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# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements symmetry-related structure forms.
"""
from typing import List, Sequence
import numpy as np
from tabulate import tabulate
from pymatgen.core.structure import PeriodicSite, Structure
class Symmetr... | materialsproject/pymatgen | pymatgen/symmetry/structure.py | Python | mit | 5,238 | [
"pymatgen"
] | b4bfde571d4ad6a8ae9a342d51a7993a8e744df3ff96a504e574fe2e9f33c08e |
# Reference: http://getblimp.github.io/django-rest-framework-jwt/
import datetime
import json
import os
import requests
base_url = 'http://127.0.0.1:8000/api/'
register_url = base_url + 'users/register/'
login_url = base_url + 'auth/token/'
verify_url = login_url + 'verify/'
refresh_url = login_url + 'refresh/'
... | loafbaker/django_blog | django_blog/tests.py | Python | mit | 6,882 | [
"DIRAC"
] | 61ff7df01b4d4704c91eda421cb18dcc54f4f38b513e6a77c22dba1db9a02e6b |
'''
This module performs a few early syntax check on the input AST.
It checks the conformance of the input code to Pythran specific
constraints.
'''
from pythran.tables import MODULES
from pythran.intrinsic import Class
import ast
class PythranSyntaxError(SyntaxError):
def __init__(self, msg, node=None):
... | pbrunet/pythran | pythran/syntax.py | Python | bsd-3-clause | 7,344 | [
"VisIt"
] | 9cf6d8573b01b8b974686e078c93711f03b84bc5072ec80ac1d1b316928fc0b6 |
########################################################################
# $HeadURL $
# File: ReTransfer.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/02 14:24:21
########################################################################
""" :mod: ReTransfer
================
.. module: ReTransfer
... | avedaee/DIRAC | DataManagementSystem/Agent/RequestOperations/ReTransfer.py | Python | gpl-3.0 | 3,900 | [
"DIRAC"
] | a3ed66b8143c12adaf621f28e4d9a362cafbc6dcfbae87435b953e4ba59f0c7f |
# see changeset 4891
import numpy as np
from ase import Atoms
from gpaw import GPAW
from gpaw.mpi import world
from gpaw.test import equal
a = 2.5
H = Atoms('H', cell=[a, a, a], pbc=True)
energy_tolerance = 0.00006
niter_tolerance = 0
if world.size >= 3:
calc = GPAW(kpts=[6, 6, 1],
spinpol=True,
... | robwarm/gpaw-symm | gpaw/test/kptpar.py | Python | gpl-3.0 | 1,300 | [
"ASE",
"GPAW"
] | e1bc6e09d4d4f6c943bd6a29da61a9869590f84ac603958936fdadbb84715685 |
# coding=utf-8
from sys import version_info
from unittest import TestCase
import sys
from nose import SkipTest
from nose.tools import eq_, assert_raises, ok_
from six import text_type
from parsimonious.exceptions import UndefinedLabel, ParseError
from parsimonious.expressions import Literal, Lookahead, Regex, Sequen... | erikrose/parsimonious | parsimonious/tests/test_grammar.py | Python | mit | 19,295 | [
"VisIt"
] | 38a76b5b820459a7fdff2e6009fd6ac0414b479d2c5f88a2d0de21e6097bbe75 |
#
# Copyright (C) 2007 by Greg Landrum
# All rights reserved
#
import copy
import time
from rdkit import Chem, Geometry
from rdkit.Chem import AllChem
from rdkit.Chem.Subshape import BuilderUtils
from rdkit.Chem.Subshape import SubshapeObjects
import pickle
class SubshapeCombineOperations(object):
UNION = 0
... | greglandrum/rdkit | rdkit/Chem/Subshape/SubshapeBuilder.py | Python | bsd-3-clause | 4,237 | [
"PyMOL",
"RDKit"
] | 7e36b18640c9eb4038eacd2cdc4a0892c1cb076d095c87b11f76e22f428a2515 |
# Copyright (c) 2012-2015 Netforce Co. Ltd.
#
# 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, merge, publ... | nfco/netforce | netforce_general/netforce_general/models/reason_code.py | Python | mit | 1,865 | [
"VisIt"
] | c6349ed4521d9c62335c3a6c79d31ac3085cde163708f2ad1f90ed500191dbd1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright INRIA
# Contributors: Nicolas P. Rougier (Nicolas.Rougier@inria.fr)
#
# DANA is a computing framework for the simulation of distributed,
# asynchronous, numerical and adaptive models... | rougier/dana | examples/DNF-1d.py | Python | bsd-3-clause | 2,505 | [
"Gaussian"
] | 384860f2a0ada690a1151022840d756f97da147e4679188af12c2aeb1d0cca40 |
import glob, re, os, operator, itertools, copy, collections
from math import sin, cos, acos,radians
import parser
import our_module
import ast
import sys
# change runjob.sh
#our_module.change_vasp_path()
open('compound_directories', 'w').close()
# we choose files to work on depending on arguments given to the script,... | cwandtj/A2P2 | a2p2_170111updated/a2p2.py | Python | mit | 13,586 | [
"VASP"
] | 62424e8ff313014505de8389475668dfc588b424f6182c44693e311da6b7a2f9 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Parser for MOPAC output files"""
# Based on parser in RMG-Py by Greg Magoon
# https://github.com/ReactionMechanismGene... | cclib/cclib | cclib/parser/mopacparser.py | Python | bsd-3-clause | 9,929 | [
"MOPAC",
"cclib"
] | b9ee90c6d65964296fd2a047cb68aebdf554c5d43cc41ec2a24fdf4466cd05cc |
from __future__ import print_function, absolute_import
import os
import warnings
import numpy as np
import mdtraj as md
from ..utils.progressbar import ProgressBar, Percentage, Bar, ETA
from ..utils import verbosedump
from ..cmdline import NumpydocClassCommand, argument, exttype, stripquotestype
from ..dataset import... | msultan/msmbuilder | msmbuilder/commands/featurizer.py | Python | lgpl-2.1 | 9,643 | [
"MDTraj"
] | 3754c4a1b5505fae8589f5a714eed7fad335e9e916660fffc40a845bd7ab18de |
""" ImportedIds gathers identifiers imported by a node. """
from pythran.analyses.globals_analysis import Globals
from pythran.analyses.locals_analysis import Locals
from pythran.passmanager import NodeAnalysis
import pythran.metadata as md
import gast as ast
class ImportedIds(NodeAnalysis):
"""Gather ids refe... | serge-sans-paille/pythran | pythran/analyses/imported_ids.py | Python | bsd-3-clause | 3,484 | [
"VisIt"
] | 0c52bcd29d069020858a98baa8bc65d43e1ccf597c91b62af633d742d97ebc42 |
#!/usr/bin/env python3
import linecache
import collections
import time
import platform
import getpass
import numpy as np
from netCDF4 import Dataset
def readheader(filename):
"""
Takes a file name and reads the header of the file
First implemented as a named tuple. So you can call
a = read_header('myfi... | andy3092/asc2netcdf | asc2netcdf/asc2netcdf.py | Python | gpl-3.0 | 5,013 | [
"NetCDF"
] | 2925a1b4f804cb3c56dbe0d96caf7794903bbc2da36e39bf70ffa3248c9de925 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
import numpy as np
from scipy.spatial import ... | mganeva/mantid | Framework/PythonInterface/plugins/algorithms/IndexSatellitePeaks.py | Python | gpl-3.0 | 6,641 | [
"CRYSTAL"
] | ad26587226c954fe5a67648c7bc0d3ac3ea155159ec6aafc90df8df49408247a |
#!/usr/bin/python
###############################################################################
#
# This script generates survival probabilities of rotameric states generated
# from the label_states output of Rotamer_Preprocessor. This gives you
# insight into the kinetics of rotameric motion. Survival probabilities
... | cing/ChannelAnalysis | ChannelAnalysis/RotamerAnalysis/Survival.py | Python | mit | 8,782 | [
"MDAnalysis"
] | 2f44bf0b1fde6ddb52fdd89457706924e826a1a16ce882f0b48d667f977c47ff |
from matplotlib import rcParams, rc
import numpy as np
import sys
from fitFunctions import gaussian
import scipy.interpolate
import scipy.signal
from baselineIIR import IirFilter
import pickle
# common setup for matplotlib
params = {'savefig.dpi': 300, # save figures to 300 dpi
'axes.labelsize': 14,
... | bmazin/SDR | Projects/SuperMatchedFilters/photonTriggersSubBase.py | Python | gpl-2.0 | 9,178 | [
"Gaussian"
] | 5479de04e359565e7600f06277dcedb02edea21b93da8550216620e658f3c073 |
# Copyright 2013 by Christian Brueffer. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Command line wrapper for the multiple sequence alignment program MSAProbs.
"""
fro... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Align/Applications/_MSAProbs.py | Python | gpl-2.0 | 3,559 | [
"Biopython"
] | 9f0b0da62bd70ae1769e0425f96b4eb91811e3a734b855d3dafdaa74ef7f7daf |
# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ...util.linalg import jitchol, DSYR, dtrtrs, dtrtri, pdinv, dpotrs, tdot, symmetrify
from paramz import ObsAr
from . import ExactGaussianInference, VarDTC
from ...util import dia... | dhhjx880713/GPy | GPy/inference/latent_function_inference/expectation_propagation.py | Python | bsd-3-clause | 18,424 | [
"Gaussian"
] | 8f2afbd0c92c3ac0a54a40fdb0cd2dfbba1c7e37921734a45dd075d99d7721d3 |
'''
This is the final wavelength calibration code that implements the
grating equation to calculate the wavelength dispersion.
The input should just be the name of a comparison lamp, taken from argv.
The function depend on some hard coded data, "WaveList" and "Parameters" which
are project spesific.
Written by Je... | joshfuchs/ZZCeti_pipeline | Wavelength_Calibration.py | Python | mit | 37,734 | [
"Gaussian"
] | 0f69cbca83c471ea004061ea2b3fe4e2f980a125bd821ea4eceb6bb79f476533 |
#!/usr/bin/env python
import h5py
import numpy as np
def grab_stat_entries(stat_file_name,name):
""" stat_file_name: .stat.h5 file name, name: ex. gofr """
stat_file = h5py.File(stat_file_name)
data = []
# find entry and extract data
for estimator in stat_file.keys():
if estimator != n... | Paul-St-Young/QMC | stat_analyzer.py | Python | mit | 15,140 | [
"QMCPACK"
] | 11d176e2e2b79199c748358aa43343e5ff285a990afbc239bdaaf0e81ec6b52f |
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import PhysicsBasics as pb
from skimage.feature import blob_log
from skimage.io import imread
from multiprocessing import Pool
from matplotlib.patches import Circle
from scipy.stats import mode
from tabulate import tabulate
import re
from io import By... | ZGainsforth/MultiLaue | Calibrations/XRDImageFeatureExtraction.py | Python | epl-1.0 | 9,245 | [
"CRYSTAL",
"Gaussian"
] | 865edde2e7aa3b8eab04ba41e83c9623ce6587910e1445aec7199d6abab60c1e |
"""
Vectors options
---------------
Vectors display options for a filter list.
* Vectors that have been loaded onto the current input state are shown in
the list. If one of the options is checked the vectors will be displayed
by drawing arrows for each of the visible atoms. The size of the arrows
is calculated... | chrisdjscott/Atoman | atoman/gui/filterListOptions/vectorsOptions.py | Python | mit | 8,581 | [
"VTK"
] | 541aab19999be74238a6c28c89519d89896b516b8b0a298b0d9685aeae0ba6e0 |
# 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.
import re
import sys
import android_commands
import json
import logging
import math
# Valid values of result type.
RESULT_TYPES = {'unimportant': 'RESU... | espadrine/opera | chromium/src/build/android/pylib/perf_tests_helper.py | Python | bsd-3-clause | 6,792 | [
"Galaxy"
] | 85939c7e0eb55ece679762cbd56c43ffaf0d0a7f2855c5886b4d9da1411a115e |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | mainglis/adminpanel | config/urls.py | Python | bsd-3-clause | 1,317 | [
"VisIt"
] | 995d8fb04f27f7a42e25261645c7d6aaa9320e009f5c39f69da8a5bab813cb57 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2015 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A Beauchamp, Jason Swails... | mpharrigan/mdtraj | mdtraj/geometry/distance.py | Python | lgpl-2.1 | 11,815 | [
"MDTraj"
] | 12cf22c0481d2a2757af6adec049b56191ed2e2064307d4653eeac7f89935544 |
#!/usr/bin/python
# Write the initial topology file for restrained simulations in swarm free energy calculations
# Grant Rotskoff, 11 July 2012
# Rewritten by Bjorn Wesen in June 2014
# This function can do two things - either get a start and end config and associated xvg's, and then interpolate
# n states between th... | gromacs/copernicus | cpc/lib/swarms/dihedral_restraints.py | Python | gpl-2.0 | 8,979 | [
"Gromacs"
] | 4891707558b5e4a87e6473f8b203288dc1c99421e03045c45ed6a91fe2e9bce5 |
import pyspeckit
# neet matplotlib so we can make mouse-click events from the script
import matplotlib
import os
# list of annotations so we can clear them
annotations = []
excesslines = []
# get the data from http://cdsarc.u-strasbg.fr/ftp/cats/II/179/sp/hr2421.fit
import urllib2
url = urllib2.urlopen('http://cdsarc... | bsipocz/pyspeckit | examples/interactive_example_hr2421.py | Python | mit | 11,292 | [
"Gaussian"
] | 3afea4cad58aa6770265925ad65b210cba8a13736fc5641f6225c8d343459476 |
"""Transforms data from third party services to Lutris compatible data"""
def clean_name(name):
"""Clean up a game name"""
extras = (
"tech demo",
"demo",
"demo 2",
"gold pack",
"complete pack",
"the final cut",
"enhanced edition",
"free preview"... | lutris/website | providers/processors.py | Python | agpl-3.0 | 1,084 | [
"Galaxy"
] | 919111c844c8b18f022588dc634e86b94ce3c3a7cc3c3cd5316cb21f7a40299d |
import sys
import re
import install_utils as utils
import config
COLLECTD_HOME = '/etc/collectd'
COLLECTD_CONF_DIR = COLLECTD_HOME + '/managed_config'
# http response header
NOT_AUTH = 401
NOT_FOUND = 404
HTTP_OK = 200
INVALID_URL = -1
def check_collectd_exists():
utils.print_step(' Checking if collectd exist... | wavefrontHQ/install | conf_collectd_plugin.py | Python | apache-2.0 | 13,057 | [
"VisIt"
] | 69a3d316f00588432db49c75cec6206704c3b7f555d8ab1f87a7a357d67be2c7 |
"""
Notifications for Android TV notification service.
For more details about this platform, please refer to the documentation at
https://home-assistant.io/components/notify.nfandroidtv/
"""
import os
import logging
import requests
import voluptuous as vol
from homeassistant.components.notify import (
ATTR_TITLE... | srcLurker/home-assistant | homeassistant/components/notify/nfandroidtv.py | Python | mit | 6,596 | [
"Amber"
] | 1d5e3a098240ac6147feff8e8e04ddb92058db6778fa864f4f1d711cd4957fcd |
'''<h1>Library for surface x-ray diffraction simulations</h1>
<p> The problem of modelling the sample is divided to four
different classes: Sample, Slab, UnitCell and Instrument.
A Slab is the basic unit that builds up a sample and can
be seen as a quasi-unitcell for the sxrd problem.
Stricitly it is a 2D unitcell with... | joshp123/genx | models/sxrd.py | Python | gpl-3.0 | 43,571 | [
"Gaussian"
] | 43d78d3f10a3226c423827d83ea32cf04f0eeda50fe3bd1cef293b57d7f2208a |
""" UserProfileDB class is a front-end to the User Profile Database
"""
import six
import cachetools
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.Helpers import Registry
from DIRAC.Core.Base.DB import DB
class UserProfileDB(DB):
"""UserProfileDB class is a front-end to the User Profile... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/DB/UserProfileDB.py | Python | gpl-3.0 | 21,018 | [
"DIRAC"
] | 92a756ec40715c9b112105a9910185333d93a9a085713951a091de616f825998 |
#!/usr/bin/env python
""" Create a DIRAC transfer/replicateAndRegister request to be executed
by the DMS Transfer Agent
"""
__RCSID__ = "$Id$"
import os
from hashlib import md5
import time
from DIRAC.Core.Base import Script
from DIRAC.Core.Utilities.List import breakListIntoChunks
Script.setUsageMessage( '\n'.joi... | fibbo/DIRAC | DataManagementSystem/scripts/dirac-dms-create-replication-request.py | Python | gpl-3.0 | 3,301 | [
"DIRAC"
] | fd3fd8086af2f2a41f1bac4c35810e0d9d119d2f6b35fa3fcaa72090e895f1a6 |
from __future__ import division, absolute_import, print_function
import numpy as np
from numpy.testing import (
TestCase, run_module_suite, assert_, assert_raises, assert_equal,
assert_warns, assert_array_equal, assert_array_almost_equal)
from numpy import random
from numpy.compat import asbytes
import... | kiwifb/numpy | numpy/random/tests/test_random.py | Python | bsd-3-clause | 61,543 | [
"Gaussian"
] | 01497b12acf37836c8887eb612411065152c92f455e4a7220b5261a5d0901e42 |
from __future__ import absolute_import, division
from django.conf import settings
from django.core import urlresolvers
from django.db import connection
from django.db.models import Sum
from django.db.models.query import QuerySet
from django.http import HttpResponseNotFound, HttpRequest, HttpResponse
from django.templa... | SmartPeople/zulip | analytics/views.py | Python | apache-2.0 | 36,568 | [
"VisIt"
] | a7f5fea377758f73b22fe17c7c33ad1e05bd05a450ab8964895a3db8fc932f2c |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/admin/action/__init__.py | Python | gpl-2.0 | 1,728 | [
"VisIt"
] | b685073eb6d9ca56e4fac95dbcf40e5f86c0f9e41125ae2edb5a20f5397263f3 |
"""
Authors: Craig Heady (craig.heady@csiro.au)
Copyright 2015 CSIRO
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... | CWSL/cwsl-mas | cwsl/vt_modules/vt_cdo_histogram.py | Python | apache-2.0 | 3,983 | [
"NetCDF"
] | 967379789d7c8d65c0132129a604aa2ecbac61063caadc28210dce58f3733de1 |
#!/usr/bin/python
"""
Copyright 2010 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | clreinki/GalaxyHarvester | getHarvesterData.py | Python | agpl-3.0 | 8,252 | [
"Galaxy"
] | 3580a26703ff9e7f3787bdd5a8626fde5c40c3d9e5ca6b66267172417222883b |
"""
Sample Mayavi customization file.
This code is not to be executed as `mayavi2 -x user_mayavi.py` or
`python user_mayavi.py`.
Put this file in ~/.mayavi2/user_mayavi.py and rerun mayavi2 to see what
it does -- the worker view may not show up by default so you will have
to go to View->Other and in the Show View dia... | liulion/mayavi | examples/mayavi/user_mayavi.py | Python | bsd-3-clause | 9,808 | [
"Mayavi"
] | 64ccfa8ec828a4b6215406ea1f15e2645af87c1d90237eee21097960651534ad |
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #
# (c) 2010... | Chuban/moose | python/chigger/misc/ChiggerBackground.py | Python | lgpl-2.1 | 1,283 | [
"MOOSE"
] | 6ca7ae064674740d07f845a54c4fdadd8ff270850205feefb7f386ad4425a870 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/bin/meta.py | Python | gpl-2.0 | 14,814 | [
"VTK",
"VisIt"
] | 091e69345f44a3f1ad4651e102af88e5359f92ce8c3a9f79aff13c629b532f0f |
#!/usr/bin/env python
from __future__ import print_function
import argparse
import calc
import env
import logging
import math
import sys
app_name = "distance"
log = logging.getLogger(app_name)
class Application(object):
def __init__(self, arg, hosted, state = {}):
ap_parents = [env.arg_parser] if not hosted... | KayJohnston/jackies-map | distance.py | Python | bsd-3-clause | 5,593 | [
"VisIt"
] | dcf6b26bbe1a1ca4e497349ee87d5d12c5af7f9b06e00fc9184e9395a48a7f75 |
from discord.ext.commands import Bot
import random
import SecretKey
import asyncio
import discord
import time
# Start the bot object
my_bot = Bot(command_prefix="S")
# All the things to say
jokes = ["Would you like sum fries with that?", "Tickle my bum and call me Samantha.",
"SUCCULENT CHINESE MEEEEEAL", "D... | AxelFl/ScottBot | ScottBott.py | Python | mit | 4,139 | [
"CRYSTAL"
] | 53923ce01ea41aa369af5741dc5308fa1c4251151697978782feeced5a84887a |
import threading
# Because eval(valenc) might require it
import datetime
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import DEncode, List
from DIRAC.Core.Utilities.ReturnValues import isReturnStructure
from DIRAC.Core.Base.ExecutorModule import ExecutorModule
from DIRAC.WorkloadManagementSystem.C... | avedaee/DIRAC | WorkloadManagementSystem/Executor/Base/OptimizerExecutor.py | Python | gpl-3.0 | 8,027 | [
"DIRAC"
] | f71f804679d57f7a676f9686b8258f93f3f66cbba28ef1a4c0b742dc68754622 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2018, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Gaussian Editor
#######################
Base class on top of exatomic.Editor for NBO Editors
"""
from exatomic import Editor as AtomicEditor
class Editor(AtomicEditor):
def... | avmarchenko/exatomic | exatomic/nbo/editor.py | Python | apache-2.0 | 548 | [
"Gaussian"
] | 2a281847b3be22dc82003ed664e530b3f27530505d24c48600a8b8185fda9839 |
from ovito import *
from ovito.io import *
from ovito.modifiers import *
# Load a simulation sequence.
node = import_file("simulation.*.dump")
# Add modifier for computing the coordination numbers of particles.
node.modifiers.append(CoordinationNumberModifier(cutoff = 2.9))
# Save the initial coordination numbers a... | srinath-chakravarthy/ovito | doc/python/example_snippets/freeze_property_modifier.py | Python | gpl-3.0 | 1,264 | [
"OVITO"
] | cebde9b8362b3d26b4ad606d374668c904ff5ea92e282613ec3bc2c3f494638d |
import random, math, GameEnvironment, npc
class neuron:
#num_inputs = total number of inputs + 1 for the bias input
def __init__(self, num_inputs):
#generating an initially random set of weights
self.weights = []
for x in range(num_inputs):
self.weights.append(random.... | scottnm/Evolving-Boss-Battles | neuron.py | Python | apache-2.0 | 4,393 | [
"NEURON"
] | c4ac2908fb023a39f3b2c326dd45cda6facd57af2096349e2f3cf81681300346 |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# 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 requ... | steckdenis/rlglue-py3 | tests/test_message_agent.py | Python | apache-2.0 | 1,944 | [
"Brian"
] | 6700988419fb5191246c3779f1ecdb5ba5b337deb62defe8edc80d72d7deba24 |
# Copyright (C) 2013 Oskar Maier
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in ... | loli/medpy | medpy/io/load.py | Python | gpl-3.0 | 4,421 | [
"NetCDF",
"VTK"
] | a719afc16e4a8bb8c1aa441582eb3dd05e6f2c2ff5acebd1c48866f183684396 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'IndicatorDomain'
db.create_table(u'profiles_indicatordomain', (
(u'id', self.g... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0001_initial.py | Python | mit | 52,131 | [
"MOE"
] | f4991629a40cc86aa2e6d7041d3239ac8c0325a9be51ab7f330655a2dc903ff4 |
# -*- 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_machine_images.py | Python | apache-2.0 | 130,071 | [
"Octopus"
] | d4169b2cb8f461b73f7b197ed5d233c1e6f63cef306cab03009d1a948e65bcbb |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 5.0.4.
Change directory to p... | dmordom/nipype | nipype/interfaces/fsl/epi.py | Python | bsd-3-clause | 28,769 | [
"Gaussian"
] | b091bff46aace680761ed63bdbf62d4f2dd7a9d91a504b25c19f872a7bfc3d1e |
#######################################################################
#
# Copyright 2009-2010 by Ullrich Koethe
#
# This file is part of the VIGRA computer vision library.
# The VIGRA Website is
# http://hci.iwr.uni-heidelberg.de/vigra/
# Please direct questions, bug reports, and contributions... | cha007/vigra | vigranumpy/lib/__init__.py | Python | mit | 78,536 | [
"Gaussian"
] | b130ac610a902d373d64e522d89989f1f0cc7bc59c672db9925cd3222bc21603 |
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
import os
import sys
from hashlib import md5
from docutils import nodes
from docutils.parsers.rst import directives
import warnings
from matplotlib import rcParams
from matplotlib.mathtext import ... | Reagankm/KnockKnock | venv/lib/python3.4/site-packages/matplotlib/sphinxext/mathmpl.py | Python | gpl-2.0 | 3,857 | [
"VisIt"
] | 05da00bfb49fd696a46f2eb84bc549ac3521dd52cdb7fa96da1cbf2fedcc6a25 |
# -*- coding: utf-8 -*-
# imports here
from aiida.parsers.plugins.vasp.instruction import BaseInstruction
__copyright__ = u'Copyright © 2016, Mario Zic, Trinity College Dublin. All Rights Reserved.'
__license__ = "Apache, Version 2.0, see LICENSE.txt file"
__version__ = "0.0.1"
__contributors__ = "Mario Zic"
__contac... | abelcarreras/aiida_extensions | plugins/parsers/vasp/instruction/error/dummy_error_parser.py | Python | mit | 889 | [
"VASP"
] | c069a263ef7b0d3a3c494994579eb20a8142c425514044e5058578aabccff101 |
# This component creates a bar chart of monthly or avrMonthlyPerHour data.
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Chris Mackey and Mostapha Sadeghipour Roudsari <Chris@MackeyArchitecture.com and Sad... | samuto/ladybug | src/Ladybug_Monthly Bar Chart.py | Python | gpl-3.0 | 58,657 | [
"EPW"
] | 5f91f37321d1f4aaced8cd7804438c65a5eaac41feebb3dc43ea35e52b0c893c |
# -*- coding: utf-8 -*-
"""Parser for the Google Chrome Cookie database."""
from plaso.containers import time_events
from plaso.lib import eventdata
# Register the cookie plugins.
from plaso.parsers import cookie_plugins # pylint: disable=unused-import
from plaso.parsers import sqlite
from plaso.parsers.cookie_plugin... | dc3-plaso/plaso | plaso/parsers/sqlite_plugins/chrome_cookies.py | Python | apache-2.0 | 5,261 | [
"VisIt"
] | 97c788df33013f4176535cfa57a79617790303b89ab30e2c7776a04251b10eb2 |
# -*- Mode: Python -*-
# vi:si:et:sw=4:sts=4:ts=4
# Flumotion - a streaming media server
# Copyright (C) 2004,2005,2006,2007,2008,2009 Fluendo, S.L.
# Copyright (C) 2010,2011 Flumotion Services, S.A.
# All rights reserved.
#
# This file may be distributed and/or modified under the terms of
# the GNU Lesser General Pub... | flumotion-mirror/flumotion-dvb | flumotion/worker/checks/dvb.py | Python | lgpl-2.1 | 21,811 | [
"CRYSTAL"
] | 9f2d30d1bfe64042f59b5e0e2d97ebd83fd4319db852cd1a328d862c4cf35975 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB ... | yashdsaraf/scancode-toolkit | tests/textcode/test_markup.py | Python | apache-2.0 | 7,898 | [
"VisIt"
] | df481314488c18466bdff5e2d4c3671020229a49a9fcb390284ba37eeb72081f |
#!/usr/bin/env python
# :noTabs=true:
# (c) Copyright Rosetta Commons Member Institutions.
# (c) This file is part of the Rosetta software suite and is made available under license.
# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
# (c) For more information, see http://www.r... | madscatt/zazzie_1.5 | trunk/sassie/build/pdbrx/salign.py | Python | gpl-3.0 | 6,769 | [
"PyMOL"
] | 96b8f4d3c750cc5031337b59e33bb84cde4ab4a0db3a9972c6ce91d5d0b210bc |
import re
import sys
import subprocess
from Bio.Blast import NCBIXML
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio import SeqIO
import time
import os
def createDatabase(db_file, force = True):
"""Create BLAST db out of elements file"""
if force or not os.path.isfile(db_file + ".nhr"):
... | karroje/RAIDER_eval | coverageBLAST.py | Python | gpl-3.0 | 3,912 | [
"BLAST",
"Biopython"
] | e98eafd9f7aadb665d014981c60f326059b52ac3d21d5ff854de799455789ba8 |
# coding: utf-8
# flake8: noqa
"""
MINDBODY Public API
No description provided (generated by Swagger Codegen https://github.com/swagger-api/swagger-codegen) # noqa: E501
OpenAPI spec version: v6
Generated by: https://github.com/swagger-api/swagger-codegen.git
"""
from __future__ import absolu... | mindbody/API-Examples | SDKs/Python/swagger_client/models/__init__.py | Python | bsd-2-clause | 15,312 | [
"VisIt"
] | 628f72a9f76917877d3d32ce3a3d230d577beb0dbebc9ad60183c8a61e5fdfe9 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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 it and/or modify
#... | jturney/psi4 | psi4/driver/procrouting/dft/hyb_functionals.py | Python | lgpl-3.0 | 15,712 | [
"Psi4"
] | b1194cc9211cfeb9c47b4687f7c892baa577d0e32237c170a178a3a94270ac2a |
"""
@author Alberto Perez de Alba Ortiz
"""
import openpathsampling as paths
try:
import mdtraj as md
except ImportError:
HAS_MDTRAJ = False
else:
HAS_MDTRAJ = True
try:
import openpathsampling.engines.openmm as peng_omm
except ImportError:
HAS_OPENMM = False
else:
HAS_OPENMM = True
try:
... | choderalab/openpathsampling | openpathsampling/tests/test_plumed_wrapper.py | Python | lgpl-2.1 | 8,235 | [
"MDTraj",
"OpenMM"
] | 241f40d5a0c068833a6933f3fb55442f6222d1e814b05a4bd55b465aefad4585 |
# coding: utf8
""" Implementation of finite DPP MCMC samplers:
- `add_exchange_delete_sampler`
- `add_delete_sampler`
- `basis_exchange_sampler`
- `zonotope_sampler`
.. seealso:
`Documentation on ReadTheDocs <https://dppy.readthedocs.io/en/latest/finite_dpps/mcmc_sampling.html>`_
"""
import time
import numpy as... | guilgautier/DPPy | dppy/mcmc_sampling.py | Python | mit | 19,068 | [
"Gaussian"
] | 3d4aa5d6a25d4f6b38867e648c3ccfbdc0c2da9f77f92a7ff94d6ca35f23372c |
#######################################################################
#
#
# Volume Text Renderer for Dreambox/Enigma-2
# Coded by Vali (c)2010
# Support: www.dreambox-tools.info
#
#
# This plugin is licensed under the Creative Commons
# Attribution-NonCommercial-ShareAlike 3.0 Unported License.
# To view ... | openatv/enigma2 | lib/python/Components/Renderer/VolumeText.py | Python | gpl-2.0 | 1,573 | [
"VisIt"
] | d7c6ced9aff7f431180bdf3f40f15edb355fda37eba734473bcb185e6ab43dc1 |
#
# Copyright (c) 2008--2016 Red Hat, Inc.
#
# This software is licensed to you under the GNU General Public License,
# version 2 (GPLv2). There is NO WARRANTY for this software, express or
# implied, including the implied warranties of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. You should have received a c... | mcalmer/spacewalk | backend/common/rhnException.py | Python | gpl-2.0 | 13,657 | [
"VisIt"
] | bf803338dfbe40944573b561baaf10dd8deb1a8cd33a8c7ac3d3d3fbc538bc64 |
#! /usr/bin/env python
"""
adds "X. to the front and ." to the end of each name in the first column if it begins with Otu
used to format network attributes file for Cytoscape so that Otu names match
assumes comma separated values and unix linebreaks
usage:
python format-for-cytoscape.py filename.csv
Copyright:
... | Brazelton-Lab/lab_scripts | format-for-cytoscape.py | Python | gpl-2.0 | 1,696 | [
"Cytoscape"
] | 1cd2e74c419df700a2d7a9c5f9c8933fe55141601dae17304d3edb4352285718 |
import pytest
import pyvista as pv
has_panel = True
try:
from panel.pane.vtk.vtk import VTKRenderWindowSynchronized
except:
has_panel = False
skip_no_panel = pytest.mark.skipif(not has_panel, reason='Requires panel')
@skip_no_panel
def test_set_jupyter_backend_panel():
pv.set_jupyter_backend('panel')
... | akaszynski/vtkInterface | tests/jupyter/test_panel.py | Python | mit | 830 | [
"VTK"
] | 56428021436947c282d6bc6ca2305b20015d72ba76562bcb6fa6f24a6206b738 |
""" Contains the GI (General Illumination) parent classes. """
# gi.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
from mpf.system.device import Device
... | spierepf/mpf | mpf/devices/gi.py | Python | mit | 3,624 | [
"Brian"
] | a03e5f3e607028d7e730b13605056e353d6d362fb7dbe3e33a3e9a14f6e6a974 |
# -*- coding: utf-8 -*-
from PyQt4 import QtCore, QtGui
from NaiveBayes import *
import numpy as np
from sklearn.naive_bayes import GaussianNB
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
def _fromUtf8(s):
return s
try:
_encoding = QtGui.QApplication.UnicodeUTF8
def _transl... | mlskit/astromlskit | FRONTEND/naiveui.py | Python | gpl-3.0 | 6,601 | [
"Gaussian"
] | 6e5fafac403642d8ef30ab9b24364ebdc51d1ccb697b70d6e77188887aef1269 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# John Ossyra
#
# Contributors:
#
# `adapt... | markovmodel/adaptivemd | adaptivemd/worker.py | Python | lgpl-2.1 | 27,583 | [
"MDTraj"
] | 8c1d7d466cb4bbd5df6df3e12c674f144363bb18696df28b0eb7255fb76659b3 |
'''
DQN approach with experience replay for different RL problems
as part of the basic series on reinforcement learning @
https://github.com/vmayoral/basic_reinforcement_learning
TODO:
- learning is just not fine
- review bins, and activation functions
Inspired by
- https://gym.openai.com/evaluations... | vmayoral/basic_reinforcement_learning | tutorial5/tests/dq-learning-experience-gym.py | Python | gpl-3.0 | 9,505 | [
"NEURON"
] | 56a0639247e9d59918d6e349a75f19bd49b65b2700fa8cd72c6a27f4df385cc1 |
#!/usr/bin/env python
"""
Turn docstrings from a single module into a markdown file.
We do this with PydocMarkdown, using custom processors and renderers defined here.
"""
import argparse
import logging
import os
import re
import sys
from collections import OrderedDict
from dataclasses import dataclass
from enum imp... | allenai/allennlp | scripts/py2md.py | Python | apache-2.0 | 18,741 | [
"VisIt"
] | 692257596676b052130091216cd48b6d678f34d8bfa06c20196060362c3447bb |
import sys
from optparse import OptionParser
def build_parser():
description = 'Generate LCAO basis sets for the specified elements.'
parser = OptionParser(usage='%prog [options] [elements]',
version='%prog 0.1', description=description)
parser.add_option('-n', '--name', default=... | robwarm/gpaw-symm | gpaw/atom/gpaw_basis.py | Python | gpl-3.0 | 6,907 | [
"GPAW",
"Gaussian"
] | 347ade01d457d7c1533ad39d4e59e865e14d810d516f6382470390075839d5f8 |
def make_basal_ganglia(net, name='Basal Ganglia', dimensions=1, neurons=100,
tau_ampa=0.002, tau_gaba=0.008, output_weight=1,
radius=1.5):
"""This function creates a subnetwork with a model of the basal ganglia
based off the paper (Gurney, Prescott, & Redgrave, 20... | jaberg/nengo | nengo/templates/basalganglia.py | Python | mit | 3,546 | [
"NEURON"
] | f57a867824c069e06dd6d197c258ec10d667ba6c07bc385ffcdf20806493e42c |
# Copyright (c) 2015-2018 Cisco Systems, Inc.
#
# 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, merge... | metacloud/molecule | test/unit/test_migrate.py | Python | mit | 5,139 | [
"Galaxy"
] | 0993415022c549f2038e3faabb926deef1966f2459b9a17c2a1cbc3f5de2921b |
"""
Python interface to the NVIDIA cuDNN library
"""
import sys
import ctypes
import ctypes.util
if sys.platform in ('linux2', 'linux'):
_libcudnn_libname_list = ['libcudnn.so', 'libcudnn.so.6.5', 'libcudnn.so.6.5.35']
elif sys.platform == 'darwin':
_libcudnn_libname_list = ['libcudnn.dylib', 'libcudnn.6.5.dy... | ttakamura/chainer | chainer/cudnn/libcudnn.py | Python | mit | 71,227 | [
"NEURON"
] | 1d4c8ec70d3d8e894a5fcfae11f79b6eb408c3459abd65b61ebc975607ab6d44 |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from lettuce import world, step
from lettuce.django import django_url
from nose.tools import assert_equals, assert_in # pylint: disable=no-name-in-module
from logging import getLogger
logger = getLogger(__name__)
@step('I navigate to an open... | cselis86/edx-platform | lms/djangoapps/courseware/features/openended.py | Python | agpl-3.0 | 2,996 | [
"VisIt"
] | 9b1319a316ba8193f6f33432e894ecec837baa65eb3a25723617badc58adb3a8 |
'''
Given a binary tree, return the postorder traversal of its nodes' values.
For example:
Given binary tree {1,#,2,3},
1
\
2
/
3
return [3,2,1].
Note: Recursive solution is trivial, could you do it iteratively?
'''
# Definition for a binary tree node.
class TreeNode(object):
... | gavinfish/leetcode-share | python/145 Binary Tree Postorder Traversal.py | Python | mit | 1,110 | [
"VisIt"
] | 635d641c4d52f265b7e91b6fe35a503efe2127eb58503cc9e4991dee3d18dd54 |
import util
import measureprocessplot
import time
import deploy
from fabric.tasks import execute
#'400.perlbench',
spec_benchmarks= ['470.lbm','462.libquantum','401.bzip2','444.namd','464.h264ref','403.gcc',
'445.gobmk','465.tonto','410.bwaves','416.gamess','450.soplex','471.omnetpp',
... | navaneethrameshan/PMU-burst | automateall.py | Python | gpl-2.0 | 1,175 | [
"GAMESS",
"Gromacs",
"NAMD"
] | 30c031ce047b7b7d8aff76fac745c6c45a51c93b5773151b7235d046611b02ed |
#!python
import math
import warnings
warnings.filterwarnings('ignore','masked')
warnings.simplefilter('ignore')
import pylab
from pylab import *
for k,v in pylab.__dict__.iteritems():
if hasattr(v,'__module__'):
if v.__module__ is None:
locals()[k].__module__ = 'pylab'
import matplotlib
impor... | ufoym/agpy | agpy/pyflagger.py | Python | mit | 109,393 | [
"Gaussian",
"NetCDF"
] | cddd0788e37890426f135b22db5644db708467952015852c1650d8d6e5d4c10e |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
# A collection of optimization algorithms. Version 0... | pizzathief/scipy | scipy/optimize/optimize.py | Python | bsd-3-clause | 123,400 | [
"Gaussian"
] | fa8ae5129def972cfb22e4c0691b4a947eb9f3e67511008b5a935f3c8c5c15a5 |
####### LICENSE #######
# This code is part of the Recombineering module, written by Gregory
# Moyerbrailean at Michigan State University, Department of Microbiology
# and Molecular Genetics.
# Copyright (C) 2010 Gregory Moyerbrailean
#
# This program is free software; you can redistribute it and/or modify
# it under... | gmoyerbrailean/PyRec | Files/export.py | Python | gpl-2.0 | 7,299 | [
"BLAST"
] | 559274a7ffd1bc3b0892da3946d563c9cc987b31932560fd522eb22502d3f8c4 |
"""
An off-screen mayavi engine.
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
from traits.api import Callable, Str
from tvtk.pyface.tvtk_scene import TVTKWindow
from mayavi.core.engine import Engine
from mayavi.preferences.api import set_scene_p... | dmsurti/mayavi | mayavi/core/off_screen_engine.py | Python | bsd-3-clause | 999 | [
"Mayavi"
] | a02838f82dfcb05b4d231db935db6c4d913ec6eef802072d4b3e61553e9d797c |
"""
Defines the plugin to return the boolean given as param
"""
from DIRAC.Resources.Catalog.ConditionPlugins.FCConditionBasePlugin import FCConditionBasePlugin
class DummyPlugin(FCConditionBasePlugin):
"""
This plugin is to be used to simply return True or False
"""
def __init__(self, conditions):... | DIRACGrid/DIRAC | src/DIRAC/Resources/Catalog/ConditionPlugins/DummyPlugin.py | Python | gpl-3.0 | 554 | [
"DIRAC"
] | 5f637f3f5012d7d41813f0866fe23da61f52c66c248e199c7ce19e72970b0621 |
# -*- coding: utf-8 -*-
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
import warnings
from collections.abc import Iterable
from functools import wraps
import ctypes
import numpy as np
from scipy._lib.doccer import (extend_notes_in_docstring,
... | e-q/scipy | scipy/stats/_continuous_distns.py | Python | bsd-3-clause | 296,959 | [
"CRYSTAL",
"Gaussian"
] | 435c6d901a0f07830cdd71cca8d5f4a4ecccbaf4625d830263dc6e5807bec722 |
# Copyright 2017 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... | kevin-coder/tensorflow-fork | tensorflow/contrib/gan/python/eval/python/classifier_metrics_impl.py | Python | apache-2.0 | 45,064 | [
"Gaussian"
] | 3d27de604defd19514051b99219ab5a047fc9dc63d672fb0ae12b770e1372fcf |
""" Client for the SandboxStore.
Will connect to the WorkloadManagement/SandboxStore service.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import six
import os
import tarfile
import hashlib
import tempfile
import re
from six im... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/SandboxStoreClient.py | Python | gpl-3.0 | 13,422 | [
"DIRAC"
] | 03c407567fb61553c198b01f7966bc4ee64c867b546f24e214d9431715cbbecf |
import numpy as np
from scipy.ndimage import gaussian_filter, gaussian_laplace
import itertools as itt
import math
from math import sqrt, hypot, log
from numpy import arccos
from ..util import img_as_float
from .peak import peak_local_max
from ._hessian_det_appx import _hessian_matrix_det
from ..transform import integ... | pratapvardhan/scikit-image | skimage/feature/blob.py | Python | bsd-3-clause | 16,619 | [
"Gaussian"
] | 90233527d06ff63aecc9c24e2639c7402e9d7ca50bdbaf0a34de980387efbb12 |
# -*- coding: utf-8 -*-
"""Node grouping utilities."""
from collections import defaultdict
from typing import Callable, Iterable, List, Mapping, Optional, Set, TypeVar
from pybel import BELGraph, BaseEntity
from pybel.constants import ANNOTATIONS, HAS_VARIANT, IS_A, ORTHOLOGOUS, PART_OF, RELATION
from pybel.dsl impo... | pybel/pybel-tools | src/pybel_tools/selection/group_nodes.py | Python | mit | 4,163 | [
"Pybel"
] | 6b72f3a90a503e129d8446a295cea998dfe59682b3b2dd890ae4040c9628d909 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Joan Massich <mailsik@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
#
# License: Simplified BSD
import os
import pytest
import importlib
import numpy as np
from ... | adykstra/mne-python | mne/viz/backends/tests/test_renderer.py | Python | bsd-3-clause | 4,174 | [
"Mayavi"
] | 8e7469f6b239d5667c2a1567b100630d49b141236405c2607756ffbe35887b61 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
from django.conf import settings
import hs_core.models
class Migration(migrations.Migration):
dependencies = [
('auth', '0001_initial'),
('pages', '__first__'),
migrations.swappable_d... | RENCI/xDCIShare | hs_app_netCDF/migrations/0001_initial.py | Python | bsd-3-clause | 7,029 | [
"NetCDF"
] | 5ade7586048fcc9bdf6cbaf50de3c289f7358e851aa967f8e109444d1c79d3b4 |
import tornado.web
import traceback
from plugins.bases.plugin import PluginBase
import os
import sys
import gdata
import gdata.youtube
import gdata.youtube.service
class HandlersBase(tornado.web.RequestHandler, PluginBase):
# Every handler must have a web path, override this in this fashion
WEB_PATH = r"/"
... | anzenehansen/wedding-photos | plugins/bases/handlers.py | Python | mpl-2.0 | 4,489 | [
"Amber"
] | 6eba9a486b0e57f6f068fcc7aded1120584c599b4505906e2d2a96cde0f3e1e2 |
'''
HolyGrail (c) University of Manchester 2015
HolyGrail is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=too-many-arguments
import random
from synbiochem.utils import seq_utils, struct_utils
def sample_s... | neilswainston/HolyGrail | holygrail/pdb_data.py | Python | mit | 1,953 | [
"VisIt"
] | 30e48697f43c7dae1f183a885eff4d9d886af57767d3312c9ccbb003cefe380a |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/integrator/BerendsenBarostat.py | Python | gpl-3.0 | 4,302 | [
"ESPResSo"
] | f7b91eeaa717333fc649382985a4f9e9aafe368044c38a0e1176c936b2b7326a |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathem... | sknepneklab/SAMoS | analysis/batch_nematic/batch_analyze_nematic_R40c.py | Python | gpl-3.0 | 2,362 | [
"VTK"
] | 48e8f0cab41d11b3be72968556f4ce4bdc4774fed9e5c1159c97d4e1179023e7 |
# -*- coding: utf-8 -*-
"""
Created on Fri Oct 30 21:51:35 2015
@author: spatchcock
"""
# %%
import numpy
from matplotlib import pyplot
import matplotlib.animation as animation
numpy.set_printoptions(precision=3)
# %% Numerical scheme
w = 0.05
D = 0.001
L = 1.
J = 500
dx = float(L)/float(J-1)
x_grid = numpy.array(... | spatchcock/models | advection_diffusion/advection_diffusion_equation_crank_nicolson.py | Python | unlicense | 2,246 | [
"Gaussian"
] | 0661af119bc4421957f2fc3ffc1c1e0690acd0ad43abdf57e02733081c337a01 |
""" Test case for DIRAC.Core.Utilities.File module
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
##
# @author Krzysztof.Ciba@NOSPAMgmail.com
# @date 2011/01/17 14:01:18
# @brief Definition of FileTestCase class.
# imports
import os
from os.path import... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/test/Test_File.py | Python | gpl-3.0 | 4,629 | [
"DIRAC"
] | e42a0cd377b0f22edba7eb78898f74d6ad85ece5dcb407119611917185736aab |
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