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from __future__ import print_function, unicode_literals, absolute_import, division
import numpy as np
from gputools import OCLArray
from .convolve import convolve
from .convolve_sep import convolve_sep2, convolve_sep3
def gaussian_filter(data, sigma=4., truncate = 4., strides=1, normalize=True, res_g=None):
"""
... | maweigert/gputools | gputools/convolve/gaussian_filter.py | Python | bsd-3-clause | 2,814 | [
"Gaussian"
] | 843d255d35e806c27ec26b42cb2aad0138f832231be011ed2170dbf5b2cfc55c |
# Made by Fulminus
# Quest 347: Go Get The Calculator.
qn = "347_GoGetTheCalculator"
import sys
from com.l2scoria.gameserver.model.quest import State
from com.l2scoria.gameserver.model.quest import QuestState
from com.l2scoria.gameserver.model.quest.jython import QuestJython as JQuest
# NPCs to talk to
BRUNON = 3052... | zenn1989/scoria-interlude | L2Jscoria-Game/data/scripts/quests/347_GoGetTheCalculator/__init__.py | Python | gpl-3.0 | 4,644 | [
"CRYSTAL"
] | 8c1ebe7734995755e07efc6234598e69e760d63134a30b9a4dcc8fdaab4fb9ef |
""" test StoragElement
"""
import os
import tempfile
import mock
import unittest
import itertools
from DIRAC import S_OK
from DIRAC.Resources.Storage.StorageElement import StorageElementItem
from DIRAC.Resources.Storage.StorageBase import StorageBase
from DIRAC.ConfigurationSystem.Client.ConfigurationData import g... | chaen/DIRAC | Resources/Storage/test/Test_StorageElement.py | Python | gpl-3.0 | 30,105 | [
"DIRAC"
] | 3efdd406af9f5860f5d41afc485d538179653e26011b857b90dd26235365f65d |
# Copyright 2015 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... | AnishShah/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 108,132 | [
"Gaussian"
] | b796462a31a7b8bb58c6881ee3b2ebc46a1ce9fddb6730e9782055ce3b424c85 |
""" This is the guy that parses and interprets the local configuration options.
"""
import re
import os
import sys
import getopt
import DIRAC
from DIRAC import gLogger
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gConfigurationData
from DIRAC.ConfigurationSystem.priva... | DIRACGrid/DIRAC | src/DIRAC/ConfigurationSystem/Client/LocalConfiguration.py | Python | gpl-3.0 | 30,480 | [
"DIRAC"
] | ea4e4a9b56f41ca99dbe5a17a1aeebadb9eaafa6ba8e2cfe12b11b0e765f06ef |
# Copyright 2015 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... | aldian/tensorflow | tensorflow/python/ops/image_grad_test.py | Python | apache-2.0 | 21,612 | [
"Gaussian"
] | fedaa46e23ed08677f48e673b0dece8a6ab13f6f525a3e95782b422439d26dd8 |
from django.conf import settings
from django.conf.urls import url
from django.conf.urls.static import static
from django.contrib import admin
from django.urls import include, path
from django.views import defaults as default_views
from django.views.i18n import JavaScriptCatalog
from graphene_django.views import GraphQL... | Flaburgan/the-federation.info | config/urls.py | Python | agpl-3.0 | 1,491 | [
"VisIt"
] | 406aaf8fcba1df5af6140ea3cb337ee4b7e6ab5e959923bd40362dc262d9bccc |
# AvsP - an AviSynth editor
#
# Copyright 2007 Peter Jang <http://avisynth.nl/users/qwerpoi>
# 2010-2013 the AvsPmod authors <https://github.com/avspmod/avspmod>
#
# 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
#... | AvsPmod/AvsPmod | build.py | Python | gpl-2.0 | 6,148 | [
"VisIt"
] | 828861576b1196b6f43df77eb77fa8e934f78a37e4926c8f31f9b94fe02b0272 |
#!/usr/bin/env python
#
# Logger post-processing script for NZBGet
#
# Copyright (C) 2013-2015 Andrey Prygunkov <hugbug@users.sourceforge.net>
#
# 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; e... | nkatsaros/nzbget | scripts/Logger.py | Python | gpl-2.0 | 3,393 | [
"VisIt"
] | a4e883ee036ba5dc9b9e82a86caad42be68e31da052aeaad7a288139c00f0ef3 |
# -*- coding: utf-8 -*-
"""
Driver classes for generating suntans input files
Matt Rayson
Stanford University
April 2013
"""
from SUNTANS.sunpy import Grid, Spatial
from sundepths import DepthDriver, adjust_channel_depth
from sunboundary import modifyBCmarker, Boundary, InitialCond
from metfile import Sun... | UT-CWE/Hyospy | Hyospy_ensemble/lib/SUNTANS/SUNTANS/sundriver.py | Python | mit | 21,028 | [
"NetCDF"
] | 73a32f60cace0d3d291bb6b41aab34678448e904386258b153bf04b03e045613 |
#
# Copyright (C) 2000 greg Landrum
#
""" handles doing cross validation with decision trees
This is, perhaps, a little misleading. For the purposes of this module,
cross validation == evaluating the accuracy of a tree.
"""
from __future__ import print_function
from rdkit.ML.DecTree import ID3
from rdkit.ML.Data ... | adalke/rdkit | rdkit/ML/DecTree/CrossValidate.py | Python | bsd-3-clause | 7,238 | [
"RDKit"
] | 45cde84cb91efeff5b663d0af08b06581b9d7d5b1f1b60b2b8b73ab1bf498196 |
"""
Galore: Gaussian and Lorentzian broadening of simulated spectra
"""
from os.path import abspath, dirname
from setuptools import setup, find_packages
import unittest
project_dir = abspath(dirname(__file__))
def unit_tests():
test_loader = unittest.TestLoader()
test_suite = test_loader.discover('test', pa... | SMTG-UCL/galore | setup.py | Python | gpl-3.0 | 3,766 | [
"Gaussian",
"VASP",
"pymatgen"
] | 879947446b1f48dc9b72c4d40fb19afcd6261da3ed29a1dcb79c06b7e8036de0 |
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE... | Dixon3/lammps | python/lammps.py | Python | gpl-2.0 | 27,272 | [
"LAMMPS"
] | 9a0712c876bce30c77badac27e527f0cd8ec8b305c2b612725ce3ee8a9296441 |
#!/usr/bin/env python
#
# Tools for working with BLAST
#
# (c) The James Hutton Institute 2016
# Author: Leighton Pritchard
import os
import subprocess
from collections import namedtuple
from .tools import is_exe, NotExecutableError
# factory class for Blastclust class returned values
Results_bc = namedtuple("Resu... | widdowquinn/THAPBI-pycits | pycits/blast.py | Python | mit | 2,218 | [
"BLAST"
] | d668d329fec7f111990b95ef1de6982f764876313d9393f9e25c4626ac7a1dfe |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Read a maf from stdin and print the chromosome number for each alignment. It
searches for 'chr' in each alignment block src, and may not be robust if other
src formats are used.
NOTE: See 'align_print_template.py' for a more general variation of this
program.
usage... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/maf_print_chroms.py | Python | bsd-3-clause | 858 | [
"Galaxy"
] | d3d95b34e61c6ed78664f5201bbd154c9c06605bae15c6851671ba641bf909fc |
#!/usr/bin/env python
#########################################################################
# Filename: fsMesher2D.py #
# Date: 2018-May-07 #
# Version: 1. #
#... | BV-DR/foamBazar | pythonScripts/oldStuff/fsMesher2D.py | Python | gpl-3.0 | 27,889 | [
"ParaView"
] | 4baba7d718f75c9bd7ccdf21ae3acaac2d820572b916ccb96434a09b2408267e |
# Copyright 2005-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# Author(s): Nicholas Carpaski (carpaski@gentoo.org), Brian Harring (ferringb@gentoo.org)
from __future__ import unicode_literals
__all__ = ["cache"]
import stat
import sys
import operator
import warnings
from ... | mm1ke/portage | pym/portage/eclass_cache.py | Python | gpl-2.0 | 5,677 | [
"Brian"
] | 10ef3913af8fd33d6ea1fd0cde193c534c5468e74a914aa9358ab235f697d77b |
"""
@name: PyHouse/Project/src/Modules/Web/web_mainpage.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2013-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 27, 2013
@Summary:
When a user wants to connect to PyHouse to monitor or control the system, th... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/Web/web_mainpage.py | Python | mit | 13,127 | [
"Brian"
] | 67fb29d03617787380b26373661263d9dbdd376b52f1bb70124bcbaac1adf12c |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines 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 by ap... | google/uncertainty-baselines | uncertainty_baselines/models/vit_gp_test.py | Python | apache-2.0 | 3,615 | [
"Gaussian"
] | 220bfa10b7fa810d6c0bec10f657a0583f0eb128dbb6b8fdece044dac4bab38a |
#!/usr/bin/env python
#
# $File: pyDuringMatingOperator.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can ... | BoPeng/simuPOP | docs/pyDuringMatingOperator.py | Python | gpl-2.0 | 1,608 | [
"VisIt"
] | bc2aca10915909cdddb710ebe9d86909db02cccdd1843c79d06823d7dcf69572 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to define a phonon band structure.
"""
import collections
import numpy as np
from monty.json import MSONable
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Str... | vorwerkc/pymatgen | pymatgen/phonon/bandstructure.py | Python | mit | 24,422 | [
"CRYSTAL",
"phonopy",
"pymatgen"
] | b64030b854d24c406eba8ece92407188bc0d9d13283f05cce6a1dd166bcbc5de |
#!/usr/bin/env python
import os
from subprocess import Popen, STDOUT, PIPE, call
import filecmp
import glob
from optparse import OptionParser
parser = OptionParser()
parser.add_option('--mpi_exec', dest='mpi_exec', default='')
parser.add_option('--mpi_np', dest='mpi_np', default='3')
parser.add_option('--exe', dest='... | bhermanmit/cdash | tests/test_track_output/test_track_output.py | Python | mit | 2,315 | [
"VTK"
] | ef43350a9828b8fce454d991bb3d244a1fe682aeae25d6557fc5f49db31fae59 |
# Copyright (c) 2011, Alex Krizhevsky (akrizhevsky@gmail.com)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# - Redistributions of source code must retain the above copyright notice,
# this ... | tund/kaggle-galaxy-zoo | cuda_convnet/layer.py | Python | bsd-3-clause | 62,899 | [
"Gaussian",
"NEURON"
] | c52cb6f65b0bf2fe540451027ce396a90e20c557a9b2bccaf1dd9dc8f0cd9ef0 |
#!/usr/bin/env python
"""
.. module:: randomNumberFunctions
:synopsis: Random number functions.
.. moduleauthor:: Hazen Babcock
"""
import numbers
import random
import opensdraw.lcad_language.interpreter as interp
import opensdraw.lcad_language.lcadExceptions as lce
lcad_functions = {}
class RandomNumberFuncti... | HazenBabcock/opensdraw | opensdraw/lcad_language/randomNumberFunctions.py | Python | mit | 4,198 | [
"Gaussian"
] | 56258413eac863c51d2490d51d364a2ba89a877e42af6764290e1244915e2df5 |
###################################################################################
## numpy extension by PJ (peter.juvan@fri.uni-lj.si)
##
## TODO: fix default axis asignment (in several funcions 0 is the dedault):
## - for numpy default is None
## - for numpy.me default is still -1 (will this be fixed in fu... | tomazc/orange-bio | orangecontrib/bio/widgets/numpyExtn.py | Python | gpl-3.0 | 37,882 | [
"Biopython"
] | e6b7c6a16278819e8ca4307ab3bf7c5d8a87b691e61ceeb0d9e70143097abfb7 |
#!/usr/bin/env python
import roslib; roslib.load_manifest('flexbe_input')
import rospy
import pickle
import actionlib
import threading
from flexbe_msgs.msg import BehaviorInputAction, BehaviorInputFeedback, BehaviorInputResult, BehaviorInputGoal
from .complex_action_server import ComplexActionServer
'''
Created on 02... | team-vigir/flexbe_behavior_engine | flexbe_input/src/flexbe_input/flexbe_input.py | Python | bsd-3-clause | 1,989 | [
"Brian"
] | 69c7d14f2b617a48bb9a3a67a647e70ecbbc6e3316366ac14a32fc3d5e09edf9 |
# 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... | mckerrj/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 92,208 | [
"VisIt"
] | 5938de22a1569c13dc6daa8c7c27b1eb1a44270ae248f9d2dc82ebc85f618fe8 |
#!/usr/bin/env python
from datetime import datetime,timedelta
import itertools
def get_1mo_dates(inyr,inmo,indate,byear,eyear):
"""
Used with netCDF4 files and py-netCDF.
From 1985-2011, a number of days range to search
for dates centered around the given date and forecast time,
returns the applicable dates ... | mogismog/PyAnalog | pyanalog/generate_dattim.py | Python | apache-2.0 | 9,575 | [
"NetCDF"
] | a91826f241843c50832f5bef72f1c63616d283f5dede8ca57e40137d9b75db16 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# BSF Auto Search: Barracuda Spam Firewall message log review with Selenium browser automation.
# Copyright (C) 2015 Michael Sincavage
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Lic... | Gormogon/BSF-Auto-Search | src/bsfas.py | Python | gpl-3.0 | 15,295 | [
"VisIt"
] | 61b89e441c7a8e2e886ad0cdf9e10fcac284781fffe2341ff531d82e63d46074 |
import logging
import signal
import sys
import unittest
from os.path import abspath, dirname, join
from robot.running import TestSuite, TestSuiteBuilder
from robot.utils import StringIO
from robot.utils.asserts import assert_equals
from resources.runningtestcase import RunningTestCase
from resources.Listener import L... | moto-timo/robotframework | utest/running/test_running.py | Python | apache-2.0 | 12,074 | [
"VisIt"
] | a77f3d63c6523c78f7f4efaad6c2b2d33b2812962ca0904202ca8bc13c744215 |
#!/usr/bin/env python
import shutil
import sys
sys.path.insert(0, '..')
from testing_harness import *
class TrackTestHarness(TestHarness):
def _test_output_created(self):
"""Make sure statepoint.* and track* have been created."""
TestHarness._test_output_created(self)
outputs = [glob.gl... | lilulu/openmc | tests/test_track_output/test_track_output.py | Python | mit | 1,883 | [
"VTK"
] | 17fb6183e0f69e38c1e5fa5e9a3a06b3f6aa014e326c572af8170774e71e538e |
__author__ = 'ddeconti'
import base64
import numpy
import sys
import pickle
from io import BytesIO
from flask import Flask, render_template, request, make_response, send_file
from rdkit import DataStructs
from rdkit.Chem import AllChem, MolFromSmiles, Draw
#from app import app
app = Flask(__name__)
@app.route('/'... | dkdeconti/PAINS-train | web_app_frontend/app/views.py | Python | mit | 2,396 | [
"RDKit"
] | 0f78e4e78e8e753171d649ce58e62473663320b308e113b6ac2fee60125624b4 |
"""Create entries for gem blocks/items for localization (lang) files.
Translators: You could optionally use this for your translations:
- In the gems dict: change the values (right of the colon ':')
- In blocks and items, edit the first part of the value as needed (gem + ' Block Name' or whatever)
- Do NOT... | SilentChaos512/SilentGems | scripts/make_loc_keys.py | Python | lgpl-3.0 | 4,346 | [
"Amber"
] | c06353da6e7c466687f18e7dca58cfc2cfff9cbfc1a00fd082044c740ebff084 |
#pylint: disable=C0111
from django.contrib.auth.models import User
from lettuce import world, step
from lettuce.django import django_url
from common import course_id
from student.models import CourseEnrollment
@step('I view the LTI and it is not rendered$')
def lti_is_not_rendered(_step):
# lti div has no class... | morpheby/levelup-by | lms/djangoapps/courseware/features/lti.py | Python | agpl-3.0 | 6,463 | [
"VisIt"
] | 0761a724e3eef9a0d33e8cb81bb09389e9c315424b08824d69139f58421c9810 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007-2008 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the Licens... | andrebellafronte/stoq | stoqlib/importers/serviceimporter.py | Python | gpl-2.0 | 2,106 | [
"VisIt"
] | 16fab26e903c5ce1e2f7b5664cf2f59f659dc67826f106f5eaba300cf2059d22 |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for problems in the LMS
See also old lettuce tests in lms/djangoapps/courseware/features/problems.feature
"""
from textwrap import dedent
from ..helpers import UniqueCourseTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.lms.courseware import ... | simbs/edx-platform | common/test/acceptance/tests/lms/test_lms_problems.py | Python | agpl-3.0 | 16,012 | [
"VisIt"
] | 62b25005eaf2054c861d75dc90ed309362d84eb82fd6fc62a664a12bb14e4b73 |
# $HeadURL: $
''' TransferCommand module
'''
from datetime import datetime, timedelta
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.AccountingSystem.Client.ReportsClient import ReportsClient
fr... | avedaee/DIRAC | ResourceStatusSystem/Command/TransferCommand.py | Python | gpl-3.0 | 8,074 | [
"DIRAC"
] | 50d4195897c39d5a5c46ee21ca47b7e8a883cb9a44259ae75fba86a7e7876e08 |
#
# @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
#... | lothian/psi4 | psi4/share/psi4/databases/S22.py | Python | lgpl-3.0 | 43,408 | [
"Psi4"
] | 7e4a6a069983688a29d0e74b8edd5b9bf3bab938be089df64cee247d635641c5 |
# SINGULAR - last updated for NodeBox 1.9.4
# Adapted from Bermi Ferrer's Inflector for Python:
# http://www.bermi.org/inflector/
# Copyright (c) 2006 Bermi Ferrer Martinez
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software to deal in this software without restriction, i... | RensaProject/nodebox_linguistics_extended | nodebox_linguistics_extended/singular.py | Python | gpl-2.0 | 6,791 | [
"Elk",
"Octopus"
] | 44bf4575a03c22e307e7e625b6c00b64215cb6ac8121a7e3b6e1a423a79b504c |
from __future__ import print_function
import bisect
import itertools
def find_bonding_info(types, bonding_info):
"""
Find the parameters for the particular pair of atom types
:param types: sequence containing either two or three atom types
:param bonds_info: either bonds or angles
:return: dictiona... | jmborr/confinedBSA | simulation/silica/cristobalite/python/silicatop.py | Python | mit | 4,906 | [
"Gromacs"
] | bd3d47b477a46873058a8a7601ec6aa0af0f0d0b1bea566644936fdf7a8ca038 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
####
# 2006/02 Will Holcomb <wholcomb@gmail.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or... | utitankaspk/SPKCAM | src/lib/MultipartPostHandler.py | Python | apache-2.0 | 5,143 | [
"Brian"
] | f81956bc42b55aff230bbb4a8dc5579051cd18369937af551923c5aa46469027 |
from __future__ import print_function, division
from sympy.core import S, C, sympify, Dummy
from sympy.core.function import Function, ArgumentIndexError
from sympy.core.logic import fuzzy_and
from sympy.ntheory import sieve
from math import sqrt as _sqrt
from sympy.core.compatibility import reduce, as_int, xrange
fro... | AunShiLord/sympy | sympy/functions/combinatorial/factorials.py | Python | bsd-3-clause | 21,030 | [
"VisIt"
] | 3fecca8d61f8333f517d9fd045ada4c77795f5b4e20b7a044447f936c54aeb88 |
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import warnings
from ase.data.colors import cpk_colors
from ase.data import covalent_radii,chemical_symbols
from matplotlib.patches import Circle
from scipy.cluster.hierarchy import linkage,fcluster
from ase import Atoms
import coll... | jacobjma/PyQSTEM | pyqstem/util.py | Python | gpl-3.0 | 7,165 | [
"ASE"
] | f2235f60af7ac278cfda9f7644adf71c0301375b560432c776eba4190c264d1d |
#
# Copyright 2016 The BigDL 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 by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/learn/optimizers/optimizers_impl.py | Python | apache-2.0 | 11,315 | [
"ORCA"
] | 18bd66bcf5fd547f364e4c0f8ca51189b451b529d097e27c5dfb1d6fceacf8eb |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure that all files contain proper licensing information."""
import json
import optparse
import os.path
import subproces... | ltilve/ChromiumGStreamerBackend | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 20,425 | [
"Galaxy"
] | f0f926100224b03168b789d90cb0fc6d51f89e8f731fc864bd1ffbd5ba7bf1d3 |
#
# @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 it and/or modify
#... | amjames/psi4 | psi4/driver/qcdb/p4regex.py | Python | lgpl-3.0 | 1,282 | [
"Psi4"
] | d06ad86d828ffe818022d73cbf1aa3e8d20e730a830e51a3d7dbd36625ff1a65 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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)
#
# Released under th... | alejob/mdanalysis | package/MDAnalysis/topology/core.py | Python | gpl-2.0 | 1,935 | [
"MDAnalysis"
] | bea34e80a0fedc292efe767fc72bb01601cc3fed7d1ea976906ff1b505cc4256 |
from math import *
from numpy import *
from scipy import integrate
from scipy.interpolate import InterpolatedUnivariateSpline
fg = open("lrg", "r")
fd = open("random", "r")
sd = open("bao", "w")
# Values for the cosmic parameters
c = 3.0*10**5
Om = 0.3
H0 = 72.0
Ol = 0.7
rty = 2.0
# Formula for radial diameter distance... | rohinkumar/galsurveystudy | correlationfunc.py | Python | mit | 5,370 | [
"Galaxy"
] | 8779a78cc614af6eed6cebd4883896f26d3698b287cb7486626f103fcc92d4c1 |
# Copyright 2011 OpenStack Foundation
# 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 requ... | CloudServer/cinder | cinder/tests/unit/api/test_xmlutil.py | Python | apache-2.0 | 27,333 | [
"VisIt"
] | 3a671b8f74c396af1b0cb410b8ca8203cc59188bf60321fac4a6df55a1d9c885 |
""" MQConsumer
"""
import queue
from DIRAC import S_ERROR, S_OK, gLogger
from DIRAC.Resources.MessageQueue.Utilities import getDestinationAddress, getMQService, generateDefaultCallback
from DIRAC.Core.Utilities.DErrno import EMQNOM
class MQConsumer(object):
def __init__(self, mqManager, mqURI, consumerId, callbac... | DIRACGrid/DIRAC | src/DIRAC/Resources/MessageQueue/MQConsumer.py | Python | gpl-3.0 | 2,562 | [
"DIRAC"
] | 6e88004dade0f1905780817a8b0baf9735063b95e54f09238c09df494d8c38c9 |
from pylab import figure,show,connect,hist,plot,legend
from numpy import array, append, arange, empty, exp
from shogun.Distribution import Gaussian, GMM
from shogun.Features import RealFeatures
import util
util.set_title('EM for 1d GMM example')
#set the parameters
min_cov=1e-9
max_iter=1000
min_change=1e-9
#setup t... | ratschlab/ASP | examples/undocumented/python_modular/graphical/em_1d_gmm.py | Python | gpl-2.0 | 1,933 | [
"Gaussian"
] | f4bae57bd36e58c4ba645d9e3e2a7bbd6764215acdf780c567aae157b75d32f8 |
"""
API operations allowing clients to determine Galaxy instance's capabilities
and configuration settings.
"""
from galaxy.web import _future_expose_api as expose_api
from galaxy.web.base.controller import BaseAPIController
import logging
log = logging.getLogger( __name__ )
class ConfigurationController( BaseAPICo... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/api/configuration.py | Python | gpl-3.0 | 1,546 | [
"Galaxy"
] | ad2257f90326faa24d029ffa04d0f1626b54c41135e449e51e00956a96f7800a |
# (c) 2015, Brian Coca <briancoca+dev@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | jaddison/ansible | lib/ansible/plugins/action/patch.py | Python | gpl-3.0 | 2,387 | [
"Brian"
] | 13a8148879fbeb9618a8927aa9dbb41e64a5bf71b59b1d55dd7da3250ac96363 |
"""
SVDSuperimposer finds the best rotation and translation to put
two point sets on top of each other (minimizing the RMSD). This is
eg. useful to superimpose crystal structures. SVD stands for singular
value decomposition, which is used in the algorithm.
"""
from SVDSuperimposer import *
| dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/SVDSuperimposer/__init__.py | Python | apache-2.0 | 294 | [
"CRYSTAL"
] | 842476f0566eaa2f32d6b72bba71ffbfa09559246828e596aff3c1ab7202952f |
#!/usr/bin/python
import json
import os
import random
import unittest
import numpy as np
from pymatgen.analysis.structure_matcher import StructureMatcher
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.core.surface import (
ReconstructionGenerator,
Slab,... | materialsproject/pymatgen | pymatgen/core/tests/test_surface.py | Python | mit | 36,521 | [
"pymatgen"
] | 493a11b7b8adae2ec959f39f063f534dc6c08a22fac6e4f4cecacdc99509244e |
#!/usr/bin/env python
# Copyright (C) 2017,2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either ... | govarguz/espressopp | examples/adress/piadress_water/AdaptivePIwater.py | Python | gpl-3.0 | 21,537 | [
"ESPResSo"
] | 596437041eb55202b09debc7dd1ccd6582d9407f7bb291bac0c09ca9f6f8c78c |
#!/usr/bin/env python
import vtk
def main():
mc_cases, rotation, label = get_program_parameters()
if not mc_cases:
mc_cases = [7]
else:
# Ensure that they are unique.
mc_cases = list(set(mc_cases))
# Check that they lie in the correct range.
badCases = []
f... | lorensen/VTKExamples | src/Python/VisualizationAlgorithms/MarchingCases.py | Python | apache-2.0 | 19,479 | [
"VTK"
] | 2db5b6632b17629f4d486113d2d12e589b8245dee53b6fb7c8830e74360ad1ea |
#!/usr/bin/env python
"""
map bisulfite converted reads to an insilico converted genome using bwa mem.
A command to this program like:
python bwameth.py --reference ref.fa A.fq B.fq
Gets converted to:
bwa mem -pCMYR ref.fa.bwameth.c2t '<python bwameth.py c2t A.fq B.fq'
So that A.fq has C's converted to T's ... | BioInfoTools/BSVF | bin/bwameth.py | Python | lgpl-3.0 | 15,252 | [
"BWA"
] | 1c5022b0123f0c7b5bc6a5f37f2f26d9f4c45eda05c27c497bb91f23b1d927f3 |
# test_archan.py ---
#
# Filename: test_archan.py
# Description:
# Author:
# Maintainer:
# Created: Sat Jun 2 11:05:22 2012 (+0530)
# Version:
# Last-Updated: Sun Jun 25 16:19:47 2017 (-0400)
# By: subha
# Update #: 8
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Chang... | BhallaLab/moose-examples | traub_2005/py/test_archan.py | Python | gpl-2.0 | 1,541 | [
"NEURON"
] | 762e847c61cf8ee7d40830848137a3eb73085b6a1f77cdc02fea746cb87a5efd |
import cryspy
from cryspy.fromstr import fromstr as fs
import cryspy.numbers as nb
import cryspy.geo as geo
import numpy as np
def calculate_twotheta(metric, wavelength, q):
assert isinstance(metric, cryspy.geo.Metric), \
"First argument of calculate_twotheta(...) must be of type cryspy.geo.Metric!"
a... | tobias-froehlich/cryspy | cryspy/utils.py | Python | gpl-3.0 | 41,432 | [
"CRYSTAL"
] | 6aba208083212e51ea98e4444dde37dac7b2da00bebb0544ba5b91a78d357c86 |
#
# Copyright (c) 2016 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/packagedcode/test_nevra.py | Python | apache-2.0 | 3,289 | [
"VisIt"
] | 8e5b7a62945804ad077d2bc2ec72d29f2ae1b68ce4698c1d2ec2ed097a48fc40 |
#!/usr/bin/env python
import httplib
import httplib2
import os
import sys
from googleapiclient.discovery import build
from googleapiclient.errors import HttpError
from oauth2client.client import flow_from_clientsecrets
from oauth2client.file import Storage
from oauth2client.tools import argparser, run_flow
httplib2.... | akilan98/FRC-YouTube-Uploader | youtubeAuthenticate.py | Python | gpl-3.0 | 2,762 | [
"VisIt"
] | 6c76d459fa23e6b34f49e27658eabd244f9ec7dc27417b7e35426c3623db4be3 |
'''classify.py
This module implements the pre-alignment process designed by Justin and John
over approx. Nov 2010 to February 2011.
The primary objects being manipulated here will be variously called 'fragments',
'hits', or 'records'. They represent BLAST hits, i.e., results from a BLAST
search. They will usua... | jpassaro/seq-align-prep | classify.py | Python | gpl-2.0 | 15,380 | [
"BLAST"
] | 4290aec2c4dc3c58f942b83edaa032be9c23f46c92c0314444f44d9337792e13 |
import math
import json
from jmespath import exceptions
from jmespath.compat import string_type as STRING_TYPE
from jmespath.compat import get_methods, with_metaclass
# python types -> jmespath types
TYPES_MAP = {
'bool': 'boolean',
'list': 'array',
'dict': 'object',
'NoneType': 'null',
'unicode'... | achang97/YouTunes | lib/python2.7/site-packages/jmespath/functions.py | Python | mit | 12,642 | [
"VisIt"
] | 133443cf73ead05ad33124d67375932a674c8dd05a752d00f09b0528ec9e1262 |
# Copyright 2021 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 by applicable law o... | tensorflow/probability | tensorflow_probability/python/distributions/student_t_process_regression_model.py | Python | apache-2.0 | 31,341 | [
"Gaussian"
] | b906685f127de035f5b7b9fbf7022e7e3f1f9f349afb917cf864c7886a84f0ec |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | CDSherrill/psi4 | psi4/driver/qcdb/pytest/addons.py | Python | lgpl-3.0 | 3,612 | [
"Psi4"
] | 2e55eb38cf6bad477fb552783029fa1e4af8a052959148f982a481c03125a422 |
#------------------------------------------------------------------------------
# Copyright (C) 2009 Richard Lincoln
#
# This program 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; version 2 dated June... | rwl/openpowersystem | cdpsm/iec61968/asset_models/open_circuit_test.py | Python | agpl-3.0 | 2,697 | [
"exciting"
] | 9068956775921c4dee554a57be01116348041484e626cac57f132d7350e63c25 |
#!/bin/env python
#
# This file is part Protein Engineering Analysis Tool (PEAT)
# (C) Copyright Jens Erik Nielsen, University College Dublin 2003-
# All rights reserved
#
# Damien Farrell April 2010
from Tkinter import *
import Pmw
class YasaraControl(Frame):
"""A yasara controller for comparison use... | dmnfarrell/peat | PEATDB/Yasara.py | Python | mit | 1,231 | [
"YASARA"
] | 96a79039731ffdcb5481a24fca6587d1ddf9b1b629f4e819f84bf6e37dfc2935 |
#~~~~~~~GLOBAL IMPORTS~~~~~~~#
# Standard library packages import
from os import path, remove
from time import time
# Local library packages
from pyDNA.Utilities import run_command, file_basename, make_cmd_str, merge_files
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~... | a-slide/pyDNA | Bwa/IndexWrapper.py | Python | gpl-2.0 | 5,474 | [
"BWA"
] | 50bd4db6bf7d6051e844a9624790d1083db9fb474fc6e9080f19636890d76091 |
from __future__ import absolute_import
input_name = '../examples/diffusion/cube.py'
output_name = 'test_cube.vtk'
from tests_basic import TestInput
class Test( TestInput ):
pass
| vlukes/sfepy | tests/test_input_cube.py | Python | bsd-3-clause | 183 | [
"VTK"
] | 86f187252342cd761c9eae3e211954f7cb67993213e3a3570a4ae57a831ac796 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import logging
from math import ceil
import sys
import numpy as np
import tensorflow as tf
class FCN8VGG:
def __init__(self, vgg16_npy_path=None):
if vgg16_npy_path is None:
... | yuxng/Deep_ISM | FCN/lib/networks/fcn8_vgg.py | Python | mit | 17,815 | [
"Gaussian"
] | 416c48cd92385d260e8ac67976ca34c7b7337d2568c286687b304891d7d48300 |
# Copyright 2011-2016 Free Software Foundation, Inc.
#
# This 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 prog... | freak97/binutils | gdb/contrib/excheck.py | Python | gpl-2.0 | 11,670 | [
"VisIt"
] | 5591fbd34119eaff7f0017a1bc7075514e519a590e2fb0f3eb40cbf067f607a2 |
"""
@name: PyHouse_Install/src/Install/mosquitto_certs.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2016-2016 by D. Brian Kimmel
@license: MIT License
@note: Created Jan 24, 2016
@Summary:
"""
# Import system stuff
# import getpass
# import os
import subprocess
# ... | DBrianKimmel/PyHouse_Install | src/Install/mosquitto_certs.py | Python | mit | 16,962 | [
"Brian"
] | 85a944cb17e22b74904ed112496d0d5bb51f66941e2cdc7d96d02fcede619844 |
"""
Acceptance tests for course creation.
"""
import uuid
from bok_choy.web_app_test import WebAppTest
from nose.plugins.attrib import attr
from common.test.acceptance.pages.studio.auto_auth import AutoAuthPage
from common.test.acceptance.pages.studio.index import DashboardPage
from common.test.acceptance.pages.studio... | louyihua/edx-platform | common/test/acceptance/tests/studio/test_studio_course_create.py | Python | agpl-3.0 | 5,834 | [
"VisIt"
] | 7ad67c75adfd82768507dacf28a62959b990c68d667bf07228cc05de519056e4 |
from django import forms
from django.contrib.admin.widgets import AdminRadioSelect, AdminRadioFieldRenderer, AdminDateWidget
from django.utils import timezone
from edc_constants.constants import ON_STUDY, YES, NO, UNKNOWN, NOT_APPLICABLE
from edc_visit_tracking.choices import VISIT_INFO_SOURCE
from edc_visit_tracking.... | botswana-harvard/ba-namotswe | ba_namotswe/forms.py | Python | gpl-3.0 | 13,077 | [
"VisIt"
] | b2b086b69dabc70ae0c87e6abbc47494dd8281632648ec0671e09eb229a32188 |
import os
import targqc.utilz.reference_data as ref
from os.path import join, splitext, dirname
from targqc import config
from targqc.Target import Target
from targqc.fastq import proc_fastq
from targqc.general_report import make_general_reports
from targqc.region_coverage import make_region_reports
from targqc.summari... | vladsaveliev/TargQC | targqc/main.py | Python | gpl-3.0 | 8,233 | [
"BWA"
] | 74b1d3bbd05b44ab61b3ee07d9b3c052720079293b43f7c070b5536a703aeeb7 |
"""
Set up the plot figures, axes, and items to be done for each frame.
This module is imported by the plotting routines and then the
function setplot is called to set the plot parameters.
"""
#--------------------------
def setplot(plotdata):
#--------------------------
"""
Specify what is to b... | clawpack/clawpack-4.x | apps/tsunami/bowl-radial/setplot.py | Python | bsd-3-clause | 11,661 | [
"NetCDF"
] | 0a0b381a2288b7c9e5d957757f2f5870c69bfb43d2eec51c3c05cf2218e2d6cd |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | wscullin/spack | var/spack/repos/builtin/packages/pexsi/package.py | Python | lgpl-2.1 | 4,759 | [
"DIRAC"
] | e828273231523b5bea443507af400bb846e42a8e0eb522dece79191547b9b414 |
#!/usr/bin/env python
# Copyright 2017 Calico 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
# https://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agr... | calico/basenji | bin/archive/basenji_hdf5_single.py | Python | apache-2.0 | 27,482 | [
"pysam"
] | 517668f53ae99c35699a28af5f6d7ba06337d6ebe9e0cae9a69b6b30d40babb5 |
from pylab import *
import numpy as np
from scipy.io.netcdf import netcdf_file
def make_plot(DIR_INP, FILTER, CUTS, nBin):
MCwant = FILTER['MCwant']
fgap = FILTER['fgap']
WangFlag = FILTER['WangFlag']
FNAME = 'MCflag%s_%dbefore.%dafter_fgap%1.1f' % (MCwant, nBin['before'], nBin['after... | jimsrc/seatos | etc/groups/src/icme.par/funcs.py | Python | mit | 1,316 | [
"NetCDF"
] | aaba2365c40bdf39a3bd09f206ef32112eec022a238e33fa495af8b7d3ea3aeb |
"""
Test functions for GEE
External comparisons are to R and Stata. The statsmodels GEE
implementation should generally agree with the R GEE implementation
for the independence and exchangeable correlation structures. For
other correlation structures, the details of the correlation
estimation differ among implementa... | bashtage/statsmodels | statsmodels/genmod/tests/test_gee.py | Python | bsd-3-clause | 79,647 | [
"Gaussian"
] | 665c89c946cdf16d813ae2d084cdf141e4e987241838afca14a84a5c25ea4964 |
#!/usr/bin/env python
"""
boundary.py
ROMS boundary utilities
Written by Brian Powell on 01/15/14
Copyright (c)2017 University of Hawaii under the MIT-License.
"""
import seapy
import numpy as np
import netCDF4
import textwrap
from collections import namedtuple
# Define the sides of ROMS boundaries along w... | ocefpaf/seapy | seapy/roms/boundary.py | Python | mit | 37,416 | [
"Brian",
"NetCDF"
] | 290f46ea12cbd66594ec43915cc33662aa7b33cf7643956b93db4c9777aa6c3c |
from SimpleCV.base import np, warnings
from SimpleCV.ImageClass import Image
class DFT:
"""
**SUMMARY**
The DFT class is the refactored class to crate DFT filters which can
be used to filter images by applying Digital Fourier Transform. This
is a factory class to create various DFT filters.
*... | tpltnt/SimpleCV | SimpleCV/DFT.py | Python | bsd-3-clause | 28,322 | [
"Gaussian"
] | 891fa6e6f03a19faa8ec318464dba7d60e3f2f764775be76a50110d3d97a043c |
#!/usr/bin/env python
#
# Copyright (C) 2014
# Brian Caswell <bmc@lungetech.com>
# Narf Industries <info@narfindustries.com>
#
# 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 res... | f0rki/cb-multios | original-challenges/FASTLANE/poller/for-testing/machine.py | Python | mit | 10,652 | [
"Brian"
] | dc688a9085a4e70ac396dafee044ad8b74ea98c549261c3d9b9088007cbe29c8 |
import re
import os
import logging
log = logging.getLogger(__name__)
from markdown.util import etree
from MooseSyntaxBase import MooseSyntaxBase
import utils
import MooseDocs
class MooseSystemSyntax(MooseSyntaxBase):
"""
Creates tables of sub-object/systems.
!subobjects = A list of subobjects /* and /<type>
... | joshua-cogliati-inl/moose | python/MooseDocs/extensions/MooseSystemSyntax.py | Python | lgpl-2.1 | 3,779 | [
"MOOSE"
] | 2ba77ea1e5407325568688954ecec99b4cbe65566aa21a2e4341b55b2ac7b3dd |
# -*- test-case-name: pyflakes -*-
# (c) 2005-2010 Divmod, Inc.
# See LICENSE file for details
import __builtin__
import os.path
import _ast
from pyflakes import messages
# utility function to iterate over an AST node's children, adapted
# from Python 2.6's standard ast module
try:
import ast
iter_child_nod... | chunjispring/environment | vim_setting/ftplugin/python/pyflakes/pyflakes/checker.py | Python | gpl-2.0 | 21,891 | [
"VisIt"
] | 7be459dcc51bcea1ad8a10df390ebef9fe8e089cca7633673d2a3511007dfadd |
"""
Demo run
"""
import enaml
from enaml.qt.qt_application import QtApplication
def run():
with enaml.imports():
from vtk_canvas_docks import Main
app = QtApplication()
view = Main(custom_title='VTK Example')
view.show()
# Start the application event loop
app.start()
run()
| viz4biz/PyDataNYC2015 | tutorial/vtk_canvas_docks_run.py | Python | apache-2.0 | 313 | [
"VTK"
] | 43860aa20021db4b32e7bd944da6d58f471e4632cd3cedf5cbb622b5269c00fd |
import os
import sys
from tango.module_loader import ModuleLoader
# from tango.parser import parse
# from tango.scope_binder import SymbolsExtractor, ScopeBinder
# from tango.type_builder import build_types
# from tango.type_solver import infer_types
# from tango.type_disambiguator import disambiguate_types
#
# from ... | kyouko-taiga/tango | run.py | Python | apache-2.0 | 3,285 | [
"VisIt"
] | 7f48cb58e8d529b77f9b80df878e080aeee8c452678980af5d14ccec3eef22a9 |
# Copyright (c) 2010 Howard Hughes Medical Institute.
# All rights reserved.
# Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
# http://license.janelia.org/license/jfrc_copyright_1_1.html
from networkx import DiGraph, dijkstra_path
import os.path, sys
from pydispatch import dis... | JaneliaSciComp/Neuroptikon | Source/network/network.py | Python | bsd-3-clause | 34,416 | [
"NEURON"
] | 6914f305396e9830698bf2e62317f1c4f5ee32c0f9a8404d42ab98c68fc64ef1 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
import urllib
from datetime import datetime, timedelta
from textwrap import dedent
import pytz
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import CourseFixture, CourseUpdateDesc, XBlockFixtureDesc
from common.test.accep... | lduarte1991/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 53,203 | [
"VisIt"
] | 3ac27180a259aeac1c8846c047b6554c9e31fbedcc57608f0047697635ed9e2b |
# Copyright (c) 2012 OpenStack Foundation.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | miyakz1192/neutron | neutron/tests/unit/test_policy.py | Python | apache-2.0 | 28,412 | [
"BLAST"
] | 89b4ed6de03e338bb423e66d89068182cd84d0a5e949e6282bf47e8a0ff98796 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
#
# This program is free software; you can redistribute i... | SNoiraud/gramps | gramps/gen/plug/docgen/paragraphstyle.py | Python | gpl-2.0 | 11,461 | [
"Brian"
] | ae1777d5875a9e9d652a8bf0b36e32f36d5a836338a627205717b8e12a812fac |
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code for the... | greglandrum/rdkit | rdkit/Chem/Pharm2D/UnitTestSignature.py | Python | bsd-3-clause | 8,784 | [
"RDKit"
] | 5dda3184c7b3c1b58b0b4cfc69bebb0f0c01c20aa20e2063e0f506a0849b5c97 |
# Copyright 2016 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 agr... | brianmoose/civet | ci/recipe/tests/test_RecipeReader.py | Python | apache-2.0 | 11,341 | [
"MOOSE"
] | 1d2732de62843bc7ccf748f3b5681711fd3de585b9c69f7d041a24b7b8b4217d |
"""
Utilities for MLP object.
Copyright (C) 2017, Lucas Ondel
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, m... | amdtkdev/amdtk | amdtk/models/mlp_utils.py | Python | mit | 8,852 | [
"Gaussian"
] | 64d334a368d10d8938e0ebc43b94542e570d710b2d29acff3c8eb35d7fb3cd3a |
from menu import Menu
# from generator._unknown.space.galaxy import GalaxyGenerator
# from generator._unknown.space.planet import PlanetGenerator
from .menu_handler import MenuHandler
galaxies = []
class GalaxyHandler(MenuHandler):
def __init__(self, galaxy):
self.galaxy = galaxy
@property
de... | d2emon/generator-pack | src/game_menu/galaxy_menu.py | Python | gpl-3.0 | 1,006 | [
"Galaxy"
] | e354649bc395d938a0c71916446e4f7202b67ce25dd428c237c176419d9f1d7e |
"""
Test course discovery.
"""
from __future__ import absolute_import
import datetime
import json
import uuid
from six.moves import range
from common.test.acceptance.fixtures.course import CourseFixture
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.common.lo... | ESOedX/edx-platform | common/test/acceptance/tests/lms/test_lms_course_discovery.py | Python | agpl-3.0 | 2,284 | [
"VisIt"
] | 0d91a44e87d1118f88c06eef8ee0c234249e74db933222ebf39d241dda1c64d8 |
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
import csv, os
from scipy.stats.kde import gaussian_kde
class protein_length(object):
'''
Probability distributions of protein lenght across different organisms.
Protein length is calculated in amino acids (AA), based on the
... | dandanvidi/weighted-proteins | protein_length/abundance_histograms.py | Python | mit | 5,710 | [
"Gaussian"
] | 3665467e2b040f82cb41fa3681db48309395d52628af63751e6b9082597b81bd |
#this script plots and writes the load (nN) vs. penetration depth (nm) data from lammps output
#also outputs the H and E of the material
import numpy as np
import glob
import matplotlib.pyplot as plt
filename = 'indent-GP2-Al2O3-15-1-10.dat' # lammps data file
flist = glob.glob(filename)
outfile = 'GP2-Al2O3_100.da... | msadat/python-scripts | indent_P-h.py | Python | gpl-3.0 | 1,780 | [
"LAMMPS"
] | 3039642bf1156f6ccb0821f7142d7e68cbc985b23005865b8ba2020d5276d623 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
# graph_tool -- a general graph manipulation python module
#
# Copyright (C) 2006-2015 Tiago de Paula Peixoto <tiago@skewed.de>
#
# 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... | jim-pansn/graph-tool | src/graph_tool/search/__init__.py | Python | gpl-3.0 | 58,109 | [
"VisIt"
] | 5c306a54f7618bc21107240ae15e92e62929112663ab1edd5b75af9e33827895 |
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