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# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jendap/tensorflow | tensorflow/tools/compatibility/tf_upgrade_v2.py | Python | apache-2.0 | 64,405 | [
"Gaussian"
] | 04672765da89acecc6d6a6cc211b0c2f7e391ec79a285831f5da97d2a71de749 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | Chuban/moose | python/chigger/tests/exodus/blocks/boundary_numeric.py | Python | lgpl-2.1 | 1,629 | [
"MOOSE",
"VTK"
] | 74859db02cd65c34230bb73f82f6dc2655856ac9a6a5c9fb77c935b8f679c3a6 |
'''
Created August 09, 2012
By Kay Perry, Frank Murphy
Distributed under the terms of the GNU General Public License.
This file is part of RAPD
RAPD is a 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 vers... | RAPD/RAPD | src/plugins/merge/rapd_agent_mergemany.py | Python | agpl-3.0 | 62,002 | [
"CRYSTAL"
] | 90ad6f4e949c7e01ce80478bbd3ae6ed4757e6121ccc51d6c21a7bd7b37fd23f |
"""
=====================================================
Prediction Intervals for Gradient Boosting Regression
=====================================================
This example shows how quantile regression can be used to create prediction
intervals.
"""
# %%
# Generate some data for a synthetic regression problem b... | shyamalschandra/scikit-learn | examples/ensemble/plot_gradient_boosting_quantile.py | Python | bsd-3-clause | 12,164 | [
"Gaussian"
] | 8f9d477338711e61a046dc003c33d1281aba59b7cfb6771b5e3fe05e1354dac9 |
import vigra
import vigra.graphs as graphs
import pylab
# parameter:
filepath = '100075.jpg' # input image path
sigmaGradMag = 3.0 # sigma Gaussian gradient
superpixelDiameter = 10 # super-pixel size
slicWeight = 10.0 # SLIC color - spatial weight
# load image and convert to LAB
img = vigra.impex.rea... | dagophil/vigra | vigranumpy/examples/graph_watersheds.py | Python | mit | 2,002 | [
"Gaussian"
] | 0a13c6eea53cb7461d4324207e34311eac5ae4503583a09b71f718c9287269d4 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Interfaces to assorted Freesurfer utility programs.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> d... | iglpdc/nipype | nipype/interfaces/freesurfer/utils.py | Python | bsd-3-clause | 56,504 | [
"Gaussian",
"VTK"
] | e2f07cdb3bdf6206eda8671f13eb799e372ab6e8c76420a10c143720384e287e |
import datetime
import ensembler
import os
import re
import numpy as np
import pandas as pd
import yaml
import mdtraj
import gzip
from ensembler.core import logger, check_ensembler_modeling_stage_complete
import warnings
class ProjectCounts(object):
def __init__(self, targetid, project_dir='.', ofile_basepath=Non... | choderalab/ensembler | ensembler/tools/inspect.py | Python | gpl-2.0 | 21,551 | [
"MDTraj"
] | 388eab0bbc0ba77b62a924b128138f20500fc511874b8e886809606fbe8b3d3f |
#------------------------------------------------------------------------------------------------------------
#
# This program carries out phase averaging of VTK output variable
# It works with both scalar and vector variables, the name only has to be specified
# In return an averaged file
#
#
# Usage : python phaseA... | blaisb/cfdemUtilities | mixing/foamTreatment/phaseAverage/phaseAverage.py | Python | lgpl-3.0 | 2,790 | [
"VTK"
] | c5fb8f0b11517749ccb0858741c75cc1030d8ee3d86b7e02841fb2f3db8baa04 |
import numpy as np
def gaussianKernel(x1, x2, sigma):
"""returns a gaussian kernel between x1 and x2
and returns the value in sim
"""
# Ensure that x1 and x2 are column vectors
# x1 = x1.ravel()
# x2 = x2.ravel()
# You need to return the following variables correctly.
sim = 0
# ============... | JediKoder/coursera-ML | ex6/gaussianKernel.py | Python | mit | 620 | [
"Gaussian"
] | f371c617785db5ba2f993ea02655da929a68717b2378676ecb33c6f22fcf4fa5 |
#!/usr/bin/env python
# CREATED:2013-03-08 15:25:18 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa core (__init__.py)
#
# Run me as follows:
# cd tests/
# nosetests -v
#
# This test suite verifies that librosa core routines match (numerically) the output
# of various DPWE matlab implementations on ... | ebattenberg/librosa | tests/testLibrosaCore.py | Python | isc | 5,518 | [
"Brian"
] | db7c9d0c33e0c9df0f03c326758725f926c6b34ad3662414743017a31a0bab44 |
""" JobEfficiencyPolicy
Policy that calculates the efficiency following the formula::
( completed + done ) / ( completed + done + failed )
if the denominator is smaller than 10, it does not take any decision.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import p... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/JobEfficiencyPolicy.py | Python | gpl-3.0 | 2,095 | [
"DIRAC"
] | f8d6339a3e54e70bb1304d22e2b86f8fa77dd2ff43463be08cc8bf1e33a575a1 |
#Written by Nick Loman (@pathogenomenick)
import os
import sys
from Bio import SeqIO
from clint.textui import colored, puts, indent
def get_nanopolish_header(ref):
recs = list(SeqIO.parse(open(ref), "fasta"))
if len (recs) != 1:
print >>sys.stderr, "FASTA has more than one sequence"
raise SystemExit
return "... | zibraproject/zika-pipeline | scripts/minion.py | Python | mit | 4,070 | [
"BWA"
] | dc3a83425824aa31a72c7233b827984fa1dc34e436d88453e6b424d0d073d8f9 |
"""
A container which is updated with the pycsp version in use. Making it possible to import pycsp.current from pycsp.common modules.
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT Li... | runefriborg/pycsp | pycsp/current/__init__.py | Python | mit | 333 | [
"Brian"
] | 79146525d30d3a68dbfb9429203e953fb1963759a6c45a85d8494905a0fa127c |
# Copyright 2021 Google 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 to in writing, ... | google-research/DBAP-algorithm | third_party/rlkit_library/examples/skewfit/sawyer_pickup.py | Python | apache-2.0 | 6,354 | [
"Gaussian"
] | 5c83b1721ba96041f1872af2bc72289d5169072578409e8124839416282d9ed4 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ThreadPoolExecutor."""
import atexit
from six import PY2
if PY2:
from . import _base
else:
from concurrent.futures import _base
import itertools
import Queue as queue
import threading
import wea... | SickGear/SickGear | lib/sg_futures/futures/thread.py | Python | gpl-3.0 | 7,291 | [
"Brian"
] | 65e146967bbcf9fe74df82336147740051dc741a37925edf76c12382073031f0 |
#!/usr/bin/env python
#/************************************************************
#*
#* 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 licen... | cac2003/incubator-singa | tool/python/singa/layer.py | Python | apache-2.0 | 26,145 | [
"Gaussian"
] | 0e74fb2fda425b9f0925ca87be7f655b840c215c78bd4b05fea86c5fd4bf4529 |
#!/usr/local/bin/python2.6
###IdentifyAltIsoforms
#Copyright 2005-2008 J. David Gladstone Institutes, San Francisco California
#Author Nathan Salomonis - nsalomonis@gmail.com
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the... | kdaily/altanalyze | IdentifyAltIsoforms.py | Python | apache-2.0 | 78,240 | [
"Biopython"
] | f545e020b512921dddf68f6266012ed79f70d57603f2df39536f5c6572ac98d2 |
import argparse
from collections import defaultdict
import numpy
import pysam
def Parser():
the_parser = argparse.ArgumentParser()
the_parser.add_argument(
'--input', action="store", type=str, help="bam alignment file")
the_parser.add_argument(
'--minquery', type=int,
help="Minim... | chamaelj/tools-artbio | tools/small_rna_signatures/signature.py | Python | mit | 9,118 | [
"pysam"
] | 005ff31fd67ea051fcaf0475452b058e3bc1ead0990175ba92ceb51a40db6dfb |
from distutils.core import setup
install_requires = []
# Test if we have built-in JSON - Python 2.6+, 3.0+.
# Older Python versions require simplejson.
try:
import json
except ImportError:
install_requires.append('simplejson')
setup(name='geopy',
version='0.94dev.zen.2',
description='Python Geocoding... | dpla/zen | thirdparty/geopy_export/setup.py | Python | apache-2.0 | 1,146 | [
"Brian"
] | e60e0c61572dde998e90dcbb02ec606c7ee6550f5973b97f5a51ce0f7b6556ea |
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------
# Copyright (c) 2009-2015 Jendrik Seipp
#
# RedNotebook 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... | jendrikseipp/rednotebook-elementary | rednotebook/info.py | Python | gpl-2.0 | 23,602 | [
"VisIt"
] | 52ef6212f56eecd9977382493e1bf77aa643fd59925aee1bab7d72a09f636f06 |
from sqlalchemy import and_
from sqlalchemy import bindparam
from sqlalchemy import case
from sqlalchemy import Column
from sqlalchemy import exc
from sqlalchemy import extract
from sqlalchemy import ForeignKey
from sqlalchemy import func
from sqlalchemy import Integer
from sqlalchemy import literal_column
from sqlalch... | kawamon/hue | desktop/core/ext-py/SQLAlchemy-1.3.17/test/sql/test_generative.py | Python | apache-2.0 | 69,886 | [
"ADF",
"VisIt"
] | 8af1b80513c10fb668ae7ef9a87dcf32d81a621b6a5e98992b153758a7bbf202 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001-2006 Donald N. Allingham
# Copyright (C) 2008-2009 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | pmghalvorsen/gramps_branch | gramps/gui/plug/report/_textreportdialog.py | Python | gpl-2.0 | 3,778 | [
"Brian"
] | be43da6859261579796081d1e9ffaf45929b3c75551cb3865fe9f5c769bb641a |
# Subject models to explicit solvent simulation.
#
# John D. Chodera <choderaj@mskcc.org> - 17 Feb 2013
#
# PREREQUISITES
#
# * OpenMM
# http://simtk.org/home/openmm
#
# TODO
# * use ff99sb-ildn-star
# * trim all systems to have the same number of waters?
# PARAMETERS
import sys
from ast import literal_eval
# Proces... | choderalab/Ensembler2 | scripts/attic/solvate-models-mpi4py.py | Python | gpl-2.0 | 4,710 | [
"OpenMM"
] | 0b1ab53c50503b16dfe615155bade268b34476cf34689d0eb185edd99170de3d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#/*
# * Copyright (c) 2011-2012 XBMC-Russia, HD-lab Team, E-mail: dev@hd-lab.ru
# * Writer (c) 2011, Kostynoy S.A., E-mail: seppius2@gmail.com
# *
# * This Program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public Licen... | sshnaidm/ru | plugin.video.rpod.ru/default.py | Python | gpl-2.0 | 12,462 | [
"Amber"
] | 94bd4b9899d2c5ba5445da35dc6411952e262b3efb44d16c0be98a0a68f6ab6a |
# -*- coding: utf-8 -*-
# URL shortener using short url services.
# Created By Abdul Hamid
# 06 March 2014
# ah@appscluster.com
import sys, time, os.path, getopt, socket
import urllib2, urllib
HEADERS = {'User-Agent':'Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.16 Safari/537.3... | appscluster/python-shorturl | shorturlpy/shorturlpy.py | Python | mit | 5,067 | [
"Galaxy"
] | af633e6ea040a29e3ad28b958c7d0fe9f875933fd3308dfc44467b61b9307539 |
# $Id$
#
# Copyright (C) 2004 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import RDConfig
import sys, os.path
from rdkit.VLib.Supply import SupplyNode
import pickle
if RDConfig.usePgSQL:
from pyPgSQL import PgSQL as sql
class _lazyDataSeq:
"""
These classes are used to speed up (a lot... | ptosco/rdkit | rdkit/VLib/NodeLib/DbPickleSupplier.py | Python | bsd-3-clause | 5,731 | [
"RDKit"
] | 89ceb1df9fd2403d4bb844b4cd15395ea59dd20d1c1e4d56eeed00a74585afe5 |
from repESP import resp, resp_helpers, graphs
from repESP.field_comparison import rms_and_rep
from repESP.charges import update_with_charges, _update_molecule_with_charges
from repESP.charges import compare_charges
import os
import matplotlib.pyplot as plt
import math
import shutil
# NOTE: This ad-hoc script has been... | jszopi/repESP | scripts/old/compromise.py | Python | gpl-3.0 | 8,488 | [
"Gaussian"
] | 0f59923785643d413b437ebfb88a1ed62905c7d7a7a1812feca1fdaefe2740e2 |
import numpy as np
import matplotlib.pyplot as plt
import scipy.io as sio
from ex8_utility import *
## Machine Learning Online Class - Exercise 8: Anomaly Detection and Collaborative Filtering
# Instructions
# ------------
#
# This file contains code that helps you get started on the
# exercise. You will need to... | cameronlai/ml-class-python | solutions/ex8/ex8.py | Python | mit | 4,241 | [
"Gaussian"
] | 59dce890054eb713ebb46ffc0715e5c14fc1df589b1f17a9d691917fc9cbb46e |
# -*- coding: utf-8 -*-
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import absolute_import
from __future__ import division
import logging
import math
from osgeo import gdal
from osgeo import osr
import netCDF4
import numpy as np
from threedilib.subgrid import datas... | lizardsystem/threedilib | threedilib/subgrid/quads.py | Python | gpl-3.0 | 4,236 | [
"NetCDF"
] | e06d03ffa6ad9f2eb54fdc7171fdb827e3603b75cc3c0cc3e31b46ff54dc4ba7 |
# coding: utf-8
"""Tools for the submission of Tasks."""
from __future__ import unicode_literals, division, print_function
import os
import time
import yaml
import pickle
from collections import deque
from datetime import timedelta
from six.moves import cStringIO
from monty.io import get_open_fds
from monty.string im... | rousseab/pymatgen | pymatgen/io/abinitio/launcher.py | Python | mit | 45,634 | [
"ABINIT",
"pymatgen"
] | 098ba94d5b4a8573cb0461be3f94db7f38c91c7cd5b6127f52d45b97768777b1 |
__author__ = 'Jayson Stemmler'
from netCDF import NetCDFFile
from netCDF import NetCDFFolder
import HDF
from ECMWF import pick_ecmwf_point
from uhsas import UHSAS | jstemmler/toolbox | toolbox/fileIO/__init__.py | Python | mit | 163 | [
"NetCDF"
] | 8c1e5bf4b3caf56bf5f1ca208a502de446efc5079b7ad76576be0b25b071892f |
r"""This module contains code to generate synthetic diffusion signal
attenuation following several state-of-the-art model, including diffusion
tensor [1]_, stick model [2]_, hindered diffusion in cylinder [3]_, and
mixture of the above. All the models described here have axial and antipodal
symmetry, and we define an a... | oesteban/phantomas | phantomas/mr_simul/synthetic.py | Python | bsd-3-clause | 5,678 | [
"Gaussian"
] | cb4788a6c6b278b13e3f140eedcae701a4a3ac635f4f9c5435869ec63df849af |
import os
import vtk
import math
import numpy
import paraview.servermanager
S = GetActiveSource()
FileName = os.path.basename(GetActiveSource().FileNames[0])
FileName = os.path.splitext(FileName)[0]
Normals = GenerateSurfaceNormals(Input=S,ComputeCellNormals=1)
Triangulate1 = Triangulate(Normals)
Surface = serverm... | vianamp/Utils | ImaginalDisk/python/flatextension.py | Python | gpl-3.0 | 1,424 | [
"ParaView",
"VTK"
] | 2398b7d2dde04c66426a2e9f8f6a3c30e0b181db619d884801804d61ff85e896 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 v... | pmghalvorsen/gramps_branch | gramps/gen/plug/menu/_style.py | Python | gpl-2.0 | 2,925 | [
"Brian"
] | 11ca5ebf4e4a75ac5b915eea84548a90c453f77017eb76ed306d8f4798a1234f |
import netCDF4 as netcdf
class NetCDF4Storage(object):
"""docstring for NetCDF4Storage"""
def __init__(self, storedir='./',natoms=None,dt=0.001,zlib=False, cmplevel=1):
super(NetCDF4Storage, self).__init__()
self._storedir = storedir
self._natoms = natoms
self._zlib = zlib
... | nrego/westpa | lib/examples/stringmethodexamples/shared/elasticnetwork-langevin/netcdf4storage.py | Python | gpl-3.0 | 2,059 | [
"Amber",
"NetCDF"
] | cfc8c57570586e8be1d1ed2d5ba138865f31814ba1a93df00735d504eb7725df |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Final/results/objects/96/test10_cross_validate_objects_96_1200ms.py | Python | mit | 4,252 | [
"Mayavi"
] | 5bf5f0b851e4e4cc6789b3c2c100604f2c981a7183a6082f2ef7eb48aa22b364 |
from pylab import *
from IPython.Debugger import Tracer; keyboard = Tracer()
#------------------------------------------------------------------------------
# Experimental code for generating samples positions which are well-distributed
# in time and space, and appropriate for use with interleaved sampling.
#
# Demo o... | karstenda/aqsis | prototypes/newcore/experiments/sample_patterns.py | Python | gpl-2.0 | 21,277 | [
"Gaussian"
] | 3b310b091cbb212dbe02724de0a0d21769c81bfac5e7236f600b6cd866266bd1 |
"""Elementary tests for wrapper_gen.py.
This test suite is not comprehensive because it is very hard to test
wrapper_gen directly.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2004, Prabhu Ramachandran, Enthought, Inc.
# License: BSD Style.
import unittest
import vtk
from tvtk import w... | dmsurti/mayavi | tvtk/tests/test_wrapper_gen.py | Python | bsd-3-clause | 2,042 | [
"VTK"
] | 3dd4d7e43fc057875ea65bf28d6533537b8ede7911ed3a45b6478786723574a5 |
#!/usr/bin/env python
# encoding: utf-8
"""
Uniweb validator project
djcheckfunc.py
Copyright (c) 2009 Brian Shumate
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, includin... | brianshumate/uniweb | share/djcheckfunc.py | Python | bsd-2-clause | 2,135 | [
"Brian"
] | e5f3dfea27b5715a360ce4a3841aafa118bee147ed39a39fcb21199b7d8a7043 |
"""Summary
"""
import cPickle as pickle
import numpy as np
from scipy.cluster.vq import kmeans2
from scipy.optimize import minimize
from scipy.spatial.distance import cdist
from config import *
from utils import ObjectiveWrapper, flatten_dict, unflatten_dict, adam
from utils import profile, PCA_reduce, matrixInverse
f... | thangbui/geepee | geepee/base_models.py | Python | mit | 58,801 | [
"Gaussian"
] | 9ed84d94900a875be56d3fe99457bc789d99b23029426c0eaf191fe2e873437a |
from arg_parse import blastargument_parser
import subprocess as sp
import multiprocessing as mp
import glob
import os
import output_parser
import sys
import gzip
try:
import Bio
except ImportError("Trouble Installing BioPython:"):
print "Can't find BioPython Module in this path. PyIgBlast is dependent on Biopy... | andrejbranch/pyigblast | run.py | Python | unlicense | 6,385 | [
"BLAST",
"Biopython"
] | 0fd78178daff928a06f928a67b637e4139514909757022fd867aba4a2e075770 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/awidgets/checkbox.py | Python | gpl-3.0 | 1,209 | [
"Brian"
] | 327f58f573a4c95ad91aefdc7d22e9919cfc17da05f03900748b256f1f6a4d3b |
#!/usr/bin/env python
#
# $File: numOff.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute it ... | BoPeng/simuPOP | docs/numOff.py | Python | gpl-2.0 | 2,852 | [
"VisIt"
] | d12c673a5f94315ef65deba46055b5b05887b0b2768143f4fa59a6233bb6e4e9 |
from pattern import Pattern
import itertools
import random
import colorsys
import time
class EqPattern(Pattern):
def __init__(self, meter_color=(255,100,50), background_color=(0,50,255)):
self.meter_r = meter_color[0]
self.meter_g = meter_color[1]
self.meter_b = meter_color[2]
self... | TheGentlemanOctopus/thegentlemanoctopus | octopus_code/core/octopus/patterns/eqPattern.py | Python | gpl-3.0 | 2,854 | [
"Octopus"
] | afe4d8544b97a473fbb511ca552a88c2f8a51011cc9d19f31dd77abaedb54118 |
# -*- coding: utf-8 -*-
"""
Created on Wed May 6 17:07:00 2015
"""
import numpy as np
from scipy.optimize import newton
_author__ = 'Julien Milli'
class Dust_distribution(object):
"""This class represents the dust distribution
"""
def __init__(self,density_dico={'name':'2PowerLaws', 'ain':5, 'aout':-5,
... | carlgogo/vip_exoplanets | vip_hci/metrics/dust_distribution.py | Python | bsd-3-clause | 15,666 | [
"Gaussian"
] | 30b9d8f45afa8e684a193b16c1440d68c325ad24e279aae75524577653867e57 |
#!/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/df/outcore.py | Python | apache-2.0 | 11,452 | [
"PySCF"
] | fc59c528a012031e8ea0a40a00156a4a3bf424cca031acd5c8159a705083a0f3 |
import numpy as np
from box.mix import phival
from math import sin,cos
from numpy import abs
from weakref import proxy
from box.mix import rotation_matrix
class Gaussian:
def __init__(self,atoms,type):
'''
Class for arbitrary Gaussian curvature.
@param: atoms hotbit.Atoms instan... | pekkosk/hotbit | hotbit/containers/gaussian.py | Python | gpl-2.0 | 3,768 | [
"Gaussian"
] | 40fba1768138deabf1fb0e8d1de83be52ad558e3b18da2c98a36f188de99fb88 |
#! /usr/bin/env python
"""Implementation of the Dakota polynomial chaos method."""
from .base import UncertaintyQuantificationBase
classname = "PolynomialChaos"
class PolynomialChaos(UncertaintyQuantificationBase):
"""The Dakota polynomial chaos uncertainty quantification method.
Designation of a coeffic... | csdms/dakota | dakotathon/method/polynomial_chaos.py | Python | mit | 5,509 | [
"Gaussian"
] | 59d5de5e310d22f83040670446c076870b76504d9b7caf0df9b3fa1fdcb1794e |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 v... | pmghalvorsen/gramps_branch | gramps/gen/plug/menu/_filter.py | Python | gpl-2.0 | 2,619 | [
"Brian"
] | f88093a71ef502b936fc8093b37da424714bef8c8e9ea44aabbb45a89a23ba05 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | dhuang/incubator-airflow | airflow/providers/microsoft/azure/hooks/azure_data_factory.py | Python | apache-2.0 | 27,951 | [
"ADF"
] | 5c26f5ee9756bf9ef18f4e97e2c2cc45b4d9079cc810acdd991ebfac044b5a86 |
#!/usr/bin/env python3
"""The influence of windowing of log. bandlimited sweep signals when using a
Kaiser Window by fixing beta (=2) and fade_out (=0).
fstart = 100 Hz
fstop = 5000 Hz
"""
import sys
sys.path.append('..')
import measurement_chain
import plotting
import calculation
import ir_imitation
impo... | spatialaudio/sweep | log_sweep_kaiser_window_bandlimited_script5/log_sweep_kaiser_window_bandlimited_script5.py | Python | mit | 2,156 | [
"DIRAC"
] | c87453f11017b825ffd5532f6aa24aa1bbc88b571949d28791cf92d5eec3c44b |
"""
Generalized Linear Models with Exponential Dispersion Family
"""
# Author: Christian Lorentzen <lorentzen.ch@googlemail.com>
# some parts and tricks stolen from other sklearn files.
# License: BSD 3 clause
import numbers
import numpy as np
import scipy.optimize
from ...base import BaseEstimator, RegressorMixin
... | shyamalschandra/scikit-learn | sklearn/linear_model/_glm/glm.py | Python | bsd-3-clause | 26,031 | [
"Gaussian"
] | 8ef2628a63395c1bbef29160d555041d032600aaf9dfd9563468b20f4a64774f |
"""Classes of fundamental atomistic concepts
Representations of fundamental atomistic concepts,
such as energy levels, Atoms,...
Uses ASE's Atoms objects.
"""
import numpy as np
import copy as cp
from ase.atoms import Atom, Atoms
class EnergyLevel(object):
"""An energy level"""
def __init__(self, energy, ... | ltalirz/asetk | asetk/atomistic/fundamental.py | Python | mit | 13,510 | [
"ASE",
"Gaussian"
] | f8c3b5d5c78c69f4703a499dc6996672e411edd0e38ac7bab8094fccfb4144e7 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkMultiThreshold(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk... | nagyistoce/devide | modules/vtk_basic/vtkMultiThreshold.py | Python | bsd-3-clause | 498 | [
"VTK"
] | 697f681602debd2edf56ceff907d9d0111b4a302c13b024d7a290fdee652f54e |
from django.utils import timezone
from edc_appointment.models import Appointment
from edc_constants.choices import YES, NOT_APPLICABLE, POS
from edc_constants.constants import FAILED_ELIGIBILITY, LOST_VISIT, IN_PROGRESS, NEW_APPT
from microbiome.apps.mb_maternal.forms import MaternalVisitForm
from microbiome.apps.mb_... | botswana-harvard/microbiome | microbiome/apps/mb_maternal/tests/test_maternal_visit.py | Python | gpl-2.0 | 4,356 | [
"VisIt"
] | 8ebdd66f848b5efba7e36726e749919b9aa844d3728bab1a48f448f96beed03d |
#!/usr/bin/python
import sys
import Tkinter
import timeit
from Tkinter import *
from tkFileDialog import askopenfilename
from copy import deepcopy
class PuzzleGUI(Tkinter.Tk):
"""Main tkinter class for GUI"""
def __init__(self,parent, puzzle):
"""
Initializer for main GUI class
"""
Tkinter.Tk._... | kpandya91/SudokuSolver | SudokuSolver.py | Python | mit | 20,859 | [
"VisIt"
] | 09231cb106c35082506229c7cecdec92c413a4be0183eb23bbefb58583ca7833 |
import matplotlib.pyplot as plt
import seaborn as sb
import os
import os.path as path
import numpy as np
import pandas as pd
import platform
import sys
if (platform.system() == "Linux"):
WORK_PATH = "/local1/xiaoxiaol/work"
else:
WORK_PATH = "/Users/xiaoxiaoliu/work"
p = WORK_PATH + '/src/morphology_analysis... | XiaoxiaoLiu/morphology_analysis | bigneuron/run_consensus_simulation.py | Python | gpl-3.0 | 7,722 | [
"NEURON"
] | 0db1533b98d382e4433f33d02191695e335398930cccada8ff2e650c753b460e |
# $Id: MurckoScaffold.py 3672 2010-06-14 17:10:00Z landrgr1 $
#
# Created by Peter Gedeck, September 2008
#
"""
Generation of Murcko scaffolds from a molecule
"""
from rdkit import Chem
from rdkit.Chem import AllChem
murckoTransforms = [AllChem.ReactionFromSmarts('[*:1]-[!#1;D1]>>[*:1][H]'),
All... | jandom/rdkit | rdkit/Chem/Scaffolds/MurckoScaffold.py | Python | bsd-3-clause | 4,215 | [
"RDKit"
] | 67ef60e199588f9d595d4b6ea1d888a60f2766b4d72d3e59a533fac6359dbe19 |
import numpy as np
from assignment2.cs231n.layers import *
from assignment2.cs231n.layer_utils import affine_relu_forward
from assignment2.cs231n.layer_utils import affine_relu_backward
from assignment2.cs231n.layer_utils import affine_relu_forward_ext
from assignment2.cs231n.layer_utils import affine_relu_backward_ex... | machinelearningnanodegree/stanford-cs231 | solutions/levin/assignment2/cs231n/classifiers/fc_net.py | Python | mit | 18,869 | [
"Gaussian"
] | 038ff4f5505f6b55be2b1380f9e095a57c8f7a8295386698fb7bedade0c7b6d2 |
#!/usr/bin/env/python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | modules/level_set/python/lsutils.py | Python | lgpl-2.1 | 3,295 | [
"MOOSE",
"VTK"
] | 4dec00af939cea520a0aebdafd5dd5e201da21ed8154387bd59f4d40bd8ad6d4 |
import requests
import json
import os
import sys
import re
import traceback
from adsputils import setup_logging
from aip.libs import enforce_schema
logger = setup_logging('solr_adapter')
ARTICLE_TYPES = set(['eprint', 'article', 'inproceedings', 'inbook'])
def get_date_by_datetype(ADS_record):
"""comp... | romanchyla/ADSimportpipeline | aip/libs/solr_adapter.py | Python | gpl-3.0 | 31,796 | [
"Galaxy"
] | 29114e6c67becb1a6c78f483780734015c1c6815d760c1220d410064b195d41d |
# Copyright 2017 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... | hehongliang/tensorflow | tensorflow/python/kernel_tests/signal/spectral_ops_test.py | Python | apache-2.0 | 14,310 | [
"Gaussian"
] | f4a44bd649cbdb044fed70fbe012e73ebf43ae0271070b945ca1db80b1843c7e |
from calendar import month_name, month_abbr
from collections import UserDict
from word2vec import WORD_EMBEDDING_FILE
from nltk.tree import Tree
import sqlite3
import re
import os
import logging
UNKNOWN_TOKEN = 'UNKNOWN'
UNKNOWN_TOKEN_INDX = 0
def tokenize(raw):
if raw.upper() == raw:
return raw
# ... | tinyHui/QuestionAnswering | preprocess/data.py | Python | mit | 16,997 | [
"Octopus"
] | 0e8a0ecbff9248edd450d6cbb76253da7e6316060582ed54b5ae027eb18d7f9a |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | jralls/gramps | gramps/plugins/webreport/contact.py | Python | gpl-2.0 | 5,550 | [
"Brian"
] | 3a4d46d66f42684b5e2d1376a5d223a6f5ea9346668569ade7fa1a3a4b1f5080 |
def parsearguments():
epilog = """============================== Alea jacta est =============================="""
parser = argparse.ArgumentParser(epilog=epilog,formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('INFNAME',help="Path to the SAM/BAM/fastq/fasta file containing the re... | tdido/tstk | tstk/seqfeatfilter.py | Python | mit | 4,592 | [
"pysam"
] | f8afa3610d5e66f6a0c121fd070e5ffda823530045f4ca0a3543524957896e05 |
from collections import defaultdict
import shutil
from defaults import *
from vcf_utils import *
from sv_interval import SVInterval, get_gaps_file, interval_overlaps_interval_list, merge_intervals, merge_intervals_recursively
from pindel_reader import PindelReader
from breakdancer_reader import BreakDancerReader
from ... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/MetaSV-0.5-py2.7.egg/metasv/main.py | Python | apache-2.0 | 17,370 | [
"pysam"
] | d27fcb6fe91a702fe42b5264853c0502b714fcada8b048703b20d5e57953bb85 |
##########################################################################
## # The Coq Proof Assistant / The Coq Development Team ##
## v # Copyright INRIA, CNRS and contributors ##
## <O___,, # (see version control and CREDITS file for authors & dates) ##
## \VV/ #########... | Zimmi48/coq | doc/tools/coqrst/notations/sphinx.py | Python | lgpl-2.1 | 5,858 | [
"VisIt"
] | e2f2eea8ca1c428e02f307e5b62904072bc32cf5f19b32d734b0951c1b2ef3ed |
#!/usr/bin/env python
#-*- coding: utf-8 -*
#
# Copyright (c) 2009 Antonio Barbuzzi <antonio.barbuzzi@gmail.com>,
# Telematics Lab, DEE, Politecnico di Bari, Italy. All rights reserved.
#
#
# This file is part of DeSRTO.
#
# DeSRTO is free software: you can redistribute it and/or modify
# it under the terms ... | antoniobarbuzzi/desrto | iptool.py | Python | gpl-2.0 | 9,587 | [
"VisIt"
] | cec94055816c9a5b158b2a3c781ed5fa872682bf18208563e1b404ee3e2c7dee |
from edc_constants.constants import (
NOT_APPLICABLE, UNKNOWN, OTHER, UNSCHEDULED, SCHEDULED, MISSED_VISIT, LOST_VISIT,
OFF_STUDY, ON_STUDY, COMPLETED_PROTOCOL_VISIT, FAILED_ELIGIBILITY, PARTICIPANT)
from .constants import NO_MODIFICATIONS, START, BREASTFEED_ONLY, DISCONTINUED, NEVER_STARTED
STUDY_SITES = (
... | botswana-harvard/microbiome | microbiome/apps/mb/choices.py | Python | gpl-2.0 | 29,452 | [
"VisIt"
] | 027be9e1d646a722f72a3af51341ef18d2ff2c042103dc13384b8e7f6f38e4f7 |
#!/usr/bin/env python
# CREATED:2013-08-22 12:20:01 by Brian McFee <brm2132@columbia.edu>
'''Music segmentation using timbre, pitch, repetition and time.
If run as a program, usage is:
./segmenter.py AUDIO.mp3 OUTPUT.lab
'''
import sys
import os
import argparse
import string
import numpy as np
import scipy.sp... | wangsix/cluster | cluster/segmenter.py | Python | gpl-3.0 | 20,128 | [
"Brian",
"Gaussian"
] | 3ba9e37aa1e0ab71111d1e868edbbdb96ae95519f272815dfba3bf209d807440 |
#!/usr/bin/env python
#import genetic
import GEN
import os
import sys
def gaussian(x, mu, sig):
import numpy as np
return np.exp(-np.power((x - mu)/sig, 2.) / 2.)
class GENBeam(genetic.GEN):
"Custom Generation Class: overload Fitness evaluation"
def evalFit(self,ind):
fit = 1.
fit *= gaussianind.getall()[0],... | iljabek/genetic | beam.py | Python | gpl-2.0 | 8,646 | [
"Gaussian"
] | c45ada33ac9eb3867c69ce48110fcbfd4d8d3b008096337dc798acc2518e9496 |
#* 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
im... | nuclear-wizard/moose | python/MooseDocs/extensions/gallery.py | Python | lgpl-2.1 | 8,104 | [
"MOOSE"
] | a4343e9d34b7489283c8545a49a558aeb71f752630d83f129643867263f4a32a |
from __future__ import division # needed for 1/2 = 0.5
import numpy as np
from scipy.misc import *
#from scipy.linalg import *
from scipy import linalg
from sympy.parsing.sympy_parser import parse_expr
from sympy import *
import math
import random
import matplotlib.pyplot as plt
#printing.init_printing(use_latex='math... | OscarES/lie | lie.py | Python | lgpl-3.0 | 18,957 | [
"Gaussian"
] | e239ab3127a263920229e4aceb0f36fc8d676236315c9744c44166334234b580 |
import pytest
from ansible.playbook.play_context import PlayContext
from openshift_health_check import ActionModule, resolve_checks
from openshift_health_check import copy_remote_file_to_dir, write_result_to_output_dir, write_to_output_file
from openshift_checks import OpenShiftCheckException, FileToSave
def fake_c... | ewolinetz/openshift-ansible | roles/openshift_health_checker/test/action_plugin_test.py | Python | apache-2.0 | 12,455 | [
"VisIt"
] | 7d821eeaee27aceaca1aafbe40003a71faf9642469a6716ab7348db8834a837a |
#!/usr/bin/python
# LICENSE: GPL2
# (c) 2015 Kamil Wartanowicz
import os
import logging
import plac
import traceback
import sim_router
import file_parser
import sim_codes
import sim_reader
import sim_backup
from util import hextools
from util import types
from util import types_g
def setupLogger():
logger = log... | kamwar/simLAB | sim/sim_shell.py | Python | gpl-2.0 | 53,411 | [
"ADF"
] | 96ddcbd64648af62dc027c9a64a32243ce1f5719e902af53cee735f921bcc9a1 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
# test_attributes.py
"""
Test the population and group functions.
"""
import numpy as np
import pytest
import nngt
def test_groups():
ids = [i for i in range(10)]
g1 = nngt.NeuralGroup(ids, neuron_type=None)
assert ids == g1.ids
assert len(ids) == len(g... | Silmathoron/NNGT | testing/test_group_pop.py | Python | gpl-3.0 | 4,047 | [
"NEURON"
] | 1c71b8f4812e5783aaa9348ec8f29cad22e14fd3e719f4e453cc3d6bc93c1724 |
#!/usr/bin/env python
# encoding: utf-8
# Thomas Nagy, 2010-2016 (ita)
"""
Classes and functions required for waf commands
"""
import os, re, imp, sys
from waflib import Utils, Errors, Logs
import waflib.Node
# the following 3 constants are updated on each new release (do not touch)
HEXVERSION=0x1081200
"""Constant ... | zhumingliang1209/Ardupilot | ardupilot/modules/waf/waflib/Context.py | Python | gpl-3.0 | 19,546 | [
"VisIt"
] | 4b487d5c5cc918c4ef26820d52e50ac6f73d119993d957f0ac3cbb72b7cd3950 |
########################################################################
# File : CSGlobals.py
# Author : Ricardo Graciani
########################################################################
"""
Some Helper functions to retrieve common location from the CS
"""
from __future__ import absolute_import
from __futu... | yujikato/DIRAC | src/DIRAC/ConfigurationSystem/Client/Helpers/CSGlobals.py | Python | gpl-3.0 | 2,914 | [
"DIRAC"
] | 3e0a3183cc21dc9ea6e08aad62fb03660faee3e5e0d01e75987d5861b078f8c7 |
#!/usr/bin/env ipython
from pylab import *
import numpy as np
from scipy.io.netcdf import netcdf_file
MCwant = '2'
nbefore = 2
nafter = 4
WangFlag = 'NaN'
fgap = 0.2
v_lo = 550.0 #550.0 #450.0 #100.0
v_hi = 3000.0 #3000.0 #550.0 #450.0
prexShift = 'wShiftCorr'
DIR_FIGS = '.... | jimsrc/seatos | mcs/src/histo.py | Python | mit | 2,345 | [
"NetCDF"
] | 83cf82fec5dd0445d32638b84a3442954f36788a6e5d27537bd637dd7f5de02e |
#!/usr/bin/env python
"""
Project-wide application configuration.
DO NOT STORE SECRETS, PASSWORDS, ETC. IN THIS FILE.
They will be exposed to users. Use environment variables instead.
See get_secrets() below for a fast way to access them.
"""
import os
"""
NAMES
"""
# Project name used for display
PROJECT_NAME = 't... | dannydb/tumblr-blog | app_config.py | Python | mit | 4,125 | [
"Brian"
] | eafc55bdbc571809c4eef95d452bf3f0156f5f3bb57588c252acfacf4531c435 |
import sys
import os
from PyQt5 import QtCore, QtWidgets
import vtk
from vtk.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
import chigger
import mooseutils
from ExodusPlugin import ExodusPlugin
class RetinaQVTKRenderWindowInteractor(QVTKRenderWindowInteractor):
"""
Currently VTK7.1 and Qt5 do... | yipenggao/moose | python/peacock/ExodusViewer/plugins/VTKWindowPlugin.py | Python | lgpl-2.1 | 16,177 | [
"VTK"
] | 83dfd03d8a06cc6751a82d6b3b37e30bc672f8e322eb6adf130acf0edea24b54 |
"""
Course Outline page in Studio.
"""
import datetime
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise
from selenium.webdriver.support.ui import Select
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.common.action_chains import ActionChains
from .course_p... | martynovp/edx-platform | common/test/acceptance/pages/studio/overview.py | Python | agpl-3.0 | 26,276 | [
"VisIt"
] | 98e3014e2e1b7a079491cf9ce48fd7b84490e0f3fd72996ae2f0891f2b274038 |
########################################################################
# $HeadURL$
########################################################################
""" DIRAC FileCatalog mix-in class to manage directory metadata
"""
__RCSID__ = "$Id$"
import os, types
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Dat... | avedaee/DIRAC | DataManagementSystem/DB/FileCatalogComponents/DirectoryMetadata.py | Python | gpl-3.0 | 31,266 | [
"DIRAC"
] | 17bc158eaa605bf1296a9a6502d4219f022a7f33c0d082c45c0120190ebf28db |
import numpy
from chainer import cuda
from chainer import function
from chainer.utils import type_check
class Gaussian(function.Function):
"""Gaussian sampling function.
In forward calculation, this funciton takes mean and logarithm of variance
as inputs, and draw a sample from a gaussian distribution.... | sou81821/chainer | chainer/functions/noise/gaussian.py | Python | mit | 2,139 | [
"Gaussian"
] | 587331957a3bd87969a3e1ad95b3de0d3350aa83cfb2d6f6900cdb1b0a91d1ca |
# -*- coding: utf-8 -*-
'''
This module (mostly) uses the XenAPI to manage Xen virtual machines.
Big fat warning: the XenAPI used in this file is the one bundled with
Xen Source, NOT XenServer nor Xen Cloud Platform. As a matter of fact it
*will* fail under those platforms. From what I've read, little work is needed
t... | stephane-martin/salt-debian-packaging | salt-2016.3.2/salt/modules/xapi.py | Python | apache-2.0 | 26,061 | [
"VMD"
] | 8ffbce50e68b499d7a97f55cda97721402f53e791cbc856916aa338995e1460f |
# !/usr/local/bin/python3.4.2
# ----Copyright (c) 2016 Carnegie Hall | The MIT License (MIT)----
# ----For the full license terms, please visit https://github.com/CarnegieHall/quality-control/blob/master/LICENSE----
# run script with 5 arguments:
# argument 0 is the script name
# argument 1 is the path to the Isilon HD... | CarnegieHall/metadata-matching | idMatching_windowcards.py | Python | mit | 5,765 | [
"VisIt"
] | 00e12e9b88c856a60253bf2ecb0ef15a9cae0d9c1cb2fdf2a62c7ca7894d0e9c |
#!/usr/bin/env python
from scitools.FunctionSelector import *
#from math import sqrt, pi
from scitools.numpyutils import *
import sys
sys.path.insert(0, os.path.join(os.environ['scripting'], 'src',
'py', 'examples', 'pde'))
from wave1D_class import WaveEq2, SolverWithViz
from Tkinter im... | sniemi/SamPy | sandbox/src1/TCSE3-3rd-examples/src/py/examples/pde/wave1D_GUI.py | Python | bsd-2-clause | 12,362 | [
"Gaussian"
] | d579581660b90be658fd759eb7fc80802faf6015b4fdd0ed3bce0190e4dba49e |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | espressomd/espresso | testsuite/scripts/tutorials/test_polymers.py | Python | gpl-3.0 | 2,487 | [
"ESPResSo"
] | d72b790503ee7b39114bda7cb48d78c4b901419699b6908bfd3d3804e7d1521e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# (c) Copyright 2003-2007 Hewlett-Packard Development Company, L.P.
#
# 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 Lice... | matrumz/RPi_Custom_Files | Printing/hplip-3.15.2/base/status.py | Python | gpl-2.0 | 70,914 | [
"ADF"
] | 46bbf77ab43f22a4fbd667d8a1ad1c624ea97501807124fffdccbb9acd9c5df3 |
from .base import *
from .commands import *
from .command import *
from .cybrowser import *
from .session import *
from .network import *
from .node import *
from .vizmap import *
from .diffusion import *
from .idmapper import *
from .edge import *
from .group import *
from .view import *
from .layout import *
from .ta... | idekerlab/py2cytoscape | py2cytoscape/cyrest/cyrest.py | Python | mit | 4,590 | [
"Cytoscape"
] | 585b1df8282c624d9bc95ead6d6634ac981038f311ff7cfab443bdf1a243b4a9 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ===========================================================================
# eXe
# Copyright 2012, Pedro Peña Pérez, Open Phoenix IT
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published b... | UstadMobile/exelearning-extjs5-mirror | exe/jsui/mainpage.py | Python | gpl-2.0 | 56,312 | [
"VisIt"
] | 382f5cbeba3ecb945b9c8aa381e18fb24c182641275aa26cb6a984892be71a4f |
__docformat__ = "restructuredtext en"
import mdp
from ica_nodes import ICANode
numx, numx_rand, numx_linalg = mdp.numx, mdp.numx_rand, mdp.numx_linalg
mult = mdp.utils.mult
class JADENode(ICANode):
"""
Perform Independent Component Analysis using the JADE algorithm.
Note that JADE is a batch-algorithm. T... | ME-ICA/me-ica | meica.libs/mdp/nodes/jade.py | Python | lgpl-2.1 | 8,744 | [
"Gaussian"
] | b7b6256363952e33e2a10775ee4c3a0492ac07378f6c6f766ae33e573d29f19b |
from argparse import RawTextHelpFormatter
import datetime
import glob
import os
import zipfile
from lxml import html
import requests
from tqdm import tqdm
from django.conf import settings
from django.core.management import BaseCommand
from openprescribing.utils import mkdir_p
class Command(BaseCommand):
help =... | annapowellsmith/openpresc | openprescribing/pipeline/management/commands/fetch_bnf_codes.py | Python | mit | 3,537 | [
"VisIt"
] | 5433b267a5c267627f43544cd598b2be9cb39b2f153708e310fe2f1b7d518635 |
# pause.py
# Aaron Taylor
# Moose Abumeeiz
#
# The pause menu takes over the game and displays the
# players current stats and seed.
#
from pygame import *
from math import *
from const import *
from func import *
def pause(screen, seed, textures, fonts, stats):
running = True
arrowpoint = 0
pausecard = textures... | ExPHAT/binding-of-isaac | pause.py | Python | mit | 2,186 | [
"MOOSE"
] | 952295d5cf4bc32862c39ee07f795ea7d73d5823bc07bfc5b9ed3f0af15ab5a4 |
import numpy as np
from sklearn.cluster import affinity_propagation
from sklearn.covariance import GraphicalLasso
from sklearn.mixture import GaussianMixture
from sklearn.neighbors import KernelDensity
from sklearn.utils.validation import check_is_fitted
from .base import BaseOutlierDetector
from ..plotting import plo... | Y-oHr-N/kenchi | kenchi/outlier_detection/statistical.py | Python | bsd-3-clause | 20,643 | [
"Gaussian"
] | 1bcf548104b208fcffa767c47d05b5a58fe1a3d4d3ac74a7e60b8fc94743bd70 |
#!/usr/bin/env python3.2
import argparse
import os
import sys
import bioannotation
import biocodeutils
import biothings
## constants
DEFAULT_PRODUCT_NAME = "hypothetical protein"
def main():
parser = argparse.ArgumentParser( description='Parses multiple sources of evidence to generate a consensus functional anno... | google-code/biocode | sandbox/jorvis/parse_ergatis_euk_functional_pipeline.py | Python | gpl-3.0 | 4,400 | [
"BLAST"
] | 544614618ebd0ac888263fe3bf7ccc380f970bd2f8edfa0c1ac5d078389ae28f |
from __future__ import print_function
import argparse
import operator
import json
import os
import sys
import shutil
import subprocess
#Parameters
# python tractographyScriptApp.py neo-0188-1-4years neo-0188-1-4year_42_DWI_QCed_VC_up1mm.nrrd
# neo-0188-1-4year-T1_SkullStripped_scaled_DWISpace_up1mm.nrrd DWI_Spac... | NIRALUser/CIVILITY | src/civility-tractography/scripts/tractographyScriptapp.py | Python | apache-2.0 | 17,621 | [
"VTK"
] | 213a17e13ce7a515ff584fa63ad7d805d2617ed543763674af22b4861bb37a1e |
"""module for performing common calculations
(c) 2007-2011 Matt Hilton
(c) 2013-2014 Matt Hilton & Steven Boada
U{http://astlib.sourceforge.net}
The focus in this module is at present on calculations of distances in a given
cosmology. The parameters for the cosmological model are set using the
variables OMEGA_M0, O... | boada/astLib | astLib/vec_astCalc.py | Python | lgpl-2.1 | 15,409 | [
"Galaxy"
] | 0d8da6dbbd1b7ed311e012e4f43da501705adc56afe14f6dbb1921f89df980ce |
#!/usr/bin/env python
#---------------- EDIT JOB NAME -------------------
#$ -N den1IFCg0
#--------------------------------------------------
#$ -S /usr/bin/python
#$ -v PYTHONPATH=/home/oliver/Library/python-lib
#$ -v LD_LIBRARY_PATH=/opt/intel/cmkl/8.0/lib/32:/opt/intel/itc60/slib:/opt/intel/ipp41/ia32_itanium/shared... | iwelland/hop | doc/examples/fulldensity_gsbp.py | Python | lgpl-3.0 | 3,284 | [
"VMD"
] | b172b49a877bbcf9e122f7296bf463a0a04a27a1f7f9d0e272fe823fe0a98100 |
from __future__ import print_function
import numpy as np
def moments(Xax, data, vheight=True, estimator=np.mean, negamp=None,
veryverbose=False, nsigcut=None, noise_estimate=None, **kwargs):
"""
Returns the gaussian parameters of a 1D distribution by calculating its
moments. Depending on the ... | low-sky/pyspeckit | pyspeckit/spectrum/moments.py | Python | mit | 4,902 | [
"Gaussian"
] | 1210f255482a257f4b1a2c0aa020440a81687418f3c44a8bebeedbd553ca44ee |
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