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#!/usr/bin/python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute... | amjames/psi4 | doc/sphinxman/document_databases.py | Python | lgpl-3.0 | 1,819 | [
"Psi4"
] | b72929d5f6bcd84ed538eaf1d6fa2dda56b9085d53d4743dc2302c0f42c4e285 |
# Authors : Denis A. Engemann <denis.engemann@gmail.com>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#
# License : BSD 3-clause
from copy import deepcopy
import math
import numpy as np
from scipy import fftpack
# XXX explore cuda optimazation at some point.
from ..io.pick import pick_type... | nicproulx/mne-python | mne/time_frequency/_stockwell.py | Python | bsd-3-clause | 10,146 | [
"Gaussian"
] | 2d32f72d958bd5cd671bce8aa0eb46338e4428c1867c4109bb03ba55505235f7 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
#
# 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; ... | pmghalvorsen/gramps_branch | gramps/gui/plug/quick/_textbufdoc.py | Python | gpl-2.0 | 12,680 | [
"Brian"
] | c21b1779c5c232e52938d0fc027031cc27b92014d26d9015a1bd90312739fa3a |
# -*- coding: utf-8 -*-
# @Date : Nov 22 2012
# @Author : Tachyon Technologies Pvt Ltd
# @Version : 1
from email.MIMEText import MIMEText
from aifc import Error
import cherrypy
from QuillSourceProcessor import QuillSourceProcessor
from QuillManual import QuillManual
import const
import MySQLdb
import... | teamtachyon/Quillpad-Server | startquill_cherry.py | Python | bsd-3-clause | 21,836 | [
"VisIt"
] | b25d61154f967362b02088990bd91e64a9ccf9499011741feb98f231e86df3e6 |
"""
langcodes knows what languages are. It knows the standardized codes that
refer to them, such as `en` for English, `es` for Spanish and `hi` for Hindi.
Often, it knows what these languages are called *in* a language, and that
language doesn't have to be English.
See README.md for the main documentation, or read it ... | LuminosoInsight/langcodes | langcodes/__init__.py | Python | mit | 65,962 | [
"ASE"
] | 4788164f1f9e7cff4e131d167b023649f832d0654a4df2b86a69014ae30277d4 |
# ==========================================================================
#
# Copyright NumFOCUS
#
# 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/... | vfonov/ITK | Wrapping/Generators/Python/itk/support/extras.py | Python | apache-2.0 | 66,365 | [
"VTK"
] | 3021de329b0492e8cb3003eb0c0272ebdb96b999225c9df63bdee774fa972ee6 |
# Encoding: utf-8
import json
import math
import numpy as np
import pymatgen as pmg
import cage.utils as utils
import pymatgen.symmetry.analyzer as syman
from itertools import combinations
from monty.io import zopen
from monty.json import MSONable
from pymatgen.core.structure import Molecule
from pymatgen.core.struc... | mbercx/cage | cage/core.py | Python | mit | 51,327 | [
"VASP",
"pymatgen"
] | 9cb4b439961acff3eaf65ee4e4d72525df613f25f89940cdf8fac0e8faf9ca22 |
#!/usr/bin/env python
import unittest
import postpic as pp
from postpic import io
#import postpic.io.common
import numpy as np
import os
class TestIO(unittest.TestCase):
def gettempfile(self, suffix=''):
import tempfile
h, f = tempfile.mkstemp(suffix=suffix)
os.close(h)
print('fi... | stetie/postpic | test/test_io.py | Python | gpl-3.0 | 2,644 | [
"VTK"
] | 2ed039d04011c6e1b90d09ffc88b66005c72eaa0069e06f31b7344b6519bb931 |
# -*- coding: utf-8 -*
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Running SageNB Tests
Functions for running SageNB tests. This can also be used a script.
NOTE:
The SageNB tests tests assume a Selenium server or Grid hub is running
with the options given in :mod:`sagenb.testing.notebook_test_case` or
set by :... | migeruhito/sagenb | sagenb/testing/run_tests.py | Python | gpl-3.0 | 8,950 | [
"VisIt"
] | dadb60d65ebbd309ba3353879b5e7c35aa88ab656e7ab9ab519bfa8770351fd9 |
# Copyright 2004-2010 PyTom <pytom@bishoujo.us>
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, mer... | MSEMJEJME/ReAlistair | renpy/display/anim.py | Python | gpl-2.0 | 20,638 | [
"VisIt"
] | ac21ccd5a522071748c6acfcedcf3fa44f57b68d2c9374e96f9b89cdf4f274ec |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/topology/test_xyz.py | Python | gpl-2.0 | 1,663 | [
"MDAnalysis"
] | 859d768da54d220e819c5fd09d9c51067641c25375d2ace5b7aa6e63d2aa55d7 |
import ast
from .base import BaseAnalyzer, Result, DeprecatedCodeVisitor
DESCRIPTION = """
``{name}`` function has been deprecated in Django 1.3 and will be removed in
1.5.
"""
class GenericViewsVisitor(DeprecatedCodeVisitor):
interesting = {
'django.views.generic.simple': ['direct_to_template', 'redir... | alfredhq/djlint | djlint/analyzers/generic_views.py | Python | isc | 2,239 | [
"VisIt"
] | ab9ae30d2c2fb218941532090a6e7baf0029e9acf2233d90eb8b6a47c2e6f124 |
#!/usr/bin/python
#=============================================================================================
# example files for reading in MD simulation files and performing
# statistical analyses according to manuscript "Simple tests for
# validity when sampling from thermodynamic ensembles", Michael
# R. Shirts... | shirtsgroup/checkensemble | examples/analyze-md.py | Python | gpl-2.0 | 11,159 | [
"CHARMM",
"Desmond",
"Gromacs"
] | 7eefba62262c1604c0b21f3cc63e7d3c7b4bf0cfda23e07597ec1f6f1f3a66ce |
#!/usr/bin/env python
# encoding: utf-8
"""
Tests that stresses are calculated correctly by Asap
Name: testStress.py
Description: Part of the Asap test suite. Tests that stresses are
calculated correctly by calculating various elastic constants from
strain and stress and comparing them with the same constan... | auag92/n2dm | Asap-3.8.4/Test/BrennerStress.py | Python | mit | 10,820 | [
"ASE",
"CRYSTAL"
] | d8facc7d363fb08489285902c886736514bf4c9af558810c352db10256041110 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | kyleabeauchamp/mdtraj | mdtraj/testing/nosetester.py | Python | lgpl-2.1 | 1,860 | [
"MDTraj"
] | cc4293ea4d74303d5d62955f4ea7fddc9ba1a794ea91928d57f593b6c18f12a0 |
#!/usr/bin/python
########################################################################
# 19 May 2014
# Patrick Lombard, Centre for Stem Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import subproce... | pdl30/pyrnatools | pyrnatools/counting.py | Python | gpl-2.0 | 9,128 | [
"HTSeq"
] | d2b16321dc7717a78c033b6cd6212e2582601bb9dcd77b8bc1779100fc935e32 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes representing non-periodic and periodic sites.
"""
import collections
import json
from typing import Optional, Tuple, Union
import numpy as np
from monty.dev import deprecated
from monty.json i... | vorwerkc/pymatgen | pymatgen/core/sites.py | Python | mit | 23,312 | [
"pymatgen"
] | 6ef6a519ab6ce28c0b866785b78c1e8a4a077c9dca98051040c98ccdb84c5090 |
# 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
from twilio.rest import Client
# Your Account Sid and Auth Token from twilio.com/user/account
account = "ACXXXXXXXXXXXXXXXXXXXXX... | teoreteetik/api-snippets | notifications/rest/bindings/retrieve-binding/retrieve-binding.6.x.py | Python | mit | 545 | [
"VisIt"
] | 4f42abef7f100e0b78a0650d9816a2b94afc17fe3c00e4da809a0c993f558e48 |
from setuptools import setup
setup(
name='galaxy-api-tools',
version='0.1.0',
author='Carlos Borroto',
author_email='carlos.borroto@gmail.com',
url="https://github.com/cjav/galaxy-api-tools",
packages=['galaxyapitools'],
scripts=["scripts/galaxy-api-tools"],
description='The Galaxy API ... | cjav/galaxy-api-tools | setup.py | Python | bsd-2-clause | 491 | [
"Galaxy"
] | e79984de5909c6e521a754d3b58024115df9aa6a2b86efdae551b4747d797be5 |
"""Utilities used in the Kadenze Academy Course on Deep Learning w/ Tensorflow.
Creative Applications of Deep Learning w/ Tensorflow.
Kadenze, Inc.
Parag K. Mital
Copyright Parag K. Mital, June 2016.
"""
import matplotlib.pyplot as plt
import tensorflow as tf
import urllib
import numpy as np
import zipfile
import os
... | AlfredNeverKog/BrainCarya | src/my/kadenze/lesson4/utils.py | Python | mit | 21,223 | [
"Gaussian"
] | c6de3641ccfad9462b5837679089e3852c92bab088c9010c4ec4472ee36392fc |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module provides a container class to store parameters for the
geometry of an ellipse.
"""
import math
from astropy import log
import numpy as np
__all__ = ['EllipseGeometry']
IN_MASK = [
[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
... | astropy/photutils | photutils/isophote/geometry.py | Python | bsd-3-clause | 19,964 | [
"Galaxy"
] | 8fccf24664c965b951502d17a35e41f79df34f2f725aa38a961886a0bfaacc53 |
from __future__ import print_function
from __future__ import unicode_literals
import argparse
import ast
import collections
import traceback
DEBUG_STATEMENTS = set(['pdb', 'ipdb', 'pudb', 'q'])
DebugStatement = collections.namedtuple(
'DebugStatement', ['name', 'line', 'col'],
)
class ImportStatementParser(a... | arahayrabedian/pre-commit-hooks | pre_commit_hooks/debug_statement_hook.py | Python | mit | 2,072 | [
"VisIt"
] | ff9cab6ca5bbeda17941c7a1922732f25c36eef9f8e4b573514106edd8baa6a7 |
import math
class NeuronConnection(object):
def __init__(self, neuron, weight=1.0):
self.neuron = neuron
self.weight = weight
class Neuron(object):
def __init__(self, input=None):
self.input = input
self.output = None
self.incoming_neurons = []
self.outgoing_... | dev-coop/neural-net-hacking-examples | python/Part 1/neural_network_with_connections.py | Python | mit | 1,475 | [
"NEURON"
] | feffa1fe5a854e2345646f77b3d405d31058928c96f2fbb4a4446f57dbfc84e3 |
#!/usr/bin/python
# -*- coding:utf-8 -*-
import functions
import Image
import math
class Anaglyph:
"Anaglyph support class"
def __init__(self, parent):
self.vergence = 0 # Horizontal separation
self.vsep = 0 # Vertical separation
self.left = self.right = '' # Right and left Images
self.height = self... | magestik/TuxStereoViewer | src/lib_anaglyph.py | Python | gpl-3.0 | 4,017 | [
"Amber"
] | 665a55bd9472e7cc195485d66223e4deb42ed92583fa5bf4ce68532d34e8e968 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Defines SymmetryGroup parent class and PointGroup and SpaceGroup classes.
Shyue Ping Ong thanks Marc De Graef for his generous sharing of his
SpaceGroup data as published in his textbook "Structure of Materials".
"""
impo... | materialsproject/pymatgen | pymatgen/symmetry/groups.py | Python | mit | 19,338 | [
"CRYSTAL",
"pymatgen"
] | 8d32b1cfec0a7cb1e3347fb2a829b8f183c80087bb19a16ec0ac3d0741308f03 |
"""Detect viral infections via bwa alignment of unaligned reads.
This is primarily useful for cancer samples where viral infection can
inform treatment.
"""
import glob
import os
from bcbio import bam, utils
from bcbio.distributed.transaction import file_transaction
from bcbio.pipeline import datadict as dd
from bcbi... | biocyberman/bcbio-nextgen | bcbio/qc/viral.py | Python | mit | 2,676 | [
"BWA"
] | 73f9db1ce9e64b90e3b95dd9bf95d87bb17a2f9c4c37d5e4f33b97f3f4a226d4 |
""" Example smearing script
This script:
* Reads in mc spectra from hdf5
* Smears spectra, default is to use weighted Gaussian method, but can
also use specify random Gaussian method via command line
* Smeared spectrum is saved to the same directory with ``_#value#ly`` or
``_#value#rs`` added to the file... | jwaterfield/echidna | echidna/scripts/dump_smeared_energy.py | Python | mit | 4,361 | [
"Gaussian"
] | f692a4b1262206df7d720667891446b90d9d33674235cb5620287398fad3128f |
#from __future__ import division, print_function
#from __future__ import absolute_import
#from __future__ import unicode_literals
from configparser import ConfigParser
from sys import platform, stdout
from os import path, sep, listdir, access, X_OK, environ, pathsep
# from pkg_resources import resource_stream, resourc... | PySCeS/PyscesToolbox | psctb/utils/config.py | Python | bsd-3-clause | 8,339 | [
"PySCeS"
] | 4d414a91522394dd03c4f5ae416968ffa529da7700837b5c9300a9e260517c65 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_clocksyn_lodens_0128/brian2_benchmark_COBAHH_clocksyn_lodens_0128.py | Python | gpl-3.0 | 3,778 | [
"Brian"
] | 1049bd588e71d8f30fd29d20aa4c6b9999fa68b6cb11e9391b8e9fc85cc872cf |
import json
import sys
import os.path
from os.path import expanduser
from Crypto.PublicKey import RSA
from Crypto.Hash import SHA256
from Crypto.Signature import PKCS1_PSS
#Author: Brian Greenberg 6/29/17
#JSON based config generator for groups to be used in conjunction with iptables like rules
#for an OpenFlow bas... | bgreenb/FireWall | GroupGen.py | Python | mit | 5,703 | [
"Brian"
] | 72a91d6561852c697c7317b5c4ac23825eaf1e312ac6ac3665e95d1ad5f08776 |
import os.path as op
import shutil
import unittest
import numpy as np
import numpy.testing as npt
from scipy.stats import truncnorm
import pyhrf
from pyhrf import Condition
import pyhrf.sandbox.physio as phy
class SimulationTest(unittest.TestCase):
def setUp(self):
# called before any unit test of the ... | philouc/pyhrf | python/pyhrf/test/test_sandbox_physio.py | Python | gpl-3.0 | 7,291 | [
"Gaussian"
] | 35d57f131cca12a792e51ccd44934cacfe554e14dc95e7169f47898dd5b06593 |
# $Id: nodes.py 6351 2010-07-03 14:19:09Z gbrandl $
# Author: David Goodger <goodger@python.org>
# Copyright: This module has been placed in the public domain.
"""
Docutils document tree element class library.
Classes in CamelCase are abstract base classes or auxiliary classes. The one
exception is `Text`, for a text... | MichaelNedzelsky/intellij-community | python/helpers/py2only/docutils/nodes.py | Python | apache-2.0 | 64,847 | [
"VisIt"
] | bd275c5bdc6b61c8bf6e0b744f251bbd93c8c3a5b86417d544fc6f24ad67ee21 |
from basecrm.configuration import Configuration
from basecrm.http_client import HttpClient
import basecrm.services
import basecrm.sync
class Client(object):
"""
The :class:`Client <Client>` is the entry point to all services and actions.
:attribute :class:`Configuration <basecrm.Configuration>` config: ... | basecrm/basecrm-python | basecrm/client.py | Python | mit | 10,350 | [
"VisIt"
] | 1e0ee313cbe07410ac8a35db90c0378e1c9bb64f261244d059f8fca04abd58b7 |
"""
Courseware views functions
"""
import logging
import urllib
import json
import cgi
from datetime import datetime
from django.utils import translation
from django.utils.translation import ugettext as _
from django.utils.translation import ungettext
from django.conf import settings
from django.core.context_process... | rhndg/openedx | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 56,833 | [
"VisIt"
] | 10d174d1c5319f0c9346827db00182c3bdf33e136500c7da889b6eb337a59754 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007-2009 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Softw... | andrebellafronte/stoq | stoqlib/gui/wizards/stocktransferwizard.py | Python | gpl-2.0 | 9,677 | [
"VisIt"
] | 45041a6f9032dfa23c3cd036847fa65b88bac857af0eeffa3118f35e54ca4476 |
from __future__ import annotations
import pytest
def test(dials_data):
from dxtbx.model.experiment_list import ExperimentListFactory
from dials.algorithms.spot_prediction import PixelToMillerIndex
from dials.array_family import flex
filename = dials_data("centroid_test_data").join("experiments.json... | dials/dials | tests/algorithms/spot_prediction/test_pixel_to_miller_index.py | Python | bsd-3-clause | 887 | [
"CRYSTAL"
] | d8efd8117d10b7ea312cd0d68a550c3407cd094e0051324401de0695cdcf9e7b |
# http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06211.html
from pymol import cmd
def print_hb(selection):
hb = cmd.find_pairs("((byres "+selection+") and n;n)","((byres "+selection+") and n;o)",mode=1,cutoff=3.7,angle=55)
pair1_list = []
pair2_list = []
dist_list = []
for pairs in hb:
... | jtprince/hydrogen_bondifier | reference/campbell_find_hb.py | Python | mit | 690 | [
"PyMOL"
] | 05cfbc622339ae19bca666be8840a25718686edfdb5220eb7d7f0c48153a9b49 |
#!/usr/bin/env python2
#
# Copyright (C) 2020(H)
# Jozef Stefan Institute
# Max Planck Institute for Polymer Research
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify... | govarguz/espressopp | testsuite/langevin_thermostat_on_group/langevin_thermostat_on_group.py | Python | gpl-3.0 | 3,244 | [
"ESPResSo"
] | e8be2c94cf295b80e90ec8e62e7ccf826454ce1384537f7cbd5183cee1960c5f |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | sonaht/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 104,645 | [
"VisIt"
] | 3a63d4c8ead1cbcd32619c9c1622066635dc8ec3d4d106096747fb706db89321 |
from time import time, ctime
import numpy as np
import pickle
from math import pi
from ase.units import Hartree
from ase.io import write
from gpaw.blacs import BlacsGrid, Redistributor
from gpaw.io.tar import Writer, Reader
from gpaw.mpi import world, size, rank, serial_comm
from gpaw.utilities import devnull
from gpaw... | robwarm/gpaw-symm | gpaw/response/bse.py | Python | gpl-3.0 | 34,879 | [
"ASE",
"GPAW"
] | 62e3fdee0a818ac9c9b2d0287e02f6d4ca43fd1e9165d3fb1c0fdd4fa73223b3 |
from __future__ import print_function
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import MultipleLocator
from astropy.io import fits
from astropy.time import Time
from PyAstronomy import pyasl
from scipy import ndimage
import pandas as pd
import gaussfitter as gf
'''
Functions used in BF_p... | mrawls/BF-simulator | BF_functions.py | Python | mit | 14,918 | [
"Gaussian"
] | ef42c8428e780e388207f76d44c9445a5ed6dc64b692d46769f63e6ee94bdc01 |
# -*- coding: utf-8 -*-
# Django settings for seahub project.
import sys
import os
import re
import random
import string
from seaserv import FILE_SERVER_ROOT, FILE_SERVER_PORT
PROJECT_ROOT = os.path.join(os.path.dirname(__file__), os.pardir)
DEBUG = False
TEMPLATE_DEBUG = DEBUG
ADMINS = (
# ('Your Name', 'your... | madflow/seahub | seahub/settings.py | Python | apache-2.0 | 18,567 | [
"VisIt"
] | 266ad4afcf0dcc2773176023bdecca6f0a317e07f5128c45e9372bdf58194875 |
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 6 12:05:13 2015
@author: landman
Test convergence
"""
import sys
#sys.path.insert(0, '/home/bester/Algorithm') #On cluster
sys.path.insert(0, 'fortran_mods/') #At home PC
from numpy import size, exp, any,loadtxt, linspace, array,zeros, sqrt, pi, mean, std, load, asarr... | landmanbester/Copernicus | Test_Convergence.py | Python | gpl-3.0 | 11,778 | [
"Gaussian"
] | 63bf2a16e790984dfb646d5d9583748d23f4b23821db9555631af3156372436d |
"""MPF plugin which implements Logic Blocks"""
# logic_blocks.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
from mpf.system.tasks import... | spierepf/mpf | mpf/system/logic_blocks.py | Python | mit | 20,301 | [
"Brian"
] | 4ac600fde5ff4cb6fa2e8bbd09a8eae5ee3abe0d8d1ee4a275f495e1b3d4aec8 |
#!/usr/bin/env python
#
# Copyright 2008-2010 by Brian Dominy <brian@oddchange.com>
#
# PYLDecider 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 lat... | bcd/PYLDecider | PylDecider.py | Python | gpl-2.0 | 26,870 | [
"Brian"
] | 6e465ec6c444658f284221c3cc0187e094a16fcbd53b2d8122b881df02c12f47 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import csv
import json
import os
import random
import unittest
import numpy as np
import scipy.constants as const
from monty.tempfile import ScratchDir
from pymatgen.analysis.diffusion_analyzer import (
... | davidwaroquiers/pymatgen | pymatgen/analysis/tests/test_diffusion_analyzer.py | Python | mit | 19,129 | [
"pymatgen"
] | 5c56799df35e173a58e1a656d25369e028b24deea65b63532e654a3c9865b624 |
"""
========================================================================
Concentration Prior Type Analysis of Variation Bayesian Gaussian Mixture
========================================================================
This example plots the ellipsoids obtained from a toy dataset (mixture of three
Gaussians) fitte... | glemaitre/scikit-learn | examples/mixture/plot_concentration_prior.py | Python | bsd-3-clause | 5,695 | [
"Gaussian"
] | da78b701898915e870cbca9aa15f72f373486bd19eb0ff8e6dc48e4edc132dff |
# Copyright 2008-2009 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of django-facebookconnect.
#
# django-facebookconnect is free software: you can redistribute it and/or modify
# it under the te... | ryszard/django-facebookconnect | facebookconnect/admin.py | Python | gpl-3.0 | 1,007 | [
"Brian"
] | 36d0769e1189a38803c3d07045fb0c88729fa392ebd32605b9eb03db7e68d104 |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2011 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Fre... | tiagocardosos/stoq | stoq/gui/admin.py | Python | gpl-2.0 | 17,432 | [
"VisIt"
] | 04bb4fdbe91afbfc7d726aaf55e31066b43476a1b24a2db8990b1c8e64dc4653 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | andysim/psi4 | psi4/driver/p4util/text.py | Python | gpl-2.0 | 7,028 | [
"Psi4"
] | 3226109478237391ec11e57ea28d3647b70d9582431dddba733b9ced22f10e5e |
#!/usr/bin/env python
# encoding: utf-8
# ======================================================================
# Package: pyclaw.plotters
# File: data.py
# Created: Aug 7, 2009
# Author: R.J. LeVeque
# ============================================================================
"""
Plotting Da... | clawpack/clawpack-4.x | python/pyclaw/plotters/data.py | Python | bsd-3-clause | 58,418 | [
"NetCDF"
] | 9b7af73544f3cf30ee33ad01775decac90ca35ed24a8e4363b8b4833b6dfc2c7 |
from .tractography import Tractography
from .trackvis import tractography_from_trackvis_file, tractography_to_trackvis_file
from warnings import warn
import numpy
__all__ = [
'Tractography',
'tractography_from_trackvis_file', 'tractography_to_trackvis_file',
'tractography_from_files',
'tractography_fr... | oesteban/tract_querier | tract_querier/tractography/__init__.py | Python | bsd-3-clause | 2,715 | [
"VTK"
] | 74f00d8a7d957fabca90b239d83f59b5c02c2f25515f8ff7d22b31c150ba7158 |
from collections import defaultdict
import json, subprocess, sys, re, magic, csv, os, logging
#STRAWMAN FIXME
#THIS WOULD BE A PROGRAMMATICALLY INGESTED JSON ON MODULE LOAD IN REAL LIFE
#DONT HATE THIS PART
#programs = defaultdict(dict)
#programs['bwa']={"default":"/opt/common/CentOS_6/bwa/bwa-0.7.12/bwa",
# ... | mskcc/cmo | cmo/util.py | Python | gpl-2.0 | 9,809 | [
"BWA"
] | 35a047cc16a5386d515f44b0f02bca38bf089df604bea4363d3165fecb8f5431 |
"""
Send an email to settings.FEED_APPROVERS with the feeds that need to
be manually approved.
"""
from django.conf import settings
from django.contrib.auth.models import User
from django.core import mail
from django.core.management import BaseCommand
from django.template import Context, Template
from ...models import... | django/djangoproject.com | aggregator/management/commands/send_pending_approval_email.py | Python | bsd-3-clause | 1,711 | [
"VisIt"
] | 59c523c7c67b34e36d82160e8c35124c5c1e49ba483c3f3ae2d3f67e3ef8e1c5 |
"""
Copyright (c) 2012-2013, Nicolas Kuttler.
All rights reserved.
License: BSD, see LICENSE for details
Source and development at https://github.com/piwik/piwik-python-api
"""
import sys
import datetime
from hashlib import md5
import logging
import os
import random
try:
import json
except ImportError:
impor... | piwik/piwik-python-api | piwikapi/tracking.py | Python | bsd-3-clause | 31,981 | [
"VisIt"
] | 99b3ad5091cfe147bfcf45b8b5936f83aaee286b5253dfe5b3b24e526f5f8c2c |
#!/usr/bin/python
"""Test of column header output."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
sequence.append(KeyComboAction("End"))
sequence.append(KeyComboAction("<Shift>Right"))
sequence.append(KeyComboAction("Down"))
sequence.append(KeyComboAction("Down"))
sequence.append(KeyComb... | h4ck3rm1k3/orca-sonar | test/keystrokes/gtk-demo/role_column_header.py | Python | lgpl-2.1 | 4,996 | [
"ORCA"
] | 81079fc2e0ca001aabf2d27159fccfcbfb31fb460c608043ce2e073d1cf5274c |
# coding: utf-8
# Deep Learning
# =============
#
# Assignment 4
# ------------
#
# Previously in `2_fullyconnected.ipynb` and `3_regularization.ipynb`, we trained fully connected networks to classify [notMNIST](http://yaroslavvb.blogspot.com/2011/09/notmnist-dataset.html) characters.
#
# The goal of this assignme... | pdedumast/ShapeVariationAnalyzer | src/py/trainlib/prediction.py | Python | apache-2.0 | 5,070 | [
"VTK"
] | 4ee6fea07ff36350a412ec7e3726b23fdf807c585de65ed88f1aaa5f7ec9a99d |
''' Test_RSS_Policy_FreeDiskSpacePolicy
'''
# pylint: disable=protected-access
import unittest
import DIRAC.ResourceStatusSystem.Policy.FreeDiskSpacePolicy as moduleTested
################################################################################
class FreeDiskSpacePolicy_TestCase(unittest.TestCase):
def... | andresailer/DIRAC | ResourceStatusSystem/Policy/test/Test_RSS_Policy_FreeDiskSpacePolicy.py | Python | gpl-3.0 | 3,636 | [
"DIRAC"
] | 08fb93d83c9842820580c9aee1c0380781fd2a67d1ee9d7f6657ac9af740a6e7 |
#!/usr/bin/env python
"""
This is a master vasp running script to perform various combinations of VASP
runs.
"""
from __future__ import division
import logging
import sys
import yaml
from custodian.custodian import Custodian
from custodian.vasp.jobs import VaspJob
from pymatgen.io.vasp import VaspInput, Incar, Kpoi... | xhqu1981/custodian | custodian/cli/run_vasp.py | Python | mit | 12,242 | [
"VASP",
"pymatgen"
] | b1ffd875ec9031d2b0778cfd0c5c80328427c28d81a16629668ad43dd9cbec25 |
#!/usr/bin/env python3
import matplotlib.pyplot as plt
import numpy as np
from pysisyphus.calculators.AnaPot import AnaPot
from pysisyphus.calculators.XTB import XTB
from pysisyphus.helpers import geom_from_xyz_file
from pysisyphus.optimizers.hessian_updates import bfgs_update, flowchart_update
def rms(arr):
... | eljost/pysisyphus | tests_staging/test_ancopt/test_ancopt.py | Python | gpl-3.0 | 4,927 | [
"xTB"
] | a6c1333870ad2f1f22ec03ca47ce8ebe02136254db522e6cb2cfbead0385f3d8 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the Google Chrome History database plugin."""
from __future__ import unicode_literals
import unittest
from plaso.formatters import chrome as _ # pylint: disable=unused-import
from plaso.lib import definitions
from plaso.parsers.sqlite_plugins import chrome... | rgayon/plaso | tests/parsers/sqlite_plugins/chrome_history.py | Python | apache-2.0 | 12,609 | [
"VisIt"
] | 03e03e3909539b93fc01157d7e3f42d4622720324a31375812357b7ea2e191c2 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImagePadFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk... | nagyistoce/devide | modules/vtk_basic/vtkImagePadFilter.py | Python | bsd-3-clause | 491 | [
"VTK"
] | d6422565e6fee860e69feaef9cb8b86502c34b842b0b5dcd54e38d89e064aa06 |
from __future__ import division, unicode_literals
import warnings
import matplotlib
matplotlib.use('pdf')
import unittest as unittest
import numpy as np
from pymatgen import Composition
from pymatgen.entries.computed_entries import ComputedEntry
from pymatgen.analysis.phase_diagram import PhaseDiagram, \
GrandP... | gpetretto/pymatgen | pymatgen/analysis/tests/test_interface_reactions.py | Python | mit | 13,779 | [
"pymatgen"
] | 14b68b8f91490ae13b43adc90db8de9e2570c39f575cbf76e59412b722b5c1ce |
# ==================================================================================================
# Copyright 2011 Twitter, Inc.
# --------------------------------------------------------------------------------------------------
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... | foursquare/commons-old | src/python/twitter/common/options/__init__.py | Python | apache-2.0 | 5,609 | [
"Brian"
] | 26bc8d002c21c86d2d91ae0b5ca87aabfb9529db46a1465a42ab7a10d56ae51b |
import warnings
warnings.simplefilter('always', DeprecationWarning)
import os
import functools
import os.path
import re
import urllib
import urllib2
import json
import imp
import random
import tabulate
from connection import H2OConnection
from job import H2OJob
from expr import ExprNode
from frame import H2OFrame, _py_... | weaver-viii/h2o-3 | h2o-py/h2o/h2o.py | Python | apache-2.0 | 76,615 | [
"Gaussian"
] | c742975c72b74d54b409f2f03bb6e4c2a8e78d892c3d4da8ad2a00b83bbd45d0 |
# Copyright 2017 Battelle Energy Alliance, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | idaholab/raven | framework/unSupervisedLearning.py | Python | apache-2.0 | 64,055 | [
"Gaussian"
] | 536f9bd8c10b065adf3a03e192cd8111c8308026047b67994d4f52a34cc67945 |
import torch
import math
import os
import shutil
import pyprob
import pyprob.diagnostics
from pyprob import Model, InferenceEngine
from pyprob.distributions import Uniform, Normal
class GaussianWithUnknownMeanMarsaglia(Model):
def __init__(self, prior_mean=1, prior_stddev=math.sqrt(5), likelihood_stddev=math.sqr... | probprog/pyprob | tests/extra/diagnostics/gum_marsaglia.py | Python | bsd-2-clause | 7,875 | [
"Gaussian"
] | fbc826020ec42535501da21898f7693c5ed9867503f7a09bf23e270370901e67 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Tests that relate to evaluating models with quantity parameters
"""
import numpy as np
import pytest
from numpy.testing import assert_allclose
from ..core import Model
from ..models import Gaussian1D
from ... import units as u
from ...units import... | funbaker/astropy | astropy/modeling/tests/test_quantities_evaluation.py | Python | bsd-3-clause | 6,581 | [
"Gaussian"
] | 828454abf5598806df52f18316004d61bc79ddf216f169b6001a8f9a8c52ff2b |
'''
Yugang Created at Aug 08, 2016, CHX-NSLS-II
Create a PDF file from XPCS data analysis results, which are generated by CHX data analysis pipeline
How to use:
python Create_Report.py full_file_path uid output_dir (option)
An exmplae to use:
python Create_Report.py /XF11ID/analysis/2016_2/yuzhang/Results/August... | yugangzhang/chxanalys | chxanalys/Create_Report.py | Python | bsd-3-clause | 62,451 | [
"VisIt"
] | 1c5c2d7e6b1755822fb44a80667aa66b1ae004ada8ddccf83cdb9c0c8dc1c8f1 |
from pymatgen.core.structure import Structure
from connectivity_from_structure import get_connectivity_matrix, Polyhedra
from effective_coordination import EffectiveCoordFinder
import unittest
__author__ = 'Tina'
"""
Each unit test checks whether the connectivities between polyhedra as well as the coordination numb... | tchen0965/structural_descriptors_repo | examples/structures_test.py | Python | mit | 47,836 | [
"pymatgen"
] | 3fc4c00a40157de745bb0692c4dcb5e7489d561d5e2cd1a1ae8a2157875585f1 |
# -*- coding: utf-8 -*-
import time
from datetime import datetime, timedelta
from dateutil.parser import parse as dateutil_parse
from loguru import logger
from sqlalchemy import Column, Date, DateTime, Integer, String, Table, Time, Unicode, and_, or_
from sqlalchemy.orm import relation
from sqlalchemy.schema import ... | malkavi/Flexget | flexget/components/trakt/db.py | Python | mit | 42,299 | [
"VisIt"
] | 7f8c202e60c7252b9948da98cc0a1bb27bb1ca24e794d42e0b941e7b4d02ebb7 |
# Copyright 2014 Roberto Brian Sarrionandia
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | sarrionandia/tournatrack | custom_room_status.py | Python | apache-2.0 | 2,445 | [
"Brian"
] | a545baa9e3e7fd12fde47dc142cce58504b58f9072114576c9a8ddd8dad2e5ff |
import xarray as xr
from .common import NetCDF4, expects_file_info
__all__ = [
'HOAPS',
]
class HOAPS(NetCDF4):
"""File handler that can read data from HOAPS NetCDF4 files.
This object handles HOAPS V3.3 NetCDF4 files such as they are
compatible with :mod:`typhon.collocations`, i.e.:
* convert... | atmtools/typhon | typhon/files/handlers/hoaps.py | Python | mit | 3,243 | [
"NetCDF"
] | f5b6bd5d1d5ad8288d7493470e61770843cb4b0e0ba4c61a6289d0567066f6a9 |
"""
Test atomic coordinates and neighbor lists.
"""
import os
import numpy as np
import unittest
from rdkit import Chem
import deepchem as dc
class TestAtomicCoordinates(unittest.TestCase):
"""
Test AtomicCoordinates.
"""
def test_atomic_coordinates(self):
"""
Simple test that atomic coordinates retur... | Agent007/deepchem | deepchem/feat/tests/test_binding_pocket_features.py | Python | mit | 1,022 | [
"RDKit"
] | 69d9af1f8482ce518a03c7ba6d1e6f639acff449f571975e252fabeac09792c5 |
"""Van der Waals energy and radii terms per AMBER atom type"""
vdw_energy = {'IP': 0.00277, 'HS': 0.0157, 'HP': 0.0157, 'Na': 0.00277, 'N*': 0.17, 'Li': 0.0183, 'HO': 0.0,
'Rb': 0.00017, 'HC': 0.0157, 'HA': 0.015, 'O3': 0.21, 'CQ': 0.086, 'C*': 0.086, 'NA': 0.17, 'NB': 0.17,
'NC': 0.17, 'O2... | brianjimenez/lightdock | lightdock/scoring/vdw/data/vdw.py | Python | gpl-3.0 | 1,634 | [
"Amber"
] | 44e9f6020e9105596d1451e0b47d28c56054519b4171e6373d61db927d9647b9 |
"""
This is our testing framework.
Goals:
* it should be compatible with py.test and operate very similarly
(or identically)
* doesn't require any external dependencies
* preferably all the functionality should be in this file only
* no magic, just import the test file and execute the test functions, that's it
* po... | Sumith1896/sympy | sympy/utilities/runtests.py | Python | bsd-3-clause | 78,928 | [
"VisIt"
] | 5dd1bccf0b8851d37cee16b250ab54da69b0b649ec50a2e89ac6b00e74d64320 |
"""cdbgui.py
Developers: Christina Hammer, Noelle Todd
Last Updated: August 19, 2014
This file contains a class version of the interface, in an effort to
make a program with no global variables.
"""
from datetime import datetime, timedelta, date
from tkinter import *
from tkinter import ttk
from cdbifunc2 import *
fr... | ChristinaHammer/Client_Database | cdbgui15.py | Python | mit | 63,159 | [
"VisIt"
] | 07c4bdb4cb8a126b351ef2f42e8106b9806b2384301de5fb01cf5eb2291493cb |
#
# Copyright (C) 2013-2018 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... | mkuron/espresso | testsuite/python/p3m_electrostatic_pressure.py | Python | gpl-3.0 | 5,881 | [
"ESPResSo"
] | f2037846325848278776233dffea9782c6795c66d0a83b0398eae29a98deb2b6 |
# Lint as: python3
# Copyright 2020 The TensorFlow Probability Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required ... | tensorflow/probability | spinoffs/inference_gym/inference_gym/tools/stan/targets.py | Python | apache-2.0 | 8,434 | [
"Gaussian"
] | 4553a26089b461cbb6174cc7d3035b9004904519df20149659476732fa57e11c |
#!/usr/bin/env python3
#
# Copyright (c) 2012 Brian Yi ZHANG <brianlions at gmail dot com>
#
# This file is part of pynebula.
#
# pynebula 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 th... | brianlions/python-nebula | nebula/asyncevent/_asyncevent.py | Python | gpl-3.0 | 30,921 | [
"Brian"
] | 6b38e7e21ee2188c75b3dd5af4067793b99db42fb00e96a334fd5bfb13ac8cba |
"""Code run on the client side for unstaging complete Pulsar jobs."""
import fnmatch
from contextlib import contextmanager
from logging import getLogger
from os.path import join, relpath
from json import loads
from ..action_mapper import FileActionMapper
from ..staging import COMMAND_VERSION_FILENAME
log = getLogger... | galaxyproject/pulsar | pulsar/client/staging/down.py | Python | apache-2.0 | 10,068 | [
"Galaxy"
] | 6d1733dc9e36bd5ef0902d27c4b1e782349271e992df6920da1021d734ce8c80 |
#region GPLv3 notice
# Copyright 2014 Damian Quiroga
#
# This file is part of depict.
#
# depict 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... | qdamian/depict | test/system/features/steps/when.py | Python | gpl-3.0 | 1,532 | [
"VisIt"
] | 665c615576a74a37b0cad21267dd37028abd39bdc2872dfe29a91a8bce9aeb42 |
# -*- coding: utf-8 -*-
# @Author: tasdik
# @Date: 2016-04-11 23:50:46
# @Last Modified by: Tasdik Rahman
# @Last Modified time: 2016-04-12 14:31:45
# @GPLv3 License
# @http://tasdikrahman.me
# @https://github.com/tasdikrahman
HAM_TEXT_2= \
"""
Bro. Hope you are fine.
Hows the work going on ? Can you send me som... | prodicus/spammy | tests/test_classifier.py | Python | gpl-3.0 | 4,039 | [
"VisIt"
] | 3d1f48fd511cdf27e06edbdefd1a3a041ef407628f2c4463eb1bbcef61c80522 |
# Copyright 2010-2011 Canonical Ltd. This software is licensed under the
# GNU Lesser General Public License version 3 (see the file LICENSE).
import inspect
import logging
from configglue.schema import (
BoolOption,
Section,
DictOption,
IntOption,
ListOption,
Schema,
StringOption,
Tup... | miing/mci_migo_packages_django-configglue | django_configglue/schema.py | Python | lgpl-3.0 | 79,058 | [
"VisIt"
] | 4325791ccf5f4c9bd2582abd25d35c5734903bf6a4ff23a5e86479ea0484f771 |
# -*- coding: utf-8 -*-
"""Tests for instantiating the manager"""
import os
import tempfile
import unittest
from pybel import Manager
from pybel.manager.base_manager import build_engine_session
try:
from unittest import mock
except ImportError:
import mock
class TestInstantiation(unittest.TestCase):
"... | pybel/pybel | tests/test_manager/test_connection.py | Python | mit | 2,903 | [
"Pybel"
] | 8ae997eb3828300b34f518f26c791cd5dfb64452208c3e2cf6fa1f752550fba7 |
"""
====================================================================
Probabilistic predictions with Gaussian process classification (GPC)
====================================================================
This example illustrates the predicted probability of GPC for an RBF kernel
with different choices of the hy... | fabianp/scikit-learn | examples/gaussian_process/plot_gpc.py | Python | bsd-3-clause | 3,958 | [
"Gaussian"
] | a5efa02004d3072f037e9fb318649658f0697b760017ef38a125a3dbf39d89a1 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS Index page (aka, Home page). Note that this is different than
what students see @ edx.org because we redirect requests to a separate web application.
"""
import datetime
from bok_choy.web_app_test import WebAppTest
from common.test.acceptance.pages.lms.index im... | louyihua/edx-platform | common/test/acceptance/tests/lms/test_lms_index.py | Python | agpl-3.0 | 2,224 | [
"VisIt"
] | de958a9d9442ca7e15329ddde57f7d3d61c5ac2ee38c6c9a12172c93b558bee5 |
#!/usr/bin/env python
"""Adaoted from the "wall" demo client for Open Pixel Control
http://github.com/zestyping/openpixelcontrol
Creates a shifting rainbow plaid pattern by overlaying different sine waves
in the red, green, and blue channels.
To run:
First start the gl simulator using the included "wall" layout
... | TheGentlemanOctopus/thegentlemanoctopus | octopus_code/core/octopus/patterns/rainbowPlaidPattern.py | Python | gpl-3.0 | 2,407 | [
"Octopus"
] | 41f2c0aa60ba82ca48b4fbc26b99131241dfb4d0f3dca8bce7d4b99509be0f32 |
import json
import networkx as nx
from itertools import imap
from functools import partial
from collections import defaultdict
from math import sqrt
from datetime import datetime
from django.core.serializers.json import DjangoJSONEncoder
from django.db import connection
from django.http import HttpResponse
from catma... | AdaEne/CATMAID | django/applications/catmaid/control/skeletonexport.py | Python | gpl-3.0 | 36,529 | [
"NEURON"
] | f85942b3e736ae0490c0bc3d4166f6151721116836f24f8d72568bf04326418f |
#!/usr/bin/env python
# Midautumn
# Copyright 2011 Ron Huang
# See LICENSE for details.
from google.appengine.dist import use_library
use_library('django', '1.2')
import os
import logging
from datetime import datetime, timedelta
from google.appengine.ext import webapp
from google.appengine.ext.webapp import util
fro... | ronhuang/adieu | backend/midautumn/api.py | Python | mit | 8,598 | [
"VisIt"
] | 8ca58a5556b154e7ef054786e6e370c862612e303e4069621ba586668ebb8b89 |
# proxy module
from __future__ import absolute_import
from mayavi.action.modules import *
| enthought/etsproxy | enthought/mayavi/action/modules.py | Python | bsd-3-clause | 90 | [
"Mayavi"
] | 1e5f16296572a44649338b1101c8cf7ad94e6a02c774de5bd07021e086898504 |
#!/usr/bin/python
# Adjust SED gratings.
#
# Copyright (C) 2010-2011 Huang Xin
#
# See LICENSE.TXT that came with this file.
from __future__ import division
import sys
from StimControl.LightStim.Core import DefaultScreen
from StimControl.LightStim.LightData import dictattr
from StimControl.LightStim.FrameControl impor... | chrox/RealTimeElectrophy | StimControl/Experiments/demo/mansed.py | Python | bsd-2-clause | 2,136 | [
"Gaussian"
] | 8edb41aeb58e48ee5b3462d1e8c6ba77a5626da335db3d242be2800a066e1902 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Filters
=======
Filter bank construction
------------------------
.. autosummary::
:toctree: generated/
dct
mel
chroma
constant_q
Window functions
----------------
.. autosummary::
:toctree: generated/
window_bandwidth
get_window
Mi... | ruohoruotsi/librosa | librosa/filters.py | Python | isc | 25,845 | [
"Gaussian"
] | 776c50892649b06fadda7093df45e1e8e0a4b87cd31f74a761bebb4c1bc5d79d |
# GALLERY_GET is a tool for downloading images from a gallery page.
#
# ABOUT THIS TOOL
# Many sites link each thumbnail to another page for displaying the image,
# which makes batch-downloading impossible (even with browser plugins).
# This tool will crawl the linked pages for the actual image and download them f... | regosen/gallery_get | gallery_get.py | Python | mit | 18,548 | [
"VisIt"
] | 68bab0099ef8f0ae1eff3549dc4ddd23c9590dda413c61ceed354db4ad461499 |
#
# Copyright (C) 2011-2021 Greg Landrum and other RDKit contributors
#
# @@ 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.
#
import base64
import copy
i... | bp-kelley/rdkit | rdkit/Chem/Draw/IPythonConsole.py | Python | bsd-3-clause | 12,511 | [
"RDKit"
] | 47e9fa45c983765240251295bb4e99117de2c912e918766d8d77407ff3bb5aa3 |
"""
Converts a dict containing a mongo query to a lambda. Doesn't support all the mongo
query $keywords, probably differs the result in subtle ways.
It only supports querying flat structures: dicts with no lists or other dicts in
them (aka subdocuments).
"""
from __future__ import absolute_import
from __future__ impor... | ionelmc/python-mongoql-conv | src/mongoql_conv/__init__.py | Python | bsd-2-clause | 14,173 | [
"VisIt"
] | 35e4115571457c2b1b996b679d57ea90b799bda1c38077e8626d0fcbc16ea677 |
# 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)
from spack import *
class RDirichletmultinomial(RPackage):
"""Dirichlet-Multinomial Mixture Model Machine Learning f... | iulian787/spack | var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py | Python | lgpl-2.1 | 1,391 | [
"Bioconductor"
] | 4d57a8bf9811ddc1f80b83a1e32a913186dcfe50ea78fc4c974038226412e508 |
#!/usr/bin/python
"""
TCP Communications Module
"""
import asyncore
import socket
import errno
import cPickle as pickle
from time import time as _time, sleep as _sleep
from StringIO import StringIO
from .debugging import ModuleLogger, DebugContents, bacpypes_debugging
from .core import deferred
from .task import F... | JoelBender/bacpypes | py27/bacpypes/tcp.py | Python | mit | 31,609 | [
"ASE"
] | 289dbe09537e5566df151ab8c1e586a3052a8b2cf4dbf4043563011536d5c947 |
"""Topology handling in gromacs"""
from ..db import ChemlabDB
from ..core import System, Molecule, Atom
from ..table import atomic_no, atomic_weight
from .energy import lorentz_berthelot as combine_lorentz_berthelot
import itertools
import time
import datetime
from itertools import combinations, combinations_with_rep... | chemlab/chemlab | chemlab/md/potential.py | Python | gpl-3.0 | 11,381 | [
"Gromacs"
] | 43091bdd31c17b7c2f271be0d327da3ba0521185cce75dcf764b08a3d82f92e1 |
# -*- coding: utf-8 -*-
"""
Created on Sat Aug 16 02:08:24 2014
@author: hangyin
"""
# a python implementation of Cross-Entropy method for stochastic optimization
import copy
import numpy as np
class GaussianCEM:
def __init__(self, x0=[0], eliteness=10, covar_full=False, covar_learning_rate=1, covar_scale=None, ... | navigator8972/vae_assoc | pygcem.py | Python | bsd-2-clause | 8,422 | [
"Gaussian"
] | 3832929afaf012580a7fd623a87adc822ec61b0acad3c48c85e16a172c4aa14c |
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