS"
] | 85581a83468e7987adecf163e3591a98bd1116d7ace0506abefd70564038c6a4 |
# Script control setup area
# script info
__script__.title = 'Find Peak Angle'
__script__.version = '1.0'
# Use below example to create parameters.
# The type can be string, int, float, bool, file.
ui_min = Par('string', 'm2om')
ui_min.title = 'Motor'
ui_min = Par('float', 179.619)
ui_min.title = 'Min'
... | Gumtree/Kookaburra_scripts | Internal/KKB_FindPeakAngle.py | Python | epl-1.0 | 5,244 | [
"CRYSTAL"
] | 471ed121e6bd74aadc9a230fd8ae08bfb2b599731e9222a8c6394ab066ea00f7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Main simulation script for setting up the model producing the data shown in
figure 7 and 8 in:
Multimodal modeling of neural network activity: computing LFP, ECoG, EEG
and MEG signals with LFPy2.0
Espen Hagen, Solveig Næss, Torbjørn V Ness, Gaute T Einevoll... | LFPy/LFPy | examples/bioRxiv281717/figure_7_8/example_parallel_network.py | Python | gpl-3.0 | 28,390 | [
"NEURON"
] | 4269bc0fe96d2d6daa41468f9ec7ffe1eb3b9636732c05d32db698f894af5622 |
from pysimm import system, lmps, cassandra
from collections import OrderedDict
import os
import re
import random
import types
def mc_md(gas_sst, fixed_sst=None, mcmd_niter=None, sim_folder=None, mc_props=None, md_props=None, **kwargs):
"""pysimm.apps.mc_md
Performs the iterative hybrid Monte-Carlo/Molecular ... | polysimtools/pysimm | pysimm/apps/mc_md.py | Python | mit | 7,333 | [
"LAMMPS"
] | 3b0706884c2b046cf9b7bd4f765c9d49e1c23e0c3750ad9c04993e5101bc55a4 |
# TODO: check format of file? guess format maybe; use BioPython to parse variety of formats?
#: set: valid IUPAC nucleotide characters for checking FASTA format
VALID_NUCLEOTIDES = {'A', 'a',
'C', 'c',
'G', 'g',
'T', 't',
'R', 'r',
... | peterk87/sistr_cmd | sistr/src/parsers.py | Python | apache-2.0 | 3,758 | [
"Biopython"
] | ee869a364dfefd4d19534374bd9ef1a8df6ff15ddd63b53adc9c4593c46b8848 |
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# 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 PyBioMed source tree.
"""
#####... | gadsbyfly/PyBioMed | PyBioMed/PyMolecule/kappa.py | Python | bsd-3-clause | 8,037 | [
"RDKit"
] | c2427c3456fb998f79baaed064f89e5c59877ed870231b7226e9825d28228983 |
#!/usr/bin/env python
'''
Quantile regression model
Model parameters are estimated using iterated reweighted least squares. The
asymptotic covariance matrix estimated using kernel density estimation.
Author: Vincent Arel-Bundock
License: BSD-3
Created: 2013-03-19
The original IRLS function was written for Matlab by... | hlin117/statsmodels | statsmodels/regression/quantile_regression.py | Python | bsd-3-clause | 15,371 | [
"Gaussian"
] | fc8ae14941dea4eade7006a0db72659c923d966289f03428d64ba12792d20984 |
import os
import external.cclib as cclib
import logging
from subprocess import Popen
import re
from rmgpy.molecule import Molecule
from qmdata import CCLibData
from molecule import QMMolecule
class Gaussian:
"""
A base class for all QM calculations that use Gaussian.
Classes such as :class:`Gaussian... | comocheng/RMG-Py | rmgpy/qm/gaussian.py | Python | mit | 18,670 | [
"Gaussian",
"MOPAC",
"cclib"
] | 05c23210fbe51f7b8bbbb4556b3b1b7db8945cf2418737793937f269dfe150c8 |
import datetime
from django.contrib.auth.decorators import login_required
from django.contrib.auth.models import User
from django.db.models.aggregates import Sum
from django.db.models import Q
from django.shortcuts import get_object_or_404
from django.views.decorators.clickjacking import xframe_options_exempt
from dja... | haystack/eyebrowse-server | extension/views.py | Python | mit | 12,847 | [
"VisIt"
] | 73f334fa33f2e33d6c631af10e707c9369c7299f0d7c6b0c289ff8968eb1af7c |
#!/usr/bin/env python
# Author: Richard Bradshaw, R.T.Bradshaw@soton.ac.uk
# Script to create and calculate SAXS scattering intensities due to individual
# atom-atom scatters. Can then create a difference matrix of atom-atom
# contributions to intensity at a given Q-value, for given reference & test
# conformations.
... | rtb1c13/scripts | SAXS_MD/Debye_differences.py | Python | gpl-2.0 | 14,306 | [
"Amber",
"CHARMM",
"MDAnalysis",
"NetCDF",
"VMD"
] | 293d1ec2e121e5aa19aba1393978a0534cfe880b4ddce1ada88be2fcfdd48faf |
import sys
import os.path
#sys.path.insert(0, '/home/andy/theano/tool_examples/theano-lstm-0.0.15')
from theano_lstm import Embedding, LSTM, RNN, StackedCells, Layer, create_optimization_updates, masked_loss
from utilities import *
import dill
import argparse
#import cPickle
import pickle
import numpy
from collections... | darongliu/Lstm_Turing_LM | lstm-neural-turing-machines-lm/exp1/v1-second-half/lm_v4.py | Python | mit | 25,619 | [
"NEURON"
] | bceeec331b7499ba7d57b1cc90cde905b589d35569383c0ec0492a0dc4ceca7a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Abinit Post Process Application
authors: Martin Alexandre, Vincent Stutzmann
last edited: May 2014
"""
from numpy import array,reshape,ones
#Fortran Code
import fortran.positions as posit
#----------------------------------------------------------------#
#----------... | jmbeuken/abinit | scripts/post_processing/appa/utility/positions.py | Python | gpl-3.0 | 2,384 | [
"ABINIT"
] | b94e010ee939765e951d5e79f1b33298b301aa651fd382083fc563c9d4c52710 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the Account Settings page.
"""
from datetime import datetime
from unittest import skip
from bok_choy.web_app_test import WebAppTest
from bok_choy.page_object import XSS_INJECTION
from flaky import flaky
from nose.plugins.attrib import attr
from pytz import timezone, utc... | tanmaykm/edx-platform | common/test/acceptance/tests/lms/test_account_settings.py | Python | agpl-3.0 | 19,660 | [
"VisIt"
] | b9a76038966b0d9b5414359b4c68b1337c0acbe16cdf42c2dbae32ca86cb8678 |
"""Support for Google - Calendar Event Devices."""
from datetime import timedelta, datetime
import logging
import os
import yaml
import voluptuous as vol
from voluptuous.error import Error as VoluptuousError
import homeassistant.helpers.config_validation as cv
from homeassistant.helpers import discovery
from homeassi... | Cinntax/home-assistant | homeassistant/components/google/__init__.py | Python | apache-2.0 | 12,952 | [
"VisIt"
] | 4fa678a3f82aa251e3897bd8c87dcae2219a784c3badbc8ed33f19b9ba5da11b |
# Copyright (C) 2011-2012 CRS4.
#
# This file is part of Seal.
#
# Seal is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Seal is dis... | crs4/seal | tests/tseal/lib/aligner/test_bwa_aligner.py | Python | gpl-3.0 | 5,542 | [
"BWA"
] | 3e5481dc1b4e905663ba334d11ed4a1b5e9664dbd1efc25e24506174bdac697a |
#!/bin/env python
"""
Create and put 'ReplicateAndRegister' request.
"""
import os
from DIRAC.Core.Base.Script import Script
from DIRAC import gLogger
import DIRAC
def getLFNList(arg):
"""get list of LFNs"""
lfnList = []
if os.path.exists(arg):
lfnList = [line.split()[0] for line in open(arg).read... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_replicate_and_register_request.py | Python | gpl-3.0 | 4,549 | [
"DIRAC"
] | 1d53e6b32295628c091f1997dda3fd000b5d7095a0521564ee1a9bccc0620261 |
"""
gp.py - a Gaussian process regression. Marcus Frean.
usage: python gp.py datafile
Gaussian process regression. Reads a datafile consisting of a matrix
in which each row is a training item. The final column in the target
and preceding columns are the input.
Hyperparameters theta control a squared exponential co... | garibaldu/ego-demo | gp.py | Python | gpl-2.0 | 11,604 | [
"Gaussian"
] | a6f93e9d4f4039ad87662275ac4272208e40bdad28e00d4bcf09d9ca5b930590 |
"""
@name: PyHouse/src/Modules/Families/Insteon/_test/test_Insteon_decoder.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com>
@copyright: (c) 2014-2017 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 18, 2014
@Summary:
Passed all 8 tests - DBK - 2017-10-08
This _test needs ... | DBrianKimmel/PyHouse | Project/src/Modules/House/Family/Insteon/_test/test_insteon_decoder.py | Python | mit | 6,574 | [
"Brian"
] | 2b659fe8e2cd7d23741f4be08afb93ab88c69a2fdf5613afa33e8ba3c6472ad3 |
# -*- coding: utf-8 -*-
import re
from setuptools import setup, find_packages
from setuptools.command.sdist import sdist as _sdist
from setuptools.command.install import install as _install
VERSION_PY = """
# This file is originally generated from Git information by running 'setup.py
# version'. Distribution tarball... | fidelram/deepTools | setup.py | Python | gpl-3.0 | 2,913 | [
"pysam"
] | c7f03584e445cf1d004ad96d09b3be603a853c0388ea3f4438bb6dd3ca4272e3 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | SNoiraud/gramps | gramps/gen/filters/rules/family/_hassourcecount.py | Python | gpl-2.0 | 1,801 | [
"Brian"
] | 8f0ccba36a97d9f87f9fc4d0b49888871bde42a9f8c90b5c2f1e78e8307c6c94 |
########################################################################
# File: Operation.py
# Date: 2012/07/24 12:12:05
########################################################################
"""
:mod: Operation
.. module: Operation
:synopsis: Operation implementation
Operation implementation
"""
# Disable inva... | vmendez/DIRAC | RequestManagementSystem/Client/Operation.py | Python | gpl-3.0 | 10,219 | [
"DIRAC"
] | f04a312ffba7ff50fc990b765f5ad3d3ad4cbc639d44eb6887f8075cd5e1c382 |
########################################################################
#
# (C) 2015, Chris Houseknecht <chouse@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Fo... | thaim/ansible | lib/ansible/galaxy/login.py | Python | mit | 4,798 | [
"Galaxy"
] | a1ce25144cff1bfab8ff55f40ae4d8e8be4796f091f919b0dc8e054e061b5143 |
import traceback
from bzt.utils import iteritems
def dameraulevenshtein(seq1, seq2):
"""Calculate the Damerau-Levenshtein distance between sequences.
This distance is the number of additions, deletions, substitutions,
and transpositions needed to transform the first sequence into the
second. Althoug... | greyfenrir/taurus | bzt/linter.py | Python | apache-2.0 | 12,248 | [
"VisIt"
] | 4351c3dda0eb00467576165135e88dc62ab7548fd0b7c8e13e4747e1b5d1bceb |
"""
Copyright (C) 2017 Roberto Bruttomesso <roberto.bruttomesso@gmail.com>
This file is distributed under the terms of the 3-clause BSD License.
A copy of the license can be found in the root directory or at
https://opensource.org/licenses/BSD-3-Clause.
Author: Roberto Bruttomesso <roberto.bruttomesso@gmail.com>
Da... | formalmethods/intrepyd | intrepyd/lustre2py/visitor.py | Python | bsd-3-clause | 4,853 | [
"VisIt"
] | 6724bf354e91e66fff964919ec89a363de8517b73a0d91ee711597c7a783caca |
#!/usr/bin/env python
###############################################################################
#
# buildtableauxdb.py - build a database of protein tableaux
#
# File: buildtableauxdb.py
# Author: Alex Stivala
# Created: May 2008
#
# $Id: buildtableauxdb.py 4251 2011-07-26 07:45:28Z alexs $
#
################... | NirBenTalLab/proorigami-ptgraph | buildtableauxdb.py | Python | mit | 12,411 | [
"Biopython"
] | 034cb347d7045a875774813f23231974d367c418bdbe860dff9edee71f1be377 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2005, Pierre Legrand
#
# 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 option) any lat... | jsburg/xdsme | XOconv/XOconv.py | Python | bsd-3-clause | 40,015 | [
"CRYSTAL"
] | b28d2d15c96b0484bcd4bd2b1f309b3466c4ddd586b16638894ff24be3b0a330 |
#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division
__author__ = "Dan Knights"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Dan Knights", "Luke Ursell"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "Dan Knights"
__email__ = "daniel.knights@colora... | antgonza/qiime | scripts/supervised_learning.py | Python | gpl-2.0 | 11,481 | [
"VisIt"
] | d45b97c1bc259527f65957ddcc55e85e275c3351973ea6c00d0256ba0db85564 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2016, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Custom Axes
###################
"""
#
#import seaborn as sns
#
#from exa.mpl import _plot_contour, _plot_surface
#from exatomic import Energy
#
#
#def _get_minimum(mindf):
# a... | avmarchenko/exatomic | exatomic/mpl.py | Python | apache-2.0 | 23,126 | [
"Gaussian"
] | 6a725e68cbd384e1e132812733d96cdb35cc6f1dbf6fb2f33a12131fe0fa2973 |
#!/usr/bin/env python
"""
Script that synchronizes the resources described on the CS with the RSS.
By default, it sets their Status to `Unknown`, StatusType to `all` and
reason to `Synchronized`. However, it can copy over the status on the CS to
the RSS. Important: If the StatusType is not defined on the CS, it will se... | petricm/DIRAC | ResourceStatusSystem/scripts/dirac-rss-sync.py | Python | gpl-3.0 | 7,927 | [
"DIRAC"
] | 3cd454d67f1a78aef83a3c80d4327572f16362d314874395fad0049a23ddc351 |
import matplotlib
matplotlib.use('Agg', warn=False)
import unittest
import warnings
from nose.tools import assert_equal
import numpy as np
import iminuit
from iminuit import describe
from iminuit.iminuit_warnings import InitialParamWarning
from probfit.funcutil import rename
from probfit.pdf import gaussian, linear
fr... | piti118/probfit | probfit/test/testfit.py | Python | mit | 3,379 | [
"Gaussian"
] | b07ccf1f4447fa87f8400b04c212030f416a3b9495a6d4621d805943ad3854e8 |
"""
Tests the forum notification views.
"""
from __future__ import absolute_import
import json
import logging
from datetime import datetime
import ddt
import pytest
import six
from django.http import Http404
from django.test.client import Client, RequestFactory
from django.test.utils import override_settings
from dja... | ESOedX/edx-platform | lms/djangoapps/discussion/tests/test_views.py | Python | agpl-3.0 | 86,765 | [
"VisIt"
] | e86a2ca26034cbd5df3fa2bc15dcecf534cb4d2d5fd78ffe1ef749d8fea997e6 |
"""Collection of DIRAC useful file related modules.
.. warning::
By default on Error they return None.
"""
# pylint: skip-file
# getGlobbedFiles gives "RuntimeError: maximum recursion depth exceeded" in pylint
import os
import hashlib
import random
import glob
import sys
import re
import errno
__RCSID__ = "$Id$"... | arrabito/DIRAC | Core/Utilities/File.py | Python | gpl-3.0 | 7,925 | [
"DIRAC"
] | eb66aaa69854b889aaa6dc2c5c13cb0d34e7cf318610cf8a9ee7b149cef1628b |
# -*- coding: utf-8 -*-
# Copyright (C) 2008-2020 Samuele Carcagno <sam.carcagno@gmail.com>
# This file is part of pychoacoustics
# pychoacoustics 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, ... | sam81/pychoacoustics | pychoacoustics/response_box.py | Python | gpl-3.0 | 438,232 | [
"Gaussian"
] | c9b0cd73094ce2980352469b0352b46a93d8600b86e3c28dccd6f19cec7737aa |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Module for BondDissociationEnergies.
"""
import logging
from monty.json import MSONable
from pymatgen.core.structure import Molecule
from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError... | fraricci/pymatgen | pymatgen/analysis/bond_dissociation.py | Python | mit | 21,090 | [
"pymatgen"
] | 1abb54643471f23dd4707be365ef83b8f7ab517568968f7fa0a5cf286b3bd51e |
''' Create rst documentation of the examples directory.
This uses screenshots in the screenshots_dir
(currently doc/sources/images/examples) along with source code and files
in the examples/ directory to create rst files in the generation_dir
(doc/sources/examples) gallery.rst, index.rst, and gen__*.rst
'''
import ... | rnixx/kivy | kivy/tools/gallery.py | Python | mit | 12,277 | [
"exciting"
] | cc8f501f826516d1cc60224a1016e7f37c0fe49ceddbe93dc0bc40abf932219a |
import intprim.basis.gaussian_model
import intprim.basis.polynomial_model
import intprim.basis.sigmoidal_model
import matplotlib.pyplot as plt
import numpy as np
import scipy.linalg
import sklearn.metrics
class Selection:
def __init__(self, dof_names, scaling_groups = None):
self.demonstration_li... | ir-lab/intprim | intprim/basis/selection.py | Python | mit | 9,321 | [
"Gaussian"
] | 0076caecc48d7894f172d3a0594eae7fea54d17f0307474aed2ae60231fdf2e1 |
"""
PlatformIO Framework for Cosa
-----------------------------
This PlaformIO framework for Cosa is developed and maintained by Sinisha Djukic as part of the Meshwork project.
NOTE: This framework provides UNOFFICIAL support for Cosa and is not in any way associated with the Cosa project or its author Mikael Patel. I... | mikaelpatel/Cosa | build/PlatformIO/platform/cosa/builder/frameworks/cosa.py | Python | lgpl-2.1 | 5,137 | [
"VisIt"
] | e95d346d81d64d4def74367681276424884a7548dafb140ca0cee7b88466f032 |
#!/usr/bin/env python
from __future__ import print_function, division
import argparse
from collections import defaultdict
import datetime
import json
import psutil
import os
import shutil
import subprocess
import time
import networkx as nx
import sys
from conda_build.metadata import parse, MetaData
CONDA_BUILD_CACHE... | ContinuumIO/ProtoCI | protoci/build2.py | Python | bsd-3-clause | 14,365 | [
"pysam"
] | ac42f6d6229c35261e0d94b160ec0acdbd3164ca4f3faf497b8b3d101da2b695 |
# -*- coding: utf-8 -*-
"""
flaskbb.configs.default
~~~~~~~~~~~~~~~~~~~~~~~
This is the default configuration for FlaskBB that every site should have.
You can override these configuration variables in another class.
:copyright: (c) 2014 by the FlaskBB Team.
:license: BSD, see LICENSE ... | jerkos/kepavi | kepavi/configs/default.py | Python | mit | 3,728 | [
"VisIt"
] | 819e6f270fa86dbe6e4c840f7bdea5b990541dd54f844a2f1549a166bbd09f42 |
#!/usr/bin/env python
"ipyrad.analysis wrapper for parallel BUCKy concordance tree analyses"
from __future__ import print_function
from builtins import range
import os
import glob
import time
import numpy as np
import subprocess as sps
from collections import Counter
from ipyrad.analysis.utils import progressbar, P... | dereneaton/ipyrad | ipyrad/analysis/bucky.py | Python | gpl-3.0 | 22,171 | [
"Bioconda"
] | 882a32b0e703c490857481b32f4352796a8c3b03f1c8ac2ce73ec8715ff903e3 |
#pylint: disable=C0111
#pylint: disable=W0621
from lettuce import world, step
from lettuce.django import django_url
from django.conf import settings
import requests
import string
import random
import os
from django.contrib.auth.models import User
from student.models import CourseEnrollment
from nose.tools import asser... | XiaodunServerGroup/ddyedx | cms/djangoapps/contentstore/features/upload.py | Python | agpl-3.0 | 6,992 | [
"VisIt"
] | 6f9aa7490c1d45526c706bd1a5cbf085f22373bcddd135504bbb7e7b8bfe4e5e |
import functools
import inspect
class Plugin(object):
def __init__(self):
self.execution_count = 0
@functools.lru_cache()
def first_name(self):
self.execution_count += 1
return 'Brian'
def last_name(self):
return 'Messiah'
def main():
p = Plugin()
print(p.f... | noelevans/sandpit | introspection.py | Python | mit | 1,080 | [
"Brian"
] | 77a46c7e023d1e8887a5b64a3790306781d61ad34ea15be338e3f0bd0e0c3c03 |
# (c) 2013, Michael DeHaan <michael.dehaan@gmail.com>
# Stephen Fromm <sfromm@gmail.com>
# Brian Coca <briancoca+dev@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by... | bezhermoso/home | lib/ansible/runner/action_plugins/assemble.py | Python | gpl-3.0 | 4,340 | [
"Brian"
] | 7d5adfe55328a4f52258de31dd9d3ee059ed1290475daedc3785ae8ac4ce44f7 |
import os
from fontbakery.profiles.universal import UNIVERSAL_PROFILE_CHECKS
from fontbakery.status import INFO, WARN, ERROR, SKIP, PASS, FAIL
from fontbakery.section import Section
from fontbakery.callable import check, disable
from fontbakery.utils import filesize_formatting
from fontbakery.message import Message
fr... | moyogo/fontbakery | Lib/fontbakery/profiles/googlefonts.py | Python | apache-2.0 | 256,068 | [
"VisIt"
] | 636dbf98c5440567fd9ad317eb874f6c7c0ff793f7af3601ba3696da2a329589 |
import numpy as np
from .widget import RepresentationViewer, TrajectoryControls
from .utils import get_atom_color
from .marchingcubes import marching_cubes
from . import gg
from traitlets import Any
__all__ = ['MolecularViewer']
# Library-agnostic molecular viewer
class MolecularViewer(RepresentationViewer):
coo... | gabrielelanaro/chemview | chemview/viewer.py | Python | lgpl-2.1 | 19,807 | [
"PyMOL"
] | 7cadcd1dafe8218a1941aa4899dc160d66d54e1efeec7a85a51450e37f141b4f |
"""
A simple VTK widget for PyQt v4, the Qt v4 bindings for Python.
See http://www.trolltech.com for Qt documentation, and
http://www.riverbankcomputing.co.uk for PyQt.
This class is based on the vtkGenericRenderWindowInteractor and is
therefore fairly powerful. It should also play nicely with the
vtk3DWidget code.
... | cjh1/VTK | Wrapping/Python/vtk/qt4/QVTKRenderWindowInteractor.py | Python | bsd-3-clause | 13,525 | [
"CRYSTAL",
"VTK"
] | 5dc943f859821acabbecf2201867d874eb1e3130e3570b335acf9c31eb43aa37 |
# -*- coding: utf-8 -*-
# cec_rpi
"""
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... | thica/ORCA-Remote | src/interfaces/cec_rpi/interface.py | Python | gpl-3.0 | 5,552 | [
"ORCA"
] | d43b0ce4f1cb372921a244d87947dbce5bc6fe6f03d208c160e980081d13d2d0 |
# coding=utf-8
"""
Reproject :class:`xarray.DataArray` objects.
Makes assumptions on the data that it matches certain NetCDF-CF criteria
The CRS is stored as the 'spatial_ref' attribute of the 'crs' data variable
Spatial dimensions are either 'latitude' / 'longitude' or 'x' / 'y',
although this should probably instead... | ceos-seo/Data_Cube_v2 | agdc-v2/datacube/api/geo_xarray.py | Python | apache-2.0 | 9,842 | [
"NetCDF"
] | 259de11e097681b5ce3f1a9692b74aa5496073fe65fa105d0b7cc7b3326faef6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# (c) Copyright 2001-2009 Hewlett-Packard Development Company, L.P.
#
# 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 Lice... | matrumz/RPi_Custom_Files | Printing/hplip-3.15.2/ui4/setupdialog.py | Python | gpl-2.0 | 49,765 | [
"VisIt"
] | 9050f6097d0fadcb61a05202a7d6d1635288758dd9d270a2f24ad8d887d65081 |
# CC0 Public Domain: http://creativecommons.org/publicdomain/zero/1.0/
extension_dict = {
'.3g2' : 'video/3gpp2',
'.3gp2' : 'video/3gpp2',
'.3gpp' : 'video/3gpp',
'.3gp' : 'video/3gpp',
'.323' : 'text/h323',
'.NMW' : 'a... | tim-janik/tobin | Mime.py | Python | agpl-3.0 | 19,803 | [
"NetCDF"
] | 8ba5d033b662c7e8d97c7887330a4f1cacfe86c09a18787251e1ad56407a791b |
__author__ = "Andre Merzky, Ole Weidner"
__copyright__ = "Copyright 2012-2013, The SAGA Project"
__license__ = "MIT"
""" PBS job adaptor implementation
"""
import threading
import saga.url as surl
import saga.utils.pty_shell as sups
import saga.adaptors.base
import saga.adaptors.cpi.job
from saga... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/saga_python-0.18-py2.7.egg/saga/adaptors/pbs/pbsjob.py | Python | apache-2.0 | 42,869 | [
"Jaguar"
] | bcab783031e34b191cda454a5074979dc22f9f7af8e3c1483abcf79dc475b1e3 |
# -*- coding: utf-8 -*-
from distutils.core import setup
import py2exe
option = {
"compressed" : 1 ,
"optimize" : 2 ,
"bundle_files" : 2
}
setup(
options = {
"py2exe" : {"includes" : ["sip"]}
},
windows = [{
'script' : 'windowsGUI.py',
'icon_r... | taiki3/grablu_casino | setup.py | Python | mit | 548 | [
"CASINO"
] | 30ecfe4234cd8bbf27efd4935116992fefb810609ff03ede72c1bd3434a187dd |
import os
from collections import OrderedDict
from __main__ import vtk, qt, ctk, slicer
from CIP.logic.SlicerUtil import SlicerUtil
class MIPViewerWidget(object):
CONTEXT_UNKNOWN = 0
CONTEXT_VASCULATURE = 1
CONTEXT_EMPHYSEMA = 2
LAYOUT_DEFAULT = -1
LAYOUT_RED_ONLY = 6
LAYOUT_SIDE_BY_SIDE = 2... | acil-bwh/SlicerCIP | Scripted/CIP_/CIP/ui/MIPViewerWidget.py | Python | bsd-3-clause | 34,531 | [
"VTK"
] | 2607389b166e43e8cee5da36281c53ee73643e141c0bb13bc39cc9b33253c81d |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import functools
import glob
import itertools
import jinja2
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import time
import urllib2
import zlib
from xml.etree import ElementTree
from cStringIO import Stri... | jmesteve/saas3 | openerp/addons/web/controllers/main.py | Python | agpl-3.0 | 74,418 | [
"VisIt"
] | 184136c8159fa4cf5edfc514d10209b39288176a5e1793bb9bbb2593396265d1 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import subp... | harterj/moose | python/TestHarness/tests/test_Diff.py | Python | lgpl-2.1 | 1,228 | [
"MOOSE"
] | 9f1ed5d777a118de0c3282557cd7ef5d9ca61743376e6291cd53a9629099f582 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/magic/catalog/synchronizer.py | Python | mit | 19,581 | [
"Galaxy"
] | 7090302f74feb45ed8dd3c3403a72234ad393fa72008be8cfe274e934be170ff |
# dataset.py
"""Module for Dataset class
Overview of Dicom object model:
Dataset(derived class of Python's dict class)
contains DataElement instances (DataElement is a class with tag, VR, value)
the value can be a Sequence instance
(Sequence is derived from Python's list),
or just a regular valu... | njvack/yadda | dicom/dataset.py | Python | mit | 24,807 | [
"VisIt"
] | 5feaff30ce601d675bb2a088007cb22b8e8454fb8335c5642f5c10bc10c22ed2 |
"""
Class for outlier detection.
This class provides a framework for outlier detection. It consists in
several methods that can be added to a covariance estimator in order to
assess the outlying-ness of the observations of a data set.
Such a "outlier detector" object is proposed constructed from a robust
covariance es... | jmargeta/scikit-learn | sklearn/covariance/outlier_detection.py | Python | bsd-3-clause | 6,778 | [
"Gaussian"
] | 4b31e35c341f0c2502f1a1d16f297f9f56c806e55b0f2a5cceb334afdb3c8d8f |
import unittest
import numpy as np
from scipy import integrate,stats
import cpnest
import cpnest.model
import matplotlib as mpl
mpl.use('Agg')
from matplotlib import pyplot as plt
class GaussianModel(cpnest.model.Model):
"""
A simple gaussian model with parameters mean and sigma
"""
def __init__(self):... | johnveitch/cpnest | tests/test_1d.py | Python | mit | 2,363 | [
"Gaussian"
] | ac5e64cccb5c52fa64caf7aed843cde59a0f7a570a8eefa0e4efad5e4ef9fe24 |
#!/usr/bin/env python
"""cssutils - CSS Cascading Style Sheets library for Python
Copyright (C) 2004-2013 Christof Hoeke
cssutils 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 ver... | bslatkin/8-bits | tools/cssutils/src/cssutils/__init__.py | Python | apache-2.0 | 15,000 | [
"VisIt"
] | 0b0d587617beca3c3194240abb23c9bd492311b272a21b286e8b8cf75d24e369 |
'''
Module of learners used to determine what parameters to try next given previous cost evaluations.
Each learner is created and controlled by a controller.
'''
from __future__ import absolute_import, division, print_function
__metaclass__ = type
import threading
import numpy as np
import random
import numpy.random... | charmasaur/M-LOOP | mloop/learners.py | Python | mit | 74,602 | [
"Gaussian"
] | 849280bdf631daf4433f56ff3bbfdbc4cb2a7eb99fb7af94f8340f01b58b23b9 |
##
# Copyright (c) 2011-2015 Apple 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 l... | red-hood/calendarserver | contrib/performance/loadtest/test_profiles.py | Python | apache-2.0 | 38,153 | [
"Gaussian"
] | cde6c4d63e26dc05d979f633072cdf9ed77bc1c78eebfdd339473cd1e40151ad |
"""Mode Grueneisen parameter band structure calculation."""
# Copyright (C) 2012 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributi... | atztogo/phonopy | phonopy/gruneisen/band_structure.py | Python | bsd-3-clause | 11,303 | [
"phonopy"
] | 8e10b948bc13b6d9274bb2946fb5c073c4cc1371e5aa908e53fa1950ee2eb72c |
#!/usr/bin/env python
# encoding: utf-8
usage = '''
Takes alignments, corresponding to piRNAs, and counts how often each nucleotide occurs in the boundaries (5' and 3') of the sequence. By default the it counts nucleotide frequency at positions -20 to +20. It also outputs results for sense and antisense piRNAs to a p... | adomingues/NGSpipe2go | tools/piRNA/piRNABaseTerminalBases.py | Python | gpl-3.0 | 10,767 | [
"pysam"
] | 278394b821200f794d27d6b6aa59bab6b2a19e08fa223c91edf1744ab64d000e |
## This file is part of Invenio.
## Copyright (C) 2008, 2009, 2010, 2011, 2012, 2013 CERN.
##
## Invenio 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 option... | Panos512/invenio | modules/miscutil/lib/dbquery.py | Python | gpl-2.0 | 20,278 | [
"BLAST"
] | e1c5b1f42901dfc4d120b745e8f3656969abaf729c89bf856975a838799c9bf8 |
#!/usr/bin/env python
# Copyright 2008, 2009
# CAMd (see accompanying license files for details).
from optparse import OptionParser, SUPPRESS_HELP
import ase.gui.gtkexcepthook
#ase.gui.gtkexcepthook.feedback = "schiotz@fysik.dtu.dk"
#ase.gui.gtkexcepthook.smtphost = "mail.fysik.dtu.dk"
def build_parser():
parse... | slabanja/ase | ase/gui/ag.py | Python | gpl-2.0 | 4,815 | [
"ASE"
] | d7b05f1e8b3e87ad6b3b087dceba59ff7905fcb2dcb156e41527f79a76f1b96c |
#
# 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
#
# This program is free software; you can redistribute i... | Forage/Gramps | gramps/gen/plug/docgen/fontstyle.py | Python | gpl-2.0 | 5,371 | [
"Brian"
] | 3e4949832bbd6bfd26f733eb91ba045c676b65faa3adef269ece0e35ffc65cfc |
"""
Python implementation of the fast ICA algorithms.
Reference: Tables 8.3 and 8.4 page 196 in the book:
Independent Component Analysis, by Hyvarinen et al.
"""
# Authors: Pierre Lafaye de Micheaux, Stefan van der Walt, Gael Varoquaux,
# Bertrand Thirion, Alexandre Gramfort, Denis A. Engemann
# License: BS... | raghavrv/scikit-learn | sklearn/decomposition/fastica_.py | Python | bsd-3-clause | 19,076 | [
"Gaussian"
] | 956c0274b41a73555b4a9be71c3ca4e01d5673c78848e37c73fcc27098bc1455 |
from __future__ import unicode_literals
import re
import nose
from django.conf import settings
from django.contrib import messages
from django.contrib.auth.models import AnonymousUser, User
from django.core.exceptions import ValidationError
from django.http import HttpResponse, HttpResponseRedirect
from django.test.c... | brennie/reviewboard | reviewboard/accounts/tests.py | Python | mit | 34,411 | [
"VisIt"
] | 5a60bde62ec5aa63118bbf84df78c442220231d88206a92d38ae2ffa8c6dfaf0 |
# Copyright (c) 2012, Cloudscaling
# 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... | sebrandon1/nova | nova/hacking/checks.py | Python | apache-2.0 | 32,473 | [
"VisIt"
] | 8b425f1bdfd107ebec0093f551b2847ce05b8c61fa3d7ea676e56f5fc69c94b8 |
""" Contains the Driver parent class. """
# driver.py
# 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
import time
from mpf.system.devices impor... | jabdoa2/mpf | mpf/devices/driver.py | Python | mit | 7,922 | [
"Brian"
] | cb26ada043f8e14c5c8ca12a2c39f5f41f5b8afcf9c2bb8fa5139e493d9d0e92 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from TestHa... | nuclear-wizard/moose | python/TestHarness/tests/test_PythonVersion.py | Python | lgpl-2.1 | 700 | [
"MOOSE"
] | 8807a998f8ecb7be4382b854ad7be1136f77937232f2b9a6d38a245249f32b8b |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from __future__ import division
from __future__ import absolute_import
from __future__ import print_function
import os
import logging
import subprocess
import multiprocessing
import itertools
try:
from subprocess import DEVNULL # py3k
except Imp... | hadim/spindle_tracker | spindle_tracker/detector/peak_detector.py | Python | bsd-3-clause | 14,979 | [
"Gaussian"
] | f57f46451d4b5f0e4fbaedb34dea4100321966587a4981e28eb38925cc6f4051 |
from __future__ import print_function
import sys
import random
import os
from builtins import range
import time
import json
sys.path.insert(1, "../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.naive_bayes import H2ONaiveBayesEstimator
from h2o.grid.grid_search import H2OGridSearch
class Tes... | mathemage/h2o-3 | h2o-py/dynamic_tests/testdir_algos/naivebayes/pyunit_naivebayes_gridsearch_over_all_params_large.py | Python | apache-2.0 | 22,200 | [
"Gaussian"
] | 3c8fff2906606beddc2e2592c0f11b7935b32d91912cf6bd4bf19ee303ff6620 |
#!/usr/bin/env python
## category General
## desc Find and mark PCR duplicates
## experimental
'''
For a BAM file, find and mark all possible PCR duplicates. This is meant to be
used primarily with paired-end reads, since these have better resolution to
verify that we care seeing a legitimate PCR duplicate and not just... | ngsutils/ngsutils | ngsutils/bam/pcrdup.py | Python | bsd-3-clause | 5,632 | [
"pysam"
] | 4b00332e233a71544f37bccdb1a349fb23f34fbd1f180934ea02167c59d501de |
"""
Views related to the Custom Courses feature.
"""
import csv
import datetime
import functools
import json
import logging
import pytz
from copy import deepcopy
from cStringIO import StringIO
from django.conf import settings
from django.core.urlresolvers import reverse
from django.http import (
Http404,
Http... | Livit/Livit.Learn.EdX | lms/djangoapps/ccx/views.py | Python | agpl-3.0 | 22,896 | [
"VisIt"
] | a25290a2619c189c3006524364fc4c9a3cc71d21c560a290c91fff759b5782a2 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | andysim/psi4 | psi4/share/psi4/databases/A24.py | Python | gpl-2.0 | 29,724 | [
"Psi4"
] | 05d7c4ba0234bf3dfa0c5e90981f65ea17048c7a6b54b1d1bb86c8b0c4b3df98 |
#!/opt/local/bin/python2.5
#=============================================================================================
# Render a replica trajectory in PyMOL
#=============================================================================================
#=============================================================... | jchodera/yank | examples/abl-imatinib-explicit/render_trajectory.py | Python | lgpl-3.0 | 13,052 | [
"Amber",
"NetCDF",
"PyMOL"
] | e26a17cca6e9ebf4e68ab3d140bf8ad9ecb1a0f5aba4fb36f9c8497f2308ae82 |
"""
.. moduleauthor:: Gillian Basso <gillian.basso@hevs.ch>
.. codeauthor:: Gilbert Maitre <gilbert.maitre@hevs.ch>
"""
import csv
import numpy as np
from gridsim.decorators import accepts, returns
from gridsim.unit import units
from gridsim.timeseries import TimeSeries
from .core import AbstractElectricalCPSElement... | gridsim/gridsim | gridsim/electrical/element.py | Python | gpl-3.0 | 21,696 | [
"Gaussian"
] | c30bcf27b6809108cf9c76a7d63a3c8589d0c48ce3403dddb4904b32c790f43d |
#!/usr/bin/env python3
from pysam import AlignmentFile
import sys, os, gzip, re, math
# The regular expression pattern for "chrXX 1234567" in both VarScan2 Output and VCF files:
pattern_major_chr_position = re.compile(r'^(?:chr)?(?:[1-9]|1[0-9]|2[0-2]|[XY]|MT?)\t[0-9]+\b')
# More lenient pattern:
pattern_chr_positio... | bioinform/somaticseq | somaticseq/genomicFileHandler/genomic_file_handlers.py | Python | bsd-2-clause | 19,338 | [
"pysam"
] | 11ee29166e7e610fe0bda06e9155dffd335a635ec9c627026f196dc78eea7f4e |
#!/usr/bin/env python
# Copyright 2014-2021 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/fci/spin_op.py | Python | apache-2.0 | 11,438 | [
"PySCF"
] | a70e3d51040e1249c20923a0be528e1c65e79c6b97ab797ea85e3d6b6495cdf8 |
import locale
from locale import atof, atoi
import datetime
from lxml import html
import json
from jsoncomment import JsonComment
import requests
year = 2017
file_name = 'PASO_2017_ultimo_provisorio'
def main():
locale.setlocale(locale.LC_NUMERIC, 'es_AR.utf8') # used to convert string to int or float correctly... | marcoshipe/AnalizandoLasElecciones | ObtenerDatos.py | Python | apache-2.0 | 7,233 | [
"VisIt"
] | c52ea48eaa6e105c9d8e11f6e2d31ee8f12940cdc675774208d73fbb6d9c0c66 |
# Copyright 2007-2011 The Hyperspy developers
#
# This file is part of Hyperspy.
#
# Hyperspy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ... | CodeMonkeyJan/hyperspy | hyperspy/tests/model/test_fancy_indexing.py | Python | gpl-3.0 | 5,704 | [
"Gaussian"
] | 0bdfa223f9664f7020db0a4aa354bb033a489665ec842c9308f03fcb7fbb16d9 |
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