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# Copyright 2002 by Katharine Lindner. 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.
"""
Module to represent the NDB Atlas structure (a minimal subset of PDB format).
Hetero,... | bryback/quickseq | genescript/Bio/Crystal/__init__.py | Python | mit | 8,385 | [
"Biopython",
"CRYSTAL"
] | 183a558b06a1b5d99090585335af91650eeb833219fac3ee22b354653e9d2a9f |
from .atom import * # NOQA
from .molecule import * # NOQA
from .crystal import * # NOQA
from .fragment import * # NOQA
from .kernel import * # NOQA
| crcollins/molml | molml/features.py | Python | mit | 153 | [
"CRYSTAL"
] | 5a876d09228d479e72468040cb6d760a0126d37de79ad436cc3be5cff7d91945 |
#!/usr/bin/env python3
import espressopp
from espressopp import Real3D, Int3D
from espressopp.tools import decomp, lattice, velocities
from mpi4py import MPI
import time
import numpy as np
def generate_particles(particles_per_direction):
num_particles = particles_per_direction**3
x, y, z, Lx, Ly, Lz = lattic... | espressopp/espressopp | examples/add_particles_numpy/add_particles_numpy.py | Python | gpl-3.0 | 2,889 | [
"Gaussian"
] | a26d56582e705503391baa49a0b09843a2f8038912398bcab387e49ce52eab14 |
#!/usr/bin/env python
"""
Solve day 1 of Advent of Code.
http://adventofcode.com/day/1
"""
# Do we go up or down based on the instruction character?
instruction_map= { '(': 1, ')': -1 }
def floor_from_instructions(instructions):
"""
Get the floor number resulting from a set of instructions.
"""
retu... | mpirnat/adventofcode | day01/day01.py | Python | mit | 979 | [
"VisIt"
] | 19a326606338108d5db8cc0cb7a40875811dbc84d9cdaef2e8e99f8e913170db |
import ast
from py14.scope import add_scope_context
from py14.context import add_variable_context
from py14.analysis import (FunctionTransformer, CalledWithTransformer,
ImportTransformer, AttributeCallTransformer,
is_void_function)
def parse(*args):
source = a... | lukasmartinelli/py14 | py14/tests/test_analysis.py | Python | mit | 2,639 | [
"VisIt"
] | 14269df1b20ba63065684103af90116c26a737794385cc34e839b4067fbcbeca |
# todo:
# * vtkVolumeMapper::SetCroppingRegionPlanes(xmin,xmax,ymin,ymax,zmin,zmax)
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
import vtkdevide
class VolumeRender(
ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_mana... | nagyistoce/devide | modules/filters/VolumeRender.py | Python | bsd-3-clause | 9,232 | [
"VTK"
] | b7d5bd52e8c7b25fdbee9770e191ed84f68225ac1b2c550c1201a8545b35d42c |
import os, sys
import numpy as np
import pandas as pd
from pytrack_analysis import Node
from pytrack_analysis.cli import colorprint, flprint, prn
import pytrack_analysis.preprocessing as prp
from pkg_resources import get_distribution
__version__ = get_distribution('pytrack_analysis').version
"""
Kinematics class: load... | degoldschmidt/pytrack-analysis | pytrack_analysis/kinematics.py | Python | gpl-3.0 | 8,362 | [
"Gaussian"
] | 100fbe6b0196e8dc7b170f25dbc5af1c50f3d5fd0bf09ba41a22035edede5120 |
# Copyright 2013 Mark Chilenski
# This program is distributed under the terms of the GNU General Purpose License (GPL).
# Refer to http://www.gnu.org/licenses/gpl.txt
#
# 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 Fr... | markchil/gptools | gptools/utils.py | Python | gpl-3.0 | 112,260 | [
"VisIt"
] | 20a7e6626e9a4905bd22d90c05671d3cb6e78af77c02f6ae820b2af4508e9cf3 |
#!/usr/bin/python
"""
Copyright 2016 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... | druss316/G-Harvestor | html/authUser.py | Python | gpl-3.0 | 4,198 | [
"Galaxy"
] | 3a62920e3d1c11864e7421b2160f62c0a1bad4ee5f8d0ce2cbe53c66a7ef211a |
# $Author: patricio $
# $Revision: 285 $
# $Date: 2010-06-18 17:59:25 -0400 (Fri, 18 Jun 2010) $
# $HeadURL: file:///home/esp01/svn/code/python/branches/patricio/photpipe/lib/gaussian.py $
# $Id: gaussian.py 285 2010-06-18 21:59:25Z patricio $
#! /usr/bin/env python
'''
Name
----
gaussian
File
--... | zkbt/mosasaurus | mosasaurus/gaussian.py | Python | mit | 25,888 | [
"Gaussian"
] | f4dbe33a24d5c108b1ed8519bf2b21137b0600872082655d23d093ca87b5d74d |
#
# 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... | beernarrd/gramps | gramps/gen/plug/docgen/paragraphstyle.py | Python | gpl-2.0 | 11,465 | [
"Brian"
] | ecbe0ecf82afc653bb6108a4e02b4a3f16eb3e528cd656c339f0580bbbf5220e |
#!/usr/bin/env python
# This is a simple volume rendering example that uses a
# vtkVolumeTextureMapper2D mapper
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the standard renderer, render window and interactor
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renW... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/VolumeRendering/Python/SimpleTextureMap2D.py | Python | gpl-3.0 | 1,868 | [
"VTK"
] | 25a2f0ae510a73cbd5fbc4723f1162dedbf7c98744932fb15f1b2994a4477568 |
# 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.
"""Top-level presubmit script for Chromium.
See http://dev.chromium.org/developers/how-tos/depottools/presubmit-scripts
for more details about the presu... | mogoweb/chromium-crosswalk | PRESUBMIT.py | Python | bsd-3-clause | 38,018 | [
"VisIt"
] | f8cc476fe8b0ce003f5a9199b7321488f12621c5714e835db4104a73f03c3276 |
from __future__ import print_function
"""
INSTRUCTIONS
This tests requires AT LEAST the following set
export FBUTILS_APP_ID=xxxxxxxxx
export FBUTILS_APP_SECRET=xxxxxxxxxx
export FBUTILS_APP_SECRETPROOF=1
export FBUTILS_APP_SCOPE=email
export FBUTILS_APP_DOMAIN=xxxxxxxxxx
export FBUTILS_REDIRE... | jvanasco/facebook_utils | test_interactive.py | Python | bsd-3-clause | 4,520 | [
"VisIt"
] | 2e5060ddd96c55d4c38ae1138f528039f3c5923553876ce83153f8655f9d65c0 |
# -*- coding: utf-8 -*-
'''
@author: Gabriele Girelli
@contact: gigi.ga90@gmail.com
@description: statistic operations library.
'''
# DEPENDENCIES =================================================================
import math
import matplotlib.pyplot as plt
import numpy as np
from scipy import stats
from pygpseq imp... | ggirelli/gpseq-img-py | pygpseq/tools/stat.py | Python | mit | 18,120 | [
"Gaussian"
] | 53f9eb33649c143a79e8acab0b1033078df2d309d9a2d07bce744ddb8cccb919 |
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#-----------------------------------------------
# Set these parameters for adjoint flagging....
# location... | clawpack/adjoint | examples/acoustics_2d_radial_mixed/setrun.py | Python | bsd-2-clause | 14,033 | [
"NetCDF"
] | c1f9bcaebbbb6fd9fcc26117b64d4109872b8316bc4fe946e18338d7b0a62281 |
"""
Results for test_glm.py.
Hard-coded from R or Stata. Note that some of the remaining discrepancy vs.
Stata may be because Stata uses ML by default unless you specifically ask for
IRLS.
"""
import os
import numpy as np
import pandas as pd
from statsmodels.api import add_constant
from statsmodels.genmod.tests.res... | jseabold/statsmodels | statsmodels/genmod/tests/results/results_glm.py | Python | bsd-3-clause | 273,613 | [
"Gaussian"
] | b40982c2a086a46ff6f1e261815694f93d39f101601a493f75c9c97b91690646 |
import os
import sys
try:
from setuptools import setup
except:
from distutils.core import setup
readme_note = '''\
.. note::
For the latest source, issues and discussion, etc, please visit the
`GitHub repository <https://github.com/pharmbio/sciluigi>`_\n\n
'''
with open('README.rst') as fobj:
long... | samuell/sciluigi | setup.py | Python | mit | 1,532 | [
"VisIt"
] | 87e6d66afcbfbab8137ebdd1c5f7537ba0d627fc9420818452487601a7017f82 |
# -*-python-*-
#
# Copyright (C) 1999-2013 The ViewCVS Group. All Rights Reserved.
#
# By using this file, you agree to the terms and conditions set forth in
# the LICENSE.html file which can be found at the top level of the ViewVC
# distribution or at http://viewvc.org/license-1.html.
#
# For more information, visit h... | marcellodesales/svnedge-console | svn-server/lib/viewvc/vclib/ccvs/__init__.py | Python | agpl-3.0 | 2,149 | [
"VisIt"
] | 0385c6dd809d243bc1012860717641d1c5496e6d6df853a57509762f5f4ec18e |
#!/usr/bin/env python2.3
################################################################################
#
# This file is part of the General Hidden Markov Model Library,
# GHMM version __VERSION__, see http://ghmm.org
#
# file: ghmm.py
# authors: Benjamin Georgi, Wasinee Rungsarityotin, Ale... | tempbottle/ghmm | ghmmwrapper/ghmm.py | Python | gpl-3.0 | 197,239 | [
"Gaussian"
] | f25524259c3925c7f7a389afbdad3875dcb1c17a60b2abe1a65c657988047b05 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module implements classes to perform bond valence analyses.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date... | Dioptas/pymatgen | pymatgen/analysis/bond_valence.py | Python | mit | 21,652 | [
"Gaussian",
"pymatgen"
] | 468027eaf19468d5f9d3f2895bf65f0179aba54c3a1d28d348d569c8185651f3 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | jdrudolph/scikit-bio | skbio/stats/ordination/_utils.py | Python | bsd-3-clause | 7,264 | [
"scikit-bio"
] | b7ccf0ce20b14fac34c3bddc74e88dbae126179149ccf78f7ac7a6d84aff13a2 |
# $Id: get_projects.py 2016-12-17 $
# Author: Coen Meerbeek <coen@buzzardlabs.com>
# Copyright: BuzzarLabs 2016
"""
This file retrieves projects from an Octopus application
"""
import logging, json, requests, time, sys
import ConfigParser
import splunk.Intersplunk as isp
import octopus_common
# Parse octopus.conf fo... | cmeerbeek/splunk-addon-octopus-deploy | TA-OctopusNT-Fwd/bin/get_projects.py | Python | mit | 1,165 | [
"Octopus"
] | d4ee0b17e94df00fc9011096b0ac840f8e886f42a5393195f801d4b74f909534 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-install-db
# Author : Ricardo Graciani
########################################################################
"""
Create a new DB on the local MySQL server
"""
__RCSID__ = "$Id$"
#
from DIRAC.... | marcelovilaca/DIRAC | Core/scripts/dirac-install-db.py | Python | gpl-3.0 | 1,527 | [
"DIRAC"
] | 97507cf195ec61a46a358aba22776120bdb0f9da3fc5d6ff0bb952ba98161685 |
"""
This sample demonstrates a simple skill built with the Amazon Alexa Skills Kit.
The Intent Schema, Built-in Slots, and Sample Utterances for this skill, as well
as testing instructions are located at http://amzn.to/1LzFrj6
For additional samples, visit the Alexa Skills Kit Getting Started guide at
http://amzn.to/1... | MaxLinCode/tardy-HackIllinois-2017 | backend/lambda_function.py | Python | mit | 6,926 | [
"VisIt"
] | b9b445b6f6e9b6d78659898c09462b3064dbe824696216c2ec07a6fe2880ce0e |
# -*- coding: utf-8 -*-
# Copyright: (c) 2020-2021, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
"""Concrete collection candidate management helper module."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import ... | felixfontein/ansible | lib/ansible/galaxy/collection/concrete_artifact_manager.py | Python | gpl-3.0 | 25,482 | [
"Galaxy"
] | dd6f7b86c973ddb7db6e3eef0bb672d0c8d201dd1014622443f53d252ef63f0f |
""" Maximally localized Wannier Functions
Find the set of maximally localized Wannier functions
using the spread functional of Marzari and Vanderbilt
(PRB 56, 1997 page 12847).
"""
import numpy as np
from time import time
from math import sqrt, pi
from pickle import dump, load
from ase.parallel import par... | slabanja/ase | ase/dft/wannier.py | Python | gpl-2.0 | 28,927 | [
"ASE",
"Gaussian"
] | d9c3de27e3ff48c0cefdd0f28db513d195d8d2df7d4486c27024669472c9dc16 |
# test_codecs.py from CPython 2.7, modified for Jython
from test import test_support
import unittest
import codecs
import locale
import sys, StringIO
if not test_support.is_jython:
import _testcapi
class Queue(object):
"""
queue: write bytes at one end, read bytes from the other end
"""
def __init_... | adaussy/eclipse-monkey-revival | plugins/python/org.eclipse.eclipsemonkey.lang.python/Lib/test/test_codecs.py | Python | epl-1.0 | 60,499 | [
"FEFF"
] | 2217904e470c216a4ee508d6d44b00821302f7cafa74c2771385c2bce459588d |
#!/usr/bin/python
import sys
from subprocess import call
print "\nUsage: bwa_protocol.py ListOfReads Reference Threads [noreduce/reduce]\n"
try:
data = sys.argv[1]
except:
data = raw_input("List of reads: ")
try:
ref = sys.argv[2]
except:
ref = raw_input("FASTA reference file: ")
try:
threads ... | fjruizruano/ngs-protocols | bwa_protocol.py | Python | gpl-3.0 | 1,605 | [
"BWA"
] | ac6b0d6e7154a3565511211cbd7cde79f9e21b5e061ebcad9857ae63b1640e2d |
""" Testing the FCConditionPaserClass
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
from DIRAC.Resources.Catalog.FCConditionParser import FCConditionParser
__RCSID__ = "$Id $"
class TestLogicEvaluation(unittest.TestCase):
""" Tests... | yujikato/DIRAC | src/DIRAC/Resources/Catalog/test/Test_FCConditionParser.py | Python | gpl-3.0 | 8,957 | [
"DIRAC"
] | 56505741b9815380d5d3f56c8d61e69b3dbf1e7c964b16f0d16ed647995ed010 |
########################################################################
# $Id$
# File : ProcessMonitor.py
# Author : Stuart Paterson
########################################################################
""" The Process Monitor utility allows to calculate cumulative CPU time and memory
for a given PID and it... | Sbalbp/DIRAC | Core/Utilities/ProcessMonitor.py | Python | gpl-3.0 | 18,429 | [
"DIRAC"
] | 9b14d6ccdabd94d05b092fe5cc6fd701d9fadace22f185c7375a050d79f355a4 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
from copy import deepcopy
from functools import partial
from gzip import GzipFile
import os
import os.path as op
import numpy as np
from scipy import sparse, linalg... | jniediek/mne-python | mne/source_space.py | Python | bsd-3-clause | 103,050 | [
"Mayavi"
] | ab896590ec898aada00a47fb814f6dd01235fbf19208b2abe150788b7430dc5b |
# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from sparse_gp import SparseGP
from numpy.linalg.linalg import LinAlgError
from ..inference.latent_function_inference.var_dtc_parallel import update_gradients, VarDTC_minibatch
impo... | TianpeiLuke/GPy | GPy/core/sparse_gp_mpi.py | Python | bsd-3-clause | 5,101 | [
"Gaussian"
] | 6600634acfdd688d0f1c6bb83652596e0b78bdce5c5810de7d03b343c76420bf |
import os
import logging
import numpy as np
import parmap
from sklearn import mixture
import scipy
from scipy.interpolate import interp1d
import datetime as dt
from tqdm import tqdm
import torch
import torch.multiprocessing as mp
from yass import read_config
from yass.reader import READER
from yass.deconvolve.match_p... | paninski-lab/yass | src/yass/deconvolve/run_original.py | Python | apache-2.0 | 105,663 | [
"NEURON"
] | 9f58c74fd8a6354db59c67fb2dc59e6e0d0817f612a43c58f21baff76c94398e |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008-2009 Brian G. Matherly
# Copyright (C) 2009 Rob G. Healey <robhealey1@gmail.com>
# Copyright (C) 2014 Vlada Perić <vlada.peric@gmail.com>
#
# This program is free ... | jralls/gramps | gramps/plugins/lib/libholiday.py | Python | gpl-2.0 | 18,137 | [
"Brian"
] | 67fb65dc098d17cdc50d1ba8052ef97a83d87e159bc40b4c91da8dd3fe29f6a9 |
#!/usr/bin/env python
#-*- coding: utf-8 -*-
""" An example python-meep simulation of a dielectric sphere scattering a broadband impulse,
illustrating the use of the convenient functions provided by meep_utils.py
(c) 2014 Filip Dominec, see http://f.dominec.eu/meep for more information
The simulated models of struc... | FilipDominec/python-meep-utils | scatter.py | Python | gpl-2.0 | 7,750 | [
"Gaussian",
"exciting"
] | e9f13dc4d15c239a40658140885affb05a052204c71058d6a628452c0da705c6 |
#
# @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
#... | ashutoshvt/psi4 | psi4/driver/wrapper_database.py | Python | lgpl-3.0 | 26,302 | [
"Psi4"
] | cc4c230191c77484ca982e83d384b8f6c7976929a2971cdb824aa774989cee16 |
from __future__ import print_function, division
import matplotlib
matplotlib.use('agg')
from os import path, remove
from nutils import *
import scipy
import numpy as np
import matplotlib.pyplot as plt
from scipy import sparse
from scipy.io import mmwrite
from mskrylov import poly_driver
from mekrylov import me_driver
i... | ManuelMBaumann/opt_tau | num_exper/elast_wedge.py | Python | mit | 11,781 | [
"VTK"
] | 5498c48598cd2ddd6ac595872a168d2df000e144437e6e0b27889ad6490be204 |
#================================================================================
# Title: Angular correlation and auto-correlation function for bubbles and YSOs
# Authors: S. Kendrew, Max Planck Institute for Astronomy, Heidelberg, 2012
#================================================================================
... | linan7788626/brut | scripts/calc_corr.py | Python | mit | 29,259 | [
"Gaussian"
] | 3a7daab8c2770b05e216536accb19e0a3940f7634b41b9f342e044ebc4777bd2 |
# algorithm to implement max-flow min-cut
def bfs(N, start, end, dist):
'find an augmenting path from start to end via dijkstra on a graph.'
visited = [False] * N
distance = [None] * N
pointer = [None] * N
distance[start] = 0
while not visited[end]:
latest_frontier = None # next vertex ... | jeeyoungk/exercise | python/maxflow.py | Python | mit | 3,762 | [
"VisIt"
] | 3cb733ccb94edf2d1213feae7bb43c7e3ad77c189b7aadd0a0c2f4f0375c4c26 |
import requests
import time
ERROR_STRING = '"ERROR, event logged"'
OSCAR_API_BASE_URL = 'http://burdellanswers.com:3000/api/oscar/'
DEPARTMENTS = { 'ACCT' : 'Accounting',
'AE' : 'Aerospace Engineering',
'AS' : 'Air Force Aerospace Studies',
'APPH' : 'Applied Physiolo... | swgillespie/pyoscar | pyoscar.py | Python | mit | 10,966 | [
"ASE"
] | f4892e42a101d5ad1611a9c49bef3616a491a05c4f4b9e9644c73fd719eefe9e |
#! /usr/bin/python
"""versioneer.py
(like a rocketeer, but for versions)
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Version: 0.7+
This file helps distutils-based projects manage their version number by just
creating version-control tags.
For developers who work from a V... | masterkorp/obfsproxy | versioneer.py | Python | bsd-3-clause | 25,767 | [
"Brian"
] | 4c54d39adb3ff998148449308cd66004230a01c3f56ad51ea0fed37f87f38d95 |
# Copyright 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... | itielshwartz/BackendApi | lib/oauth2client/old_run.py | Python | apache-2.0 | 6,106 | [
"VisIt"
] | 33430b91f4cefef2bad403164ca0fa96ca089a86b2559f4d203ef4aed699517a |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/test.py | Python | bsd-3-clause | 527 | [
"scikit-bio"
] | 80d1f1bdabad91da70430121020aee41b30ea50990ca88479a6b876c8cd83e86 |
import sys
from galaxy.datatypes.tabular import Tabular
from galaxy.util.json import loads
class BaseDataProvider( object ):
"""
Base class for data providers. Data providers (a) read and package data from datasets;
and (b) write subsets of data to new datasets.
"""
def __init__( self, converted_d... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/visualization/data_providers/basic.py | Python | gpl-3.0 | 7,444 | [
"Galaxy"
] | 8b83b3335225bfb18c37da57cf8f2ba43e9e7c67807d2af48b1588139cd2fda0 |
import unittest
from kalliope.core.SignalModule import MissingParameter
from kalliope.core.Models import Brain
from kalliope.core.Models import Neuron
from kalliope.core.Models import Synapse
from kalliope.core.Models.Signal import Signal
from kalliope.signals.geolocation.geolocation import Geolocation
class Test_... | kalliope-project/kalliope | kalliope/signals/geolocation/tests/test_geolocalisation.py | Python | gpl-3.0 | 3,673 | [
"NEURON"
] | 58f38d2eb38acbd364253fe2e01bdfa92f1b31400ca1f835d810a452a204cc98 |
"""
Here we generate the interaction tables for the dimerized gromacs input.
If PME are used, the tables will consider it and remove half of it for the beads.
Otherwise the standard coulomb table is passed.
"""
| marckn/dimerizer | dimerizer/tables/__init__.py | Python | gpl-3.0 | 214 | [
"Gromacs"
] | 47a1aa82cfdbdc46b351a9705ee60bafb000279ba8df405ca2c0a397e8c3df3f |
# Copyright 2008 by Norbert Dojer. All rights reserved.
# Adapted by Bartek Wilczynski.
# 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.
"""Approximate calculation of appropriate thresholds for motif ... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Motif/Thresholds.py | Python | gpl-2.0 | 3,439 | [
"Biopython"
] | 27bab89035c058614f69346d214c70387df09474bda80881077263ce0248720e |
"""Miscellaneous utilities."""
from functools import reduce, partial
import os
import os.path as op
import re
import shutil
import subprocess
import warnings
import numpy as np
import mne
from mne import (pick_types, pick_info, make_sphere_model, DipoleFixed, Epochs,
Dipole, make_forward_dipole, Proj... | LABSN/mnefun | mnefun/_utils.py | Python | bsd-3-clause | 17,637 | [
"Mayavi"
] | ee207dbd056b75f59076c852e1c0d9bd6108497c72e2f225d1ef8299803bbb69 |
# -------------------------------------------------------------------------
# Name: Data handling
# Purpose: Transforming netcdf to numpy arrays, checking mask file
#
# Author: PB
#
# Created: 13/07/2016
# Copyright: (c) PB 2016
# -------------------------------------------------------------------... | CWatM/CWatM | cwatm/management_modules/data_handling.py | Python | gpl-3.0 | 60,787 | [
"NetCDF"
] | 0166837f160b584344c4f0c3827420fa2405a5d16e8a77413fb44b9dec15aa62 |
# -*- 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... | kain88-de/mdanalysis | package/MDAnalysis/analysis/lineardensity.py | Python | gpl-2.0 | 10,626 | [
"MDAnalysis"
] | 6ed32f848989ec3ef00b5d4894c04c5095b3e2c8afc07a7a679576b6ccf4429f |
#makes use of Michigan Tech's Directory
name = raw_input("Enter the first name of the person you wish to look up: ")
from splinter import Browser
with Browser() as browser:
url = "https://www.mtu.edu/mtuldapweb/web_lookup/"
browser.visit(url)
browser.fill('advtext', name)
#find and click the 'search' bu... | frankcash/Web_Scraping | test2.py | Python | mit | 465 | [
"VisIt"
] | 02d98c32025c1c4d8d82e3881d05eb867f33f0188ff488c70b7a5d5128fb17b2 |
""" Transformation Database Client Command Line Interface.
"""
__RCSID__ = '$Id: $'
#! /usr/bin/env python
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
import sys, cmd
from DIRAC.Core.Base.API import API
from DIRAC.Core.Utilities.Subprocess ... | Sbalbp/DIRAC | TransformationSystem/Client/TransformationCLI.py | Python | gpl-3.0 | 18,292 | [
"DIRAC"
] | 1153463d740d18e7244e6238202d52b99ba71238cfbf2c573c86a0d33191807b |
#!/usr/bin/env python3
"""
cv_algorithms difference-of-gaussian example
"""
import cv2
import cv_algorithms
# Read example file which contains some fractals (generated by GIMP fractal renderer)
img = cv2.imread("thinning-example.png")
# Convert to grayscale
imgGray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# Difference... | ulikoehler/cv_algorithms | examples/difference-of-gaussian.py | Python | apache-2.0 | 513 | [
"Gaussian"
] | 0a91d940b0e5b867333b7a4e6c5d44db9b1655921c776b81152098de3d708392 |
"""Soundex algorithm
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.3 $"
__date__ = "$Date: 2004/05/11 19:11:21 $"
__copyright__ ... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/soundex/stage3/soundex3a.py | Python | mit | 1,677 | [
"VisIt"
] | b6219a7963635f397a0afce91f4f095f11109338748198d18b2b47f4d5af9aa0 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
from pymatgen.electronic_structure.cohp import (
Cohp,
CompleteCohp,
IcohpCollection,
IcohpValue,
get_integrated_cohp_in_energy_range,
)
from pymatgen.electronic_struc... | materialsproject/pymatgen | pymatgen/electronic_structure/tests/test_cohp.py | Python | mit | 56,785 | [
"pymatgen"
] | f3c6e44f94564880acfc73f4a4d788a08a59c0967797ed5c0f972ab3407c8dee |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# showfreeze - front end to freezing files into write-once archive
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of th... | heromod/migrid | mig/cgi-bin/showfreeze.py | Python | gpl-2.0 | 1,104 | [
"Brian"
] | 5260cff1de8ea9fcc05a2379a5d2a40898ced99f55b2764fd6a63c0146c91118 |
import numpy as np
from math import exp, sqrt
from ase.calculators.calculator import Calculator
class MorsePotential(Calculator):
"""Morse potential.
Default values chosen to be similar as Lennard-Jones.
"""
implemented_properties = ['energy', 'forces']
default_parameters = {'epsilon': 1.0,
... | grhawk/ASE | tools/ase/calculators/morse.py | Python | gpl-2.0 | 1,494 | [
"ASE"
] | fc37666f7caef9812b076070308e276555c23c3dfeb002c0d220ed2c23fef4c2 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['architectures', 'name','version','moduleid','descripti... | shodanuk/firebase-titanium | iphone/build.py | Python | mit | 8,646 | [
"VisIt"
] | c65dc8a639d13923df6efb21953d041f719b379a293c81409dc9f0b01d366f97 |
#!/usr/bin/python
# Copyright (C) 2012,2013,2014 The ESPResSo project
# Copyright (C) 2011 Olaf Lenz
# Copyright 2008 Marcus D. Hanwell <marcus@cryos.org>
#
# 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 F... | mgusenbauer/espresso | maintainer/git2changelog.py | Python | gpl-3.0 | 4,726 | [
"ESPResSo"
] | bcff87acaa80b86a9dfb297f9092092fb7b0791503b469b0a9a06833c8ad115e |
#!/usr/bin/env python2.5
#
# Copyright 2011 the Melange 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 applic... | adviti/melange | app/soc/views/helper/access_checker.py | Python | apache-2.0 | 37,137 | [
"VisIt"
] | 0067d1ace032ef639cbc4c88b89bc1dff94154400f570a1c361e5d15fd9a645b |
from neuron import h, gui
import matplotlib
matplotlib.use('TkAgg')
import matplotlib.pyplot as pyplot
import math
import random
#neuron.load_mechanisms("./mod")
from cfiber import cfiber
from onefibersimulation import balance
#paralleling NEURON interface
pc = h.ParallelContext()
rank = int(pc.id())
nhost = int(pc.... | research-team/robot-dream | Nociception/parallelsimulation.py | Python | mit | 3,866 | [
"NEURON"
] | c31047456f443338442f72d64a19c411f8cd19d5843e4836872c051def3ba33f |
#!/usr/bin/env python
from traits.api import HasTraits, List, Instance, Bool, Str, File, Dict
from traitsui.api import View, Item, VGroup, HGroup, Group, \
RangeEditor, TableEditor, Handler, Include,HSplit, EnumEditor, HSplit, Action, \
CheckListEditor, ObjectColumn
from ..streamlines.track_dataset import Tra... | mattcieslak/DSI2 | dsi2/database/track_datasource.py | Python | gpl-3.0 | 7,393 | [
"Mayavi"
] | a9c6a5febcb2942c17cc7ac4c12fde0378bf6d324fb2d04e650e7afc7902e1e6 |
from bayesflare import Lightcurve
import bayesflare as pf
from math import *
import numpy as np
from random import random
__all__ = ["SimLightcurve", "simulate_single"]
class SimLightcurve(Lightcurve):
"""
Contains methods to simulate various light curves; builds upon the framework of the :class:`Lightcurve` c... | BayesFlare/bayesflare | bayesflare/simulate/simulate.py | Python | gpl-2.0 | 5,965 | [
"Gaussian"
] | 8f1b83e725593d5944471e55c7bad8328414e6bede0d238ac676e0a5a35230a5 |
# encoding: utf-8
# Copyright (c) Marnik Bercx
from monty.json import MSONable
from cage.core import Cage
from matplotlib.pyplot import subplots
import json
import math
import os
import warnings
import matplotlib.pyplot as plt
import pymatgen as pmg
import pymatgen.io.nwchem as nw
import numpy as np
import cage.util... | mbercx/cage | cage/landscape.py | Python | mit | 25,423 | [
"NWChem",
"pymatgen"
] | f8089587425b4aa8afd37e3bc569809c206eddb1bc3f4c5bd338b3bba736e8ea |
#! /usr/bin/env python
import os, sys, optparse
import PEATSA.Core as Core
import PEATSA.Core.Matrix
import MySQLdb
import matplotlib.pyplot as plt
import numpy as np
"""
Requires ProteinComplexTool_execute.py to do calculations!
"""
class ProteinComplexTool:
def __init__(self):
return
def ... | dmnfarrell/peat | sandbox/ProteinComplexTool_pypar_.py | Python | mit | 15,460 | [
"MDAnalysis"
] | ae4cb4e8f9a354f73b072211ced23b49f53920b77abbbde791c699359af57fba |
#!/usr/bin/env python
#encoding=utf8
#Copyright [2014] [Wei Zhang]
#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 ... | anthonylife/TaobaoCompetition2014 | src/MTL-LR/train.py | Python | gpl-2.0 | 2,562 | [
"Gaussian"
] | 6bb01d5b743c5847aad64e2a36f2a951a747583029416faad62e09c675dea861 |
"""
vtkImageImportFromArray: a NumPy front-end to vtkImageImport
Load a python array into a vtk image.
To use this class, you must have NumPy installed (http://numpy.scipy.org/)
Methods:
GetOutput() -- connect to VTK image pipeline
SetArray() -- set the array to load in
Convert python 'Int' to VTK_UNSIGNED_S... | chapering/PyVolRender | imageImportFromArray.py | Python | gpl-2.0 | 4,251 | [
"VTK"
] | ad26c82923f09f6ed79f73cbc6640d2967c26236053bbe5e2540525450715049 |
"""Streaming pickle implementation for efficiently serializing and
de-serializing an iterable (e.g., list)
Created on 2010-06-19 by Philip Guo
http://code.google.com/p/streaming-pickle/
Modified by Brian Thorne 2013 to add base64 encoding to support
python3 bytearray and the like.
"""
import base64
from pickle imp... | mjirik/lisa | lisa/extern/sPickle/sPickle.py | Python | bsd-3-clause | 2,170 | [
"Brian"
] | d2c9ad31d9165ea3b71beda6488dba6ec23a1fde32c473522f088db041e309dc |
#!/bin/python3
# coding: utf-8
"""
A Sphinx extension that enables watermarks for HTML output.
https://github.com/kallimachos/sphinxmark
Copyright 2021 Brian Moss
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 ... | kallimachos/sphinxmark | sphinxmark/__init__.py | Python | apache-2.0 | 6,205 | [
"Brian"
] | cd9d8f00878b9e2cc7746f89f673ac0fc0008a4f7cc7f88f2d1421218aae0eb6 |
# -*- coding: utf-8 -*-
"""
SUNTANS bathymetry interpolation tools
Created on Fri Oct 05 11:24:10 2012
@author: mrayson
"""
from interpXYZ import Inputs, interpXYZ
import numpy as np
import sunpy
import matplotlib.pyplot as plt
from SUNTANS.sunpy import Grid
from trisearch import TriSearch
import ti... | UT-CWE/Hyospy | Hyospy_ensemble/lib/SUNTANS/SUNTANS/sundepths.py | Python | mit | 8,258 | [
"Mayavi",
"VTK"
] | d3b07f10ccef49cafddd0dd4cd277c677f5c522b326cae2338c8a10ef6958f8f |
"""
Define common steps for instructor dashboard acceptance tests.
"""
# pylint: disable=C0111
# pylint: disable=W0621
from __future__ import absolute_import
from lettuce import world, step
from nose.tools import assert_in # pylint: disable=E0611
from courseware.tests.factories import StaffFactory, InstructorFacto... | TangXT/GreatCatMOOC | lms/djangoapps/instructor/features/common.py | Python | agpl-3.0 | 3,515 | [
"VisIt"
] | 705d40226167e6920c5bab097e6a7acb6ce8ec7ba0f6098b60ab798e62b1c5c3 |
import os
import time
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
import mdtraj.reporters
import sys
code = "2evn"
which_forcefield = "amber99sbildn.xml"
which_water = 'tip3p-fb.xml'
platform_name = "CUDA"
timestep = 2.0 * u.femtoseconds
cutoff = 0.95 * u.nanometers
output_freq... | hainm/open-forcefield-group | nmr/2EVN/code/production.py | Python | gpl-2.0 | 1,817 | [
"MDTraj",
"OpenMM"
] | 0049ea058c4a8b6488443d80dc9640c70f26ef29d0499d3d67bb58ca5336ac85 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Abinit Post Process Application
author: Martin Alexandre
last edited: May 2014
"""
import sys,os,time,commands
import string, math
#GUI
import gui.graph as Graph
import gui.conv as Conv
#Utility
import utility.writeHIST as Write
import utility.analysis as Analysis... | jmbeuken/abinit | scripts/post_processing/appa/gui/netcdf.py | Python | gpl-3.0 | 2,757 | [
"ABINIT",
"NetCDF"
] | 217c262cdde23c84a858fa0e96c23565a1307bf94cf72971b32a8bdcc070e5c9 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jun 12 20:20:03 2018
@author: BallBlueMeercat
"""
import time
import dnest4
import numpy as np
import numpy.random as rng
import pickle
#from numba import jitclass, int32
import datasim
import results
import tools
#from scipy.special import erf
# slow ... | lefthandedroo/Cosmo-models | zprev versions/Bfactor_bad_prior.py | Python | mit | 8,675 | [
"Gaussian"
] | 58572b51c3e58696a462bc4ef3b15fa8aa2f50b7605fb1d43620ef3b5fed9e07 |
# Authors: Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
# Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD (3-clause)
# Many of the computations in this code were derived from Matti Hämäläinen's
# C code.
from copy import deepcopy
from functools import partial
from gzip import GzipFile
import ... | olafhauk/mne-python | mne/source_space.py | Python | bsd-3-clause | 125,513 | [
"Mayavi"
] | d77b3b69e5e9a5a2061a0a4b4b292962a759b1927bead8704326a35776768bb1 |
# this lets me be lazy..starts the cloud up like I want from my json, and gives me a browser
# copies the jars for me, etc. Just hangs at the end for 10 minutes while I play with the browser
import unittest
import time,sys
sys.path.extend(['.','..','py'])
import h2o_cmd, h2o, h2o_hosts, h2o_glm
import h2o_browse as h2... | janezhango/BigDataMachineLearning | py/testdir_hosts/glm_bench_gaussian.py | Python | apache-2.0 | 6,075 | [
"Gaussian"
] | 5f2b0357f771a609f0214f87270bc86ac55024c7713aa306a357f2f2610a4698 |
#pylint: disable=C0111
#pylint: disable=W0621
from lettuce import world, step
from nose.tools import assert_false, assert_equal, assert_regexp_matches # pylint: disable=E0611
from common import type_in_codemirror, press_the_notification_button
KEY_CSS = '.key input.policy-key'
VALUE_CSS = 'textarea.json'
DISPLAY_NAM... | TangXT/GreatCatMOOC | cms/djangoapps/contentstore/features/advanced_settings.py | Python | agpl-3.0 | 4,393 | [
"VisIt"
] | 3f07b84cf0c96d4cef8d690703dc5a8bfdf49fa50cb28a7a4356eae8bcd1c222 |
#!/usr/bin/env python
#
# fa2lens - Extract length data from a fasta file
#
# Copyright (C) 2013, Jian-Long Huang
# Licensed under The MIT License
# http://opensource.org/licenses/MIT
#
# Author: Jian-Long Huang (jianlong@ntu.edu.tw)
# Version: 0.2
# Created: 2013.1.26
#
# Required:
# * Biopython: http://biopython.org
... | jlhg/bdorpy | bdorpy/fa2lens.py | Python | mit | 1,611 | [
"Biopython"
] | 4bcc5597e32479d859db95047c911da598195f22f04d62ba3c9871450ff3f8e3 |
# $HeadURL$
"""
Encoding and decoding for dirac, Ids:
i -> int
I -> long
f -> float
b -> bool
s -> string
z -> datetime
n -> none
l -> list
t -> tuple
d -> dictionary
k -> DError
"""
__RCSID__ = "$Id$"
import types
import datetime
from DIRAC.Core.Utilities.DErrno import DError
_dateTimeObject = datetime.da... | vmendez/DIRAC | Core/Utilities/DEncode.py | Python | gpl-3.0 | 7,767 | [
"DIRAC"
] | f99231715b3893ebbdcd8779d3f54fc3337f82dbd849b2f543c9ca868b14110c |
# -*- coding: utf-8 -*-
#!/usr/bin/python
"""Test of sayAll output."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
########################################################################
# We wait for the focus to be on a blank Firefox window.
#
sequence.append(WaitForWindowActivate(uti... | h4ck3rm1k3/orca-sonar | test/keystrokes/firefox/sayAll_bug-591351-1.py | Python | lgpl-2.1 | 2,537 | [
"ORCA"
] | c6e58783221ec9b724585ce9ed54bc667ec9b385271841eb5d7ac9f3c990230f |
#
import numpy as np
import healpy as hp
import astropy.io.fits as pyfits
from multiprocessing import Pool
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
from quicksipManera import *
import fitsio
### ------------ A couple of useful conversions -----------------------
def zeropointToScale(z... | legacysurvey/pipeline | validationtests/DESIccdManera.py | Python | gpl-2.0 | 38,903 | [
"Galaxy"
] | b246960abd393e9b2282d3789c29aa1730bc8bd625e3f2e35610a4445c702f89 |
# -*- coding: utf-8 -*-
"""
sphinx.pycode.nodes
~~~~~~~~~~~~~~~~~~~
Parse tree node implementations.
:copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
class BaseNode(object):
"""
Node superclass for both terminal and nonterminal ... | havard024/prego | venv/lib/python2.7/site-packages/sphinx/pycode/nodes.py | Python | mit | 6,387 | [
"VisIt"
] | fc38fbd08a8799f6a6167e186fdecfa58028b90510ba06fedb02d8049b722c80 |
"""
This script tests the SPMP2 module.
"""
import numpy as np
from frankenstein import sgscf, mp
from frankenstein.tools.pyscf_utils import get_pymol
import pytest
@pytest.mark.parametrize("geom, basis, spin_proj, ngrid, eref",
[
("geom/c2h4.zmat", "6-31g", 0, 6, -0.1269558397)
])
def test_spmp2(geom... | hongzhouye/frankenstein | tests/spmp2_test.py | Python | bsd-3-clause | 748 | [
"PyMOL"
] | 79a4fbadceebb5167f7c358e37471a6f82509c33baad0bdd66f7ae383f3f45f5 |
# pylint: disable=C0111
# pylint: disable=W0621
from lettuce import world, step
from lettuce.django import django_url
@step('I register for the course "([^"]*)"$')
def i_register_for_the_course(_step, course):
url = django_url('courses/%s/about' % world.scenario_dict['COURSE'].id.to_deprecated_string())
worl... | LICEF/edx-platform | lms/djangoapps/courseware/features/registration.py | Python | agpl-3.0 | 1,763 | [
"VisIt"
] | bb6141b2b402f08c25fb7e14cfd7300c601e18b6bea021a6417fd6b844e467d6 |
from builtins import range
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.gbm import H2OGradientBoostingEstimator
def offset_gaussian():
# Connect to a pre-existing cluster
insurance = h2o.import_file(pyunit_utils.locate("smalldata/glm_test/insurance.csv")... | nilbody/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_offset_gaussian_gbm.py | Python | apache-2.0 | 2,019 | [
"Gaussian"
] | 9e9e2fae88312e9800011a5a73ab5f6d709bd196e79fdb8bf3c281c778b43eb0 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import os
im... | harterj/moose | python/MooseDocs/extensions/config.py | Python | lgpl-2.1 | 2,751 | [
"MOOSE"
] | af2359d032bbf5d3b370037f80ce6bc91692c8ee0877948581ec4d68829f0881 |
import operator as op
from functools import partial
from itertools import permutations, combinations
import logging
import lib.const as C
import lib.visit as v
from ... import add_artifacts
from ... import util
from ... import sample
from ...encoder import add_ty_map
from ...meta import class_lookup
from ...meta.temp... | plum-umd/pasket | pasket/rewrite/gui/observer.py | Python | mit | 28,595 | [
"VisIt"
] | c3541e9211f85ae7248d7e6e1c6a940803be597869ccd207ec9558cfd25047fb |
# -*- coding: utf-8 -*-
# LICENCE
#
# This File is part of the Webbouqueteditor plugin
# and licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported
# License if not stated otherwise in a files head. To view a copy of this license, visit
# http://creativecommons.org/licenses/by-nc-sa/3.0/... | E2OpenPlugins/e2openplugin-OpenWebif | plugin/controllers/BouquetEditor.py | Python | gpl-3.0 | 28,113 | [
"VisIt"
] | 7fa14312816064af8c56ada9a84f50bd0a4e074ecb3db0cd1406d1f1babb93a0 |
import json, os, time
from solver.commonSolver import CommonSolver
from logic.helpers import Pickup
from utils.utils import PresetLoader
from solver.conf import Conf
from solver.out import Out
from solver.comeback import ComeBack
from utils.parameters import easy, medium, hard, harder, hardcore, mania, infinity
from u... | theonlydude/RandomMetroidSolver | solver/standardSolver.py | Python | mit | 7,846 | [
"VisIt"
] | 181ef660ee1eec7e9082989be965636f8598414e659fb32d0da947a6cd3e6f2e |
from numpy.testing import assert_array_equal, assert_allclose, assert_raises
import numpy as np
from skimage.data import camera
from skimage.util import random_noise, img_as_float
def test_set_seed():
seed = 42
cam = camera()
test = random_noise(cam, seed=seed)
assert_array_equal(test, random_noise(c... | paalge/scikit-image | skimage/util/tests/test_random_noise.py | Python | bsd-3-clause | 8,005 | [
"Gaussian"
] | 73bad0fff841ebbc21b507d21fe6d92e716e89403a31e117e8d03d3aff1f72f4 |
# Copyright 2004 by James Casbon. 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.
"""
Code to deal with COMPASS output, a program for profile/profile comparison.
Compass is des... | LyonsLab/coge | bin/last_wrapper/Bio/Compass/__init__.py | Python | bsd-2-clause | 14,957 | [
"Biopython"
] | 6306e215b3df74a9ea1a3362263b9017bac851dafc4b58662542c5f4aad1ecca |
"""
Copyright (C) since 2013 Calliope contributors listed in AUTHORS.
Licensed under the Apache 2.0 License (see LICENSE file).
io.py
~~~~~
Functions to read and save model results.
"""
import os
import xarray as xr
from calliope._version import __version__
from calliope import exceptions
def read_netcdf(path):... | calliope-project/calliope | calliope/core/io.py | Python | apache-2.0 | 4,033 | [
"NetCDF"
] | 935c1273bc0273a1f933ff0a7aa5001c5468d05c0f51b8227cf820913c39ed1c |
"""
Acceptance tests for the teams feature.
"""
import json
import random
import time
from dateutil.parser import parse
import ddt
from nose.plugins.attrib import attr
from uuid import uuid4
from unittest import skip
from ..helpers import EventsTestMixin, UniqueCourseTest
from ...fixtures import LMS_BASE_URL
from ...... | nanolearningllc/edx-platform-cypress-2 | common/test/acceptance/tests/lms/test_teams.py | Python | agpl-3.0 | 80,479 | [
"VisIt"
] | ff0a785480564d8686c8cf907bf2db9138cb3d0df1ca95e3536ea95183e22c43 |
#!/usr/bin/env python
'''
Master loader for CANON October (Fall) Campaign 2020
'''
import os
import sys
from datetime import datetime
parentDir = os.path.join(os.path.dirname(__file__), "../")
sys.path.insert(0, parentDir)
from CANON import CANONLoader
import timing
cl = CANONLoader('stoqs_canon_october2020', 'CANO... | stoqs/stoqs | stoqs/loaders/CANON/loadCANON_october2020.py | Python | gpl-3.0 | 6,445 | [
"NetCDF"
] | 4aaa242da3c7f15fa8aaa84ede8a3a805483526dbc9aa9038191d8e0c0219e41 |
import numpy as np
from galaxy_analysis.plot.plot_styles import *
import matplotlib.pyplot as plt
import yt
from yt.fields.api import ValidateParameter
from matplotlib.colors import LogNorm
from galaxy_analysis.analysis import Galaxy
from multiprocessing import Pool
from contextlib import closing
import itertools
imp... | aemerick/galaxy_analysis | misc/mixing_experiment_plot.py | Python | mit | 7,363 | [
"Galaxy"
] | e622f789c1d029318a8c0e2c606ea730a6a7eda51367de3de61296d101c3f287 |
# Modified from moose-example/synapse_tutorial.py ---
import moose
import random
import numpy as np
def test_synapse():
"""
In this example we walk through creation of a vector of IntFire
elements and setting up synaptic connection between them. Synapse on
IntFire elements is an example of ElementFi... | dilawar/moose-core | tests/core/test_synapse.py | Python | gpl-3.0 | 4,253 | [
"MOOSE"
] | 8549be44643281b74f3525bd12f47d1c99bf2f8c2224a96be246723f31f7a456 |
# vi: ts=8 sts=4 sw=4 et
#
# model.py: the Draco model
#
# This file is part of Draco2. Draco2 is free software and is made available
# under the MIT license. Consult the file "LICENSE" that is distributed
# together with this file for the exact licensing terms.
#
# Draco2 is copyright (c) 1999-2007 by the Draco2 autho... | geertj/draco2 | draco2/model/model.py | Python | mit | 3,882 | [
"VisIt"
] | 1337d5d13cbade816f027f22e71a1184d82c52fcfa72aa7dbdf16c431698bb0a |
# suppyrrs.py ---
#
# Filename: suppyrrs.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Fri Aug 7 13:59:30 2009 (+0530)
# Version:
# Last-Updated: Fri Oct 21 17:12:04 2011 (+0530)
# By: Subhasis Ray
# Update #: 605
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary: Superf... | BhallaLab/moose-thalamocortical | DEMOS/pymoose/traub2005/py/suppyrRS.py | Python | lgpl-2.1 | 4,890 | [
"MOOSE",
"NEURON"
] | 3e43603d3765e3b4fe374bc60bb538f28680fc1964d287e9bcdd6c5eef97d6ca |
from django.conf import settings
from django.contrib import admin
from django.urls.base import reverse
from django.urls.exceptions import NoReverseMatch
from edc_model_admin.model_admin_audit_fields_mixin import audit_fieldset_tuple,\
audit_fields
from edc_visit_schedule.fieldsets import visit_schedule_fieldset_tup... | botswana-harvard/edc-visit-tracking | edc_visit_tracking/modeladmin_mixins.py | Python | gpl-2.0 | 5,335 | [
"VisIt"
] | f2c46fba5e6f507863bb394f3e2e50bf8972137ccb365c72272225b3ab66d4d8 |
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