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''' CacheFeederAgent
This agent feeds the Cache tables with the outputs of the cache commands.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN CacheFeederAgent
:end-before: ##END
:dedent: 2
:caption: CacheFeederAgent options
'''
__RCSID__ = '$Id$'
from DIRAC import S_OK
from DIRAC.Core.Bas... | petricm/DIRAC | ResourceStatusSystem/Agent/CacheFeederAgent.py | Python | gpl-3.0 | 6,425 | [
"DIRAC"
] | ba00d2814ee72009da4ee62625e8f1fba6e68667041aca102460b5010c7b7e48 |
'''
Check the speed of different Brian 2 configurations (with additional models for brian2cuda)
'''
import brian2
from brian2 import *
from brian2.tests.features import SpeedTest
from brian2.tests.features.speed import *
from brian2cuda.tests.features.cuda_configuration import insert_benchmark_point
from brian2.tests... | brian-team/brian2cuda | brian2cuda/tests/features/speed.py | Python | gpl-2.0 | 30,610 | [
"Brian",
"NEURON"
] | 35dd339f9aa266a2907f18cf9c65011aabfa831aa047f24bed46abb106b866b9 |
1 #!/usr/bin/env python
2 """Module cma implements the CMA-ES (Covariance Matrix Adaptation Evolution Strategy).
3
4 CMA-ES is a stochastic optimizer for robust non-linear non-convex
5 derivative- and function-value-free numerical optimization.
6
7 This implementation can be us... | raphaelvalentin/qtlayout | syntax/optimize/cma/cma-1.0.07/cma-1.0.07.py | Python | gpl-2.0 | 391,778 | [
"exciting"
] | 7ff36957f19e7b40a1c5c1a95e5c15b1a0a9e723e9b6a9ab1e00283acb03bb53 |
#!/usr/bin/env python
""" refresh CS
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from DIRAC.Core.Base import Script
Script.parseCommandLine()
from DIRAC.ConfigurationSystem.private.Refresher import gRefresher
res = gRefresher.forceRefresh()
if not r... | yujikato/DIRAC | tests/Jenkins/dirac-refresh-cs.py | Python | gpl-3.0 | 354 | [
"DIRAC"
] | 18244feceff47eebc63e27ce9bf3709c7142e1b3c6b102e0757e678f2877b35c |
__author__ = 'williewonka'
import json
from splinter import Browser
import argparse
import sys
import openpyxl
parser = argparse.ArgumentParser(description='queries a give list of patents from json object')
parser.add_argument('--janus', dest='janus', action='store_true', help='activates logging in from janus')
parse... | williewonka/USE-patents-project | querymaker.py | Python | gpl-2.0 | 5,222 | [
"VisIt"
] | e5613858d22fd9b22c8317f1ae98f5f1394711b11aa998dab4ce9f7448a1162b |
# -*- coding: utf-8 -*-
try:
# Python 2.7
from collections import OrderedDict
except:
# Python 2.6
from gluon.contrib.simplejson.ordered_dict import OrderedDict
from gluon import current
from gluon.html import *
from gluon.storage import Storage
from gluon.validators import IS_NOT_EMPTY
from s3.s3fie... | gnarula/eden_deployment | private/templates/Philippines/config.py | Python | mit | 128,063 | [
"Amber"
] | 62f65749e38298b41b0e9361ae3b8f1eebe384588da89aa8d3b9f4287bdb0b90 |
import os, sys
import argparse
import types
import glob
import numpy as np
import pickle
import tensorflow as tf
import data
import model
from util import *
from learning import LearnerCls, LearnerDACls, LearnerClsSelf, LearnerConfPred
from learning import TempScalingCls as CalibratorCls
##TODO: clean-up tf options... | googleinterns/intern2020_cocal | uncertainty/plots/compute_stats.py | Python | apache-2.0 | 23,245 | [
"Gaussian"
] | 0c2975d78e027b523d7a52c031c2c6b8a514b993741f9ab4ad92362357c52223 |
#!/usr/bin/env python
from __future__ import print_function
import argparse
import glob
import sys
import numpy as np
import pysam
import time
import os
from contextlib import closing
TAG_HAPLOTYPE = "ht"
TAG_CHUNK_ID = "mp"
PB_HAP1_READS = "pb_hap1"
PB_HAP2_READS = "pb_hap2"
PB_LENGTH = "pb_len"
PB_BLOCK_ID = "pb_b... | benedictpaten/marginPhase | toil/src/toil_marginphase/scripts/merge_chunks.py | Python | mit | 23,945 | [
"pysam"
] | a46af808076a34d4d0562b1456bfb538334b590eb27aadcc423f59033a548fdd |
# -*- coding: utf-8 -*-
# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry
# and reaction kinetics.
# Copyright (C) 2008-2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, An Ghysels
# <An.Ghysels@UGent.be> and Matthias Vandichel <Matthias.Vandichel@UGent.be>
# Center for Molecular Modeling... | molmod/tamkin | tamkin/io/cp2k.py | Python | gpl-3.0 | 8,743 | [
"CP2K"
] | 70e5c2b9b77c83b76c5de5a3d10e16666f36af9ec1d0b5ceb62b7fce499790ce |
"""
Django module container for classes and operations related to the "Course Module" content type
"""
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime... | nagyistoce/edx-platform | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 62,216 | [
"VisIt"
] | 0efb137ef016c17ffdbe04ff018a905b2b01119cbf29a3402a799cbbf300633e |
"""
@file outputs.py
@author Yun-Pang Wang
@author Daniel Krajzewicz
@author Michael Behrisch
@date 2007-12-25
@version $Id: outputs.py 12595 2012-08-24 14:07:33Z dkrajzew $
This script is for generating the outputs from the choosed traffic assignment.
SUMO, Simulation of Urban MObility; see http://sumo.sour... | rudhir-upretee/Sumo_With_Netsim | tools/assign/outputs.py | Python | gpl-3.0 | 6,838 | [
"MOE"
] | 083e0099ae1da68e706a99d0ed0b3b59285d4fb7eb57b8bfe4afa4d8b4613cf8 |
import os
import distutils.spawn
import external.cclib as cclib
import itertools
import logging
from subprocess import Popen
import re
from rmgpy.molecule import Molecule
from qmdata import parseCCLibData
from molecule import QMMolecule
class Gaussian:
"""
A base class for all QM calculations that use Gaussi... | pierrelb/RMG-Py | rmgpy/qm/gaussian.py | Python | mit | 19,822 | [
"Gaussian",
"MOPAC",
"cclib"
] | 84b98cd79b46f33a84e451dfe99dd90a32372d79d0328b1c8bafd88629d39502 |
from sympy import *
from sympy.parsing.sympy_parser import parse_expr, standard_transformations, convert_xor, auto_number
from sympy.printing.latex import LatexPrinter
import re
import ANNarchy.core.Global as Global
from ANNarchy.core.Random import RandomDistribution
from ..Extraction import *
from ANNarchy.parser.Ana... | vitay/ANNarchy | ANNarchy/parser/report/LatexParser.py | Python | gpl-2.0 | 16,861 | [
"NEURON"
] | e7d4d2b1c47cf7e71b2907c6e969d3516611d5fb954835a7b5390f10739cca1f |
#!/usr/bin/python
#
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required b... | wubr2000/googleads-python-lib | examples/adwords/v201506/campaign_management/validate_text_ad.py | Python | apache-2.0 | 2,766 | [
"VisIt"
] | bd1eea17d886f6aecc4d11071fa0e0845db9589da1260ab64f90322819a65ec7 |
# Default Django settings. Override these with settings in the module
# pointed-to by the DJANGO_SETTINGS_MODULE environment variable.
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
gettext_noop = lambda s: s
#################... | disqus/django-old | django/conf/global_settings.py | Python | bsd-3-clause | 21,172 | [
"VisIt"
] | b697fe703f417262438515faedfe6cfc7f1e54ea1ecd8b10aff48e7f4557ec7e |
#!/usr/bin/env python
try:
from magpy.stream import *
from magpy.absolutes import *
from magpy.transfer import *
from magpy.database import *
except:
from magpy.stream import *
from magpy.absolutes import *
from magpy.transfer import *
from magpy.database import *
import wx
from matpl... | hschovanec-usgs/magpy | magpy/gui/analysispage.py | Python | gpl-3.0 | 5,932 | [
"Gaussian"
] | 9d7b7c90a252418fe532f28fa9822dc62a8f3ee57c084377bad7433c8bfe3d53 |
# common.py - shared symbols and globals
import os, errno
# exception class so you know where exception came from
class FsDriftException(Exception):
pass
def myassert(bool_expr):
if (not bool_expr):
raise FsDriftException('assertion failed!')
NOTOK = 1
OK = 0
BYTES_PER_KiB = 1 << 10
BYTES_PER_MiB =... | parallel-fs-utils/fs-drift | common.py | Python | apache-2.0 | 2,976 | [
"Gaussian"
] | 111324dec7cb8b1c8fa8de38ab145d87b5d60967f963109de81797ab8f4f47c1 |
# This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed... | marcioweck/PSSLib | reference/deap/examples/es/onefifth.py | Python | lgpl-3.0 | 2,795 | [
"Gaussian"
] | a9fab1d811c0780d85aafdc7b1dc25515b83ff881aaa1197292af3e1adfe9415 |
"""MNIST AutoEncoder Test"""
import numpy as np;
import matplotlib.pyplot as plt;
import theano;
import theano.tensor as T;
import telaugesa.datasets as ds;
from telaugesa.fflayers import ReLULayer;
from telaugesa.fflayers import SigmoidLayer;
from telaugesa.model import AutoEncoder;
from telaugesa.optimize import g... | duguyue100/telaugesa | scripts/mnist_ae_test.py | Python | mit | 2,845 | [
"Gaussian"
] | 904bfd55b94387d545b93b08d0f9146b2658b8444a1e817e6e5e8d60570a3123 |
import numpy as np
from parabem.airfoil.conformal_mapping import VanDeVoorenAirfoil
from parabem.vtk_export import VtkWriter
from parabem.utils import check_path
####################################################
# analytic solution of vandevooren-airfoils #
################################################... | booya-at/paraBEM | examples/vtk/vtk_airfoil_vandevooren.py | Python | gpl-3.0 | 2,780 | [
"VTK"
] | b7c046e3527d7f73daa6ef81fd996839e3fb700c07c340999c588cce356af3ec |
from __future__ import division, print_function, absolute_import
import unittest
import GPy
import numpy as np
import networkx as nx
from numpy.testing import *
from .utilities import *
from safemdp.SafeMDP_class import reachable_set, returnable_set
from safemdp.grid_world import compute_true_safe_set, grid_world_gr... | befelix/SafeMDP | safemdp/test.py | Python | mit | 10,232 | [
"Gaussian"
] | b45b3288991e28cffcbb781ddeccac52fae219eb289b170602cfa734e6f692c0 |
# to do
# handle files that don't exist in all 3 directories
import os
import subprocess
import shutil
import hashlib
import log
from uvsconst import UVSConst
# TODO: return results from this service
# shouldnt have trouble found flag set. hard conflict found is ok, refactor trouble found to raise error
# this ... | kouritron/uvs | libuvs/automergeservice.py | Python | bsd-3-clause | 25,097 | [
"VisIt"
] | 0a6489b6a7848feb92bc91459316a951592b612f6846141f58b2b6200cdd6cd9 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/lammps/package.py | Python | lgpl-2.1 | 4,781 | [
"LAMMPS",
"NetCDF"
] | e26feeb047348541fd2fe5efa235c7a32227c30879ee4eee2a64275d644168d9 |
# Orca
#
# Copyright 2010 Joanmarie Diggs.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library i... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/epiphany/script.py | Python | gpl-3.0 | 2,923 | [
"ORCA"
] | 42be9e41b9f631e9928ece1157f98c13b9fa34c7b0a412a4ac72aa3f05bb88c8 |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# Redistribution and use in ... | hainm/scikit-xray | skxray/core/spectroscopy.py | Python | bsd-3-clause | 13,125 | [
"Gaussian"
] | 10e378c08bd02e0f01acf15bd334049c433aeb8fb3cc7e94bda0c29ca5437be7 |
#! encoding: utf-8
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# Redistr... | tacaswell/scikit-beam | skbeam/core/roi.py | Python | bsd-3-clause | 26,488 | [
"Gaussian"
] | 4bc1c8f223a430db1c28772256f869ebb2ee1cfbff275ad02132cf881a3b9038 |
#!/usr/bin/env python
#! -*- coding: utf-8 -*-
from __future__ import print_function
import unittest
import sys, os.path
pkg_dir = os.path.dirname(os.path.realpath(__file__)) + '/../'
sys.path.append(pkg_dir)
from CRPGaussianSamplers import *
class TestCRPGaussianCollapsedGibbs(unittest.TestCase):
def se... | AusterweilLab/MPBNP | unittests/CRPGaussianCollapsedGibbsTest.py | Python | mit | 1,859 | [
"Gaussian"
] | 76d9c047b1f70d7eb6e1b750807f5d0afc25921c1e0b7b034857dafb1c06f882 |
"""
Add a state column to the history_dataset_association and library_dataset_dataset_association table.
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from sqlalchemy.exc import *
from migrate import *
from migrate.changeset import *
from galaxy.model.custom_types import *
import datetime
now = datetime.d... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py | Python | gpl-3.0 | 2,434 | [
"Galaxy"
] | fa954332e4c6d60d50ce6c93b8eedf2fee3e313e67634652a6ddf468dc70a47f |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2015 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | dilawar/moose-full | moose-examples/snippets/insertSpinesWithoutRdesigneur.py | Python | gpl-2.0 | 3,531 | [
"MOOSE",
"NEURON"
] | 68f7fea979614c1e900ab3feaa0bf3d37391601da43d2a9dd07d5b0244fa4ef3 |
#!/usr/bin/python
import click
import os
from sidr import default
from sidr import runfile
CONTEXT_SETTINGS = dict(help_option_names=['-h', '--help'])
def validate_taxdump(value, method):
if (os.path.isfile("%s/%s" % (value, "names.dmp")) and
os.path.isfile("%s/%s" % (value, "nodes.dmp")) and
os... | damurdock/SIDR | sidr/cli.py | Python | mit | 6,054 | [
"BLAST"
] | dd62026aba57be1899a6aa67df1957ee31bc4ac95c46a9fdb506c9da7d13a2d5 |
import ocl
import pyocl
import camvtk
import time
import datetime
import vtk
def main(filename="frame/f.png"):
print ocl.revision()
myscreen = camvtk.VTKScreen()
myscreen.camera.SetPosition(20, 12, 20)
myscreen.camera.SetFocalPoint(0,0, 0)
# axis arrows
camvtk.drawArrows(my... | davidwusea/opencamlib | scripts/ocode/cutsim_test_1.py | Python | gpl-3.0 | 2,975 | [
"VTK"
] | a47f752340b04ec32292b307b0637dc0c39366ed405a87f46f372c90565f721c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Unit tests for StructureNL (SNL) format
"""
__author__ = "Anubhav Jain"
__credits__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Pro... | aykol/pymatgen | pymatgen/matproj/tests/test_snl.py | Python | mit | 9,898 | [
"pymatgen"
] | 421294271be39fd42acec747605fb662f6c5895e806338b88326938f07507513 |
"""
Main class of the phone loop model.
Copyright (C) 2017, Lucas Ondel
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, ... | amdtkdev/amdtk | amdtk/models/phone_loop.py | Python | mit | 19,108 | [
"Gaussian"
] | e8a557d7fb5b4e59d7f08c5fe0dc90ee1e185dd292c38b38104f96612d8787ff |
"""
"""
from wheezy.http import WSGIApplication
from wheezy.http.middleware import http_cache_middleware_factory
from wheezy.web.middleware import bootstrap_defaults
from wheezy.web.middleware import http_error_middleware_factory
from wheezy.web.middleware import path_routing_middleware_factory
from config import opt... | lajto/ww-i18n | src/app.py | Python | gpl-3.0 | 928 | [
"VisIt"
] | 17dc0c9f35605175aeb9adfee713448348f5b7e8008491cfbc75316e31ff5564 |
#!/usr/bin/python
"""Test of line navigation."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
# Work around some new quirk in Gecko that causes this test to fail if
# run via the test harness rather than manually.
sequence.append(KeyComboAction("<Control>r"))
sequence.append(PauseAction(... | pvagner/orca | test/keystrokes/firefox/line_nav_wiki_down.py | Python | lgpl-2.1 | 41,454 | [
"ORCA"
] | 5a97e78cf3fe43e68438fbc50ebceb5f1c026d95c3a0db5849101828d8272329 |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/fciqmcscf/fciqmc.py | Python | apache-2.0 | 39,629 | [
"PySCF"
] | 7506175a321c98a863533baa16f5f569faf20888b92f70344fd8a08591986b10 |
from tapiriik.settings import WEB_ROOT, HTTP_SOURCE_ADDR, GARMIN_CONNECT_USER_WATCH_ACCOUNTS
from tapiriik.services.service_base import ServiceAuthenticationType, ServiceBase
from tapiriik.services.service_record import ServiceRecord
from tapiriik.services.interchange import UploadedActivity, ActivityType, ActivityS... | cpfair/tapiriik | tapiriik/services/GarminConnect/garminconnect.py | Python | apache-2.0 | 41,473 | [
"VisIt"
] | 129e1bf96f6f8180f1b5b31a16f79683dfe91895a0e23270cb64869e73159b0e |
"""
.. module:: CosmicX
:synopsis: Remove cosmic rays from an astronomical image.
kludged from PyCosmic to run _lacosmicx instead, which is faster
"""
import time
import argparse
import numpy as np
import astropy.io.fits as pf
try:
import _lacosmicx
except ImportError:
print("Please install lacosmicx from ... | scizen9/kpy | SEDMr/CosmicX.py | Python | gpl-2.0 | 5,410 | [
"Gaussian"
] | 0d9d6b01368f73614e680725842bf017451676c161a4dfe5b074c2d86f159bd0 |
'''
synbiochem (c) University of Manchester 2015
synbiochem is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
import re
__ELEMENTAL_MASSES = {
'H': 1.007825032,
'He': 3.01602932,
'Li': 6.015122887,
'Be': 9.012... | synbiochem/synbiochem-py | synbiochem/utils/chem_utils.py | Python | mit | 4,634 | [
"VisIt"
] | 9412657898363c93af9ad61d88a2eaf48c2c2f8ab7a529fecb84bbcd1cd50acd |
# -*- coding: utf-8 -*-
'''
CuBIC is a statistical method for the detection of higher order of
correlations in parallel spike trains based on the analysis of the
cumulants of the population count.
Given a list sts of SpikeTrains, the analysis comprises the following
steps:
1) compute the population histogram (PSTH) wi... | pietroquaglio/elephant | elephant/cubic.py | Python | bsd-3-clause | 6,870 | [
"Gaussian"
] | e51618bfdb517f90c537195a4ba07c0f1200a73d26fe85209bb13cc8435a7c4c |
# -*- coding: utf-8 -*-
"""
=================================================
==================== Common Configuration
================================================= """
# Which will be the default atlas?
# Options: Swanson, PaxinosWatson
ATLAS = "Swanson"
# Should multithreading be used when matching?
# If True, ... | DeveloperJose/Vision-Rat-Brain | feature_matching_v2/config.py | Python | mit | 4,836 | [
"Gaussian"
] | 4ffac9bc2044d19fdbea092d1a0f48f1dbd9a8a89f48514539a65bf6d98f5164 |
# -*- coding: utf-8 -*-
"""Functions for inducing random sub-graphs."""
import bisect
import logging
import random
from operator import itemgetter
from typing import Any, Iterable, Mapping, Optional, Set, Tuple
from ..utils import remove_isolated_nodes
from ...graph import BELGraph
from ...pipeline import transforma... | pybel/pybel | src/pybel/struct/mutation/induction/random_subgraph.py | Python | mit | 7,301 | [
"Pybel"
] | 852b7de4400d985e4efb49decc25ad7e6eeb95e4d95cf6f7a40c618c46beb5ae |
import unittest
import sam.sam_handler
import os
import subprocess
import Utility
import shutil
import tempfile
import sam_test_case
import config.settings as settings
settings.setup_logging()
# Simulation Configs
SIM_DIR = os.path.dirname(os.path.realpath(__file__)) + os.sep + "simulations"
SIM_DATA_FILENAME_PREFIX ... | cfe-lab/Umberjack | test/Test_sam_handler.py | Python | bsd-2-clause | 22,038 | [
"BWA"
] | 3d1d7a2db81bddaf618e2a685b6df3d1c6cbb960ceb2eefe181101b58386a2c7 |
import unittest
import numpy as np
from spglib import get_symmetry_dataset, get_hall_number_from_symmetry
from vasp import read_vasp
from os import listdir
dirnames = ('cubic',
'hexagonal',
'monoclinic',
'orthorhombic',
'tetragonal',
'triclinic',
... | sauliusg/cod-tools | src/externals/spglib/python/test/test_hall_number_from_symmetry.py | Python | gpl-2.0 | 2,575 | [
"VASP"
] | 578382370a2f02ad49fbbf11c8d481b7b3a08be78e2600df9a90e24f0b73ae12 |
#!/usr/local/bin/python
# encoding: utf-8
"""
*Import Multi Unit Spectroscopic Explorer (MUSE) IFS galaxy stream into sherlock-catalogues database*
:Author:
David Young
"""
from __future__ import print_function
import sys
import os
os.environ['TERM'] = 'vt100'
import readline
import glob
import pickle
import codec... | thespacedoctor/sherlock | sherlock/imports/ifs.py | Python | mit | 5,686 | [
"Galaxy"
] | e6a5e3340029b6c8e7ef48a51ebc9ee2d24915b275429116bed9a404bed3beca |
#
# Copyright (C) 2013,2014,2015,2016 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... | lahnerml/espresso | samples/python/minimal-polymer.py | Python | gpl-3.0 | 1,793 | [
"ESPResSo"
] | cde69044723fec30e09302390f1769b020ef3ed9ac94a4eec921e2ab8194310e |
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit https://code.google.com/p/feedparser/ for the latest version
Visit http://packages.python.org/feedparser/ for the latest documentation
Required: Python 2.4 or later
Recommended: iconv_codec <http://cjkpython.i18n.org... | flavour/eden | modules/feedparser5213.py | Python | mit | 159,859 | [
"NetCDF",
"VisIt"
] | e8d336a0233778a5974036fa60d87cc8408e05ae93abcde0fdbbba78153a60bb |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | lothian/psi4 | psi4/driver/procrouting/interface_cfour.py | Python | lgpl-3.0 | 18,937 | [
"CFOUR",
"Psi4"
] | 9c57664b4e20d410611d717d73824f6f6425ab90a6d44f05016d075126f84c06 |
########################################################################
# File: Operation.py
# Date: 2012/07/24 12:12:05
########################################################################
"""
:mod: Operation
.. module: Operation
:synopsis: Operation implementation
Operation implementation
"""
# Disable inva... | andresailer/DIRAC | RequestManagementSystem/Client/Operation.py | Python | gpl-3.0 | 10,421 | [
"DIRAC"
] | b65e9eb9c832f90c66f4310f2aeb0b94c9c230ddfee469a0ec3d195aa8273e10 |
# -*- coding=utf-8 -*-
from __future__ import absolute_import, print_function, unicode_literals
import unittest
import copy
import math
import numpy as np
from chemfiles import Frame, UnitCell, Topology, Atom, Residue, ChemfilesError
from chemfiles import BondOrder, CellShape
from _utils import remove_warnings
class... | Luthaf/Chemharp-python | tests/frame.py | Python | mpl-2.0 | 7,425 | [
"Chemfiles"
] | 1759ffb59b30cbd9b5cbd28bffd40488bc60186bdecc6827ad8323c8434f04e9 |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/sklearn/ensemble/forest.py | Python | mit | 79,027 | [
"Brian"
] | bac84a3ef771ac8a0d0fec9db2d1f8d2d6aa1ceb87dd8a2aa577ede5682dab08 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
for a group of sequences,calculate pairwise identity
then use igraph to find non-redundant sets of sequences
please install python-igraph,BioPython,numpy first
usage: python igraph_maximal_clique_seq.py seq.fa
"""
import sys
import os
import igraph
import numpy as np... | lituan/tools | igraph_maximal_clique_seq.py | Python | cc0-1.0 | 3,920 | [
"Biopython"
] | f211dbc0ded87260b31d65a949f113bbc8c9c479a782ba7c83aa02016ce4348c |
#!/usr/bin/env python
"""
This data and module are in the public domain.
http://inamidst.com/phenny/
"""
data = (
("AYGA", -6.08166666667, 145.391666667),
("AYMD", -5.20694444444, 145.788611111),
("AYMH", -5.82611111111, 144.296111111),
("AYNZ", -6.56972222222, 146.726111111),
("AYPY", -9.443333333... | NeoMahler/rc-vikidia | icao.py | Python | mit | 180,282 | [
"FEFF"
] | 73e2309227401ef20f9014448325a4fc7283fda925798adbbb68751d2a8e1d6c |
# -*- coding: utf-8 -*-
"""OpenERP addons manifest aka __openerp__.py checker"""
import os
try:
import ast
from ast import NodeVisitor
except ImportError:
from flake8.util import ast
from ast import NodeVisitor
from common_checker.base_checker import BaseChecker
AGPL = 'AGPL-3'
ALLOWED_KEYS = ['name'... | nbessi/openerp-conventions | v7/manifest_checker.py | Python | mit | 5,069 | [
"VisIt"
] | 5bd61bb0bed11416664835795d94904f7b8663d24dcde20909e5f04cd330837a |
# This file is part of xrayutilities.
#
# xrayutilities 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 later version.
#
# This program is distributed... | dkriegner/xrayutilities | examples/simpack_xrr_effectivedensityslicing.py | Python | gpl-2.0 | 2,533 | [
"CRYSTAL"
] | c5278d8c7814947dab3dbaba1cef1cd5d1b50d38edf03d77443b258c15058fff |
""" The TimeLeft utility allows to calculate the amount of CPU time
left for a given batch system slot. This is essential for the 'Filling
Mode' where several VO jobs may be executed in the same allocated slot.
The prerequisites for the utility to run are:
- Plugin for extracting information from lo... | yujikato/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/TimeLeft/TimeLeft.py | Python | gpl-3.0 | 8,046 | [
"DIRAC"
] | b423af86c57d5e87fc9cf963665d106e1a2c80b4aaf76ca49ee7d4dc616fe485 |
##############################################################################
##############################################################################
# Default settings and helpers for
# Maximum-likelihood inference
#
# Copyright (c) 2016 Johan Dahlin
# liu (at) johandahlin.com
#
###############################... | compops/gpo-abc2015 | para/ml_helpers.py | Python | mit | 9,739 | [
"Gaussian"
] | 690b288a754ee960e152e57d0f3a21bc3f5a9bc14712dcada8b4a598d8c2289f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from CTFd.models import Users, Solves, Challenges, WrongKeys, Keys, Tags, Files, Tracking, Teams
from CTFd import create_app
from random import randint
import datetime
import random
import hashlib
import os
import sys
app = create_app()
USER_AMOUNT = 50
TEAM_AMOUNT = 10
CHA... | RITC3/RC3_CTFD | populate.py | Python | apache-2.0 | 16,078 | [
"Amber",
"Brian",
"CRYSTAL"
] | 308a36dddb2ba07e63022e84cc97561aa953e2c0f19cba4780aca25c270c52b2 |
import os
import cmd
import sys
import shlex
import pprint
import argparse
import synapse.neuron as s_neuron
import synapse.eventbus as s_eventbus
import synapse.datamodel as s_datamodel
class Cmd(cmd.Cmd,s_eventbus.EventBus):
def __init__(self, neu):
cmd.Cmd.__init__(self)
self.prompt = 'neu> '
... | imjonsnooow/synapse | synapse/tools/neutool.py | Python | apache-2.0 | 3,150 | [
"NEURON"
] | 398f1a5cd5df91d30d2e151a16df152c114b1f74847c0cd428922778c3fa90c1 |
#!/usr/bin/env python
"""
Framework to start a simulated vehicle and connect it to MAVProxy.
Peter Barker, April 2016
based on sim_vehicle.sh by Andrew Tridgell, October 2011
"""
import atexit
import getpass
import optparse
import os
import os.path
import signal
import subprocess
import sys
import tempfile
import ti... | Block137/Dual2 | Tools/autotest/sim_vehicle.py | Python | gpl-3.0 | 31,138 | [
"Firefly"
] | 0e2fdc7e32f4d561f20edd7b6ce031bb1261fd3ebc3e626a57d6abfae083f7d6 |
"""
Extractor for gridded data
y.wang@bom.gov.au
"""
from datetime import date, timedelta
import numpy as np
from scipy.io import netcdf
from .cod import CoD
from .mask import Mask
from .gridded import AwapDailyData
class GriddedExtractor(object):
def __init__(self, cod_base_dir=None, mask_base_dir=None, gridd... | paolap/cwsl-ctools | sdm/sdm/extractor.py | Python | apache-2.0 | 3,948 | [
"NetCDF"
] | 98110f59572080ba38a46b16f95d792891cc8e83db240e2517578825f59c0687 |
# Copyright 2014-2019 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
#
# Unless required by appl... | sunqm/pyscf | pyscf/adc/test/test_radc/test_H2CO_radc_outcore_small_mem.py | Python | apache-2.0 | 3,532 | [
"PySCF"
] | af09b821d616a3313ba30290e102ae70dec0058193544a5905b6b5697f9474bc |
"""
JSON Renderer
"""
from . import json_template
from .. import renderer_result
from ...visitors import data_visitor as dv
class JsonPrimitiveRenderer(dv.DataVisitor):
def __init__(self, string_stream, new_line, render_name=True):
self.string_stream = string_stream
self.new_line = new_line
... | svperbeast/plain_data_companion | src/templates/json/json_renderer.py | Python | mit | 5,861 | [
"VisIt"
] | bb22b20e930148dce847ac34f9c2cd343c5fc97aa861e795f71f207f49faf927 |
###############################################################################
#
# Copyright (c) 2011 Ruslan Spivak
#
# 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... | moses-palmer/slimit | src/slimit/visitors/ecmavisitor.py | Python | mit | 12,856 | [
"VisIt"
] | d5547a546d4bd5134691b51078994537fe3da311337036853b62af3b51bccae0 |
#!/usr/bin/env python
"""
binreads is a simple script that uses pysam to find retrieve reads over a region
from read mapping analysis (BAMfiles).
Script requires a **sorted** BAM file and you need to specify the name of the
reference sequence used (Just check with samtool view). If you want to specify
a subregion u... | happykhan/binreads | binreads/binreads.py | Python | gpl-3.0 | 4,388 | [
"pysam"
] | 60e1efe3287b063d5b221489634c2b0047a1c851430ebfe2c9619d5df1ace6dc |
# Copyright 2014, Brian Coca <bcoca@ansible.com>
# Copyright 2017, Ken Celenza <ken@networktocode.com>
# Copyright 2017, Jason Edelman <jason@networktocode.com>
# Copyright 2017, Ansible Project
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of ... | privateip/ansible | lib/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 8,342 | [
"Brian"
] | 9ef5cb1549dcf8d71a6431d5a33688694e1b71bb72214a43b2265f84f31127eb |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | hkariti/ansible | lib/ansible/modules/network/avi/avi_virtualservice.py | Python | gpl-3.0 | 26,779 | [
"VisIt"
] | fd05a879056d9a426380c867e3bae2ea39d27f4942483825e9a6c725c8f899b3 |
########################################################################
# File: TracedTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/08/08 15:21:32
########################################################################
""" :mod: TracedTests
=======================
.. module: TracedTests
... | andresailer/DIRAC | Core/Utilities/test/Test_Traced.py | Python | gpl-3.0 | 2,735 | [
"DIRAC"
] | c32ba93c0a66b0030c487494c90674da84b58f80d5867a365de4979a69bb71c7 |
# $Id$
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import doctest
import unittest
from rdkit import Chem
from rdkit import rdBase
from rdkit.... | bp-kelley/rdkit | rdkit/Chem/Fraggle/UnitTestFraggle.py | Python | bsd-3-clause | 7,513 | [
"RDKit"
] | 4f4df51365e6507d32689396d69249ad028fed851b9772175153c78bc400d066 |
# Copyright 2018 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... | tensorflow/privacy | tensorflow_privacy/privacy/analysis/rdp_accountant.py | Python | apache-2.0 | 19,387 | [
"Gaussian"
] | b93d3ab1494468627e4fa704d36a928f48056846c707e9ef007dd8b2dcd85567 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/vasp/incar/test_npar.py | Python | gpl-3.0 | 1,976 | [
"CRYSTAL",
"VASP"
] | 07354f8285d5ea967d7a02bcf00541c060a7b6677b4eff844c70c8117d2d900b |
from setuptools import setup, find_packages
version = '1.1.0'
setup(name='pyrabbit',
version=version,
description="A Pythonic interface to the RabbitMQ Management HTTP API",
long_description="""\
The main documentation lives at http://pyrabbit.readthedocs.org
There's no way to easily write progra... | bkjones/pyrabbit | setup.py | Python | bsd-3-clause | 1,641 | [
"Brian"
] | e23f2a3e025018b9aaf6123ef1352e3a1e57d30ed5a7d52a28a876ffb005419e |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/ajax/eventdescription.py | Python | gpl-2.0 | 4,498 | [
"VisIt"
] | 480255f7adc3071ec3cad832e62be941a4e58ac945ba568829c828eaa568313f |
"""
Spatial Error Models module
"""
__author__ = "Luc Anselin luc.anselin@asu.edu, \
Daniel Arribas-Bel darribas@asu.edu, \
Pedro V. Amaral pedro.amaral@asu.edu"
import numpy as np
from numpy import linalg as la
import ols as OLS
from pysal import lag_spatial
from utils import power_expansion, set_end... | TaylorOshan/pysal | pysal/spreg/error_sp.py | Python | bsd-3-clause | 43,203 | [
"COLUMBUS"
] | 6389fbec2f9234f74fdd79c6ac9d392c11e2f7a820f3d3271055620bf4ae2ad7 |
from cd_perf_promotion.engines.argumentengine import ArgumentEngine
from cd_perf_promotion.engines.configengine import ConfigEngine
from cd_perf_promotion.engines.dataengine import DataEngine
from cd_perf_promotion.engines.comparisonengine import ComparisonEngine
from cd_perf_promotion.engines.outputengine ... | CDKGlobal/cd-performance-promotion | cd_perf_promotion/main.py | Python | mit | 1,639 | [
"CDK"
] | 6c7c14a98ecd15051d9fdaa84fd8605fbada39f9a697d1724d4a97b7f86ff0f4 |
"""Functions to process IPython magics with."""
from functools import lru_cache
import dataclasses
import ast
from typing import Dict, List, Tuple, Optional
import secrets
import sys
import collections
if sys.version_info >= (3, 10):
from typing import TypeGuard
else:
from typing_extensions import TypeGuard
... | psf/black | src/black/handle_ipynb_magics.py | Python | mit | 13,534 | [
"VisIt"
] | b38d02a3cf5ea529c7573f4c7dd96866a58299488a294ec1ba66bd8fe139cacb |
##########################################################################
#
# This file is part of OCEMR.
#
# OCEMR 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,... | ph1l/ocemr | ocemr/views/visit.py | Python | gpl-3.0 | 23,918 | [
"VisIt"
] | e9f6f5fa66f7a614ffc98a67d40e972c0cb6a1abe670c08bd318d5039b94c4b5 |
#!/usr/bin/env python
# coding: utf-8
#
# Copyright 2007 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | nicko96/Chrome-Infra | appengine/chromium_rietveld/upload.py | Python | bsd-3-clause | 100,822 | [
"VisIt"
] | a5aa5356014496c5d2ef63b7f023532caa8dfdb83b62b1af44d783d60916285d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import logging
import numpy as np
import time
from pymatgen.core.structure import Structure
from pymatgen.core.sites import PeriodicSite
from monty.json import... | czhengsci/pymatgen | pymatgen/analysis/chemenv/coordination_environments/voronoi.py | Python | mit | 40,650 | [
"pymatgen"
] | b501a3e98e18cef05c823d435fb8ead845086feeddf92c4d7a98f5323ed3818b |
from nanopore.analyses.abstractAnalysis import AbstractAnalysis
from nanopore.analyses.utils import AlignedPair, getFastaDictionary, getFastqDictionary, samIterator
import os
import numpy
import pysam
import xml.etree.cElementTree as ET
from jobTree.src.bioio import reverseComplement, fastaRead, fastqRead, prettyXml, s... | mitenjain/nanopore | nanopore/analyses/coverage.py | Python | mit | 9,851 | [
"pysam"
] | 9d4c0de9d4512154c109bc0262f930fc2f472b2c20488b528ed03195cc4e7a6d |
""" unit tests for Transformation Clients
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=protected-access,missing-docstring,invalid-name
import six
import unittest
import json
import mock
from DIRAC.RequestManagementSystem.Client.Req... | ic-hep/DIRAC | src/DIRAC/TransformationSystem/Client/test/Test_Client_TransformationSystem.py | Python | gpl-3.0 | 13,918 | [
"DIRAC"
] | c4fde540d2f8a2ba7027d29392d9220d3f33ccb79d72d29a2853991e16d4195e |
#
# $Revision: 738 $
# $Date: 2009-02-12 15:32:12 -0700 (Thu, 12 Feb 2009) $
# $Author: brian@tannerpages.com $
# $HeadURL: http://rl-glue-ext.googlecode.com/svn/trunk/projects/codecs/Python/src/rlglue/versions.py $
def get_svn_codec_version():
SVN_GLUE_VERSION="$Revision: 738 $"
justTheNumber=SVN_GLUE_VER... | okkhoy/rlglue-python3-codec | src/rlglue/versions.py | Python | apache-2.0 | 422 | [
"Brian"
] | d2f25a9e305d7aef1fa9488b183c4b13d639dd3540d331b927c5b59ff467d090 |
"""
utilities
=========
Collection of classes and functions for components and services of ApBsInT:
- Potential manager
- Model (PM and B factor)
- Representation
"""
import numpy as np
import scipy.sparse as ssp
import scipy.linalg as sla
import numbers
import time # For profiling
import apbsint.helpers as helper... | mseeger/apbsint | python/apbsint/utilities.py | Python | bsd-3-clause | 26,130 | [
"Gaussian"
] | dfac4bd8ce06cb63d650c43497bc20a23a54c51f9f27d1697731b8c090971067 |
import ocl as cam
import camvtk
import time
import vtk
import math
import datetime
def main():
myscreen = camvtk.VTKScreen()
focal = cam.Point(5, 5, 0)
r = 30
theta = (float(45)/360)*2*math.pi
fi=45
campos = cam.Point( r*math.sin(theta)*math.cos(fi), r*math.sin(theta)*math.sin(f... | aewallin/opencamlib | examples/python/kdtree_debug_0.py | Python | lgpl-2.1 | 3,657 | [
"VTK"
] | 147bb08c9d36afdb10021b79894a47ad5856f3b7782e7a5c474108c125c779cc |
import numpy as np
import rdkit.Chem.Descriptors as Descriptors
import rdkit.Chem.rdMolDescriptors as rdMolDescriptors
import rdkit.Chem.EState as EState
import rdkit.Chem.rdPartialCharges as rdPartialCharges
import rdkit.Chem.rdChemReactions as rdRxns
att_dtype = np.float32
def oneHotVector(val, lst):
'''Converts a... | connorcoley/ochem_predict_nn | utils/descriptors.py | Python | mit | 7,409 | [
"RDKit"
] | 30bb6fd608b7a537ffec3460f9dcf75a83033e9b6e68fe15940d42eb9dbc607a |
# Storage filtering classes
#
# Copyright (C) 2013 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed... | sujithshankar/anaconda | pyanaconda/ui/gui/spokes/filter.py | Python | gpl-2.0 | 27,986 | [
"VisIt"
] | f2ce42cb0078e8eb5a1cf68b8a82674d94a3a70fba8a610402517ced39fd5316 |
# -*- 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/coordinates/test_memory.py | Python | gpl-2.0 | 14,202 | [
"MDAnalysis"
] | aeb0649b4ebb060035ce4befdac7681ed46d5f92420e5a70c3a1b47b7979a7ae |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | frreiss/tensorflow-fred | tensorflow/python/ops/gradients_util.py | Python | apache-2.0 | 40,873 | [
"VisIt"
] | f26aecbefb7fb35333942ad97945cdea9ba2284d2ac866cb1ae8c41fe5408e02 |
#!/usr/bin/env python3
import torch
class _feature_flag(object):
_state = False
@classmethod
def on(cls):
return cls._state
@classmethod
def off(cls):
return not cls._state
@classmethod
def _set_state(cls, state):
cls._state = state
def __init__(self, state... | jrg365/gpytorch | gpytorch/settings.py | Python | mit | 20,168 | [
"Gaussian"
] | 00c18c0fc65e1dd02e92f46b8bca9c7f03b4ab39f35a05e2299d6d1d0ec24446 |
# Copyright 2010 Google Inc.
#
# 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, modify, merge, publish, dis-
# trib... | matthappens/taskqueue | taskqueue/venv_tq/lib/python2.7/site-packages/boto/gs/key.py | Python | mit | 42,415 | [
"VisIt"
] | f5f22a1b54733c212399512bde0047feea8beaebcaec2eb8870bee3c7704fa0f |
"""
Copyright (c) 2014 Brian Muller
Copyright (c) 2015 OpenBazaar
"""
import heapq
from operator import itemgetter
from protos import objects
class Node(object):
def __init__(self, node_id, ip=None, port=None, pubkey=None,
relay_node=None, nat_type=None, vendor=False):
self.id = node_id
... | saltduck/OpenBazaar-Server | dht/node.py | Python | mit | 4,175 | [
"Brian"
] | 82b7369279f3637d8fbcb1097c390eae2dcec2b7498af0099c49bc609671f5e1 |
#!/usr/bin/env python3
# coding:utf-8
# Based on GAppProxy 2.0.0 by Du XiaoGang <dugang.2008@gmail.com>
# Based on WallProxy 0.4.0 by Hust Moon <www.ehust@gmail.com>
# Contributor:
# Phus Lu <phus.lu@gmail.com>
# Hewig Xu <hewigovens@gmail.com>
# Ayanamist Yang <ayanamist@gmail.com>... | Suwmlee/XX-Net | gae_proxy/local/proxy.py | Python | bsd-2-clause | 11,261 | [
"VisIt"
] | 90b489de07f3d02de70f2455c4a8ce3a387116f0bd80c9348d072926b0b2d206 |
#!/home/paulk/software/bin/python
from __future__ import division
from sys import argv,exit,stderr
from key_functions import *
import pysam
from cPickle import load
f = open("resources/exons.hg19.Ens66.0-based.pic")
exons = load(f)
f.close()
print "exon\tincl\texcl\ttotal\tupintrlen\texonlen\tdownintrlen"
f = open("t... | polarise/RP-python | intronLen2ExonInclRate.py | Python | gpl-2.0 | 862 | [
"pysam"
] | 27eab0a1f4f01a7327bcc3d4a95d5223e979019915ff7217709846392aa9502d |
# -----------------------------------------------------------------------------
# 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.
# -------------------------------------------... | Kleptobismol/scikit-bio | skbio/parse/sequences/clustal.py | Python | bsd-3-clause | 3,294 | [
"scikit-bio"
] | ba6e1e6643a1dc091eec83770bcfdff4164f97a706ced4911b116f9a2e3b2703 |
"""
/******************************************************************************
This source file is part of the Avogadro project.
Copyright 2013 Kitware, Inc.
This source code is released under the New BSD License, (the "License").
Unless required by applicable law or agreed to in writing, software
di... | cjh1/mongochemweb-avogadrolibs | avogadro/qtplugins/quantuminput/inputGenerators/gamessuk.py | Python | bsd-3-clause | 5,941 | [
"Avogadro",
"GAMESS"
] | b8c63a84d8e8b965ad0c7659f792f15e4c04de8f382209bf2e0e1ef318d1583b |
#!/usr/bin/env python
from pymatgen.io.vasp import Poscar
import cProfile
import pstats
import os
import logging
logging.basicConfig(level=logging.DEBUG)
p = Poscar.from_file("../test_files/POSCAR.LiFePO4", check_for_POTCAR=False)
s = p.structure
def test():
nn = s.get_all_neighbors(20)
print len(nn)
def c... | matk86/pymatgen | dev_scripts/profile_structure.py | Python | mit | 949 | [
"VASP",
"pymatgen"
] | 008853eb1ae304d90cde113b63c6dae1af2f1d66502727103d85bc77913348ef |
import click
import os
import requests
import sys
import json
from soccer import leagueids
from soccer.exceptions import IncorrectParametersException, APIErrorException
from soccer.writers import get_writer
BASE_URL = 'http://api.football-data.org/alpha/'
LIVE_URL = 'http://soccer-cli.appspot.com/'
LEAGUE_IDS = leag... | thurask/soccer-cli | soccer/main.py | Python | mit | 11,507 | [
"VisIt"
] | aacce4295ff475e9674341bea511d19ff7d98511e9b9ba4f0a3af75bca4abbbb |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf.urls.static import static
from django.views import defaults as default_views
from django.conf.urls import include, url
from django.conf import settings
from django.conf.urls.i18n import i18n_patterns
from django.contrib import admin
from... | jeremy-c/unusualbusiness | config/urls.py | Python | bsd-3-clause | 1,693 | [
"VisIt"
] | 3019c7f99d9f3cd8507b008c2580690563bb1106ddfc107d6e6f0e990fd4a813 |
from __future__ import absolute_import
import logging
import click
import cachetools
try:
import cPickle as pickle
except ImportError:
import pickle
from copy import deepcopy
from pathlib import Path
from pandas import to_datetime
from datetime import datetime
import datacube
from datacube.api.core import Dat... | ceos-seo/Data_Cube_v2 | agdc-v2/datacube/scripts/ingest.py | Python | apache-2.0 | 11,891 | [
"NetCDF"
] | 5e870ddae3e1e7095c3e4f17d7caeb20684a56f588ad146c3379ee80e413e5e1 |
"""
Use the greedy-terrain-decimator to display a decimated terrain view.
This example illustrates decimating a terrain. We use the
greedy-terrain-decimator to create a reduced mesh with an optimized grid that
approximates the initial regular grid.
The initial grid is displayed in white, and the optimized grid is dis... | liulion/mayavi | examples/mayavi/mlab/canyon_decimation.py | Python | bsd-3-clause | 3,293 | [
"Mayavi"
] | 8b60bea759a74796a30b8499ae49a064c4c6b8e957cf3461fd05d01dcb98516d |
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