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# $Id: docutils_xml.py 8368 2019-08-27 12:10:14Z milde $
# Author: David Goodger, Paul Tremblay, Guenter Milde
# Maintainer: docutils-develop@lists.sourceforge.net
# Copyright: This module has been placed in the public domain.
"""
Simple document tree Writer, writes Docutils XML according to
http://docutils.sourceforg... | sonntagsgesicht/regtest | .aux/venv/lib/python3.9/site-packages/docutils/writers/docutils_xml.py | Python | apache-2.0 | 7,134 | [
"VisIt"
] | 3fc03ca3c62711941798742b5c5f83def5c29b6f51644d7ce45bddfec2562178 |
#!/usr/bin/python
import argparse
import math
import numpy
from pnoise import noise2D, noise3D
def create_grid(width = 128, height = 128, roughness = 0.2, nc_file = None, vtk_file = None):
#init arrays
nc_x = []
nc_y = []
nc_values = {}
### Try to import netcdf ##
if nc_file:
try:
import netCDF4
from n... | Manuel1605/ASAGI | preprocess/gen_noise/create_noise_grid.py | Python | gpl-3.0 | 2,898 | [
"NetCDF",
"VTK"
] | 53dc5ce2134331a7280b4f26cf286f7e2d2bb4481918d371c7ad8d713531788d |
# -*- coding: utf-8 -*-
import json
import time
from django.db import connection, transaction, InternalError
from django.test import TestCase, TransactionTestCase
from django.test.client import Client
from guardian.shortcuts import assign_perm
from catmaid import history
from catmaid.control import tracing
from catma... | tomka/CATMAID | django/applications/catmaid/tests/test_skeleton_summary_tables.py | Python | gpl-3.0 | 13,264 | [
"NEURON"
] | 584617c6fc8bcb6edbbf20866d15b5eb18439b3b2d4cb1d6a49910642968a9f5 |
import ast
import random
import re
class CommentParser(ast.NodeVisitor):
def visit_Module(self, node):
self.strings = set()
self.generic_visit(node)
return list(self.strings)
def visit_Str(self, node):
self.strings.add(node.s)
@classmethod
def get_safe_prefix(cls, sour... | kybp/pyformat | pyformat/parser.py | Python | gpl-3.0 | 3,814 | [
"VisIt"
] | 57a6be8da8d60b5c97dca92284732185f7bd008cf094af2f50e9c6a6c5b3e579 |
#!/usr/bin/env python
#=========================================================================
#
# Copyright Insight Software Consortium
#
# 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
... | 151706061/SimpleITK | Examples/SimpleGaussianProcedural.py | Python | apache-2.0 | 1,305 | [
"Gaussian"
] | 81f14f4bccc84e13b7fb6078a250a681f79f3b687301429dedeb3f8ca91b2d65 |
# 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/middleware/threadlocals.py | Python | gpl-3.0 | 1,723 | [
"Brian"
] | 0116212cc9ade2c78a92ed1314fb1249d8e70678a1a9a35a7dfad78cd2fcb9ca |
# coding=utf-8
# --------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# Code generated by Microsoft (R) AutoRest Code Generator.
# Changes may ... | Azure/azure-sdk-for-python | sdk/hybridnetwork/azure-mgmt-hybridnetwork/azure/mgmt/hybridnetwork/models/_models.py | Python | mit | 75,375 | [
"ASE"
] | 5075c2848f16c03598493ad68aaeff4d3cf81e65b2475b485ddee3023140edaa |
from ase.asec.run import RunCommand
class PluginCommand(RunCommand):
def __init__(self, logfile, args, calculate_function):
RunCommand.__init__(self, logfile, args)
self.calculate_function = calculate_function
def calculate(self, atoms, name):
data = self.calculate_function(atoms, name... | alexei-matveev/ase-local | ase/asec/plugin.py | Python | gpl-2.0 | 389 | [
"ASE"
] | 412be9edf8d0759d64d3b9679ab98a7bf6ae34b20a3925acc49f498c3f815b90 |
# $HeadURL: $
''' DIRAC.ResourceStatusSystem.Policy package
'''
__RCSID__ = '$Id: $'
################################################################################
#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF#EOF | andresailer/DIRAC | ResourceStatusSystem/Policy/__init__.py | Python | gpl-3.0 | 251 | [
"DIRAC"
] | 8ffe2c63d26bec8f49e3eef1a750dd635faddc93cd9b17cba38212e911b2c518 |
#!/usr/bin/python
# Author: Felipe Molina (@felmoltor)
# Date: 05/2015
# Summary: Download nvd.nist.gov XML files containing CVE details.
# Parse it and saves in sqlite3 db
# LICENSE: GPLv2
from mechanize import *
from lxml import etree
import os
import datetime
import time
import gzip
import sqlite3
i... | felmoltor/NVDparser | nvdparser.py | Python | gpl-2.0 | 15,511 | [
"VisIt"
] | a36e8c1491bd52cd91fca10220862b09a90329656a32be33d97feae0faf493ab |
#import matplotlib.pyplot as plt
#%matplotlib inline
import nengo
import numpy as np
import scipy.ndimage
#import matplotlib.animation as animation
#from matplotlib import pylab
from PIL import Image
import nengo.spa as spa
import cPickle
import random
from nengo_extras.data import load_mnist
from nengo_extras.vision ... | science-of-imagination/nengo-buffer | Project/mental_scaling_training.py | Python | gpl-3.0 | 7,557 | [
"NEURON"
] | 75f7e5bf7cdfa1cdf7676f0079247dd6c5692d3d2c0748e807ccbff2150f38c9 |
import numpy as np
import PIL
import netCDF4
from giss import runlength
from PIL import Image # Necessary
import shutil
maskname = 'gmask1m.nc'
incname = 'ZETOPO1.NCEI.nc'
ivname = 'FOCEAN'
ofname = 'focean1m_gmask.png'
oncname = 'ZETOPO1.NCEI-SeparateGreenland.nc'
# Read continents from ETOPO1
with netCDF4.Datase... | citibeth/twoway | topo/regenerate_focean1_gmask.py | Python | gpl-3.0 | 3,002 | [
"NetCDF"
] | 6c1c75a42ff130dca017faac7c7b5ef79abd41c1d3bc40f8de96e9138c19e84a |
# -*- coding: utf-8 -*-
__author__ = 'Brian Jacobowski'
__email__ = 'bjacobowski.dev@gmail.com'
__version__ = '0.1.0' | ychaim/bbg | bbg/__init__.py | Python | bsd-3-clause | 118 | [
"Brian"
] | e0dae8399f6d882085ddd91d503ae3b166304dc398b3df8c3b43ef2b865f90d1 |
from mumax2 import *
from mumax2_geom import *
from math import *
Nx = 64
Ny = 32
Nz = 2
sX = 160e-9
sY = 80e-9
sZ = 5e-9
setgridsize(Nx, Ny, Nz)
setcellsize(sX/Nx, sY/Ny, sZ/Nz)
load('micromagnetism')
load('solver/rk12')
savegraph("graph.png")
setv('Msat', 800e3)
# setmask('Msat', ellipse())
setv('Aex', 13e-... | mumax/2 | certification/stdproblem5a/mumax/std5a.py | Python | gpl-3.0 | 2,184 | [
"VTK"
] | 89efe023f59693f14824cf011dcbc36b3c0d1ea1bb72fdf8fcc1ce5468befe3f |
"""Plotting functions for visualizing distributions."""
from numbers import Number
from functools import partial
import warnings
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.transforms as tx
from matplotlib.colors import to_rgba
from matplotlib.colle... | anntzer/seaborn | seaborn/distributions.py | Python | bsd-3-clause | 72,099 | [
"Gaussian"
] | adeaedea41153c863c7803b0859f088d0211a6ac066bce54444f8013ed5e272f |
# Copyright 2012 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of ngs_crumbs.
# ngs_crumbs 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, ... | JoseBlanca/ngs_crumbs | test/test_mapping.py | Python | gpl-3.0 | 14,354 | [
"BWA",
"pysam"
] | 9b3197ec5c8d457e2a1648faa6ad869a9795db07f8042c8a0a72fab393a5e232 |
import argparse
import csv
import os
import shlex
import shutil
import subprocess
import sys
import numpy
parser = argparse.ArgumentParser(description='''
Part II: Conducting the alignments to the psuedogenomes. Before\
doing this step you will require 1) a bamfile of the unique\
... | drosofff/tools-artbio | tools/repenrich/RepEnrich.py | Python | mit | 22,611 | [
"Bowtie"
] | 2dc0fb1b913e0bba86c25e099e329291637f29d2694eab350cee9112aa4e33b6 |
# Copyright 2011-2013 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# SPDX-License-Identifier: GPL-3.0-or-later
#
#
'''
Blocks and utilities for digital modulation and demodulation.
'''
# The presence of this file turns this directory into a Python package
import os
try:
from .digital_pyt... | dl1ksv/gnuradio | gr-digital/python/digital/__init__.py | Python | gpl-3.0 | 1,172 | [
"Gaussian"
] | 7195722b0b0f3144a5af018f0f7d118d8b8238a4f7cda9a17381879040831bc4 |
import sys
import os
import csv
import numpy
import logging
logger = logging.getLogger(__name__)
# NOTE: This file depends on numpy.add.at(), which requires numpy v1.8.0
def downsample_pointcloud( pointcloud_csv_filepath,
output_filepath,
scale_xyz=None,
... | nielsbuwen/ilastik | bin/downsample_pointcloud.py | Python | gpl-3.0 | 17,044 | [
"Gaussian"
] | 2ab0f7e610cc50a9eb09714eecf31ad6637b27ef52a6f4c72a117a344372e1fe |
"""
function for merging objects of Bayesflow Gaussian mixture models
"""
import numpy as np
import copy as cp
from logisticnormal import tMd
import scipy.optimize as spo
from mpi4py import MPI
class HGMMMerge(object):
"""
Object used to merging classes in a hGMM obj
if one wants non deafult i... | JonasWallin/Mixture | Mixture/Bayesflow/GmmMerge.py | Python | gpl-3.0 | 7,918 | [
"Gaussian"
] | 68863ee277948c87445569fb8805adeae4cc4f5ed9ea16590cd8a4cacd131c57 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2013, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | elkingtonmcb/nupic | src/regions/PictureSensorExplorers/rotate_block.py | Python | agpl-3.0 | 3,076 | [
"VisIt"
] | 38b684cb0e0b0c6d1fa63d0ab86f222270d24449f57f2820c71cbbc905e552bc |
"""Module for easy compartmental implementation of a `BRIAN network`_.
Build parts of a network via subclassing :class:`~pypet.brian.network.NetworkComponent` and
:class:`~pypet.brian.network.NetworkAnalyser` for recording and statistical analysis.
Specify a :class:`~pypet.brian.network.NetworkRunner` (subclassing op... | nigroup/pypet | pypet/brian/network.py | Python | bsd-3-clause | 33,480 | [
"Brian",
"NEURON"
] | f3a5188c583339315cc2be08f9c35581008705f1019e55fd80aa0aaa255301eb |
from __future__ import print_function
import functools
import os
import sys
from wadl2rst.nodes.char import CharNode
def resolve_external_code(base_path, tree, samples_path):
""" Resolve the code that <xsdxt:code> nodes refer to. """
# find all the code nodes
code_nodes = []
code_visitor = functoo... | annegentle/wadl2rst | wadl2rst/transformations/resolve_external_code.py | Python | apache-2.0 | 1,937 | [
"VisIt"
] | 5e2b453ccaa3484203adea3851cccc4849b72a1ab2f0f5f6638e94892237e458 |
#!/usr/bin/env python
# Copyright 2018 Informatics Matters Ltd.
#
# 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... | InformaticsMatters/pipelines | src/python/pipelines/rdkit/standardize.py | Python | apache-2.0 | 3,592 | [
"RDKit"
] | a9b8439e042a3ebfb1089f496837afe45815f217aebac8d228d28e5a91ea8833 |
#!/opt/local/bin/python
u"""
Make in.const.linreg and in.params.linreg to be used in linreg potential.
"""
import sys,os,random,math
#============================================================ Parameters
constfname='in.const.linreg'
paramfname='in.params.linreg'
#.....number of species
nsp = 2
#.....cutoff radiu... | ryokbys/nap | pmd/util/make_const-params_linreg.py | Python | mit | 5,729 | [
"Gaussian"
] | af3dd390b1b68ca77f5d43e8fe997525e3b8a8ea582652fc2f4fdfa45f193400 |
import time
from django.core.management import call_command
from fabric.api import local
from lettuce import step, world, before, after
from lettuce.django import django_url, mail
from splinter import Browser
####################
# Setup and teardown
####################
@before.all
def setup():
"""
Setup ea... | robrechtdr/inonemonth | inonemonth/core/features/terrain.py | Python | mit | 4,059 | [
"VisIt"
] | b578d84d329e4541d0782f13c4b9a124d15007d4e06cd847865dfc5c3ae8cf82 |
import radical.utils as ru
from radical.entk import Pipeline, Stage, Task
import os
import tarfile
import writeInputs
import time
class Replica(object):
#A replica class to hold replica information, potentially useful for replica states in asynchronous exchange
def __init__(self, rid, Temp, EPtot, rstate):
... | radical-cybertools/radical.repex | old/examples/Sync.py | Python | mit | 12,243 | [
"Amber",
"Gromacs"
] | 8fb09d597db3edeb7e5558db0bd66a05f1bd288c8ec9f0afedf0b616706bb7ae |
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..compat import compat_urllib_parse_unquote
from ..utils import (
clean_html,
ExtractorError,
determine_ext,
sanitized_Request,
)
class XVideosIE(InfoExtractor):
_VALID_URL = r'https?://(?:www\.)?xvideos\.co... | nandhp/youtube-dl | youtube_dl/extractor/xvideos.py | Python | unlicense | 2,556 | [
"Galaxy"
] | 0c7817f08d1d127a672f8acf2d607946fb409c935b7b3eafa73ad4fbc206d8b0 |
""" DIRAC FileCatalog component representing a directory tree with
a closure table
General warning: when we return the number of affected row, if the values did not change
then they are not taken into account, so we might return "Dir does not exist"
while it does.... t... | andresailer/DIRAC | DataManagementSystem/DB/FileCatalogComponents/WithFkAndPs/DirectoryClosure.py | Python | gpl-3.0 | 21,043 | [
"DIRAC"
] | 5790a6893d8fb6c5961c728e14352ae95d09b5c638d31ef2cb55d1796340b41a |
import core
import tappedout
import gracefulstats
import praw
import logging
import time
import traceback
import datetime
import getpass
import deckstatscom
TESTING = False
PRAW = praw.Reddit(user_agent=core.USER_AGENT)
PRAW.login(raw_input('user name: ').strip(), getpass.getpass().strip())
BOT_NOTICE = """
\n\nI'm ... | donaldpminer/edhrec | reddit.py | Python | mit | 7,549 | [
"VisIt"
] | 1f7e393541852a6074488259e606a5fc467600273c1b8ff862a57b6ae76b7bff |
"""
Summary:
Contains the ATool class an interface that all tools (i.e. file loaders,
etc) should inherit.
This was a integral part of these tools when they were written in Java
as they allowed the user interface to communicate with the tools through
an observer. In Python it's not needed becaus... | duncan-r/SHIP | ship/utils/atool.py | Python | mit | 3,436 | [
"VisIt"
] | 434d248431f63fc6462a75c00da0b48ee34d3df33eaf300a0ce0ddcd91089830 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2017 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | FarnazH/horton | horton/io/__init__.py | Python | gpl-3.0 | 1,573 | [
"CP2K",
"Gaussian",
"Molpro",
"VASP"
] | a600acd84396aa612fe8d9825f2296b6462b90db62c75984cb45deb23e432458 |
"""
Example ThirdWay experimentations.
"""
from __future__ import absolute_import, print_function
import matplotlib.pyplot as plt
import numpy as np
from thirdway.lightcurve import LightCurve, generate_lc_depth
from thirdway.fitting import run_emcee, summed_gaussians
# Load light curve from jrad's text archive
light_c... | jradavenport/ThirdWay | example.py | Python | mit | 1,928 | [
"Gaussian"
] | 1f0bbc7c5121c1d857344b6a02d429363f56aa1e1215f8475e9652419feb6774 |
# -*- coding: utf-8 -*-
"""
========================
Gaussian KDE and Extents
========================
Smooth marginalised distributions with a Gaussian KDE, and pick custom extents.
Note that invoking the KDE on large data sets will significantly increase rendering time when
you have a large number of points. You c... | Samreay/ChainConsumer | examples/customisations/plot_kde_extents.py | Python | mit | 1,039 | [
"Gaussian"
] | d8fc7bb99a55be4ab0e7acaca82a21ee1414b60b475c2c70ca934c8bfeca1baf |
#!/usr/bin/env python
from setuptools import setup, find_packages
"""
Documentation can be found at https://docs.python.org/2/distutils/index.html, but usually you only need to do the
following steps to publish a new package version to PyPI::
# Update the version tag in this file (setup.py)
python setup.py re... | pretix/cleanerversion | setup.py | Python | apache-2.0 | 2,313 | [
"Brian"
] | 8399aa95a3cd47fdb6cee2d77c30cea58b4407d180ace6cf75c6725bf33825e8 |
#!/usr/bin/env python
#
# $File: InitSex.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute it... | BoPeng/simuPOP | docs/InitSex.py | Python | gpl-2.0 | 1,369 | [
"VisIt"
] | 1ed007750ad61aa8e25781c58bc54faca07283bc86d0441cc18321160b0f639a |
#!/p/home/sblair/anaconda2/bin/python
# -*- coding: utf-8 -*-
"""
Pipe flow problem
Created on Thu Aug 3 11:32:57 2017
@author: stu
"""
import sys
sys.path.insert(1,'.')
import FluidChannel as fc
import argparse
parser = argparse.ArgumentParser(prog='pipe_flow_geom.py',
descriptio... | stu314159/pyNFC | pipe_flow_geom.py | Python | mit | 1,020 | [
"VTK"
] | 8a8e15ca33207b789b1ea8a46fdf24104f73ea93361d25c5dd0e27ca13cf91f3 |
#
# @file TestEvent.py
# @brief SBML Event unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file located at
# ... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestEvent.py | Python | bsd-3-clause | 7,729 | [
"VisIt"
] | 93eae4c917ef0a4a91abc1e30a2656f5b87ad48eb039f9c134d900f07e5980a5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# proteinExtractor_netcdfToPdb.py
#
# Copyright 2016 Carlos Eduardo Sequeiros Borja <casebor@gmail.com>
#
# 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 Soft... | casebor/labioscripts | python/proteinExtractor_netcdfToPdb.py | Python | gpl-3.0 | 3,068 | [
"MDTraj",
"NetCDF"
] | 008f45d0230f36a2d5f65cc78721d7de27384f5151fac5d1af908e08bf9020e2 |
from __future__ import print_function, division
import unittest
from hypothesis import given, assume
from hypothesis.strategies import integers, floats, builds
from numpy import pi, allclose, cos, sin, array, zeros
from elastic.elastic import get_deformed_cell, get_lattice_type
from elastic.elastic import get_vecang_c... | jochym/Elastic | test/test_elastic.py | Python | gpl-3.0 | 3,526 | [
"ASE"
] | 7b19746c262fe596fc71c1eb3e7aed26738046bd64d35e1964f963fd062c61fe |
# This file is part of xrayutilities.
#
# xrayutilities 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 distributed... | dkriegner/xrayutilities | lib/xrayutilities/materials/plot.py | Python | gpl-2.0 | 8,429 | [
"CRYSTAL"
] | ba612b1887aa25aa211a321c012e33ab7b8e96f4b39146d55f7e86c92d7c95eb |
#!/usr/env/bin python
# -*- coding: utf-8 -*-
"""
unit testing for MolVS steps for PubChem Substances
tests include
molvs.standardize_smiles
Standardizer().normalize
Standardizer().disconnect_metals
Standardizer().reionize
molvs.standardize.canonicalize_tautomer_smiles
molvs.validate.Validator()
Standardizer().fragment... | bp-kelley/rdkit | rdkit/Chem/MolStandardize/UnitTestMolVS.py | Python | bsd-3-clause | 8,981 | [
"RDKit"
] | 6d8887992fb1fac9d1a324186220a11aeb69ef1e1960e2461ed978ca77f675de |
#!/usr/bin/env python
#
# Data manager for reference data for the 'mothur_toolsuite' Galaxy tools
import json
import optparse
import os
import shutil
import sys
import tarfile
import tempfile
import urllib2
import zipfile
from functools import reduce
# When extracting files from archives, skip names that
# start with ... | Delphine-L/tools-iuc | data_managers/data_manager_mothur_toolsuite/data_manager/fetch_mothur_reference_data.py | Python | mit | 19,170 | [
"Galaxy"
] | 2a8d48d1bbd13d07d51680f6350194787e1a297df6c9ab6d1e78bb1ac50131b8 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'NeuronEphysLink'
db.create_table('neuroelectro_neuronephyslink', (
... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0012_auto__add_neuronephyslink__add_ephyspropsyn__add_ephysprop__add_datata.py | Python | gpl-2.0 | 13,218 | [
"NEURON"
] | 37e2a92523dadfcf063a17de47ec52bace1c3faa9c7794938b1793580e9a4ecb |
from ase.data import atomic_numbers, chemical_symbols, reference_states
from ase.units import *
from . import fcc
from . import hcp
from . import au
lattice = {'fcc': fcc.data,
'hcp': hcp.data,
}
element = {79: au.data, #Au
}
| suttond/MODOI | ase/cluster/data/__init__.py | Python | lgpl-3.0 | 260 | [
"ASE"
] | de7ea65e5ad22258b9c65d0e8ecef09808e4e38979bf7d4f4cb2c893fa2a671f |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | tests/licensedcode/test_tokenize.py | Python | apache-2.0 | 22,250 | [
"VisIt"
] | 952e93fda8f25438240e2f527746d88117b056964b3fcdb42a16a92734c21f2d |
# .. coding: utf-8
# $Id: __init__.py 7745 2014-02-28 14:15:59Z milde $
# Author: Engelbert Gruber, Günter Milde
# Maintainer: docutils-develop@lists.sourceforge.net
# Copyright: This module has been placed in the public domain.
"""LaTeX2e document tree Writer."""
__docformat__ = 'reStructuredText'
# code contributi... | ruibarreira/linuxtrail | usr/lib/python2.7/dist-packages/docutils/writers/latex2e/__init__.py | Python | gpl-3.0 | 124,497 | [
"VisIt"
] | ea56b35d2afa5829a782c90c3d28a86dd7c7b830e0601f7733316ee6e7b177bd |
"""
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 glob
import hashlib
import json
import os
import random
import re
import pysam
import google.protobuf.... | ohsu-computational-biology/server | ga4gh/datamodel/variants.py | Python | apache-2.0 | 53,277 | [
"pysam"
] | 7b043837dd989ad705558360d77a2ac0eddb89d9c688731ba30bb5b761396edc |
"""
Functions for the contacts script
"""
import numpy as np
import mdtraj as md
import itertools
import seaborn as sns
from matplotlib import pyplot as plt
import pandas as pd
import datetime
import uncertainties.unumpy as unumpy
def figure_dims(width_pt, factor=0.45):
"""
I copied this from here:
https:... | jeiros/Scripts | AnalysisMDTraj/contact_utils.py | Python | mit | 15,036 | [
"MDTraj"
] | ec88d4a0a77ae6641b87641f29b95353fe58f00f144b31a1663789116d23d91f |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Nodes for PPAPI IDL AST"""
#
# IDL Node
#
# IDL Node defines the IDLAttribute and IDLNode objects which are constructed
# by th... | blackenough/mediaAdapter | ppapitest/sdk/ppapi/generators/idl_node.py | Python | gpl-3.0 | 13,144 | [
"VisIt"
] | 791e7d3afe863eadc8faa6d2b64ce685146990ae23c2d7e0f2127f01f384bacc |
import math
import theano.tensor as T
# ----------------------------------------------------------------------------
# this is all taken from the parmesan lib
c = - 0.5 * math.log(2*math.pi)
def log_bernoulli(x, p, eps=1e-5):
"""
Compute log pdf of a Bernoulli distribution with success probability p, at valu... | kuleshov/deep-learning-models | models/distributions/distributions.py | Python | mit | 2,861 | [
"Gaussian"
] | e46f4d51a093b25f74632f5d14f1ed3c46ee98bc0c0066511c5701e59379a8d8 |
"""
Solving functions for neural network exploitation.
"""
import os
import random
import itertools
from functools import partial
from collections import deque
from neural_world import actions
from neural_world import default
from neural_world import atoms
from neural_world import commons
from neural_world import s... | Aluriak/neural_world | neural_world/neural_network.py | Python | gpl-2.0 | 6,445 | [
"NEURON"
] | 6c4b0882eb49e5aee3535e0827b83bb79555426c3f952914254510314ee0621c |
import numpy as np
import tempfile
from pele.systems import BaseSystem, dict_copy_update
from pele.angleaxis import MinPermDistAACluster, ExactMatchAACluster
from pele.angleaxis import TakestepAA
from pele.landscape import smoothPath
from pele.utils.elements import elements
from pele.utils.xyz import write_xyz
from p... | cjforman/pele | pele/angleaxis/aasystem.py | Python | gpl-3.0 | 7,254 | [
"PyMOL"
] | 0f7d5103e7ceb3bda1f22e8a65d0abe48e8de0499b4d25bc2e4b36518fbb5224 |
#!coding:utf-8
# Transmageddon
# Copyright (C) 2009 Christian Schaller <uraeus@gnome.org>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Library General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at you... | hailongqiu/new-deepin-media-player | src/format_conv/transmageddon.py | Python | gpl-3.0 | 64,866 | [
"DIRAC"
] | 9cbbf9aa40a0dbcdc5b3d4951aefe5d5c2db75a2cc3f9b9b0f82e89c328c0fed |
#!/usr/bin/env python
from sys import argv
import os
job = argv[1]
nodes = argv[2]
time = argv[3] + ":00"
if '--exclusive' in argv:
is_exclusive = True
argv.remove('--exclusive')
else:
is_exclusive = False
if len(argv) > 4:
gpaw_options = ' '.join(argv[4:])
else:
gpaw_options = ' '
#options = '-l... | RKBK/gpaw-customize-files | sherlock.stanford.edu.run_gpaw.py | Python | mit | 1,489 | [
"GPAW"
] | c295afa44894d9fe2ccd0b1661806bee1993d43bc8e4b561e5bfd3e52f9e6a04 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Module implementing classes and functions to use Zeo++.
Zeo++ Installation Steps:
========================
1) Zeo++ requires Voro++. Download Voro++ from code.lbl.gov using
subversion:
"svn checkout ... | gVallverdu/pymatgen | pymatgen/io/zeopp.py | Python | mit | 18,485 | [
"GULP",
"pymatgen"
] | 39b31c7b009c22b26950853d7a4cd5dfd45fb5e472c7f1f305374a07364cc55c |
#!/bin/python
import vtk
import vtk.util.colors
points = vtk.vtkPoints()
points.InsertNextPoint(0, 0, 0)
points.InsertNextPoint(0, 1, 0)
points.InsertNextPoint(1, 0, 0)
points.InsertNextPoint(0, 0, 1)
unstructuredGrid = vtk.vtkUnstructuredGrid()
unstructuredGrid.SetPoints(points)
unstructuredGrid.InsertNextCell(vtk.... | trianam/tests | python/vtkTetrahedron.py | Python | gpl-2.0 | 946 | [
"VTK"
] | 40b64c7869ae81a14b574a260085e890570a20221e4762448c4cb27fb3cb458b |
#!/usr/bin/env python
#
# uses pygmsh:
# https://github.com/nschloe/pygmsh
# https://pygmsh.readthedocs.io/en/latest/
#
# install with:
# pip install -U pygmsh
#
# this alreay includes module meshio. in case needed separately, install with:
# pip install -U meshio
#
# in case you have already created an input f... | geodynamics/specfem3d | EXAMPLES/Gmsh_simple_lddrk/mesh_example_with_Gmsh_simple.py | Python | gpl-3.0 | 24,097 | [
"VTK"
] | 5984fc39fcef6403bd4dcfd09fa0ed19d57fcc16a5d353f588b90605edcbfd32 |
import pyspeckit
# Grab a .fits spectrum with a legitimate header
sp = pyspeckit.Spectrum('G031.947+00.076_nh3_11_Tastar.fits')
""" HEADER:
SIMPLE = T / Written by IDL: Tue Aug 31 18:17:01 2010
BITPIX = -64
NAXIS = 1 / number of array dimensions
NAXIS1 = 8192... | bsipocz/pyspeckit | examples/ammonia_fit_example.py | Python | mit | 3,096 | [
"Gaussian"
] | 00d67c7fe785f38c8bbdb30746aa355d9a5a88ca8bf509a22add9067063b99c4 |
import vtk
import math
def map_to_blue_red_rgb(value):
tanh_value = math.tanh(value)
# Compute the hue
if tanh_value <= 0.0:
hue = 0.6 # blue
else:
hue = 0.0 # red
# Compute the saturation
sat = abs(tanh_value)
# Convert to RGB
return vtk.vtkMath.HSVToRGB((hue, sat, 1.0))
| zibneuro/brainvispy | vis/visutils.py | Python | bsd-3-clause | 304 | [
"VTK"
] | f04616acb149739e8ef1a50ce51ea24e03aa17f3e8e5219213cfdfd4ba071e10 |
import collections
class Solution(object):
def findItinerary(self, tickets):
"""
:type tickets: List[List[str]]
:rtype: List[str]
"""
targets = collections.defaultdict(list)
for a,b in sorted(tickets)[::-1]:
targets[a] += b,
route = []
prin... | quake0day/oj | Reconstruct Itinerary.py | Python | mit | 831 | [
"VisIt"
] | 2ada77d21f66b182c5125fc4fc51aec3b6fa06d44cea44a83a0f4f3fa14381f4 |
import numpy as np
class AdalineGD(object):
"""ADAptive LInear NEuron classifier.
Parameters
------------
eta : float
Learning rate (between 0.0 and 1.0)
n_iter : int
Passes over the training dataset.
Attributes
-----------
w_ : 1d-array
Weights after fitting.
... | 1iyiwei/pyml | code/ch02/adaline_gd.py | Python | mit | 1,648 | [
"NEURON"
] | 30d171b46fd9dc2ad08110bbbe4f41d80823bfe723440a52a81e19ab7a6326fe |
# -*- coding: utf-8 -*-
# Copyright (C) 2012, Almar Klein, Ant1, Marius van Voorden
#
# This code is subject to the (new) BSD license:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of s... | algrant/scrabble15 | images2gif.py | Python | mit | 36,936 | [
"NEURON"
] | 9aea3d7c4b9e3890a52115db906b06c50d35ecd2bdee33eccd225d17b244f740 |
from flask import Flask, render_template, session, request, redirect
import random
app = Flask(__name__)
app.secret_key = 'my_secret_key'
@app.route('/')
def index():
if not 'gold' in session:
session['gold'] = 0
if not 'activities' in session:
session['activities'] = []
return render_temp... | authman/Python201609 | Sparks_Steven/Assignments/Flask Olympics/olympics8/server.py | Python | mit | 1,501 | [
"CASINO"
] | 3d06c5388dca6092075cd44934c2f252987ae83e2822ed824164b0c792325a57 |
from sparktk.loggers import log_load; log_load(__name__); del log_load
from sparktk.propobj import PropertiesObject
import os
def train(frame,
observation_columns,
column_scalings,
k=2,
max_iterations=20,
convergence_tol=0.01,
seed=None):
"""
Creates ... | shibanis1/spark-tk | python/sparktk/models/clustering/gmm.py | Python | apache-2.0 | 7,465 | [
"Gaussian"
] | ed34a57d80b87ddd449059789a1077f3be935fbe7cf0dc0b92beee8f3948a8ec |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Test the cf module.
"""
# import iris tests first so that some things can be initialised before importing anything else
i... | pp-mo/iris | lib/iris/tests/test_cf.py | Python | lgpl-3.0 | 14,857 | [
"NetCDF"
] | 4965d5904aca73a192537feae1370707af1ff57510f6c51d18fe06a8424e6549 |
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
import numpy
from Bio.Cluster.cluster import *
def _treesort(order, nodeorder, nodecounts, tree):
# Find the order of the nodes consistent wit... | zjuchenyuan/BioWeb | Lib/Bio/Cluster/__init__.py | Python | mit | 24,900 | [
"Biopython"
] | 79cd9b02e4214d79eeecd14bc26c335970b14617987db807d5354b68dd4fa232 |
"""
The slice plane helper
@author: Chris Scott
"""
from __future__ import absolute_import
from __future__ import unicode_literals
import vtk
################################################################################
class SlicePlane(vtk.vtkActor):
"""
Slice plane.
"""
def __init__(self,... | chrisdjscott/Atoman | atoman/rendering/slicePlane.py | Python | mit | 1,665 | [
"VTK"
] | 3be2877c67304a2e4b340080029edb4c0321847fd432a09e8cdbab184a9d913e |
# Copyright (c) 2018 PaddlePaddle 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 app... | Canpio/Paddle | python/paddle/fluid/initializer.py | Python | apache-2.0 | 14,199 | [
"Gaussian"
] | eb086b55b2673fd91939849ae3d6d27df2aa5dd313e0404e5648ef1e0275dac3 |
"""setuptools.command.bdist_egg
Build .egg distributions"""
from distutils.dir_util import remove_tree, mkpath
from distutils import log
from types import CodeType
import sys
import os
import re
import textwrap
import marshal
from pkg_resources import get_build_platform, Distribution, ensure_directory
from setuptool... | martbhell/wasthereannhlgamelastnight | src/lib/setuptools/command/bdist_egg.py | Python | mit | 16,604 | [
"VisIt"
] | faea6207a7c5b66f1c412423d4b4435691b5f93d78dc3b170af5747e1d37bbb5 |
#
# Copyright 2014-2015, 2021 Lars Pastewka (U. Freiburg)
# 2017 Punit Patel (Warwick U.)
# 2014-2016 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or m... | libAtoms/matscipy | scripts/fracture_mechanics/energy_barrier.py | Python | lgpl-2.1 | 13,362 | [
"ASE",
"Matscipy"
] | 74e33cf1db1e7910fcf52dc31addfa2bad8393ded3eb05510ad826f06de821e6 |
#!/usr/bin/env python
# This application is released under the GNU General Public License
# v3 (or, at your option, any later version). You can find the full
# text of the license under http://www.gnu.org/licenses/gpl.txt.
# By using, editing and/or distributing this software you agree to
# the terms and condition... | solo2101/Tilo-Menu | src/lib/tilo/Tilo-Settings.py | Python | gpl-2.0 | 38,250 | [
"VisIt"
] | 834f3bd9c317ee5aaa7a63d85504cfc5f9a003e811439a64aafbf419a2718295 |
"""Analyze python import statements."""
from __future__ import absolute_import, print_function
import ast
import os
from lib.util import (
display,
ApplicationError,
)
VIRTUAL_PACKAGES = set([
'ansible.module_utils.six',
])
def get_python_module_utils_imports(compile_targets):
"""Return a dictiona... | tsdmgz/ansible | test/runner/lib/import_analysis.py | Python | gpl-3.0 | 8,617 | [
"VisIt"
] | 63ccf1cd362182597c93a34139df4e3dd1c89b53c43168a9c0a2af9b208bc430 |
api_number = {
# 500 - 599 - Internal File I/O API calls
"FILE_CREATE_AN": 500,
"FILE_OPEN_AN": 501,
"FILE_WRITE_AN": 502,
"FILE_CLOSE_AN": 503,
"FILE_LSEEK_AN": 504,
"FILE_READ_AN": 505,
"FILE_UNLINK_AN": 506,
"FILE_MKDIR_AN": 507,
"FILE_CHMOD_AN": 508,
"FILE_RMDIR_AN": 509,... | trel/irods-qgis | irods/api_number.py | Python | gpl-2.0 | 5,297 | [
"NetCDF"
] | e60b8a4a42a0eb6756d6f5ce0696f7e84134128986b2380f18a7465f7d9472bb |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2012 Nick Hall
# Copyright (C) 2012 Brian G. Matherly
# Copyright (C) 2012-2014 Paul Franklin
#
# 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
# t... | SNoiraud/gramps | gramps/plugins/textreport/alphabeticalindex.py | Python | gpl-2.0 | 4,553 | [
"Brian"
] | 58b5272bf0a019baa08642f08551ba70e001e7c0a0e5b4624264b410d962fc39 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Peter Eastman, Robert McGibbon
# Contributors: Kyle A. Beaucha... | marscher/mdtraj | MDTraj/core/topology.py | Python | lgpl-2.1 | 30,937 | [
"MDTraj",
"OpenMM"
] | 2ac19610ac6936c3acbe986cdf42537e407aa9d8b06a3b5bdade1645ea23602e |
import accumulator
import resultset
import masterdirac.models.run as run_mdl
import json
import logging
import collections
import boto
from boto.exception import S3ResponseError
from boto.s3.lifecycle import Lifecycle,Expiration
DEL_LIFECYCLE_PATTERN = '%s-lc-delete-all'
#the pattern for marking a bucket as deletable... | JohnCEarls/DataDirac | datadirac/aggregator/controller.py | Python | gpl-3.0 | 8,510 | [
"DIRAC"
] | 7552d073338ebbca1a0c89e9546986d75e3f19a8dd57476e5074583de7de88d7 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# logger - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of th... | heromod/migrid | mig/mig-xsss/logger.py | Python | gpl-2.0 | 2,455 | [
"Brian"
] | fe39f9ae3e76ff01ed89a55051794e46d29e54f021e8438f37b25ba2e645fa6f |
import nltk
import xml.etree.ElementTree as ET
from mimetypes import guess_type
from nltk.stem import PorterStemmer
from nltk.corpus import wordnet
from tokenizer import *
class MAE_Document:
"""A document object is constructed from an XML document file whose c_path is supplied as an initialization parameter. The ... | sethmachine/iaa | Corpora/mae_document.py | Python | mit | 12,862 | [
"Amber"
] | 97d095c51cd70c44431544381b672da7cde31c2d218b9bce1ac27564291d3c3e |
#!/usr/bin/env python
# Lint as: python3
"""This is the setup.py file for the GRR client.
This is just a meta-package which pulls in the minimal requirements to create a
full grr server.
"""
import configparser
import itertools
import os
import shutil
import subprocess
from setuptools import find_packages
from setup... | google/grr | grr/server/setup.py | Python | apache-2.0 | 7,872 | [
"GULP"
] | 50f31ff4cfce32d988760a82a20501511d6801f975e6150f587cb149cc1408a5 |
# -*- coding: utf-8 -*-
# Copyright 2007-2011 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | sillvan/hyperspy | hyperspy/_signals/simulation.py | Python | gpl-3.0 | 1,753 | [
"Gaussian"
] | 519cd7ec815eccdf6d9fc49a7113577afa4146374a215f8ee258bf6954b79004 |
#!/usr/bin/env python
# Copyright (c) 2015, Palo Alto Networks
#
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" A... | PaloAltoNetworks-BD/SplunkforPaloAltoNetworks | SplunkforPaloAltoNetworks/bin/lib/environment.py | Python | isc | 3,598 | [
"Brian"
] | 5a9858761796dde9dbf5562a9cbbac9602ecf806982360e6348a4e81f87f2efe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
PDB related functions used in the SCT suite of programs
"""
# Copyright 2014 University College London
# 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 L... | dww100/sct | python/sct/pdb.py | Python | apache-2.0 | 17,056 | [
"CHARMM"
] | 558d4062f4f5419f5b6091869ed4ebf7ad839c797583e39e66fd495dd6b3b8c3 |
from edc_constants.constants import YES, NO, NOT_APPLICABLE
from django import forms
from ..models import InfantFeeding
from .base_infant_model_form import BaseInfantModelForm
class InfantFeedingForm(BaseInfantModelForm):
def clean(self):
cleaned_data = super(InfantFeedingForm, self).clean()
sel... | botswana-harvard/tshilo-dikotla | td_infant/forms/infant_feeding_form.py | Python | gpl-2.0 | 13,306 | [
"VisIt"
] | 1588b40ef4fcdb08f255ec34f77e846f90306c7ae1060ae8ec29d121d4c920be |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | Garrett-R/scikit-learn | sklearn/cluster/k_means_.py | Python | bsd-3-clause | 53,933 | [
"Gaussian"
] | 2c75f4923b84c18d3c067bd1bd4b574fb6f55a8fab2ca70172760c09a9c040c1 |
from django.shortcuts import render, redirect
from django.http import HttpResponse
from django.db.models import Min, Count, Max
from django.conf import settings
from django.views.decorators.cache import cache_page
from django import forms
from construct.models import *
from structure.models import Structure
from prote... | protwis/protwis | construct/tool.py | Python | apache-2.0 | 81,937 | [
"CRYSTAL"
] | 12ee5a61a54c52b807eaffe85b0097cc41d6e6f9c6dfd64944e74d086d404b1a |
#!/usr/bin/env pvbatch
from paraview.simple import *
import pviz
import sys
oviz = pviz.viz(sys.argv) # instantiate viz object (and load data)
pviz.makeSlice( z = 0. ) # make slice
# Clip and zoom on a specific region around (x0,y0)
x0 =0.0
y0 =0.0
length=1.0
xmin=x0-length/2.; xmax= x0+length/... | ruizanthony/pviz | examples/simple/cut_z0_box.py | Python | lgpl-3.0 | 783 | [
"ParaView"
] | 7d5e4055c52012e90a0bc0332272fb94e6748bf8cd0347be2f46d73391d2e070 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS that utilize the
progress page.
"""
from __future__ import absolute_import
from contextlib import contextmanager
import ddt
from six.moves import range
from ...fixtures.course import CourseFixture, XBlockFixtureDesc
from ...pages.common.logout import LogoutPag... | ESOedX/edx-platform | common/test/acceptance/tests/lms/test_progress_page.py | Python | agpl-3.0 | 16,839 | [
"VisIt"
] | 3325fa76adf9a4347fc3c7288a0f98c38ffc55b30077501ddaf9636ac145f2ed |
# $Id$
#
# Copyright (C) 2008 Greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from aggdraw import Brush, Pen #@UnresolvedImport #py... | adalke/rdkit | rdkit/Chem/Draw/aggCanvas.py | Python | bsd-3-clause | 5,894 | [
"RDKit"
] | 19cf8090ad17efbe2149ac62317cde7a5e2132505d2bf0bef90b6b2d78f7efa4 |
from __future__ import division, absolute_import, print_function
import warnings
import sys
import collections
import operator
import numpy as np
import numpy.core.numeric as _nx
from numpy.core import linspace, atleast_1d, atleast_2d
from numpy.core.numeric import (
ones, zeros, arange, concatenate, array, asarr... | rudimeier/numpy | numpy/lib/function_base.py | Python | bsd-3-clause | 143,330 | [
"Gaussian"
] | 5ef37dd96c1f832b010e64f0386fb81485af147729b01dad8dec135cab69a1c8 |
# sql.py
# Copyright (C) 2005, 2006, 2007, 2008 Michael Bayer mike_mp@zzzcomputing.com
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Defines the base components of SQL expression trees.
All components are derived from a common base... | santisiri/popego | envs/ALPHA-POPEGO/lib/python2.5/site-packages/SQLAlchemy-0.4.5-py2.5.egg/sqlalchemy/sql/expression.py | Python | bsd-3-clause | 128,057 | [
"VisIt"
] | 248170ea323176d81dcbd5f08eb9d860d19d014ed7a62a239aaca42fda99bb01 |
"""
A number of function that enhance IDLE on MacOSX when it used as a normal
GUI application (as opposed to an X11 application).
"""
import sys
import tkinter
from os import path
_appbundle = None
def runningAsOSXApp():
"""
Returns True if Python is running from within an app on OSX.
If so... | theheros/kbengine | kbe/res/scripts/common/Lib/idlelib/macosxSupport.py | Python | lgpl-3.0 | 6,503 | [
"VisIt"
] | 454404f2e46b46394499f7a09e63dcc3c081d09a55d1cd638eb292529f094b7c |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import print_function
import ast
import gyp.common
import gyp.simple_copy
import multiprocessing
import os.path
import re
import shlex
import sig... | nodegit/node-gyp | gyp/pylib/gyp/input.py | Python | mit | 127,669 | [
"VisIt"
] | 54302ca528b3d118707084570fe732aa3d580d169be60b98b54c18bbeb0dfab3 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/dealii/package.py | Python | lgpl-2.1 | 17,758 | [
"NetCDF"
] | 6e93bb8b5552526c4df27e634633c95d6f8f370ad1a4511fd45fecacf70e1232 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
# Legal Notice
# ------------
# OPENFOAM is a trademark owned by OpenCFD Ltd
# (producer and distributor of the OpenFOAM s... | iulian787/spack | var/spack/repos/builtin/packages/foam-extend/package.py | Python | lgpl-2.1 | 16,449 | [
"ParaView"
] | 41f48a40102df07bc1e5c41bf3f563d3673cbd10d7088e7761161bc0ea24e81d |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy, ... | alexholcombe/dot-jump | dataRaw/Fixed Cue/test_dot-jump27Oct2016_11-29.py | Python | gpl-3.0 | 25,275 | [
"Gaussian"
] | b2a0541e301ddc6674a22e938f4baedc3af524fee8242c1e7ddf24563e9c54f5 |
# coding=utf-8
# --------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# Code generated by Microsoft (R) AutoRest Code Generator.
# Changes may ... | Azure/azure-sdk-for-python | sdk/databoxedge/azure-mgmt-databoxedge/azure/mgmt/datab/models/_models.py | Python | mit | 198,400 | [
"ASE"
] | fb2c487e25dcdd566e0989ea6c430aeeb50f701ea5a35ae57004b598fdc9e45e |
# Copyright 2011 by Eric Talevich. All rights reserved.
# 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.
"""Command-line wrapper for the tree inference program PhyML."""
__docformat__ = "restructuredte... | LyonsLab/coge | bin/last_wrapper/Bio/Phylo/Applications/_Phyml.py | Python | bsd-2-clause | 9,818 | [
"Biopython"
] | 633a3b839bb86f152e775fa01c24e405ee9c24d79f41110922ffc8905df09d1d |
# -*- coding: utf-8 -*-
#
# test_rate_instantaneous_and_delayed.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 vers... | lekshmideepu/nest-simulator | testsuite/pytests/test_rate_instantaneous_and_delayed.py | Python | gpl-2.0 | 3,690 | [
"NEURON"
] | 6cbcd4b3de0b972ffcbaa135ea4d764b4ca2cb06c1b6abebbb9c1301711f47fc |
"""
Core Harmonic Convolution Implementation
"""
import numpy as np
import tensorflow as tf
def h_conv(X, W, strides=(1,1,1,1), padding='VALID', max_order=1, name='h_conv'):
"""Inter-order (cross-stream) convolutions can be implemented as single
convolution. For this we store data as 6D tensors and filters a... | deworrall92/harmonicConvolutions | harmonic_network_ops.py | Python | mit | 14,546 | [
"Gaussian"
] | dbcfeb26bfabd3f3def3a666a4525445d668a320a17a602b2bfd348ebf156a8e |
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