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# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import numpy as np
from math import pi
import unittest
import os
from monty.os.path import which
from pymatgen.analysis.local_env import ValenceIonicRadiusEvaluator, \... | nisse3000/pymatgen | pymatgen/analysis/tests/test_local_env.py | Python | mit | 41,017 | [
"Jmol",
"pymatgen"
] | 1a17f24032cefbd5cbde666b35ade3b3eab81568694483c0cdcb73b1cc761e6e |
# (C) British Crown Copyright 2014 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris 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 3 of the License, or
# (at your option) any l... | decvalts/iris | lib/iris/tests/unit/fileformats/netcdf/test__load_aux_factory.py | Python | gpl-3.0 | 5,682 | [
"NetCDF"
] | 59a7c63933e030f654541b91868b65e2c3fcd6c76371ee3c623eb9debbf64c6b |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# PMDA
# Copyright (c) 2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher ve... | MDAnalysis/pmda | pmda/test/test_custom.py | Python | gpl-2.0 | 3,737 | [
"MDAnalysis"
] | af07676e7d3c601675ed0309a2a2404b74d0dece3edc12222677b12702886000 |
#!/usr/bin/env python
""" File Catalog Client Command Line Interface. """
# TODO: This should be modernised to use subprocess(32)
try:
import commands
except ImportError:
# Python 3's subprocess module contains a compatibility layer
import subprocess as commands
import os.path
import time
import sys
import ... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/Client/FileCatalogClientCLI.py | Python | gpl-3.0 | 80,558 | [
"DIRAC"
] | 8a731fc07272b162b611df2c37799be2d63cc3a98c590547e7c1c00fcee73929 |
# modified from https://gist.github.com/sorenbouma/6502fbf55ecdf988aa247ef7f60a9546
import gym
import numpy as np
import matplotlib.pyplot as plt
env = gym.make('CartPole-v0')
env.render(close=True)
#vector of means(mu) and standard dev(sigma) for each paramater
mu=np.random.uniform(size=env.observation_space.shape)
s... | vmayoral/basic_reinforcement_learning | tutorial11/code/cross_entropy_method.py | Python | gpl-3.0 | 2,825 | [
"Gaussian"
] | 1296f0b676c19fd0beb6b80a5b036b71785f062358edc329a0edb3bc02daf761 |
# Copyright 2019 DeepMind Technologies Limited
#
# 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 agr... | deepmind/open_spiel | open_spiel/python/pytorch/policy_gradient.py | Python | apache-2.0 | 19,835 | [
"Gaussian"
] | 433c7306ce0e5719d2be6cf3e9fde630ce313984863bbb6405a4283f139b4eef |
#!/usr/bin/python
# <!--------------------------------------------------------------------------
# This file is part of libSBMLSim. Please visit
# http://fun.bio.keio.ac.jp/software/libsbmlsim/ for more
# information about libSBMLSim and its latest version.
#
# Copyright (C) 2011-2013 by the Keio University, Yok... | TheCoSMoCompany/biopredyn | Prototype/src/libsbmlsim-1.1.0/examples/python/Test.py | Python | bsd-3-clause | 2,272 | [
"VisIt"
] | e7a1c98d0be2e731a02b1529d6cd7eb12bdb1ef93ef500eb139f753a9e00cc2e |
from aiida.orm.calculation.job import JobCalculation
from aiida.orm.data.parameter import ParameterData
from aiida.orm.data.structure import StructureData
from aiida.common.exceptions import InputValidationError
from aiida.common.datastructures import CalcInfo, CodeInfo
from aiida.common.utils import classproperty
fro... | abelcarreras/aiida_extensions | plugins/jobs/lammps/md.py | Python | mit | 9,997 | [
"Gaussian",
"LAMMPS",
"phonopy"
] | 8bbdb1ecde24ae231e4123d7c2b04c650e0f6ed911d957f6b1b21dc7e82695bc |
#!/usr/bin/env python
from __future__ import division
from __future__ import print_function
from builtins import zip
from builtins import map
from builtins import range
from builtins import object
from past.utils import old_div
import os
import sys
import glob
import math
from pyfits import getheader, getval
#import a... | boada/planckClusters | MOSAICpipe/legacy/CLUSTERpipe/find_position_SOI.py | Python | mit | 50,780 | [
"Galaxy"
] | 9494d79bf5779480935c4aebc2c29e8e785d9109b4b999c9c1d3e9a09b73bba8 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_fermi_dirac.py | Python | apache-2.0 | 1,194 | [
"DIRAC",
"PySCF"
] | aab15127ce01850b6bc345ba4028f151bc7014e519c29c9e66255c1afbcf9974 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import numpy as np
from matplotlib.ticker import AutoMinorLocator
from matplotlib.backends.backend_pdf import PdfPages
from ph_plotter.sf_plotter import SFPlotter
... | yuzie007/ph_plotter | ph_plotter/points_sf_plotter.py | Python | mit | 5,230 | [
"VASP",
"phonopy"
] | 9c0d3268ccea852f109e001281a9c3c1c1fba80f24d39f5458e34e4f5d81f822 |
import traceback
import os
import argparse
import multiprocessing
import subprocess
import hashlib
from functools import partial
import json
import base64
from external_cmd import TimedExternalCmd
import pysam
import pybedtools
from spades_contig import SpadesContig
from tigra_contig import TigraContig
from svregion ... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/MetaSV-0.5-py2.7.egg/metasv/run_age.py | Python | apache-2.0 | 17,773 | [
"pysam"
] | d7e8a7712f1befe392c8593bc4fada432f34512e9ea04ea3af930c8e67548a03 |
#!/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.
""" Generator for C style prototypes and definitions """
from __future__ import print_function
import glob
import os
import re
im... | chromium/chromium | ppapi/generators/idl_c_header.py | Python | bsd-3-clause | 12,596 | [
"VisIt"
] | f767fb2f0a2738526477cd5c3ec2915ded47d49dcc16ab142a6357cd2c6f3dc6 |
import numpy as np
from pybbn.gaussian.inference import GaussianInference
def get_cowell_data():
"""
Gets Cowell data.
:return: Data and headers.
"""
n = 10000
Y = np.random.normal(0, 1, n)
X = np.random.normal(Y, 1, n)
Z = np.random.normal(X, 1, n)
D = np.vstack([Y, X, Z]).T
... | vangj/py-bbn | docs/source/code/gaussian-cowell.py | Python | apache-2.0 | 1,275 | [
"Gaussian"
] | aaeaeab1ff77995bab808298617513a675b6196d1c760a5451a51e6f19683be0 |
#!/usr/bin/env python
"""
midi.py -- MIDI classes and parser in Python
Placed into the public domain in December 2001 by Will Ware
Python MIDI classes: meaningful data structures that represent MIDI events
and other objects. You can read MIDI files to create such objects, or
generate a collection of objects and use t... | zlv/peach | musicConvert/midi.py | Python | gpl-2.0 | 15,262 | [
"CRYSTAL"
] | 56327bf3aae8ff8885385927dcb5dee0ee64a4ab94101adc4e680006e3fa5418 |
#!/bin/python
### see 0926params.dict to change variables. This program creates an image stack of the data which is then input into sdssfitpsf.py. There a 2-d gaussian is fit to each image, and the resulting file is used to create a lightcurve using sdsslightcurve.py, or plotFullData.py
import numpy as np
from util.O... | bmazin/ARCONS-pipeline | examples/Pal2012-sdss/sdss_display_stack.py | Python | gpl-2.0 | 4,584 | [
"Gaussian"
] | f281e2f4ada73144dbf5cd0f32a3d2a95b50e411a7248b06f4c8feb48022a34b |
#!/usr/bin/python
# spud - keep track of photos
# Copyright (C) 2008-2013 Brian May
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | brianmay/spud | spud/management/commands/process_actions.py | Python | gpl-3.0 | 2,944 | [
"Brian"
] | a596d99b17efe0e3806950e7423e530d5922058cbca7fa21d322ec6f6c59e958 |
import configparser
import logging
import multiprocessing
import multiprocessing.managers
import multiprocessing.synchronize
import numbers
import os
import re
from typing import Optional, Set, Iterable, List, Tuple, Final, Iterator, Union
import appdirs
import numpy as np
from PyQt5 import QtCore
from .calculations.... | awacha/cct | cct/core2/processing/settings.py | Python | bsd-3-clause | 17,026 | [
"Gaussian"
] | 0caafcdf6eaa877365148da44f2c128b57c4a7b2cb1dc28cc4b784c58e5d3663 |
#!/usr/bin/python
#coding=utf8
##----------------------------------------------------------------------------##
## █ █ ##
## ████████ ##
## ██ ██ ... | AmazingCow/Linux_USBBootCreator | usbbootcreator.py | Python | gpl-3.0 | 14,421 | [
"VisIt"
] | 08cd3f51caf5e483ccc02f17f94d4677b3fb891c58bd681ad62dba4d739698f2 |
# -*- coding: utf-8 -*-
import numpy as np
#def hho(w,w0,q):
# return w0*w0/(w0*w0-w*w + i*w*w0/Q)
def Xd(w,w0,Q):
return (w0*w0*w0*w0-w0*w0*w*w)/( (w0*w0-w*w)*(w0*w0-w*w) + w*w*w0*w0/Q/Q )
def Yd(w,w0,Q):
return -w0*w0*w0*w/Q/( (w0*w0-w*w)*(w0*w0-w*w) + w*w*w0*w0/Q/Q )
def Xr(t,w,w0,Q):
return np.e**(-w*t/... | benschneider/dephasing_ringdown_sim | equations.py | Python | gpl-2.0 | 4,627 | [
"Gaussian"
] | 91bedb7c684e1f3021557af84550d572477aa6e66b341dcbf60b78088d3234bc |
# -*- coding:utf-8 mode:python; tab-width:4; indent-tabs-mode:nil; py-indent-offset:4 -*-
import os
import cPickle as pickle
import sys
import yaml
import sharedutilities
import geoprep
try:
from ebsel.src import EMSL_local
except ImportError:
msg = "Warning! Unable to import ebsel. Attempts to prepare calcula... | mattbernst/polyhartree | cpinterface.py | Python | gpl-3.0 | 18,738 | [
"Amber",
"GAMESS",
"NWChem"
] | 9001cda6cad1007e6df2c020b405b3b5d9fd31cc3473aaf5183f301b049f0763 |
import ocl
import pyocl
import camvtk
import time
import datetime
import vtk
import math
def main():
print(ocl.revision())
myscreen = camvtk.VTKScreen()
myscreen.camera.SetPosition(-15, -8, 15)
myscreen.camera.SetFocalPoint(0,0, 0)
# axis arrows
#camvtk.drawArrows(myscreen,center=(0,0,0... | aewallin/opencamlib | src/attic/cutsim/cutsim_07_circle.py | Python | lgpl-2.1 | 3,255 | [
"VTK"
] | bbb1a3a56fd155b8bf64455c273e29c51039d461f26096478c9ef27a32a6ee75 |
"""Perform GATK based filtering, perferring variant quality score recalibration.
Performs cutoff-based soft filtering when VQSR fails on smaller sets of variant calls.
"""
import os
from bcbio import broad, utils
from bcbio.distributed.transaction import file_transaction
from bcbio.log import logger
from bcbio.pipeli... | biocyberman/bcbio-nextgen | bcbio/variation/gatkfilter.py | Python | mit | 9,937 | [
"BWA"
] | 70d5a854009d6379dd0494f7f888b0516545da341b8496a15ff1df1c9b7f1533 |
#!/usr/bin/python
#FILE DESCRIPTION=======================================================
#~ Python script used for post-processing automatization of the rivulet
#~ flow down the experimental plate in Freiberg
#~
#~ NOTES:
#~ - before running, the main file has to be highlighted
#~ - can be ran from command l... | MartinIsoz/CFD_oF | 05_freibergExpSetUp/00_Scripts/rivuletPostProc.py | Python | gpl-2.0 | 6,765 | [
"ParaView"
] | 512c3ec0a61d351e2b1a41f96d20e3bc0989cc35b93ea30f5b5a7217c24a920b |
#!/usr/bin/env python
from AlGDock.BindingPMF import *
# vmd procedure to align the principal axes of the ligand to y and x.
vmd_principal_axes_procedure = '''
package require Orient
namespace import Orient::orient
set sel [atomselect 0 "all"]
set I [Orient::calc_principalaxes $sel]
set M1 [orient $sel [lindex $I 2]... | CCBatIIT/AlGDock | AlGDock/BindingPMF_plots.py | Python | mit | 18,368 | [
"VMD"
] | b94de257d59a47413f46cc7b26972e8ef8feea64a0c1ac26089c619957a6f152 |
#! /usr/bin/python
## \file menu.py
# \brief General Menu Class
# \author Scott Barlow
# \date 2009
# \version 1.0.3
#
# This is a menu class written for pygame/Python. The menu is designed to work
# with a program using a finite state machine (but it could also be easily
# modified to have the 'buttons' retu... | Spinnk/Robot-Murder-Investigation | menu.py | Python | gpl-3.0 | 34,276 | [
"TINKER"
] | 66d3cc7e6fc79d410d140403ab76aaa716b281736c60fa03dedcb777d49ebcfb |
__all__ = [
'PackedBinariesReader',
'MadagascarReader',
]
__displayname__ = 'Binary/Serialized File I/O'
import warnings
import numpy as np
import vtk
from .. import _helpers, interface
from ..base import ReaderBase
class PackedBinariesReader(ReaderBase):
"""This reads in float or double data that is ... | banesullivan/ParaViewGeophysics | PVGeo/readers/binaries.py | Python | bsd-3-clause | 7,433 | [
"VTK"
] | dbc35fed01377ccf08e03c6e14bb8ea4932443451caf3b3fc9da534b0d45153b |
#!/usr/bin/env python
# author : Kanika Sood
# Date : Aug 24, 2015
#This program takes in csv file (file with the predicted classes from Weka) and gives the top 10 most used solvers for PETSc
#python top10goodSolvers.py -f moose-petscRS2J48Results.csv
import csv, argparse, os
from collections import OrderedDict
impo... | LighthouseHPC/lighthouse | sandbox/petsc/solvers/scripts/top10goodSolvers.py | Python | mit | 3,070 | [
"MOOSE"
] | 34840c21273cd4be68c3aeb40fa1e87af15e54992a23d3c0d7b6e2b2fd60cc1a |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/widgets/core/FileBrowser.py | Python | gpl-3.0 | 22,567 | [
"ORCA"
] | 78e864c98b5870eafceaa563f0479d1be583bdd62107058bd3d4e324ed2a1a2f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This file is part of the PyNeurActiv project, which aims at providing tools
# to study and model the activity of neuronal cultures.
# Copyright (C) 2017 SENeC Initiative
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of th... | SENeC-Initiative/PyNeurActiv | models/fardet_2017_synchronous_bursting.py | Python | gpl-3.0 | 49,989 | [
"DIRAC"
] | 934ff33dd5f5a1ab96140842d2dc66ebbb36228bba33a403ec8073bdd3324dc3 |
"""
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
(at your option) any later version.
Written (W) 2013 Heiko Strathmann
Written (W) 2013 Dino Sejdinovic
"""
fro... | karlnapf/kameleon-mcmc | kameleon_mcmc/distribution/MixtureDistribution.py | Python | bsd-2-clause | 3,526 | [
"Gaussian"
] | 858f094f14a89e88051ab3613d8647a141eefdef7279ba283669c335b06b6eb6 |
# Copyright 2013 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | pombredanne/pytype | pytype/pytd/parse/node_test.py | Python | apache-2.0 | 6,979 | [
"VisIt"
] | e02254250f85f61aa6a47db2f827f8f4b5b122668057fdd73928d4103921f729 |
"""
Wrappers for calls to Mayavi2's `mlab` module for plotting
:mod:`fatiando.mesher` objects and automating common tasks.
**Objects**
* :func:`~fatiando.vis.myv.prisms`
* :func:`~fatiando.vis.myv.polyprisms`
* :func:`~fatiando.vis.myv.points`
* :func:`~fatiando.vis.myv.tesseroids`
**Misc objects**
* :func:`~fatian... | seancug/python-example | fatiando-0.2/fatiando/vis/myv.py | Python | gpl-2.0 | 32,551 | [
"Mayavi",
"VTK"
] | 9794f479a3124d06a7db22e28673af1926516f183823f5aa1119357a8dc2c4a2 |
# Storage filtering classes
#
# Copyright (C) 2013 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed... | kparal/anaconda | pyanaconda/ui/gui/spokes/filter.py | Python | gpl-2.0 | 27,523 | [
"VisIt"
] | 2b8c7d5c878e9883dc23de4f74ed6db4e4f4a4b2e364cf6c8f7d9e7161efda07 |
import logging
import os
from igraph import Graph
from parvusdb import GraphDatabase
_path = os.path.dirname(__file__)
class GraphJoinerVisitor:
__logger = logging.getLogger(__name__)
def __init__(self, drs):
self._rules = """
CREATE %s;
""" % str(drs)
def visit(self, g):
... | fractalego/pynsett | pynsett/discourse/global_graph_visitors.py | Python | mit | 2,046 | [
"VisIt"
] | bcec1786f71964c006f40ee1ab7b2506cb4278917f22283c75567de94add5ed0 |
#
# QAPI command marshaller generator
#
# Copyright IBM, Corp. 2011
# Copyright (C) 2014-2015 Red Hat, Inc.
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
# Michael Roth <mdroth@linux.vnet.ibm.com>
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
#... | akairain/QEMU | scripts/qapi-commands.py | Python | gpl-2.0 | 12,197 | [
"VisIt"
] | fa2ba490e0c0485bd729735c64db0ed61b35b1558cc5391802a7894e44355121 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Non-interactive command line front end to NBody implementation"""
import time
from nbodyphysics_original import move, random_galaxy
def nbody_benchmark(bodies_list, time_step):
"""Run benchmark simulation without visualization"""
x_max = 500
y_max = 500
... | dikujepsen/OpenTran | matlab/NBody/NBodyPy/nbody.py | Python | mit | 833 | [
"Galaxy"
] | 7fe0f1e878864f502ee67538077277fcf5e584258063df39dfb1293d9022f562 |
import collections
import optparse # using optparse as hyrda still python 2.6
import re
import sys
def report_error(error):
"""Prints the error, and exits -1"""
print error
sys.stderr.write(error)
sys.stderr.write("\n")
sys.stderr.flush()
sys.exit(1)
def clean_part(part, tab_replace=" "):
... | Christian-B/galaxy_shedtools | multi_merger/merge_files.py | Python | gpl-2.0 | 13,066 | [
"Galaxy"
] | 6f7e0d805c84e32d973ea58963d5ca279ed453436a999ee0a8d07419e3c34f10 |
from hotbit import Hotbit
from hotbit import LinearResponse
from hotbit.test.misc import default_param
from ase import *
from box import Atoms
plot=True
try:
import pylab as pl
except:
plot=False
import numpy as np
from box import mix
from ase.units import Hartree
Na3=Atoms('Na3',positions=[(1.6964... | pekkosk/hotbit | hotbit/test/test_lr.py | Python | gpl-2.0 | 1,022 | [
"ASE"
] | 957ede1c2617b2dbf5b87f9828fe4b202e81cf9b846a6731215101e2cd07af30 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005, 2006 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 Licen... | andrebellafronte/stoq | stoqlib/gui/base/slaves.py | Python | gpl-2.0 | 1,749 | [
"VisIt"
] | ecf7a4941cc84391d3e9564c466a7015e919758749ab4e021dfd9fd7dcc045ba |
import importlib
class FactoryMixIn:
def _get_data_area(self, module, classname):
"""Helper function to instantiate a data area or return a cached instance."""
if hasattr(self, "_cache_" + module):
return getattr(self, "_cache_" + module)
da_mod = importlib.import_module(f"{sel... | DiamondLightSource/ispyb-api | src/ispyb/interface/factory.py | Python | apache-2.0 | 1,516 | [
"CRYSTAL"
] | 4bfc33da91cca43a5afec30060bad912bb7a3f39ae9b7246793ba9a46c815192 |
from setuptools import setup, find_packages
version = '1.1.0'
setup(name='pyrabbit',
version=version,
description="A Pythonic interface to the RabbitMQ Management HTTP API",
long_description="""\
The main documentation lives at http://pyrabbit.readthedocs.org
There's no way to easily write progra... | vshn/pyrabbit-debian | setup.py | Python | bsd-3-clause | 1,641 | [
"Brian"
] | 3f58f1f554106dc29aefd27f8b8ccfc49b13ad66e4ee85f4c401380ae4f02157 |
#!/opt/local/bin/python2.5
#=============================================================================================
# Analyze a set of datafiles produced by YANK.
#=============================================================================================
#=====================================================... | choderalab/brokenyank | tools/analyzeall.py | Python | lgpl-3.0 | 10,892 | [
"Amber",
"NetCDF"
] | b23e31e675f1fc2b816926dcfa5e38d6443ff2709fb8a761d4a113e59a9b1caf |
#!/usr/bin/env python3
"""
This script is a python version of TimingAccuracyDHC. We use numpy functions to
simplify the creation of random coefficients.
"""
import time
import numpy as np
from pyshtools import expand
from pyshtools import spectralanalysis
# ==== MAIN FUNCTION ====
def main():
TimingAccuracyDHC(... | SHTOOLS/SHTOOLS | examples/python/TimingAccuracy/TimingAccuracyDHC.py | Python | bsd-3-clause | 2,762 | [
"Gaussian"
] | 51025c7e39b0ebe3073aa7f0cf2367946451b6be82b01079caa037c76b40aea6 |
''' targets.py
=========================
AIM: Class headers for the target_list class and load a catalogue of objects of interest
INPUT: function depend
OUTPUT: function depend
CMD: To include: from resources.targets import *
ISSUES: <none known>
REQUIRES: standard python libraries, specific libraries in resources... | kuntzer/SALSA-public | resources/targets.py | Python | bsd-3-clause | 5,222 | [
"VisIt"
] | 291f10fa5a2d1ffbf1dd04ee8a05d6ce32c7738ed3942af7104f5abbac9cb46c |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import argparse
import os
import sys
import logging
from os.path import join, dirname, abspath
import zeroinstall.injector.config
from zeroinstall import SafeException
from repo... | gfxmonk/0repo | repo/cmd/__init__.py | Python | lgpl-2.1 | 2,849 | [
"VisIt"
] | dc1c2a516f50ae31ddfcf4692b0cca065c2edf3d864978748d6c05031c2b6261 |
import unittest
import numpy as np
import pysal.lib
from pysal.model.spreg.ols import OLS
from pysal.model.spreg.ols_regimes import OLS_Regimes
from pysal.lib.common import RTOL
PEGP = pysal.lib.examples.get_path
class TestOLS_regimes(unittest.TestCase):
def setUp(self):
db = pysal.lib.io.open(pysal.lib.e... | lixun910/pysal | pysal/model/spreg/tests/test_ols_regimes.py | Python | bsd-3-clause | 7,529 | [
"COLUMBUS"
] | 9dbefed0bf20605ad53ba8f69312066ae76bd91b11542daef4982ec7fbbba57a |
import collections
import king_phisher.plugins as plugin_opts
import king_phisher.server.plugins as plugins
import king_phisher.server.signals as signals
import king_phisher.server.database.manager as db_manager
import king_phisher.server.database.models as db_models
import requests
EXAMPLE_CONFIG = """\
api_key: ... | securestate/king-phisher-plugins | server/ifttt_on_campaign_success.py | Python | bsd-3-clause | 3,222 | [
"VisIt"
] | fdf6a5430a6c165f1ec2d5610b232424e082c67e58e0317dc05dc32fc7c4e857 |
"""High level parallel SNP and indel calling using multiple variant callers.
"""
import os
import collections
import copy
import pprint
import six
import toolz as tz
from bcbio import bam, utils
from bcbio.cwl import cwlutils
from bcbio.distributed.split import (grouped_parallel_split_combine, parallel_split_combine)... | a113n/bcbio-nextgen | bcbio/variation/genotype.py | Python | mit | 22,094 | [
"Octopus"
] | 78007d29122598c16d08063cda35bcd7fc225f912496f5f3a8e8af0833da0091 |
# Original Version: Taehoon Kim (http://carpedm20.github.io)
# Source: https://raw.githubusercontent.com/carpedm20/DCGAN-tensorflow/master/model.py
# Modifications for image inpainting: Zack Soliman
import os
import time
import math
from glob import glob
import tensorflow as tf
import numpy as np
from ops import *
fro... | zacksoliman/conditional-image-generation | imagegen/models/dcgan/model.py | Python | mit | 18,520 | [
"Gaussian"
] | 7d439cc80f19a2fc084cb172f8cb9d5cda361ffade328899dcd0836540c4dd6a |
# $Id$
'''Deal with the tinker .prm file'''
from itcc.tinker import molparam
__revision__ = '$Rev$'
__all__ = ['Parameter', 'Torsionparameter', 'Parameters']
class Parameter:
pass
class Torsionparameter(Parameter):
def __init__(self, data):
assert 7 <= len(data) <= 10, str(data)
self.data = ... | lidaobing/itcc | itcc/tinker/parameter.py | Python | gpl-3.0 | 1,934 | [
"TINKER"
] | 5ab9b04074918a079365582c4966ad5914a0acb956ebba3e3bb39ff46becf238 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Support for reading XCrysDen files.
"""
from pymatgen.core.periodic_table import Element
__author__ = "Matteo Giantomassi"
__copyright__ = "Copyright 2013, The Materials Project"
__version__ = "0.1"
__mai... | gVallverdu/pymatgen | pymatgen/io/xcrysden.py | Python | mit | 3,625 | [
"CRYSTAL",
"pymatgen"
] | 0ea52612973d4b3af66be18b88dccc52e251710ea310e8c96496dab5637fb759 |
"""Generate self-contained HTML reports from MNE objects."""
# Authors: Alex Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Mainak Jas <mainak@neuro.hut.fi>
# Teon Brooks <teon.brooks@gmail.com>
#
# License: BSD (3-clause)
import base64
import os
import os.path as op
import fnmatch
import re
i... | teonlamont/mne-python | mne/report.py | Python | bsd-3-clause | 69,880 | [
"Mayavi"
] | beaf612ff9d09d55e9f402e36b2243d57ff2fd5265a3ccbb216478573be43a5e |
# $Id$
#
# Copyright (C) 2003-2006 Rational Discovery LLC
#
# @@ 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.
#
"""unit testing code for graph-theoret... | soerendip42/rdkit | rdkit/Chem/UnitTestGraphDescriptors.2.py | Python | bsd-3-clause | 24,674 | [
"MOE",
"RDKit"
] | 11cb816a98065667cd326c4d4a6fe0fce707d8d90f1f44f06bbf22e4ee06caac |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jiaphuan/models | research/differential_privacy/multiple_teachers/deep_cnn.py | Python | apache-2.0 | 21,836 | [
"Gaussian"
] | 6a38c3df06bd2188ea4a9d6e462c146a650819ef552bcf817e5cc7c2b8db09aa |
prior_dic = {}
def gaussian(pars, prior_pars=None, name=None):
''' Gaussian prior that returns a chi2 '''
mu = prior_pars[0]
sigma = prior_pars[1]
par = pars[name]
return (par-mu)**2/sigma**2
def gaussian_norm(pars, prior_pars=None, name=None):
''' Gaussian prior that returns a normalized lik... | igmhub/picca | py/picca/fitter2/priors.py | Python | gpl-3.0 | 554 | [
"Gaussian"
] | e4db475efed345c235cef1a53ef276a3d84c1037a2ce9cf91ece937a356dc77f |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | samples/reaction_ensemble.py | Python | gpl-3.0 | 3,578 | [
"ESPResSo"
] | 8cf2e9c2da3d1e17e2fbebba3cf6abb9b6df8ad9a9e72f0f8fdb89b349fe80cf |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# (c) The James Hutton Institute 2016-2019
# (c) University of Strathclyde 2019-2020
# Author: Leighton Pritchard
#
# Contact:
# leighton.pritchard@strath.ac.uk
#
# Leighton Pritchard,
# Strathclyde Institute for Pharmacy and Biomedical Sciences,
# 161 Cathedral Street,
# ... | widdowquinn/pyani | pyani/scripts/pyani_script.py | Python | mit | 6,228 | [
"BLAST",
"Biopython"
] | 1b414969a88250ad6bf8d739b535e0d8936703fd26eaf8b54f95245f49dbb958 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkWeightedTransformFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkWeightedTransformFilter.py | Python | bsd-3-clause | 507 | [
"VTK"
] | 0ba9db535df3cfd4fa3bdb7e19e799240f2d3b033340f969dd00d91a847d8fe3 |
"""Additional docstring for the DErrno module."""
class CustomDErrno(object): # pylint: disable=too-few-public-methods
"""Add the ERRNO constants to the docstring automatically."""
def __init__(self):
"""Create a string containing restructured text documentation for all the defined error numbers.
... | DIRACGrid/DIRAC | docs/diracdoctools/CustomizedDocs/CustomDErrno.py | Python | gpl-3.0 | 1,284 | [
"DIRAC"
] | 9def372b00a6705e8542e1fe1d36b6e9d375a02ea42324d6020f1989fe8740d0 |
import os.path
import time, random
import Krakatau
import Krakatau.ssa
from Krakatau.error import ClassLoaderError
from Krakatau.environment import Environment
from Krakatau.java import javaclass
from Krakatau.verifier.inference_verifier import verifyBytecode
from Krakatau import script_util
def findJRE():
try:
... | sahilshekhawat/ApkDecompiler | javadecompiler/decompile.py | Python | gpl-2.0 | 4,949 | [
"VisIt"
] | dc88eb6133fa86663974e543a67215c93250bdb199a68e91b0e79bd9282a89f7 |
# -*- coding: utf-8 -*-
import bson
import os
import pickle
import unittest
import uuid
import weakref
from datetime import datetime
from bson import DBRef, ObjectId
from tests import fixtures
from tests.fixtures import (PickleEmbedded, PickleTest, PickleSignalsTest,
PickleDynamicEmbedded, ... | cogniteev/mongoengine | tests/document/instance.py | Python | mit | 106,290 | [
"exciting"
] | 5888d67fa6fa62abc0d1a5a7d4b7ec355ffaf590cdc407636512a9557ee4ee5d |
import functools
import inspect
import os
import sys
import warnings
from collections import defaultdict
from collections import deque
from pathlib import Path
from types import TracebackType
from typing import Any
from typing import Callable
from typing import cast
from typing import Dict
from typing import Generator
... | nicoddemus/pytest | src/_pytest/fixtures.py | Python | mit | 65,428 | [
"VisIt"
] | 516837b37523dab8e9c78cc02dc315435bf6ec9590f3c0ec8ce504d69f7b5475 |
# Copyright 2016-2020 Amazon.com, Inc. or its affiliates. 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. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
#
# or in the "license" f... | gregbdunn/aws-ec2rescue-linux | tools/moduletests/unit/test_enadiag.py | Python | apache-2.0 | 15,925 | [
"VisIt"
] | 72e50f7fda603f546639528e5e8bd2d8e2a97013d51a49dd0573c7798b3e7c0e |
# adaptation of the lowess function from BioPython to work in isolation
import numpy as np
import numpy.random as rng
def lowess(x, y, f=2. / 3., iter=3):
n = len(x)
r = int(np.ceil(f * n))
h = [np.sort(abs(x - x[ii]))[r] for ii in xrange(n)]
w = np.clip(abs(([x] - np.transpose([x])) / h), 0.0, 1.0)
... | buck06191/BayesCMD | batch/lowess.py | Python | gpl-2.0 | 1,463 | [
"Biopython"
] | 8c1177de0b7f19849d4abc6f36f021ae071c52d435f003cdf681c65173e0c272 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Merging of spatially overlapping components that are temporally correlated
Created on Tue Sep 8 16:23:57 2015
@author: agiovann
"""
#\package caiman/source_extraction/cnmf
#\version 1.0
#\copyright GNU General Public License v2.0
from builtins import range
import n... | agiovann/Constrained_NMF | caiman/source_extraction/cnmf/merging.py | Python | gpl-2.0 | 13,849 | [
"NEURON"
] | 8ac3fd4da777f48476b567017d19043ccf4b326bb0c7c5409f960ec7978e8ec7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import math
import itertools
import warnings
from six.moves import map, zip
import numpy as np
from numpy.linalg import inv
from numpy import pi, dot, transpo... | matk86/pymatgen | pymatgen/core/lattice.py | Python | mit | 42,030 | [
"ABINIT",
"CRYSTAL",
"pymatgen"
] | 671b5a39eb86b2330ac3b3f84ebd4eb98406db7348f9feb675eacff62ad298a8 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-compute | tests/unit/gapic/compute_v1/test_region_notification_endpoints.py | Python | apache-2.0 | 82,634 | [
"Octopus"
] | 25069676cd01d01976c1446a3fa2946091131af4602063d8bdc2fa80cb85ac57 |
import tkSimpleDialog
import tkMessageBox
from pymol.wizard import Wizard
from pymol import cmd, preset
import os,sys
cmd.load('{prot}_avedye.pdb')
cmd.load('{prot}_point.pdb','point')
#initial view
preset.publication('all')
cmd.hide("sticks")
cmd.show("sticks",'{dyes}')
cmd.set ('ray_opaque_background', 'off')
#cmd... | tmorrell/SamStruct | inputs/pymol_cloud.py | Python | gpl-2.0 | 578 | [
"PyMOL"
] | ff61eff2c20fbe16eaa01d325635af849621c1181b1c46cd4eeb9df2ea27e354 |
from collections import defaultdict
from itertools import count
from operator import attrgetter
from os import path as op
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
from tqdm import tqdm
import pickle
from ..exceptions import PipelineException
try:
import cv2
except ImportError:
pr... | cajal/pipeline | python/pipeline/utils/eye_tracking.py | Python | lgpl-3.0 | 45,889 | [
"Gaussian"
] | f244c42dda70e3fbcaa52499c17f6024147509aa3ae0315f53534bdb4d13ea24 |
#!/usr/bin/env python
import mango
import mango.io
import mango.image
import mango.fmm
import mango.mpi as mpi
import scipy as sp
import numpy as np
import logging
import re
import os
import os.path
import sys
haveArgParse = False
try:
import argparse
haveArgParse = True
except:
import optparse
logger, ... | pymango/pymango | misc/python/mango/application/srskull/label_spherical_cavities.py | Python | bsd-2-clause | 16,524 | [
"NetCDF"
] | 365335972749be22c2a33ef820302ca1c96abca72ec1bab3190acd2f2481f019 |
# Copyright (c) 2012 OpenStack Foundation.
#
# 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... | projectcalico/calico-neutron | neutron/tests/unit/test_policy.py | Python | apache-2.0 | 27,049 | [
"BLAST"
] | c449f697441387c1ece393948f9c641d36f297c2ede2009d64d2d6423d794bf9 |
from __future__ import division, print_function, absolute_import
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, around, unique, asarray,
zeros, arange, sort, amin, amax, any, atleast_1d,
sqrt, ceil, floor, a... | Eric89GXL/scipy | scipy/stats/morestats.py | Python | bsd-3-clause | 106,197 | [
"Gaussian"
] | be127e13308a15730795f2251d275379ef5070009bb918fab98d21830cd60241 |
# Copyright 2012, SIL International
# All rights reserved.
#
# 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 License, or
# (at your option) any lat... | moyogo/pysilfont | examples/gdl/__init__.py | Python | mit | 975 | [
"VisIt"
] | 94d0dc03bfa0c4ea84c8c5b471af7f2c4b4c7c481481f72a0ccbe9a8c301ed84 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | pkreissl/espresso | testsuite/python/coulomb_mixed_periodicity.py | Python | gpl-3.0 | 4,010 | [
"ESPResSo"
] | 69b6e10f8d366027135e6e16594d37c325c639356fdc537901e5aad6a5c623c7 |
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | dllatas/deepLearning | local/cifar10.py | Python | mit | 19,297 | [
"Gaussian"
] | f15e3e0bf2a11fe9ae071970f69fa23c8f442427e1850f19d7d4561145820640 |
import logging
import unittest
import numpy
from scipy import signal
from cam_server.pipeline.data_processing.functions import gauss_fit, calculate_slices, linear_fit, find_index, chunk_copy
class FunctionsTest(unittest.TestCase):
def test_gauss_fit(self):
size = 101
standart_deviation_set = 6.3
... | datastreaming/cam_server | tests/test_functions.py | Python | gpl-3.0 | 8,171 | [
"Gaussian"
] | 7966e3854a9acc8daf8580293ecf6781e67d4e036407a7c816ddef26f85de2a0 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-get-banned-sites
# Author : Stuart Paterson
########################################################################
"""
Get banned sites
Example:
$ dirac-admin-get-banned-sites
LCG.IN2P3.fr ... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_get_banned_sites.py | Python | gpl-3.0 | 1,084 | [
"DIRAC"
] | 3ab10c6cdb88e10e53ff0be81e532c6c1c69806c63f108b769d2d5956f7ed90c |
version = 39
versions = {22: "1.0.6.1",
12: "1.0.5",
36: "1.1",
39: "1.1.2",
100: "1.2.4",
102: "1.2.4.1",
175: "1.3.3",
176: "1.3.3.1",
}
cmod = False
npclist = ["Merchant", "Nurse", "Arms Dealer", "Dryad", "Guide", "Cloth... | Berserker66/omnitool | omnitool/database.py | Python | mit | 101,667 | [
"Amber",
"CRYSTAL",
"Firefly"
] | 14293b41b6b47a333464f03efc85897fa3ceb446a9af3c74c4075b612ed603fa |
# NOTE: This example uses the next generation Twilio helper library - for more
# information on how to download and install this version, visit
# https://www.twilio.com/docs/libraries/python
import os
from twilio.rest import Client
# Your Account Sid and Auth Token from twilio.com/user/account
# To set up environmenta... | TwilioDevEd/api-snippets | notifications/rest/credentials/delete-credential/delete-credential.7.x.py | Python | mit | 566 | [
"VisIt"
] | 17734d0338b6d5442ca14017f2b2aee32332d453adcd353b4d9a3109614aeba0 |
#Dan Blankenberg
#takes fasta alignments, a distance metric and builds neighbor joining trees
import os, sys
from galaxy import eggs
from galaxy.tools.util import hyphy_util
#Retrieve hyphy path, this will need to be the same across the cluster
tool_data = sys.argv.pop()
HYPHY_PATH = os.path.join( tool_data, "... | volpino/Yeps-EURAC | tools/hyphy/hyphy_nj_tree_wrapper.py | Python | mit | 2,259 | [
"Galaxy"
] | e64db5720823b8028d7e4f9081cd0dc51de23896fb55bc028596b7a00d4e6db9 |
"""
An expression language for Raco: functions, booleans, aggregates, etc.
Most non-trivial operators and functions are in separate files in this package.
"""
from abc import ABCMeta, abstractmethod
import logging
from raco.utility import Printable
from raco import types
LOG = logging.getLogger(__name__)
class Typ... | uwescience/raco | raco/expression/expression.py | Python | bsd-3-clause | 21,303 | [
"VisIt"
] | 05f476773fcdb507fb30696bd7cc1854f7a86ec4ed4c6007b48de16e05f1d9a4 |
#!/usr/bin/env python
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
import argparse
import json
import os
import os.path
import sys
import requests
from socorro.li... | Tayamarn/socorro | socorro/scripts/fetch_crash_data.py | Python | mpl-2.0 | 4,969 | [
"VisIt"
] | 25bd71b46ba5d9e394e8fa15609f1d4a3af5b6371d89f4815770225d46bfb292 |
# Copyright 2018 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.
"""Helpers for dealing with translation files."""
from __future__ import print_function
import ast
import os
import re
import xml.etree.cElementTree as Ele... | endlessm/chromium-browser | tools/translation/helper/translation_helper.py | Python | bsd-3-clause | 9,381 | [
"xTB"
] | 6c4722c05369997153e913acc92b90d4a863a2c426f03cf4bc4e74834658dc72 |
"""
Utility file containing helper functions that perform various dimensionality
reduction technique.
"""
import numpy as np
from sklearn.decomposition import PCA
from sklearn.random_projection import GaussianRandomProjection as GRP
from lib.utils.data_utils import get_data_shape
from lib.utils.DCA import DCA
from li... | arjunbhagoji/ml_defense | lib/utils/dr_utils.py | Python | mit | 9,242 | [
"Gaussian"
] | 7c29f5fb4be7fe5fdcb1a0eba5069b3ffe4e0b57cf6fabe4e8a9cd857bb9aad2 |
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
""" unit tests for the model and descriptor packager """
from rdkit import RDConfig
from rdkit.ML.Data import DataUtils
import unittest,os,cPickle,sys
from rdkit.ML.ModelPackage imp... | rdkit/rdkit-orig | rdkit/ML/ModelPackage/UnitTestPackage.py | Python | bsd-3-clause | 4,053 | [
"RDKit"
] | dd86b9d6964869f6036c056e8e26ab5692d0127cc715425fb771fb1ef4749989 |
from __future__ import print_function, division
from sympy.core.basic import C
from sympy.core.singleton import S
from sympy.core.function import Function
from sympy.core import Add
from sympy.core.evalf import get_integer_part, PrecisionExhausted
from sympy.core.relational import Gt, Lt, Ge, Le
#####################... | AunShiLord/sympy | sympy/functions/elementary/integers.py | Python | bsd-3-clause | 5,972 | [
"VisIt"
] | c8daa502b98af56afde10a0bd5ea8b51ff552d1648d925ae252f85af578281a4 |
"""
@Name: Modules/Computer/Internet/internet.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2012-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Mar 20, 2012
@summary: This module determines the IP address of the ISP connection.
All nodes currently ru... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/Internet/internet.py | Python | mit | 5,223 | [
"Brian"
] | 2ac5de090c5b04f1be09a8c22b03eba18079b23ba341ff9ec6d042853c32bd86 |
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | annarev/tensorflow | tensorflow/tools/compatibility/update/generate_v2_reorders_map.py | Python | apache-2.0 | 5,386 | [
"VisIt"
] | e588ea9fe0e388992f969f1d9ceecc104819311088f5974716e8d13f964a4cae |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import xml.etree.cElementTree as ET
from pymatgen.io.exciting import ExcitingInput
from pymatgen.core import Structure, Lattice
"""
Tests the module to parse exciting input
Created 1s... | tschaume/pymatgen | pymatgen/io/exciting/tests/test_inputs.py | Python | mit | 5,068 | [
"CRYSTAL",
"exciting",
"pymatgen"
] | 1d233e42ad1992616563e2c1a7a88d09dd506152894692de10427b74aca4cfd0 |
import theano
import numpy as np
from .base import Layer
from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams
__all__ = [
"DropoutLayer",
"dropout",
"GaussianNoiseLayer",
]
class DropoutLayer(Layer):
"""Dropout layer [1]_,[2]_.
Sets values to zero with probability p. See note... | ebattenberg/Lasagne | lasagne/layers/noise.py | Python | mit | 4,423 | [
"Gaussian"
] | b3da37ada72998e14fd9599dd824cf5d2a873fbb6534672ffd8f7acf9be67863 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2017 The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this s... | jasperges/blenderseed | properties/nodes/specular_brdf.py | Python | mit | 3,515 | [
"VisIt"
] | acd7e0fcf47efd4633320a6abf3d118fa97a71f7ed4b2480507f89b2464c9af8 |
# -*- coding: utf-8 -*-
u"""SRW template fixups
:copyright: Copyright (c) 2019 RadiaSoft LLC. All Rights Reserved.
:license: http://www.apache.org/licenses/LICENSE-2.0.html
"""
from __future__ import absolute_import, division, print_function
from pykern import pkcollections
from pykern.pkdebug import pkdc, pkdexc, pk... | radiasoft/sirepo | sirepo/template/srw_fixup.py | Python | apache-2.0 | 2,823 | [
"CRYSTAL"
] | b9c978cbde68bf3e299e1bd0cbafb1b6de3c53845aad0651d8ca168d5c47150f |
# -*- coding: utf-8 -*-
"""
This script opens data files and extracts relevant data. Then, using a sklearn
gaussian process package, fits a gaussian to the crosswind (1d) temperature
measurements and interpolates temparture values (relative, not absolute) at a
2 mm interval.
TODO: make gaussian process it's own scrip... | isomerase/GP-temperature-interpolation | gptempdata.py | Python | mit | 5,482 | [
"Gaussian"
] | 59cf5aba181006575d4ae4e323a21a16fa26f1f0350d4856367a1cb381e5a84d |
from ase import *
from ase.lattice.surface import *
from ase.lattice.surface import surface
from ase.optimize import *
from ase.constraints import *
from ase import io
#create a (111) or (110) surface slab of 2x2x4
#(2x2) surface area; 3 layers along surface normal)
#7 angstrom vacuum layer added on each side
# run t... | CBE544/CBE544.github.io | ASE/Getting_Started/setup_surf.py | Python | gpl-2.0 | 1,455 | [
"ASE"
] | 0d577c4e47bfad3106dcbfcaa119886fdbca43dd9fdf49cfa928ba3cc015ac54 |
# Copyright 2021 DeepMind Technologies Limited. 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 ... | deepmind/mctx | mctx/_src/tests/tree_test.py | Python | apache-2.0 | 7,560 | [
"VisIt"
] | e56c8f49a7cd3e24f2408306d7e6832a9be21e15327b049f16be1612e571912b |
import os
import re
import logging
from datetime import datetime
from django.contrib.auth.models import User
from django.db import models
from django.db.models import Q
from django.utils.html import escape
from django.utils.safestring import mark_safe
from django.utils.translation import ugettext_lazy as _
from djble... | chazy/reviewboard | reviewboard/reviews/models.py | Python | mit | 65,610 | [
"VisIt"
] | 41b1560d2f09d3f1d213f110f3ebc0569c4d5d85c42e0cb78e371251d1d6a78a |
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jart/tensorflow | tensorflow/contrib/autograph/pyct/static_analysis/liveness.py | Python | apache-2.0 | 6,838 | [
"VisIt"
] | a0844a43405ae52697c2bf1df8eca2e36e962ae33ea37453eda74d98af1161e4 |
"""
Paul Rozdeba (prozdeba@physics.ucsd.edu)
Department of Physics
University of California, San Diego
May 23, 2017
NeuralNetVA
Carry out variational annealing (VA) to train a neural network model. Network
states and activation function parameters are estimated from training data
consisting of many input/output pair... | paulrozdeba/varanneal | varanneal/va_nnet.py | Python | mit | 26,673 | [
"Gaussian",
"NEURON"
] | f44d086460e34e01228f62c8a09aedb5561846cf55ad55381439135d6d639f36 |
"""
Visit the Twitter developer page and create a new application:
https://dev.twitter.com/apps/new
This will get you a CONSUMER_KEY and CONSUMER_SECRET.
When users run your application they have to authenticate your app
with their Twitter account. A few HTTP calls to twitter are required
to do this. Please see ... | fjacob21/pycon2015 | elpiwear/twitter/oauth.py | Python | mit | 4,710 | [
"VisIt",
"exciting"
] | a784c060573dad3e437a07aee5c66c739344a3adbb135e1fd67cf158c82c8117 |
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