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"""
SOM and NoveltySOM classes
$Id;$
"""
from Numeric import *
from plastk.vq import VQ
from plastk.base import BaseObject
from plastk.utils import norm,inf,gaussian,decay
from plastk.params import Number,Magnitude,PositiveInt,NonNegativeInt
import plastk.rand
class SOM(VQ):
dim = NonNegativeInt(default=2)
... | ronaldahmed/robot-navigation | neural-navigation-with-lstm/MARCO/plastk/vq/som.py | Python | mit | 7,348 | [
"Gaussian"
] | 5d2bb9738db146c060d06e7039754b567a1992bc2bc0d48be876201ab24b69b3 |
"""
====================================================================
Linear and Quadratic Discriminant Analysis with confidence ellipsoid
====================================================================
Plot the confidence ellipsoids of each class and decision boundary
"""
print(__doc__)
from scipy import lin... | RPGOne/Skynet | scikit-learn-c604ac39ad0e5b066d964df3e8f31ba7ebda1e0e/examples/classification/plot_lda_qda.py | Python | bsd-3-clause | 4,794 | [
"Gaussian"
] | 10a728c0ee774fc35208d99981c0b172995dc9d0fa50d00289de3e1c9bdf68b7 |
# -*- coding: utf-8 -*-
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.go... | invesalius/invesalius3 | invesalius/data/viewer_volume.py | Python | gpl-2.0 | 84,093 | [
"VTK"
] | 62ac2bb5c0e004240cfdd13d663d51ebb11df9892392b146dfa0e7f5fe98a0d1 |
__author__ = 'Christoph Heindl'
__copyright__ = 'Copyright 2017, Profactor GmbH'
__license__ = 'BSD'
import glob
import os
import numpy as np
import matplotlib.pyplot as plt
from sensor_correction.utils import sensor_unproject
from sensor_correction.gp_cpu import GPRegressor
def select_data(temps, poses, all_depths_... | cheind/rgbd-correction | sensor_correction/apps/train.py | Python | bsd-3-clause | 3,582 | [
"Gaussian"
] | 1d16a9232c167fb37fab599f2c201f07e56a9d17cdfa7a8cadc718e99429d943 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | dreamfields/dreamfields/augment.py | Python | apache-2.0 | 4,860 | [
"Gaussian"
] | 26c842e3d3c558fbf00a3751242f015b4200e7f9f2cfd5c3af96609be1bead4a |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/conf/urls.py | Python | gpl-3.0 | 2,677 | [
"Brian"
] | 66bd49beef5605e2e7103d85c2133ea4d8430436e569affe7e3c6a00290f2a0f |
### Example for using CATMAID Frontend to retrieve a neuron's skeleton
### including the synaptic connectors
import urllib, json
import http.cookiejar as cj
from catmaid_frontend import *
remote_instance = None
#Provide Credentials for CATMAID Server
http_user = ''
http_pw = ''
catmaid_user = ''
catmaid_pw = ''
#S... | catsop/CATMAID | scripts/remote/example.py | Python | gpl-3.0 | 1,242 | [
"NEURON"
] | 446a36cd3156ba0c670242bcc7bee406ed4b5d6aed76417d76c67ca691772fbe |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either vers... | marscher/PyEMMA | pyemma/coordinates/data/featurization/misc.py | Python | lgpl-3.0 | 13,896 | [
"MDTraj"
] | bd9432108b1ad4c584de92a21022c72e60c70f82f8194606d0106c6cfea838c6 |
import textwrap
import csv
import argparse
from collections import defaultdict
import sys
from jinja2 import Environment, FileSystemLoader
import os
import consts
encoding = sys.getfilesystemencoding()
EXEC_DIR = os.path.dirname(unicode(__file__, encoding))
def save_or_print_json(json_str, outdir, json_name):
i... | Duke-GCB/GGR-cwl | draft-3/json-generator/run.py | Python | mit | 15,031 | [
"Bowtie"
] | 059b2b25be234f3e0795466f273961ac0bf265aa57e733050c904445988ad986 |
from __future__ import print_function
import math
import simtk.unit as units
from intermol.exceptions import (UnimplementedFunctional, UnsupportedFunctional,
UnimplementedSetting, UnsupportedSetting,
GromacsError, InterMolError)
def convert_nothing(x... | ctk3b/InterMol | intermol/forces/convert_dihedrals.py | Python | mit | 6,907 | [
"Gromacs"
] | cfcb848b49e9f4aadd355279de05b53683bc1c128ce67c0c1c82f996e2cbd355 |
# 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... | ghchinoy/tensorflow | tensorflow/contrib/bayesflow/python/kernel_tests/monte_carlo_test.py | Python | apache-2.0 | 10,209 | [
"Gaussian"
] | 61abd14222218af36847f72525e5b509e2215b589e78420a72922f20e725c8dd |
#
# Copyright 2016 The BigDL 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 or agreed to in ... | intel-analytics/BigDL | python/orca/test/bigdl/orca/torch/test_torch.py | Python | apache-2.0 | 8,381 | [
"ORCA"
] | e03c989e5d247fb50bf53a6ffa5d6fd4a7a23d72f8bc7300e5b60b6b48eb2df4 |
# Copyright (c) 2016-2021, The Bifrost Authors. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditi... | ledatelescope/bifrost | python/bifrost/pipeline.py | Python | bsd-3-clause | 34,609 | [
"GULP"
] | 099adae1282ede96c99c516d1759a19ef22427e5c2e297209fd3d16bda67bc2b |
#!/usr/bin/python
import os, sys
#specify the location of ncs.py in ncs_lib_path
ncs_lib_path = ('../../../../')
sys.path.append(ncs_lib_path)
import ncs
def run(argv):
sim = ncs.Simulation()
regular_spiking_parameters = sim.addNeuron("regular_spiking","izhikevich",
{
"a": 0.02,
"b": 0.2,
... | BrainComputationLab/ncs | python/samples/models/izh/regular_spiking_izh.py | Python | bsd-2-clause | 938 | [
"NEURON"
] | 5d3153bf7ebcd76e79195a3fc1bf8c3171c2d50fe2a3d6234060b5585e6ecdc6 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes to generate point defect structures
"""
import logging
from abc import ABCMeta, abstractmethod
from monty.json import MSONable
from pymatgen.analysis.bond_valence import BVAnalyzer
from pymat... | materialsproject/pymatgen | pymatgen/analysis/defects/generators.py | Python | mit | 10,954 | [
"pymatgen"
] | 71574349cc386206b37e2fba01e734c4d8f65242a7a09cfb2c29e435c959d292 |
from __future__ import print_function
from __future__ import division
from builtins import str
from builtins import range
from past.utils import old_div
import numpy as np
from boututils import file_import
from mayavi import mlab
from tvtk.tools import visual
def zinterp( v, zind):
#v = REFORM(v)
nz = np.size(v)... | kevinpetersavage/BOUT-dev | tools/pylib/boututils/plotpolslice.py | Python | gpl-3.0 | 3,616 | [
"Mayavi"
] | 3f2042dbdef4b1aa3dbfb113c1fbf779e70517fcc03f4df42d450332c003cb99 |
# -*- coding: utf-8 -*-
"""
Definition of a hierarchy of classes for kernel functions to be used
in convolution, e.g., for data smoothing (low pass filtering) or
firing rate estimation.
Symmetric kernels
*****************
.. autosummary::
:toctree: _toctree/kernels/
RectangularKernel
TriangularKernel
... | INM-6/elephant | elephant/kernels.py | Python | bsd-3-clause | 29,017 | [
"Gaussian"
] | 9a2f45d19e90651a05be0b8f0526428d09b399eb29fbca524e004ec91e801b80 |
# -*- coding: utf-8 -*-
"""
Output Plugin for Ogg Vorbis Encoder (OggEnc).
Copyright (c) 2006-2008 by Nyaochi
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... | rinrinne/cueproc-alternative | src/ce_oggenc.py | Python | gpl-2.0 | 3,528 | [
"VisIt"
] | 43f9aadb5b284e8ae79507d41cfde6c9bd9bda965875699fb88555b6dd8f01eb |
import logging
logger = logging.getLogger(__name__)
from os import path , mkdir, listdir
import ocgis
def get_equation(culture_type='fallow', climate_type=2):
"""
returns the equation as basis to calculate the segetal flora
:param culture_type: Type of culture. Possible values are
'fallo... | KatiRG/flyingpigeon | flyingpigeon/segetalflora.py | Python | apache-2.0 | 10,121 | [
"NetCDF"
] | 49f0597c00d512be95507025a69d65c750ddd3f9daff8dde72c58cb229a42716 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
import time
m = 200
n = 400
numLambdas = 5
st... | justusc/Elemental | examples/interface/DSDense.py | Python | bsd-3-clause | 1,721 | [
"Gaussian"
] | 00f8e57a156c344479a18315aac73742ed0b28fbcc03397353fc9c290d01edac |
from __future__ import division
from numpy import arange, array, linspace, ones, zeros
from scipy.linalg import solve_banded
import interp as _spline
def cal_coefs(a, b, y, c=None, alpha=0, beta=0):
'''
Return spline coefficients
Parameters
----------
a : float
lower bound of the grid.
... | mjvakili/supermean | code/inter.py | Python | mit | 5,097 | [
"Mayavi"
] | 70d20984996d34045b70edc527f20016d55114a5614ed5bf5cd5d615dd881af8 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009-2010 Andrew I Baznikin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Ge... | arunkgupta/gramps | gramps/plugins/rel/rel_ru.py | Python | gpl-2.0 | 17,584 | [
"Brian"
] | 3a983174a1d3f5726157cae0f6353033ed281f6226a872fce68a671e12e7b132 |
## Antonio Díaz Pozuelo - IA - PEC2 - adpozuelo@uoc.edu
## Python 3.6
import csv
import numpy as np
from sklearn.decomposition import PCA
import matplotlib.pyplot as plt
from sklearn import manifold
from sklearn.neighbors import KNeighborsClassifier
from sklearn.svm import SVC
from sklearn.tree import DecisionTreeClas... | adpozuelo/Master | IAA/PEC2/adpozuelo_IA_PEC2.py | Python | gpl-3.0 | 11,393 | [
"Gaussian"
] | a60f56481c7f510f19d5ef7bb2c6b846565b4d3e5b036bbf1efe90382f104f5f |
# Copyright (C) 2010-2019 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 v... | espressomd/espresso | testsuite/python/analyze_chains.py | Python | gpl-3.0 | 5,703 | [
"ESPResSo"
] | a80eec897c8240cff6169930edbaa9bccc0917ebe8f4a2b74d96a79259e45e33 |
########################################################################
# File : SSHComputingElement.py
# Author : Dumitru Laurentiu
########################################################################
""" SSH (Virtual) Computing Element: For a given list of ip/cores pair it will send jobs
directly through ... | DIRACGrid/DIRAC | src/DIRAC/Resources/Computing/SSHBatchComputingElement.py | Python | gpl-3.0 | 8,533 | [
"DIRAC"
] | f497b252f22699e4a8bfb952c1dcc5e58270ac81e79825b33513765acecaa7d0 |
# 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/Scaled_Features/best_kNN_PCA/objects/test11_cross_validate_objects_1200ms_scaled_method_iii.py | Python | mit | 4,917 | [
"Mayavi"
] | 9d79e6c4e9b1896d4977cf5a7f3f1b7897d3f10843901cd84985a07296d18db4 |
"""
usage: scramble.py [egg_name]
With no arguments, scrambles all eggs necessary according to the
settings in universe_wsgi.ini.
egg_name - Scramble only this egg (as defined in eggs.ini) or 'all'
for all eggs (even those not required by your settings).
"""
import os, sys, logging
root = logging.getLogg... | dbcls/dbcls-galaxy | scripts/scramble.py | Python | mit | 1,037 | [
"Galaxy"
] | f0fdbaf2feeb6a12c75979dc4b34784d9d0ad27a37dfb52f000747e8472e4193 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2009 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 | stoqlib/gui/editors/saleeditor.py | Python | gpl-2.0 | 14,541 | [
"VisIt"
] | 79d35c4caf0531038068d7e85a4a30e43d97153247150b1ffe7aec59705d8a96 |
"""Copyright 2012 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.8'
__date__ = 'May 17 2010'
import threading
from ctypes ... | danielsuo/mobot | src/move/PhidgetsPython/Phidgets/Devices/AdvancedServo.py | Python | mit | 31,175 | [
"VisIt"
] | 4ab3f21105a59ca62009e77123e2db0abf927b10c550cec9b645b78491668b13 |
class Node(object):
def __init__(self, value):
self._value = int(value)
self._connections = set()
@property
def value(self):
return self._value
def __int__(self):
return self.value
def __float__(self):
return float(self.value)
def connect(self, *nodes)... | satyrius/traversal | traversal.py | Python | mit | 1,311 | [
"VisIt"
] | e0c45724730ece7ebd1f2bb6101c159f3156e83ea83888ccc18384db0d232fda |
#-------------------------------------------------------------------------------
# . File : MopacInputFile.py
# . Program : MolarisTools
# . Copyright : USC, Mikolaj Feliks (2015-2018)
# . License : GNU GPL v3.0 (http://www.gnu.org/licenses/gpl-3.0.en.html)
#----------------------------------------------... | mfx9/MolarisTools | MolarisTools/Parser/MopacInputFile.py | Python | gpl-3.0 | 3,870 | [
"MOPAC"
] | 1014c65371df41ef91fc298d280f28046ca92a9a0a10a59b9fb3a495b71828a7 |
#!/usr/bin/env python
__author__ = 'Danelel Cline'
__copyright__ = '2016'
__license__ = 'GPL v3'
__contact__ = 'dcline at mbari.org'
__doc__ = '''
Creates interpolated netCDF files for all LRAUV data; engineering and science data
@var __date__: Date of last svn commit
@undocumented: __doc__ parser
@status: pr... | danellecline/stoqs | stoqs/loaders/CANON/toNetCDF/makeLRAUVNetCDFs.py | Python | gpl-3.0 | 11,209 | [
"NetCDF"
] | 5593930bae44718ef86a7d3338e843cc1b600eb4919ab04ac54d746d365836f3 |
from ANNarchy import *
from ANNarchy.extensions.image import *
from ANNarchy.extensions.convolution import Convolution, Pooling
# Definition of the neurons
Linear = Neuron(equations="r=sum(exc): min=0.0")
DNF = Neuron(parameters="tau=10.0", equations="tau*dr/dt + r = sum(exc) + sum(inh): min=0.0, max=1.0")
# Popula... | vitay/ANNarchy | examples/image/Webcam.py | Python | gpl-2.0 | 2,959 | [
"NEURON"
] | 59f4787819fa94892331e85a28ea7ab003e48a298f8b0a6fb1952fccd95dccff |
#!/usr/bin/env python3
# Use the astroalign module to align and stack a series of astro images.
# Suggested Workflow;
# If starting with raw images, process them in darktable:
# - darktable *.cr2 (probably including your dark frame,
# though this script doesn'tsubtract dark frames yet)
# or if that doesn't work (... | akkana/scripts | astro/starstack.py | Python | gpl-2.0 | 18,652 | [
"Gaussian"
] | 121ccb4c327efc0ed49ecccaa6b44e8f7ffb96ce54bc518fc6de47d701fa2db2 |
import discord
from discord.ext import commands
import aiohttp
from bs4 import BeautifulSoup
import random
class Nsfw:
"""Nsfw commands."""
def __init__(self, bot):
self.bot = bot
@commands.group(pass_context=True)
async def nsfw(self, ctx):
"""Nsfw commands."""
... | FishyFing/FishBot | cogs/nsfw.py | Python | gpl-3.0 | 7,068 | [
"MOE"
] | 0cd5fe54d22972e40c7073a7530c74a337b602e443b601d1d4251e3865be5049 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
SO-ECP Integrals
'''
import numpy
from pyscf import gto, lib
mol = gto.M(
verbose = 0,
atom = 'C 0 0 0; O 0 0 1.5',
basis = {'C': 'crenbl', 'O': 'ccpvdz'},
ecp = {'C': 'crenbl'}
)
#
# SO-ECP integrals in real spherical Gaussia... | gkc1000/pyscf | examples/gto/20-soc_ecp.py | Python | apache-2.0 | 1,010 | [
"Gaussian",
"PySCF"
] | c1e0916bcff99fa3771d376ddd72416b38e056c2ad1fd35f948cfba30fdf5a67 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Copyright (C) 2012 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at yo... | LFPy/LFPy | LFPy/test/test_cell.py | Python | gpl-3.0 | 73,160 | [
"NEURON"
] | d1abc3e773a304d11da1dd099a0ba3eee51f2c99f9d6de57efee1ccef83af3a5 |
#
# Copyright (C) 2010-2019 The ESPResSo project
# Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
# Max-Planck-Institute for Polymer Research, Theory Group
#
# 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... | KaiSzuttor/espresso | doc/tutorials/02-charged_system/scripts/nacl_units.py | Python | gpl-3.0 | 5,879 | [
"ESPResSo"
] | 5cf44b965372cc6c39ab11e8378f94072d2c754e87f537d4712a7377e100318f |
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under th... | hammerlab/isovar | isovar/dna.py | Python | apache-2.0 | 1,476 | [
"Biopython"
] | 5784109b7ffb2c4d9e62773193140cd33de98056002d23b2db11eb7baf5fa3be |
import PythonQt
from PythonQt import QtCore, QtGui, QtUiTools
from director import objectmodel as om
from director import visualization as vis
from director import transformUtils
from director import vtkAll as vtk
from director import cameracontrol
from director import propertyset
from director import pointpicker
impo... | RobotLocomotion/director | src/python/director/cameracontrolpanel.py | Python | bsd-3-clause | 5,855 | [
"VTK"
] | 3550ddcce44cb8981258d4a270e055745d8ba20184d5aa38c4d14a57f20bee3a |
# Filename: cider.py
#
# Description: Describes the class to compute the CIDEr (Consensus-Based Image Description Evaluation) Metric
# by Vedantam, Zitnick, and Parikh (http://arxiv.org/abs/1411.5726)
#
# Creation Date: Sun Feb 8 14:16:54 2015
#
# Authors: Ramakrishna Vedantam <vrama91@vt.edu> and Tsung... | cesc-park/attend2u | utils/pycocoevalcap/cider/cider.py | Python | mit | 1,670 | [
"Gaussian"
] | 544562f4f8aa79bd2c7bad30bd5c875a6aa7e5ca64f0956cf12f734d2a212c11 |
#!/usr/bin/env python
# File created on 05 Oct 2009.
from __future__ import division
from os.path import split, basename, abspath, exists, join
from subprocess import PIPE, Popen
from skbio.util import remove_files
from burrito.parameters import ValuedParameter
from burrito.util import (which, CommandLineApplicatio... | ssorgatem/qiime | qiime/identify_chimeric_seqs.py | Python | gpl-2.0 | 46,969 | [
"BLAST",
"Brian"
] | dff18ed521a9671c8078ae3dfacdc09d324c641a56de15f70f5eeb615031caca |
# Made by Mr. Have fun! Version 0.2
# Shadow Weapon Coupons contributed by BiTi for the Official L2J Datapack Project
# Visit http://forum.l2jdp.com for more details
import sys
from com.l2scoria.gameserver.model.quest import State
from com.l2scoria.gameserver.model.quest import QuestState
from com.l2scoria.gameserver.m... | zenn1989/scoria-interlude | L2Jscoria-Game/data/scripts/quests/417_PathToScavenger/__init__.py | Python | gpl-3.0 | 15,562 | [
"VisIt"
] | 71b72de68627dfb846d08131dd1d113954014e2233ada8fa9960b962615d3c97 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the main LMS Dashboard (aka, Student Dashboard).
"""
import datetime
from nose.plugins.attrib import attr
from ..helpers import UniqueCourseTest
from ...fixtures.course import CourseFixture
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.dashboard impo... | antoviaque/edx-platform | common/test/acceptance/tests/lms/test_lms_dashboard.py | Python | agpl-3.0 | 10,222 | [
"VisIt"
] | f59a43a5b86395cb9cb2d9ff4e5a924a076a821c607eb8f9ddadafa026ed0454 |
#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import srwl_uti_smp
def set_optics(v=None):
el = []
pp = []
names = ['M1', 'M1_Grating', 'Grating', 'GA', 'GA_M3A', 'M3A', 'M3', 'M3_SSA', 'SSA', 'SSA_KBAp... | mrakitin/sirepo | tests/template/srw_generate_data/nsls-ii-esm-beamline.py | Python | apache-2.0 | 33,095 | [
"Gaussian"
] | dc7e71db6c4ea081691849f33fced8ca0bd30c2d953ffac40fe40698acebece8 |
#!/usr/bin/env python3
# Copyright (C) 2015-2017(H)
# Max Planck Institute for Polymer Research
#
# 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, eit... | espressopp/espressopp | examples/stillinger_weber_Si/stillinger_weber_silicon.py | Python | gpl-3.0 | 9,186 | [
"ESPResSo"
] | c8abeb73f225feb9caf21d5dd251faaa2bc01e421b1bd36e54b9456de9add4af |
###
# Emin Bugra Saral
# http://www.eminbugrasaral.com/
# version: 0.8
# 2014
#
# Using the API of http://www.solutions4mobiles.com for SMS Messaging
# Please contact http://www.solutions4mobiles.com to use their paid services
#
# NOTE: This Python class is written by using examples from
# http://www.solutions4mobiles... | ebsaral/s4m-python-api | python/SMS.py | Python | gpl-3.0 | 3,914 | [
"VisIt"
] | cdfd4b7adc121502ffa19a8e10b9d4645a6448446fbcebb071abcd317327f194 |
import bs4
import copy
import datetime
import functools
import time
from django.conf import settings as django_settings
from django.core import management
from django.core import serializers
import django.core.mail
from django.core.urlresolvers import reverse
from django.test import TestCase
from django.test.client imp... | coffenbacher/askbot-devel | askbot/tests/email_alert_tests.py | Python | gpl-3.0 | 46,177 | [
"VisIt"
] | 92a89788ee125aa2b9c244e9678670e2171f7ca47230aa97259c0eb1195decbd |
"""
Collection of tools for PISI
This file is part of Pisi.
Pisi is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Pisi is distributed in th... | kichkasch/pisi | pisitools.py | Python | gpl-3.0 | 4,421 | [
"VisIt"
] | 02fa55277c1fa0c54e7f733b0cd66a4c1dfda387c570ab063b9806401e68d69d |
#!/usr/bin/python
# Copyright 2009, Stephen Molloy, Stewart Boogert
#
# This file is part of Serpentine.
#
# Serpentine 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... | OscarES/serpentinetracker | serpentine.py | Python | gpl-3.0 | 12,630 | [
"Gaussian"
] | 0734b469bc27c1f05aa311af90354d3cab9a6403020f880576e2a65a0062e1ec |
"""
File argtest.py: (3.X + 2.X) function decorator that performs
arbitrary passed-in validations for arguments passed to any
function method. Range and type tests are two example uses;
valuetest handles more arbitrary tests on a argument's value.
Arguments are specified by keyword to the decorator. In the act... | simontakite/sysadmin | pythonscripts/learningPython/argtest.py | Python | gpl-2.0 | 5,114 | [
"MOOSE"
] | d4b4ae80251c5226cd390961427d2f4c117d94bc2ba39a4a39d782fb9bba6e09 |
import scrapy
from scrapy.selector import Selector
from scrapy.http import FormRequest,Request
from crawlers.items import SchoolItem
class AllSchoolSpider(scrapy.Spider):
name = "allSchool"
allowed_domains = ["moe.edu.sg"]
def start_requests(self):
prim_school_codes = ['1150', '1234', '12... | jackliusr/scrapy-crawlers | crawlers/crawlers/spiders/allSchool.py | Python | apache-2.0 | 4,682 | [
"MOE"
] | c4c79271340903365e8e6f1cf392308fd6fd2ef0e773f00b2038818ccc757024 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkClipPolyData(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.v... | nagyistoce/devide | modules/vtk_basic/vtkClipPolyData.py | Python | bsd-3-clause | 499 | [
"VTK"
] | 48bd3306f47fefc35cd87f5bf2e60173691681e3e6bcb5b893773b20e4895611 |
# coding=utf-8
import collections as coll
import numpy as np
from scipy import ndimage as ndi
import warnings
from ..util import img_as_float, regular_grid
from ..segmentation._slic import (_slic_cython,
_enforce_label_connectivity_cython)
from ..color import rgb2lab
def slic(image... | benjaminirving/perfusion-slic | perfusionslic/slic_superpixels_upstream.py | Python | bsd-3-clause | 7,616 | [
"Gaussian"
] | 2ef4dfacf6f11a0876c0d46a21d1ad63fb023a3bd2f4d952b2a184be72c20457 |
"""
Fabric file for installing application portal servers for AWS and Mukurtu
Copyright (C) 2016 Cameron Poole
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at... | Pooli3/YMAC_Returns | fabfile.py | Python | gpl-3.0 | 47,673 | [
"VisIt"
] | 1d62524edd840140eba946f76be3803af5d7ea65e61fd36c81f503a323cc96d4 |
#!/usr/bin/env python
# coding=utf-8
# Draw a cylindrical maze suitable for plotting with the Eggbot
# The maze itself is generated using a depth first search (DFS)
# Written by Daniel C. Newman for the Eggbot Project
# Improvements and suggestions by W. Craig Trader
# 20 September 2010
# Update 26 April 2011 by Dan... | evil-mad/EggBot | inkscape_contributed/eggbot_maze.py | Python | gpl-3.0 | 24,814 | [
"VisIt"
] | 1f73e655ce81d1e3e7fabc624c51fa229db14b733c6355b3db3bb0d3de9f3773 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import os
import unittest
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.transition_state import NEBAnalysis
import json
"""
TODO: Modi... | xhqu1981/pymatgen | pymatgen/analysis/tests/test_transition_state.py | Python | mit | 2,867 | [
"pymatgen"
] | 634a93e2a517fc1a13c69f5f05484050cc1552e9c4c81d531274b8eabc853916 |
""" Few unit tests for LCG clients
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import mock
from datetime import datetime, timedelta
from DIRAC.Core.LCG.GOCDBClient import GOCDBClient
mockRSS = mock.MagicMock()
GOCCli = GOCDBCli... | yujikato/DIRAC | src/DIRAC/Core/LCG/test/Test_LCG.py | Python | gpl-3.0 | 30,395 | [
"DIRAC"
] | 0976bbb68716c85217643f3dee0b05491e9a515e5e1e133f337ac166cb4df571 |
# -*- coding: utf-8 -*-
# Copyright (c) 2006-2016 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2010 Maarten ter Huurne <maarten@treewalker.org>
# Copyright (c) 2012 FELD Boris <lothiraldan@gmail.com>
# Copyright (c) 2012-2014 Google, Inc.
# Copyright (c) 2013-2016 Claudiu Popa <pcmanticore@gmail.co... | axbaretto/beam | sdks/python/.tox/lint/lib/python2.7/site-packages/pylint/checkers/classes.py | Python | apache-2.0 | 48,423 | [
"VisIt"
] | eda7551a87a9b3f86c1346ae2051488ca574428202123bdac57077f1671471e3 |
compass_directions = set(('north', 'east', 'south', 'west'))
directions = {'north': 0, 'east': 1, 'south': 2, 'west': 3, 'up': 4, 'down': 5}
inverted_directions = {'north': 2, 'east': 3, 'south': 0, 'west': 1, 'up': 5, 'down': 4}
road_directions = set(('secret pass', 'secret route', 'old road',
... | olympiag3/olypy | olypy/details.py | Python | apache-2.0 | 9,957 | [
"CRYSTAL"
] | 28478f4de39b35d92ad6d521ab938cf4c420a943e98982a256f50fb91bfe6e0c |
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 18 11:27:46 2016
@author:
Maximilian N. Guenther
Battcock Centre for Experimental Astrophysics,
Cavendish Laboratory,
JJ Thomson Avenue
Cambridge CB3 0HE
Email: mg719@cam.ac.uk
"""
import warnings
import numpy as np
import matplotlib.pyplot as plt
#from astropy.modeling ... | DJArmstrong/autovet | Features/old/Centroiding/scripts/old/stacked_images.py | Python | gpl-3.0 | 13,046 | [
"Gaussian"
] | f141a0ef5d74178a29aa0db6d894f4d21f28b786be40f78f44b08b1ab5c81281 |
#!/usr/bin/env python3
"""
BBS-format file source object for GSM.
Author: Alexey Mints (2012).
"""
import os.path
import healpy as hp
from copy import copy
from math import radians
from src.errors import SourceException
from src.gsmlogger import get_gsm_logger
class GSMBBSFileSource(object):
"""
Reads source ... | kernsuite-debian/lofar | CEP/GSM/bremen/src/bbsfilesource.py | Python | gpl-3.0 | 6,646 | [
"Gaussian"
] | d053a1e278acd7b4cbcb5d532aaefa03d4a553554e87577a6bba780e3f18dc51 |
#!/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/ccn/test.py | Python | apache-2.0 | 9,757 | [
"ORCA",
"PySCF"
] | f82d0c1290249e926d06379bf7a6b5a08cd617e4e73e14161facd37c170efb5b |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2013 Jan Decaluwe
#
# The myhdl library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License as
# published by t... | forrestv/myhdl | myhdl/_intbv.py | Python | lgpl-2.1 | 16,319 | [
"VisIt"
] | f406e4bcefe20c10f0b93515215e2433b0b0f371e42534d0f25428cd40764399 |
import numpy as np
from pysam import FastaFile
"""Bioinformatics helpers."""
comp = {
'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C', 'X': 'X', 'N': 'N',
'a': 't', 't': 'a', 'c': 'g', 'g': 'c', 'x': 'x', 'n': 'n',
#'-': '-'
}
comp_trans = str.maketrans(''.join(comp.keys()), ''.join(comp.values()))
def reverse_c... | nanoporetech/pomoxis | pomoxis/bio.py | Python | mpl-2.0 | 2,577 | [
"pysam"
] | 5243d4296d0f23265be9f1ed8f2514f931c2974907ddc7a0ef3e0a1710654042 |
# module pyparsing.py
#
# Copyright (c) 2003-2018 Paul T. McGuire
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to u... | sonntagsgesicht/regtest | .aux/venv/lib/python3.9/site-packages/setuptools/_vendor/pyparsing.py | Python | apache-2.0 | 232,056 | [
"VisIt"
] | 99a86d920729de0acd003d2b7bff51d032ef067be3ce978bc2026a4fedc7d421 |
#!/usr/bin/env python
import unittest
import os
import smact
from smact.properties import compound_electroneg, band_gap_Harrison
from smact.builder import wurtzite
import smact.screening
import smact.lattice
import smact.lattice_parameters
import smact.distorter
import smact.oxidation_states
from pymatgen.... | WMD-group/SMACT | smact/tests/test.py | Python | mit | 9,617 | [
"pymatgen"
] | 9f89d8e52665475d4dad9eb41b7b0badea76817794076ceb8cc84697a98a6599 |
#!/usr/bin/env python3
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# 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, e... | espressopp/espressopp | testsuite/ewald/ewald_eppDeserno_comparison.py | Python | gpl-3.0 | 7,620 | [
"ESPResSo"
] | 421c1c7469522f6950d1e531641b801e9c0f837cfc8d35c6ab83b35d6f84424a |
# Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
# Revisions copyright 2008-2009 by Peter Cock.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# Contact: Leighton Pritchard,... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Graphics/GenomeDiagram/_Graph.py | Python | gpl-2.0 | 9,565 | [
"Biopython"
] | 834952bf12476fbdff68a5d5d36e659a459e1ec3716a69ef1270dc267ebb6911 |
# $HeadURL$
"""
Collection of DIRAC useful operating system related modules
by default on Error they return None
"""
__RCSID__ = "$Id$"
from types import StringTypes
import os
import multiprocessing
import DIRAC
from DIRAC.Core.Utilities.Subprocess import shellCall
from DIRAC.Core.Util... | marcelovilaca/DIRAC | Core/Utilities/Os.py | Python | gpl-3.0 | 6,068 | [
"DIRAC"
] | 7c467340dbfd1ee44a5fe4d0a692127fa2d212c52d0a777c77f9ef2e629969f3 |
# This file is part of OpenDrift.
#
# OpenDrift 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
#
# OpenDrift is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without ev... | OpenDrift/opendrift | opendrift/models/sealice.py | Python | gpl-2.0 | 19,003 | [
"Gaussian"
] | 0cff8747875d6808168dde66625c33149b3557bbb3a84ab50d7cbceaf5e12209 |
#!/usr/bin/env python
#App="$1" # argument is the application to fixup
#LibrariesPrefix="Contents/Libraries"
#echo ""
#echo "Fixing up $App"
#echo "All required frameworks/libraries will be placed under $App/$LibrariesPrefix"
#echo ""
#echo "----------------------------"
#echo "Locating all executables and dylibs alr... | Sprunth/RGG | meshkit/Projects/apple/fixup_bundle.py | Python | bsd-3-clause | 13,677 | [
"ParaView"
] | 12cf850446b0f89a1ce21fb2ceed0e670d358981c7ed9ed943a71c28ac0b7035 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the Account Settings page.
"""
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.web_app_test import WebAppTest
from bok_choy.page_object import XSS_INJECTION
from ...pages.lms.account_settings import AccountSettingsPage
from ...pages.lms.aut... | solashirai/edx-platform | common/test/acceptance/tests/lms/test_account_settings.py | Python | agpl-3.0 | 17,581 | [
"VisIt"
] | c8dd7540233d6f9540573b275bf03067560ba481e8ea28cbb44172f3e8f96e52 |
#!/usr/bin/env python3
import sys
import argparse
import shlex
import copy
import _pathfix
from mhapi.db import MHDB, MHDBX
from mhapi.damage import MotionValueDB, WeaponMonsterDamage
from mhapi.model import SharpnessLevel, Weapon, ItemStars
from mhapi import skills
from mhapi.util import ELEMENTS, WEAPON_TYPES, WTY... | bd4/monster-hunter-scripts | bin/mhdamage.py | Python | mit | 21,107 | [
"BLAST"
] | b138654bced96ab9a17b4d473109cc2aacf4a9c7d2389b91440e152dbe720e5f |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... | userzimmermann/robotframework | src/robot/model/message.py | Python | apache-2.0 | 2,594 | [
"VisIt"
] | 0fd6e495724aaea2c9f002856e13b272bfd46a1927dbe6870a2150cac4310632 |
import sys
if len(sys.argv) != 3:
print "command is 'python <python driver code> <script name> <number of time steps>'"
sys.exit(1)
import paraview
import paraview.vtk as vtk
import paraview.simple as pvsimple
import math
# initialize and read input parameters
paraview.options.batch = True
paraview.options.sym... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/CoProcessing/PythonCatalyst/Testing/Cxx/waveletdriver.py | Python | gpl-3.0 | 2,590 | [
"ParaView",
"VTK"
] | db4f3322bd2004edbc4caba6daa76c9a1fc607a8ea2a17eea5bf99077a01db51 |
# coding: utf-8
#------------------------------------------------------------------------------------------------------------------------------------------------
############################################################## EL BRAYAN ##############################################################
#--------------------... | dagaros/Videojuego | ElBrayan.py | Python | mit | 184,339 | [
"Brian"
] | ff74bfaa9e5020dbd254d0a20530a68a8f37edfb400e3ee8f7a6fd89b44a729c |
# Copyright 2008-2009 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of django-facebookconnect.
#
# django-facebookconnect is free software: you can redistribute it and/or modify
# it under the te... | ryszard/django-facebookconnect | facebookconnect/urls.py | Python | gpl-3.0 | 1,493 | [
"Brian"
] | 4303e4aca7073f8b395e8e35c13154a73b991fb600d929b9ef42900ab6b0238c |
#! /usr/bin/env python
#
# Copyright (C) 2014 Xiabo LI
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This progr... | xmimi/diracfs | diracfs.py | Python | gpl-2.0 | 13,032 | [
"DIRAC"
] | f5014adcd825a9a9a27daa73c502b33ae9c2d276c1f1c6d496848eefce6cf1f1 |
# coding=utf-8
# Copyright 2014 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
from __future__ import absolute_import, division, print_function, unicode_literals
from textwrap import dedent
from pants.backend.docgen.targets.doc import Page, Wiki, Wik... | twitter/pants | tests/python/pants_test/backend/docgen/targets/test_wiki_page.py | Python | apache-2.0 | 4,669 | [
"exciting"
] | b7ac6aa1962c4b3fbe678ed49632083f6cb696a375727f15df278c13fe653466 |
"""Next gen sequence alignments with Bowtie (http://bowtie-bio.sourceforge.net).
"""
import os
from bcbio.pipeline import config_utils
from bcbio.utils import file_exists
from bcbio.distributed.transaction import file_transaction
from bcbio.provenance import do
galaxy_location_file = "bowtie_indices.loc"
def _bowtie... | elkingtonmcb/bcbio-nextgen | bcbio/ngsalign/bowtie.py | Python | mit | 2,206 | [
"Bowtie"
] | 2d322345b3c6852cc44c9234188fe1edfb38e51c38162d178027049fc9091e96 |
"""
Copyright (C) 2015, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Barbara Harmon (bharmon@jaguarlandrover.com)
"""
from django.conf.urls import patterns, u... | afan1/rvi_backend | web/sota/urls.py | Python | mpl-2.0 | 588 | [
"Jaguar"
] | e905bef51ce951bf46d20366297e07af86f6b64674d2b1e2f9afce1b1f4f9e2d |
#!/usr/bin/python3
# The MIT License (MIT)
# Copyright (c) 2015 Brian Wray (brian@wrocket.org)
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limita... | wrocket/Tulip-Chess | utils/generate_tree.py | Python | mit | 2,285 | [
"Brian"
] | a739d196c4edae94657a7a3cb8b76098b763d7a3c01074edd7c1e5a36dc4fcc6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# benchmark_alternating - benchmark alternating read/write
# Copyright (C) 2003-2011 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU ... | heromod/migrid | mig/grsfs-fuse/benchmarks/code/benchmark_alternating.py | Python | gpl-2.0 | 5,766 | [
"Brian"
] | cc1010c1b12494e5a514b5f291e88d3169ff8983dbea323746fd2abe5507018a |
NAME = "Minbias1PV"
#from tempfile import mkstemp
#from shutil import move
#from os import remove, close
#
#def replace(file_path, pattern, subst):
# #Create temp file
# fh, abs_path = mkstemp()
# with open(abs_path,'w') as new_file:
# with open(file_path) as old_file:
# for line in old_file... | saschastahl/ridge-analysis | scripts/GangaMC.py | Python | mit | 1,322 | [
"DIRAC"
] | 6c8ffa9de94c6e96a865de34258abc136eb23599a9b01392c0c5c2a636b771bb |
"""
$Revision: 1.2 $ $Date: 2009/04/22 07:30:27 $
Author: Martin Kuemmel (mkuemmel@stecf.org)
Affiliation: Space Telescope - European Coordinating Facility
WWW: http://www.stecf.org/software/slitless_software/axesim/
"""
import os
import os.path
import sys
import math
import string
from axesimutils import *
from axesi... | nfourmanoit/TIPS | python/axesim/configfile.py | Python | gpl-3.0 | 47,897 | [
"Gaussian"
] | 83a1e796c05a07c7dcc385bd2d488f824d32ccc4389523180bcb6059969bf1ac |
#!/usr/bin/env python
'''Gets contact webform URLs for the intersection of members with bioguide ids
and with correlating contact form steps in unitedstates/contact-congress:
args:
<bioguide_id bioguide_id ...>
A list of bioguide ids to import.
options:
--debug[=True]
Whether or not verbose output should be prin... | gautamsrin/congress-legislators | scripts/contact_forms.py | Python | cc0-1.0 | 2,134 | [
"VisIt"
] | f7ed4df22579ef1a988f81e89c5e7c2744dc34a9ac20783f528cc03200859b46 |
# ## Copyright (c) 2013, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
import itertools, logging
from ..kern import Kern
from ..core.parameterization.variational import NormalPrior
from ..core.parameterization import Param
from paramz import ObsAr
from .... | befelix/GPy | GPy/models/mrd.py | Python | bsd-3-clause | 15,289 | [
"Gaussian"
] | 1002adce1577c9387310458b86a4f32ce4ebbddc1988abbde4c395f4c965645a |
"""
unit testing code rdkit.Chem.Pharm2D.Generate
"""
import unittest
from rdkit.Chem.Pharm2D import Generate
class TestCase(unittest.TestCase):
def test_Gen2DFingerprint(self):
# The code is run from most of the other tests. This is only
# to test the assertions
self.assertRaises(ValueError, Generat... | rvianello/rdkit | rdkit/Chem/Pharm2D/UnitTestGenerate.py | Python | bsd-3-clause | 430 | [
"RDKit"
] | e72e0935f4d279d7419e1b367a48b460de1b651d88313201788970e0eabb8165 |
# -*- coding: utf-8 -*-
"""
This scripts sets an initial layout for the ProEMOnline software. It uses the
PyQtGraph dockarea system and was designed from the dockarea.py example.
Keaton wrote this.
"""
#Import everything you'll need
from __future__ import absolute_import, division
import pyqtgraph as pg
from pyqtgr... | ccd-utexas/ProEMOnline | ProEMOnline.py | Python | mit | 57,911 | [
"Gaussian"
] | cda4d379e5d78da4357e4e8c1fe24304ef0605acee1d49d304705ca27e6852ab |
from builtins import object
import numpy as np
from cs231n.layers import *
from cs231n.fast_layers import *
from cs231n.layer_utils import *
class ThreeLayerConvNet(object):
"""
A three-layer convolutional network with the following architecture:
conv - relu - 2x2 max pool - affine - relu - affine - sof... | DavidQiuChao/CS231nHomeWorks | assignment2/cs231n/classifiers/cnn.py | Python | mit | 6,012 | [
"Gaussian"
] | 27d7480aa59104bfe12b9e38bcdd6a313efd5ea4f5e0ca3f969ebf3a00921921 |
"""
Helper function for running Grizli redshift fits in AWS lambda
event = {'s3_object_path' : 'Pipeline/j001452+091221/Extractions/j001452+091221_00277.beams.fits'}
Optional event key (and anything to grizli.fitting.run_all):
'skip_started' : Look for a start.log file and abort if found
'check_wcs' : check... | gbrammer/grizli | grizli/aws/lambda_handler.py | Python | mit | 29,824 | [
"Galaxy"
] | 01b160c8132d2e16efd3b8589d8bcfbc3f50bb726350db35902a052c6234d47c |
#!/usr/local/bin/python
#Created on 4/2/2013
__author__ = 'Juan A. Ugalde'
def split_sequence_fragments(sequence, block_size):
"""
Function that takes a sequence of letters (usually a DNA sequence), and returns
fragments of a defined block size
"""
fragments = []
total_size = len(sequence)
... | juanu/ANI_analysis | ANI_blastn.py | Python | mit | 11,775 | [
"BLAST"
] | 97a38d8f72c5328983fb869094e32a02f7c937e948bc195478dd63ebf2099785 |
"""
======================================================================
Time-frequency on simulated data (Multitaper vs. Morlet vs. Stockwell)
======================================================================
This example demonstrates the different time-frequency estimation methods
on simulated data. It shows ... | jaeilepp/mne-python | examples/time_frequency/plot_time_frequency_simulated.py | Python | bsd-3-clause | 8,415 | [
"Gaussian"
] | bd30f4819d0d5b8b3cbc463d14195abd1e19ed3a7e3c418972f10ee4d23d5aa3 |
#!python
# coding=utf-8
import os
import tempfile
import operator
from glob import glob
import pytz
try:
import pyncml
except ImportError:
raise ImportError("You must install the 'pyncml' library to use this functionality.")
import netCDF4
import numpy as np
from pyaxiom.utils import DotDict
from pyaxiom im... | axiom-data-science/pyaxiom | pyaxiom/netcdf/grids/collection.py | Python | mit | 8,456 | [
"NetCDF"
] | 7d541c3934416c95d3da25db09f96dca1c2cb8245c908ade65b8c682a63ddeae |
#
# The OpenDiamond Platform for Interactive Search
#
# Copyright (c) 2011-2018 Carnegie Mellon University
# All rights reserved.
#
# This software is distributed under the terms of the Eclipse Public
# License, Version 1.0 which can be found in the file named LICENSE.
# ANY USE, REPRODUCTION OR DISTRIBUTION OF T... | cmusatyalab/opendiamond | opendiamond/server/listen.py | Python | epl-1.0 | 9,733 | [
"BLAST"
] | 78d9b0ec9e121580fa8caf7011d071b04265ca9244a9381cf33826f8d35e397a |
########################################################################
# File : JobWrapper.py
# Author : Stuart Paterson
########################################################################
""" The Job Wrapper Class is instantiated with arguments tailored for running
a particular job. The JobWrapper starts ... | fstagni/DIRAC | WorkloadManagementSystem/JobWrapper/JobWrapper.py | Python | gpl-3.0 | 63,187 | [
"DIRAC"
] | 29976cd5a3d506ca65b0c41297623341a9c3955dd8b6446b757c28694d67cd20 |
import logging
import time
from fsi import *
from gui import *
import vtk
import Tkinter
import tkFileDialog
import tkColorChooser
import ttk
from vtk.tk.vtkTkRenderWindowInteractor import vtkTkRenderWindowInteractor
import sys
import tkFont
from PIL import Image, ImageTk
from distutils.core import setup
from distutils... | beauof/FSIViewer | main.py | Python | lgpl-3.0 | 37,423 | [
"VTK"
] | b9a64260fc2e709a559fca14159d25560919974422cdc2d3d46f8db61559d699 |
#
# co_co_current_buffers_not_specified.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 License, or... | kperun/nestml | pynestml/cocos/co_co_current_buffers_not_specified.py | Python | gpl-2.0 | 2,304 | [
"NEURON"
] | 32f651a5e97953dece14f7c2d905bd7f44be8237ec50bd9e0b3701b2c4fa4442 |
#!/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... | veger/ansible | lib/ansible/modules/files/find.py | Python | gpl-3.0 | 16,054 | [
"Brian"
] | 282e8aa9994d9bfb86aebf18bf8525afddb35db66f41c25c625529b33bcb82a2 |
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