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""" Class that contains client access to the JobStateUpdate handler. """
from DIRAC.Core.Base.Client import Client, createClient
@createClient("WorkloadManagement/JobStateUpdate")
class JobStateUpdateClient(Client):
"""JobStateUpdateClient sets url for the JobStateUpdateHandler."""
def __init__(self, url=No... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/JobStateUpdateClient.py | Python | gpl-3.0 | 747 | [
"DIRAC"
] | 2cdc4449cc823d5ad34939dea2c629f4f60e0297951cdcc7bc41698900d8084b |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | horance-liu/tensorflow | tensorflow/contrib/seq2seq/python/ops/attention_wrapper.py | Python | apache-2.0 | 57,798 | [
"DIRAC"
] | 2de2a74051e2fad4328045e451e5ec2d7961795c6181893cbc57049a07e6d2de |
import tempfile
import cgi
from .base import Cleaver
from .compat import urlencode, parse_qsl
from .backend import CleaverBackend
from .identity import CleaverIdentityProvider
class SplitMiddleware(object):
def __init__(self, app, identity, backend, environ_key='cleaver',
allow_override=False, ... | ryanpetrello/cleaver | cleaver/middleware.py | Python | bsd-3-clause | 7,263 | [
"VisIt"
] | 7287a028167272df0a800db226bd671af3ae78a9cc2c42fdc85a8a5eff231702 |
"""
Module for plotting and analysis of reaction/diffusion-related results
"""
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
try:
basestring
except NameError:
basestring = str
from future import standard_l... | Neurosim-lab/netpyne | netpyne/analysis/rxd.py | Python | mit | 4,498 | [
"NEURON"
] | 38a8e1a08cf13fb27dc88efa58f6ec12854fc889ee099fa6b41531ff489f3fef |
# -*- coding: utf-8 -*-
"""
NEST v2 implementation of the PyNN API.
:copyright: Copyright 2006-2016 by the PyNN team, see AUTHORS.
:license: CeCILL, see LICENSE for details.
"""
import numpy
import nest
import logging
from itertools import repeat
try:
xrange
except NameError: # Python 3
xrange = range
from ... | anupkdas-nus/global_synapses | pyNN-dispackgaes/nest/projections.py | Python | gpl-3.0 | 18,779 | [
"NEURON"
] | 773e6aaad191475dd82b85a3ef9e9ba05f609aa0f725e4ea2d60fd08b599c26a |
import vtk
import numpy
from vtk.util.numpy_support import numpy_to_vtk, vtk_to_numpy
import sys
sys.dont_write_bytecode = True
def assignElements2Dlin(mesh, elements):
numRows, numCols = elements.shape
# TODO can we do this faster?
for i in range(numRows):
v0, v1, v2, v3, v4, v5 = elemen... | beauof/FSIViewer | organiseData.py | Python | lgpl-3.0 | 6,548 | [
"VTK"
] | 8946166b052361570fa1e7a9172e933993fb872d5d7945a8aac6b10e5a49b8df |
from random import random
from ase.io import write
from ase.optimize import BFGS
from ase.calculators.emt import EMT
from ase.ga.data import DataConnection
from ase.ga.population import Population
from ase.ga.standard_comparators import InteratomicDistanceComparator
from ase.ga.cutandsplicepairing import CutAndSpliceP... | askhl/ase | ase/test/ga/basic_example_main_run.py | Python | gpl-2.0 | 3,181 | [
"ASE"
] | b7b21e09f7c967e5e0c3ca9d8764f18ef469d92e15f49f9d5b4f14545da5b90e |
#!/usr/bin/env python
#
# @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 file is part of Psi4.
#
# Psi4 is free software; you can redistri... | jH0ward/psi4 | psi4/share/psi4/basis/primitives/diff_gbs.py | Python | lgpl-3.0 | 4,565 | [
"Psi4"
] | 6a43893b963d53cd96bf8b034c8a15068676536cf941c07a55aff4cf6cf9c9e3 |
# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, so... | googlecodelabs/migrate-python2-appengine | mod13b-memorystore/main.py | Python | apache-2.0 | 2,028 | [
"VisIt"
] | 5712e161ef4ff920a1c5f73c24b7e8a2f5a97e71b09899c1931b7fb87a975c62 |
#!/bin/env python
""" Show request given its ID, a jobID or a transformation and a task """
__RCSID__ = "$Id: $"
import datetime
def convertDate( date ):
try:
value = datetime.datetime.strptime( date, '%Y-%m-%d' )
return value
except:
pass
try:
value = datetime.datetime.utcnow() - datetime.timede... | coberger/DIRAC | RequestManagementSystem/scripts/dirac-rms-show-request.py | Python | gpl-3.0 | 6,894 | [
"DIRAC"
] | 1adea7a50eeaf547775b838f277ecea86abe4af16a79e00a8f785c2dbf4e9c75 |
"""
BNL NSLS-2 Computer Vision Module
Author: William Watson
Date: 2016-7-14
This Module contains numerous functions designed to
help in the data manipulation of images on the Beam-lines within NSLS-2.
It Uses the numpy and cv2 libraries to construct a simple module to
make image processing and computer vision easie... | nextBillyonair/compVision | XPD/cvlibNoEpics.py | Python | mit | 82,776 | [
"Gaussian"
] | a39e497f2e7bb5669589970325c64376cf0b3460ef101838022134f69148067b |
""" FileReport module defines the FileReport class, to report file status to the transformation DB
"""
import copy
from DIRAC import S_OK
from DIRAC.Core.Utilities import DEncode
from DIRAC.TransformationSystem.Client.TransformationClient import TransformationClient
from DIRAC.Re... | andresailer/DIRAC | TransformationSystem/Client/FileReport.py | Python | gpl-3.0 | 2,385 | [
"DIRAC"
] | 7002c9812a9cc8e9db4ba96eaf5aadd3534084084c391dbdabef83d6e251e98b |
import os
import itertools
import math
import re
import numpy as np
import scipy.linalg as spla
import hail as hl
import hail.expr.aggregators as agg
from hail.expr import construct_expr, construct_variable
from hail.expr.expressions import (expr_float64, matrix_table_source, expr_ndarray,
... | hail-is/hail | hail/python/hail/linalg/blockmatrix.py | Python | mit | 99,722 | [
"Gaussian"
] | cf7d765e0ba54a5c3ca24c1c1a92901e2fc6d08d357ff2fa6de19ea478fcbeb5 |
"""MSAView - PyMol support.
Copyright (c) 2011 Joel Hedlund.
Contact: Joel Hedlund <yohell@ifm.liu.se>
MSAView is a modular, configurable and extensible package for analysing and
visualising multiple sequence alignments and sequence features.
This package provides support for viewing structures using custom
visu... | yohell/msaview | msaview_plugin_pymol/__init__.py | Python | mit | 5,546 | [
"PyMOL"
] | 89fd1bcd318beaf97509b44f035fa32e11ed392c57543f5e6baedde083efff50 |
#!/usr/bin/env python
__author__ = "Mike McCann"
__copyright__ = "Copyright 2012, MBARI"
__license__ = "GPL"
__maintainer__ = "Mike McCann"
__email__ = "mccann at mbari.org"
__doc__ = '''
Script to read data from CSV formatted data that Monique makes from the ESP Drifter
platform and write them to netCDF files.
... | josephmfaulkner/stoqs | stoqs/loaders/CANON/toNetCDF/espDriftToNetcdf.py | Python | gpl-3.0 | 11,311 | [
"NetCDF"
] | 8ceb2b3783776956cf2d703346df76724c657ab1f93051a1d39fea25e8640afc |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, divi... | mganeva/mantid | Framework/PythonInterface/test/python/plugins/algorithms/CorrectTOFTest.py | Python | gpl-3.0 | 5,020 | [
"Gaussian"
] | 392a52d82e1c6d7620aa86cf49ab8429fe666752d9debb210ceeed865650bcba |
from threading import Lock
class ResponsibleGenerator(object):
"""A generator that will help clean up when it is done being used."""
__slots__ = ['cleanup', 'gen']
def __init__(self, gen, cleanup):
self.cleanup = cleanup
self.gen = gen
def __del__(self):
self.cleanup()
... | gloaec/trifle | src/rdflib/plugins/stores/concurrent.py | Python | gpl-3.0 | 2,686 | [
"VisIt"
] | fedc78b7156b6ec561277e1971ce86ce3c278e856b86a6ff1cd6d9d0ae2c0537 |
from pyibex.thickset import *
from pyibex import Interval, IntervalVector
from vibes import vibes
def ex_circle():
t = ThickDisk(0,0,2)
X0 = IntervalVector(2, [-5,5])
# P = ThickPaving(X0, lambda x: opNot(t.test(x)), 0.05)
P = ThickPaving(X0, t, 0.05)
P.visit(ToVibes(1000, "Disk"))
t2 = ThickTranslateIn... | benEnsta/pyIbex | pyibex/thickset/examples/ex_translate.py | Python | lgpl-3.0 | 889 | [
"VisIt"
] | 9699be0fef675a756eb7c88a82a4407ad0e65921eecab7e7a94b7cd31f7fa931 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | taroplus/spark | python/pyspark/pandas/tests/test_dataframe.py | Python | apache-2.0 | 238,076 | [
"Elk"
] | 819a8b5095eb83a3881ca94fbd203094eab1f8baed4672f809d09828f69fe978 |
#!/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... | simonwydooghe/ansible | lib/ansible/modules/network/avi/avi_stringgroup.py | Python | gpl-3.0 | 4,256 | [
"VisIt"
] | 0a0a2a4363d6b6ca6534437a65690bfbfd06addabe16fbed9d09951e69e36634 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | andreaso/ansible | lib/ansible/modules/network/avi/avi_tenant.py | Python | gpl-3.0 | 3,806 | [
"VisIt"
] | ab154eb1599e41fa8c2c9f4ae69acd4e7e2a68d5f678d8fc07eb01fcea5d64a8 |
#!/usr/bin/python
# Howto, Code license, Credits, etc: http://code.google.com/B/BCI-Project-Triathlon/
noGL = False # Set noGL to True for disabling the use of OpenGL (to gain speed, or to avoid python-wx-opengl problems)
import pyfann
from pyfann import libfann
import string
import os
import sys
import random
im... | Buggaboo/Triathlon | TriathlonBeta-orig/Triathlon-Breeder.py | Python | mit | 34,534 | [
"Gaussian"
] | 00f4273d43624aba4cfc6093f4b19e65acaffb736e1a60b5b374973a2a17e068 |
#!/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/v201502/error_handling/handle_policy_violation_error.py | Python | apache-2.0 | 4,149 | [
"VisIt"
] | 5dbe05134131b08fb433a1ca65abd6b04270cea4bd4573290eca4393c107e0f5 |
"""
Created on 29/06/2015
@author: vgil
@brief: Performs some automatic analysis over the trajectories. The kind of analysis to be done are
specificied using the command line (rmsf, sasa, radius of gyration or a report analysis if it is a
PELE result)
"""
import os
import glob
import numpy
from optparse import Opti... | victor-gil-sepulveda/PhD-ANMPythonHelpers | trajectory_comparison/trajectory_full_analysis.py | Python | mit | 10,635 | [
"MDTraj",
"VMD"
] | d2d76df4a054fb720919ea7b91a67349d3d279a5a6492c9b5d519d9223addfa2 |
import pickle
from io import BytesIO
import numpy as np
import scipy.sparse
from sklearn.datasets import load_digits, load_iris
from sklearn.cross_validation import cross_val_score, train_test_split
from sklearn.externals.six.moves import zip
from sklearn.utils.testing import assert_almost_equal
from sklearn.utils.te... | mblondel/scikit-learn | sklearn/tests/test_naive_bayes.py | Python | bsd-3-clause | 17,567 | [
"Gaussian"
] | edcc24c305473c079e2eb7e8709108ee3a89670925cb510d56fb43769004d30f |
"""Dataset generation for simulation.
"""
from __future__ import division, absolute_import
import abc
from copy import deepcopy
import numpy as np
from scipy.stats import pearsonr
from bcn.bias import BiasLowRank, BiasUnconstrained
from bcn.redundant_signal import RedundantSignal
from bcn.missing import Missing
d... | a378ec99/bcn | bcn/data.py | Python | mit | 13,971 | [
"Gaussian"
] | 83d5f9640dbcc61c03e8d754a4411195e158c2791e8b0a8e181655fdbfb7c9f1 |
from .config import *
from .compute_lst import compute_lst
def compute_lsrk(wf):
""" Computes the LSR in km/s
Computes the Local standard of rest kinematic using the time (MJD),
RA and DEC of the observation to compute along with the telescope location.
Requires pyslalib
Args:
wf (bl.Wate... | UCBerkeleySETI/blimpy | blimpy/ephemeris/compute_lsrk.py | Python | bsd-3-clause | 2,089 | [
"Galaxy"
] | a5eb40418ee44bf09c57e9916b298b41ad31359ebfa98fe5877b322273cbc543 |
# This file is part of ts_wep.
#
# Developed for the LSST Telescope and Site Systems.
# This product includes software developed by the LSST Project
# (https://www.lsst.org).
# See the COPYRIGHT file at the top-level directory of this distribution
# for details of code ownership.
#
# This program is free software: you ... | lsst-ts/ts_wep | tests/task/test_estimateZernikesScienceSensorTask.py | Python | gpl-3.0 | 10,126 | [
"VisIt"
] | 59bd3159186e51b35afb58a4240a3bc53a728639d6b392b2b02ce9ad8b9c2976 |
"""
Message Queue Handler
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import json
import logging
import socket
from DIRAC.Resources.MessageQueue.MQCommunication import createProducer
class MessageQueueHandler(logging.Handler):
... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/private/standardLogging/Handler/MessageQueueHandler.py | Python | gpl-3.0 | 1,589 | [
"DIRAC"
] | e17b62e4d70c3ccf2156307484137d171373bad0a05b49aeab619f96d6b47a84 |
#!/usr/bin/env python
"""
Runs a simulation under NVT conditions.
Outputs a portable state (.xml) file with positions and velocities,
to allow restarting and/or continuation.
.2019. joaor@stanford.edu
"""
from __future__ import print_function, division
import argparse
import logging
import math
import os
import ra... | csblab/md_scripts | openmm/amberff/equilibrate_NVT.py | Python | mit | 12,419 | [
"OpenMM"
] | 9ad0a52ddc8a98ded07448404a1164c356324345d0651417ba7e99353edbff65 |
from __future__ import with_statement
__author__ = 'Tom Schaul, tom@idsia.ch; Justin Bayer, bayerj@in.tum.de'
import gc
import pickle
import logging
import threading
import os
import operator
from itertools import count
from math import sqrt
from random import random, choice
from string import split
from scipy impo... | fxsjy/pybrain | pybrain/utilities.py | Python | bsd-3-clause | 23,298 | [
"NetCDF"
] | 40727179af4098573798c34752607b97b7f5a017261313ae46ef11e2a073663a |
from __future__ import print_function
import numpy as np
import matplotlib.pyplot as plt
import h5py
from plotstuff import params, colours
reb = params()
cols = colours()
from gatspy.periodic import LombScargle
import sys
import multiprocessing as mp
from multiprocessing import Pool
from GProtation import make_plot, ln... | RuthAngus/LSST-max | code/recover_LSST.py | Python | mit | 5,566 | [
"Gaussian"
] | fb1bdece3176cb3b657826478a13d6c53dd5c518705a0d28fefa07f7e6817511 |
import numpy as np
from unittest import TestCase
from diffprivlib.mechanisms import Gaussian
from diffprivlib.utils import global_seed
class TestGaussian(TestCase):
def setup_method(self, method):
if method.__name__ .endswith("prob"):
global_seed(314159)
self.mech = Gaussian
def... | IBM/differential-privacy-library | tests/mechanisms/test_Gaussian.py | Python | mit | 2,994 | [
"Gaussian"
] | dc19559303e7460713e52ee2311406219827f28e09848be9713f942770a81d56 |
# GromacsWrapper environment.py
# Copyright (c) 2011 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
:mod:`gromacs.environment` -- Run time modification of behaviour
========================================================... | jandom/GromacsWrapper | gromacs/environment.py | Python | gpl-3.0 | 8,025 | [
"Gromacs",
"MDAnalysis"
] | 310af7d6d79cfd17b4cab3787239ddc9a9cc3c15ee621a305fa8a7f53ca2bc2a |
# es.po
val = {" days." : " días.",
"(all)" : "(todo)",
"(any)" : "(cualquier)",
"(anyone)" : "(cualquiera)",
"(available)" : "(disponible)",
"(blank)" : "(en blanco)",
"(both)" : "(ambos)",
"(everyone)" : "(todos)",
"(master user, not editable)" : "(usuario maestro, no editable)",
"(no change)" : "(sin cambios)",
"(n... | bobintetley/asm3 | src/asm3/locales/locale_es.py | Python | gpl-3.0 | 204,743 | [
"Amber",
"VisIt"
] | c789f15b240550901e606a2f0f5cfda6398ce33d48ee6692a7a4a34ce6086dd3 |
"""
====================
Voigt Profile Fitter
====================
"""
from . import model
import numpy as np
from ...spectrum.moments import moments
import types
try:
import scipy.special
scipyOK = True
except ImportError:
scipyOK = False
def voigt(xarr, amp, xcen, sigma, gamma, normalized=False):
""... | mikelum/pyspeckit | pyspeckit/spectrum/models/inherited_voigtfitter.py | Python | mit | 3,431 | [
"Gaussian"
] | 184c27aa45a522b2aae144b0d95b3442dd23aee4e8fc162632848b08daaa995a |
# ******************************************************************************
# Copyright 2014-2018 Intel Corporation
#
# 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.apa... | NervanaSystems/neon | neon/optimizers/optimizer.py | Python | apache-2.0 | 43,255 | [
"Gaussian"
] | 25d72d3ecf948198f7e57b50d49bb3d3095cc07249afa2b07bb5d126f4ebea40 |
import webapp2
from google.appengine.api import mail
from google.appengine.api import users
from google.appengine.api.taskqueue import taskqueue
import gig
import member
import assoc
import logging
import re
import pickle
import os
from webapp2_extras import i18n
from webapp2_extras.i18n import gettext as _
# need t... | bklang/GO2 | goemail.py | Python | gpl-3.0 | 10,926 | [
"exciting"
] | 1afd6c553bbb38530416db1bdc575a48429147f9b636622660b10e37f825de5c |
"""
Tools for different procedure estimations
"""
__author__ = "Luc Anselin luc.anselin@asu.edu, \
Pedro V. Amaral pedro.amaral@asu.edu, \
David C. Folch david.folch@asu.edu, \
Daniel Arribas-Bel darribas@asu.edu,\
Levi Wolf levi.john.wolf@gmail.com"
import numpy as np
from ... | schmidtc/pysal | pysal/spreg/utils.py | Python | bsd-3-clause | 27,878 | [
"COLUMBUS"
] | d53c6ba6777be1e2ebb25755703aa088d06ff83bafddf3a6d55708235a40331f |
import os
import util
import urllib
import helper
from util import *
from xml.etree.ElementTree import *
#friendly name : db column, missing filter statement
gameproperties = {'Title' : ['name', "name = ''"],
'Description' : ['description', "description = ''"],
'Genre' : ['genre', "Id NOT IN (SELECT Gam... | azumimuo/family-xbmc-addon | script.games.rom.collection.browser/resources/lib/config.py | Python | gpl-2.0 | 27,831 | [
"Jaguar"
] | 1a557d9bdfc3241e3bc173d760faf1196b413f4db1a4a7f1b4361263809a884b |
"""Probit regression class and diagnostics."""
__author__ = "Luc Anselin luc.anselin@asu.edu, Pedro V. Amaral pedro.amaral@asu.edu"
import numpy as np
import numpy.linalg as la
import scipy.optimize as op
from scipy.stats import norm, chisqprob
import scipy.sparse as SP
import user_output as USER
import sum... | AlanZatarain/pysal | pysal/spreg/probit.py | Python | bsd-3-clause | 26,628 | [
"COLUMBUS"
] | 0aa975c9573fca190039ef53298af1bdb8e794db9df94b2a3ae7d333c01a9f43 |
########################################################################
# $HeadURL$
# File: ReqProxyHandler.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/06/04 13:18:41
########################################################################
"""
:mod: RequestProxyHandler
.. module: ReqtProxyHandler
:syn... | Sbalbp/DIRAC | RequestManagementSystem/Service/ReqProxyHandler.py | Python | gpl-3.0 | 7,200 | [
"DIRAC"
] | 0c43dd5820faae1234dcc0367e733243853d8371b266c53c8d6bb75849704705 |
import pytest
import psi4
pytestmark = [pytest.mark.quick]
def test_dft_grid_threaded_raise():
dimer = psi4.geometry("""
1 1
K -4.067042 -1.894214 0.002270
""")
psi4.set_options({
"dft_grid_name": "SG1",
"dft_vv10_radial_points": 50,
"dft_vv10_spherical_points": 1... | ashutoshvt/psi4 | tests/pytests/test_raises.py | Python | lgpl-3.0 | 617 | [
"Psi4"
] | 7e1e0b397238d4bb58534668c1db538678f427b87cc02c38db4817e26deccb5c |
#!/usr/bin/env python -Es
"""
Script that creates bcbio-compatible inputs in case of multiple files samples
"""
import os
import yaml
from collections import defaultdict
from argparse import ArgumentParser
from cluster_helper import cluster as ipc
from bcbio import log
from bcbio.log import logger
from bcbio.install... | Cyberbio-Lab/bcbio-nextgen | scripts/bcbio_prepare_samples.py | Python | mit | 5,871 | [
"Galaxy"
] | 7073483c01cebd9addab9818db0a998cccda782611c03d5a0393353708a0dd81 |
"""
This module contains classes for representing ProblemStatistics object
For further information visit http://codeforces.com/api/help/objects#ProblemStatistics
"""
from . import BaseJsonObject
__all__ = ['ProblemStatistics']
class ProblemStatistics(BaseJsonObject):
"""
Represents a statistic data about ... | soon/CodeforcesAPI | codeforces/api/json_objects/problem_statistics.py | Python | mit | 2,497 | [
"VisIt"
] | 24b7be8c94ff12b7c437638ffa3f065b4c5cc7a688597f1fe82449af7d0fb754 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Created on Mar 19, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Mar 19, 2012"
import os
import uni... | yanikou19/pymatgen | pymatgen/entries/tests/test_compatibility.py | Python | mit | 22,208 | [
"pymatgen"
] | 074f2c11b7011a33792977057d17e94bed5a33a4672d703859d64d730b1a9541 |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
from contextlib import contextmanager
from unittest.mock import patch
from odoo.tests.common import TransactionCase, HttpCase
from odoo import Command
class TransactionCaseWithUserDemo(TransactionCase):
def setUp... | jeremiahyan/odoo | odoo/addons/base/tests/common.py | Python | gpl-3.0 | 14,419 | [
"Amber"
] | b8f834c33a6d12376581cc3dbe7a03c7893db2aef902b4e8ad7acc2abd5a8bb3 |
import time
import numpy as np
import theano
import theano.tensor as T
import ops
def expressions_YTYpR_byY(Y, lambda_reg):
f = Y.shape[1] - 1 # f = number of factors
Y_e = T.set_subtensor(Y[:, f], T.ones((Y.shape[0],))) # factors with biases replaced by a column of ones.
YTY = T.dot(Y_e.T, Y_e)
... | benanne/theano_wmf | theano_wmf.py | Python | mit | 8,156 | [
"Gaussian"
] | fe85592313aeaf84c3b7a410cfa6c8bd5f805a85f51f5cd9a47bd70ab70d19ca |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-kill
# Author : Stuart Paterson
########################################################################
"""
Issue a kill signal to a running DIRAC job
Example:
$ dirac-wms-job-kill 1918
Killed... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_job_kill.py | Python | gpl-3.0 | 1,520 | [
"DIRAC"
] | 2df944cf9d98e51521b85b437f6f8eb2d6baaf8d663d89a468ea9f155ddc2719 |
# -*- coding: utf-8 -*-
u"""SRW execution template.
:copyright: Copyright (c) 2015 RadiaSoft LLC. All Rights Reserved.
:license: http://www.apache.org/licenses/LICENSE-2.0.html
"""
from __future__ import absolute_import, division, print_function
from pykern import pkcompat
from pykern import pkinspect
from pykern imp... | mkeilman/sirepo | sirepo/template/srw.py | Python | apache-2.0 | 80,889 | [
"CRYSTAL",
"VTK"
] | 78aec70861737c4f84a4572dfd56239b3b4e3220fc2fdc0dd6118116f66453c5 |
# python_version >= '3.5'
#: Okay
class C:
async def __init__(*args, **kwargs):
pass
#: N805:4:17
class C:
@decorator(
'a')
async def m(cls, k='w'): # noqa: N805
pass
#: N805(--staticmethod-decorators=exstatik,stcmthd)
class ButWeLostTheOriginalStaticMethodLateDecorator(object):
... | flintwork/pep8-naming | testsuite/N805_py35.py | Python | mit | 394 | [
"exciting"
] | f4bb5fc6bdfa13097a1f32251567167ca14ca9b64a62ff9b64a3d759374b0c75 |
from django.shortcuts import render
from django.http import JsonResponse
from django.db import connections
from django.db.models import Count
from django.contrib import admin
from visitor.models import Apache
import json
admin.site.register(Apache)
# Create your views here.
def text(request):
apachelogs_list = Ap... | za/dd3 | dd3/visitor/views.py | Python | apache-2.0 | 1,183 | [
"VisIt"
] | 1e0b8134cfd9abd50611c9b5431c25627efb2b46f535d4e7c3dd47006752045c |
"""Extensions to the ase Atoms class
"""
import numpy as np
from ase import Atoms
from ase.io import read, write
from ase.data import covalent_radii
from ase.calculators.neighborlist import NeighborList
class Cluster(Atoms):
"""A class for cluster structures
to enable simplified manipulation"""
def __in... | qsnake/gpaw | gpaw/cluster.py | Python | gpl-3.0 | 6,110 | [
"ASE",
"GPAW"
] | ba97dfcead6e5c580b0d14f779994bafae54c3b7dd23be59e5ae27ffd4b61d87 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes that operate on points or vectors in 3D space.
"""
import re
import string
import warnings
from math import cos, pi, sin, sqrt
import numpy as np
from monty.json import MSONab... | davidwaroquiers/pymatgen | pymatgen/core/operations.py | Python | mit | 22,058 | [
"CRYSTAL",
"pymatgen"
] | e997da2099c7f7b618010af3acd281a9db72a56d2f74e1eea97b7e84b1efd9f9 |
import pycuda.driver as cuda
import pycuda.autoinit
from pycuda.compiler import SourceModule
from pycuda import gpuarray
from pylab import *
from numpy import *
from time import time
from ..model.sample_prep import Q_space
from .approximations import wavefunction_format
import numpy
import time
def loadkernelsrc(nam... | reflectometry/osrefl | osrefl/theory/DWBA_Cuda.py | Python | bsd-3-clause | 18,701 | [
"Gaussian"
] | abe18cee881fdda79cc7e5fad2a8c863174c60ba7cc535d956172239aba2695d |
# pymol -c generate2.py
from chempy import io
from glob import glob
from copy import deepcopy
# backbone-independent rotamers
lines = io.lst.fromFile("bbdep02.May.lib")
chi = { 'CYS' :
{ '1': ('N' , 'CA' , 'CB' , 'SG' ) },
'ASP' :
{ '1': ('N' , 'CA' , 'CB' , 'CG' ),
'2': ('CA' ... | gratefulfrog/lib | python/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py | Python | gpl-2.0 | 4,774 | [
"ChemPy",
"PyMOL"
] | 7ad01b9aa365b07f0f296367e873c8cb72b181b89967e6678acc85e99172f743 |
#* 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_RequiredApps.py | Python | lgpl-2.1 | 881 | [
"MOOSE"
] | 82c091c79ba13999a5c658e99407886fe259efaeea503d2c96e7b6d167fe7257 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from io import BytesIO
from threading import Lock
import contextlib
import itertools
import os.path
import pickle
import shutil
import tempfile
import unittest
import sys
import numpy as np
import pandas as pd
... | jhamman/xray | xarray/tests/test_backends.py | Python | apache-2.0 | 81,552 | [
"NetCDF"
] | 4d5674fdf22048c73d73e598deb446650ae7e631083d0f7f395f1c2afd9a1b2f |
#!/usr/bin/env python
import ts
import matplotlib.pyplot as plt
import numpy as np
import mdtraj as md
from argparse import ArgumentParser
parser = ArgumentParser( description = 'Calculate Mutual Information')
#
# INPUT FILES
#
parser.add_argument("-f","--traj",dest="traj",action="store",type=str,default=None,help="In... | sherpaman/MolToolPy | bin/calc_transfer_info_traj_fluct.py | Python | gpl-2.0 | 2,175 | [
"MDTraj"
] | 585134ac84626d210363e6a807fd3f5aa4250cca1fadf4c13a2224d40ec0fd87 |
from __future__ import division
from __future__ import print_function
""" 30.06.2016 copied from "produce_forecasts_nrt.py"
which was operational on SatLive
"""
from datetime import datetime
import sys, string, os
import logging
sys.path.insert(0, "/home/lom/users/cll/pytroll/install/lib/python2.6/site-packages")
f... | meteoswiss-mdr/monti-pytroll | scripts/produce_forecasts_develop.py | Python | lgpl-3.0 | 49,128 | [
"NetCDF"
] | b32e8e93c5b5c1d51637f5bb734bf0848335e996660b8defa56f6ee185de49a3 |
#!/usr/bin/env python
# -*- coding: utf-8
# Functions that perform mathematical operations on an image.
import logging
import numpy as np
from skimage.morphology import erosion, dilation, disk, ball, square, cube
from skimage.filters import threshold_local, threshold_otsu
from scipy.ndimage.filters import gaussian_f... | neuropoly/spinalcordtoolbox | spinalcordtoolbox/math.py | Python | mit | 9,798 | [
"Gaussian"
] | ec77fc75e939432cc9a5a5de51b830e505827a4d9dd1bba9f54d5a320a53b2f0 |
"""
GEMPRO
======
"""
import logging
import os
import os.path as op
import shutil
from copy import copy
import pandas as pd
from Bio import SeqIO
from bioservices import KEGG
from bioservices import UniProt
from cobra.core import DictList
from six.moves.urllib.error import HTTPError
from slugify import Slugify
impor... | nmih/ssbio | ssbio/pipeline/gempro.py | Python | mit | 78,176 | [
"BLAST",
"Biopython"
] | 4a62773d0aaa5200b47e2dce40c7e58067ab7ff507b32c064684e34a565169bf |
from pssh import ParallelSSHClient
import paramiko
import argparse
import pssh.utils
parser = argparse.ArgumentParser(description='Take an SSH Key and Blast it across the network.')
parser.add_argument('-i', '--input', required=True, help='The input file containing hosts')
parser.add_argument('-s', '--sudo', default=F... | sleventyeleven/badkeys_checker | SSHScanner.py | Python | gpl-2.0 | 1,896 | [
"BLAST"
] | f17921a8907946dc903e91567c7469890c2bf17b6b38f658a7caf1ac399d9d82 |
#!/usr/bin/env python
""" pure utilities (other)
generally useful functions for CaImAn
See Also
------------
https://docs.python.org/3/library/urllib.request.htm
"""
#\package Caiman/utils
#\version 1.0
#\bug
#\warning
#\copyright GNU General Public License v2.0
#\date Created on Tue Jun 30 21:01:17 2015
#\autho... | agiovann/Constrained_NMF | caiman/utils/utils.py | Python | gpl-2.0 | 25,059 | [
"NEURON"
] | 032f693cb7c40ef625a38ae2e34f256c62a7e7bafa033c8927965623682f936a |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'DataDomain.order'
db.add_column(u'profiles_datadomain', 'order', self.gf('django.db.models... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0068_auto__add_field_datadomain_order.py | Python | mit | 22,873 | [
"MOE"
] | 127ede2b8dbe5d0c866ecaa6cae1af7b87aa197458d48f5fe1f29eb6ff93a845 |
import unittest
import test_vers
from streamsx.topology.topology import *
from streamsx.topology import context
from streamsx.topology.schema import CommonSchema
from streamsx.topology.tester import Tester
from streamsx.spl import op
import time
import os
import datetime
class Person(object):
def __init__(self, ... | wmarshall484/streamsx.topology | test/python/topology/test2_python_window.py | Python | apache-2.0 | 8,492 | [
"DIRAC"
] | 53f087963cd1df1fd62a93e32e76732351d37401cb29896f486186b0b864203d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Unit tests for data_ingestion.py"""
__version__ = '$Id: 568a6aaef622d61870862a94f33f8c743cf2f7f3 $'
import os
import unittest
import test_utils
import pywikibot
import data_ingestion
class TestPhoto(unittest.TestCase):
def setUp(self):
self.obj = data_inges... | races1986/SafeLanguage | CEM/tests/test_data_ingestion.py | Python | epl-1.0 | 2,763 | [
"CRYSTAL"
] | b50b3cd58ad0e75101a1c828524c48546dcc154cbe8d948d92c629c12cf34ed0 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
"""Analysis of results from mdevents_optimize... | mganeva/mantid | Framework/DataObjects/scripts/analysis.py | Python | gpl-3.0 | 5,578 | [
"Mayavi"
] | 1d82261ce5c3af97e6b3eb40a61a6f31ae6b531ca645e011042c15947c092bad |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007-2014 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Softw... | tiagocardosos/stoq | stoqlib/reporting/transfer.py | Python | gpl-2.0 | 2,250 | [
"VisIt"
] | 5ec5f1a9708e56fcc75f9b033d2238dad2807b8c500b3697ce48d0f11fc3f502 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | CDSherrill/psi4 | psi4/driver/qcdb/molpro2.py | Python | lgpl-3.0 | 27,439 | [
"CFOUR",
"Psi4"
] | 5069105b7f7403132b84358e3010cd61cc87972ca008acb6cfbe1194339c3f54 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# settings - back end for the settings page
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Li... | heromod/migrid | mig/shared/functionality/settings.py | Python | gpl-2.0 | 40,926 | [
"Brian"
] | 91914e523ba4749724e7b1ead245aa6b7db67304f6f5e6d84ab4a1e23b27e6ff |
__author__ = "Christian Kongsgaard"
__license__ = 'MIT'
# -------------------------------------------------------------------------------------------------------------------- #
# IMPORTS
# Modules
import numpy as np
import pandas as pd
from scipy.optimize import curve_fit
import os
import matplotlib.pyplot as plt
fro... | thp44/delphin_6_automation | test_files/driving_rain_model.py | Python | mit | 8,199 | [
"Gaussian"
] | 812d2285abe85e1c12f332513bc691b4a3224bf1c1fd2d600b050a41c3258bca |
from __future__ import print_function
"""An experimental package for making plots during a simulation.
A PrimiPlotter can plot a list of atoms on one or more output devices.
"""
from numpy import *
from ase.visualize.colortable import color_table
import ase.data
import sys, os, time, weakref
import collections
class... | suttond/MODOI | ase/visualize/primiplotter.py | Python | lgpl-3.0 | 35,589 | [
"ASE",
"RasMol"
] | 0e6107e465c5adc24d49133d771615ef134001474f6d26d487bf58c690ab41c2 |
##############################################################################
# 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... | krafczyk/spack | var/spack/repos/builtin/packages/r-gosemsim/package.py | Python | lgpl-2.1 | 2,171 | [
"Bioconductor"
] | 75e4554b5ab8a6f50e506f0006749737bbc7dfb33eb47c5d6a0bea0d48cfd341 |
# coding=utf-8
"""
Unit Tests for sickbeard/numdict.py
"""
# pylint: disable=line-too-long
from __future__ import print_function, unicode_literals
import os.path
import sys
import unittest
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), '../lib')))
sys.path.insert(1, os.path.abspath(os.p... | terbolous/SickRage | tests/numdict_tests.py | Python | gpl-3.0 | 19,849 | [
"Octopus"
] | b4abda4ec178ed0d9a715cfbb4bfaedf9223dc65f40579f0323f5223f223b2fb |
from __future__ import absolute_import
import six
import inspect
from parsimonious.grammar import Grammar, NodeVisitor
from parsimonious.exceptions import ParseError
from sentry.stacktraces.platform import get_behavior_family_for_platform
from sentry.grouping.utils import get_rule_bool
from sentry.utils.safe import ... | mvaled/sentry | src/sentry/grouping/fingerprinting.py | Python | bsd-3-clause | 10,477 | [
"VisIt"
] | 407d9f79b9398d078360c6f21fb70d2889f7ecdfef2c0bfd980ee5ac57ab9c9b |
# Copyright (C) 2016 Christopher M. Biwer, Collin Capano
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This progr... | ahnitz/pycbc | pycbc/distributions/gaussian.py | Python | gpl-3.0 | 10,663 | [
"Gaussian"
] | a39b9b8fadb885919b1e5a29cb1a2009b46349253268fc576d14c20a920dab7f |
#!/home/psilocaluser/toolchainconda/bin/python
# CDS:
# need to get the right python... we have to update the line above if
# python moves (sigh). /usr/bin/env python3 wouldn't work for me
# when this is called as a crontab (even though it works when called
# as a user). Only thing I found that worked was hardwiring... | psi4/psi4meta | github-feed/parse_gh_commits.py | Python | gpl-2.0 | 3,546 | [
"Psi4"
] | 5dd106ee537302e2a20c30d95f9286a8cef9beaa31060da221e564d5275b2265 |
#
# iqcalc.py -- image quality calculations on FITS data
#
# Eric Jeschke (eric@naoj.org)
#
# Copyright (c) 2011-2012, Eric R. Jeschke. All rights reserved.
# This is open-source software licensed under a BSD license.
# Please see the file LICENSE.txt for details.
#
import math
import logging
import numpy
import thre... | astrofrog/ginga | ginga/iqcalc.py | Python | bsd-3-clause | 13,125 | [
"Gaussian"
] | a697333c39f6768dd36d68cd85ac7a53bfbf77e47d578f6921559c9f4de24981 |
"""
Demo by G. Brammer
"""
import numpy as np
from voronoi import bin2d
import matplotlib.pyplot as plt
# Noisy gaussian
yp, xp = np.indices((100,100))
R = np.sqrt((xp-50)**2+(yp-50)**2)
sigma = 10
g = 10*np.exp(-R**2/2/sigma**2)
s = 1
noise = np.random.normal(size=R.shape)*s
pix_bin, bin_x, bin_y, bin_sn, bin_npix, ... | lauralwatkins/voronoi | example/test.py | Python | bsd-2-clause | 1,615 | [
"Gaussian"
] | 80c33a160e643949ff26ff863678e1599f99ead64cd307d7ca35e13c330c9419 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | capoe/espressopp.soap | src/integrator/LiquidGasLB.py | Python | gpl-3.0 | 4,569 | [
"ESPResSo"
] | 3b48a40e5cbb3b04c933aa85a4fc09ae328648b4adb5b3d4e35e22bd7c0534f3 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-dialogflow-cx | tests/unit/gapic/dialogflowcx_v3/test_transition_route_groups.py | Python | apache-2.0 | 108,247 | [
"Octopus"
] | f7f98474c6e8f546dc235555a0d7042c83f973acafdca83cb763dfdc7fbcb22f |
#!/usr/bin/env python
"""
The expressions module contains classes to represent an expression. The main
class is ExpressionNode. ExpressionNode's most useful method is py_string(),
which returns a Python string representing that expression.
"""
import sys
from .ctypedescs import *
import keyword
# Right now, the obj... | davidjamesca/ctypesgen | ctypesgen/expressions.py | Python | bsd-2-clause | 11,176 | [
"VisIt"
] | 6db17d9efd163e042bc6854ea219ff667776e1278cefd36f67d0a25f3734fd44 |
import numpy as np
colors = 'brgmck'
def sample_clusters(amps, means, varis, N=100, D=2, bounds=None):
'''
Draws samples from a set of clusters.
*amps*: [iterable] cluster weights; fraction of points drawn from each
*means*: [iterable of D-vectors] cluster centers, eg
[ [0,0], [1,2] ] describ... | dstndstn/Unsupervised | utils.py | Python | gpl-2.0 | 10,718 | [
"Gaussian"
] | 3f37e2537ba325e17a20edbdbd8c7edeab44b304e72802bafab784e14080d2e8 |
# The MIT License (MIT)
#
# Copyright (c) 2015 Philippe Proulx <eeppeliteloop@gmail.com>
# Copyright (c) 2015 Simon Marchi <simon.marchi@polymtl.ca>
#
# 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 S... | simark/pygdbmi | pygdbmi/visitors.py | Python | mit | 7,906 | [
"VisIt"
] | 6d9c10c75dd867b539a4a227ae2b31bc205dffccad34b0a284f69b79bca8d01d |
# Copyright (c) 2018 Santosh Philip
# =======================================================================
# Distributed under the MIT License.
# (See accompanying file LICENSE or copy at
# http://opensource.org/licenses/MIT)
# =======================================================================
"""home of e... | jamiebull1/eppy | eppy/easyopen.py | Python | mit | 4,982 | [
"EPW"
] | a7116287f9c6bd1bd06f3964fef255b581cd32ed49c68f3338d93ea869b9ed31 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Tests for the Popularity Contest (popcontest) parser."""
import unittest
from plaso.formatters import popcontest # pylint: disable=unused-import
from plaso.lib import eventdata
from plaso.lib import timelib
from plaso.parsers import popcontest
from tests import test_lib ... | dc3-plaso/plaso | tests/parsers/popcontest.py | Python | apache-2.0 | 7,240 | [
"ORCA"
] | 652ab09478727eb3a6614c056faf74016ef7d71d31b1ca81fe6de4ac13221cfe |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems 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
#
# ... | nhynes/neon | examples/mnist_merge.py | Python | apache-2.0 | 2,572 | [
"Gaussian"
] | f083e21dad9292405aacfe031312c970b2c082e2e30ab4c0940ade05d1bd9409 |
import pybedtools
import os, difflib, sys
from textwrap import dedent
from nose import with_setup
from nose.tools import assert_raises, raises
from pybedtools.helpers import BEDToolsError
from pybedtools import featurefuncs
from tfuncs import setup, teardown, testdir, test_tempdir, unwriteable
def fix(x):
"""
... | jos4uke/getSeqFlankBlatHit | lib/python2.7/site-packages/pybedtools/test/test1.py | Python | gpl-2.0 | 47,373 | [
"BWA"
] | 4d93774960541edb28d138b33635e5885bea463e6786c1ee720fbea8a3b34777 |
"""
Module simplifying manipulation of XML described at
http://libvirt.org/formatdomain.html
"""
import logging
from autotest.client.shared import error
from virttest import virsh, xml_utils
from virttest.libvirt_xml import base, accessors, xcepts
from virttest.libvirt_xml.devices import librarian
class VMXMLDevices... | sathnaga/virt-test | virttest/libvirt_xml/vm_xml.py | Python | gpl-2.0 | 24,993 | [
"VisIt"
] | 3ea305c24492227774a4e14dca88c057a2184f92fb220205235e263bdede147e |
import numpy as np
import scipy as sp
import scipy.interpolate
import scipy.spatial
import pickle
import vtk
import vtk.util.colors
import math
import warnings
warnings.filterwarnings("error")
class Plotter:
COLOR_BG = vtk.util.colors.light_grey
COLOR_BG_PLOT = vtk.util.colors.ghost_white
#vtk.util.colors.... | trianam/voropath | plotter.py | Python | gpl-2.0 | 22,000 | [
"VTK"
] | 430365ddca2f9ec4fde18b1c9836632ac2f359fe59d1ea5ac1e04ea2391047b2 |
"""
Set up the plot figures, axes, and items to be done for each frame.
This module is imported by the plotting routines and then the
function setplot is called to set the plot parameters.
"""
from __future__ import print_function
from clawpack.geoclaw import topotools
import pylab
import glob
from numpy imp... | clawpack/adjoint | examples/adjoint_CrescentCity/setplot.py | Python | bsd-2-clause | 5,998 | [
"NetCDF"
] | 58398ac7fdd4c9d56a7dd64998c9370e65ffddb318ab304cf9155740141a5783 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import re
import time
import numpy as np
from pair_correlation import *
import omero.scripts as scripts
import omero.util.script_utils as script_util
from omero.gateway import BlitzGateway
import omero
from omero.rtypes import *
from email.MIMEMultipart import ... | QBI-Microscopy/omero-user-scripts | PALM-STORM/Pair_Correlation_Function.py | Python | gpl-2.0 | 20,571 | [
"Gaussian"
] | b66af0fb6d54e61edc8abbf5cf5903d08bbade6053b1c8b3b2050bca69b6a197 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# restartfe - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of... | heromod/migrid | mig/shared/functionality/restartfe.py | Python | gpl-2.0 | 3,973 | [
"Brian"
] | 45d5df440cce7bd5cd436c4a2a536ae0b14c3c0221d72c0e465ffbe80875dbcd |
#!/usr/local/bin/env python
#=============================================================================================
# Analyze datafiles produced by YANK.
#=============================================================================================
#=============================================================... | choderalab/brokenyank | src/yank/analysis.py | Python | lgpl-3.0 | 33,936 | [
"Amber",
"NetCDF"
] | 858f38099a74df20ebf8aad7f48db26af6229e02ac087d690965835101dc5558 |
skills = [
{
"id" : "0001",
"name" : "Liver of Steel",
"type" : "Passive",
"isPermable" : False,
"effects" :
{
"maximumInebriety" : "+5",
},
},
{
"id" : "0002",
"name" : "Chronic Indigestion",
"type" : "Combat",
... | KevZho/buffbot | kol/data/Skills.py | Python | mit | 27,396 | [
"MOOSE",
"SIESTA"
] | 1c78c2042432896d542f2987209bd10a6429ae5a62040ff0e8d4d4dd5edb1b12 |
"""Fetch the NASA POWER Dataset.
For now, we just run each Monday for the current year RUN_2AM.sh
"""
import sys
import time
import datetime
import subprocess
from tqdm import tqdm
import requests
import numpy as np
from pyiem import iemre
from pyiem.util import ncopen, logger, exponential_backoff
LOG = logger()
d... | akrherz/iem | scripts/dl/fetch_power.py | Python | mit | 4,562 | [
"NetCDF"
] | 93bdb68d9684e3f41e9d1e55ee0f6db61236e533d736df5d819cb71e0717a2d5 |
"""Testing out vtk
"""
import os
import string
import time
import pdb
import numpy as np
import vtk
from vtk.util import numpy_support
from vtk.util.colors import tomato
from vtk.util.misc import vtkGetDataRoot
from point_cloud import wavefront, raycaster
from visualization import graphics
def vtk_example():
# ... | skulumani/asteroid_dumbbell | integration/vtk_examples.py | Python | gpl-3.0 | 24,601 | [
"VTK"
] | c33b96742ab0592db7a0ccee939c97cbcef53262a5b070a93768942afaf2dfaa |
"""Test correctness of vdW-DF potential."""
import os
from math import pi
from gpaw.grid_descriptor import GridDescriptor
import numpy as np
from gpaw.test import equal
from gpaw.xc import XC
from gpaw.mpi import world
N = 8
a = 2.0
gd = GridDescriptor((N, N, N), (a, a, a))
# Spin paired:
def paired():
xc = XC('v... | qsnake/gpaw | gpaw/test/vdw/potential.py | Python | gpl-3.0 | 1,303 | [
"GPAW"
] | 73c7a5d727bce3794fb78f50a3d6288393289ec3d9ddeeea15a8f47f99dba6a6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import numpy as np
import scipy.constants as const
from monty.json import MSONable
from pymatgen.analysis.structure_matcher import StructureMatcher, \
Or... | aykol/pymatgen | pymatgen/analysis/diffusion_analyzer.py | Python | mit | 38,730 | [
"VASP",
"pymatgen"
] | 245cf3d76e72b7bf9e081680874e79b2cbb0f065a21a6826da81a9b48e2721ea |
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