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#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""\
Wrapper script around Rietveld's upload.py that simplifies working with groups
of files.
"""
import json
import optparse
impo... | chinmaygarde/depot_tools | gcl.py | Python | bsd-3-clause | 51,974 | [
"VisIt"
] | d2b55bfb548920cc510808e7f8f741252f869cd503da26cc7234be6c677bfd66 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Oct 11 14:36:29 2017
@author: derek
"""
import os
import tensorflow as tf
import numpy as np
def _parse_function(example_proto):
"""Reads tfrecords with features {shape: (height,width,depth) of cube data,
label: (malignancy, lobulation, spicul... | dereknewman/cancer_detection | train_label_cat_cubes_3d.py | Python | mit | 13,908 | [
"Gaussian"
] | eba1a468ea4f0119c76aad2f42fb1b1dcc725e4ae40746ce839905b68d590df4 |
'''
Guestbook Parser
Guestbook analyzes an Apache log file and returns information about who
visited a site, or a particular part of a site. For example, it can be used
to retrieve information about visitors' geographic location, or the most frequent
visitors by IP address.
It uses the freegeoip.net location API.
*... | Brian-Lam/Guestbook | guestbook.py | Python | mit | 7,342 | [
"VisIt"
] | 9a1d233b23f94aa95003b0b1a89f13521c0783464e01cca53c61db254c75b10b |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | src/typecode/magic2.py | Python | apache-2.0 | 8,508 | [
"VisIt"
] | 552bcb74ffb24f46463d4161b0b206f47daf9fdb0947ba56cdd82d3128727c1c |
try:
from __builtin__ import unicode as str
except ImportError:
pass
import os
import sys
import time as timer
import math
import traceback
try:
import Queue as queue
except ImportError:
import queue
import logging
import multiprocessing
import numpy as np
import netCDF4
from paegan.location4d import ... | axiom-data-science/paegan-transport | paegan/transport/parallel_manager.py | Python | gpl-3.0 | 20,674 | [
"NetCDF"
] | a04a970dca281cd2e6b3e5352f0e70f3a70240af95d77d647890240a4e375446 |
# coding: utf-8
from __future__ import unicode_literals
import base64
import binascii
import collections
import ctypes
import email
import getpass
import io
import itertools
import optparse
import os
import platform
import re
import shlex
import shutil
import socket
import struct
import subprocess
import sys
import xm... | remitamine/youtube-dl | youtube_dl/compat.py | Python | unlicense | 93,360 | [
"Bowtie"
] | 8fdb4c807e592bc91cbd7e4a2fde2cf38646d382770b80d9dfb83c6de99f0f47 |
#!/usr/bin/env python
from setuptools import setup, find_packages
exec(open('yeadon/version.py').read())
setup(
name='yeadon',
version=__version__,
author='Chris Dembia',
author_email='chris530d@gmail.com',
url="https://github.com/chrisdembia/yeadon/",
description='Estimates the inertial prop... | chrisdembia/yeadon | setup.py | Python | bsd-3-clause | 1,238 | [
"Mayavi"
] | 1298ffa7ddbaf5c863b6811fe9c100e5996e79fa03196e38db08da837fd4fc0d |
# coding: utf-8
from __future__ import unicode_literals, division, print_function
import os
import datetime
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.abinit import events
_test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
'test_files', "abinit")... | migueldiascosta/pymatgen | pymatgen/io/abinit/tests/test_events.py | Python | mit | 2,940 | [
"ABINIT",
"pymatgen"
] | 5767b7a7cb7e30c89e512ef026459e65848fd4d64660852a45efe2cd63f45283 |
from __future__ import absolute_import
from typing import Any, Dict, List, Set, Tuple, TypeVar, \
Union, Optional, Sequence, AbstractSet
from typing.re import Match
from zerver.lib.str_utils import NonBinaryStr
from django.db import models
from django.db.models.query import QuerySet
from django.db.models import Ma... | paxapy/zulip | zerver/models.py | Python | apache-2.0 | 55,239 | [
"VisIt"
] | ddf6e02b3e7adfea41cf3410e3782263a302009bc27cc2799def50da64ab8c4a |
import math
import numpy as np
from PyQt5.QtCore import Qt, QPoint, QRect, pyqtSignal
from PyQt5.QtGui import QPainter, QImage, QPen, QColor, QBrush
from PyQt5.QtWidgets import QWidget
# FIXME[todo]: improve the display of the activations: check that the
# space is used not only in a good, but in an optimal way. Chec... | JarnoRFB/qtpyvis | qtgui/widgets/activationview.py | Python | mit | 13,724 | [
"NEURON"
] | a53f9bdbaf1f7854b70e9e2583d0a00a501f5df1803b569c99a09ecbc3a88a8b |
""" FreeDiskSpacePolicy
FreeDiskSpacePolicy.__bases__:
DIRAC.ResourceStatusSystem.PolicySystem.PolicyBase.PolicyBase
"""
__RCSID__ = '$Id$'
from DIRAC import S_OK
from DIRAC.ResourceStatusSystem.PolicySystem.PolicyBase import PolicyBase
class FreeDiskSpacePolicy(PolicyBase):
"""
The FreeDiskSpacePolic... | chaen/DIRAC | ResourceStatusSystem/Policy/FreeDiskSpacePolicy.py | Python | gpl-3.0 | 2,000 | [
"DIRAC"
] | 0cea9324f49111fd63dfe0c471d4bdea9d7982f74c39a034e7ceebe952977a77 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | espressomd/espresso | samples/visualization_npt.py | Python | gpl-3.0 | 2,563 | [
"ESPResSo"
] | 3d09a1e4e9669dd69653a3d02a292f7f1b60f3230ac370bcf70b403619f7a9f3 |
# Sample module in the public domain. Feel free to use this as a template
# for your modules (and you can remove this header and take complete credit
# and liability)
#
# Contact: Brian Carrier [carrier <at> sleuthkit [dot] org]
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is f... | APriestman/autopsy | pythonExamples/July2015FileTutorial_BigRound/FindBigRoundFiles.py | Python | apache-2.0 | 6,704 | [
"Brian"
] | 57b4fcd652c3596476d431ecbc3d8ccf165d2e14f33dc06a3f85ef711f5ce377 |
#!/usr/bin/env python
"""
Upwind discretization of advection equation
@author Alexander Pletzer
"""
import pnumpy
import numpy
import sys
from mpi4py import MPI
import sys
import operator
import saveVTK
class Upwind:
def __init__(self, velocity, lengths, numCells):
self.rk = MPI.COMM_WORLD.Get_rank()
se... | pletzer/fidibench | upwind/python/upwindMPI.py | Python | mit | 5,436 | [
"VTK"
] | b46bef49878b02169b345491da6b95b532045321dcc1e40705195678b5cc219c |
"""
Some generic utility routines for number handling and
calculating (specific) variances
"""
import logging
import itertools
import numpy
from tkp.utility import containers
from tkp.utility.memoize import Memoize
from tkp.sourcefinder import utils
from tkp.sourcefinder import stats
from tkp.sourcefinder import extra... | bartscheers/tkp | tkp/sourcefinder/image.py | Python | bsd-2-clause | 37,484 | [
"Gaussian"
] | 6dcd0c5fc52cb04d904ad2310956cbd43066b2f196b191516c3160444f11963e |
../../../../../../../share/pyshared/orca/scripts/apps/Eclipse/__init__.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/Eclipse/__init__.py | Python | gpl-3.0 | 73 | [
"ORCA"
] | 3e474af4e6664ef5db25cb625e12f88146a29c48187afa5e4f8e2c1d99913aac |
"""
Python dot expression completion using Pymacs.
This almost certainly needs work, but if you add
(require 'pycomplete)
to your init.el file and have Pymacs installed, when you hit M-TAB it will
try to complete the dot expression before point. For example, given this
import at the top of the file:
import... | paulgriepentrog/python-mode | completion/pycomplete.py | Python | gpl-3.0 | 25,005 | [
"VisIt"
] | 3226c80ef437e3a552d7429d4948a5fdc79a8ff3fcb95d4c85dbc2e769a46688 |
'''
ustvnow XBMC Plugin
Copyright (C) 2015 t0mm0, Lunatixz
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 versi... | aplicatii-romanesti/allinclusive-kodi-pi | .kodi/addons/plugin.video.ustvnow/default.py | Python | apache-2.0 | 4,591 | [
"VisIt"
] | 65936512dea7aeb8e66594e5a324eb8425e66a7982aa33132e01a96615490ab2 |
import numpy as np
from gpaw.lfc import BasisFunctions
from gpaw.utilities import unpack
from gpaw.utilities.tools import tri2full
from gpaw import debug
from gpaw.lcao.overlap import NewTwoCenterIntegrals as NewTCI
from gpaw.utilities.blas import gemm, gemmdot
from gpaw.wavefunctions.base import WaveFunctions
from gp... | robwarm/gpaw-symm | gpaw/wavefunctions/lcao.py | Python | gpl-3.0 | 37,969 | [
"ASE",
"GPAW"
] | 7f59300d22de5fa69f646c411db1085034057d399646a81c1dd4dba3f17b9077 |
# -*- test-case-name: buildbot.broken_test.test_buildreq -*-
from twisted.trial import unittest
from twisted.internet import defer
from buildbot import sourcestamp
from buildbot.buildrequest import BuildRequest
from buildbot.status.builder import SUCCESS, FAILURE
from buildbot.changes.changes import Change
from build... | centrumholdings/buildbot | buildbot/broken_test/unit/test_buildreq.py | Python | gpl-2.0 | 12,862 | [
"Brian"
] | bdbd6ccf7833ac6ee3f46174eb2aed71b8a562428adb519d842edcd6cdee873f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010 Radim Rehurek <radimrehurek@seznam.cz>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Tests for Vowpal Wabbit LDA wrapper.
Will not be run unless the environment variable 'VOWPAL_WABBIT_PATH' is set
and points to the ... | markroxor/gensim | gensim/test/test_ldavowpalwabbit_wrapper.py | Python | lgpl-2.1 | 7,796 | [
"Jaguar"
] | 71d1402cd8952fafd4951c2512b6c835ff068075116b61dcbe47379f7fa5d43f |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module is used to estimate the cost of various compounds. Costs are taken
from the a CostDB instance, for example a CSV file via CostDBCSV.
For compounds with no cost listed, a Phase Diagram style convex hull
optimiza... | materialsproject/pymatgen | pymatgen/analysis/cost.py | Python | mit | 6,163 | [
"pymatgen"
] | 2febcf27999386bbf20905755a01b26c00a28178278c4de88c7db3dc6966a10a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import os
import tempfile
import shutil
from pymatgen.util.testing import PymatgenTest
from monty.functools import lazy_property
from pymatgen.... | johnson1228/pymatgen | pymatgen/io/abinit/tests/test_flows.py | Python | mit | 11,432 | [
"ABINIT",
"pymatgen"
] | f5db368c834f6f2516ed9059bb0b4f5eadc6c173b504b5e236b17d949f821981 |
import re
import sys
import os
###############################################################################
# lexer
###############################################################################
# opaque? unsigned? void?
_keywords = frozenset(["typedef", "namespace", "void", "unsigned", "enum",
... | OkCupid/okws | tools/ast_gen.py | Python | gpl-2.0 | 21,231 | [
"VisIt"
] | 734aad806bbef031d7f6edd32dda6ee5d4b14054f931997e6b6c8e8f9aa2cc62 |
# GromacsWrapper plugin: ls.py
# Copyright (c) 2010 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
ls plugin
=========
This simply lists the files on disk. It is useful for testing the
plugin architecture.
Plugin class... | pslacerda/GromacsWrapper | gromacs/analysis/plugins/ls.py | Python | gpl-3.0 | 3,435 | [
"Gromacs"
] | 9ab65c44bfb04a5bcb6e86cc8df3f308b84a45353f99964aca48d29551c4368b |
#!/usr/bin/env python2.7
#Ryan G. Coleman, Brian K. Shoichet Lab
#reads in file containing terminal rotatable hydrogen definitions.
import string, sys
import math
import geometry_basic
import combinatorics
from collections import defaultdict
class Hydrogens(object):
'''holds parameters that determine what a rotata... | ryancoleman/mol2db2 | hydrogens.py | Python | gpl-2.0 | 10,279 | [
"Brian"
] | ae7019f85e975bf423db944228a7cc28c4107ec400d8ebf765aa07dc8634f3ad |
# Lint as: python3
# 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 ... | tensorflow/lingvo | lingvo/core/rnn_layers_test.py | Python | apache-2.0 | 60,274 | [
"Gaussian"
] | c5bc4d373b3589b604fae506726ffb16b5533d620f2cfb9b1299c7103d67a476 |
# -*- coding: utf-8 -*-
"""
A real simple app for using webapp2 with auth and session.
It just covers the basics. Creating a user, login, logout
and a decorator for protecting certain handlers.
Routes are setup in routes.py and added in main.py
"""
# standard library imports
import logging
import ran... | rchaber/publishbay | boilerplate/handlers.py | Python | lgpl-3.0 | 65,778 | [
"VisIt"
] | c3cbb35e14e8fcd432f652eb84d4ed6e607610293c41cfcc923c46c6d080e18d |
##############################################################################
# Copyright (c) 2013-2017, 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... | TheTimmy/spack | var/spack/repos/builtin/packages/netcdf/package.py | Python | lgpl-2.1 | 8,015 | [
"NetCDF"
] | e44e89a8ddfe99648e9bdf5e506af250e3ce1f64e794c6548e192b73fe54d19e |
# This file is part of Merlin.
# Merlin is the Copyright (C)2008,2009,2010 of Robin K. Hansen, Elliot Rosemarine, Andreas Jacobsen.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; ... | ellonweb/merlin | Hooks/intel/bumchums.py | Python | gpl-2.0 | 2,299 | [
"Galaxy"
] | badf135dee3da231841c02821570ac8f64c3ab5dfe0aeabc7b73a0130a24495c |
#!/usr/bin/env python
"""
Created on Mon Feb 01 15:03:56 2016
@author: Nablaquabla
"""
import h5py
import os
import numpy as np
import easyfit as ef
import sys
# ============================================================================
# Run program
# ================================... | Nablaquabla/csi-analysis | _getSPEQIndex.py | Python | gpl-3.0 | 2,267 | [
"Gaussian"
] | 2229d86c4f6daeb47145daa3a515473346b9182d11e488c89b1a482a692c72a9 |
## Automatically adapted for numpy.oldnumeric Mar 26, 2007 by alter_code1.py
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg & Johan Leckner
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Ge... | ostrokach/biskit | Biskit/PDBParseNCBI.py | Python | gpl-3.0 | 9,024 | [
"Biopython"
] | 1f5a991dab9e26456be6bd0cb87651c36968813a967730c84851c83b8bad1282 |
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import numpy as np
from . import MinCovDet
from ..utils.validation import check_is_fitted
from ..metrics import accuracy_score
from ..base import OutlierMixin
class EllipticEnvelope(OutlierMixin, MinCovDet):
"""An object for detecting... | manhhomienbienthuy/scikit-learn | sklearn/covariance/_elliptic_envelope.py | Python | bsd-3-clause | 8,996 | [
"Gaussian"
] | 6f7f6b48697aad3c00e4b0251cec12e77dcde8c8209cd6f3d6b75957208de226 |
"""
========================================================
Time-frequency on simulated data (Multitaper vs. Morlet)
========================================================
This examples demonstrates on simulated data the different time-frequency
estimation methods. It shows the time-frequency resolution trade-off
a... | rajegannathan/grasp-lift-eeg-cat-dog-solution-updated | python-packages/mne-python-0.10/examples/time_frequency/plot_time_frequency_simulated.py | Python | bsd-3-clause | 4,504 | [
"Gaussian"
] | 7eb9de660e9ef0716cc32c88a5513da7460ddbb6d9e22058aa22a777fdfa8e59 |
# Orca
#
# Copyright 2008 Sun Microsystems Inc.
#
# 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 libr... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/dbusserver.py | Python | gpl-3.0 | 6,167 | [
"ORCA"
] | 05695ae56b15464e6d802c56d22f8e210e3b3410381b75c7b66a827502e25680 |
#!/usr/bin/env python3
import argparse
import razer.client
import sys
def _clamp_u8(value):
if value > 255:
return 255
elif value < 0:
return 0
else:
return value
def _print_table(header_list, rows):
column_lengths = [len(header_item) for header_item in header_list]
for r... | z3ntu/razer-drivers | scripts/daemon/controller.py | Python | gpl-2.0 | 7,782 | [
"Firefly"
] | db5ed729e7eafb0b12eb5dd0a6f74065103dc8fc30ca298c1dbd2a20e559a933 |
#!/usr/bin/env python
"""
compliance_checker/protocols/cdl.py
"""
import os
def is_cdl(filename):
"""
Quick check for .cdl ascii file
Example:
netcdf sample_file {
dimensions:
name_strlen = 7 ;
time = 96 ;
variables:
float lat ;
... | ioos/compliance-checker | compliance_checker/protocols/cdl.py | Python | apache-2.0 | 822 | [
"NetCDF"
] | 7ccaa0f44c95d97eb93ae16e9acfd7fea16117c37fd66d405058e6f925947d5e |
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
D = 126.0
downstreamPosition = [-1.0, 0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 11.0, 12.0, 13.0, 14.0, 15.0, 16.0, 17.0, 18.0, 19.0, 20.0];
lineDir = '../lineData'
time = 1050.0
controlDi... | gzt200361/SOWFA | tutorials/turbine/NREL5MWRef.uniformFlow/system/sampleLine.py | Python | gpl-3.0 | 4,368 | [
"ParaView"
] | 51f918ac90d8b06553ce0cb67df739cc108b227b7352394bf02655cdfd3dd69c |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/inference/inference_model.py | Python | apache-2.0 | 7,656 | [
"ORCA"
] | a392baf1b0b67434b201fc0fbda2a11d4bd9d2b52541c76afd2b2224a03b20cf |
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# Licence: BSD 3 clause
from __future__ import print_function
import numpy as np
from scipy import linalg, optimize
from ..base import BaseEstimator, RegressorMixin
from ..metrics... | RPGOne/Skynet | scikit-learn-c604ac39ad0e5b066d964df3e8f31ba7ebda1e0e/sklearn/gaussian_process/gaussian_process.py | Python | bsd-3-clause | 34,397 | [
"Gaussian"
] | e3d86093b4e2ed630f9ba5a030737011f56196b23c05985d06c6dd3887a154dd |
# 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 u... | nudles/incubator-singa | test/python/test_tensor.py | Python | apache-2.0 | 16,386 | [
"Gaussian"
] | b516c39cc914ad7bd108b7ed1990da63a5981b56276ab040d1e75c0891fd40bc |
#!/usr/bin/env python
# Copyright 2008, 2009
# CAMd (see accompanying license files for details).
import os
from optparse import OptionParser, SUPPRESS_HELP
import ase.gui.i18n
from gettext import gettext as _
# Grrr, older versions (pre-python2.7) of optparse have a bug
# which prevents non-ascii descriptions. Ho... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/gui/ag.py | Python | gpl-2.0 | 5,192 | [
"ASE"
] | 98c68b17fceed590e5a54455efab281f8707899ceaa35638e5991efc56e918af |
#!/usr/bin/env python
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg & Johan Leckner
##
## 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 Softwar... | ostrokach/biskit | scripts/Mod/search_templates.py | Python | gpl-3.0 | 4,647 | [
"BLAST"
] | a5737262273482bc2e4d887a0437034db236613d663ddc19abfac646677e6b1d |
#!/usr/bin/env python
##########################################################################
#
# Copyright 2011 Jose Fonseca
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in th... | PeterLValve/apitrace | scripts/jsondiff.py | Python | mit | 8,804 | [
"VisIt"
] | ef83ceaf62e7f56babc9c6af09b3c399ef1865c9bae1329ced57546743507101 |
# Settings for Zulip Voyager
### MANDATORY SETTINGS
#
# These settings MUST be set in production. In a development environment,
# sensible default values will be used.
# The user-accessible Zulip hostname for this installation, e.g.
# zulip.example.com
EXTERNAL_HOST = 'zulip.example.com'
# The email address for the ... | zachallaun/zulip | zproject/local_settings_template.py | Python | apache-2.0 | 9,628 | [
"VisIt"
] | ac3d3fa82130cbf02ff10f884c6905ad601582c2b41bd3680c40e97aa2962778 |
# $Id$
#
# Copyright (C) 2001-2008 greg Landrum
#
# @@ 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.
#
"""utility functions for clustering
"""
def Ge... | ptosco/rdkit | rdkit/ML/Cluster/ClusterUtils.py | Python | bsd-3-clause | 4,413 | [
"RDKit"
] | feadea0bbee542253218bfbc41f5516bd3ced24cbe43dab5b0da9928255f229e |
"""
.. _point_spread:
Corrupt known signal with point spread
======================================
The aim of this tutorial is to demonstrate how to put a known signal at a
desired location(s) in a :class:`mne.SourceEstimate` and then corrupt the
signal with point-spread by applying a forward and inverse solution.
"... | nicproulx/mne-python | tutorials/plot_point_spread.py | Python | bsd-3-clause | 6,797 | [
"Gaussian",
"Mayavi"
] | b7eb4454ab07b2fa293585fa7f48945ca7f09f326b909c943ab97b31c416f624 |
## Absolute location where all raw files are
RAWDATA_DIR = '/home/cmb-06/as/skchoudh/dna/Oct_10_2016_HuR_Human_Mouse_Liver/rna-seq/Penalva_L_08182016/human'
## Output directory
OUT_DIR = '/staging/as/skchoudh/Oct_10_2016_HuR_Human_Mouse_Liver/RNA-Seq_human'
## Absolute location to 're-ribo/scripts' directory
SRC_... | saketkc/ribo-seq-snakemake | configs/Oct_10_2016_HuR_Human_rna.py | Python | bsd-3-clause | 2,343 | [
"HTSeq",
"pysam"
] | b348557fe16a6b8833f944f40f9fdb32374b165727381e1dbd860ea3dea1d0ca |
# pylint: disable=missing-docstring, invalid-name
import unittest
import numpy as np
from obsoper.exceptions import StepNotFound
from obsoper import (cell,
cursors,
walk)
class TestWalk(unittest.TestCase):
def setUp(self):
longitudes, latitudes = np.meshgrid([100,... | met-office-ocean/obsoper | obsoper/test/test_walk.py | Python | bsd-3-clause | 10,332 | [
"ORCA"
] | c18cfe94bfd948ad4c8a42d686fe0b946ee1d822a07546e61e38bf089999630b |
#!/usr/bin/env python
#from sumatra.projects import load_project
#from sumatra.parameters import build_parameters
#from sumatra.decorators import capture
from ruffus import *
import sys
import os
import time
import datetime
import drmaa
from omics_pipe.utils import *
from omics_pipe.parameters.default_pa... | adammaikai/OmicsPipe2.0 | omics_pipe/WGS_GATK_group_calling.py | Python | mit | 3,992 | [
"BWA"
] | 0e222f0e4da5ee562b34049249244efdd95a4fdb9bed44bbbdc4aa6242a6f3ed |
""" The MJF utility calculates the amount of wall clock time
left for a given batch system slot or VM. This is essential for the
'Filling Mode' where several jobs may be executed in the same slot.
Machine Job/Features are used following HSF-TN-2016-02 if available.
Otherwise values are filled in using ... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/MJF.py | Python | gpl-3.0 | 7,448 | [
"DIRAC"
] | 5c992eb2d426f55bcdc41bb70fac25076d4514cd299f303b7649059fd099bdd0 |
"""
Traits View definition file.
The view trait of the parent class is extracted from the model definition
file. This file can either be exec()ed or imported. See
core/base.py:Base.trait_view() for what is currently used. Using exec()
allows view changes without needing to restart Mayavi, but is slower than
importi... | dmsurti/mayavi | mayavi/core/ui/module_manager.py | Python | bsd-3-clause | 1,127 | [
"Mayavi"
] | b2b88f550429f400ef3b8c754f63737c97a73c0aa9136db251745987b1dbf75d |
"""Optimise the cache."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import _, logger
import os, sys
def _already_linked(a, b):
ai = os.stat(a)
bi = os.stat(b)
return (ai.st_dev, ai.st_ino) == (bi.st... | dsqmoore/0install | zeroinstall/zerostore/optimise.py | Python | lgpl-2.1 | 3,568 | [
"VisIt"
] | bbc7e3ebe2a7dfa93526623502b81e557b1d0f10261d2f7c27d981ff22c22ef1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
try:
from urllib.parse import urlsplit, urlparse, parse_qs, urljoin
except:
from urlparse import urlsplit, urlparse, parse_qs, urljoin
import json
import os
import re
import time
import urllib
from base64 import b64decode
from core import httptools
from platformc... | alfa-jor/addon | plugin.video.alfa/lib/unshortenit.py | Python | gpl-3.0 | 17,786 | [
"ADF"
] | 9079d165a7fe4f54123350ef8f04182101ad646aa2c2478e6bac763ce7df90a9 |
from flask_restful import Resource
class Status(Resource):
def get(self):
status = {
'serviceName': 'GO Analysis Service',
'description': 'Perform GO enrichment analysis with Bioconductor',
'apiVersion': 'v1',
'buildVersion': '0.1.0'
}
ret... | cytoscape-ci/go-enrichment | api/status.py | Python | mit | 331 | [
"Bioconductor"
] | 0a50d1a46afb6a432c768deaeb1c05c56ca4f42fb98533ada48564dc35613fd1 |
from PyQt5.QtCore import pyqtSlot, pyqtSignal, Qt, QVariant, QTimer
from PyQt5.QtWidgets import QWidget, QFrame, QMenu, QAction, \
QPushButton, QLabel, QVBoxLayout, QHBoxLayout, QLineEdit, QToolButton, \
QMessageBox, QGridLayout, QScrollArea, QLayout
from PyQt5.QtGui import QIcon, QCursor, QPixmap, QFont
from ... | minlexx/xnovacmd | ui/planet_widget.py | Python | gpl-2.0 | 37,758 | [
"CRYSTAL",
"Galaxy"
] | 7963953c4684e8f33973a510385d68f782e263d8b33e852948e2b8e99e7afdb8 |
'''
This program is to identify those multiply mapped reads which are mapped to different isoform of the same genes.
This program has three steps.
1. Load the realtions of ENSTs and ENSGs.
2. Select the reads which maps to different ENSTs of the same ENSG
3. Dump them to the output file
The Ensembl Annotation... | claudejrogers/RNASEQR | selected_the_multiply_mapped_reads_of_the_same_genomic_position.py | Python | gpl-3.0 | 35,467 | [
"BLAST",
"BWA",
"Bowtie"
] | 53cac7bc4d97da902543a4ae73166c40558763562d610dceb414967daad405d9 |
# classification.py
"""
Description: This file contains a set of python functions for conducting
machine learning classification on remote sensing data contained in an
Open Data Cube instance.
License: The code in this notebook is licensed under the Apache License,
Version 2.0 (https://www.apache.org/licenses/LICENSE-... | ceos-seo/data_cube_utilities | dea_tools/dea_tools/classification.py | Python | apache-2.0 | 62,134 | [
"Gaussian"
] | c85fdc08e416d2c1ad95ac185300bd0dfba14efdf7d6149976a75f392ab00a75 |
#
# Copyright (C) 2020 Kevin Thornton <krthornt@uci.edu>
#
# This file is part of fwdpy11.
#
# fwdpy11 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... | molpopgen/fwdpy11 | fwdpy11/genetic_values.py | Python | gpl-3.0 | 18,005 | [
"Gaussian"
] | a71097351925075c796c36834d3f2b2621c6d25ed82c986c57f59000e8aac5ba |
from django.core.urlresolvers import reverse_lazy
from django.utils.translation import ugettext_lazy as _
from django.core.urlresolvers import reverse
from horizon import exceptions
from horizon import forms
from horizon import workflows
import json
from crystal_dashboard.api import projects as api
from crystal_dashbo... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/projects/groups/views.py | Python | gpl-3.0 | 1,490 | [
"CRYSTAL"
] | d15e513631f2bac3531f911cf3b71664c057589823c0f73083748bbdf11697b4 |
import os
import re
import string
import random
import json
import time
import markovify
from textblob import TextBlob
from textblob import Word
from flask import Flask
from flask import render_template, url_for, request, jsonify
import requests
import twitter
app = Flask(__name__)
# Used to build up ... | tkah/wriwenis | app.py | Python | mit | 17,132 | [
"VisIt"
] | 7a10d26f6145afc24ce0583085a7e35448d059e6befb5b0ffc2dca6558b6aabe |
import ast
from myhdl._convutils import _makeAST, _genfunc
from myhdl._util import _flatten
from myhdl._enum import EnumType
from myhdl._Signal import SignalType
class Data():
pass
def _resolveRefs(symdict, arg):
gens = _flatten(arg)
data = Data()
data.symdict = symdict
v = _AttrRefTransformer(d... | forrestv/myhdl | myhdl/_resolverefs.py | Python | lgpl-2.1 | 1,977 | [
"VisIt"
] | 163e9f65464dddbc44b2d6962741bbf7e127a82dd022f7e3dea12934b5152024 |
from nac.common import retrieve_hdf5_data
from nac.workflows.input_validation import process_input
from nac.workflows import workflow_stddft
from os.path import join
from .utilsTest import remove_files, copy_basis_and_orbitals
import numpy as np
import pkg_resources as pkg
import os
import tempfile
# Environment dat... | felipeZ/nonAdiabaticCoupling | test/test_absorption_spectrum.py | Python | mit | 2,093 | [
"NAMD"
] | 5e4d222919727e13dd72efbcb017b88839ff32916ba7006fbbc7b26450f3aa00 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; ... | Forage/Gramps | gramps/gui/pluginmanager.py | Python | gpl-2.0 | 12,518 | [
"Brian"
] | 2499664f50a4a15136a16f2463779356594050bb059424ea749b8619751df39c |
"""loader_moose.py:
Load a SWC file in MOOSE.
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2015, Dilawar Singh and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer__ = "Dilawar Singh"
_... | BhallaLab/benchmarks | neuro_morpho/loader_moose.py | Python | gpl-2.0 | 6,492 | [
"MOOSE"
] | 650304f9db6ff26e1ee44cfb76ff24fc84e037f4879da9d0eab2f5f0150182e2 |
"""Integration with Python standard library module urllib2: OpenerDirector
class.
Copyright 2004-2006 John J Lee <jjl@pobox.com>
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD or ZPL 2.1 licenses (see the file
COPYING.txt included with the distribution).
"""
import o... | deanhiller/databus | webapp/play1.3.x/samples-and-tests/i-am-a-developer/mechanize/_opener.py | Python | mpl-2.0 | 14,502 | [
"VisIt"
] | e77b2e62eeb5596d11d8c4757b3a5830541fc7ea10c67cb0e79a49ebc694c1ea |
import json
import math
import os
import random
import getdist
import getdist.plots
import matplotlib.pyplot as pyplot
import numpy
import pymultinest
#
# Model parameter information
#
params_min = [
0,
0,
50,
0
]
params_max = [
1000,
1000,
1000,
1000
]
params_count = len(params... | caseresearch/code-review | code-review/2015--2016/multinest_demo.py | Python | mit | 4,355 | [
"Gaussian"
] | 3ac8a8163070f8af574c40116f09d6eb4b70ad94597ded68c7be624fe309505f |
"""
This module generates fake curves by "drawing" them from common sourcesplines, adding noise, tweaking microlensing.
"""
import sys, os, time
import numpy as np
import pycs.gen.lc
import pycs.gen.util
import pycs.sim.src
import scipy.ndimage.filters
def sample(lc, spline):
"""
You give me a lightcurve, ... | COSMOGRAIL/PyCS | pycs/sim/draw.py | Python | gpl-3.0 | 22,455 | [
"Gaussian"
] | 9f4a25c2e810cd976c5cca6e8c092c7601779a261f88857df537c7909e344efe |
# This file is part of PyEMMA.
#
# Copyright (c) 2014-2017 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 versi... | marscher/PyEMMA | pyemma/_base/serialization/mdtraj_helpers.py | Python | lgpl-3.0 | 5,240 | [
"MDTraj"
] | 7c357ba4aed3e0d59abcabc50beadee3be5a0f0aae1aa2342f5205f31b06b5d7 |
from __future__ import absolute_import, unicode_literals
from django.test import TestCase
from .models import (Building, Child, Device, Port, Item, Country, Connection,
ClientStatus, State, Client, SpecialClient, TUser, Person, Student,
Organizer, Class, Enrollment)
class SelectRelatedRegressTests(TestCase)... | rebost/django | tests/regressiontests/select_related_regress/tests.py | Python | bsd-3-clause | 6,546 | [
"Brian"
] | f87fb6a4d856eb27089eb4c8c22824474183aa3e95ef555af6f4a6bd119a9d1a |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module provides classes to create phase diagrams.
"""
from six.moves import filter
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "2.0"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyue... | Dioptas/pymatgen | pymatgen/phasediagram/pdmaker.py | Python | mit | 18,351 | [
"pymatgen"
] | c895eed4e7d3d4b308cce4ebf3678d2506bed4d9da1e69f0d28c4769418296ac |
##############################################################################
#
# Copyright (c) 2003 Zope Foundation and Contributors.
# All Rights Reserved.
#
# This software is subject to the provisions of the Zope Public License,
# Version 2.1 (ZPL). A copy of the ZPL should accompany this distribution.
# THIS SOF... | mdworks2016/work_development | Python/05_FirstPython/Chapter9_WebApp/fppython_develop/lib/python3.7/site-packages/zope/interface/advice.py | Python | apache-2.0 | 7,612 | [
"VisIt"
] | 0a91e1b804fc9db69aca60c1117bb1bc9bfd651304b6aedf8139a850ec2c4b78 |
#!/usr/bin/python -u
import os, subprocess
import collections
from argparse import Namespace
from gmx_lib import run_setup
from gmx_lib.run_setup import WorkdirStructure
from gmx_lib.gmx_engine import GmxEngine
from gmx_lib.gmx_params import GmxParameters
from modeling_lib.scwrl_engine import ScwrlEngine
from modeli... | ivanamihalek/smallmol | gmx03_mutation_scan.py | Python | gpl-2.0 | 6,294 | [
"Gromacs"
] | b03eeba6e63933b8335d527b7b376383e9256ea112ea659cc3d8c56decee75b5 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | Karaage-Cluster/karaage | karaage/common/context_processors.py | Python | gpl-3.0 | 1,348 | [
"Brian"
] | 789a8ff0539e4c04842138966c381bb1987129db9d3491fa160a561fec6e30de |
# -*- coding: utf-8 -*-
"""Main IPython class."""
#-----------------------------------------------------------------------------
# Copyright (C) 2001 Janko Hauser <jhauser@zscout.de>
# Copyright (C) 2001-2007 Fernando Perez. <fperez@colorado.edu>
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distribu... | lmregus/Portfolio | python/design_patterns/env/lib/python3.7/site-packages/IPython/core/interactiveshell.py | Python | mit | 148,339 | [
"VisIt"
] | 889f260ac6e89e5dcb6ce94130492b41c2314c0702ab462e68a206399a5df2cc |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris 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 l... | Jozhogg/iris | lib/iris/tests/test_netcdf.py | Python | lgpl-3.0 | 39,602 | [
"NetCDF"
] | 64a81974b47bc0d4fb6e706d14d1d6d3aae8a75b3334a6b52723460f670ed702 |
# -*- coding: utf-8 -*-
"""Functional tests using WebTest.
See: http://webtest.readthedocs.org/
"""
from innovator.admin.models import Event
class TestEvent:
def test_event_public_display(self, event, testapp):
res = testapp.get('/events/')
assert res.status_code == 200
assert 'test even... | B-O-P/innovator | tests/test_event.py | Python | bsd-3-clause | 3,976 | [
"MOE"
] | 0b077ceadf2fcda24108b556720eb75c29f7b30de66a4382eb90c72af0fea4bd |
"""
Copyright (c) 2012-2017, Zenotech Ltd
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and th... | zCFD/zutil | zutil/farm.py | Python | mit | 55,488 | [
"ParaView",
"VTK"
] | c7bfda0facaaa9b27c25bef806a1deb8fb9224e6d3153de0241484e6931f5dec |
#!/usr/bin/env python
from setuptools import setup, find_packages
import os
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
setup(
name='junit-xml',
author='Brian Beyer',
author_email='brian@kyr.us',
url='https://github.com/kyrus/python-junit-xml',
license=... | desolat/python-junit-xml | setup.py | Python | mit | 1,086 | [
"Brian"
] | 7f7a721ea5eedd42c0a4700a57db971a9918f6e9ad3146bb3310db923e830e4e |
"""
This library allows you to quickly and easily use the SendGrid Web API v3 via
Python.
For more information on this library, see the README on Github.
http://github.com/sendgrid/sendgrid-python
For more information on the SendGrid v3 API, see the v3 docs:
http://sendgrid.com/docs/API_Reference/api_v3... | blackpioter/sendgrid-python | sendgrid/sendgrid.py | Python | mit | 3,305 | [
"VisIt"
] | 65e7b98dff1921cb3409ac77419811f32872a3997656edc4d9a412f12ecef007 |
import ocl
import camvtk
import time
import datetime
import vtk
def drawTree(myscreen,t,color=camvtk.red,opacity=0.2, offset=(0,0,0)):
nodes = t.get_nodes()
black=0
for n in nodes:
cen = n.point()
#print "cen=",cen.str()
scale = n.get_scale()
#print "col=", n.color
... | aewallin/opencamlib | src/attic/ocode/ocode_movie1.py | Python | lgpl-2.1 | 4,981 | [
"VTK"
] | 942913d309ea9dd8a26a09ba2719862bd00166b7b9f9b9d62ec40582168f453e |
# (c) 2015, Brian Coca <briancoca+dev@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | axilleas/ansible | lib/ansible/plugins/action/patch.py | Python | gpl-3.0 | 2,341 | [
"Brian"
] | 5e47c7002b351ee3154ed79308e19ff74ff4e0e6792cb8ff41c0c889499e6329 |
import time
import RPi.GPIO as io
from servo import set_servo
import logging
from logging.handlers import RotatingFileHandler
from logging import Formatter
import sys
logger = logging.getLogger('bergro')
logger_format = ("%(asctime)s %(levelname)s: %(message)s"
" [%(pathname)s:%(lineno)d]")
logger_f... | erikulven/flapmagick | flapmagick.py | Python | bsd-2-clause | 3,432 | [
"VisIt"
] | dc54f1db2b05800f58f8edd58737c930a44df1cf5f8f7372599636b68fa1e549 |
"""
Module for rendering clusters
"""
from __future__ import absolute_import
from __future__ import unicode_literals
import copy
import logging
import vtk
import numpy as np
from . import baseRenderer
from . import povrayWriters
from .. import utils
from ...filtering import _clusters
from ...filtering import cluste... | chrisdjscott/Atoman | atoman/rendering/renderers/clusterRenderer.py | Python | mit | 5,229 | [
"VTK"
] | 42e33c96bd9d241f0a15f9525f246852ecaf1710f5d579fb920c0c0adb1225b4 |
#!/usr/bin/env python
# Copyright 2014-2018 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/cc/test/test_ccsd_lambda.py | Python | apache-2.0 | 5,644 | [
"PySCF"
] | 46ee5e1df4ae43090c6c65de7c76419ad155b32bdc61cce7764a23d5295a3a5a |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import sys
import numpy as np
from ...core.parameterization.parameterized import Parameterized
from kernel_slice_operations import KernCallsViaSlicerMeta
from ...util.caching import Cache_this
from GPy.core... | fivejjs/GPy | GPy/kern/_src/kern.py | Python | bsd-3-clause | 11,771 | [
"VisIt"
] | b06c1891c1f7598f0debd76368ee3ca010d35b65f4916c783c0d5a3e0701598e |
#!/usr/bin/env python
###############################################################################
# Copyright 2015-2016 University of Florida. All rights reserved.
# This file is part of UF CTS-IT's NACCulator project.
# Use of this source code is governed by the license found in the LICENSE file.
################... | ZacZZZ/Nacculator_Github | nacc/backup/redcap2nacc_flask-8-17-before debugging.py | Python | bsd-2-clause | 9,596 | [
"VisIt"
] | 2221bc0fc35994b4f23a6746a56f234f11d3a52158946db59f82efe853f82f29 |
#!/usr/bin/env
"""
Chuckchi_Winds_NARR_model_prep.py
Retrieve NARR winds for one locations
Icy Cape Line, Ckip2
Latitude = 70.8401 Longitude = 163.2054
Filter NARR winds with a triangular filter (1/4, 1/2, 1/4) and output every 3hrs
Provide U, V
Save in EPIC NetCDF standard
"""
#System Stack
import datetim... | shaunwbell/FOCI_Analysis | NARR_3hr_WindsSFCtemp_Station.py | Python | mit | 11,955 | [
"NetCDF"
] | 36e41587254da5fcf0001815e589fd9962bf8b06780d62895e3c4c32e859a813 |
# -*- coding: utf-8 -*-
'''
@author: Hung-Hsin Chen
@mail: chenhh@par.cse.nsysu.edu.tw
'''
from __future__ import division
import numpy as np
import pandas as pd
import os
import sys
from datetime import date
import time
from stats import Performance
import scipy.stats as spstats
from cStringIO import StringIO
import s... | chenhh/PySPPortfolio | PySPPortfolio/buyHoldPortfolio.py | Python | gpl-3.0 | 7,631 | [
"ADF"
] | cd873ed32e4c781d0ab1712e084fc3db02ee651dc43884f4f9be4013bd88d3f1 |
"""Test the server of Geckoboard data."""
import json
import copy
from twisted.trial import unittest
from twisted.internet.defer import inlineCallbacks, returnValue
from twisted.web.client import getPage
from vumidash.gecko_server import GeckoServer
from vumidash.base import MetricSource
class DummySource(MetricSour... | praekelt/vumi-dashboard | vumidash/tests/test_gecko_server.py | Python | bsd-3-clause | 7,475 | [
"Amber"
] | 2e14e23098a995ca58f0a32d4e25256268dab007198dd541a8c82cab49848ced |
# Copyright 2007-2020 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ve... | dnjohnstone/hyperspy | hyperspy/tests/model/test_chi_squared.py | Python | gpl-3.0 | 3,332 | [
"Gaussian"
] | 9711984481c1fce2fae1e2419451161d82e0a3b03e2f08ee5780718f17b4b0ef |
import os
import socket
import codecs
from math import floor
from threading import Lock
try:
import mmap
except ImportError: # pragma: no cover
mmap = None
import socket
import binascii
try:
from StringIO import StringIO
except ImportError:
from io import StringIO, BytesIO
from platform import ... | irrgit/hexchat-plugins | hexchat-oper/extras/pygeoip.py | Python | gpl-3.0 | 59,717 | [
"BWA",
"COLUMBUS"
] | 92601f132c76a6973a0bfc971b10c8cfc524f932c1a539ef91400170547ff0a0 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import os.path
import numpy as np
import matplotlib.pyplot as plt
import abel
# This example demonstrates a BASEX transform of an image obtained... | rth/PyAbel | examples/example_basex_photoelectron.py | Python | mit | 2,703 | [
"Gaussian"
] | 92a344f8e1bb8a401f4f8beb5b796cffb336eaaafe0d83b40166456bd9bc31ae |
#!/usr/bin/python
# -*- coding: iso-8859-1 -*-
"""Various helper functions related to VTK.
"""
import vtk
def set_mapper_input(mapper, data):
""" VTK 5 and 6 function to set a mapper input """
try:
mapper.SetInput(data)
except AttributeError:
mapper.SetInputData(data)
def pointCloudActor... | BenoitLBen/runtime | tools/vtk_utils.py | Python | mit | 5,115 | [
"VTK"
] | 00270fbd448ad56b666cf949d0489cd08e33fe25ac0d60619ff0b572c52cd4c0 |
"""
Alpha diversity measures (:mod:`skbio.diversity.alpha`)
=======================================================
.. currentmodule:: skbio.diversity.alpha
This package provides implementations of alpha diversity measures, including
measures of richness, dominance, and evenness. Some functions generate
confidence in... | gregcaporaso/scikit-bio | skbio/diversity/alpha/__init__.py | Python | bsd-3-clause | 2,159 | [
"scikit-bio"
] | dcfe0261c7004cb4af467385b26cd034bd2075e8dedf7f816535427e430cb6d2 |
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import sys, os, socket, ssl
from zeroinstall import _
from zeroinstall.injector import download
from zeroinstall.support import ssl_match_hostname
if sys.version_info[0] > 2:
from urllib import request as urllib2
... | slovenwd/0install | zeroinstall/injector/_download_child.py | Python | lgpl-2.1 | 4,719 | [
"VisIt"
] | 47599cf7e11d483567c770764447470afcc56efe48f74fec220ee27a0d13c3b0 |
import inspect
import math
import json
import weakref
from jmespath import exceptions
from jmespath.compat import string_type as STRING_TYPE
from jmespath.compat import get_methods
# python types -> jmespath types
TYPES_MAP = {
'bool': 'boolean',
'list': 'array',
'dict': 'object',
'NoneType': 'null',... | mruse/aliyun-cli | aliyuncli/jmespath/functions.py | Python | apache-2.0 | 12,257 | [
"VisIt"
] | 8193a6ba5e6a72a3b1ccbf564ec75b1b915b6b829501eb078820ab29802f3b8e |
"""
Tests for discussion pages
"""
import datetime
from pytz import UTC
from unittest import skip
from uuid import uuid4
from nose.plugins.attrib import attr
from .helpers import BaseDiscussionTestCase
from ..helpers import UniqueCourseTest
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.courseware ... | IndonesiaX/edx-platform | common/test/acceptance/tests/discussion/test_discussion.py | Python | agpl-3.0 | 46,842 | [
"VisIt"
] | c7e1e34c3e9d1f30d2c68f967d1a0e4f1269a97a673a8fca25eee899300671ca |
import pysam
is_paired = 0
is_proper = 0
for read in pysam.AlignmentFile("ex1.bam", "rb"):
is_paired += read.is_paired
is_proper += read.is_proper_pair
print ("there are alignments of %i paired reads" % is_paired)
print ("there are %i proper paired alignments" % is_proper)
| brendanofallon/pysam | tests/python_flagstat.py | Python | mit | 285 | [
"pysam"
] | 63dd340dfb76609b1405f21a31b8a3ab755fed66d9235dc19056d29b72ccc176 |
#!/usr/bin/python
# break : break is a keyword which takes you out of a loop.
# sys.exit: takes you out of the program.
# Task : make sure you give your friend only 3 chances.
import sys
my_answer = raw_input("do you want to play the game? y/n :")
if my_answer == 'n':
sys.exit()
my_num = 7 # hidden in my palm
#tes... | tuxfux-hlp-notes/python-batches | archieves/batch-58/my_game.py | Python | gpl-3.0 | 773 | [
"VisIt"
] | 2f27efa49cb302c7f38ca849d247281e91f22410228c2bca53ed2104ce4913a6 |
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