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import os
import math
import vtk
from ddapp.consoleapp import ConsoleApp
from ddapp import ioUtils
from ddapp import segmentation
from ddapp import segmentationroutines
from ddapp import applogic
from ddapp import visualization as vis
from ddapp import transformUtils
from ddapp import filterUtils
from ddapp import robo... | gizatt/director | src/python/tests/testAmazonPod.py | Python | bsd-3-clause | 5,747 | [
"VTK"
] | b0102b14019df5794134728aa49a5f4821ec53e168879b386e82ecd90fdacc3c |
"""
Module that provides lookups of references and names of Delphix objects.
"""
import re
from datetime import datetime
from dateutil import tz
from delphixpy.v1_8_0.exceptions import HttpError
from delphixpy.v1_8_0.exceptions import JobError
from delphixpy.v1_8_0.exceptions import RequestError
from delphixpy.v1_8_... | CloudSurgeon/delphixpy-examples | lib/GetReferences.py | Python | apache-2.0 | 9,856 | [
"ASE"
] | 33f32c73f37b85175cb767bdb8b990134302305f2c69504cd63f5e6a7b20e809 |
# Test the vtkCellIntegrator
from paraview import smtesting
import os
import os.path
import sys
import paraview
paraview.compatibility.major = 3
paraview.compatibility.minor = 4
from paraview import servermanager
from paraview import util
smtesting.ProcessCommandLineArguments()
servermanager.Connect()
file1 = os.pa... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/ParaViewCore/ServerManager/Default/Testing/Python/CellIntegrator.py | Python | gpl-3.0 | 2,526 | [
"ParaView",
"VTK"
] | 3360d3fff6c0d6d6ea60d2ad2351d05ac2c50b658134a8a4949dba3247609483 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# pickle_file_sizes - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the ... | heromod/migrid | mig/wwwuser/pickle_file_sizes.py | Python | gpl-2.0 | 1,433 | [
"Brian"
] | 2e162980fc8207f820c07f3ddf3761d1360174d3ab4655825fe689a23c26b735 |
"""
# Notes:
- This simulation seeks to emulate the CUBA benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008).
- The time taken to si... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_CUBA_nosyn_compiled_0008.py | Python | gpl-3.0 | 2,137 | [
"Brian"
] | eab11c2c73241241e8e6afe902e4425dba3e800d6a210c4056a29dc6043670e4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import copy
import pprint
import jinja2
import proteindf_bridge as bridge
from . import __version__
from .qccontrolobject import QcControlObject
from .qcprotonate import QcProtonate
from .qcremovewat import QcRemoveWAT
from .qcneutralize import QcNeutralize
fro... | ProteinDF/QCLObot | qclobot/qcmodeler.py | Python | gpl-3.0 | 6,754 | [
"Amber"
] | 7a9c0182c48f9079f7f8e234c3abb548373c099e7cd6a7748b460acc87543c78 |
'''
mayavi interface to plot atoms, unit cells, and volumetric data
'''
import numpy as np
from enthought.mayavi import mlab
mlab.figure(1, bgcolor=(1,1,1), size=(350, 350))
mlab.clf()
def plot_cylinder(start,end,tube_radius=0.1,color=(0,0,0)):
mlab.plot3d([start[0],end[0]],[start[1],end[1]],[start[2],end[2]]... | freephys/python_ase | ase/calculators/jacapo/mayavis.py | Python | gpl-3.0 | 1,901 | [
"ASE",
"Mayavi"
] | 4c2c86793caa547b70b9dec373f52b622d0682af9040d1c91015830ae35abae8 |
#!/usr/bin/env python
import argparse
import pandas as pd
import numpy as np
#from matplotlib import pyplot as plt
#from upsetplot import UpSet
def getOptions():
# Parse command line arguments
parser = argparse.ArgumentParser(
description=(
"Flag maize genotype detection (CCS gene read cou... | McIntyre-Lab/papers | nanni_maize_2022/scripts/flag_detect_analyze_gene_file.py | Python | lgpl-3.0 | 11,575 | [
"HTSeq"
] | e423926fdcd38b1fc001ed6a9997ffc9ae7aeba3948f44743abf52909d3021eb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Unittests for search helper utilities.
"""
from unittest import TestCase
from search.utils import *
from django.db.models import Q
class PhraseQSeriesTestCase(TestCase):
def setUp(self):
return
def test_output_q_series_is_q(self):
output_q_ser... | access-missouri/am-django-project | am/search/tests/test_search_utils.py | Python | bsd-2-clause | 1,786 | [
"MOOSE"
] | 0c303b91a8ba6549553fdeb625f534b3b7cdcbba44976ba73c3e7fbd017a6299 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | ashutoshvt/psi4 | psi4/share/psi4/databases/JSCH.py | Python | lgpl-3.0 | 287,170 | [
"Psi4"
] | d4aed0b1cf611ab2d4f0e62aff44665df7e70149688112f552a27a7f2f856603 |
from django.core.checks import Error
from django.core.checks.translation import (
check_language_settings_consistent, check_setting_language_code,
check_setting_languages, check_setting_languages_bidi,
)
from django.test import SimpleTestCase
class TranslationCheckTests(SimpleTestCase):
def setUp(self):
... | EmadMokhtar/Django | tests/check_framework/test_translation.py | Python | mit | 4,263 | [
"ASE"
] | 6c05248eb18df885c2d1c35a81cf89005f471bea070d523aab77039cf53d69c0 |
''' Synchronizer
Module that keeps the database synchronized with the CS
Module that updates the RSS database ( ResourceStatusDB ) with the information
in the Resources section. If there are additions in the CS, those are incorporated
to the DB. If there are deletions, entries in RSS tables for those elements ... | rajanandakumar/DIRAC | ResourceStatusSystem/Utilities/Synchronizer.py | Python | gpl-3.0 | 17,332 | [
"DIRAC"
] | 38f0826f6c13c35c315aff0b8517ac1845ff8853fc92c6fc1625c3c7696dab32 |
#!/usr/bin/env python
# flake8: noqa
# pylint: disable=C0103,C0301,R0903
#
# A library that provides a Python interface to the Telegram Bot API
# Copyright (C) 2015-2016
# Leandro Toledo de Souza <devs@python-telegram-bot.org>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms... | nelsongoh/shanhousebot | libs/telegram/emoji.py | Python | apache-2.0 | 39,926 | [
"Octopus"
] | bbc82a449b6c57ab1705c598e0f871cfdd03546481bde4b2ece5827ae4313412 |
import mdtraj as md
import tensorflow as tf
import tftraj.rmsd_op
import numpy as np
import math
from matplotlib import pyplot as plt
def main(n_clusters=2, cluster_diff_multiplier=1.0):
rmsd_op = tftraj.rmsd_op.load()
traj = md.load(['../../fs_peptide/trajectory-{}.xtc'.format(i + 1) for i in range(28)],
... | mdtraj/tftraj | examples/rmsd-cluster/rmsd-cluster.py | Python | mit | 2,225 | [
"MDTraj"
] | 437a5393e0c28e14e16d802ab1250edfcc0c9bef9e7b9b628d99d865e4e1bf1d |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Parser for Molcas output files"""
import re
import string
import numpy
from cclib.parser import logfileparser
from c... | berquist/cclib | cclib/parser/molcasparser.py | Python | bsd-3-clause | 48,683 | [
"MOLCAS",
"cclib"
] | 6a55a5732b8c1b7916d2ad52428386dfff3ed902487a5fca5491da3980c86a8c |
import os, sys; sys.path.insert(0, os.path.join(os.path.dirname(__file__), "..", ".."))
from pattern.server import App
from pattern.server import MINUTE, HOUR, DAY
from pattern.text import language
app = App("api")
# The language() function in pattern.text guesses the language of a given string.
# For example: lan... | krishna11888/ai | third_party/pattern/examples/08-server/02-api/api.py | Python | gpl-2.0 | 3,618 | [
"VisIt"
] | a0bf6e22f79f3c8bcc156c83d3b3102683b214d5db3495457b3c1a77f5b03dc4 |
from django.db import models
from apps.reporters.models import *
from apps.locations.models import *
class AmbulanceDriver(models.Model):
phonenumber = models.CharField(max_length = 20)
name = models.CharField(max_length = 100)
identity = models.CharField(max_length = 20)
car = None # Ini... | pivotaccess2007/RapidSMS-Rwanda | apps/ambulances/models.py | Python | lgpl-3.0 | 2,284 | [
"BWA"
] | cfd939f8b9d36ba0c94201e77d5bc05ceeb196a49fcc6b89327fdff0442be587 |
#Copyright ReportLab Europe Ltd. 2000-2012
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/platypus/paraparser.py
__version__=''' $Id: paraparser.py 3959 2012-09-27 14:39:39Z robin $ '''
__doc__='''The parser used to process markup within... | nickpack/reportlab | src/reportlab/platypus/paraparser.py | Python | bsd-3-clause | 44,963 | [
"VisIt"
] | b415aa9131b9904c370b90ae7275ceef82f8b0800062ecdf74fb9361cb2f058f |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://pythonhosted.org/setuptools/easy_install.html
"""
from... | harshita-gupta/Harvard-FRSEM-Catalog-2016-17 | flask/lib/python2.7/site-packages/setuptools/command/easy_install.py | Python | mit | 86,722 | [
"VisIt"
] | 8d648847ad15bc1471569ab8341ad16a447dc5f7065268ae1d3011384490d6f3 |
"""
Creates an augmented version of the Labeled Faces in the Wild dataset.
Run with:
python generate_dataset.py --path="/foo/bar/lfw"
"""
from __future__ import print_function, division
import os
import random
import re
import numpy as np
from scipy import misc
from ImageAugmenter import create_aug_matrices
from sk... | aleju/face-generator | dataset/generate_dataset.py | Python | mit | 7,921 | [
"Gaussian"
] | 78d0415df887d448ab53d11aa7f52ef343748a1aab48e0d2f5d8c4dfcc15530d |
import numpy as np
import unittest
from caffe2.python import core, workspace, test_util
class TestToyRegression(test_util.TestCase):
def testToyRegression(self):
"""Tests a toy regression end to end.
The test code carries a simple toy regression in the form
y = 2.0 x1 + 1.5 x2 + 0.5
... | ryfeus/lambda-packs | pytorch/source/caffe2/python/toy_regression_test.py | Python | mit | 2,822 | [
"Gaussian"
] | 6149a1d9d0e2124542df6bd9a5e97a825133de16ea64445cc851e0b287de5d56 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/procrouting/dft/libxc_functionals.py | Python | lgpl-3.0 | 13,135 | [
"Psi4"
] | 31f7427ef1120267b6d49fe09c20411b324ac34576569f9288bca8a19049f696 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | DataReplyUK/datareplyuk | GenesAssociation/spark-2.0.0-bin-hadoop2.7/python/pyspark/mllib/clustering.py | Python | apache-2.0 | 36,924 | [
"Gaussian"
] | a3b44dca52ced46ef236c0e18b997017811a9c0955b0054813b5f2f7c0f14f0c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# -------------------------------------------------------------------
# Filename: input_handler.py
# Purpose: reading option flags and generate input_dics
# Author: Kasra Hosseini
# Email: kasra.hosseinizad@earth.ox.ac.uk
# License: GNU Lesser General... | kasra-hosseini/obspyDMT | obspyDMT/utils/input_handler.py | Python | gpl-3.0 | 62,269 | [
"ParaView",
"VTK"
] | 995324411730986a84bce4e2a4de8a3c88f09251292d01abbbff3f629017053e |
import numpy, math
def kernel(name, k = 3):
return {
'sobel': numpy.array([[-1, 0, 1], [-2, 0, 2], [-1, 0, 1]])/8,
'gauss': gauss_kernel(k)
}.get(name)
def convolution(img, kernel):
kernel = numpy.array(kernel)
rowk = kernel[0]
colk = kernel.transpose()[0] / kernel[0,0]
if not (abs(colk.reshape(-1,1).dot... | The-BFG/GenericCV | src/neighborhoodOperators.py | Python | gpl-3.0 | 2,307 | [
"Gaussian"
] | 96ad19ace563f051ae191c1457d5913516713883ceba41325064fac7eb523010 |
"""
This module contain solvers for all kinds of equations:
- algebraic or transcendental, use solve()
- recurrence, use rsolve()
- differential, use dsolve()
- nonlinear (numerically), use nsolve()
(you will need a good starting point)
"""
from __future__ import print_function, division
f... | grevutiu-gabriel/sympy | sympy/solvers/solvers.py | Python | bsd-3-clause | 120,616 | [
"Gaussian"
] | 81f791f7fb91589a72b0b1e5255b6985c4866359ae4f10156d0810c8ee096944 |
import random
import numpy as np
import copy
import MDAnalysis
def rate_sum_update(hopgraph,oneway=True):
h=hopgraph
if oneway==True:
h.filter(exclude={"bulk":True,"outliers":True,"unconnected":True,'oneway':True})
else:
h.filter(exclude={"bulk":True,"outliers":True,"unconnected":True})
... | iwelland/hop | hop/walker.py | Python | lgpl-3.0 | 9,798 | [
"MDAnalysis"
] | 00d839781b98582bbb4c09f5e3fa02eb296085a7feaf735b10aba2c149c615db |
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
AUTHORS
The original version of this software, called LMFIT, was written in FORTRAN
as part of the MINPACK-1 package by XXX.
Craig Markwardt converted the FORTRAN code to IDL. The information for ... | keflavich/pyspeckit-obsolete | pyspeckit/mpfit/mpfit.py | Python | mit | 93,165 | [
"Gaussian"
] | ccca1442e2315528e828769c5d52569aac12be210faaccfe0e53bdc0157e49b0 |
# test_deeplts.py ---
#
# Filename: test_deeplts.py
# Description:
# Author:
# Maintainer:
# Created: Mon Jul 16 16:12:55 2012 (+0530)
# Version:
# Last-Updated: Thu Nov 8 18:00:47 2012 (+0530)
# By: subha
# Update #: 501
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# C... | BhallaLab/moose-examples | traub_2005/py/test_deeplts.py | Python | gpl-2.0 | 1,516 | [
"MOOSE"
] | 10c1d5ca968e624a6083f432bd3376d224403bf811825d9045548ea0210cbda6 |
from __future__ import division
from .. import Gratoms
from . import symmetry
from . import utils
from . import adsorption
from . import defaults
import numpy as np
import itertools
import warnings
import scipy
import ase
try:
from math import gcd
except ImportError:
from fractions import gcd
class SlabGenera... | jboes/CatKit | catkit/gen/surface.py | Python | gpl-3.0 | 25,028 | [
"ASE"
] | 3ddef904498667e19e27f3fd53015d146a12c2e3775caad3841836f45204e8e4 |
# This code is licensed under the New BSD License
# 2009, Alexander Artemenko <svetlyak.40wt@gmail.com>
# For other contacts, visit http://aartemenko.com
try:
from setuptools import setup, find_packages
except ImportError:
from ez_setup import use_setuptools
use_setuptools()
from setuptools import setu... | svetlyak40wt/gtdzen | setup.py | Python | bsd-3-clause | 1,684 | [
"VisIt"
] | ccd29397b881f1b56399953476d4d76fd724385eff325db1f17ac47aa6001bb7 |
import random
# Third-party libraries
import numpy as np
class Network(object):
def __init__(self, sizes):
"""The list ``sizes`` contains the number of neurons in the
respective layers of the network. For example, if the list
was [2, 3, 1] then it would be a three-layer network, with the... | vvvvcp/NeverMore | mathtype/lib/NN/network.py | Python | apache-2.0 | 6,575 | [
"Gaussian",
"NEURON"
] | f6113936c05bd9bd7fb0db67f5a5070a3b794f9c092a3aed09412006706e6a0a |
# 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.
import re
line_floats_re = re.compile("-*\d+\.\d+")
try:
float("nan")
_nan_float... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Phylo/PAML/_parse_codeml.py | Python | gpl-2.0 | 21,488 | [
"Biopython"
] | 6db7daf73b09498f5b7859ea3968f848e791502db14c53a5be5c0b4277d46d62 |
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under t... | openstack/python-openstacksdk | openstack/tests/unit/test_proxy.py | Python | apache-2.0 | 16,473 | [
"Brian"
] | 90b22dbb5e7aa135e61b3551fb4043987e4c5a28b90328ec2b19009f90c52a85 |
# search.py
# ---------
# Licensing Information: Please do not distribute or publish solutions to this
# project. You are free to use and extend these projects for educational
# purposes. The Pacman AI projects were developed at UC Berkeley, primarily by
# John DeNero (denero@cs.berkeley.edu) and Dan Klein (klein@cs.be... | sumitb/cse537 | search/search.py | Python | gpl-2.0 | 7,132 | [
"VisIt"
] | e2dce1b2cddfc62875e5b895ebbf6da1999b56618b616343469cb458675a1017 |
#
# Created by Gareth Jones on 5/30/2020.
#
# Copyright 2020 Schrodinger, Inc
# @@ 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.
""" A rough test of Tauto... | bp-kelley/rdkit | Code/GraphMol/TautomerQuery/Wrap/rough_test.py | Python | bsd-3-clause | 3,673 | [
"RDKit"
] | a2d38db306d3267e904c694b577bda5d60e1b5ffd73879911be449ab073faa1e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | andysim/psi4 | psi4/share/psi4/databases/BAKERJCC96.py | Python | gpl-2.0 | 16,177 | [
"Psi4"
] | cb5757c0307169f3e342c468b05319a382493187b729401d07c7ecb5d27b543f |
import myast as ast
from symboltable import *
class Visitor():
def visit(self, *args, **kwargs):
node = args[0]
if node == None:
return
assert isinstance(node, ast.ASTNode), "node is no ASTNode: %r" % node
foo = "visit_" + node.__class__.__name__
visitor = getatt... | Paradyx/mcc | mcc/visitor.py | Python | gpl-3.0 | 44,327 | [
"VisIt"
] | 3ce2191d3c68ac974e90e4a74b09210d11afd66be23549c19c4ec59eb2af8312 |
################################################################################
# This program will read in a SAINT 'list.txt' file and the interactions from
# the consensus path db database and return all the interactions that we saw in
# our experiment in a format suitable for cytoscape. This allows us to filter
# b... | bornea/APOSTL | ProteinInteractions/toolshed_version/ProteinInteractions.py | Python | gpl-2.0 | 7,144 | [
"Cytoscape"
] | 27d8bc26e28982457d580aa9fcbdbb18380955b7cccf9ceab10f0e3b75d7a713 |
import pygame
import math
hillelakamariya = 9*32
class Ballo(pygame.sprite.Sprite):
def __init__(self, SCREEN, inip):
self.HMAX = 0
self.v = 0
self.offset = 0
self.upright = False
self.upleft = False
self.left = False
self.right = False
self.falling =... | krux8/Amazing-Tacos | Ball.py | Python | gpl-2.0 | 4,526 | [
"DIRAC"
] | ffe07ee5a09f733589ffb6294e92d51d160ad4847a5bb5e9ed541add0c903a1a |
r"""
Homology :mod:`homology`
========================
Tools for "symmetrizing" a period matrix.
There exists a symplectic transformation on the period matrix of a real curve
such that the corresponding a- and b-cycles have certain transformation
properties until the anti-holomorphic involution on said Riemann surfac... | abelfunctions/abelfunctions | abelfunctions/homology.py | Python | mit | 14,849 | [
"Gaussian"
] | 652690324cac6621ed68674ccdd535abd6405a89a849539a800a3cdc9732bec5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Image tools interfaces
~~~~~~~~~~~~~~~~~~~~~~
"""
import nibabel as nb
import numpy as np
from skimage import morphology as sim
from scipy.ndimage.morphol... | oesteban/preprocessing-workflow | fmriprep/interfaces/nilearn.py | Python | bsd-3-clause | 5,856 | [
"Gaussian"
] | 9309759233e4bddc0debc80351383610fc57e7c0c633b9d5ac092f11da55665a |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/tddft/__init__.py | Python | apache-2.0 | 660 | [
"PySCF"
] | a4ce96f15c179abcce9bbbc627f44e2c669e0d9c75b38ce7069b8828356dc788 |
# -*- coding: utf-8 -*-
from pylayers.simul.link import *
import pylayers.util.pyutil as pyu
import pylayers.signal.standard as std
from pylayers.util.project import *
import json
# TEST
import matplotlib
matplotlib.use('Qt4Agg')
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from m... | buguen/pylayers | pylayers/gui/PylayersGui.py | Python | lgpl-3.0 | 23,167 | [
"Mayavi"
] | 5acfb2a4348d3b47bb09925b577cffcb74c9a97d5164ac063523e100a8d8e8ab |
#
# Copyright (C) 2000 greg Landrum
#
""" unit tests for the ID3 implementation """
from __future__ import print_function
import unittest
import io
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit.ML.DecTree import ID3,DecTree
from rdkit.ML.Data import MLData
class ID3TestCase(unittest.Test... | adalke/rdkit | rdkit/ML/DecTree/UnitTestID3.py | Python | bsd-3-clause | 6,334 | [
"RDKit"
] | 25e12c5815fa9e5e02101178648385d569fb7af318d78d84a166aa68ca589fba |
"""Check specific required program versions required during the pipeline.
"""
from distutils.version import LooseVersion
import subprocess
from bcbio.pipeline import config_utils
from bcbio.log import logger
def samtools(config, items):
"""Ensure samtools has parallel processing required for piped analysis.
"... | Cyberbio-Lab/bcbio-nextgen | bcbio/provenance/versioncheck.py | Python | mit | 2,823 | [
"BWA"
] | a77a3a1a72a7972d4cb41cec064a5c5205b6fef4cdceb07cd1e2dd0071b32e99 |
"""
Test the mlab null engine.
"""
import unittest
from mayavi import mlab
from mayavi.core.engine import Engine
from mayavi.tools.engine_manager import engine_manager
from mayavi.core.registry import registry
from mayavi.tests.common import get_example_data
##########################################################... | dmsurti/mayavi | mayavi/tests/test_mlab_null_engine.py | Python | bsd-3-clause | 2,051 | [
"Mayavi"
] | e1bad5c1fbd68fac13f123dc6a41f16082136ff5dc9d5f9842d57b016dbd493c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""A module to generate a saliency map from an RGB image
This code is based on the approach described in:
[1] X. Hou and L. Zhang (2007). Saliency Detection: A Spectral Residual
Approach. IEEE Transactions on Computer Vision and Pattern Recognition
... | mbeyeler/opencv-python-blueprints | chapter5/saliency.py | Python | gpl-3.0 | 8,524 | [
"Gaussian"
] | ccb3a6fea751dfe4df938cb4bcd577de9bf3de44513498245e08bc07bc52c3da |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/qcdb/libmintsgshell.py | Python | gpl-2.0 | 14,621 | [
"GAMESS",
"Psi4"
] | f9a009d30418e45e6486857a42bbf4ceda853a8872dd37f6b2a8c631b5d23f5c |
#!/usr/bin/python
initial_text = """
Welcome to The Nilya Quest!
You are on a quest to find the nilya, and do amazing things with it.
"""
##
## Items
##
## List of tuples of the form [('id', 'short name', 'longer description'),...]
##
items = [
( 'stockton-key',
'key',
"""A small silver key. It only... | blandford/nilya | data.py | Python | gpl-3.0 | 5,170 | [
"CRYSTAL"
] | 874671b2b5c119c7f4c889e0e34e075234522a03bcdfbff2b9d613f132490b0c |
# DENISE_out functions
#
# Daniel Koehn
# Kiel, 24.06.2019
# Import Libraries
# ----------------
import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
import numpy as np
from matplotlib.colors import LightSource, Normalize
from matplotlib.pyplot import gca
from pylab import rcParams
from matplo... | daniel-koehn/DENISE-Black-Edition | par/pythonIO/denise_IO/denise_out.py | Python | gpl-2.0 | 28,084 | [
"Gaussian"
] | a4670cf6154374010f54421458f73a1dee32418a215d483140238c59b1d6cba2 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module define the various drones used to assimilate data.
"""
import abc
import glob
import json
import logging
import os
import warnings
from monty.io import zopen
from monty.json import MSONable
from pymatgen.ent... | materialsproject/pymatgen | pymatgen/apps/borg/hive.py | Python | mit | 16,272 | [
"Gaussian",
"VASP",
"pymatgen"
] | 41acff888134cedb4a685c42d176dd05182bd6f9d2f26aaf0ac32bc2a5857f91 |
#
# commands.py - the GraalVM specific commands
#
# ----------------------------------------------------------------------------------------------------
#
# 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 ... | smarr/GraalVM | mx.graal/mx_graal.py | Python | gpl-2.0 | 101,942 | [
"VisIt"
] | a0feca2befa1cecdcb95afdaff92a6ffe32bcb993d1b8d03bb4fdf20cdc9eb16 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Achuth17/scikit-bio | skbio/tree/tests/test_tree.py | Python | bsd-3-clause | 40,995 | [
"scikit-bio"
] | c62ca869cf7bd66757c584df1638fce75f84f5fb38e3fac71ab4a924a48e9aa2 |
import unittest
from deepchem.feat import MACCSKeysFingerprint
class TestMACCSKeysFingerprint(unittest.TestCase):
"""
Test MACCSKeyFingerprint.
"""
def setUp(self):
"""
Set up tests.
"""
from rdkit import Chem
smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O'
self.mol = Chem.MolFromSmiles(smiles)
... | deepchem/deepchem | deepchem/feat/tests/test_maccs_keys_finerprint.py | Python | mit | 528 | [
"RDKit"
] | 02b336fc118b74ac31db98aa8528b1f003083a77d439a43fe4d4b8182c24cfb0 |
from sfepy.base.base import *
from sfepy.base.ioutils import get_print_info
from sfepy.fem import extend_cell_data
from sfepy.homogenization.utils import coor_to_sym
from sfepy.base.conf import get_standard_keywords, ProblemConf
from sfepy.fem import ProblemDefinition
from sfepy.homogenization.coefficients import Coeff... | olivierverdier/sfepy | sfepy/homogenization/recovery.py | Python | bsd-3-clause | 17,380 | [
"VTK"
] | 12c780ca120c184e55772bafde106da2cf9eecf129fbccdc0f0a33a10ff7cfe8 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2013 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 Licens... | tiagocardosos/stoq | stoqlib/gui/search/searcheditor.py | Python | gpl-2.0 | 11,873 | [
"VisIt"
] | a4cc2ad705894122b07ca930bd92fc1cebf5728d3e52e3f2520c8a8b97d4fa2f |
#!/usr/bin/env python
# Copyright (c) 2014, Palo Alto Networks
#
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" A... | PaloAltoNetworks-BD/SyncServiceNow | syncServiceNowAssets.py | Python | isc | 7,688 | [
"Brian"
] | 5d292e62b3a4ae97d828126afdf4118a8e04d2b54b35a507b365dc8c73fe6830 |
"""The ants module provides basic functions for interfacing with ants functions.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
>>> os.chdir(... | gerddie/nipype | nipype/interfaces/ants/registration.py | Python | bsd-3-clause | 42,648 | [
"Gaussian",
"VTK"
] | be967b2cbf425b624e91d2b40d2a390b7f2ce6d9ebe644ebdbb5a47e2aa48382 |
"""
urlresolver XBMC Addon
Copyright (C) 2011 t0mm0
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.
... | azumimuo/family-xbmc-addon | script.mrknow.urlresolver/lib/urlresolver9/plugins/vidup_me.py | Python | gpl-2.0 | 3,505 | [
"VisIt"
] | 8dc4144b894e153638717622a88977f07b3b2672b04b9d96d1430e6fb775e90d |
from __future__ import division, print_function
import argparse
from functools import partial
from glob import glob
import os
from pathlib import Path
import sys
import traceback
import h5py
import numpy as np
import pandas as pd
from .featurize import (
get_embeddings,
read_file_chunks,
LinearFeaturizer,... | dougalsutherland/pummeler | pummeler/cli.py | Python | mit | 20,286 | [
"Gaussian"
] | 42446a9fe6128cab0c2c0fb8457de9a6bfa933f5337966fb79878e6e24b4b0e6 |
# Gambit scripts
#
# Copyright (C) USC Information Sciences Institute
# Author: Nibir Bora <nbora@usc.edu>
# URL: <http://cbg.isi.edu/>
# For license information, see LICENSE
import os
import sys
import csv
import pickle
import anyjson
import numpy as np
import lib.geo as geo
import lib.PiP_Edge as pip
import matplotl... | nbir/gambit-scripts | scripts/gang_activity_analysis/src/calc_rnr_visits.py | Python | apache-2.0 | 6,495 | [
"VisIt"
] | 3a53859794975c7e112a29d7e28df506e50a14a895d1a72534de6da725fbdb39 |
# -*- coding: utf-8 -*-
# ramaplot.__init__.py
#
# Copyright (C) 2015 Karl T Debiec
# All rights reserved.
#
# This software may be modified and distributed under the terms of the
# BSD license. See the LICENSE file for details.
"""
General functions.
"""
################################### MODULES ##########... | KarlTDebiec/Ramaplot | __init__.py | Python | bsd-3-clause | 1,945 | [
"Amber"
] | 61ec49d4c7a64f8ca17a49fb9650493c0ccb1911759e28a0d69fb783d037f9d3 |
tests=[
("python","UnitTestDbConnect.py",{}),
("python","UnitTestDbUtils.py",{}),
("python","UnitTestDbResultSet.py",{}),
("python","StorageUtils.py",{}),
]
longTests=[
]
if __name__=='__main__':
import sys
from rdkit import TestRunner
failed,tests = TestRunner.RunScript('test_list.py',0,1)
sys... | adalke/rdkit | rdkit/Dbase/test_list.py | Python | bsd-3-clause | 344 | [
"RDKit"
] | 5cf9a5ac3c1d15e92b336cbd04c402ce3d0d2c53c9a759e9e62e311fa2c84ecd |
#!/usr/bin/python
#
# HOW TO INSTALL/RUN "GeorgeCraft":
# pip install pyglet
# https://github.com/ajones74/GeorgeCraft.git
# cd GeorgeCraft
# python GeorgeCraft.py
# ---OR, SIMPLY:---
# ./GeorgeCraft.py
#
#
import math
import random
import time
from collections import deque
from pyglet import image
from pygle... | ajones74/GeorgeCraft | GeorgeCraft.py | Python | mit | 31,181 | [
"BLAST"
] | fb527362bcd2fa1cdcfa8ae01869208e1304170b259d869d8f03ed677b263ea7 |
# -*- coding: utf-8 -*-
import datetime
import json
import os
import shutil
from django.conf import settings
from django.core.files.storage import default_storage as storage
from django.core.urlresolvers import reverse
import mock
from nose.tools import eq_, ok_
from pyquery import PyQuery as pq
import amo
import am... | ngokevin/zamboni | mkt/submit/tests/test_views.py | Python | bsd-3-clause | 38,560 | [
"exciting"
] | 358c7313ebbfcc4972dd9caed2be08e00ae8d364d85d04c0936756f2484cf886 |
# -*- coding: utf-8 -*-
# Copyright (C) 2012, Almar Klein, Ant1, Marius van Voorden
#
# This code is subject to the (new) BSD license:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of s... | h42i/harryplotter | server/images2gif.py | Python | gpl-3.0 | 36,929 | [
"NEURON"
] | 1de30de06429b59fdc8a04629b46f9a2a961ef73ded4347afc97b6d08d29f096 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides a base class for tensor-like objects and methods for
basic tensor manipulation. It also provides a class, SquareTensor,
that provides basic methods for creating and manipulating rank 2 tensors
"""
im... | materialsproject/pymatgen | pymatgen/core/tensors.py | Python | mit | 39,581 | [
"CRYSTAL",
"pymatgen"
] | e8c3e48d0a6fbea449ba7c51a6e7eb4895b7160c2d9f15f9bfe45b62d145877e |
#
#
# File to test behaviour of the Granule Cell.
#
# To execute this type of file, type '..\..\..\nC.bat -python XXX.py' (Windows)
# or '../../../nC.sh -python XXX.py' (Linux/Mac). Note: you may have to update the
# NC_HOME and NC_MAX_MEMORY variables in nC.bat/nC.sh
#
# Author: Padraig Gleeson
#
#... | pgleeson/TestArea | models/Cerebellum/pythonScripts/Test_SingleGolgi.py | Python | gpl-2.0 | 2,975 | [
"NEURON"
] | f0702822025e938b4dc683e0169ea74d7df79f3bf2438b8eb0824b233ee8abfa |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Generated Wed Mar 30 10:13:50 2016 by generateDS.py version 2.20b.
#
# Command line options:
# ('-o', '../../Work/libSpineML/experiment.py')
#
# Command line arguments:
# ../SpineML/Schema/SpineMLExperimentLayer.xsd
#
# Command line:
# generateDS.py -o "../../Wor... | AdamRTomkins/libSpineML | libSpineML/smlExperiment.py | Python | gpl-3.0 | 238,438 | [
"NEURON"
] | 32cd8e21be9bd51606f3b699643ea7e7f69607db5af2de8cfb345521f7a560b8 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/editors/timeeditor.py | Python | gpl-2.0 | 2,153 | [
"VisIt"
] | e471b38b5128143577fe98b369c33f59da1ee880da84e259f7d06146fe8d8689 |
# 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 RKegggraph(RPackage):
"""KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor... | LLNL/spack | var/spack/repos/builtin/packages/r-kegggraph/package.py | Python | lgpl-2.1 | 1,515 | [
"Bioconductor"
] | d7636945fda88a9ccb4c6b04f9aa274ed7a6e3ad7d9eed90f790341880c21db4 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/plugins/__init__.py | Python | gpl-2.0 | 5,270 | [
"MDAnalysis"
] | 837546d42ff909850dcd2c8c57167305c9b704e186e6bc4372e119a3f6ac9182 |
# Import our stuff.
import numpy as np
import matplotlib.pyplot as plt
import seaborn
# For image processing
import skimage.io
import skimage.filters
import skimage.segmentation
import skimage.measure
# Do the same procedure as yesterday.
image = skimage.io.imread('data/lacI_titration/O2_delta_phase_pos_16.tif')
# R... | RPGroup-PBoC/gist_pboc_2017 | code/inclass/project_part2_in_class.py | Python | mit | 2,436 | [
"Gaussian"
] | 176767e4fbe271cf2d15cf663ee498d210d35b7045fb9cf9bcc8c769949f8762 |
"""contain SecurityTests Class"""
import unittest
from pyramid.paster import get_appsettings
from pyramid import testing
from askomics.libaskomics.Security import Security
from interface_tps import InterfaceTPS
class SecurityTests(unittest.TestCase):
"""Test for the Security class"""
def setUp(self):
... | ofilangi/askomics | askomics/test/security_test.py | Python | agpl-3.0 | 13,552 | [
"Galaxy"
] | efe8195f65ae3c2b73993952e5cd9fe516ce97f8dd0f280ecde917c0120b56cc |
'''A class is provided to contain a single node of a treap - multiple instances for multiple nodes of course'''
# actually, it's a little faster with the standard random module than the lcgrng module; although random is a more time
# consuming algorithm, it's coded in C.
import random as random_module
#import lcgrng ... | tomasdelvechio/ir-dev | TreapII/treapii/treap/py_treap_node.py | Python | gpl-3.0 | 5,834 | [
"VisIt"
] | 5d4eb4d27ff86f4187efab1ff071fdfc7e6657aa7b100a96938cf3a133377b02 |
import numpy as np
import quantities as pq
def create_delta_ft(shift_x=0*pq.deg, shift_y=0*pq.deg):
"""
Create delta_ft closure
Parameters
----------
shift_x : float/quantity scalar
Shift in x-direction
shift_y : float/quantity scalar
Shift in y-direction
Returns
----... | miladh/pylgn | pylgn/kernels/spatial.py | Python | gpl-3.0 | 2,721 | [
"Gaussian"
] | 89fc7073b1697db559f65f00736b772b76729f5e56b6e68ae0605a537e0ce32f |
from OpenGL.GL import *
from OpenGL.GL.ARB.vertex_buffer_object import *
from pymol.callback import Callback
from pymol import cmd
# this is an example of creating a callback object which
# uses GL arrays. Requires Numeric Python:
# NOTE: NUMERIC NOT SUPPORTED BY PYMOL 1.1 and up
from numpy import *
# define a cal... | gratefulfrog/lib | python/pymol/pymol_path/examples/devel/gl02.py | Python | gpl-2.0 | 1,626 | [
"PyMOL"
] | c38a0293a7185612ce941e8084e7ae2affd9bb2a271afe4ac4edc50ff5b98c0f |
"""
The MIT License (MIT)
Copyright (c) 2014 Melissa Gymrek <mgymrek@mit.edu>
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, ... | mgymrek/pybamview | pybamview/bam_alignment.py | Python | mit | 17,540 | [
"pysam"
] | bdc73f81eaf0e34033c56b0a9f468487e2f99c1b2614bd63aaeb021dc3e2eeea |
import collections
import copy
import warnings
import numpy
import six
from chainer import cuda
from chainer import link as link_module
from chainer import serializer as serializer_module
from chainer import variable
def _sum_sqnorm(arr):
sq_sum = collections.defaultdict(float)
for x in arr:
with cu... | kashif/chainer | chainer/optimizer.py | Python | mit | 26,479 | [
"Gaussian"
] | 26f13a323a67764938cea5eabf14b402f67d43c5f29dd92b159904a68fa9c929 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
This module defines useful physical constants and conversion factors.
All units are in SI units except for conversion factors.
.. attribute:: ELECTRON_CHARGE or e
... | sonium0/pymatgen | pymatgen/core/physical_constants.py | Python | mit | 1,495 | [
"pymatgen"
] | 0fbf7480f48199def5a0e23b92650b654464d4ff68d72eed8cda1e6dab17245e |
from __future__ import division
from __future__ import print_function
from past.utils import old_div
import sys
sys.path.insert(1, "../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.gam import H2OGeneralizedAdditiveEstimator
from h2o.grid.grid_search import H2OGridSearch
# I copied Karthik's te... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/gam/pyunit_PUBDEV_7860_PUBDEV_7367_random_gridsearch_subspaces_thin_plate_gaussian.py | Python | apache-2.0 | 5,400 | [
"Gaussian"
] | 4b04474e39a5997f3560bf77c40049d861afd9d7f520cabd9862a6ac894ab8e4 |
#!/usr/bin/env python
# Copyright 2015 Allen Institute for Brain Science
# This file is part of Allen SDK.
#
# Allen SDK 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, version 3 of the License.
#
# Allen SDK... | wvangeit/AllenSDK | allensdk/ephys/extract_cell_features.py | Python | gpl-3.0 | 24,812 | [
"ORCA"
] | dbfd7d766591e7b9059a6355c9e776accba8f9e25980fcecc03339adbea3c64d |
# pylint: disable=C0111
# pylint: disable=W0621
from __future__ import absolute_import
import time
from lettuce import world, step
from lettuce.django import django_url
from django.contrib.auth.models import User
from django.core.urlresolvers import reverse
from student.models import CourseEnrollment
from xmodule.mo... | geekaia/edx-platform | lms/djangoapps/courseware/features/common.py | Python | agpl-3.0 | 7,827 | [
"VisIt"
] | 49d59e9ff274acb866eacc0152a94b8b7a85f305f03d5f663aec7f66778e47e0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/utilities.py
#
# 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 l... | guitarmanj/king-phisher | king_phisher/utilities.py | Python | bsd-3-clause | 18,144 | [
"VisIt"
] | 1ea7a17202037654296cfed3d0e2797011edc478895e43db5d5d01b5630e8a09 |
# 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... | sunqm/pyscf | pyscf/data/nist.py | Python | apache-2.0 | 2,616 | [
"Avogadro",
"PySCF"
] | f2df585dd6bf10e65a98c778216f28bdf744650d82ed381a717787bcdf0292fc |
import img_scale
import pyfits as pyf
import pylab as pyl
from mpl_toolkits.axes_grid1 import axes_grid
import cPickle as pickle
import os
from scipy.stats import scoreatpercentile
def mk_image(galaxy):
base = './../../images_v5/GS_2.5as_matched/gs_all_'
i_img = pyf.getdata(base+str(galaxy)+'_I.fits')
j_i... | boada/ICD | sandbox/legacy_plot_code/plot_icd_clump_montage.py | Python | mit | 4,114 | [
"Galaxy"
] | 4a54cec7c325bc028e1e911fbec4b1d4ab13e584ae08f774cf18c1e1866c5e77 |
# -*- coding: utf-8 -*-
import mock
import unittest
from nose.tools import * # noqa
import tempfile
from bs4 import BeautifulSoup
from robobrowser.compat import builtin_name
from robobrowser.forms.form import Form, Payload, fields, _parse_fields
from robobrowser import exceptions
class TestPayload(unittest.TestCa... | palaniyappanBala/robobrowser | tests/test_forms.py | Python | bsd-3-clause | 23,688 | [
"Brian"
] | bddab6989020d6166cdf1185b1eb46d253ab6f00d57ceeccb73335e0a09196c8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgecontrib/simulation/synapse_templates/exponential_form/exp2synnmda/__init__.py | Python | bsd-2-clause | 1,584 | [
"NEURON"
] | d1d1cfe24830da64653d6fe754848485e36223edc33797971c9b2608487512ff |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
"""Brillouin zone classes
=========================
The Brillouin zone objects are all special classes enabling easy ma... | zerothi/sisl | sisl/physics/brillouinzone.py | Python | mpl-2.0 | 83,252 | [
"Gaussian"
] | 19f20b17523ba28f5bbd35e2dc09ba3cbd626fcc2e8fa34ad70204dc1589222f |
"""
==========================================================
Comparison of kernel ridge and Gaussian process regression
==========================================================
Both kernel ridge regression (KRR) and Gaussian process regression (GPR) learn
a target function by employing internally the "kernel trick... | ltiao/scikit-learn | examples/gaussian_process/plot_compare_gpr_krr.py | Python | bsd-3-clause | 5,039 | [
"Gaussian"
] | db76e7c24bb3c9aa3cbf6c6fc4a931f616cbc52363eb9741871cbdc26d3636e5 |
''' TransferCommand module
'''
__RCSID__ = '$Id$'
from datetime import datetime, timedelta
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.ConfigurationSystem.Client.Helpers.Resources import getSites
from DIRAC.AccountingSystem.Client.ReportsClient import ReportsClient
fr... | andresailer/DIRAC | ResourceStatusSystem/Command/TransferCommand.py | Python | gpl-3.0 | 7,081 | [
"DIRAC"
] | b0cd4973c1f0337d0b7eb13abdf7ce972e64ad9663676dcc86f576efcb1ed7bd |
"""
Tests for the vacancy renderer
"""
from __future__ import absolute_import
from __future__ import unicode_literals
import unittest
import numpy as np
import vtk
from vtk.util import numpy_support
from .. import vacancyRenderer
from ... import utils
from ....filtering.filters import pointDefectsFilter
from six.mo... | chrisdjscott/Atoman | atoman/rendering/renderers/tests/test_vacancyRenderer.py | Python | mit | 2,795 | [
"VTK"
] | 08217256848231c69cb01ef4a5f33aa276396a59c7ab0600d5b38ce7603eea00 |
# -*- coding: utf-8 -*-
###############################################################################
# Name: arpeggio.py
# Purpose: PEG parser interpreter
# Author: Igor R. Dejanović <igor DOT dejanovic AT gmail DOT com>
# Copyright: (c) 2009-2015 Igor R. Dejanović <igor DOT dejanovic AT gmail DOT com>
# License: MI... | leiyangyou/Arpeggio | arpeggio/__init__.py | Python | mit | 58,758 | [
"VisIt"
] | 5d920958f6b3a2dedb83db53f80215bd79e32560e85384a407c852b61a06f4e7 |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
# A collection of optimization algorithms. Version ... | jdavidrcamacho/Tests_GP | 02 - Programs being tested/02 - optimization test files/optimization tests 1/teste_sc_optimize.py | Python | mit | 101,090 | [
"Gaussian"
] | 16a9b26589f2c73b5c1ae6a5c0b9526ccc64be784623338240c8deacc9d3a510 |
import os.path
import tempfile
import numpy as np
import orca
import pandana as pdna
import pandas as pd
import pytest
from .. import networks
@pytest.fixture(scope="module")
def sample_osm(request):
store = pd.HDFStore(
os.path.join(os.path.dirname(__file__), 'osm_sample.h5'), "r")
nodes, edges = s... | apdjustino/urbansim | urbansim/utils/tests/test_networks.py | Python | bsd-3-clause | 1,879 | [
"ORCA"
] | a3cbb02b81f2756264654498cc61ac7835636036abd66e2f8fc8529af745a27e |
#!/usr/bin/python
from multiprocessing import Pool
import time
import os
import sys
import argparse
# Copyright(C) 2013 David Ream
# Released under Biopython license. http://www.biopython.org/DIST/LICENSE
# Do not remove this comment
# This exists to make the main function easier to read. It contains code to run th... | idoerg/BOA | tools/blast_script.py | Python | gpl-3.0 | 7,800 | [
"BLAST",
"Biopython"
] | a04fbc2a9f2fd98ea3a3dfd62c58ef7d11e0bd4bb1506b461e0fe767773d44af |
import os
import subprocess
import re
import uuid
from markdown.blockprocessors import BlockProcessor
from MooseCommonExtension import MooseCommonExtension
from markdown.util import etree
import logging
log = logging.getLogger(__name__)
class MooseDiagram(BlockProcessor, MooseCommonExtension):
"""
Extension to all... | vityurkiv/Ox | python/MooseDocs/extensions/MooseDiagram.py | Python | lgpl-2.1 | 2,161 | [
"MOOSE"
] | e4f5f67cc21d19f280d83a59bbdf07f2586ef5b157a3c9ee7f0a094a980d741a |
#####################################################################
# $HeadURL $
# File: ReqManagerHandler.py
########################################################################
"""
:mod: ReqManagerHandler
.. module: ReqManagerHandler
:synopsis: Implementation of the RequestDB service in the DISET framework
... | miloszz/DIRAC | RequestManagementSystem/Service/ReqManagerHandler.py | Python | gpl-3.0 | 12,725 | [
"DIRAC"
] | 5bdc26fa2c9f469b384e5296902968c9dae31b05ff0369ba7002e3e6a28c80b3 |
#########################################
## Last revision on September 12, 2017 ##
#########################################
import numpy as np
import math
import linecache
import sys
import os
#######################
## GLOBAL VARIABLES ###
#######################
try:
name = sys.argv[1]
dca = sys.argv[2]
xl =... | mcubeg/DCAXL | sbmbuild.py | Python | mit | 9,769 | [
"Gaussian",
"Gromacs"
] | 23711b203370ac7b6784a804a7dc2c735bea7cd304bb9814c654a2874eb731f5 |
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