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# Copyright (c) 2014-2018. Mount Sinai School of Medicine
#
# 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 ... | hammerlab/varlens | setup.py | Python | apache-2.0 | 2,375 | [
"pysam"
] | de7b7fa6e101ddd73047b49b9e3376760b75da44f2580574c8fd1e7ae817dc5b |
import numpy as np
from .dtype import img_as_float
__all__ = ['random_noise']
def random_noise(image, mode='gaussian', seed=None, clip=True, **kwargs):
"""
Function to add random noise of various types to a floating-point image.
Parameters
----------
image : ndarray
Input image data. Wi... | Hiyorimi/scikit-image | skimage/util/noise.py | Python | bsd-3-clause | 7,628 | [
"Gaussian"
] | 76968f7e0b827c652e9a807193692ec11c4abbb20c90ee7200c9b192591559eb |
# Copyright 2012 Hewlett-Packard Development Company, L.P.
#
# 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... | madAndroid/jenkins-job-builder | jenkins_jobs/modules/scm.py | Python | apache-2.0 | 49,040 | [
"Octopus"
] | ffa986cd83d22ce6e280544e0bbeb833ec360425cf3ab2bdcff956bf40b68a8e |
from mpi4py import MPI
import sys
import os
import glob
import subprocess
import shutil
def cleanPDB(pdbfile):
# This function will look for and remove duplicate atoms
# It will permanently modify the PDB that the user loaded
# This shouldn't cause problems for other programs though
data = []
taken... | schenc3/InteractiveROSETTA | InteractiveROSETTA/server/antibody_mpi.py | Python | gpl-2.0 | 6,537 | [
"BLAST",
"Biopython"
] | b55e4e22fcde19fa603a5c1015410db48b5db39de183c87621a1daa809055760 |
# Copyright 2017 Battelle Energy Alliance, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | idaholab/raven | framework/SupervisedLearning/ScikitLearn/NaiveBayes/GaussianNBClassifier.py | Python | apache-2.0 | 4,245 | [
"Gaussian"
] | 8c5871c82791ba9cc83703258827a5c150f6931c2e3e5d10947b3d45b41fd4f2 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import print_function
import ast
import gyp.common
import gyp.simple_copy
import multiprocessing
import os.path
import re
import shlex
import sig... | onecoolx/picasso | tools/gyp/pylib/gyp/input.py | Python | bsd-3-clause | 128,903 | [
"VisIt"
] | 0221fafcb23edcba5643f457ee7ec39cebafc7b735a4176e9ea58c343e61c02c |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Contribution 2009 by Reinhard Mueller <reinhard.mueller@bytewise.at>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2013-2014 Paul Franklin
#
# This program is free software; you c... | sam-m888/gprime | gprime/plugins/textreport/kinshipreport.py | Python | gpl-2.0 | 17,158 | [
"Brian"
] | cae3f56230289efd1779a392868bdb2246cce011c91402850287ac9cfcbc82f8 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2016 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | crisely09/horton | horton/io/cube.py | Python | gpl-3.0 | 5,383 | [
"Gaussian"
] | 0e32547ae0b3a7be6e8bcbc0db0a621fd33d81f45d798c51a106bdc38c9c5f99 |
class Module:
def __init__(self, mainMenu, params=[]):
# metadata info about the module, not modified during runtime
self.info = {
# name for the module that will appear in module menus
'Name': 'Linux PillageUser',
# list of one or more authors for the module
... | EmpireProject/Empire | lib/modules/python/collection/linux/pillage_user.py | Python | bsd-3-clause | 5,008 | [
"BLAST"
] | 7b665c36bc3f0de941a7c5db1c9a547dbc4496339cfd3b8e2d78bd2d8379d9ee |
import os
import sys
from utils import *
import operator
from time import localtime, strftime
import argparse
import re
import sh
import pandas as pd
# cd /nfs3/PHARM/Morgun_Lab/richrr/Type2_Diabetes/RNA-Seq/analysis/summarize_per_sample
# usage: python ~/Morgun_Lab/richrr/scripts/python/sum_data_from_la... | richrr/scripts | python/sum_data_from_lanes_per_sample.py | Python | gpl-3.0 | 5,060 | [
"HTSeq"
] | 13b264fe01ad2f053142eb4bb2ccb031544b57129fdffcda886ec0e45498ffa5 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | tests/test_tables.py | Python | gpl-2.0 | 3,219 | [
"VisIt"
] | 1e932770888376be4c2b88fa6aeadf2dcc6dc265d71b542572c6ed7b5252b66e |
import unittest, re, sys, random
sys.path.extend(['.','..','py'])
import h2o, h2o_cmd, h2o_hosts, h2o_import as h2i
class Basic(unittest.TestCase):
def tearDown(self):
h2o.check_sandbox_for_errors()
@classmethod
def setUpClass(cls):
global localhost
localhost = h2o.decide_if_localh... | woobe/h2o | py/testdir_single_jvm/test_parse_many_cases_fvec.py | Python | apache-2.0 | 9,060 | [
"Dalton"
] | c6ed6b6d9135a3f84a767b2feb6a7d278acf3d2a96c518c67163cb09605a462f |
# coding=utf-8
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... | AlexEKoren/grumpy | compiler/stmt.py | Python | apache-2.0 | 29,002 | [
"VisIt"
] | 346e560c6db95c2cde8714c8f98c9d641e8620d42d893820262878ec78d5e881 |
# Author: Jake VanderPlas
# License: BSD
# The figure produced by this code is published in the textbook
# "Statistics, Data Mining, and Machine Learning in Astronomy" (2013)
# For more information, see http://astroML.github.com
# To report a bug or issue, use the following forum:
# https://groups.google.com... | sniemi/EuclidVisibleInstrument | sandbox/GaussianMixtureModel.py | Python | bsd-2-clause | 3,599 | [
"Gaussian"
] | 31aae935ec53c129e15eb836dd8877dd700198d24f385b5b1f32b857cfc15ee7 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/analysis/polymer.py | Python | gpl-2.0 | 5,509 | [
"MDAnalysis"
] | 085605092323885aec24bf368d2c3110e72a4349a5cc535cd6dae3221e6c8c7f |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | casawa/mdtraj | mdtraj/formats/mdcrd.py | Python | lgpl-2.1 | 18,394 | [
"Amber",
"MDTraj"
] | 6e734626b347df330c9daeee0cbb7937537be02dc4cddf23b998957dd261fca3 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# License: MIT License (See LICENSE.md)
# Copyright (c) 2013
"""
bonds_by_type.py reads a LAMMPS data file (or an excerpt of a LAMMPS)
data file containing bonded many-body interactions by atom type
(and bond type), and generates a list... | smsaladi/moltemplate | moltemplate/bonds_by_type.py | Python | bsd-3-clause | 16,486 | [
"LAMMPS"
] | 9bba8d033623e09568034dc73e0a78756006dda45fbcd95ae26b5544c9d51364 |
# expression.py
# Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010 Michael Bayer mike_mp@zzzcomputing.com
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Defines the base components of SQL expression trees.
All components are derived... | obeattie/sqlalchemy | lib/sqlalchemy/sql/expression.py | Python | mit | 141,178 | [
"VisIt"
] | 670312249027d556036f315056158b277b97c7a38546fee8470669531adc42cf |
# Pyggy
#
# Author: Anton Samson <anton@antonsamson.com>
# Available freely at: https://github.com/antsam/pyggy
#
# A web crawler that will save all the pages/files from a specific
# domain/subdomain onto disk.
#
# To start with default settings: python pyggy.py -v
# The -v flag will turn on verbose output so you can s... | antsam/pyggy | pyggy.py | Python | agpl-3.0 | 11,949 | [
"VisIt"
] | 1acff71040f45fd8b17d542fc3cbf9c55d75a4ed7770ae8d55fbc8775b6c01f1 |
# Storage filtering classes
#
# Copyright (C) 2013 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed... | itoed/anaconda | pyanaconda/ui/gui/spokes/filter.py | Python | gpl-2.0 | 23,725 | [
"VisIt"
] | 2f99f5c96ab3473448ec421da998c88d6077b594a2014acfded032e5582866b7 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/core/ui/filerenameform.py | Python | gpl-2.0 | 2,842 | [
"Brian"
] | 264fea9242d72451cebdf81356acf8d3f4fed5fa164fe3490e5afe8a9c94a647 |
# Author: Suyog Dutt Jain <suyog.jain@aero.iitb.ac.in>
# Copyright (c) 2009-2015, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
import unittest
# Local imports.
from .common import get_example_data
# Enthought library imports
from mayavi.sources.poly_data_reader import PolyDataReader
from mayavi... | dmsurti/mayavi | mayavi/tests/test_poly_data_reader.py | Python | bsd-3-clause | 10,834 | [
"Mayavi",
"VTK"
] | b1d80c0d8b6f1a428849aef5beb106bd1b0ebaa30d1dcd4ac6106fb6dc748f07 |
##############################################################################
# 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-complexheatmap/package.py | Python | lgpl-2.1 | 2,261 | [
"Bioconductor"
] | 3f51ac0480195271dd3dc4da0f621bbe1e4bfcd76d2ed3bd97797726fa091703 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'NeuronEphysLink.num_reps'
db.add_column('neuroelectro_neuronephyslink', 'num_re... | lessc0de/neuroelectro_org | neuroelectro/south_migrations/0016_auto__add_field_neuronephyslink_num_reps.py | Python | gpl-2.0 | 10,641 | [
"NEURON"
] | 15c7b912899d08b86faeec7d5c3e0a774e9549e8adc88fb00d5b17c13251b45c |
#!/usr/bin/env python
#
# This example creates a polygonal model of a cone, and then renders it to
# the screen. It will rotate the cone 360 degrees and then exit. The basic
# setup of source -> mapper -> actor -> renderer -> renderwindow is
# typical of most VTK programs.
#
#
# First we include the VTK Pytho... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Tutorial/Step1/Python/Cone.py | Python | bsd-3-clause | 2,419 | [
"VTK"
] | 9cea435c570b40824ece37eaced3b7b806778c0cd31a50f4e39d10b64ce7a1a4 |
''' This is a test of the chain
ResourceManagementClient -> ResourceManagementHandler -> ResourceManagementDB
It supposes that the DB is present, and that the service is running
The DB is supposed to be empty when the test starts
'''
# pylint: disable=invalid-name,wrong-import-position
import sys
import ... | andresailer/DIRAC | tests/Integration/ResourceStatusSystem/Test_ResourceManagement.py | Python | gpl-3.0 | 12,465 | [
"DIRAC"
] | 7578ec163952fc6fbe856f5db101f42c33ca08af45baa89e8b4a210f4d5bee90 |
import pybel
import openbabel
import csv
from openmoldbmolecules.models import Molecule
"""
THIS IS OBSOLETE! USE add2db.py
"""
def add_mols(data):
namec = ""
altnamec = ""
suppc = ""
suppidc = ""
storc = ""
storidc = ""
amountc = ""
unitc = ""
casc = ""
altsupplierc = ""
... | samoturk/openmolDB | managemols.py | Python | bsd-3-clause | 8,833 | [
"Pybel"
] | f99466187cce69628286e8c67225b4a1349ef8c7818c8cdd9188325470e5293d |
#!/usr/bin/env python3
import sys
import argparse
import numpy as np
from mapTools import *
from utilities import filesFromList, writeLog
from plotTools import addImagePlot, addScatterPlot
import matplotlib.pyplot as plt
'''
Description:
Author: Mikko Auvinen
mikko.auvinen@fmi.fi
Finnish Meteorologica... | mjsauvinen/P4UL | pyRaster/processDomain.py | Python | mit | 3,976 | [
"Gaussian"
] | 5798d6aec854308400111111ed30683bab23bce4ef14e8c0e15fc6336bc2c424 |
#!/bin/ipython
# ---LICENSE-BEGIN - DO NOT CHANGE OR MOVE THIS HEADER
# This file is part of the Neurorobotics Platform software
# Copyright (C) 2014,2015,2016,2017 Human Brain Project
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as p... | roberthangu/snn_object_recognition | video-test.py | Python | gpl-2.0 | 3,417 | [
"NEURON"
] | be0be512000af8173a4887523a103100bbae7afcd17837612c4817b2ee17ef25 |
import glob
import pandas as pd
import numpy as np
pd.set_option('display.max_columns', 50) # print all rows
import os
os.chdir("/gpfs/commons/home/biederstedte-934/evan_projects/correct_phylo_files")
normalB = glob.glob("binary_position_RRBS_normal_B_cell*")
mcell = glob.glob("binary_position_RRBS_NormalBCD19pCD27... | evanbiederstedt/RRBSfun | trees/chrom_scripts/normal_chr14.py | Python | mit | 25,844 | [
"MCell"
] | 8c87a0fdbacb7487201d271d86bab066d4dd598756fc785bb7b0bf8c74bf2ac6 |
from _graph import *
from _graph import __doc__
import numpy as np
"""
This module implements the main graph classes of fff2
Graph: basic topological graph, i.e. vertices and edges. Not well developed
WeightedGraph (Graph): Idem plus values asociated with vertices
BipartiteGraph (WeightedGraph): Idem but the graph is ... | yarikoptic/NiPy-OLD | nipy/neurospin/graph/graph.py | Python | bsd-3-clause | 44,792 | [
"Gaussian"
] | 80bfb2570da31ca771363d22a28e4ab3f245e22bf28ba61f7a25ba3c540f06a6 |
import numpy as np
from IPython import embed
def coords2str(x):
return " ".join(("%d" % n for n in x))
def str2coords(s):
return np.fromstring(s, dtype=int, sep=" ")
def index_lookup_map(x):
return {coords2str(x): i for i,x in enumerate(x)}
def bounding_box(voxels):
mins=np.min(voxels,axis=0)
ma... | kharris/allen-voxel-network | voxnet/plotting.py | Python | bsd-2-clause | 9,519 | [
"VTK"
] | cf372d8f905e57317508791af8e03afe1a401fbd417208e2f498e435efe252b1 |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for problems in the LMS
See also old lettuce tests in lms/djangoapps/courseware/features/problems.feature
"""
from nose.plugins.attrib import attr
from textwrap import dedent
from common.test.acceptance.tests.helpers import UniqueCourseTest
from common.test.accept... | jzoldak/edx-platform | common/test/acceptance/tests/lms/test_lms_problems.py | Python | agpl-3.0 | 37,565 | [
"VisIt"
] | 641cc740c096d2e233807a8053b60560d33cde80f7b3fa90caa9c7a06a01bd9e |
#!/usr/bin/python
"""
# Created on Aug 12, 2016
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com) GitHub ID: grastogi23
#
# module_check: not supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
"... | thaim/ansible | lib/ansible/modules/network/avi/avi_api_session.py | Python | mit | 9,021 | [
"VisIt"
] | 79f3cb7f5577b5072180d7df821f6073abbf9bf990093eade8a3b838489c4c3e |
# -*- coding: utf-8 -*-
#
# Copyright 2008 - 2019 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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 Foundati... | dursobr/Pythics | pythics/__init__.py | Python | gpl-3.0 | 802 | [
"Brian"
] | cebca798a813b39dbb1096e1f6aeb998f64106a0f74b588e1ed13e8b6eff5edd |
from functools import reduce
from syntax import *
from collections import namedtuple
class NoRuleApplies(RuntimeError):
pass
# ------------------------ EVALUATION ------------------------
def isnumericval(term):
t_term = type(term)
if t_term is TmZero:
return True
elif t_term is TmSucc:
... | habibutsu/tapl-py | recon/core.py | Python | mit | 6,891 | [
"VisIt"
] | c46e7ac60bc4b20aa4197186291b6d5a52df2f6bd5a423b860c319df7853797f |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
# -*- coding: utf-8 -*-
"""
desitarget.randoms
==================
Monte Carlo Legacy Surveys imaging at the pixel level to model the imaging footprint
"""
import os
import numpy as np
import astropy.io.fits as fits
from astropy.wcs import WCS
from time im... | desihub/desitarget | py/desitarget/randoms.py | Python | bsd-3-clause | 67,844 | [
"Galaxy"
] | faec90c2b2ede025827538a844c6ff2019102f9bac989d5e9a84d5d61cbb7464 |
"""
This module contains the Location class.
"""
# Will Holmgren, University of Arizona, 2014-2016.
import datetime
import pandas as pd
import pytz
from pvlib import solarposition, clearsky, atmosphere, irradiance
class Location(object):
"""
Location objects are convenient containers for latitude, longitu... | anomam/pvlib-python | pvlib/location.py | Python | bsd-3-clause | 12,154 | [
"EPW"
] | d39392b57291b1f27aa488ebfc8467e38dccbda98a9d96639c6905adedfd1d56 |
# -*- coding: utf-8 -*-
#
# test_erfc_neuron.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Licens... | terhorstd/nest-simulator | pynest/nest/tests/test_erfc_neuron.py | Python | gpl-2.0 | 4,419 | [
"NEURON"
] | 42013530851eb1af6cec53e2229d93c90ce83889e8ea24bd1093afb35f6e9256 |
#!/usr/bin/env python
# File: plot_histograms3.py
# Created on: Mon Aug 20 22:14:33 2012
# Last Change: Tue Jan 15 16:03:45 2013
# Purpose of script: <+INSERT+>
# Author: Steven Boada
import pylab as pyl
from mk_galaxy_struc import mk_galaxy_struc
galaxies = mk_galaxy_struc()
verylow =[]
low =[]
med=[]
high=[]
appen... | boada/ICD | sandbox/legacy_plot_code/plot_pie_IH.py | Python | mit | 2,930 | [
"Galaxy"
] | c6453a595a231a0280aa98d94f2f9326dddc190e6943378a663060636ec32ca7 |
import unittest2 as unittest
import ROOT
from monitoring_app import tasks
class TestPages(unittest.TestCase):
def setUp(self):
self.fextension = 'root'
# The fname and keys match those of the data generated by
# `generate_histograms.py`
self.dummy_fname = 'histograms.root'
... | alexpearce/example-monitoring-app | tests/test_tasks.py | Python | mit | 3,930 | [
"Gaussian"
] | 9c4a576ad1275b8089e197e5fc5482f168da960dc7bc03dac5ffc99a4ae5b5ba |
import ecdsa
import hashlib, base64, ecdsa, re
import hmac
import subprocess
import thread
import random
import urllib
from ecdsa.curves import SECP256k1
from ecdsa.util import string_to_number, number_to_string
from ecdsa.ecdsa import curve_secp256k1, generator_secp256k1
#!/usr/bin/env python
#
# Electrum - lightweigh... | ohadcn/vanityBrain | old_mnemonic.py | Python | gpl-3.0 | 23,497 | [
"CRYSTAL",
"VisIt"
] | ca9f2876a3f740d9506ea819c80d2f4c9bf7f317a9266c73906df9fbc6ddd569 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from TestHa... | nuclear-wizard/moose | python/TestHarness/schedulers/RunParallel.py | Python | lgpl-2.1 | 3,186 | [
"MOOSE"
] | 7571612ddccd774a69d9fbdd1a9e0ce7a1d5a9c47459ccfe912c61f42b2d0cf9 |
import numpy as np
import stsci.tools.nmpfit as mpfit
from numpy.polynomial.chebyshev import Chebyshev as CC
def gaussian4(p, x):
''' gaussian model
p[0] -- scale factor
p[1] -- centroid
p[2] -- sigma
p[3] -- offset
Area: (p[0]-p[3]) x p[2] x np.sqrt(2 x pi)
'''
u = (x - p[1])/p[2]
... | nickkonidaris/kpy | NPK/Fit.py | Python | gpl-2.0 | 2,232 | [
"Gaussian"
] | cfcd6effb0f0b665af50a8d5b0811a5e059a8bb6866bfe1e54d448e5425c2706 |
import unittest
from Ann import Ann
import numpy as np
import random
import copy
import os
import pickle
class Test(unittest.TestCase):
def test_1(self):
# Test for Ann Architecture#
# First architecture test#
n_i1 = 4 # Number of input neurons
n_h1 = 2 # Number of hidde... | kod3r/Ann | Ann-py/Ann_test.py | Python | mit | 27,969 | [
"NEURON"
] | 7c2d8a297a3e92417528862efa8fe23d2ee45a937b8a3c92e35987fb2c7a104f |
#
# Copyright (C) 2020 Greg Landrum and T5 Informatics GmbH
# @@ 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.
#
from rdkit import Chem
from rdkit.Ch... | bp-kelley/rdkit | Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py | Python | bsd-3-clause | 5,160 | [
"RDKit"
] | f15b380eadae1eb1d3da7d83de5f6c3525a1905fab1e165a073c7ee457237b05 |
# 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... | jart/tensorflow | tensorflow/contrib/autograph/converters/list_comprehensions.py | Python | apache-2.0 | 2,297 | [
"VisIt"
] | 968e34ad9f3c6a60715489e114b679c454567bf8c1d3c31c133f4e1657bb297d |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2007 Marcos Pinto ('markybob') <markybob@gmail.com>
#
# This file is part of Deluge and is licensed under GNU General Public License 3.0, or later, with
# the additional special exception to link portions of this program with the OpenSSL library.
# See LICENSE for more details.... | bendykst/deluge | deluge/ui/gtkui/aboutdialog.py | Python | gpl-3.0 | 17,847 | [
"Gaussian"
] | 7ff7edb59dfb2d03ebae0650e708dbd96d2e09b783e502d11627730450f9278d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides objects describing the basic parameters of the
pseudopotentials used in Abinit, and a parser to instantiate pseudopotential objects..
"""
import abc
import collections
import json
impor... | montoyjh/pymatgen | pymatgen/io/abinit/pseudos.py | Python | mit | 63,324 | [
"ABINIT",
"pymatgen"
] | f44d7eac1a680462eac59039b1cc22f51ad78c8f365fad0f04a2212b6420fe80 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# Copyright: (c) 2015, Brian Coca <bcoca@ansible.com>
# Copyright: (c) 2016-2017, Konstantin Shalygin <k0ste@k0ste.ru>
# Copyright: (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING... | rahushen/ansible | lib/ansible/modules/files/find.py | Python | gpl-3.0 | 14,992 | [
"Brian"
] | a000232998a2cbab5ae2ece55c4d7b0a541be10d0621047ab85f56efe3dd46db |
from ..instrumenters import InstrumentPlugin
from ...metrics import formatting
import time
import logging
log = logging.getLogger( __name__ )
GALAXY_SLOTS_KEY = "galaxy_slots"
START_EPOCH_KEY = "start_epoch"
END_EPOCH_KEY = "end_epoch"
RUNTIME_SECONDS_KEY = "runtime_seconds"
class CorePluginFormatter( formatting.Jo... | jmchilton/lwr | galaxy/jobs/metrics/instrumenters/core.py | Python | apache-2.0 | 3,192 | [
"Galaxy"
] | 1ceb63fe46c7c63902396fd548310d38b5fad8c3150938ad188379465c516286 |
class ObjectVisitor(object):
def visit_objects(self, objects):
for tag, obj in objects.iteritems():
self.visit(obj)
def generic_visit(self, obj):
pass
def visit(self, obj):
visitor_name = 'visit_%s' % obj['class']
return getattr(self, visitor_name, self.generic_... | fredreichbier/babbisch | babbisch/client.py | Python | mit | 332 | [
"VisIt"
] | b6d52e013130c62caca1e686883de75f53380c0ff545cab0c370f6f90be17f1d |
import pickle
import os.path as osp
import numpy as np
from rdkit import Chem
inputs_path = osp.realpath("../../examples/sEH-TPPU")
TPPU_MOL_path = osp.join(inputs_path, "TPPU.mol")
TPPU_MOL_rdkit = Chem.MolFromMolFile(TPPU_MOL_path, sanitize=True)
TPPU_PDB_path = osp.join(inputs_path, "TPPU.pdb")
TPPU_PDB_rdkit = C... | salotz/mast | prototypes/profile_system/make_pkls.py | Python | mit | 1,463 | [
"RDKit"
] | beb1af1da0eec98c2c41afcf55ca24435cf1bd584d415ca19de85bcee802af0d |
#!/usr/bin/env python
"""
Provides wrappers and utilities for working with MAF files and alignments.
"""
#Dan Blankenberg
import pkg_resources; pkg_resources.require( "bx-python" )
import bx.align.maf
import bx.intervals
import bx.interval_index_file
import sys, os, string, tempfile
import logging
from copy im... | volpino/Yeps-EURAC | lib/galaxy/tools/util/maf_utilities.py | Python | mit | 27,158 | [
"Galaxy"
] | 348f1820f9e02b492e1b53b3f7e72259fed413610ae0c4c3da96659162513f1a |
#!/usr/bin/env python
import os
import argparse
import logging
import importlib
import tempfile
import subprocess
import pandas
from Bio import SeqIO
from cref.app import BaseApp
from cref.libs import rcsb
logger = logging.getLogger('CReF')
class TerminalApp(BaseApp):
"""
App to be run on the terminal
... | mchelem/cref2 | cref/app/terminal.py | Python | mit | 4,737 | [
"PyMOL"
] | 186f38ec15ade06b82bcc6ac837bf46e22481607cd669bffcdcd8b3632ae10c0 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General... | Azulinho/ansible | lib/ansible/modules/network/avi/avi_microservicegroup.py | Python | gpl-3.0 | 3,753 | [
"VisIt"
] | 504d92c0d4ef423c197c1773d61216dc79dc53388bea664c9f56fbd622f11ba7 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
# Copyright (c) 2014 Mikkel Schubert <MikkelSch@gmail.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 ... | MikkelSchubert/paleomix | paleomix/main.py | Python | mit | 5,185 | [
"pysam"
] | 9ba7395cc04df74cd57859e6155eaab23a98ba01e317a88e3b8d669d6ff6ef68 |
"""
Generates a PostView file from a .nc file. The three methods are for three of the
types of coordinate system used in NetCDFs: lat-lon, x-y, and x/y start/stop with x/y step.
"""
import os
from numpy import *
from time import gmtime, strftime, clock
import datetime
from Scientific.IO import NetCDF
class UnsuportedR... | janhui/test_engine | dev/StandAloneScripts/PosFileConverter.py | Python | lgpl-2.1 | 3,478 | [
"NetCDF"
] | f3a715437643bdb53ee928b4d9081400d5974dae0c8026a1612b8180378dae8c |
#!/usr/bin/python
# File created on 27 Jan 2012.
from __future__ import division
__author__ = "Kishori M Konwar"
__copyright__ = "Copyright 2013, MetaPathways"
__credits__ = ["r"]
__version__ = "1.0"
__maintainer__ = "Kishori M Konwar"
__status__ = "Release"
try:
import os, re, traceback
from os import make... | kishori82/MetaPathways_Python.3.0 | libs/python_scripts/MetaPathways_refscore.py | Python | mit | 11,218 | [
"BLAST"
] | 8010793efbf5f852a9b1e82df941ea2b5c4fbe9a85bc61cef8a343be67ce312b |
from galaxy.util import xml_text
DEFAULT_REQUIREMENT_TYPE = "package"
DEFAULT_REQUIREMENT_VERSION = None
class ToolRequirement( object ):
"""
Represents an external requirement that must be available for the tool to
run (for example, a program, package, or library). Requirements can
optionally asser... | ssorgatem/pulsar | galaxy/tools/deps/requirements.py | Python | apache-2.0 | 3,413 | [
"BWA",
"Galaxy"
] | 020de31c8c31142d12ec6e5e14201b947c3d55213a647d7efa07a7ece5b88b71 |
# ksp-compiler - a compiler for the Kontakt script language
# Copyright (C) 2011 Nils Liberg
#
# 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 2
# of the License, or (at your opt... | nojanath/SublimeKSP | ksp_compiler3/ksp_compiler.py | Python | gpl-3.0 | 105,491 | [
"VisIt"
] | 528c11f6503241a36b3e84487e33ba0df729c92ed674ba310f7d48c36bea2dd8 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import peaco... | nuclear-wizard/moose | python/peacock/ExodusViewer/plugins/ExodusPlugin.py | Python | lgpl-2.1 | 3,108 | [
"MOOSE"
] | 99fbb999751c90febb2cd8d1542b01277a3caddbe4e582f373c6af8d3d81b77d |
import ast
import inspect
import os
if __name__ == '__main__':
import django
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "sapl.settings")
django.setup()
if True:
from scripts.lista_urls import lista_urls
def get_decorators(cls):
target = cls
decorators = {}
def visit_FunctionDef(n... | LeandroRoberto/sapl | scripts/lista_permissions_in_decorators.py | Python | gpl-3.0 | 4,034 | [
"VisIt"
] | d816c1457902b4b194fdce6be2ed001488b8c1ef635a67bb1cf7ce1be5197441 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2016 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | crisely09/horton | horton/part/test/test_proatomdb.py | Python | gpl-3.0 | 8,738 | [
"CP2K"
] | 777e0a54f81ccbc99bd034740e2b769df920e751ff01c3e969d8aae788efebbd |
import numpy as np
import pylab as pl
'''
This script contains all the functions you will use for the assignments.
Have a look at them and don't be afraid to ask, if you have questions about the code here!
'''
'''
Function to compute the correlation coefficient given a certain time-window [time_window in ms]
Note, t... | h-mayorquin/camp_india_2016 | tutorials/Network Correlations/network_correlations.py | Python | mit | 6,684 | [
"NEURON"
] | 13f9cb6ff6ba511bb285fd8da432ed10ca65c7dad5e95f8976c7656f0e52a867 |
import subprocess
from .exceptions import PyperclipException
from pandas.compat import PY2, text_type
EXCEPT_MSG = """
Pyperclip could not find a copy/paste mechanism for your system.
For more information, please visit https://pyperclip.readthedocs.org """
def init_osx_clipboard():
def copy_osx(text):
... | louispotok/pandas | pandas/io/clipboard/clipboards.py | Python | bsd-3-clause | 4,244 | [
"VisIt"
] | 3699ea4cc3934d7d506bae8190fbaa093df8a0efffc5e3f775a5065ac453d804 |
import os
import numpy as np
import cPickle as pickle
import gzip
def load_pkl_gz(FN):
if os.path.isfile(FN) and os.path.getsize(FN) > 0:
F = gzip.open(FN, 'r')
try:
data = pickle.load(F)
except:
print(' error loading ' + FN)
F.close()
return None
F.close()
return data
... | CCBatIIT/AlGDock | AlGDock/IO.py | Python | mit | 17,074 | [
"Amber",
"NetCDF",
"VMD"
] | cdb57cea45c3deef4bc7e8a47bd9a960a63502dbb09b7b060a10a178856a7283 |
""" VOMSSecurityManager class implements access permissions based on VOMS roles
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import os
import datetime
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.Helpers.R... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/SecurityManager/VOMSSecurityManager.py | Python | gpl-3.0 | 23,076 | [
"DIRAC"
] | a744f9e153c1373774c7340ad63af7ebb5bf243202157303db55703f65f282b5 |
"""
Test objconfig.Config
"""
import pytest
from objconfig.exception import RuntimeException
from objconfig.exception import InvalidArgumentException
from objconfig import Config
def test_empty_instantiation():
try:
config = Config({})
except Exception:
assert False, "Empty Dictionary Instanti... | asherwunk/objconfig | tests/test_config.py | Python | mit | 3,046 | [
"Brian"
] | b8dfc28633fbc87d4382d790d704b9f91e51385983973f2f9bf28e57182ac643 |
#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# viz_gl.py
# Purpose: viz running LAMMPS simulation via GL tool in Pizza.py
# Syntax: viz_gl.py in.lammps Nfreq Nsteps
# in.lammps = LAMMPS input script
# Nfreq = dump and viz shapshot every this many steps
# ... | slitvinov/lammps-sph-multiphase | python/examples/viz_gl.py | Python | gpl-2.0 | 1,846 | [
"LAMMPS"
] | 862e020766cc3620da229a6af2bb9a5478bcf1310b4e43aef32b9f9dde0c4913 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The freesurfer module provides basic functions for interfacing with
freesurfer tools.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os... | dgellis90/nipype | nipype/interfaces/freesurfer/model.py | Python | bsd-3-clause | 63,042 | [
"Gaussian"
] | 4458a0019af6b1dd34ca8ee1c88c7745feae3ab5aeb1f716eccd4a772fbf9d22 |
from __future__ import (absolute_import, division, print_function)
import unittest
from mantid.api import IFunction1D, FunctionFactory
class TestFunction(IFunction1D):
def init(self):
pass
class FunctionFactoryTest(unittest.TestCase):
def test_get_function_factory_does_not_return_None(self):
... | wdzhou/mantid | Framework/PythonInterface/test/python/mantid/api/FunctionFactoryTest.py | Python | gpl-3.0 | 1,409 | [
"Gaussian"
] | 801ee71bd425e9068587a16d43cd7e1f228870d2931c49303364dd032cd6a28b |
import sys, os, getpass, logging, time, inspect, requests, json, pprint
import h2o_test_utils
from h2o_test_utils import log, log_rest
import h2o_print as h2p
class H2O(object):
# static (class) variables
ipaddr_from_cmd_line = None
debugger = False
json_url_history = []
python_test_name = inspect.... | YzPaul3/h2o-3 | py/h2o.py | Python | apache-2.0 | 46,466 | [
"Gaussian"
] | 90148baf5ca32fae738ec681f67b5a8b15f3e110c130fa25da3fa1df87927d1a |
"""
cell/compartCell.py
Contains compartCell class
Contributors: salvadordura@gmail.com
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import absolute_import
from builtins import super
from builtins import next
from builtins import ... | thekerrlab/netpyne | netpyne/cell/compartCell.py | Python | mit | 67,771 | [
"NEURON"
] | cdaae240cdadac0f4a7eac9fce8b11bda6a209467c870fcb25ccb51f03e8f38b |
""" Base corrector for the group and ingroup shares
"""
from DIRAC import S_OK, S_ERROR
__RCSID__ = "$Id$"
class BaseCorrector(object):
def __init__(self, opsHelper, baseCSPath, group):
self.__opsHelper = opsHelper
self.__baseCSPath = baseCSPath
self.__group = group
def initialize(self):
retur... | chaen/DIRAC | WorkloadManagementSystem/private/correctors/BaseCorrector.py | Python | gpl-3.0 | 929 | [
"DIRAC"
] | e2f8d605f08d864eb429aae52ab7a1cfa33e866bc7e620408142512785482932 |
#!/usr/bin/env python
'''
File name: main_ripp_mod.py
Author: Guillaume Viejo
Date created: 16/08/2017
Python Version: 3.5.2
'''
import sys
import numpy as np
import pandas as pd
import scipy.io
from functions import *
# from pylab import *
from multiprocessing import Pool
import os
import neurose... | gviejo/ThalamusPhysio | python/main_make_SWS_scalar_product.py | Python | gpl-3.0 | 14,308 | [
"Gaussian"
] | a30ff515be9adcb8aa14f7103d3361dbf84bf50414006f9d98c03bb5e437024b |
#
# GFSK modulation and demodulation.
#
#
# Copyright 2005-2007,2012 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# SPDX-License-Identifier: GPL-3.0-or-later
#
#
# See gnuradio-examples/python/digital for examples
import numpy
from gnuradio import gr
from gnuradio import analog
from gnuradio ... | trabucayre/gnuradio | gr-digital/python/digital/gfsk.py | Python | gpl-3.0 | 10,789 | [
"Gaussian"
] | 43b463174f42236c3a97261e77dc45ed3d35ed09e2c653cdb8a27ee6cf4c1de7 |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
datatypes_repository_name = 'emboss_datatypes_0110'
datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This reposit... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py | Python | gpl-3.0 | 12,412 | [
"Galaxy"
] | 0f26b1e7a45e37c765ecdb45a8c96633d7f13bf91b25a16cb899ce2af5629f1d |
# Copyright 2018 The TensorFlow Probability Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | tensorflow/probability | tensorflow_probability/python/vi/optimization.py | Python | apache-2.0 | 34,769 | [
"Gaussian"
] | d35d60dea675aa2d09f89bf379057b3dc0dff0ffe40bfa4e40b8c7b0a513f023 |
# -*- coding: utf-8 -*-
'''
Copyright (c) 2015 by Tobias Houska
This file is part of Statistical Parameter Estimation Tool (SPOTPY).
:author: Tobias Houska
This class holds the MaximumLikelihoodEstimation (MLE) algorithm.
'''
from . import _algorithm
import numpy as np
import time
class mle(_algorithm):
'''
... | gitporst/spotpy | spotpy/algorithms/mle.py | Python | mit | 5,553 | [
"Gaussian"
] | 0ec85855c572dc5db79aee012d9860396e27ce7b2b9996bec004004eb8fca74f |
# $Id$
#
# Copyright (C) 2004 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import RDConfig
import os,sys
import unittest
from rdkit import Chem
from rdkit.Geometry import Point3D
def feq(v1,v2,tol2=1e-4):
return abs(v1-v2)<=tol2
def ptEq(pt1, pt2, tol=1e-4):
return feq(pt1.x,pt2.x,tol) and ... | soerendip42/rdkit | Code/GraphMol/Wrap/testConformer.py | Python | bsd-3-clause | 3,539 | [
"RDKit"
] | 4922143632fa2168228ad0066728ea1284dfbf0e5b1d024026ab4518d74c0a48 |
"""
Module: audit_tie_breaker
Author: Berj K. Chilingirian
Date: 7 August 2016
Description:
The Australian Senate Election (ASE) may require an Australian Election
Official (AEO) to break a tie. There are three cases in which ties must
be broken manually by an AEO:
Case 1:
If mul... | ron-rivest/2016-aus-senate-audit | rivest/audit_tie_breaker.py | Python | apache-2.0 | 13,136 | [
"ASE"
] | a23eac3bc113f45eb9cb463a0a72dec3089ea027593adcb0c8d9aa71a04a4592 |
# This file is part of Buildbot. Buildbot 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 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without eve... | anish/buildbot | pkg/buildbot_pkg.py | Python | gpl-2.0 | 8,359 | [
"GULP"
] | a585d12ff7c4658962a0a5778ef2f6298cf1fc3c634edc57c818da3976bca4f2 |
import itertools
from datetime import datetime
from typing import Any, Dict, List, Optional, Set, Tuple
from django.db import connection
from django.db.models.query import QuerySet
from django.http import HttpRequest, HttpResponse, HttpResponseNotFound
from django.shortcuts import render
from django.utils.timezone imp... | eeshangarg/zulip | analytics/views/realm_activity.py | Python | apache-2.0 | 7,466 | [
"VisIt"
] | 321f1a37e9a0d65e34a6619e1c0c7a421216dcd740cfda04fa027e9175bf6d1a |
"""
Miscellaneous modules
Modules:
txt2alt(txt): read altitude[ft] from txt (FL ot ft)
txt2spd(spd,h): read CAS or Mach and convert to TAS for given altitude
tim2txt(t) : convert time[s] to HH:MM:SS.hh
i2txt(i,n) : convert integer to string of n chars with leading zeros
Created by : Jacco M. Ho... | ethertricity/bluesky | bluesky/tools/misc.py | Python | gpl-3.0 | 7,322 | [
"Amber"
] | 2641973c247af2126477595d8358f5e696f244b8ea258da75db20c75954808d5 |
# ----------------------------------------------------------------------
# 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... | epfl-cosmo/lammps | python/lammps.py | Python | gpl-2.0 | 29,726 | [
"LAMMPS"
] | 2ae700a82a79748f2d7e939d6804c980df39cd963d4aab1198d16599cc77179a |
from core import settings, uploader, filesystem
from core.logger import log
import os
class Backup(object):
"""
Class used to make a backup, in other words, the "kernel".
"""
def __init__(self, backup_path):
"""
Constructor. It used settings file
"""
self.recursive = Tr... | plutec/megup | core/backup.py | Python | gpl-2.0 | 11,984 | [
"VisIt"
] | 0aab3e6feca634d0accf1ec3567ade3ac576f8b9042816d1dbe4e98c56a21622 |
import collections as coll
import numpy as np
from scipy import ndimage
import warnings
from ..util import img_as_float
from ..color import guess_spatial_dimensions
__all__ = ['gaussian_filter']
def gaussian_filter(image, sigma, output=None, mode='nearest', cval=0,
multichannel=None):
"""Mul... | bennlich/scikit-image | skimage/filters/_gaussian.py | Python | bsd-3-clause | 3,998 | [
"Gaussian"
] | 62e548eb8727a122de0390ca7594fd20e7ba8b3309c340e42ed99e01c10f5af1 |
import os
import cdo
cdo = cdo.Cdo()
def split(name):
""" Returns the name of a file without the directory path
"""
path, filename = os.path.split(name)
return filename
def sample(ifile, **kwargs):
print 'called external function'
return ifile
def field_integral(ifile, **kwargs):
... | fallisd/validate | validate/functions/external.py | Python | gpl-2.0 | 684 | [
"NetCDF"
] | ab7a48260f428f7e2b843d6323b5ecadb921380bbca1580212602706638ad59e |
import os
from setuptools import setup
from pip.req import parse_requirements
# Utility function to read the README file. Used for the long_description.
# It's nice, because now 1) we have a top level README file and 2) it's easier
# to type in the README file than to put a raw string in below.
def read(fname):
w... | anchor/ceilometer-publisher-vaultaire | setup.py | Python | apache-2.0 | 1,372 | [
"Desmond"
] | f28f8952ee97e349f2c4bd6b0c89d686b0a5f9f1fd0bb48decf90132f4937903 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import os
i... | harterj/moose | python/mooseutils/VectorPostprocessorReader.py | Python | lgpl-2.1 | 5,970 | [
"MOOSE"
] | ac4caabd3ea0a5a58dcf7019b6491539f991dd74cecafe428a8c0cccd663f327 |
#!/usr/bin/env python
disk = vtk.vtkDiskSource()
disk.SetRadialResolution(2)
disk.SetCircumferentialResolution(9)
clean = vtk.vtkCleanPolyData()
clean.SetInputConnection(disk.GetOutputPort())
clean.SetTolerance(0.01)
piece = vtk.vtkExtractPolyDataPiece()
piece.SetInputConnection(clean.GetOutputPort())
extrude = vtk.vt... | ashray/VTK-EVM | Filters/Parallel/Testing/Python/TestExtrudePiece.py | Python | bsd-3-clause | 1,283 | [
"VTK"
] | e31861d713b994880af03c49fbc13b2f7de2a1caecf954cdcf2803915345b4d3 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | samples/visualization_constraints.py | Python | gpl-3.0 | 3,725 | [
"ESPResSo"
] | 6cd381761483cb51878463040f277c17a864e3f7f8f438304faa4246dab8d8bf |
from ddapp import objectmodel as om
from ddapp import affordanceitems
from ddapp import lcmobjectcollection
from ddapp import visualization as vis
from ddapp.timercallback import TimerCallback
from ddapp.uuidutil import newUUID
from ddapp import vtkAll as vtk
from ddapp.thirdparty import numpyjsoncoder
import traceback... | gizatt/director | src/python/ddapp/affordancemanager.py | Python | bsd-3-clause | 4,772 | [
"VTK"
] | 156b6fad8da5542ef8768009b0a4b58e52bcc1dd798e35227d85d45059ddb2a6 |
#!/usr/bin/env python3
# Author: LukeBob
#
# Requires: argparse, shodan, requests pip install them if needed.
# Run with: python3 synPwn.py --key <Shodan API Key> --cmd "<Command to try and execute>"
#
# python3 script for testing the (Synology StorageManager 5.2 - Root Remote Command Execution) exploit found by, (Weib... | LukeBob/bobstools-py | synpwn.py | Python | mit | 3,694 | [
"VisIt"
] | a3cd57c23ded6be2a406b8d0095d8a23d38695539ca914da6006b1d16d0d372d |
"""
Compute saddle-point integrals over trajectories traveling on adiabataic
potentials
This currently uses first-order saddle point.
"""
import numpy as np
import nomad.math.constants as constants
import nomad.core.glbl as glbl
import nomad.compiled.nuclear_gaussian_ccs as nuclear
# Let propagator know if we need d... | mschuurman/FMSpy | nomad/integrals/mca.py | Python | lgpl-3.0 | 6,533 | [
"Gaussian"
] | c021577aae4f94e8f9f2db48769fdf0d8ac43ab9aee9942844c719313910331d |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | leeping/mdtraj | tests/test_rmsd.py | Python | lgpl-2.1 | 6,778 | [
"MDTraj"
] | 0d84fef93e5ea6c2a903a316d855bf097d7f0072dacaffdd96fc5760e78cc3ed |
#!/usr/bin/env python
import clang
from clang.cindex import Index
import argparse
import os
import re
import sys
indent_spaces = 4
indentation = ' ' * indent_spaces
output = ['']
class client_data:
def __init__(self):
self.tu = None
self.current_namespaces = [] # cursors
self.current_st... | tzlaine/type_erasure | emtypen/emtypen.py | Python | mit | 17,634 | [
"VisIt"
] | 4873371b3d7d26807c8bf78ad2855a7c32765a79d55ba3d9530fd65349f82a1a |
import pandas
import numpy as np
import scipy
import statsmodels.api as sm
import matplotlib.pyplot as plt
import traceback
import os
from multiprocessing import Process
from time import time
from settings import ALGORITHMS
from os.path import dirname, join, abspath
"""
This is no man's land. Do anything you want in h... | astanway/crucible | src/algorithms.py | Python | mit | 7,970 | [
"ADF"
] | be10a275facad9baefbf3bf93ce607bdb544afc7d94e27e2da192ca55c5bff19 |
"""This module contains the "Viz" objects
These objects represent the backend of all the visualizations that
Superset can render.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import copy
import hashlib
import l... | FrederichCheng/incubator-superset | superset/viz.py | Python | apache-2.0 | 55,055 | [
"VisIt"
] | a61b29d16139c6d5de9ae1b30336d67fe776653fd60187ba4f042f395971d931 |
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