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"""Probit regression class and diagnostics."""
__author__ = "Luc Anselin luc.anselin@asu.edu, Pedro V. Amaral pedro.amaral@asu.edu"
import numpy as np
import numpy.linalg as la
import scipy.optimize as op
from scipy.stats import norm, chisqprob
import scipy.sparse as SP
import user_output as USER
import sum... | pastephens/pysal | pysal/spreg/probit.py | Python | bsd-3-clause | 34,383 | [
"COLUMBUS"
] | 01072466a3b3bf22f38f5cd735b17aae45ac0836086d320e99a68ac767d66be0 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Building the density matrix from data parsed by cclib."""
import logging
import random
import numpy
fr... | Schamnad/cclib | src/cclib/method/density.py | Python | bsd-3-clause | 2,968 | [
"cclib"
] | c4fcb2b7651d2f0d717b056513db8ce3e50bb5c4048ccb57a343c4ee78148369 |
import numpy as np
def collapse(j, data):
"""Collapses samples into a single row"""
uniques = np.unique(j)
return uniques, np.array([data[j == u].sum() for u in uniques])
def nearest(coords, shape, **kwargs):
valid = ~(np.isnan(coords).all(1))
valid = np.logical_and(valid, np.logical_and(coords[:,... | gallantlab/pycortex | cortex/mapper/samplers.py | Python | bsd-2-clause | 3,673 | [
"Gaussian"
] | 7f530ccfed5877222fe93158d9119cfc60ac12c168f15aa404954e8d11458208 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','... | joseandro/TitaniumiOSUniqueIDs | build.py | Python | mit | 6,810 | [
"VisIt"
] | be35b7771e10ac8e10cdd4910abfc638f78e654755bf87974ee906e59204a9ba |
"""
This file is a mess, it is a merge of random stuff that is in galaxy.util and
stuff that was in lwr.util. This should be reworked to only contain stuff in
galaxy.util and the rest should be moved into galaxy.util.lwr_io or something
like that.
"""
import os
import platform
import stat
try:
import grp
except Imp... | jmchilton/lwr | galaxy/util/__init__.py | Python | apache-2.0 | 5,762 | [
"Galaxy"
] | 7ece96b2417df56404c1cc7305890160453cb152d282cee42be1ee04a1dac995 |
#!/usr/bin/env python
from __future__ import absolute_import
#----------------------------------------------------------------------
# Copyright (c) 2012-2015 Raytheon BBN Technologies
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and/or hardware specification (th... | plantigrade/geni-tools | src/gcf/omnilib/amhandler.py | Python | mit | 362,512 | [
"ORCA"
] | d6d199e1d17955bbb02f6804b779485c37e0b6189de6e4e44e15161dae2c8987 |
""" :mod: SRM2Storage
=================
.. module: python
:synopsis: SRM v2 interface to StorageElement
"""
# # imports
import os
import re
import time
import errno
from types import StringType, StringTypes, ListType, IntType
from stat import S_ISREG, S_ISDIR, S_IMODE, ST_MODE, ST_SIZE
# # from DIRAC
from ... | sposs/DIRAC | Resources/Storage/SRM2Storage.py | Python | gpl-3.0 | 88,519 | [
"DIRAC"
] | 05e874c4b0313a203d6308f5b80455263da86646797ba22af8fee7eb9493cd20 |
"""
This module contains the CharmmMatcher class. It is used to apply
atom names from known topologies to the molecule by using a graph-based
representation of each molecule.
Author: Robin Betz
Copyright (C) 2019 Robin Betz
"""
# This program is free software; you can redistribute it and/or modify it under
# th... | Eigenstate/dabble | dabble/param/charmmmatcher.py | Python | gpl-2.0 | 26,364 | [
"CHARMM",
"VMD"
] | e22e062d448ffb0f4f1ca42b052dc465d025fbd354aaa1b2ae8d491c948a4e12 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/ParticleAccess.py | Python | gpl-3.0 | 1,591 | [
"ESPResSo"
] | b8cca7e1ba34af30697c2082753d807a53b77315ef7646916d1e851cae731eca |
from __future__ import absolute_import
from __future__ import division
from six import text_type
from typing import Any, Dict, List, Tuple, Optional, Sequence, Callable, Union
from django.db import connection
from django.db.models.query import QuerySet
from django.template import RequestContext, loader
from django.cor... | umkay/zulip | analytics/views.py | Python | apache-2.0 | 28,114 | [
"VisIt"
] | 369731c1ffecc0cc1d7d9fc7117465bcf78f928c627c211bc97b3ca1bf9d7afd |
from data import *
import numpy as np
import sys, math
""" fix_image_flags.py
- reads in LAMMPS data file
- looks for bonds that span periodic boundaries
- adds image flags
- writes new LAMMPS data file
note:
- completely ignores existing image flags
- assumes 'atom_style full'
- r... | musab-k/fix-image-flags | fix_image_flags.py | Python | mit | 3,997 | [
"LAMMPS"
] | 074b013615c1204d705bf5c2684729cb9d08ae764a0fe571412f41cf24432e41 |
from __future__ import division, print_function, absolute_import
import numpy as np
from numpy.dual import eig
from scipy.misc import comb
from scipy import linspace, pi, exp
from scipy.signal import convolve
__all__ = ['daub', 'qmf', 'cascade', 'morlet', 'ricker', 'cwt']
def daub(p):
"""
The coefficients f... | Universal-Model-Converter/UMC3.0a | data/Python/x86/Lib/site-packages/scipy/signal/wavelets.py | Python | mit | 10,266 | [
"Gaussian"
] | 91387ceb7aa672db763418a8658ad4ee8325296d3c00be34b700f9a04471ada1 |
#!/usr/bin/env python2
# 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... | kkreis/espressopp | examples/local_pressure_tensor/local_pressure_tensor.py | Python | gpl-3.0 | 6,109 | [
"ESPResSo"
] | 8ed33e805b06f59a174326cf840299f307f24c98398a1129b4cb4c7f05073b69 |
"""
ex20170209_SIMEX1.py
Build Model SIMEX from Godley & Lavoie (Chapter 3, section 3.7.1.
Uses the model builder from the sfc_models.gl_book sub-package.
Copyright 2017 Brian Romanchuk
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
Y... | brianr747/SFC_models | sfc_models/examples/scripts/intro_5_04_SIMEX1.py | Python | apache-2.0 | 2,355 | [
"Brian"
] | 3115292d57794d894844f40d824214b730b7c5d344fc546f6894a867bb93971c |
import unittest, logging
from pyquante2 import molecule, rhf, uhf, rohf, cuhf, h2, h2o, lih, li, oh, ch4, basisset
from pyquante2.ints.integrals import libint_twoe_integrals, twoe_integrals_compressed
from pyquante2.geo.molecule import read_xyz
from pyquante2.scf.iterators import SCFIterator, AveragingIterator, USCFIte... | Konjkov/pyquante2 | tests/test_scf.py | Python | bsd-3-clause | 11,974 | [
"NWChem"
] | c7fc040a386fca983725821e03d9c0423bc4711eebb6796074821ba24c945d93 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.defects.generators import VacancyGenerator, \
SubstitutionGenerator, InterstitialGenerator, VoronoiInterstitialGenerat... | gVallverdu/pymatgen | pymatgen/analysis/defects/tests/test_generators.py | Python | mit | 5,141 | [
"pymatgen"
] | 75a0ff9ba078c4660ce49389a564e9869f71784e090b332a54cf022b70f3df73 |
#!/usr/bin/env python3
from setuptools import setup, find_packages
setup(
name='chronoplot',
version='0.1.0',
description='Timeline maker.',
long_description='',
keywords='',
url='https://github.com/darkfeline/chronoplot',
author='Allen Li',
author_email='darkfeline@felesatra.moe',
... | darkfeline/chronoplot | setup.py | Python | gpl-3.0 | 786 | [
"MOE"
] | efe831c2a9c06911ba43e12a608f4fa038610b6bf23237e8e8b0acb6bcb9c189 |
"""
sentry.web.frontend.accounts
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:copyright: (c) 2012 by the Sentry Team, see AUTHORS for more details.
:license: BSD, see LICENSE for more details.
"""
from __future__ import absolute_import
import logging
from functools import partial, update_wrapper
import six
from django.conf import... | gencer/sentry | src/sentry/web/frontend/accounts.py | Python | bsd-3-clause | 21,398 | [
"VisIt"
] | a600dcbddfc84c579130136d3bbb69d14d980c5522d3c4e8376d97459aeddb30 |
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under t... | briancurtin/rackspace-sdk-plugin | rackspace/tests/unit/test_connection.py | Python | apache-2.0 | 2,699 | [
"Brian"
] | 42e152a84315dbdb8d7f194770dabf0d33a88abbbf8cc82558754ce2bd9fd582 |
##
# Copyright 2009-2020 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | IGB-UIUC/easybuild | easyblocks/trinity.py | Python | gpl-3.0 | 14,491 | [
"BWA"
] | 9988d74e32c9a74e58f480c0b25cf9a222ba6ffed4a3188237704eae6f3e0b92 |
# This file is part of PyEMMA.
#
# Copyright (c) 2014-2017 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 versi... | markovmodel/PyEMMA | pyemma/_base/serialization/pickle_extensions.py | Python | lgpl-3.0 | 5,874 | [
"MDTraj"
] | 8b0d49335359acbaf15edda756ce4b0bad9620de367c36e56c9c3ca828c616cc |
# encoding=utf-8
# Created by xupingmao on 2017/04/16
# @modified 2022/03/08 22:18:33
# @filename dao.py
"""资料的DAO操作集合
DAO层只做最基础的数据库交互，不做权限校验（空校验要做），业务状态检查之类的工作
一些表的说明
note_full:<note_id> = 笔记的内容，包含一些属性（部分属性比如访问时间、访问次数不是实时更新的）
note_index:<note_id> = 笔记索引，不包含内容
note_tiny:<user>:<note_id> ... | xupingmao/xnote | handlers/note/dao.py | Python | gpl-3.0 | 47,559 | [
"VisIt"
] | c5c3cd956517342e1660d591e558bc6400df7d5b6bb8caa739d5f1c354ab15ab |
from __future__ import division
import numpy as np
import paraBEM
from paraBEM.pan2d import doublet_2_0, doublet_2_0_v, source_2_0, source_2_0_v
from paraBEM.vtk_export import VtkWriter
from paraBEM.utils import check_path
p1 = paraBEM.PanelVector2(-1, -10)
p2 = paraBEM.PanelVector2(0, -10)
p3 = paraBEM.PanelVector2(1... | looooo/paraBEM | examples/vtk/vtk_heat_test.py | Python | gpl-3.0 | 3,051 | [
"VTK"
] | 15e0da7a6d8938770460bb02bb371bb292c7fde0572b5d72e33c8fb6fc62a732 |
from pathlib import Path
from os import chdir
import unittest
from math import sqrt
from nipype.interfaces.base import CommandLine
from qipype.commands import NewImage, Diff, ZShim
from qipype.fitting import ASL, ASE, ASESim, ASEDBV, ASEDBVSim
vb = True
CommandLine.terminal_output = 'allatonce'
class Perfusion(unitt... | spinicist/QUIT | Python/Tests/test_perfusion.py | Python | mpl-2.0 | 4,560 | [
"ASE"
] | 14993c722cf6d25309d808ba0511f3575406840e500cc5bdf98e168109f74932 |
from __future__ import unicode_literals
import os
from fabric.api import env, execute, task
from fabric.colors import red
from fabric.contrib.project import rsync_project
from fabric.utils import abort
from fabfile import run_local, cd, require_env, run, step
@task(default=True)
@require_env
def deploy():
"""D... | lucacorsato/feincms-in-a-box | fbox/fabfile/deploy.py | Python | bsd-3-clause | 3,356 | [
"GULP"
] | f5dc68a98f5c717f116bd7ea864ac8a327bbf2d40bceec001c7cbffd335a28b2 |
"""
Adapted from https://github.com/tornadomeet/ResNet/blob/master/train_resnet.py
Original author Wei Wu
Implemented the following paper: DenseNet-BC
Gao Huang, Zhuang Liu, Kilian Q. Weinberger, Laurens van der Maaten. "Densely Connected Convolutional Networks"
Coded by Lin Xiong Mar-2, 2017
"""
import... | bruinxiong/densenet.mxnet | train_densenet.py | Python | apache-2.0 | 11,053 | [
"Gaussian"
] | eba56cd87cdc8c4c3669309ff0f799a54908cd2aeb0462fd8bc2796221a017ed |
# 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.
#
"""Dynamic Programming algorithms for general usage.
This module contains classes which implement Dynamic Programming
algorithms that can be used ge... | zjuchenyuan/BioWeb | Lib/Bio/HMM/DynamicProgramming.py | Python | mit | 12,779 | [
"Biopython"
] | f8ddd80a1fe62a820ddfcb0ff5efff4837f0b66e41b708466f7cf0206ee60acf |
"""
@name: PyHouse/src/Modules/_test/test_Irrigation.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2017 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 31, 2015
@Summary:
"""
__updated__ = '2016-11-21'
from twisted.trial import unittest, reporter, ... | DBrianKimmel/PyHouse | Project/src/Modules/House/_test/test_Irrigation.py | Python | mit | 769 | [
"Brian"
] | 2b4a4dc1693bdd291ea453b90bc5a8b32dcfa9d8ba551c36da202462c7d4b47e |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | wizmer/NeuroM | neurom/check/tests/test_runner.py | Python | bsd-3-clause | 8,698 | [
"NEURON"
] | 9d11eb001b03dd244e5b262861f359d2c58e2838ff24072740f39ce2df8b0fc5 |
from common import *
from ex.plott import *
from ex.pp import *
class GMM:
'''gaussian mixure model
'''
def __init__(self, weights = None, means = None, covars = None):
'''initialize the parameters.
means: size [K, dim] each row is a mean vector
covars: size [K, dim, dim]
'... | excelly/xpy-ml | ex/ml/gmm.py | Python | apache-2.0 | 6,367 | [
"Gaussian"
] | 3e77bc1dee0316624c94af618e8ddf2d78577dce91f41ca85a7c50c8fca1e09a |
"""
Authentication example using Flask-Login
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This provides a simple example of using Flask-Login as the authentication
framework which can guard access to certain API endpoints.
This requires the following Python libraries to be installed:
* Flask
... | ternaris/flask-restless | examples/server_configurations/authentication/__main__.py | Python | bsd-3-clause | 4,489 | [
"VisIt"
] | 10653be80f9ad50ea342367a406d8542fb81461b54fdf1be309e0dedf04d5511 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Ansible module to manage PaloAltoNetworks Firewall
# (c) 2016, techbizdev <techbizdev@paloaltonetworks.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publish... | anryko/ansible | lib/ansible/modules/network/panos/_panos_op.py | Python | gpl-3.0 | 5,064 | [
"Galaxy"
] | a8c93f62a430ed52b8c60180612fe2bf8d9322391a9c211fb95ed2a9c35ef486 |
"""
bvp1.py solves the 1D Poisson equation using FEniCS
Copyright (C) 2013 Greg von Winckel
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
... | gregvw/FEniCS-examples | bvp1.py | Python | mit | 1,840 | [
"VTK"
] | 907e4cf2de9091c5bb034abc5f7ebbf83b4020bbaf7062f1e1fd352b5b039d2b |
#!/usr/bin/env python
########################################################################
# File : tornado-start-CS
# Author : Louis MARTIN
########################################################################
# Just run this script to start Tornado and CS service
# Use dirac.cfg (or other cfg given in the co... | yujikato/DIRAC | src/DIRAC/Core/Tornado/scripts/tornado_start_CS.py | Python | gpl-3.0 | 2,120 | [
"DIRAC"
] | 9aa2401c3369549f0cbd00a63c991cfca6ab20ace0d5195dcbc96a512fc6d871 |
"""
Backports. Mostly from scikit-learn
"""
import numpy as np
from scipy import linalg
from scipy.stats import (poisson, expon)
###############################################################################
# For scikit-learn < 0.14
def _pinvh(a, cond=None, rcond=None, lower=True):
"""Compute the (Moore-Penros... | mvictor212/hmmlearn | hmmlearn/utils/fixes.py | Python | bsd-3-clause | 7,426 | [
"Gaussian"
] | 9f609b109925d29163a8efd49da967d091363e0c88ed03906d9ad64413f6bc1f |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2008 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the License, or... | andrebellafronte/stoq | plugins/ecf/cat52.py | Python | gpl-2.0 | 32,816 | [
"VisIt"
] | 7aed4140e5d02fb83ce2246b1ff5881165151161418c492e6cd5469a23e6812e |
import subprocess
import os
import threading
import sys
from glutton.utils import get_log, tmpfile, openmp_num_threads, rm_f
from glutton.blast import Blast
from glutton.job import BlastJob
from glutton.queue import WorkQueue
class All_vs_all_search(object) :
def __init__(self, batch_size=100) :
self.nuc... | ajm/glutton | glutton/localsearch.py | Python | gpl-3.0 | 3,613 | [
"BLAST"
] | 00aec41fbe0db40aa6086c88b9c45d7962c79d32723778a3442b01190c0d6c65 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2017 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | dwhswenson/mdtraj | tests/test_reporter.py | Python | lgpl-2.1 | 10,148 | [
"MDTraj",
"OpenMM"
] | 8dd56a4aa407f9bc48782c944a8b52129ee62115ef21866e6e8b5cbaf1af15c2 |
#!/usr/bin/env python
# vim:fileencoding=UTF-8:ts=4:sw=4:sta:et:sts=4:ai
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2011, Kovid Goyal <kovid@kovidgoyal.net>'
__docformat__ = 'restructuredtext en'
import os, ppr... | nozuono/calibre-webserver | src/calibre/web/jsbrowser/browser.py | Python | gpl-3.0 | 27,188 | [
"VisIt"
] | 12a88fb12bcab16139106867466d2f59270624f6b11eb2ab42e69ded80e5a02d |
#!/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/pathintegral_water/water.py | Python | gpl-3.0 | 8,159 | [
"ESPResSo",
"Gromacs"
] | 4ac73773c31dd34bfcd04cfdea62e8a3567e8b5d9b24185d7a81f8372ecf0a2f |
__all__ = ['threshold_adaptive',
'threshold_otsu',
'threshold_yen',
'threshold_isodata',
'threshold_li', ]
import numpy as np
import scipy.ndimage
from ..exposure import histogram
from .._shared.utils import assert_nD
def threshold_adaptive(image, block_size, method='gauss... | bennlich/scikit-image | skimage/filters/thresholding.py | Python | bsd-3-clause | 13,942 | [
"Gaussian"
] | d6c611cce65d5bc0caf76306d205bb7fb6d66796fde25834677ddaccbaf5efab |
"""
Example Kernels
---------------
Figure 6.2
A comparison of the three kernels used for density estimation in figure 6.3:
the Gaussian kernel (eq. 6.2), the top-hat kernel (eq. 6.3), and the
exponential kernel (eq. 6.4).
"""
# Author: Jake VanderPlas
# License: BSD
# The figure produced by this code is published i... | eramirem/astroML | book_figures/chapter6/fig_kernels.py | Python | bsd-2-clause | 1,770 | [
"Gaussian"
] | 7e79e65bee0b56f42c60bc6007c00d98e0311944b4653183cd2942f5e9b29de9 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/ascent/package.py | Python | lgpl-2.1 | 12,381 | [
"VTK"
] | 0067fbd938d8af41542ccf3e7b9e5a31b97a66bc8cd24af7ba101179c6fc9ec6 |
# GromacsWrapper plugins
# Copyright (c) 2009-2012 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
:mod:`analysis.plugins` -- Plugin Modules
=========================================
Classes for :class:`gromacs.analysis.co... | jandom/GromacsWrapper | gromacs/analysis/plugins/__init__.py | Python | gpl-3.0 | 4,957 | [
"Gromacs"
] | 8b6850a2d6e1dbbd43fa97a206ecdf988f0d11496651810dfd8bd3b5a724b6e9 |
"""
======================================================================
Time-frequency on simulated data (Multitaper vs. Morlet vs. Stockwell)
======================================================================
This example demonstrates the different time-frequency estimation methods
on simulated data. It shows ... | rkmaddox/mne-python | examples/time_frequency/time_frequency_simulated.py | Python | bsd-3-clause | 8,475 | [
"Gaussian"
] | 948472db6ec443845ca68ce537296ff24282e848f9f0fc358e655df351187d53 |
'''
@file : testFile14.py
@author (A) : Madhu Kumar Dadi.
@project : Social List
@function :
test14(parsedTag,postag) : Searches parsedTag on google for popularity and precision at 10 and 20 urls
@parsedTag : hashtag that is searched on google
@postag : pos tags of the parsedTag
return : a list containi... | SummerProject16/project | CMUTweetTagger/testFile14.py | Python | cc0-1.0 | 3,538 | [
"VisIt"
] | 73cade9e883765263b79190fb000de2e0c7fd71d85435c5dd86703a5c926efaa |
##
# Copyright (C) 2012 Jasper Snoek, Hugo Larochelle and Ryan P. Adams
#
# This code is written for research and educational purposes only to
# supplement the paper entitled
# "Practical Bayesian Optimization of Machine Learning Algorithms"
# by Snoek, Larochelle and Adams
# Advances in Neural Information Processing... | ninjin/spearmint-lite | GPEIOptChooser.py | Python | gpl-3.0 | 20,831 | [
"Gaussian"
] | 7886097274459012a7c6b277611c96551bc9dd0141f6bdf0f9adfbca50691e1b |
import numpy as np
import pandas as pd
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
pd.set_option('display.width', 1000)
n_steps = 3000
temperature = 300. * u.kelvin
collision_rate = 1.0 / u.picoseconds
timestep = 2.0 * u.femtoseconds
steps_per_hmc = 12
k_m... | kyleabeauchamp/HMCNotes | code/old/test_xhmc_compare_ghmc.py | Python | gpl-2.0 | 1,196 | [
"OpenMM"
] | 994a5faa3d38fc53a8e0f3b86b7450616fb0161aa9287a76b0e33d3f06b681e6 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/web/tvbrowser.py | Python | gpl-2.0 | 5,220 | [
"VisIt"
] | 3d844fb6ef1270c3825a91bebb098f2bc73954d78b2e818ea8aceb42642d9767 |
import multiprocessing as MP
import itertools as IT
import progressbar as PGB
import os, warnings
import numpy as NP
import healpy as HP
from astropy.table import Table
from astropy.io import fits, ascii
import h5py
import warnings
from astropy.coordinates import Angle, SkyCoord
from astropy import units
import scipy.c... | nithyanandan/general | astroutils/catalog.py | Python | mit | 88,092 | [
"Gaussian"
] | 80f18084082b306adf0c376cfa99ad72a16e51b5489f585f52656f765bffc4eb |
from os.path import dirname, join
from rabix.common.ref_resolver import from_url
from rabix.main import TEMPLATE_JOB, init_context
def test_remap_job():
job = TEMPLATE_JOB
tool = from_url(join(dirname(__file__), 'bwa-mem.json#tool'))
context = init_context(tool)
app = context.from_dict(tool)
inpu... | rabix/rabix | rabix/tests/test-mount/test.py | Python | agpl-3.0 | 539 | [
"BWA"
] | e8c1fc79a7315d1481c494aa67d5f30a70060293f05a1b59dc71589d5b6a4fc3 |
#! /usr/bin/env python
# --------------------------------------------------
# Plot temperature at 50 m, using the SGrid class
#
# Bjørn Ådlandsvik, <bjorn@imr.no>
# Institute of Marine Research
# Created: 2010-01-20
# --------------------------------------------------
# ---------
# Imports
# ---------
import numpy a... | bjornaa/roppy | examples/plot_temp50.py | Python | mit | 1,684 | [
"NetCDF"
] | a1b2f021141cee7f92bd8fb231ce4d4d4edab0b2302214de6e108fcfbbd6a7b7 |
# compiler.py
# Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010 Michael Bayer mike_mp@zzzcomputing.com
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`~sq... | obeattie/sqlalchemy | lib/sqlalchemy/sql/compiler.py | Python | mit | 55,170 | [
"VisIt"
] | 81b91b7b6f11b3a4d3b98f9dfa1a24075ca777f7657206c0d60d118cb2f40da5 |
# encoding: utf-8
r"""Modules contains information about the aux array used in the multi-layer
swe computations."""
import numpy as np
# Define aux array indices
bathy_index = 0
wind_index = 1
h_hat_index = [2,3]
kappa_index = 4
# ==============================================
# = Sets values of h_hat for linearize... | mandli/multilayer-examples | 1d/multilayer/aux.py | Python | mit | 3,435 | [
"Gaussian"
] | f403006ee43e0d8f8389e8ff07b5c1286a0912a009276d58b82a4c0838162db7 |
from __future__ import print_function
from datetime import datetime
import logging
import re
from nameparser import HumanName
from openelex.base.transform import Transform, registry
from openelex.models import Candidate, Contest, Office, Party, RawResult, Result
from openelex.lib.text import ocd_type_id
from openelex... | openelections/openelections-core | openelex/us/wa/transform/__init__.py | Python | mit | 19,231 | [
"MOOSE"
] | 5ac2c70f7e6b28b8d260e174cb23abd7abf2fd1e999b3a17962edad6e9ae36f2 |
#!/usr/bin/python
"""
detangler.py - Copyright (c) 2012, Howard C. Shaw III
Licensed under the GNU GPL v3
detangler.py [filename] ...
Pass any number of filenames, detangler will extract all trees using BioPython,
and optimize them all simultaneously, minimizing on all combinations of trees.
"""
from sys import arg... | TheGrum/Tangled | detangler.py | Python | gpl-3.0 | 1,884 | [
"Biopython"
] | 11123e15e94fe5ea7dd25ead5453794ebdf45100f99c585757a063c5fe8b2da2 |
# Orca
#
# Copyright 2010 Joanmarie Diggs.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library i... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/evolution/script_utilities.py | Python | gpl-3.0 | 19,166 | [
"ORCA"
] | dcdbb0b0b6338b3ca0b52a430681bebc0421f72dad1329d4a89f0ad4bc4236f0 |
# -*- coding: utf-8 -*-
#------------------------------------------------------------
# pelisalacarta - XBMC Plugin
# Canal para somosmovies
# http://blog.tvalacarta.info/plugin-xbmc/pelisalacarta/
#------------------------------------------------------------
import re
import urlparse
from core import config
from core... | Hernanarce/pelisalacarta | python/main-classic/channels/somosmovies.py | Python | gpl-3.0 | 18,309 | [
"ADF"
] | 438724944d98b1618c2753bd84fab170e9f21cc6590abef94c4eace7b2bd1c6f |
import os
import tempfile
import StringIO
import pwd
import subprocess
from cgi import FieldStorage
from galaxy import datatypes, util
from galaxy.util.odict import odict
from galaxy.datatypes import sniff
from galaxy.util.json import dumps
from galaxy.model.orm import eagerload_all
from galaxy.exceptions import Object... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/tools/actions/upload_common.py | Python | gpl-3.0 | 22,064 | [
"Galaxy"
] | ba8457a8becd10212ef89b90e8062030c3386a579e1be5824150bc5900fa5320 |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or ... | ack8006/Python-mode-klen | pymode/libs/pylama/lint/pylama_pylint/pylint/checkers/exceptions.py | Python | lgpl-3.0 | 13,694 | [
"VisIt"
] | a2a2408e00b96f41a66f9582d1be056a8a6c1ef2eac2d2c3d1c477223568592c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# (c) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
#... | grimmjow8/ansible | lib/ansible/modules/files/find.py | Python | gpl-3.0 | 13,484 | [
"Brian"
] | a3fdd51ff3f2b0619a50cd76c361bf609ae7a148d7b7a0cbdbf046eff9574530 |
# -*- coding: utf-8 -*-
# This file as well as the whole tsfresh package are licenced under the MIT licence (see the LICENCE.txt)
# Maximilian Christ (maximilianchrist.com), Blue Yonder Gmbh, 2016
"""
This module contains the feature calculators that take time series as input and calculate the values of the feature.
Th... | blue-yonder/tsfresh | tsfresh/feature_extraction/feature_calculators.py | Python | mit | 81,590 | [
"ADF",
"DIRAC"
] | 5f86218a78f663cc5d8d7c27c88cc3142bd67cf12fe32e743d03e98d23d19d1d |
# coding: utf-8
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import random
import re
import socket
import sys
import time
import math
from ..compat import (
compat_cookiejar_Cookie,
compat_cookies,
compat_etree_Element,
compat_... | Orochimarufan/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 141,278 | [
"VisIt"
] | 022b324a59b7970fe089bb17e473e491836853a6990af821db7e3b80e10acb3e |
""" This module contains the function
to generate core-shell A@B nanoparticle with FCC structure.
"""
from __future__ import print_function
import random
import copy
from math import sqrt
from ase.neighborlist import NeighborList
from ase.cluster.cubic import FaceCenteredCubic
import numpy as np
from qsar import QSA... | lavakyan/ase-bimetall | coreshell.py | Python | gpl-2.0 | 20,123 | [
"ASE",
"CRYSTAL"
] | 01f21c24122a9e35fa7a11aefd83c1edf07f22986ea85e06c5723e89ec965955 |
#!/usr/bin/env python
# Copyright 2012-2014 VPAC
#
# 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, or
# (at your option) any later ... | Karaage-Cluster/karaage-applications | setup.py | Python | gpl-3.0 | 2,622 | [
"Brian"
] | 9756f8b5f4c602d67a2279f7c611e6f414b2fa6f8484ac67186e7951f3373fc0 |
#!/usr/bin/env python
import respirnet
import numpy as np
import networkx as nx
import sys
import argparse
'''
This class outputs a file (.gml) that contains a network for the pre-bot and botzinger complex based on the desired network parameters. This class allows you to vary the architecture based on the amount... | kharris/prebotc-graph-model | graphs/genPreBotBot_gamma.py | Python | bsd-3-clause | 3,156 | [
"NEURON"
] | 8f0b19b0ec51abb38cb3b36896a3ebab8b0b6fb11079219bc2d4e559a8b3bc54 |
import ast
import logging
class InvalidSortError(Exception):
pass
def sort_parse(clause):
"""
Parses sort clause.
Sort Clause Identifier Rules:
Prefix + Identifier
Prefix Rules:
Is optional
Must start with a-z OR A-Z
Can contain a-z OR A-Z OR 0-9 OR _
Mu... | pegasus-isi/pegasus | packages/pegasus-python/src/Pegasus/service/_sort.py | Python | apache-2.0 | 2,470 | [
"VisIt"
] | 268d163e80bf7acf46d8a0d494522b5b51896586f772f2ba6fd81c5b780bd0cf |
from glob import glob
from subprocess import Popen, PIPE
from math import pow
from math import floor
#from rpy2.robjects.packages import importr
import os
import re
import sys
from tiffparser import TiffParser
def getDaymetData(tiffName, ulLat, ulLon, lrLat, lrLon, startYear=2013, endYear=2013, option='tmin'):
""... | Nocsaron/Sol | ua_hpc_version/sol/0.0.1/process_dem.py | Python | gpl-3.0 | 9,450 | [
"NetCDF"
] | 6dec87157246715b5f46f29ac1aa944d441ab243bf6caf0853dfbb236ad50c03 |
"""
This module contains updated code for providing user updates on searches in Goat.
Not sure if this will work properly without threading, but will try; either way,
trying to separate user information for searches from the search itself, and
provide a better way to feed back the callback from a search to the main GUI... | chris-klinger/Goat | gui/searches/new_threaded_search.py | Python | gpl-3.0 | 17,902 | [
"BLAST"
] | 97a720b460c62211869ff57fbc42d6d9df6f96fb0487545746593b8419ec684e |
import math, scipy, numpy as np
class Lin_Alg:
'''
CLASS CONTAINING STATIC LINEAR ALGEBRA HELPER FUNCTIONS
'''
@staticmethod
def update_mat_inv(M_inv, X, mu = None):
'''
FUNCTION TO GET DYNAMICALLY CHANGING MATRIX'S INVERSE
ARGUMENTS: 2
M_inv : Curren... | rakshify/GLM_MAB | code/policies/helper.py | Python | mit | 4,433 | [
"Gaussian"
] | 47eb377e373a5ba53a445193aacc4892f008f1094ca5fb167b18ef38eafe239c |
from math import sqrt
import numpy as np
from sklearn.gaussian_process.kernels import Kernel as sk_Kernel
from sklearn.gaussian_process.kernels import ConstantKernel as sk_ConstantKernel
from sklearn.gaussian_process.kernels import DotProduct as sk_DotProduct
from sklearn.gaussian_process.kernels import Exponentiation... | scikit-optimize/scikit-optimize | skopt/learning/gaussian_process/kernels.py | Python | bsd-3-clause | 14,794 | [
"Gaussian"
] | 693247542d875f8ebbe6bd362348151e5a517a8f17bcd7703a4087ff2457e4a1 |
from __future__ import print_function, division, absolute_import
from mdtraj.utils.six import PY2
import abc
import re
import numpy as np
import warnings
from mdtraj import io
from msmbuilder.metrics.baseclasses import AbstractDistanceMetric, Vectorized
import inspect
class RedDimPNorm(Vectorized, AbstractDistanceMet... | msmbuilder/msmbuilder-legacy | MSMBuilder/metrics/projection.py | Python | gpl-2.0 | 4,136 | [
"MDTraj"
] | df9a9ecfc594cf3e905767e0ec4ef9b7acc0021a7de98f48faf40d85549f95f1 |
input_name = '../examples/multi_physics/thermo_elasticity_ess.py'
output_name = 'test_thermo_elasticity_ess.vtk'
from tests_basic import TestInput
class Test(TestInput):
pass
| RexFuzzle/sfepy | tests/test_input_thermo_elasticity_ess.py | Python | bsd-3-clause | 180 | [
"VTK"
] | 758a3fb3e535b0280de2c85dee98abfd9a5801f4fb6c07983b7826b3e7ddc4e0 |
r"""OS routines for Mac, DOS, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, mac, or ce, e.g. unlink, stat, etc.
- os.path is one of the modules posixpath, ntpath, or macpath
- os.name is 'posix', 'nt', 'os2', 'mac', 'ce' or 'riscos'
- os.curdir is a string r... | OS2World/APP-INTERNET-torpak_2 | Lib/os.py | Python | mit | 21,064 | [
"VisIt"
] | fb137bff7a9a43ebf54ba75251caf71317c26e8950093eb97320c65ec0634a2e |
# coding: utf-8
# In[ ]:
from Geometry import *
import numpy as np
#import matplotlib
import os
#os.environ['ETS_TOOLKIT'] = 'qt4'
#os.environ['QT_API'] = 'pyqt'
from PlotOctTree import mayaviPlot,plotOctTree
import astropy.units as au
import astropy.time as at
import astropy.coordinates as ac
#from E... | Joshuaalbert/IonoTomo | src/ionotomo/geometry/oct_trees/Inversion.py | Python | apache-2.0 | 38,631 | [
"Mayavi"
] | f088a8af0c766ad57658d515e746e92e3e7dbe9b8deee7f4c9a066949b0ceb89 |
# This Python file uses the following encoding: utf-8
# !/usr/local/bin/python3.4
####################################################
# This file is part of MULLPY.
#
# MULLPY is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the F... | enanablancaynumeros/mullpy | mullpy/classifiers.py | Python | mit | 70,005 | [
"Gaussian",
"NEURON"
] | 928c26c7fa29bec6a74060f069e5dcad416e3059ac340c5e225dbeea46cb3559 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Use callback method to save CASSCF orbitals in each iteration.
See also pyscf/examples/scf/24-callback.py
'''
import numpy
from pyscf import gto, scf, mcscf
mol = gto.M(
atom = [
["F", (0., 0., 0.)],
["H", (0., 0., 1.6)],]... | gkc1000/pyscf | examples/mcscf/24-callback.py | Python | apache-2.0 | 943 | [
"PySCF"
] | f5de79d6061bd316eeff51e62a06db523356e5d13264b350a2019f9192a07802 |
#!/bin/env python
""" script to obtain release notes from DIRAC PRs
"""
from collections import defaultdict
from datetime import datetime, timedelta
import argparse
from pprint import pformat
import logging
import textwrap
import requests
try:
from GitTokens import GITHUBTOKEN
except ImportError:
raise ImportErro... | andresailer/DIRAC | docs/Tools/GetReleaseNotes.py | Python | gpl-3.0 | 9,834 | [
"DIRAC"
] | 3a4de5f8cc827262e3b1d060be8ce703db05c36bc19da642b23c1ea3c6f1a35b |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'SurveyQuestion.statistic'
db.delete_column(u'survey_sur... | myvoice-nigeria/myvoice | myvoice/survey/migrations/0005_auto__del_field_surveyquestion_statistic.py | Python | bsd-2-clause | 12,627 | [
"VisIt"
] | 781ddfd92160c9b669811fefb9ea2a32720c5775e612661de63dd79be66b863a |
# Copyright 2014 Roberto Brian Sarrionandia
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | sarrionandia/tournatrack | main.py | Python | apache-2.0 | 1,267 | [
"Brian"
] | f0668d5cc9f44d844fbc2d9591eddd663c16fdfff10a6186a8095228b5ec8bca |
# -*- coding: utf-8 -*-
# This file is part of Shuup.
#
# Copyright (c) 2012-2021, Shuup Commerce Inc. All rights reserved.
#
# This source code is licensed under the OSL-3.0 license found in the
# LICENSE file in the root directory of this source tree.
import decimal
import os
import pytest
import selenium
from seleni... | shoopio/shoop | shuup_tests/browser/admin/test_refunds.py | Python | agpl-3.0 | 5,946 | [
"VisIt"
] | c71a6e8b823c1208c40278b1b8ea521694a32ca9cd70ed9013678f6b72271ff0 |
import sys
sys.path.insert(1, "../../")
import h2o, tests
def metric_accessors(ip,port):
cars = h2o.import_file(path=h2o.locate("smalldata/junit/cars_20mpg.csv"))
r = cars[0].runif()
train = cars[r > .2]
valid = cars[r <= .2]
# regression
response_col = "economy"
distribution = "gaussian"... | bospetersen/h2o-3 | h2o-py/tests/testdir_misc/pyunit_metric_accessors.py | Python | apache-2.0 | 39,151 | [
"Gaussian"
] | 2fa3166140c9ca1b7534655ef655426eeff3f54bb37caefc7713d019e9bf8a9f |
# ##### BEGIN GPL LICENSE BLOCK #####
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distrib... | Passtechsoft/TPEAlpGen | blender/release/scripts/addons_contrib/io_scene_fpx/__init__.py | Python | gpl-3.0 | 6,269 | [
"CRYSTAL"
] | 0a6163ddfabfcde4340a182f060e1375cb690dd3fda8fd75b4faa2a3df5fbd9c |
from __future__ import print_function
import numpy as np
from ..utils import Util2d, Util3d, Transient2d, MfList, \
HeadFile, CellBudgetFile, UcnFile, FormattedHeadFile
from ..mbase import BaseModel
from ..pakbase import Package
from . import NetCdf, netcdf
from . import shapefile_utils
NC_UNITS_FORMAT = ... | bdestombe/flopy-1 | flopy/export/utils.py | Python | bsd-3-clause | 38,049 | [
"NetCDF"
] | 084f395428ed599857bcab053e67da17354da8f2a684421cbc5c330bffe8ff8a |
#!/usr/bin/env python
# -*- coding: utf-8
from __future__ import division
from __future__ import absolute_import
from __future__ import print_function
import msvcrt
import os
import ConfigParser
import sys
import argparse
import logging
import json
import urllib
import urllib2
import urlparse
import base64
import sub... | jalandra/cool_scripts | crucible.py | Python | gpl-3.0 | 47,518 | [
"VisIt"
] | f0e7e3d692c4b42eec18542e8ea02f5b9615b174ce9253da588f1324a6173c92 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2014 - 2019 Adam.Dybbroe
# Author(s):
# Adam.Dybbroe <adam.dybbroe@smhi.se>
# 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, ei... | adybbroe/mesan_compositer | mesan_compositer/make_ctth_composite.py | Python | gpl-3.0 | 17,392 | [
"NetCDF"
] | b40724a55e36aaa1c5f92eaa05718c3de5dda2bcfc9d259b35ee4b98b2a22d8b |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def GetRGBColor(colorName):
'''
Return the red, green and blue components for a
color as doubles.
'''
rgb = [0.0, 0.0, 0.0] # black
vtk.vtkNamedColors... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Common/DataModel/Testing/Python/SelectionLoop.py | Python | gpl-3.0 | 2,191 | [
"VTK"
] | 6e334d589a8739ed0dfbcce03865a715a325f2c7db14c58a8a7abd7464c335f0 |
"""
============================================
Reading BEM surfaces from a forward solution
============================================
"""
# Author: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#
# License: BSD (3-clause)
print(__doc__)
import mne
from mne.datasets import sample
data_path = sampl... | effigies/mne-python | examples/plot_read_bem_surfaces.py | Python | bsd-3-clause | 1,129 | [
"Mayavi"
] | 2268d04bb143fa57178e91f08dc9be1bffa08c8f02175ec45c568cefddfa3963 |
# -*- coding: utf-8 -*-
"""
Created on Tue Sep 22 14:23:47 2015
@author: lpinello
"""
import os
import errno
import sys
import subprocess as sb
import glob
import argparse
import unicodedata
import string
import re
import multiprocessing
import logging
logging.basicConfig(level=logging.INFO,
... | lucapinello/CRISPResso | CRISPResso/CRISPRessoPooledCORE.py | Python | agpl-3.0 | 50,699 | [
"Bowtie"
] | 35f8fb15dca2d7a34dd2b7c730feb607a9112ae057f54c55d7268f8a58696f8e |
"""Translate a Python AST to JavaScript
"""
import ast
import contextlib
import functools
import inspect
import textwrap
from collections import ChainMap
import ibis.expr.datatypes as dt
from .find import find_names
from .rewrite import rewrite
class SymbolTable(ChainMap):
"""ChainMap subclass implementing sco... | ibis-project/ibis-bigquery | ibis_bigquery/udf/core.py | Python | apache-2.0 | 17,287 | [
"VisIt"
] | bb3be62ec5d12cef85f793d2aec14ec809a4dcdf69062dfc1ad0b8692cf69543 |
import copy
import cv2
from matplotlib import pyplot as plt
import numpy as np
import regional
from scipy import interpolate
from skimage import segmentation
from skimage.draw import ellipse
from skimage.feature import peak_local_max
class ImageProcModel():
# Amount to increase around a neuron when extracting a t... | gvanhorn38/active_neurofinder | baselearners/imageproc/model.py | Python | mit | 8,168 | [
"NEURON"
] | a3457af0410d3efacd3218b48fe2ea32324fc6d0986739922a5be2119fe99c00 |
## @namespace pygenn.genn_model
"""
This module provides the GeNNModel class to simplify working with pygenn module and
helper functions to derive custom model classes.
GeNNModel should be used to configure a model, build, load and
finally run it. Recording is done manually by pulling from the population of
interest a... | genn-team/genn | pygenn/genn_model.py | Python | gpl-2.0 | 78,477 | [
"NEURON"
] | 81f054a976bd86229712a46e649b84cd53b5b9dbe07c99e7034bd10c5c7ddd76 |
"""
Module responsible for translating variant data into GA4GH native
objects.
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import datetime
import random
import hashlib
import pysam
import ga4gh.protocol as protocol
import ga4gh.exceptions as excep... | ekalosak/server | ga4gh/datamodel/variants.py | Python | apache-2.0 | 19,752 | [
"pysam"
] | 6cc8f6c13ebfb35a5fb3b261f29d90e536dace6ffafb4c0f2d55a2cad92dc9c4 |
# -*- coding: utf-8 -*-
# ---
# jupyter:
# jupytext:
# formats: ipynb,py
# text_representation:
# extension: .py
# format_name: light
# format_version: '1.5'
# jupytext_version: 1.13.4
# kernelspec:
# display_name: Python 3
# language: python
# name: python
# ---
# # Rie... | pymanopt/pymanopt | examples/notebooks/mixture_of_gaussians.py | Python | bsd-3-clause | 11,003 | [
"Gaussian"
] | 6f6c55d3421f2514021c4dd7e47e0825e4599ebc52ca9d2a91184f049fd5a3a0 |
import abc
from collections import OrderedDict
from ctypes import POINTER, c_void_p, c_int, sizeof
from functools import reduce
from itertools import product
from operator import mul
from sympy import Integer
from devito.data import OWNED, HALO, NOPAD, LEFT, CENTER, RIGHT, default_allocator
from devito.ir.equations i... | opesci/devito | devito/mpi/routines.py | Python | mit | 42,676 | [
"VisIt"
] | 3b4bffe727ea2a34c3b9067489ccf1b685828077602cb1eaa0a8c1b9cdbdfa05 |
# Extract matrices from Gauusian .log files and write them to text.
# Copyright (C) 2013 Joshua J Goings
#
# 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
... | jjgoings/gaussian_matrix_parser | gauss_parse.py | Python | gpl-3.0 | 6,566 | [
"Gaussian"
] | ebaefb0c78f9ae68ba276347e6a92e27a3fc2df68068b24ac9f09af99620b115 |
from __future__ import division
from rdkit import RDConfig
import unittest
from rdkit.DataManip.Metric import rdMetricMatrixCalc as rdmmc
import numpy
import random
from rdkit import DataStructs
def feq(v1, v2, tol2=1e-4):
return abs(v1 - v2) <= tol2
class TestCase(unittest.TestCase):
def setUp(self):
pass... | rvianello/rdkit | Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py | Python | bsd-3-clause | 3,864 | [
"RDKit"
] | ddd25a60dd3ca99edacbe4fdbd314571d5bee7aa4723de2388761643461e18f6 |
#
# game.py - core game functionality
#
# Space Travel
# Copyright (C) 2014 Eric Eveleigh
#
# 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
... | mre521/space-travel | game.py | Python | gpl-3.0 | 31,233 | [
"Gaussian"
] | da904a72eda3e749d265368a353224fdfdac9c97503e83a933fd321cbf44582f |
"""Create index file for atoms or distance pairs.
This index file can be used by for RMSD distance calculations, to specify
pairs of atoms for AtomPairsFeaturizer, or to specify particular atoms
for SuperposeFeaturizer.
The format of the index file is flat text, with each line containing either
1 or 2 0-based atom in... | msultan/msmbuilder | msmbuilder/commands/atom_indices.py | Python | lgpl-2.1 | 3,793 | [
"MDTraj"
] | ed7049d9b7ed7e24710795410b41f38630d6b4ca908e30d4b707bbf7e07fa527 |
# This file is part of the Printrun suite.
#
# Printrun 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.
#
# Printrun is distributed in ... | hg42/Printrun | printrun/pronsole.py | Python | gpl-3.0 | 71,843 | [
"Firefly"
] | 5e7d28b31856d05d93e0fd11df1d0cf34a7a122b0310929d9facacb861564009 |
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