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#!/usr/bin/env python
#
# $File: simpleExample.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistrib... | BoPeng/simuPOP | docs/simpleExample.py | Python | gpl-2.0 | 1,449 | [
"VisIt"
] | 618013f12a94c6226a0c19b449afaebd628da175d6d0a153fb0e23895f68f574 |
# Copyright 2012-2014 Brian May
#
# This file is part of python-tldap.
#
# python-tldap 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.... | Karaage-Cluster/python-tldap | tldap/utils.py | Python | gpl-3.0 | 1,651 | [
"Brian"
] | 48d29ad5c570eb7097ff56dc57628738eaedb0ba8eba753328b71ad4843ca796 |
#!/usr/bin/env python2.7
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redis... | BunnyWei/truffle-llvmir | mxtool/mx.py | Python | gpl-2.0 | 222,574 | [
"VisIt"
] | e3b506a219b60fb99ff244d98ad3c4f2463d03882de0b4429497a58e6cc6ced2 |
# -*- coding: utf-8 -*-
#
# lin_rate_ipn_network.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Li... | terhorstd/nest-simulator | pynest/examples/lin_rate_ipn_network.py | Python | gpl-2.0 | 5,743 | [
"NEURON"
] | 0943a3ef0d190d28589850a124cc4f97647b6a95685bc93cbf2fb15f14018c7f |
# import to process args
import sys
import os
import math
import json
try:
import argparse
except ImportError:
# since Python 2.6 and earlier don't have argparse, we simply provide
# the source for the same as _argparse and we use it instead.
import _argparse as argparse
# import annotations
from aut... | jcfr/Midas | modules/pvw/apps/midas.py | Python | apache-2.0 | 15,740 | [
"ParaView",
"VTK"
] | 4050684293dce10e65c53eefdab626a9fc022d96ccd2aff8b673f24f63d01e9c |
from owmeta_core.command import OWM
def save_schema():
owm = OWM()
for module in ('owmeta.neuron',
'owmeta.worm',
'owmeta.biology',
'owmeta.cell',
'owmeta.channel',
'owmeta.channelworm',
'owmeta.... | openworm/PyOpenWorm | save_schema.py | Python | mit | 1,131 | [
"NEURON"
] | efb5b60dd8da26578df55919e0bec8c9708af7ce942f8292a3384ec8751018e5 |
"""Test input validation functionality."""
import pytest
from qmflows import cp2k, run
from qmflows.type_hints import PathLike
from scm import plams
from nanoqm.common import read_cell_parameters_as_array
from nanoqm.workflows.input_validation import process_input
from .utilsTest import PATH_TEST, cp2k_available, rem... | SCM-NV/qmworks-namd | test/test_input_validation.py | Python | mit | 1,752 | [
"CP2K"
] | 3844f1a33f5547f92da5f46852b04e0b41932dcc12a7af08c703bd4ae88ca420 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | samples/widom_insertion.py | Python | gpl-3.0 | 4,371 | [
"ESPResSo"
] | 0a9320ab19594a01cd0b42b43df2b9364b412c74b59bb292fbb1cd7bfebb2909 |
# Copyright (c) 2018, NVIDIA CORPORATION. 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 applic... | mlperf/training_results_v0.5 | v0.5.0/nvidia/submission/code/single_stage_detector/pytorch/coco.py | Python | apache-2.0 | 19,010 | [
"VisIt"
] | 744f8d3a3e4ffabaac7029b22c0aff68e70f8f64a5e308a7d97173b98c9ef8b5 |
#GLM2 bench
import os, sys, time, csv, re, requests, string
sys.path.append('../py/')
sys.path.extend(['.','..'])
import h2o_cmd, h2o, h2o_hosts, h2o_browse as h2b, h2o_import as h2i, h2o_rf, h2o_jobs
from pprint import pprint
csv_header = ('h2o_build','nMachines','nJVMs','Xmx/JVM','dataset','nTrainRows','nTestRows','... | janezhango/BigDataMachineLearning | bench/BMscripts/glm2Bench.py | Python | apache-2.0 | 11,359 | [
"Gaussian"
] | 86b0d3f1934bf2d38f7b868fd6c0517587f53e179fb57f6bc992bc4b5110eb70 |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | yipenggao/moose | python/MooseDocs/extensions/gchart.py | Python | lgpl-2.1 | 11,198 | [
"MOOSE"
] | 59b1e3408a89b34708b80e5675a8077b1f61c97f1b349b5eb7c6065bfa0292d0 |
#!/usr/bin/env python2.6
# Zeckviz IRC bot
# Copyright (C) 2011 Bruno Rahle
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any la... | brahle/I-Rcbot | irc/ircstart.py | Python | agpl-3.0 | 1,673 | [
"VisIt"
] | 7f5d53819af50643eb2de114282156f5cb79d8ad900a18107f31096a41235b5c |
"""
Conformer generation.
"""
import numpy as np
from typing import Any, List, Optional
from deepchem.utils.typing import RDKitMol
class ConformerGenerator(object):
"""
Generate molecule conformers.
Notes
-----
Procedure
1. Generate a pool of conformers.
2. Minimize conformers.
3. Prune conformers u... | lilleswing/deepchem | deepchem/utils/conformers.py | Python | mit | 8,816 | [
"RDKit"
] | 3e7344e97c86b2fa348c1e0313d65aeb7bd10cd917a66a644050bd2e77b7e3d2 |
######################################################################
##
## Copyright 2011 Christian Iversen <ci@sikkerhed.org>
##
## Permission is hereby granted, free of charge, to any person
## obtaining a copy of this software and associated documentation
## files (the "Software"), to deal in the Software without
... | buchuki/pyjaco | pyjaco/__init__.py | Python | mit | 6,141 | [
"VisIt"
] | 3f0f9cbff05fa9b119b1f26f9a86e1413ae34784a4844df650bb54eae2ce8306 |
import ast
import datetime
import re
import secrets
import time
from datetime import timedelta
from typing import (
AbstractSet,
Any,
Callable,
Dict,
List,
Optional,
Pattern,
Sequence,
Set,
Tuple,
TypeVar,
Union,
)
import django.contrib.auth
from bitfield import BitField... | punchagan/zulip | zerver/models.py | Python | apache-2.0 | 144,942 | [
"VisIt"
] | a8967e4c5455b162391ebfa4bc3c8e4547b2b87e4d245c71ed7ee9cf398f3555 |
"""Dirac notation for states."""
from __future__ import print_function, division
from sympy import (cacheit, conjugate, Expr, Function, integrate, oo, sqrt,
Tuple)
from sympy.core.compatibility import range
from sympy.printing.pretty.stringpict import stringPict
from sympy.physics.quantum.qexpr imp... | NikNitro/Python-iBeacon-Scan | sympy/physics/quantum/state.py | Python | gpl-3.0 | 29,156 | [
"DIRAC"
] | 61b6e9de04276cbcabea9480343c5ac94823ebda932b9121572223bc6c48051f |
'''
Created on Oct 21, 2014
@author: sergio
'''
import numpy as np
import ctypes
import numpy.ctypeslib as npct
import matplotlib.pyplot as plt
#cfsfd = ctypes.cdll.LoadLibrary('/home/sergio/iibm/sandbox/t.so')
#cfsfd.get_dc.restype = ctypes.c_float
#dc = cfsfd.get_dc("dbname=demo host=192.168.2.2 user=postgres pass... | sergio2pi/NeuroDB | test/test5.py | Python | gpl-2.0 | 2,324 | [
"Gaussian"
] | bc4487b44497305eba850ed2756feb9ea78b1088b2860d9fc4c62e4fad8fbda5 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""PhyloXML reader/parser, writer, and associated functions.
Instantiates tree elements... | bryback/quickseq | genescript/Bio/Phylo/PhyloXMLIO.py | Python | mit | 31,591 | [
"Biopython"
] | 120ae5cab5a6bb71c221a369f5fb65791dd63fec83093e6fc1936745235c5a26 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# "THE BEER-WARE LICENSE" (Revision 42):
# Christian Brueffer <christian@brueffer.de> wrote this file. As long as you
# retain this notice you can do whatever you want with this stuff. If we meet
# some day, and yo... | jessicachung/rna_seq_pipeline | scripts/fix_tophat_unmapped_reads.py | Python | mit | 3,571 | [
"pysam"
] | f46f59d18cfdafb63b0ff1b405700a452f29372bb4a83f689d051cb9c0cc248c |
''' Some tests for filters '''
from __future__ import division, print_function, absolute_import
import sys
import numpy as np
from numpy.testing import (assert_equal, assert_allclose,
assert_array_equal, assert_almost_equal)
from pytest import raises as assert_raises
import scipy.ndimage a... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/scipy/ndimage/tests/test_filters.py | Python | mit | 14,796 | [
"Gaussian"
] | 891598c78114ac96eb196f966bce246929326ba3b0a620d4e51d6a63d1a78edb |
import os
from ase import Atom, Atoms
from ase.optimize import BFGS
from ase.io import read
from gpaw import GPAW
from gpaw.test import equal
a = 4. # Size of unit cell (Angstrom)
c = a / 2
d = 0.74 # Experimental bond length
molecule = Atoms('H2',
[(c - d / 2, c, c),
(c + d / 2,... | robwarm/gpaw-symm | gpaw/test/relax.py | Python | gpl-3.0 | 3,003 | [
"ASE",
"GPAW"
] | c0bd4b975e5364aad0ffa39d0216bb2680a50ce4b2fc77a9e03c39dac85aa104 |
"""Test check utilities."""
# Authors: MNE Developers
# Stefan Appelhoff <stefan.appelhoff@mailbox.org>
#
# License: BSD-3-Clause
import os
import os.path as op
import sys
import numpy as np
import pytest
from pathlib import Path
import mne
from mne import read_vectorview_selection
from mne.datasets import t... | pravsripad/mne-python | mne/utils/tests/test_check.py | Python | bsd-3-clause | 8,752 | [
"Mayavi"
] | 723033fafc06ea8016915ea6fc2b67e3701dae1845a6a1ccd8ec0b853d460f8e |
# Copyright 2006-2013 by Peter Cock. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.AlignIO support for "stockholm" format (used in the PFAM database).
You are expe... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/AlignIO/StockholmIO.py | Python | gpl-2.0 | 23,641 | [
"BioPerl",
"Biopython"
] | b656f78d78800d5ffba2b768116ce536f369656cde0c938c5f9ee7d8c8f7faf1 |
#!/usr/bin/env python
# Author: Brian Tomlinson
# Contact: brian@brianctomlinson.com, darthlukan@gmail.com
# Description: Simple update notifier for Arch Linux,
# meant to be run via ~/.config/autostart/lupdater.desktop but
# can also be run from the applications menu.
# License: GPLv2
import os
import pwd
import sys
... | darthlukan/lupdater | lupdater.py | Python | gpl-2.0 | 7,248 | [
"Brian"
] | 862814445a12b9073ac402d6755905b11f4b0fdaa118284e83c015927d1078e2 |
#
# Import an entire NetCDF file into memory
#
from boututils import DataFile
def file_import(name):
f = DataFile(name) # Open file
varlist = f.list() # Get list of all variables in file
data = {} # Create empty dictionary
for v in varlist:
data[v] = f.read(v)
f.close()
retu... | boutproject/BOUT-2.0 | tools/pylib/boututils/file_import.py | Python | gpl-3.0 | 328 | [
"NetCDF"
] | d6b59940f8680fd5c372dc9fc301b315641852bb8d021aad84e4e418a0ac5616 |
import nose.tools
from unittest import TestCase
from nose import SkipTest
from nose.plugins.attrib import attr
import tempfile
from netCDF4 import Dataset
from ocgis import RequestDataset, OcgOperations
from ocgis.util.large_array import compute
from flyingpigeon.utils import local_path
from tests.common import pre... | sradanov/flyingpigeon | tests/test_ocgis.py | Python | apache-2.0 | 2,517 | [
"NetCDF"
] | e4ecb390eb0c6e5e33161ddb1a0e1c4713888019589998ecacc2d23ace4e7bcc |
'''
synbiochem (c) University of Manchester 2015
synbiochem is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
class Vertex():
'''Class to represent a vertex.'''
def __init__(self, name, attributes):
self.__at... | synbiochem/synbiochem-py | synbiochem/utils/graph_utils.py | Python | mit | 2,356 | [
"VisIt"
] | ff0c3a6be20aa36ef8a9102e4e49b0407589d15777c497dacb73db3f8c4c44a4 |
"""
This module defines export functions for decision trees.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Dawe <noel@dawe.me>
# Satrajit Gosh <satrajit.ghosh@gmail.com>
# Trevor... | vortex-ape/scikit-learn | sklearn/tree/export.py | Python | bsd-3-clause | 17,978 | [
"Brian"
] | 48b6a7dc2985c30e6c131bfbee35679e45c0d319235899ab3a6effce248be344 |
#
# Copyright (c) 2008--2015 Red Hat, Inc.
#
# This software is licensed to you under the GNU General Public License,
# version 2 (GPLv2). There is NO WARRANTY for this software, express or
# implied, including the implied warranties of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. You should have received a c... | xkollar/spacewalk | backend/server/rhnServer/server_class.py | Python | gpl-2.0 | 30,794 | [
"CDK"
] | 1ca20f2f8f895db1811f4fef931c729ba4be2c5c09ae1b2cf2b366fe329885c6 |
#!/usr/bin/env python
import vtk
def main():
# Create 5 points (vtkPolyData)
pointSource = vtk.vtkPointSource()
pointSource.SetNumberOfPoints(5)
pointSource.Update()
polydata = pointSource.GetOutput()
print "points in polydata are",polydata.GetNumberOfPoints()
# Create 2 po... | lorensen/VTKExamples | src/Python/Filtering/AppendFilter.py | Python | apache-2.0 | 1,730 | [
"VTK"
] | ead1332d8a391d3e0710026ea95713ac5117797ddaf8dc3ebdfeef4d6a06107a |
# -*- coding: utf-8 -*-
#
# Zesty Technology documentation build configuration file, created by
# sphinx-quickstart on Tue Apr 25 13:45:35 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated fi... | ZestyTechnology/zesty-docs | docs/conf.py | Python | agpl-3.0 | 5,385 | [
"Brian"
] | b2b5825d76b38b3c63709a0ebf2e141777d64d6b460252cdedd8ff9a65607b11 |
import pymongo
from pymongo import MongoClient
import uuid
import unittest
import pprint
from pymatgen.db.query_engine import QueryEngine, QueryResults
from pymatgen.db.tests import common
has_mongo = common.has_mongo()
class SandboxTest(unittest.TestCase):
SBX = "testing"
N = 100
def qtx(self, crit, ... | materialsproject/pymatgen-db | pymatgen/db/tests/test_postfuncs.py | Python | mit | 4,608 | [
"pymatgen"
] | b3acd6c6f8be166954eb4894cb3e15ef12187ee97d68ac5fe853aecf276a706b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# jobfeasible - Check current job feasibility for queued job
# Copyright (C) 2003-2011 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 ... | heromod/migrid | mig/cgi-bin/jobfeasible.py | Python | gpl-2.0 | 1,099 | [
"Brian"
] | ce35a7a0989ed6927e56f8e03fae2e2599b222c98af8a521b212974acc026943 |
"""Collaborative Password Database"""
__author__ = "Brian Wiborg <baccenfutter@c-base.org>"
__license__ = "GNU/GPLv2"
__version__ = "0.1.4-alpha"
| baccenfutter/cpassdb | cpassdb/__init__.py | Python | gpl-2.0 | 146 | [
"Brian"
] | d24de4ec11a87c83e4eb5a43843e1f548931d241399ff281665248b2b2bb1305 |
# This file is part of Viper - https://github.com/viper-framework/viper
# See the file 'LICENSE' for copying permission.
import os
import re
import string
from socket import inet_pton, AF_INET6, error as socket_error
from viper.common.abstracts import Module
from viper.common.objects import File
from viper.core.sessi... | MeteorAdminz/viper | viper/modules/strings.py | Python | bsd-3-clause | 13,823 | [
"Brian"
] | 992f42bbbf147e23a199a686e6f8a50bce12908f9e353330bb92ecc75bb63f9b |
#
# Copyright (C) 2017-2018 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... | hmenke/espresso | testsuite/python/accumulator.py | Python | gpl-3.0 | 2,519 | [
"ESPResSo"
] | ac61f1355252cfc55a09fa1625df052508485b71d1c19ea6f5d3e47cf4629e34 |
""" Test functions for stats module
"""
import warnings
import re
import sys
import pickle
import os
from numpy.testing import (assert_equal, assert_array_equal,
assert_almost_equal, assert_array_almost_equal,
assert_allclose, assert_, assert_warns,
... | aeklant/scipy | scipy/stats/tests/test_distributions.py | Python | bsd-3-clause | 165,416 | [
"Gaussian"
] | 2848bd3bdd670a537097ef55723363c850bd2d2d0fc5bdf3f04a059e76e0f177 |
# -*- coding: utf-8 -*-
from pyaxiom.netcdf import CFDataset
class OrthogonalMultidimensionalTimeseriesProfile(CFDataset):
@classmethod
def is_mine(cls, dsg):
try:
assert dsg.featureType.lower() == 'timeseriesprofile'
assert len(dsg.t_axes()) >= 1
assert len(dsg.x_... | axiom-data-science/pyaxiom | pyaxiom/netcdf/sensors/dsg/timeseriesProfile/om.py | Python | mit | 1,732 | [
"NetCDF"
] | 51aa6312af54f514a19eb24e4011451ddf417036d68f59df17f4e305fde72b16 |
import numpy as np
import loudness as ln
class BinauralInhibitionMG2007:
def __init__(self, cams):
nFilters = cams.size
camStep = cams[1] - cams[0]
g = np.arange(nFilters) * camStep
gaussian = np.exp(-(0.08 * g) ** 2)
self.fullGaussian = np.hstack((gaussian[::-1], gaussi... | faroit/loudness | python/tests/test_BinauralInhibitionMG2007.py | Python | gpl-3.0 | 2,403 | [
"Gaussian"
] | 53f6568470ae151626bac3cb859c6b3984d50e878cdf3ac4ceef1915353084c5 |
""" DIRAC API Base Class """
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
from DIRAC.Core.Utilities.List import sortList
from DIRAC.Core.Security.ProxyInfo import getProxyInfo, formatProxyInfoAsString
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import getDNForUser... | avedaee/DIRAC | Core/Base/API.py | Python | gpl-3.0 | 4,564 | [
"DIRAC"
] | 6271b8564171d2907c51874458d1c44b5dc646765eaeca5c7ad6c19312771b55 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import logging
from monty.json import MSONable
from pymatgen.core import Structure
from pymatgen.analysis.defects.corrections import FreysoldtCorrection, \
KumagaiCorrection, BandFillingCorrection, BandEdge... | fraricci/pymatgen | pymatgen/analysis/defects/defect_compatibility.py | Python | mit | 28,273 | [
"pymatgen"
] | fa78f77dc0daccf74b7adce8249a390e254bbd17b0c1d692daa50a775219a87f |
#!/usr/bin/env python
"""The X12.map.source module emits Python source definitions from an :mod:`X12.parse` structure.
There are two flavors of Python source that can be produced:
- :class:`PythonVisitor` creates a single definition.
A single Python constructor defines the entire message.
- :clas... | jdavisp3/TigerShark | tigershark/X12/map/source.py | Python | bsd-3-clause | 6,021 | [
"VisIt"
] | a331071e6c07e809e165b3f8347ad60bce4533db95b1653f7bc1a2c0308b9e2e |
"""
Actions manager for transcripts ajax calls.
+++++++++++++++++++++++++++++++++++++++++++
Module do not support rollback (pressing "Cancel" button in Studio)
All user changes are saved immediately.
"""
import copy
import os
import logging
import json
import requests
from django.http import HttpResponse, Http404
fro... | jbassen/edx-platform | cms/djangoapps/contentstore/views/transcripts_ajax.py | Python | agpl-3.0 | 20,955 | [
"FEFF"
] | 65fcba1f9542e6cb25ecad70caa6e496c064789304b5afef6cea95ac1960c093 |
#!/usr/bin/python
import numpy as np
import scipy.interpolate as si
import mayavi.mlab as mylab
def calc_points(line):
points = np.zeros((len(line),3)) # indicies -> point coordinates
for i in range(points.shape[0]):
#points[i,0] = 2 * 0.556 * (line[i][0]-0.5)
#points[i,1] = 2 * 0.556 * (line[i][1]-0.5)
... | jrugis/cell_mesh | poly.py | Python | gpl-3.0 | 1,938 | [
"Mayavi"
] | a0e23534d1f78b2f02a5034322cf83912fe0857b26c95d1923aca652ac724e84 |
# -*- coding: utf-8 -*-
import numpy as np
import numpy.ma as ma
import itertools
import scipy.optimize
from pytmatrix.psd import GammaPSD
import csv
from datetime import datetime
import os
from netCDF4 import Dataset, num2date
from ..DropSizeDistribution import DropSizeDistribution
from ..io import common
def read_... | josephhardinee/PyDisdrometer | pydsd/aux_readers/ARM_APU_reader.py | Python | lgpl-2.1 | 4,263 | [
"NetCDF"
] | 3dbc51206da924baf838b8380da82882303be353327c3d14b032907538230829 |
import argparse
import sys
import skimage.io
import skimage.transform
import scipy.misc
from PIL import Image
def scale_image(input_file, output_file, scale, order=1):
Image.MAX_IMAGE_PIXELS = 50000*50000
img_in = skimage.io.imread(input_file)
if order == 0:
interp = 'nearest'
elif order == 1... | BMCV/galaxy-image-analysis | tools/scale_image/scale_image.py | Python | mit | 1,364 | [
"Galaxy"
] | 318d80f9e071a1972fc8a03db095a4666c218c560ef54b4eda0fd8e84a06daa9 |
from enum import Enum, unique
from functools import wraps
from django.contrib.auth.decorators import login_required
from django.http import (
HttpResponseRedirect,
HttpResponseForbidden,
HttpResponseBadRequest,
)
from django.shortcuts import render, get_object_or_404
from django.urls import reverse
from dj... | dracidoupe/graveyard | ddcz/views/tavern.py | Python | mit | 10,915 | [
"VisIt"
] | 9fb943ab0c0fe6d3171779dbbf65efe03fa9c7418c1a4e42a7f77250cf978614 |
#!/usr/bin/env python
# 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 program is distributed in the hope that ... | dmnfarrell/smallrnaseq | smallrnaseq/config.py | Python | gpl-3.0 | 4,475 | [
"Bowtie"
] | df4ad14acdbc00178fe9e190c8702880e2dc1ff98c539f6896efcc45993bcffd |
DEVICE_TEMPLATE='''
<div class="col-md-3">
<br>
<center>
<button type="button" class="btn btn-primary" data-toggle="modal" data-target=".bs-example-modal-MODID" style="width:90%;height:45px;text-align: center; ">TITLE</button>
<div class="modal fade bs-example-modal-MODID" tabindex="-1" role="dialog" aria-labelledb... | zpriddy/Firefly | Firefly/web_ui/templates/old_design.py | Python | apache-2.0 | 8,964 | [
"Firefly"
] | 8197cc327c369ba40e410d7e29a90a86f37cc527d356d9b04e4fd0b4f46a23ba |
#!/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... | dav1x/ansible | lib/ansible/modules/network/avi/avi_sslkeyandcertificate.py | Python | gpl-3.0 | 5,738 | [
"VisIt"
] | 528e2fdd0caeaf821412e8269589e78173574a45e0440604d5cd7892d8db06b8 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2012 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the term... | sam-m888/gramps | gramps/gen/plug/_manager.py | Python | gpl-2.0 | 25,784 | [
"Brian"
] | 1652b9b1e2717e9cb69ad507112f8c9df854910aa58d8d961640823376c697fe |
# This plugin is adapted from the Python Console plugin and the IPython
# cookbook at:
# http://ipython.scipy.org/moin/Cookbook/EmbeddingInGTK
# Copyright (C) 2009-2010 Brian Parma
# Updated 2012 Brian Parma
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU... | exaile/exaile | plugins/ipconsole/__init__.py | Python | gpl-2.0 | 8,594 | [
"Brian"
] | 5f2e0dc5acca33ee5802b8ba00d180eae325eac8f8201cb696c38a34df4f7914 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-a4base/package.py | Python | lgpl-2.1 | 2,219 | [
"Bioconductor"
] | 6106d1d50293d81abbf0755f9a4f2f39e641a934062868fd8ad04428bcd72966 |
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 25 14:02:59 2015
by LW March 2015
set of utility functions for beamline alingment and commissioning
v 0.0.1 (this version): might have created a typo in E-calibration!!!
added dcm_roll for calculating DCM Roll correction
"""
import datetime ... | NSLS-II-CHX/ipython_ophyd | startup/95-utilities.py | Python | bsd-2-clause | 38,175 | [
"CRYSTAL",
"Gaussian"
] | 6947761c7c758e9bbee5c1d4db0a48d0cdc14e285758c04c508468b088b18d63 |
import numpy as np
import regreg.api as rr
from selection.randomized.glm import pairs_bootstrap_glm, bootstrap_cov
from ..sampling.langevin import projected_langevin
from ..distributions.api import discrete_family
from ..distributions.api import discrete_family, intervals_from_sample
class M_estimator(object):
d... | selective-inference/selective-inference | selectinf/randomized/sandbox/M_estimator_group_lasso.py | Python | bsd-3-clause | 19,747 | [
"Gaussian"
] | 883841cc8c1cc8d90261625e71d9dd35d0cc534ee437248ba81b13a7fdaa566f |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | valerymelou/cookiecutter-django-gulp | {{cookiecutter.project_slug}}/config/urls.py | Python | bsd-3-clause | 1,394 | [
"VisIt"
] | c06277cda98f629b44c3147e5e45fc37f9394bccc751597b35eb339455908e39 |
from __future__ import absolute_import, division, print_function
import contextlib
import logging
import multiprocessing
import threading
import time
import traceback
import warnings
from collections import Mapping, OrderedDict
import numpy as np
from ..conventions import cf_encoder
from ..core import indexing
from ... | jcmgray/xarray | xarray/backends/common.py | Python | apache-2.0 | 15,762 | [
"NetCDF"
] | 4f7a438679bc5da90fba5d11328d1b6590850920922bf84d6a93c624cb47c4fd |
import sys
from collections import namedtuple
from ua_parser import user_agent_parser
PY2 = sys.version_info[0] == 2
PY3 = sys.version_info[0] == 3
if PY3:
string_types = str
else:
string_types = basestring
MOBILE_DEVICE_FAMILIES = (
'iPhone',
'iPod',
'Generic Smartphone',
'Generic Feature... | zpzgone/python-user-agents | user_agents/parsers.py | Python | mit | 7,147 | [
"Galaxy"
] | e0b165c03267b7a6d00d564b0d6101404994bb5b17e9b364563d1291dcdc4b53 |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ 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.
#
"""unit testing code ... | adalke/rdkit | rdkit/Chem/EState/UnitTestTypes.py | Python | bsd-3-clause | 2,103 | [
"RDKit"
] | 7869770c3c1c539f6ba8191f5b73b0b137c7dcaa6aa52b8b0100df8b28ba2a80 |
from collections import OrderedDict, namedtuple
from contextlib import contextmanager
from functools import reduce
from operator import mul
from pathlib import Path
from subprocess import DEVNULL, PIPE, run
from time import time as seq_time
import os
import cgen as c
from sympy import S
from devito.ir.iet import (Exp... | opesci/devito | devito/operator/profiling.py | Python | mit | 17,233 | [
"VisIt"
] | 4725347a8a3b308f11f396ce1d2d0cc05590779f22a4d21129a776f99bfaba8e |
"""
A collection of functions to find the weights and abscissas for
Gaussian Quadrature.
These calculations are done by finding the eigenvalues of a
tridiagonal matrix whose entries are dependent on the coefficients
in the recursion formula for the orthogonal polynomials with the
corresponding weighting function over ... | nvoron23/scipy | scipy/special/orthogonal.py | Python | bsd-3-clause | 34,897 | [
"Gaussian"
] | dea1c27161e265a28f68705c91469e1dedf0b7bb4ae5d1f60dc9c92db6d2abf5 |
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
class manualTransform(ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._config.scale = (1.0, 1.0, 1.0)
... | nagyistoce/devide | modules/misc/manualTransform.py | Python | bsd-3-clause | 2,750 | [
"VTK"
] | b7bd546c6a3265983a0e1da71e5e644166aa3c6a1c264ea98439609de9c936d4 |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/changeAvailability.py | Python | gpl-3.0 | 6,314 | [
"Galaxy"
] | d5508fd3931798107ca10693bc0cd4bff596e15788519e68a66f40bd66f6a936 |
import Bio
import os
import numpy as np
import random as r
import time
import sys
#print sys.path
#sys.path.append("C:\\Users\\Andrey\\SkyDrive\\Guttlab\\Python")
import pydna
import genbankUtils as gbU
import fileUtils as filU
import bioUtils as biU
import stochastickinetics as stoc
def makeOverhangs(... | dr3y/gibsonsimulator | gibson_simulator.py | Python | mit | 7,516 | [
"BLAST"
] | eb271de90604c846849a35aa306bd270c21fe210bfaa5f3e8fbd606d1b93762b |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
'''Method collection to obtain optical system information
This module contains a method collection to obtain information, and analize
optical systems
'''
from pyoptools.raytrace.ray import Ray
from pyoptools.misc.pmisc import cross
from pyoptools.raytrace.system import ... | coupdair/pyoptools | pyoptools/raytrace/calc/calc.py | Python | bsd-3-clause | 24,577 | [
"Gaussian"
] | c7b7bb3941933e22a3d84161873efb22200ed3378a0482f0b49e84ead62862fb |
# moosehandler.py ---
#
# Filename: moosehandler.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Thu Jan 28 15:08:29 2010 (+0530)
# Version:
# Last-Updated: Fri Feb 25 11:18:27 2011 (+0530)
# By: Subhasis Ray
# Update #: 868
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary... | BhallaLab/moose-thalamocortical | pymoose/gui/qt/moosehandler.py | Python | lgpl-2.1 | 24,389 | [
"MOOSE"
] | deb77c56d448070b64cd93b1804dfc13ea5dfb129ad702d050ffaf60db2a9c7d |
"""Fork of urllib2.
When reading this, don't assume that all code in here is reachable. Code in
the rest of mechanize may be used instead.
Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Python
Software Foundation; All Rights Reserved
Copyright 2002-2009 John J Lee <jjl@pobox.com>
This... | odicraig/kodi2odi | addons/plugin.video.roggerstream-4.0.0/mechanize/_urllib2_fork.py | Python | gpl-3.0 | 50,481 | [
"VisIt"
] | 29f2553d12fb8b76d11b7beef7fdcf18f24761e9feca133068fa56b06ee07cdd |
##############################################################################
# State estimation in LGSS and SV models using Kalman and particle filters
#
# Johan Dahlin <liu (at) johandahlin.com.nospam>
# Documentation at https://github.com/compops/pmh-tutorial
# Published under GNU General Public License
###########... | compops/pmh-tutorial | python/helpers/stateEstimation.py | Python | gpl-2.0 | 6,082 | [
"Gaussian"
] | c410be9c600af79b3d6767d7b964537f8ecf385ef0c075cdb7454f4acca5b6ba |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-install-web-portal
# Author : Ricardo Graciani
########################################################################
"""
Do the initial installation of a DIRAC Web portal
"""
__RCSID__ = "$Id... | avedaee/DIRAC | Core/scripts/dirac-install-web-portal.py | Python | gpl-3.0 | 766 | [
"DIRAC"
] | 37fab7ff851ee3a6ed662253457984a3c87563d3ec72ff929d0251f209bfb3d1 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RAlsace(RPackage):
"""ALS for the Automatic Chemical Exploration of mixtures
Alter... | LLNL/spack | var/spack/repos/builtin/packages/r-alsace/package.py | Python | lgpl-2.1 | 1,487 | [
"Bioconductor"
] | 263e30dbccd2b0d2202f26a0ff6612afb5919a7a8fa64abe1b3a778ceaa4d10e |
"""
The alignment pipeline.
We start with the .fastq files and the reference for a particular genome
and carry out the gauntlet of steps to perform alignments, alignment
cleaning, snv calling, and effect prediction.
"""
from datetime import datetime
import os
import time
from celery import group
from celery import t... | woodymit/millstone | genome_designer/pipeline/pipeline_runner.py | Python | mit | 16,101 | [
"BWA"
] | 7dced44b5cffc80c390af7acf3f6693e55a90508612a68e18922a24e6b191ef7 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Modify CCSD object to get CCD method.
'''
from pyscf import gto, scf, cc
mol = gto.M(
atom = 'H 0 0 0; F 0 0 1.1',
basis = 'ccpvdz')
mf = scf.RHF(mol).run()
mycc = cc.CCSD(mf)
mycc.frozen = 1
old_update_amps = mycc.update_amps
def up... | gkc1000/pyscf | examples/cc/43-ccd.py | Python | apache-2.0 | 500 | [
"PySCF"
] | c4e2c81be567204a2e487e08d3d1c1606a85d6d81a6b79ff45d13bb678123f3d |
#!/usr/bin/env python2.4
##############################################################################
#
# Copyright (c) 2003 Zope Corporation 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 thi... | Donkyhotay/MoonPy | zope/app/locales/extract.py | Python | gpl-3.0 | 14,466 | [
"VisIt"
] | 9233fbfc5273dddd28514a9c8fe7d0544ad04d1ebb9ff3a6eb6b5ab1af3c6231 |
'''
Set up Visual Sudio to build a specified MPIR configuration
Copyright (C) 2011, 2012, 2013, 2014 Brian Gladman
'''
from __future__ import print_function
from operator import itemgetter
from os import listdir, walk, unlink, makedirs
from os.path import split, splitext, isdir, relpath, join, exists
from os.path imp... | omco/mpir | build.vc10/mpir_config.py | Python | lgpl-3.0 | 31,141 | [
"Brian"
] | 5bccf05960d5fb0e520749775a57a27ad29967080dae9503cef939dc2d18be23 |
import os
import pyscf
from pyscf.lib.logger import perf_counter, process_clock
def setup_logger():
log = pyscf.lib.logger.Logger(verbose=5)
with open('/proc/cpuinfo') as f:
for line in f:
if 'model name' in line:
log.note(line[:-1])
break
with open('/pro... | sunqm/pyscf | examples/2-benchmark/benchmarking_utils.py | Python | apache-2.0 | 534 | [
"PySCF"
] | 09ad38c5c241080519c67cbf42ab64aa7431bd81ebebdc1d3e7bc64b3e61dea0 |
#
# Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
# 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 copyrigh... | adalke/rdkit | rdkit/Chem/MolKey/MolKey.py | Python | bsd-3-clause | 16,577 | [
"RDKit"
] | b313bb98e3a397335c835f2ddbb065d0167443b21cb59aef3140a66f52980c87 |
#!/usr/bin/env python
""" This script instantiate a DFC client against a given service,
and hammers it with read request (listDirectory) for a given time.
It produces two files : time.txt and clock.txt which contain time measurement,
using time.time and time.clock (see respective doc)
It assumes that th... | Andrew-McNab-UK/DIRAC | tests/Performance/DFCPerformance/readPerf.py | Python | gpl-3.0 | 2,365 | [
"DIRAC"
] | cda0a516f797be070891ae72d05e02d67319b1bfb07de2748dfb92f748650756 |
# dump stokes-netcdf
# Copyright (C) 2007-2008 Kengo Ichiki <kichiki@users.sourceforge.net>
# $Id: stncdump.py,v 1.11 2008/06/03 02:55:55 kichiki Exp $
#
# 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 Foun... | kichiki/stokes | python/stncdump.py | Python | gpl-2.0 | 6,474 | [
"NetCDF"
] | ba99f198be2e96c64962f3034fd0d4b878270fbde9422e3b779ce96ee55f5f26 |
import numpy as np
import Grid
import pf_dynamic_sph
import os
import sys
from timeit import default_timer as timer
if __name__ == "__main__":
start = timer()
# ---- INITIALIZE GRIDS ----
(Lx, Ly, Lz) = (21, 21, 21)
(dx, dy, dz) = (0.375, 0.375, 0.375)
xgrid = Grid.Grid('CARTESIAN_3D')
xgr... | kseetharam/genPolaron | datagen_qdynamics_imdyn_sph.py | Python | mit | 8,468 | [
"Gaussian"
] | 8a466b74517e26672fe087de4a2c33e535d269a5f2665bc3f7f28fcbe4965803 |
# -*- coding: UTF-8 -*-
# Copyright 2017 Luc Saffre
#
# License: BSD (see file COPYING for details)
from lino.api import rt, _
from lino.utils.mldbc import babel_named as named
def objects():
Group = rt.models.groups.Group
User = rt.models.users.User
UserTypes = rt.models.users.UserTypes
yield name... | khchine5/xl | lino_xl/lib/groups/fixtures/demo.py | Python | bsd-2-clause | 625 | [
"Galaxy"
] | 2b879edf5eb7da37a9fc53079377332d55767d639ae7e688798bec45afe0cffb |
import numpy as np
from layers import *
from connections import *
from neurons import *
from util import *
from train import *
from cost import *
class NetworkConstructor(object):
def set_input_layer(self, NeuronLayer):
self.InputLayer = NeuronLayer
def set_output_layer(self, NeuronLayer):
... | yohanyee/simple-neural-net | classes/construct.py | Python | mit | 4,902 | [
"NEURON"
] | 55a0e8534dbf851c4634f8afaf336ba205313ca922fba2112cc203616d15ec10 |
# Author: Jake VanderPlas
# License: BSD
# The figure produced by this code is published in the textbook
# "Statistics, Data Mining, and Machine Learning in Astronomy" (2013)
# For more information, see http://astroML.github.com
# To report a bug or issue, use the following forum:
# https://groups.google.com... | AndrewRook/machine_learning | figure_5-24.py | Python | mit | 6,544 | [
"Gaussian"
] | 114c12d877635de7add2edc61816eb5baf922b1924e1171c83d3ad0892662a8a |
#!/usr/bin/env python
"""
With this command you can log in to DIRAC.
There are two options:
- using a user certificate, creating a proxy.
- go through DIRAC Authorization Server by selecting your Identity Provider.
Example:
# Login with default group
$ dirac-login
# Choose another group
$ dirac-login di... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_login.py | Python | gpl-3.0 | 13,913 | [
"DIRAC"
] | 2a70fbaaa94a664dd42f7c7f0c344ff4e12756b9dd1003b3fa2e1ca135562527 |
"""Simple XML-RPC Server.
This module can be used to create simple XML-RPC servers
by creating a server and either installing functions, a
class instance, or by extending the SimpleXMLRPCServer
class.
It can also be used to handle XML-RPC requests in a CGI
environment using CGIXMLRPCRequestHandler.
A list ... | ktan2020/legacy-automation | win/Lib/SimpleXMLRPCServer.py | Python | mit | 26,386 | [
"Brian"
] | 430838afdf189553318cfeb3a48aa5765372845366cf66b15a12f2b7e96d6f38 |
# Copyright Tilde Materials Informatics
# Distributed under the MIT License
from __future__ import print_function
from setuptools import setup, find_packages
from codecs import open
import os
import sys
# Search for required system packages
missing_packages = []
try:
import numpy
from numpy import linalg
ex... | ansobolev/tilde | setup.py | Python | mit | 3,058 | [
"ASE",
"CRYSTAL",
"ESPResSo",
"VASP"
] | f9c052dbeb8984985324776d53add883e84a48255e4202d22bf40517d91f064e |
# -*- coding: utf-8 -*-
"""
The module contains the basic network architectures
+-------------------------+------------+---------+-----------------+----------+
| Network Type | Function | Count of|Support train fcn| Error fcn|
| | | layers | | ... | blagasz/python-ann | neurolab/net.py | Python | gpl-2.0 | 10,929 | [
"NEURON"
] | bfb50d6a4a7f23c79357c208063aff98fef5199af349a6ff156d0d7793d235d3 |
#!/usr/bin/python
# -*- encoding: utf-8; py-indent-offset: 4 -*-
# +------------------------------------------------------------------+
# | ____ _ _ __ __ _ __ |
# | / ___| |__ ___ ___| | __ | \/ | |/ / |
# | | | | '_ \ / _ \/ __| |/ /... | v-a/check_mk | web/htdocs/dashboard.py | Python | gpl-2.0 | 27,831 | [
"VisIt"
] | 6a96a3452a0847f354c4516fa6451f369eb97289776590b660530596524d5825 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# first, create an image to warp
imageGrid = vtk.vtkImageGridSource()
imageGrid.SetGridSpacing(16,16,0)
imageGrid.SetGridOrigin(0,0,0)
imageGrid.SetDataExtent(0,255,0,255,0,... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Hybrid/Testing/Python/TestGridWarpLinear.py | Python | bsd-3-clause | 2,541 | [
"VTK"
] | 4be0ed7bd523daa107c5ea56db527abe96532d7fc937e19d13926ceceb5af7f2 |
# Copyright (c) 2011, Joerg Raedler (Berlin, Germany)
# 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 cond... | arktools/openfdm | python/pyopenfdm/deps/DyMat/DyMat/Export/__init__.py | Python | gpl-3.0 | 2,525 | [
"NetCDF"
] | ec7e99bd0d526950117c9ed673eaad289ae8f83d5523917b6091c71028c35427 |
"""Test Axis device."""
from copy import deepcopy
from unittest import mock
from unittest.mock import Mock, patch
import axis as axislib
from axis.event_stream import OPERATION_INITIALIZED
import pytest
import respx
from homeassistant.components import axis, zeroconf
from homeassistant.components.axis.const import (
... | rohitranjan1991/home-assistant | tests/components/axis/test_device.py | Python | mit | 16,933 | [
"VMD"
] | dd5d71f990f20dc90f517ebe69abf131d146f7d2272718be09053f795395734e |
# L. Amber Wilcox-O'Hearn 2011
# test_article_randomiser.py
from recluse import article_randomiser
import unittest, StringIO, random, subprocess, bz2, os
class ArticleRandomiserTest(unittest.TestCase):
def test_randomise(self):
r = random.Random(999)
article_separation_line = "---END.OF.DOCUME... | ambimorph/recluse | recluse/test/test_article_randomiser.py | Python | agpl-3.0 | 2,916 | [
"Amber"
] | bc9eae0d7f373dd2dddb4f75ae3dcb512320591059b7cd330e86ac6a57f7a73d |
#!/usr/bin/env python
from __future__ import division
__author__ = "Jens Reeder"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Jens Reeder", "Jai Ram Rideout",
"Jose Antonio Navas Molina"]
__license__ = "GPL"
__version__ = "1.8.0-dev"
__maintainer__ = "Greg Caporas... | wasade/qiime | scripts/parallel_identify_chimeric_seqs.py | Python | gpl-2.0 | 9,500 | [
"BLAST"
] | 2018815a1a7b48ccba4f1c6dc2e5f5f7aef5800ea361b450690ace710d3f64a7 |
import unittest
from splinter import Browser
from .fake_webapp import EXAMPLE_APP
from .base import WebDriverTests
class PhantomJSBrowserTest(WebDriverTests, unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.browser = Browser("phantomjs")
@classmethod
def tearDownClass(cls):
... | lrowe/splinter | tests/test_webdriver_phantomjs.py | Python | bsd-3-clause | 2,438 | [
"VisIt"
] | 02c3da19b27b8fb825b056e6405d1a817f20996d0450b84ec24bde42bf75029f |
from __future__ import print_function, division
from brian import (Network, NeuronGroup, SpikeMonitor,
PoissonGroup, Connection,
mV, ms, Hz)
import sys
import matplotlib.pyplot as plt
import numpy as np
import itertools as itt
fin = [f*Hz for f in range(10, 41, 5)]
win = [w*mV for... | achilleas-k/brian-scripts | thesis_stuff/test_in_out.py | Python | apache-2.0 | 2,076 | [
"Brian"
] | bccb34702e7ba4b14f642085118cb832d5d6425656e93489726a562743d2d4ba |
"""The suite of window functions."""
from __future__ import division, print_function, absolute_import
import warnings
import numpy as np
from scipy import special, linalg
from scipy.fftpack import fft
from scipy._lib.six import string_types
__all__ = ['boxcar', 'triang', 'parzen', 'bohman', 'blackman', 'nuttall',
... | Dapid/scipy | scipy/signal/windows.py | Python | bsd-3-clause | 54,555 | [
"Gaussian"
] | f3b3a94f17e77105769de67c906804ded45642f4ce360dd1e24fe308405b6854 |
import urllib,xbmcplugin,xbmcgui,xbmcaddon,xbmc,os
ADDON = xbmcaddon.Addon(id='plugin.video.kodi_maintenance')
DIR=os.path.join(ADDON.getAddonInfo('profile'))
THEHTML = xbmc.translatePath(os.path.join(ADDON.getAddonInfo('path'),'theemail.html'))
def CATEGORIES():
if ADDON.getSetting('email')=='':
Show_Di... | repotvsupertuga/repo | instal/plugin.program.tvsupertugamanutencao/resources/mail/mail_file.py | Python | gpl-2.0 | 6,183 | [
"VisIt"
] | fe96adcb35898f38ad626d9a203e522a23facafe7bc1cb681ce8b3d9ca138ca7 |
# Photovoltaics surface
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Djordje Spasic and Jason Sensibaugh <djordjedspasic@gmail.com and sensij@yahoo.com>
# Ladybug is free software; you can redistribute i... | samuto/ladybug | src/Ladybug_Photovoltaics Surface.py | Python | gpl-3.0 | 38,221 | [
"EPW"
] | 925849b5b407e211fd765360f10ef4483b9b740e7e983d2e26760c3df2411edb |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy, ... | alexholcombe/dot-jump | dataRaw/Fixed Cue/test_dot-jump21Nov2016_12-01.py | Python | gpl-3.0 | 25,538 | [
"Gaussian"
] | 1109737c86df2ab38104444b8e9a5e1e569073a1652bcca9fcf853b6688ee5b8 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... | fingeronthebutton/RIDE | src/robotide/lib/robot/output/console/dotted.py | Python | apache-2.0 | 3,029 | [
"VisIt"
] | da492b76c461520f472f398fe93371df4b1be6cabe840c0e760527e6f0556361 |
# -*- coding: utf-8 -*-
import datetime
from collections import OrderedDict
from gluon import current, IS_IN_SET, URL
from gluon.storage import Storage
from s3 import S3Method, S3Represent
from .controllers import deploy_index, inv_dashboard
RED_CROSS = "Red Cross / Red Crescent"
def config(settings):
"""
... | flavour/eden | modules/templates/RMS/config.py | Python | mit | 296,245 | [
"VisIt"
] | c6c902abd338c8431581456d0acfaa79a2ff2e229a2f32d5bb1f2d2ac4eb0bb5 |
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