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"""
LMS Course Home page object
"""
from __future__ import absolute_import
from collections import OrderedDict
from bok_choy.page_object import PageObject
from bok_choy.promise import BrokenPromise
from six import text_type
from .bookmarks import BookmarksPage
from .course_page import CoursePage
from .courseware im... | ESOedX/edx-platform | common/test/acceptance/pages/lms/course_home.py | Python | agpl-3.0 | 12,185 | [
"VisIt"
] | 73418071cdbea487a5b767a392189136b596a6e0389287e3dc269024e68073b3 |
import headering
import glob
import pprint
import sys
import os
if len(sys.argv)>1:
p = sys.argv[1:]
else:
print "Usage: pymol -cq ./headerTest.py -- MTZTestDirectory"
sys.exit(1)
for curPath in p:
print "Processing MTZ files in path: '%s'" % curPath
l = glob.glob(curPath + os.sep + "*.mtz")
d = {}
for mtz... | gratefulfrog/lib | python/pymol/pymol_path/test/headerTest.py | Python | gpl-2.0 | 650 | [
"PyMOL"
] | 41b4e3160fea68f98999b48386a825dede6d309ee8ed708ab170b3c213482d27 |
# Copyright (c) 2020 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... | luotao1/Paddle | python/paddle/fluid/dygraph/dygraph_to_static/ifelse_transformer.py | Python | apache-2.0 | 20,452 | [
"VisIt"
] | f3b82d5741c755b25d647a6a979e517c7b73db2fc35342523a56b743acf21310 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | representation_batch_rl/representation_batch_rl/policies_pixels.py | Python | apache-2.0 | 18,009 | [
"Gaussian"
] | 6a3a3a56ee33c6069b56bdba3172227893ad7ba6e5e641aa756793e1b8c932de |
from ovito.io import import_file
from ovito.vis import ParticleDisplay
node = import_file("simulation.dump")
node.add_to_scene()
particle_display = node.source.particle_properties.position.display
particle_display.shape = ParticleDisplay.Shape.Square | srinath-chakravarthy/ovito | doc/python/example_snippets/particle_display.py | Python | gpl-3.0 | 251 | [
"OVITO"
] | 528263718231786dc4b3cd1b45b395133e93818998ce774591dd2573338f6350 |
# Copyright (C) 2011 by Brandon Invergo (b.invergo@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.
from __future__ import print_function
import os
import subprocess
try:
from os.path... | zjuchenyuan/BioWeb | Lib/Bio/Phylo/PAML/_paml.py | Python | mit | 6,463 | [
"Biopython"
] | afecf2f53565747a0288e6fc986e6dba536cf4ee7b00bb21120dd8163cfc1f2e |
#!/usr/bin/env python
#
# $File: debug.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 redistribute it a... | BoPeng/simuPOP | docs/debug.py | Python | gpl-2.0 | 2,006 | [
"VisIt"
] | f6d8d06f6d96661486315551bea183413ff67f562558f43d31e624fa6a0d4373 |
'''
PathwayGenie (c) GeneGenie Bioinformatics Ltd. 2018
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=invalid-name
# pylint: disable=too-many-arguments
import sys
from scripts.writer import w... | neilswainston/PathwayGenie | scripts/plasmid_writer.py | Python | mit | 754 | [
"VisIt"
] | b89bd5071df6753732fb57ff435a3e57cfc8b81b5741ffa50038c8bfa4624a35 |
# -*- coding: utf-8 -*-
"""
Module for using a trained CNN model to predict network connectivity.
Includes funtions for computing connection scores, generating a null
distribution with surrogate shuffles, and reconstructing the estimated
adjacency matrix of a network.
Created on Wed Aug 23 14:24:32 2017
@author: pau... | orlandi/netcal | internal/networkInference/Connectomics/cnn/prediction.py | Python | mit | 10,834 | [
"NEURON"
] | 5893873e8a432490086da4de5b84045c04f771beb1e8f1d1f2fd043996efefbb |
# xarray removed version -- due to some SEVERE issues in pd.TimeStamp
import rasterio, os
import numpy as np
import pandas as pd
import geopandas as gpd
from downscale import utils
class DatasetFF( object ):
'''
THIS SHOULD BE SUBCLASSED FROM `Dataset`, but is not because that class
is poorly written and the __ini... | ua-snap/downscale | downscale/dataset_ff.py | Python | mit | 7,316 | [
"NetCDF"
] | 7076e6459d85aa489719c259c59a0f92a69a2141f948a75b52b21ee7b607fa8d |
# Copyright 2004-2017 Tom Rothamel <pytom@bishoujo.us>
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, m... | kfcpaladin/sze-the-game | renpy/display/image.py | Python | mit | 21,827 | [
"VisIt"
] | 9120faedc2f018e62abb728b3d43c5a6246b82fc57d8b7c909c8ae54b8272e2a |
"""
Copyright (C) 2004-2015 Pivotal Software, Inc. All rights reserved.
This program and the accompanying materials are made available under
the terms of the 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
... | CraigHarris/gpdb | src/test/tinc/tincrepo/mpp/gpdb/tests/storage/aoco_alter/aoco_alter_sql_test/test_aoco_altercol.py | Python | apache-2.0 | 1,273 | [
"ORCA"
] | 9c0c6cbcd4114a5b5d58b4c07d765a90300a712941cf3ee0bd900e2d48e96adb |
# -*- coding: utf-8 -*-
""" Base Hamiltonian Monte Carlo algorithm. """
import theano as th
import theano.tensor as tt
class HamiltonianSampler(object):
"""Hamiltonian / Hybrid Monte Carlo sampler (Duane et al. 1987).
Markov chain Monte Carlo sampler with transition operator constructed from
simulated H... | matt-graham/thermodynamic-monte-carlo | thermomc/hmc.py | Python | mit | 18,432 | [
"Gaussian"
] | 6514566e825c676ae6e309c9fc5645a8bee4823b76eebc312474dc6ebc1cd74a |
########################################################################
#
# File Name: Visitor.py
#
# Documentation: http://docs.4suite.com/4DOM/Visitor.py.html
#
"""
WWW: http://4suite.com/4DOM e-mail: support@4suite.com
Copyright (c) 2000 Fourthought Inc, USA. All Rights Reserve... | carvalhomb/tsmells | guess/src/Lib/xml/dom/ext/Visitor.py | Python | gpl-2.0 | 2,485 | [
"VisIt"
] | 3a60d91201686de6f9b61a497f5cd3a41f8a051e7b3d0b14b26b1a250821949f |
"""
MIT License
Copyright (c) 2017 Joris Gillis, KU Leuven
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge... | jgillis/simscape2casadi | run.py | Python | mit | 24,768 | [
"VisIt"
] | d7333995b002f0e043644f2a5b75ebd9c6d467b69a73a89693832669301ebb4a |
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE... | milfeld/lammps | python/lammps.py | Python | gpl-2.0 | 7,036 | [
"LAMMPS"
] | bd6b2f54411cb187b38e79b4d576522a368c4aa62c149b4905de1f40f917a227 |
""" TokenAgent
This agent inspect all elements, and resets their tokens if necessary.
The following options can be set for the TokenAgent.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN TokenAgent
:end-before: ##END
:dedent: 2
:caption: TokenAgent options
"""
__RCSID__ = '$Id$'
from date... | fstagni/DIRAC | ResourceStatusSystem/Agent/TokenAgent.py | Python | gpl-3.0 | 6,701 | [
"DIRAC"
] | 355d5e4d86b13f869abe9580a63aaa5b711597956ca3b1ae51ddbc0ff340d2c7 |
# Unit tests for cache framework
# Uses whatever cache backend is set in the test settings file.
import copy
import io
import os
import pickle
import re
import shutil
import tempfile
import threading
import time
import unittest
import warnings
from unittest import mock
from django.conf import settings
from django.core... | denys-duchier/django | tests/cache/tests.py | Python | bsd-3-clause | 91,107 | [
"Brian"
] | f0336b4c0ec016411f0a60997fd63ed2bf436b18fc322bec09ea328b98f09629 |
import numpy as np
import matplotlib.pyplot as plt
from Other_samples.Regularization.reg_utils import sigmoid, relu, plot_decision_boundary, initialize_parameters, \
load_2D_dataset, predict_dec
from Other_samples.Regularization.reg_utils import compute_cost, predict, forward_propagation, \
backward_propagation... | adexin/Python-Machine-Learning-Samples | Other_samples/Regularization/regularization.py | Python | mit | 11,652 | [
"NEURON"
] | 29e13724e5edbadeef9dc142c23038ccd47b8ca7a7eaaac591957492009d92ba |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | soarpenguin/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 112,500 | [
"VisIt"
] | beb265f5a84d553acf84c9a50e40b2a396a29dd360747296d173c645c842b6fb |
# Made with contributions from :
# disKret, Skeleton & DrLecter.
# this script is part of the Official L2J Datapack Project.
# Visit http://forum.l2jdp.com for more details.
import sys
from com.l2scoria.gameserver.model.quest import State
from com.l2scoria.gameserver.model.quest import QuestState
from com.l2scoria.gam... | zenn1989/scoria-interlude | L2Jscoria-Game/data/scripts/quests/17_LightAndDarkness/__init__.py | Python | gpl-3.0 | 4,047 | [
"VisIt"
] | 4c9a198a63ce7a7c353a5bd864ba31e24d73382a34c9244f97abd04ae520fa07 |
import time
import numpy as np
import matplotlib.pyplot as plt
from test_farfield import make_meshes
from tectosaur.ops.sparse_integral_op import RegularizedSparseIntegralOp
from tectosaur.ops.dense_integral_op import RegularizedDenseIntegralOp
from tectosaur.ops.sparse_farfield_op import TriToTriDirectFarfieldOp
from ... | tbenthompson/tectosaur | tests/test_regularized.py | Python | mit | 8,089 | [
"Gaussian"
] | e11fd7d87881a2946e4ff6a0b647f88ecae590c1154b47907883bcb184c6796d |
"""Module containing functions for an MLP network"""
# assumes all input features precede output(s)
import random
import math
import mlp_exceptions
def initialise_bias(params):
"""Function to initialise the neuron input biases to 1.0"""
outputs_l_j = []
# plus one for input layer
for _ in range(len(p... | farthir/msc-project | mlp_functions.py | Python | mit | 9,441 | [
"NEURON"
] | 0af46924460604c20f3bf6389f059835e578aaf82e28ec708f4d0cfcf0d8b3ca |
import unittest
import scipy
import pysal
import numpy as np
#from pysal.spreg import error_sp_regimes as SP
#from pysal.spreg.error_sp import GM_Error, GM_Endog_Error, GM_Combo
from functools import partial
from pysal.contrib.handler import Model
GM_Error = partial(Model, mtype='GM_Error')
GM_Endog_Error = partial(M... | schmidtc/pysal | pysal/contrib/handler/tests/test_error_sp_regimes.py | Python | bsd-3-clause | 15,309 | [
"COLUMBUS"
] | a2189479b2298afe2da53f48372a2fa3ed28d22e946b1851c6c93c370372ec82 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import collections
import importlib
from pymatgen.util.plotting import pretty_plot
"""
This module defines generic plotters.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Pr... | nisse3000/pymatgen | pymatgen/vis/plotters.py | Python | mit | 5,202 | [
"pymatgen"
] | c2a1749a2cd7699e0fef8c7babb1e5faeff8525075dbf27322eeccf3af3620c0 |
#!/usr/bin/env python3
########################################################################
# Solves problem 8 from projectEuler.net.
# Finds the greatest product of five consecutive digits from the
# 1000-digit number.
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software: you can ... | salessandri/programming-contests | project-euler/problem008.py | Python | gpl-3.0 | 2,423 | [
"VisIt"
] | 35aec2f1fc510afe93cf82fd0e5b9c829e1bc947a894e1951510da31b19627ac |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | modeling/decomposition/decomposition.py | Python | agpl-3.0 | 36,896 | [
"Galaxy"
] | 9fdd3127109569bb5ee6f1510e79e1d9fa4af79c8a99cf74103a54f102ce573f |
# Copyright (C) 2015
# Jakub Krajniak (jkrajniak at gmail.com)
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free softw... | capoe/espressopp.soap | src/System.py | Python | gpl-3.0 | 7,799 | [
"ESPResSo"
] | fec6e4597d84fcf8e66785fb94a01066b7ae1a296a117b4b78f586fef27b2380 |
# coding: utf-8
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 o... | fccoelho/pypln.backend | tests/test_worker_palavras_noun_phrase.py | Python | gpl-3.0 | 2,073 | [
"NAMD"
] | 796adf171a941f7adc2d465c547605169a5d2e8f1c9227384de49b241fd46798 |
#!/usr/local/bin/env python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Test that all OpenMM systems in simtk.pyopenmm.extras.testsystems.* give the ... | choderalab/YankTools | testsystems/test_energies.py | Python | gpl-2.0 | 7,093 | [
"OpenMM"
] | 7a2e42c59b4434dda274d8e8d96ec3aad9f6a77fd69776012182bc7f83424ec4 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageSobel2D(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.v... | nagyistoce/devide | modules/vtk_basic/vtkImageSobel2D.py | Python | bsd-3-clause | 487 | [
"VTK"
] | c27ddd73d8ca8c89ee0c66c5643404059b24f4475d163760fb2bde4bca59235e |
from __future__ import unicode_literals
import argparse
import ast
import collections
import sys
from typing import List
from typing import Optional
from typing import Sequence
from typing import Set
BUILTIN_TYPES = {
'complex': '0j',
'dict': '{}',
'float': '0.0',
'int': '0',
'list': '[]',
's... | Harwood/pre-commit-hooks | pre_commit_hooks/check_builtin_literals.py | Python | mit | 3,219 | [
"VisIt"
] | 49ed28f24cb0af00c9f95d3cb797cffcf608094d98b82023cf13ed273f0c9c9d |
import multiprocessing
import warnings
import copy
import sys
import PyQt5.QtCore as QtCore
from PyQt5.QtCore import pyqtSlot, QObject
from PyQt5.QtWidgets import (QMainWindow, QTabWidget, QLabel, QDialog,
QApplication, QGridLayout, QFileDialog, QWidget)
from PyQt5.Qt import Qt
from PyQt5.... | maxscheurer/pycontact | PyContact/gui/MainWindow.py | Python | gpl-3.0 | 22,094 | [
"VMD"
] | 61e65db536c7df92fa11d2b43635dc1e7d7e232662ddc5fd9f510833f846e551 |
from __future__ import print_function, division
import collections
from sympy.core.add import Add
from sympy.core.basic import Basic, C, Atom
from sympy.core.expr import Expr
from sympy.core.function import count_ops
from sympy.core.power import Pow
from sympy.core.symbol import Symbol, Dummy, symbols
from sympy.core.... | ojengwa/sympy | sympy/matrices/matrices.py | Python | bsd-3-clause | 127,348 | [
"DIRAC",
"Gaussian"
] | 894d157b1bf96fafe1167baa4384ca77138acc05dcb9573f98cc5eee5137717f |
import os
import re
import json
import logging
import itertools
import numpy as np
import scipy.signal
from mako.template import Template
# initialize log
logger = logging.getLogger(__name__)
class WindsurfConfigurator:
n = 0 # question counter
supported_models = {
'xbeach':'xbeach',
... | openearth/windsurf | windsurf/configurator.py | Python | gpl-2.0 | 9,272 | [
"NetCDF"
] | cedbb771005209819db89757a8fcfabbc7fe0330a57043c0870962d984a3e10f |
# Orca
#
# Copyright 2013 The Orca Team.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library is ... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/gnome-documents/script.py | Python | gpl-3.0 | 2,488 | [
"ORCA"
] | 03bfe0d762fecfd359f352342cf377b632767f60640b33089f3f8d2d01a29738 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# relevant imports
import sys
import time
import espressopp
import mpi4py.MPI as MPI
import Tetracryst # Preparation of tetrahedral crystal and constuctions of bonds in tetrahedral liquid
from espressopp import Real3D, Int3D
from espressopp.tools import decomp
from espre... | capoe/espressopp.soap | examples/hadress/hadressDensityPressure/hadressDensity.py | Python | gpl-3.0 | 8,087 | [
"CRYSTAL"
] | ac06155432c0c964d6253ef9bab28c7f124109a27944bbffbc013d0d50020809 |
#!/usr/bin/env/python
##============================================================
"""
Some tests for deconvolution
They aren't extreme
"""
import sys
sys.path.append("../decon/")
sys.path.append("../misc/")
import DeconvolveToTargetPSF as DT
import numpy,scipy
import time
def decontest():
## Original... | drphilmarshall/HumVI | attic/test/decontest.py | Python | mit | 5,714 | [
"Gaussian"
] | 250b0aa61814fafa1418fdf6c796d874849938df77e7a0f1ebb5914a7d2945cd |
# Import of the relevant tools
import time
import numpy as np
import theano
import theano.tensor as T
from theano import pp, config
from plotly.tools import FigureFactory as FF
import plotly.graph_objs as go
from .curves import Curve
class CurvesManifold :
"""
Encapsulates a few useful io + type conversion meth... | jeanfeydy/lddmm-ot | LDDMM_Python/lddmm_python/modules/manifolds/curves_manifold.py | Python | mit | 4,841 | [
"DIRAC"
] | fdb2b83bb0b42ee0c33483b390be8001f517f1e6e7a18e379a71b66991339332 |
# Copyright 2008-2009 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of django-facebookconnect.
#
# django-facebookconnect is free software: you can redistribute it and/or modify
# it under the te... | ryszard/django-facebookconnect | facebookconnect/management/commands/installfacebooktemplates.py | Python | gpl-3.0 | 2,621 | [
"Brian"
] | 4902a2a9e00d2ecf18492d4d36bafc72c91eff956ef0d87b588dc59d500591de |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the License, or... | tiagocardosos/stoq | stoqlib/lib/environment.py | Python | gpl-2.0 | 1,083 | [
"VisIt"
] | d77528ea11ecca0039daa3b108ab0ad200fd2d4d47fc89f4b50c45ce8f16270e |
#!python
# ChristmasTime.py
# An Interactive Fiction game by Christopher "avarisclari" Weigle
# IFID = B25D3DDC-238D-4D68-8AE7-956ACFF9110E
import textwrap
import sys
import string
import os
sys.stdout.write("\x1b]2;Christmas Time\x07")
scenes = {
"title": {
"description": "\n"
" ... | avarisclari/HeartoGold | Examples/ChristmasTime.py | Python | mit | 68,967 | [
"VisIt"
] | 198b00add42716fbf4500cfd5a9720687be81643bacce7540381551937795234 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/interaction/DihedralHarmonicCos.py | Python | gpl-3.0 | 3,028 | [
"ESPResSo"
] | fdfca8985a6b1da8c22b1afa99ac12c4c6478da6f368da952da622a556730d50 |
#!/usr/bin/env python
"""
utils for vasp only.
"""
import numpy as np
import os.path
from ase.io import read
from ase.io.vasp import read_vasp
from pyDFTutils.ase_utils.symbol import symbol_number, symnum_to_sym
from ase.atoms import Atoms
import re
def read_sort(sort_file='ase-sort.dat'):
"""
get the second ... | mailhexu/pyDFTutils | pyDFTutils/vasp/vasp_utils.py | Python | lgpl-3.0 | 4,626 | [
"ASE",
"VASP"
] | 5e61e6ca3b9ab5ca8015de25d683b772b2745156fecefe35eeb1f4ad7970b333 |
##############################################################################
# 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-variantannotation/package.py | Python | lgpl-2.1 | 2,615 | [
"Bioconductor"
] | 4a3c2194cd2b532478e23e027242824f07cd8219e4178597411c80e98506a5fa |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
from zeroinstall.support import tasks
from zeroinstall.injector import handler, download
gobject = tasks.get_loop().gobject
glib = tasks.get_loop().glib
version = '2.3.3'
class GUIHandler(... | rammstein/0install | zeroinstall/0launch-gui/gui.py | Python | lgpl-2.1 | 3,029 | [
"VisIt"
] | abe63a6d39dfa4f33d34ebd3185ea2d965dab05d0b193aa3a52d98de5d925f82 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import math
import vtk
import vtk.test.Testing
# ------------------------------------------------------------
# Purpose: Test more parametric functions.
# ------------------------------------------------------------
class TestMoreParametricFunctions(vtk.test... | hlzz/dotfiles | graphics/VTK-7.0.0/Common/ComputationalGeometry/Testing/Python/TestMoreParametricFunctions.py | Python | bsd-3-clause | 11,232 | [
"VTK"
] | a0fa7ef580edf9d2578c3ab38e6106f82cb3e9aca634b0fb13f6e637328aa07b |
#!/usr/bin/env python
import sys
import random
import bisect
import pysam
import gzip
try:
import cPickle as pickle
except:
import pickle
import numpy
from time import time
import argparse
import math
import os
inds = {'A': 0, 'T': 1, 'G': 2, 'C': 3, 'N': 4,
'a': 0, 't': 1, 'g': 2, 'c': 3, 'n': 4}
M... | hchyang/phyloVars | wes/wessim/__sub_wessim2.py | Python | gpl-3.0 | 34,602 | [
"pysam"
] | 47a870ffb7726272c979e02fee0dc931d9dd092df3aec434b2a558ef595f6992 |
'''
Examine the line shapes that result from a mixture of thermal line width
Gaussian components.
I'm getting the moments of the normal mixture model from:
http://onlyvix.blogspot.ca/2011/05/mixture-of-normal-formulas-for-skew-and.html
which uses the derivation from:
GENERATING DAILY CHANGES IN MARKET VARIABLES
USING... | e-koch/VLA_Lband | 14B-088/HI/analysis/mixture_of_normals.py | Python | mit | 10,965 | [
"Gaussian"
] | 426a67fd07a7de757dad4c93181285006196b61ed22aac46b7e08344e4a8264f |
import numpy as n
import glob
import h5py
import os
import time
import sys
h5_files = n.array(glob.glob(os.path.join(os.environ['MD10'], "h5", "hlist_?.?????_emerge.hdf5")))
h5_files.sort()
bins = n.arange(6,13,0.1)
xb = (bins[1:] + bins[:-1]) / 2.
hh = 0.6777
def measureSMF(h5_file, volume=1000.**3./hh**3., update=... | JohanComparat/pyEmerge | bin/measure_SMF.py | Python | unlicense | 1,980 | [
"Galaxy"
] | b8e52afa0f6f0a9ec312c93772b2364142837cad9257aef39838840cd786004b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import logging
from pymatgen.io.qchem.inputs import QCInput
from pymatgen.io.qchem.utils import lower_and_check_unique
# Classes for reading/manipulating/writing QChem output files.
__author__ = "Samuel Blau,... | dongsenfo/pymatgen | pymatgen/io/qchem/sets.py | Python | mit | 7,699 | [
"pymatgen"
] | 250140063c8c076ff96ff80bf564b172c30d39a25f9ac8ef4cb06f4ed69698ed |
import os
from box import Atoms
from box import md
import numpy as np
import ase
from box.interpolation import VectorSplineFunction
#from box.calculators import Calculator
from scipy.linalg import norm
import pylab as pl
vec=np.array
class LEPS_Calculator:
""" ase Calculator class """
def __init__(self):... | pekkosk/hotbit | box/barriers.py | Python | gpl-2.0 | 13,845 | [
"ASE",
"VTK"
] | 2be16a541d2dc381ef6b96469077b2e3e6ea102cb82278d855838930bcb90719 |
#!/usr/bin/python
from __future__ import division
from builtins import range
import numpy as np
import os.path as op
import subprocess as sp
import sys
import tempfile as tf
from optparse import OptionParser
import forgi.threedee.utilities.average_atom_positions as ftua
import forgi.threedee.utilities.pdb as ftup
im... | ViennaRNA/forgi | examples/plot_average_atom_positions.py | Python | gpl-3.0 | 3,537 | [
"PyMOL"
] | 50088290b8109fc429aa0be0f5e0748eeed2261ba81628a09422706dcd25a4ec |
# Copyright 2014 Mirantis Inc.
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... | openstack/osprofiler | osprofiler/tests/unit/cmd/test_shell.py | Python | apache-2.0 | 6,136 | [
"Galaxy"
] | c9d79d89c27861edef62e153a94f5ecbc8b2527ea814f16dd8dc223e42d90508 |
# -*- coding: utf-8 -*-
# Copyright © 2012-2013 Roberto Alsina and others.
# Permission is hereby granted, free of charge, to any
# person obtaining a copy of this software and associated
# documentation files (the "Software"), to deal in the
# Software without restriction, including without limitation
# the rights t... | zhukite/nikola-install | nikola/main.py | Python | mit | 5,111 | [
"VisIt"
] | 4287ad1cafc808c974e8aafc9a80c427472795858cc8b826f64dbd0f64c1d346 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""HPMC updaters."""
from . import _hpmc
from . import integrate
from hoomd import _hoomd
from hoomd.logging import log
from hoomd.data.parameterdicts import Ty... | joaander/hoomd-blue | hoomd/hpmc/update.py | Python | bsd-3-clause | 27,980 | [
"HOOMD-blue"
] | f81bb3396e847c1c8f353def9df4430886f88412f900c6f59b3b2b9e004b3e43 |
#!/usr/bin/env python
import os
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# This example demonstrates the reading of a field and conversion to PolyData
# The output should be the same as polyEx.tcl.
# Create a reader and write out the field
reade... | biddisco/VTK | Filters/Core/Testing/Python/fieldToPolyData.py | Python | bsd-3-clause | 2,400 | [
"VTK"
] | 1fc615ae6d71efc4644d1d9be479576d8ffadd589b4bf1ff955480b25d680c30 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Works for Abinit:
"""
from __future__ import unicode_literals, division, print_function
import os
import shutil
import time
import abc
import collections
import numpy as np
import six
import copy
from six.... | sonium0/pymatgen | pymatgen/io/abinitio/works.py | Python | mit | 44,493 | [
"ABINIT",
"Gaussian",
"NetCDF",
"pymatgen"
] | 6d9d26553d5ca6e0c925d67dcd8cc426e7d77d6c04c567dbfd83d4c76e31c2e2 |
# coding: utf-8
"""
Task history related objects
"""
import collections
import traceback
import logging
from monty.json import MontyDecoder, jsanitize, MSONable
from pymatgen.util.serialization import pmg_serialize
logger = logging.getLogger(__name__)
class TaskHistory(collections.deque, MSONable):
"""
His... | gmatteo/abiflows | abiflows/fireworks/utils/task_history.py | Python | gpl-2.0 | 4,925 | [
"ABINIT",
"pymatgen"
] | 859a99f82a5d6b5398284e88f6286576dfaaa0ed3ebccdf85de1d573bfeee340 |
# -*- coding:utf-8 -*-
from rdkit import Chem
from rdkit.DataStructs import cDataStructs
from rdkit.Chem import MACCSkeys
from rdkit.Chem import AllChem
from rdkit.Chem.Fingerprints import FingerprintMols
import os
class SimOperation: # compute similarities, create sim_table, write sims
p = {'maccs': 0.25, 'ecf... | HaoboGu/Structure-Similarity | Preprocess.py | Python | mit | 3,473 | [
"RDKit"
] | ef75a19b65bdaff4ae11854ff0eeb5dafb1d55e7a318ff3bf32993e5718b930f |
"""
Standard cells for nest
:copyright: Copyright 2006-2016 by the PyNN team, see AUTHORS.
:license: CeCILL, see LICENSE for details.
"""
from pyNN.standardmodels import cells, build_translations
from .. import simulator
class IF_curr_alpha(cells.IF_curr_alpha):
__doc__ = cells.IF_curr_alpha.__doc__
tran... | anupkdas-nus/global_synapses | pyNN-dispackgaes/nest/standardmodels/cells.py | Python | gpl-3.0 | 12,609 | [
"NEURON"
] | b7930a014252af89fb8a67310252120c52cf13cc8c460010e321d86bf5830aab |
#!/usr/bin/env python3
import espressopp
from espressopp.tools import replicate, readxyz
from espressopp import Real3D
import time, sys
import numpy as np
def bench_lj(xyz_file):
# read from xyz file
print("reading from: ", xyz_file)
pid, type, xpos, ypos, zpos, xvel, yvel, zvel, Lx, Ly, Lz = readxyz(xy... | espressopp/espressopp | testsuite/potential_array/potential_array_test.py | Python | gpl-3.0 | 6,093 | [
"ESPResSo"
] | 2f12c0020f9a21329e724fbfcebb8a65fe31fece525498b1ca20457092b4ac8b |
#!/usr/bin/env python
import os
import re
try:
from setuptools import setup # , Extension
# from setuptools.command.build_ext import build_ext as _build_ext
except ImportError:
from distutils.core import setup # , Extension
# from distutils.command.build_ext import build_ext as _build_ext
from Cyt... | karenyyng/george | setup.py | Python | mit | 6,172 | [
"Gaussian"
] | 765d82cfd96d126c9030f3644e8c9400addda369d56676da77c559fb7865ee73 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import json
import numpy as np
from pymatgen.analysis.structure_matcher import StructureMatcher, \
ElementComparator, FrameworkC... | xhqu1981/pymatgen | pymatgen/analysis/tests/test_structure_matcher.py | Python | mit | 30,773 | [
"pymatgen"
] | 053624b929c04ed0886b3d3e22fdc069a7ac2f7b5b5b1d8484621ebfcb9271ec |
#!/usr/bin/env python
""" Setuptools script for pseudogenerator
"""
from setuptools import setup, find_packages
from os.path import join, dirname
from pseudogen import __version__
setup(
name='pseudogen',
description='Siesta Pseudopotential Generator',
version=__version__,
packages=find_packages(),
... | ansobolev/PseudoGenerator | setup.py | Python | mit | 397 | [
"SIESTA"
] | 42f3494ffcfc0ff2fad47c6f6dbbd8cc734b643b3d5a6f7d38a0fc0a30923d2e |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | adit-chandra/tensorflow | tensorflow/python/ops/linalg/linear_operator_test_util.py | Python | apache-2.0 | 36,518 | [
"Gaussian"
] | 2486444f7006f2a6319542a328e5be53f87afe7f6e60eb7712abc39d3fafecf4 |
"""
Tests for miscellaneous utilities.
"""
import cPickle
import unittest
from rdkit import Chem
from rdkit_utils import PicklableMol
class TestPicklableMol(unittest.TestCase):
def setUp(self):
"""
Set up for tests.
"""
self.mol = Chem.MolFromSmiles('CC(C)(C)NC[C@@H](C1=CC(=C(C=C... | skearnes/rdkit-utils | rdkit_utils/tests/test_init.py | Python | bsd-3-clause | 933 | [
"RDKit"
] | 178a78e3fcc75c47940c15f8e4c1225587e4221d08dabc9f91b9b4c92fe8bf2e |
# This module is an interface of the diceseq output,
# with which you could easily access to the results,
# also visualize the data.
import sys
import gzip
import numpy as np
import matplotlib.pyplot as plt
class SampleFile:
"""docstring for SampleFile"""
def __init__(self, sample_file):
fid = gzip.op... | huangyh09/diceseq | diceseq/utils/out_utils.py | Python | apache-2.0 | 7,323 | [
"Gaussian"
] | a476a24944770c3a701ca6203b2ceb993e7bd36923412dd3af862cfe6a48c6f5 |
'''The script reads a BAM file and report SNPs
according to a position on a read.
Note for a coordinate in SAM/BAM format:
In SAM file, it is 1-based.
In BAM file, it is 0-based.
(http://genome.sph.umich.edu/wiki/SAM)
'''
import sys
import pysam
def find_snp(md):
'''Note for Cigar tag:
I ... | likit/BioUtils | read_error_profile.py | Python | bsd-2-clause | 4,185 | [
"pysam"
] | 142c52c488eb179afda9427c3e8a9c25ee00edabea6c95f989925f8d70d4e6cd |
# -*- coding: utf-8 -*-
"""
Created on Mon May 15 10:18:49 2017
@author: S.Y. Agustsson
module containing general purpouse function, usually shornamed wih gfs
"""
# %% imports
import tkinter as tk
from tkinter import filedialog
from datetime import datetime
import pickle
import os
import re
import scipy.constants as... | steinnymir/RegAscope2017 | lib/utils.py | Python | mit | 8,915 | [
"Gaussian"
] | f17488b06bec9eb9b07b90dc5991e448dc3ba1e111a0d215b6657305586f8521 |
#!/usr/bin/env python
#
# Copyright (C) 2014 Brian Caswell <bmc@lungetech.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights... | f0rki/cb-multios | tools/generate-polls/generator/graph.py | Python | mit | 13,991 | [
"Brian"
] | 4f34850ef039fddecc6ac06d9870102aee63e99a82493267e2b39fe4f5889002 |
"""
Copyright (c) 2011-2015 Nathan Boley
This file is part of GRIT.
GRIT 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.
GRIT is distribut... | nboley/grit | setup.py | Python | gpl-3.0 | 2,074 | [
"pysam"
] | 5f29e3b1b6785f61c6580d4808f6d60f8177eb2a69a42c177abbf1ae73cb5c3b |
#!/usr/bin/env python
"""
CEDA_download.py - Download CMIP5 output from the [Centre for
environmental Data Archival][CEDA].
You'll need your own login (username/password) in order to use this. Once
that's been obtained, these tools should help make it very easy to
download batches of data, even when you don't know ex... | darothen/cmip5_download | CEDA_download.py | Python | mit | 10,517 | [
"NetCDF"
] | b1a97153bc440e6dfd4eb024957278d296c9624027540b709032937abb151783 |
#
# Copyright Applied Language Solutions 2012
#
# This file is part of Pypeline.
#
# Pypeline 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... | ianj-als/pypeline | src/pypeline/core/types/state.py | Python | gpl-3.0 | 2,742 | [
"Brian"
] | b28ad46d9ac0cc729cb58b9a23da580fcabd725946eec161d9dea44daf848e73 |
# coding: utf-8
from __future__ import division, unicode_literals
'''
Created on Sep 23, 2011
'''
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Sep 23, 2011"
import os
import rand... | Dioptas/pymatgen | pymatgen/transformations/tests/test_standard_transformations.py | Python | mit | 16,838 | [
"pymatgen"
] | eed2e3fd9b3acc8084d0bbd4b0d6f824b88f38dbbf589dcb2a7c86e64cb77639 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/postprocessor_tab/test_VectorPostprocessorViewer.py | Python | lgpl-2.1 | 5,619 | [
"MOOSE"
] | 5fb7f204c2e80ae369778968cdce915ecc6d2cc961263277c2ad12d826c1eea7 |
# 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_color.py | Python | apache-2.0 | 1,190 | [
"PySCF"
] | 9343ce851e32ebc09542c0189169aa7d57fbe8eba66029a4abca071614850b13 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010-2017 GEM Foundation
#
# The OQ-CATK (Lite) 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 ... | klunk386/CatalogueTool-Lite | OQCatk/Exploration.py | Python | agpl-3.0 | 12,357 | [
"Gaussian"
] | f446fe0c7f66a10331c353bad0b0794acaa9766f4aa1267bafdf797814a6533f |
""" Test class for plugins
"""
# imports
import unittest
import importlib
from mock import MagicMock
from DIRAC import gLogger
#sut
from DIRAC.TransformationSystem.Agent.TransformationPlugin import TransformationPlugin
paramsBase = {'AgentType': 'Automatic',
'DerivedProduction': '0',
'... | vmendez/DIRAC | TransformationSystem/Agent/test/Test_Plugins.py | Python | gpl-3.0 | 3,344 | [
"DIRAC"
] | 796923f823d710ac63ad947d4a6f3f9b33b04c6522c96b34b4671c8ff5abf7df |
#!/usr/bin/env python
# Core
from __future__ import print_function
from decimal import *
from functools import wraps
import logging
import math
import pprint
import random
import re
import time
import ConfigParser
# Third-Party
import argh
from clint.textui import progress
import funcy
import html2text
from PIL im... | metaperl/revadbu | src/main.py | Python | mit | 14,096 | [
"VisIt"
] | bf1dc87f7ff93f311f7afdc4537ba951caddc5e0695486c29d4305e067138eba |
from account.models import Team
from milkyway.models import Solves, Challenge, Category
import datetime
import json
from django.contrib import messages
from django.shortcuts import redirect
from django.shortcuts import render
from django.views.generic.base import TemplateView
from django.views.generic.detail import De... | galaxy-ctf/milky-way | milkyway/views.py | Python | agpl-3.0 | 5,615 | [
"Galaxy"
] | 6f492ee6d0fae164e51cc76ceb45ffe8299bb69e12c5e2071f9a369314e83d56 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Adapted from Graphviz.py (now deprecated)
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2005-2006 Eero Tamminen
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Cont... | ennoborg/gramps | gramps/plugins/graph/gvrelgraph.py | Python | gpl-2.0 | 40,729 | [
"Brian"
] | c64f0c2f8ffa56a838183efaaf4ca3ace7b6115eab63dd8a080ba3bdfb352ec9 |
# Copyright (C) 2000 Greg Landrum
#
# 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 of the License, or (at your option) any later version.
#
# This library is distribu... | jandom/rdkit | rdkit/sping/SVG/pidSVG.py | Python | bsd-3-clause | 23,927 | [
"RDKit"
] | 25ed362f16233ffdbc1989fee9051108837f2629a486d4943c3b916c2474602d |
# Regular Scripted module import
from __main__ import vtk, qt, ctk, slicer
# Other scripted modules import
import SkinModelMaker
#
# Workflow
#
class Workflow:
def __init__(self, parent):
import string
parent.title = "Bender FEM Workflow"
parent.categories = ["", "Segmentation.Bender"]
parent.contr... | ricortiz/BenderCraniosynostosis | Modules/Scripted/Workflow/Workflow.py | Python | apache-2.0 | 115,724 | [
"VTK"
] | 217007a982d04dc9af74cefac3635c9d181b2daefc440a6f3b669195148a9ae3 |
import requests
import pytest
import json
import demistomock as demisto
bundle_index = 0
submitted_indicators = 0
mocked_get_token_response = """{"access_token": "fababfafbh"}"""
iocs_bundle = [
{
"id": "bundle--f00374ec-429c-40cb-b7bb-61f920814775",
"objects": [
{
"cre... | demisto/content | Packs/Cybersixgill-DVE/Integrations/CybersixgillDVEFeed/CybersixgillDVEFeed_test.py | Python | mit | 41,917 | [
"Amber"
] | 2836d8f67429291f6bc15eb7fd051d05b87b8e43571e8267e7e2dea6cdf3fcfc |
###
### This script demonstrates the use of the new generic cinema io api to create
### a small dataset based on the Wavelet source. Several contours are created,
### and then images are saved from a set of camera angles.
###
### To use this script, follow the command example below, after changing the
### variable "o... | Kitware/cinema | scripts/data_generation/generateWaveletNewApi.py | Python | bsd-3-clause | 4,656 | [
"ParaView"
] | 921b3591c6a753b0de2b31ad28db5ab68d86a83dbec9156470dc7ef3bcc3b80e |
# Copyright (c) 2015-2018 Cisco Systems, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge... | metacloud/molecule | molecule/model/schema_v2.py | Python | mit | 30,692 | [
"Galaxy"
] | 98300e66bbc727163e80a4c49a98b516bde0b8775cb1e3250b236db1c586818a |
###############################################
## PLANETOPLOT ##
## --> PPCLASS ##
## A generic and versatile Python module ##
## ... to read netCDF files and plot ##
###############################################
## Author: Aymeric Spiga. 02-03/... | aymeric-spiga/planetoplot | modules/ppclass.py | Python | gpl-2.0 | 111,044 | [
"NetCDF"
] | a4bba8fc937b3a34941e22fae3e536f619880f2c814d48b0d883a0f44b64854b |
#
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option)... | KonradBreitsprecher/espresso | samples/load_properties.py | Python | gpl-3.0 | 4,526 | [
"ESPResSo"
] | 391528d4148cd9b996938c5dfc1d54878037576a7c06beb957a8a7d88b281ab4 |
"""
Brian T. Bailey
ITM 513 - MP4
Client program file
"""
import sys
from socket import *
from mp4domain.crypto import *
import mp4domain.ioutils
# Configure client for server address
server_hostname = 'localhost'
server_port = 48001
# Process Message File and send to server
if len(sys.argv) > 1:
messageobj = ... | briantbailey/ITM-513 | mp4/src/client.py | Python | mit | 875 | [
"Brian"
] | d1761c08bc481f000d9cbb83e19004b6bf4add145249e539e71bab99f665568e |
#!/usr/bin/env python3
#-*- coding: utf-8 -*-
# Copyright 2017, National University of Ireland and The James Hutton Insitute
# Author: Nicholas Waters
#
# This code is part of the riboSeed package, and is governed by its licence.
# Please see the LICENSE file that should have been included as part of
# this package.
i... | nickp60/riboSeed | riboSeed/make_riboSeed_config.py | Python | mit | 15,909 | [
"BWA"
] | 715c3fcd7719a0564f8104fd22f7a2e8cdbfb73d143362153608393634c9c69c |
"""Arithmetic simplification module using sympy.
This module simplifies symbolic expressions using only arithmetic operators.
"""
# pylint: disable=unused-import,exec-used
import ast
import sympy
from copy import deepcopy
from sspam.tools import asttools
def run(expr_ast, nbits):
'Apply sympy arithmetic simplif... | quarkslab/sspam | sspam/arithm_simpl.py | Python | bsd-3-clause | 2,082 | [
"VisIt"
] | 79975232ad89747bd7033f156974f54b41582e3af2bf5c69fce378c49172b22b |
# coding: utf-8
"""
Demonstrate how to use MPI with kombine. Run this module with
mpiexec -n <nprocesses> python mpi-demo.py
where <nprocesses> is the number of processes to spawn.
"""
from __future__ import division, print_function
__author__ = "adrn <adrn@astro.columbia.edu>"
# Standard library... | stevertaylor/kombine | examples/mpi-demo.py | Python | mit | 1,597 | [
"Gaussian"
] | 7b3b39d449e7e4a7c2f51d7b72bea596299933a58b15a51e9f8c2d4ce6b0fc25 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2010-2012 Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License v... | epuzanov/ZenPacks.community.SQLDataSource | ZenPacks/community/SQLDataSource/services/SqlPerformanceConfig.py | Python | gpl-2.0 | 9,744 | [
"VisIt"
] | 9baaa9ff5cdb236c64a0e096d9b197f75a5a165dc58654adf3e6872afdffbcd5 |
### Part One ###
with open('01.in') as input:
line = input.read().rstrip().split(', ')
# Convert our Ls and Rs to machine readable tuples
rel_dirs = [((-1,1)[(x[0] == 'R')],int(x[1:])) for x in line]
# Sum through all the directions
D = 0
sums = [0,0,0,0]
for dir in rel_dirs:
D = (D + dir[0]) % 4
sums[D] += dir[1]
#... | ghlmtz/advent16 | 01/01.py | Python | gpl-3.0 | 877 | [
"VisIt"
] | 166066a9918f80c3411014118ea641054a98b8ba62a31f0500f799333b066ea1 |
"""
Extract and cluster EOD waverforms of pulse-type electric fish.
## Main function
- `extract_pulsefish()`: checks for pulse-type fish based on the EOD amplitude and shape.
"""
import os
import numpy as np
from scipy import stats
from scipy.interpolate import interp1d
from sklearn.preprocessing import StandardSca... | tillraab/thunderfish | thunderfish/pulses.py | Python | gpl-3.0 | 80,646 | [
"Gaussian"
] | 218d6dfad9cf4dd7acea373f65b0d3ab91209ba9015f14fc95464e6aaf2562c9 |
import functools
import itertools
from collections import defaultdict
from datetime import timedelta
from distutils.version import LooseVersion
from typing import Any, Dict, Hashable, Mapping, TypeVar, Union
import numpy as np
import pandas as pd
import xarray as xr # only for Dataset and DataArray
from . import ar... | jhamman/xarray | xarray/core/variable.py | Python | apache-2.0 | 82,893 | [
"NetCDF"
] | 107257bd050b0aba6103d394d361d42815660b06baee7b9e955860af00f6b9d6 |
import pytest
from stix2 import exceptions
from stix2.v20 import (
TLP_AMBER, TLP_GREEN, TLP_RED, TLP_WHITE, MarkingDefinition, TLPMarking,
)
def test_bad_id_marking_tlp_white():
with pytest.raises(exceptions.TLPMarkingDefinitionError):
MarkingDefinition(
id='marking-definition--4c9faac1... | oasis-open/cti-python-stix2 | stix2/test/v20/test_marking_definition.py | Python | bsd-3-clause | 4,217 | [
"Amber"
] | 47938233661f8cac4d14d389d0b90d4f74bb2692732c6c0328905723208ac0b5 |
"""Testing for Gaussian process classification """
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# License: BSD 3 clause
import numpy as np
from scipy.optimize import approx_fprime
import pytest
from sklearn.gaussian_process import GaussianProcessClassifier
from sklearn.gaussian_process.kernels impor... | vortex-ape/scikit-learn | sklearn/gaussian_process/tests/test_gpc.py | Python | bsd-3-clause | 5,989 | [
"Gaussian"
] | a2019b07a9130608a410ed7b86ea48e5127368636115b8fdccd0cc1d068f9f8a |
# -*- coding: utf-8 -*-
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General ... | upibhalla/moose-core | tests/python/testXreacs5a.py | Python | gpl-3.0 | 4,219 | [
"MOOSE"
] | d0d8d0b5aa2b417d080d675a120bb3f16362863476d8dd8544f56c8713d4e8aa |
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