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#!/usr/bin/env python
"""
Deploy all scripts and extensions for python2 installations.
Useless in python3.
This script is not meant to be called by users (it's automatically called by dirac-install).
Usage:
dirac-deploy-scripts [options] ... ... <python path>
Arguments:
python path: you can specify the folder... | yujikato/DIRAC | src/DIRAC/Core/scripts/dirac_deploy_scripts.py | Python | gpl-3.0 | 6,198 | [
"DIRAC"
] | 137e85384cb88788914373be526e96bd13cd82844024ca3672cfcdc1d979553b |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | szha/mxnet | python/mxnet/symbol/numpy_extension/random.py | Python | apache-2.0 | 10,667 | [
"Gaussian"
] | bd57a88acc35573c65cb0b42f7908b85ec4a5af8af270f12e32872fccc1cd8e1 |
from __future__ import absolute_import, division, print_function
import inspect
import sys
import warnings
import py
from py._code.code import FormattedExcinfo
import _pytest
from _pytest import nodes
from _pytest._code.code import TerminalRepr
from _pytest.compat import (
NOTSET, exc_clear, _format_args,
ge... | iulian787/spack | lib/spack/external/_pytest/fixtures.py | Python | lgpl-2.1 | 45,468 | [
"VisIt"
] | b8dfc4c89e7c3b9ab315b343a42eafa08bd282aaaf488717b5f37acc2fa54240 |
#!/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.
"""\
Wrapper script around Rietveld's upload.py that simplifies working with groups
of files.
"""
import json
import optparse
impo... | Teamxrtc/webrtc-streaming-node | third_party/depot_tools/gcl.py | Python | mit | 52,013 | [
"VisIt"
] | c5b0c683eb0f4a4140bc592fae1df9c2c6dd3e684bbe7bdee862bee010f6435d |
# Copyright 2019 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... | tensorflow/kfac | kfac/python/ops/estimator.py | Python | apache-2.0 | 29,042 | [
"Gaussian"
] | d938fea326af71a7c90f2a78030d06a26f61f03318ab194f4636646ee36e63f8 |
import struct
import json
import zlib
import numpy as np
import scipy.io.wavfile
import scipy.signal
import scipy.sparse
from scipy.interpolate import interp1d
from aston.spectra.Scan import Scan
class AstonSeries(object):
def __init__(self, data, index=None, name=''):
#TODO: reenable this without having ... | molliewebb/aston | aston/trace/Trace.py | Python | gpl-3.0 | 16,306 | [
"Gaussian"
] | ce3a8acfb45125cfdcf65ddcf7bd1d32a8e8779d1de76d80deaf40a697da66b7 |
# Tutorial2.py
# Author : Jose Guzman
# Mail : jose.guzman __at__ physiologie.uni-freiburg.de
#! /usr/bin/env python
import neuron
import nrn
from neuron import h
# create soma object
soma = nrn.Section()
# soma attributes
soma.L = 30
soma.nseg = 3
soma.diam = 30
h('''
NDEND = 2
create soma, basal[NDEND], axon
... | nmsutton/MemoryModule | python_version/examples/Tutorial3.py | Python | mit | 382 | [
"NEURON"
] | d69698b4ae3b748c72dd0f5f097d650a9de3d029e76f2b40185eda97f4287cbb |
import os
from collections import OrderedDict
from distutils.version import LooseVersion
import warnings
import numpy as np
from .. import DataArray
from ..core import indexing
from ..core.utils import is_scalar
from .common import BackendArray
try:
from dask.utils import SerializableLock as Lock
except ImportEr... | jcmgray/xarray | xarray/backends/rasterio_.py | Python | apache-2.0 | 11,220 | [
"NetCDF"
] | ad80f63effa381869906c2bf2a3839628a8085f2a07cfa1ea9b1e415691bc97e |
import os
import sys
import random
from pandac.PandaModules import HTTPClient
from pandac.PandaModules import HTTPCookie
from pandac.PandaModules import URLSpec
from pandac.PandaModules import Ramfile
from pandac.PandaModules import DocumentSpec
from direct.task.Task import Task
from direct.directnotify.DirectNotifyGlo... | linktlh/Toontown-journey | toontown/toonbase/UserFunnel.py | Python | apache-2.0 | 26,059 | [
"Jaguar"
] | e6ac33c00e93e35aba44b955f11b906cc88da079463843e005a01a65d1d5709f |
# $Id$
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
``analysis.plugins.dist`` --- Helper Class for ``g_dist``
=========================================================
:mod:`dist` contains helper c... | jandom/GromacsWrapper | gromacs/analysis/plugins/dist.py | Python | gpl-3.0 | 8,559 | [
"Gromacs"
] | 9d60942ae9b07d6bd7ea059f690d0e141228bf5c828686d06be46ae364241e94 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This scipt builds a centreline tree from a nested list representing the tree topology.
# The fist item in each list is the current domain, followed by the left
# and right branches if any.
#
# Parameters to control the generated tree points are to be set in this file.
#... | BlueFern/DBiharMesher | util/CentrelineGenerator.py | Python | gpl-2.0 | 11,052 | [
"VTK"
] | 86a740853fe748833d7626f7680126755e7947365d4ac253b057d956de1e4b2b |
# Author: Samuel Genheden samuel.genheden@gmail.com
"""
Program to duplicate atom types in a include file
The default output is the input include file with a "_mod" string appended
Example:
lmp_duplicate_atype.py forcefield.elba
"""
import argparse
from sgenlib import lammps
if __name__ == '__main__' :
# Com... | SGenheden/Scripts | Lammps/lmp_duplicate_atype.py | Python | mit | 1,045 | [
"LAMMPS"
] | 64771932c209466250528a5127acb71e1c437cf33f4139a2ea56d6a62dabb2f6 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for Student's Profile Page.
"""
from contextlib import contextmanager
from datetime import datetime
from nose.plugins.attrib import attr
from common.test.acceptance.pages.common.logout import LogoutPage
from common.test.acceptance.pages.lms.account_settings import AccountS... | romain-li/edx-platform | common/test/acceptance/tests/lms/test_learner_profile.py | Python | agpl-3.0 | 34,901 | [
"VisIt"
] | 64bc701fee091532565b1b15a48ec94f85fc326b44c1d8324672f630db934e31 |
"""
Computational Neurodynamics
Exercise 5
Run an example with two coupled neural oscillators.
(C) Murray Shanahan et al, 2016
"""
import sys
sys.path.append('../Exercise_2')
import numpy as np
import numpy.random as rn
import matplotlib.pyplot as plt
from SynchronisationIndex import SynchronisationIndex
import IzN... | pmediano/ComputationalNeurodynamics | Fall2016/Exercise_5/Sync2Run.py | Python | gpl-3.0 | 5,168 | [
"NEURON"
] | cbb4410f62627518f1b001309eb7f8e30ea3ed114875a20078a0e6e394dfce3d |
from ase import *
from ase.lattice.surface import fcc100, add_adsorbate
# 2x2-Al(001) surface with 3 layers and an
# Au atom adsorbed in a hollow site:
slab = fcc100('Al', size=(2, 2, 3))
add_adsorbate(slab, 'Au', 1.7, 'hollow')
slab.center(axis=2, vacuum=4.0)
# Make sure the structure is correct:
#view(slab)
# Fix ... | freephys/python_ase | doc/tutorials/constraints/diffusion4.py | Python | gpl-3.0 | 778 | [
"ASE"
] | 138d55fa852b2bf0f6da74ae557da1d65d518c78dc5afcfeed1c295419d040e9 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-site-info
# Author : Stuart Paterson
########################################################################
"""
Print Configuration information for a given Site
Usage:
dirac-admin-site-info [opti... | yujikato/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_site_info.py | Python | gpl-3.0 | 1,467 | [
"DIRAC"
] | ff15f4f5faab804aa9f2de9dde3ce01175d58d585e2156f4b8b97214ddb590bb |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/drug_package.py | Python | apache-2.0 | 13,263 | [
"VisIt"
] | d0356dda25bd1d894b7ee75921fb44f247edeb2698ef7c61b0c817cb843565d3 |
# -*- coding: utf-8 -*-
#
# test_clopath_synapse.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Li... | sdiazpier/nest-simulator | testsuite/pytests/test_clopath_synapse.py | Python | gpl-2.0 | 9,563 | [
"NEURON"
] | 4b9a6586d68b9776023a9504932029e8219ac05a65e4e0271da623fd39231d0d |
# Adverserial Variational Optimization
import math
import numpy as np
import random
import sys
import torch
import torch.nn.functional as F
from sklearn.utils import check_random_state
from torch.autograd import Variable
def main():
# Assume there exists some true parameterization.
# Beam Energy = 45 Gev, ... | JoeriHermans/ml-scripts | scripts/adverserial-variational-optimization/avo-gp.py | Python | gpl-3.0 | 8,808 | [
"Gaussian"
] | 89bdd51eb602ee9b51090c2aa13806d061cd041ec5a98825afd32bf013395cdc |
#!/usr/bin/env python
# $HeadURL$
"""
Compile the externals
"""
__RCSID__ = "$Id$"
import sys, os, getopt, tarfile, urllib2, imp, signal, re, time, stat, types, shutil
try:
import zipfile
zipEnabled = True
except:
zipEnabled = False
executablePerms = stat.S_IWUSR | stat.S_IRUSR | stat.S_IXUSR | stat.S_IRGRP | ... | Sbalbp/DIRAC | Core/scripts/dirac-install.py | Python | gpl-3.0 | 57,009 | [
"DIRAC"
] | 93fa1fcc0a66a09cfac2f8a647e86efa6025c31ab0d940ea727e5be1a4ba7d55 |
# Copyright (c) 2013 Per Unneberg
#
# 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 writing,... | percyfal/ratatosk | test/test_commands.py | Python | apache-2.0 | 8,972 | [
"BWA"
] | 48670b9b02a72e0436c4640592cf38a05ae07a9dc02c7cc82682742c13a0e347 |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2018-07-31 23:52:31
# @Last modified by: Brian Cherinka
# @Last Modified time: 2018-08-01 03:34:02
from __future__ import print_function, division, absolute_import
import os
import sys
imp... | albireox/marvin | python/marvin/utils/general/images.py | Python | bsd-3-clause | 21,667 | [
"Brian",
"Galaxy"
] | c3fe747687f3037357158a27599f4e90890ca49ae4bf79fea5ad36f426a68e53 |
# -*- coding: utf-8
# pylint: disable=line-too-long
"""File/Path operations"""
import os
import json
import time
import pysam
import shutil
import tarfile
import tempfile
import anvio
import anvio.fastalib as u
import anvio.constants as constants
from anvio.terminal import Run
from anvio.terminal import Progress
fro... | meren/anvio | anvio/filesnpaths.py | Python | gpl-3.0 | 26,628 | [
"pysam"
] | 5a607888fae6b468bde2f59cec1d68c0afc3f61f3b22be174b53fe22e5181984 |
#!/usr/bin/env python
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.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 ... | Censio/ansible-dev | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 10,440 | [
"Galaxy"
] | 22d81e3eafa6a148caca58b34b45340150283025ca59ce1d2e90d51ddac6577a |
from rdkit import RDConfig
import unittest,os
from rdkit.SimDivFilters import rdSimDivPickers
from rdkit.DataManip.Metric import rdMetricMatrixCalc as rdmmc
from rdkit import DataStructs
import numpy
import random
class TestCase(unittest.TestCase):
def setUp(self) :
self.n = 1000
self.m = 80
self.d... | adalke/rdkit | Code/SimDivPickers/Wrap/testPickers.py | Python | bsd-3-clause | 8,105 | [
"RDKit"
] | d00c4bce2722390c023865615543f8d882695ad659eb8949bc8479c9961032b6 |
# coding: utf-8
"""
A Flow is a container for Works, and works consist of tasks.
Flows are the final objects that can be dumped directly to a pickle file on disk
Flows are executed using abirun (abipy).
"""
from __future__ import unicode_literals, division, print_function
import os
import sys
import time
import collect... | Dioptas/pymatgen | pymatgen/io/abinitio/flows.py | Python | mit | 57,614 | [
"ABINIT",
"pymatgen"
] | eda5d893a1b6eb45d43820dcf1e500ae219f9870f9a5a25dfde65ccff99ce9ad |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/gui/search/workordersearch.py | Python | gpl-2.0 | 4,100 | [
"VisIt"
] | f36ed1afc4bcfd48a65abec6d68fa0cf9ae5555d806271bd4e0d4d80c5ec3eea |
# Natural Language Toolkit: Corpus Reader Utilities
#
# Copyright (C) 2001-2011 NLTK Project
# Author: Steven Bird <sb@ldc.upenn.edu>
# Edward Loper <edloper@gradient.cis.upenn.edu>
# URL: <http://www.nltk.org/>
# For license information, see LICENSE.TXT
import os
import sys
import bisect
import re
import temp... | tadgh/ArgoRevisit | third_party/nltk/corpus/reader/util.py | Python | apache-2.0 | 31,013 | [
"VisIt"
] | 84cfb3f586578bdfa2f272e193af00fbfff8e7f30355c9fdae525b1ea51211b2 |
#!/usr/bin/env python
import numpy as np
import scipy as sp
def get_fft(y, Fs, upper_frequency=0):
"""
Computes a single-sided amplitude spectrum of y(t), and returns freq, amplitude
"""
N = len(y) # length of the signal
max_freq = Fs / 2
nfreqs = N / 2
if 0 < upper_frequency < max_freq... | williampierce/cc | tools/dsp/dspUtils.py | Python | mit | 1,522 | [
"Gaussian"
] | 2d0d25308654b1d8122917e663b32d3b540a2d8cf2652489424c8ea9cbea3046 |
import os
import sys
import platform
import itertools
import numpy as np
import pytest
from vtk import VTK_QUADRATIC_HEXAHEDRON
from pyvista._vtk import VTK9
import pyvista
from pyvista import examples
from pyvista.core.errors import VTKVersionError
normals = ['x', 'y', '-z', (1, 1, 1), (3.3, 5.4, 0.8)]
skip_py2_n... | akaszynski/vtkInterface | tests/test_filters.py | Python | mit | 57,431 | [
"VTK"
] | bbb7c87c1de061e6e7d172e2d2203b660a97fd203a503f1b691abb460bacb4d6 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/champ/__init__.py | Python | gpl-2.0 | 9,454 | [
"ChemPy",
"PyMOL"
] | 5d0635845e9b061a53d6195f6ed4b857d89d25252e07fab2aac6517f37f6493a |
""" Python test discovery, setup and run of test functions. """
import fnmatch
import functools
import py
import inspect
import sys
import pytest
from _pytest.mark import MarkDecorator, MarkerError
from py._code.code import TerminalRepr
import _pytest
import pluggy
cutdir2 = py.path.local(_pytest.__file__).dirpath()
... | untitaker/pytest | _pytest/python.py | Python | mit | 82,714 | [
"VisIt"
] | 76af6270176f631e814b521fe954e32b56c846aa0e17dc8c07a307992235563a |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# math2html: convert LaTeX equations to HTML output.
#
# Copyright (C) 2009-2011 Alex Fernández
#
# Released under the terms of the `2-Clause BSD license'_, in short:
# Copying and distribution of this file, with or without modification,
# are permitted in any m... | burzillibus/RobHome | venv/lib/python2.7/site-packages/docutils/utils/math/math2html.py | Python | mit | 182,250 | [
"Bowtie"
] | 4959a1171f8618c23d36f372eb4dc9abd0290c941392911383429f51d6452585 |
from util.dispatch import method_store, multimethod
import node
class ConstantPool(object):
'''
A pool for holding compile time constants.
'''
_store = method_store()
def __init__(self):
self._pool = []
self._add(node.Bool('0'), lambda n: int(n.value))
self._add(node.Boo... | dacjames/mara-lang | bootstrap/mara/constant.py | Python | mit | 976 | [
"VisIt"
] | 6020d157bbd1202bc34e77ca1d869290214b46e3b245d6ff9075173b7afed51e |
#! /usr/bin/python3
# unsupported 20091104 ...
# ['set_sequence_number', dtime, sequence]
# ['raw_data', dtime, raw]
r'''
This module offers functions: concatenate_scores(), grep(),
merge_scores(), mix_scores(), midi2opus(), midi2score(), opus2midi(),
opus2score(), play_score(), score2midi(), score2opus(), sco... | ike709/FTL13 | tools/midi2piano2016/midi/midi.py | Python | agpl-3.0 | 65,440 | [
"BWA",
"CRYSTAL"
] | f0c6c7ec3909c4132276eb60d08e4dc4e94f2994ebbb4504174939c05a1b7ca5 |
#pylint: disable=missing-docstring
#* 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/... | harterj/moose | python/chigger/exodus/MultiAppExodusReader.py | Python | lgpl-2.1 | 1,452 | [
"MOOSE"
] | 268c676af7eabbe86c73c6b0bda2bd98af2d25296caadc542ba76d6029771a89 |
# -*- coding: utf-8 -*-
# Copyright (c) 2017, Frappe Technologies Pvt. Ltd. and Contributors
# See license.txt
from __future__ import unicode_literals
import frappe
import unittest
from frappe.utils import nowdate
from erpnext.hr.doctype.employee_advance.employee_advance import make_bank_entry
from erpnext.hr.doctype.... | libracore/erpnext | erpnext/hr/doctype/employee_advance/test_employee_advance.py | Python | gpl-3.0 | 1,400 | [
"VisIt"
] | 93775f911fbce9d59f079f339d4e67f66e612471bbe117cf63097a8581c2018a |
#!/usr/bin/env python
"""
Start a given production
Example:
$ dirac-prod-start 381
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Utilities.DIRACScript import DIRACScript as Script
@Script()
def main... | ic-hep/DIRAC | src/DIRAC/ProductionSystem/scripts/dirac_prod_start.py | Python | gpl-3.0 | 952 | [
"DIRAC"
] | 904a5fff23b81a6945fef9e8413999e2416fbf937273e9171741ab108546d77b |
__author__ = 'xiaoxiaol'
import sys
import os
import platform
import matplotlib.pyplot as plt
import seaborn as sb
if (platform.system() == "Linux"):
WORK_PATH = "/local1/xiaoxiaol/work"
else:
WORK_PATH = "/Users/xiaoxiaoliu/work"
p = WORK_PATH + '/src/morphology_analysis'
sys.path.append(p)
import bign... | XiaoxiaoLiu/morphology_analysis | bigneuron/median_compare_to_consensus.py | Python | gpl-3.0 | 13,289 | [
"NEURON"
] | 0a5e999992bbd55ab14aa909b7fae136a568ed81864a5bc985c2a57866e79e31 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: ... | fabio-otsuka/invesalius3 | invesalius/data/viewer_volume.py | Python | gpl-2.0 | 42,298 | [
"VTK"
] | 4d97c2d2ee5052d1719e794fed14dc8adae4bdd4ab219b28aa07a10085412543 |
# Copyright (c) 2016 Universidade Federal Fluminense (UFF)
# Copyright (c) 2016 Polytechnic Institute of New York University.
# This file is part of noWorkflow.
# Please, consult the license terms in the LICENSE file.
"""Trial Dot Object"""
from __future__ import (absolute_import, print_function,
... | gems-uff/noworkflow | capture/noworkflow/now/persistence/models/trial_dot.py | Python | mit | 2,788 | [
"VisIt"
] | b0ce3fbee59d6317a028fc8060f43bcbfe4ee4de56fe942d5669978924c97deb |
# -*- coding: utf-8 -*-
"""
Tests for user authorization password-related functionality.
"""
import json
import logging
import re
import ddt
from django.conf import settings
from django.contrib.auth import get_user_model
from django.core import mail
from django.test import TestCase
from django.test.client import Reque... | edx-solutions/edx-platform | openedx/core/djangoapps/user_authn/views/tests/test_password.py | Python | agpl-3.0 | 12,799 | [
"VisIt"
] | 240bcd968f485f50046c465baf9c35481187264dd0f7d4ba2c66f3ac3f10703b |
# -*- coding: utf-8 -*-
"""
molvs.normalize
~~~~~~~~~~~~~~~
This module contains tools for normalizing molecules using reaction SMARTS patterns.
:copyright: Copyright 2016 by Matt Swain.
:license: MIT, see LICENSE file for more details.
"""
import logging
from rdkit import Chem
from rdkit.Chem import AllChem
from... | bp-kelley/rdkit | rdkit/Chem/MolStandardize/normalize.py | Python | bsd-3-clause | 9,649 | [
"RDKit"
] | 2fa49ac426cce27146e6bbce6e49b164fe03e162414dc5171e699647ba496cc9 |
#!/usr/bin/python
#
# Copyright 2012 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 b... | kbdick/RecycleTracker | recyclecollector/scrap/gdata-2.0.18/samples/apps/list_group_members.py | Python | gpl-3.0 | 4,061 | [
"VisIt"
] | 80948cbdeaa02cd3fb4e4118ca7745c2ba430176de0ad6c8251137ed269af6c4 |
"""
Views for user API
"""
import logging
log = logging.getLogger(__name__)
from django.conf import settings
from django.shortcuts import redirect
from django.utils import dateparse
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import UsageKey
from rest_framework import generics, views
from rest_f... | proversity-org/edx-platform | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 13,417 | [
"VisIt"
] | e669220e753dbbf8d635042e07289d718cae98a753675cd7b5e10f66d267cbe6 |
# Copyright (c) 2000 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
__revision__ = "$Id: randsource.py,v 1.6 2003/02/10 17:26:16 zooko Exp $"
from egtp.crypto import evilcryptopp
__doc__ =... | zooko/egtp_new | egtp/crypto/randsource.py | Python | lgpl-2.1 | 1,324 | [
"VisIt"
] | 23a5faf1e9592eec4dbd481ea04c43845cfcfca40b50fd7ab9f0d08f92eb0173 |
#!/usr/bin/env python
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
import sys
if len( sys.argv ) < 2:
print 'Usage: dirac-transformation-archive transID [transID] [transID]'
sys.exit()
else:
transIDs = [int( arg ) for arg in sys.argv[1:]]
from DIRAC.TransformationSystem.Agent.Transfor... | vmendez/DIRAC | TransformationSystem/scripts/dirac-transformation-archive.py | Python | gpl-3.0 | 930 | [
"DIRAC"
] | 301178077fc837b561e008dad4e38c3cfda1e3ddde99d1ebccc14e91ad339fce |
# *****************************************************************************
# Copyright (c) 2020, Intel Corporation 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 sou... | IntelLabs/hpat | sdc/hiframes/sort.py | Python | bsd-2-clause | 19,432 | [
"VisIt"
] | e53c439c5f47d31269610b90d6db5fef6474a2ceb74cb9e7ae36809853646201 |
# Created by: Aditya Dua
# 30 September 2017
from __future__ import print_function
from abc import ABC
import math
from math import pi
import numpy as np
import vtk
from . import transforms
from .graphics import VtkPipeline
from .graphics import axesCube
from .graphics import axesCubeFloor
from .graphics import vtk_nam... | adityadua24/robopy | robopy/base/serial_link.py | Python | mit | 11,798 | [
"VTK"
] | e8bba6a73baadabea34c53ff294ffe13bc18c5b1d74b825b8018584df613e5b2 |
from math import sqrt
import numpy as np
from gpaw.symmetry import Symmetry
from ase.dft.kpoints import monkhorst_pack
# Primitive diamond lattice, with Si lattice parameter
a = 5.475
cell_cv = .5 * a * np.array([(1, 1, 0), (1, 0, 1), (0, 1, 1)])
spos_ac = np.array([(.00, .00, .00),
(.25, .25, .25... | robwarm/gpaw-symm | gpaw/test/symmetry.py | Python | gpl-3.0 | 2,647 | [
"ASE",
"GPAW"
] | f81f0ae0f1cd3cb0ac0ef29e3a8cf8db3ea66adf4033b47ab518ea7a6a56b62a |
"""
=========================================
Segmenting the picture of Lena in regions
=========================================
This example uses :ref:`spectral_clustering` on a graph created from
voxel-to-voxel difference on an image to break this image into multiple
partly-homogenous regions.
This procedure (spec... | florian-f/sklearn | examples/cluster/plot_lena_segmentation.py | Python | bsd-3-clause | 2,411 | [
"Brian"
] | a3e926aeac0e04377be0e1e2161600fc667c6f12de5bc1868497595691f1cda2 |
# (c) 2005 Ian Bicking and contributors; written for Paste (http://pythonpaste.org)
# Licensed under the MIT license: http://www.opensource.org/licenses/mit-license.php
# Mostly taken from PasteDeploy and stripped down for Galaxy
import inspect
import os
import re
import sys
from typing import Callable, Dict, List, O... | natefoo/pulsar | pulsar/util/pastescript/loadwsgi.py | Python | apache-2.0 | 26,364 | [
"Galaxy"
] | ee1d05e4dc8d129f831b616012c47faf59300c45b2d893fec48dab1395e57758 |
# Copyright 2010 United States Government as represented by the
# Administrator of the National Aeronautics and Space Administration.
# Copyright 2012 Hewlett-Packard Development Company, L.P.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the L... | phenoxim/nova | nova/tests/unit/matchers.py | Python | apache-2.0 | 20,289 | [
"VisIt"
] | bd6a39ef640012a044895f6a076cbafaa8c95a7d4f01ddd16d3c126f955b8f11 |
import numpy as np
#from Numeric import asarray as Numeric_asarray
#from ase.units import Bohr
#from ase.parallel import paropen
fast = False
# -------------------------------------------------------------------
from vtk import vtkStructuredPoints, vtkDoubleArray, vtkXMLImageDataWriter
def write_vti(filename, atom... | suttond/MODOI | ase/io/vtkxml.py | Python | lgpl-3.0 | 5,349 | [
"ASE",
"VTK"
] | 8fe9d6eeaeb8908eb86a2da5c815f6fc6398c41d2275318b2f7c8289bec22bfc |
# -*- coding: utf-8 -*-
import sys
sys.path.append('../..')
from clastic.cline import route, run, get
@route('/')
@route('/hello/<name>')
def hello_world(name='world'):
return '<html><body><h1>Hello %s!</h1></body></html>' % name
@route('/query_params')
def show_query_params(request):
"""to access the req... | kezabelle/clastic | examples/cline/basic.py | Python | bsd-3-clause | 938 | [
"VisIt"
] | 52be3384bb3867006023e5de98237e759bbe9f96e1ced2d12c30372d525e226a |
import unittest
import shutil
import tempfile
from simlammps.io.lammps_process import LammpsProcess
class TestLammpsProcess(unittest.TestCase):
def setUp(self):
self.temp_dir = tempfile.mkdtemp()
self.lammps = LammpsProcess(log_directory=self.temp_dir)
def tearDown(self):
shutil.rmt... | simphony/simphony-lammps-md | simlammps/io/tests/test_lammps_process.py | Python | bsd-2-clause | 855 | [
"LAMMPS"
] | 910dadcb44b4befc7c664267a4a50d02cc814d654557cf387f75b004edd225e3 |
import numpy as np
from def_get_mags import get_zdistmod, get_kcorrect2, aper_and_comov, abs2lum, lumdensity, abs_mag
from scipy import interpolate
import math
from halflight_second import meanlum2, get_errors
from def_halflight_math import get_halfrad
def upper_rad_cut(loglum, lograd, logden, m, proof=False):
from d... | anewmark/galaxy_dark_matter | halflight_first.py | Python | mit | 10,219 | [
"Galaxy"
] | bbd3ad752848d17fe39f4e40f6f1d760911456a046674dd9f83234739263a954 |
from behave import *
import json
import server_promotion as server
@when(u'I visit the "home page"')
def step_impl(context):
context.resp = context.app.get('/')
@then(u'I should see "{message}"')
def step_impl(context, message):
assert message in context.resp.data
@then(u'I should not see "{mes... | NYU-DEVOPS-INDIA/PROMOTIONS | features/steps/promotion_steps.py | Python | apache-2.0 | 5,128 | [
"VisIt"
] | 3610c1cd3605649df500fc5e4d50af3bafb8e0263fe9518ca5e6cb83aa4fb535 |
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2014-2018 Florian Bruhin (The Compiler) <mail@qutebrowser.org>
# This file is part of qutebrowser.
#
# qutebrowser 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 So... | toofar/qutebrowser | scripts/dev/pylint_checkers/qute_pylint/openencoding.py | Python | gpl-3.0 | 3,068 | [
"VisIt"
] | 6a81a6098555f9aea573bc1b60172b0e7e525ae92da116821126829155287661 |
#!/usr/bin/env python
"""
pretty_lefse.py
~~~~~~~~~
A simple command line application to beautify multiple LEfSe outputs.
:copyright: (c) 2015 by Thomas W. Battaglia.
:license: BSD, see LICENSE for more details.
"""
__author__ = 'Thomas W. Battaglia'
__copyright__ = 'Copyright 2015'
__license__ = 'BSD'
__version... | twbattaglia/koeken | koeken/pretty_lefse.py | Python | mit | 3,485 | [
"Galaxy"
] | f59979e74d0d6b2b140b5943b0da2812bed03829b5fbb0490fba6926b57b6a40 |
# We only import librairies needed for plotting
# Other librairies are imported in the class definition file, G3D_class.py,
# which contains all process and variables function definition.
import matplotlib
matplotlib.use('pdf')
import matplotlib.pyplot as plt
import matplotlib.dates as mdates
import datetime as dt
imp... | acapet/GHER-POSTPROC | Examples/RiverTrack.py | Python | gpl-3.0 | 2,772 | [
"NetCDF"
] | 3bb83432f49952e11270503ea5e04ca33cab27ad89c6ec4b8320fb1a84fc7543 |
#! /usr/bin/env python
"""Test script for the bsddb C module by Roger E. Masse
Adapted to unittest format and expanded scope by Raymond Hettinger
"""
import os, sys
import copy
import bsddb
import dbhash # Just so we know it's imported
import unittest
from test import test_support
class TestBSDDB(unittest.TestCase)... | zephyrplugins/zephyr | zephyr.plugin.jython/jython2.5.2rc3/Lib/test/test_bsddb.py | Python | epl-1.0 | 10,228 | [
"Brian"
] | d87b08ec7853024f2fe37765ba0b0dd6de3764a29d191b397dc4ae5602ab084c |
import sys
class Node(object):
def children(self):
""" A sequence of all children that are Nodes
"""
pass
def show(self, buf=sys.stdout, offset=0, _my_node_name=None):
""" Pretty print the Node and all its attributes and
children (recursively) to a buffer.
... | dikujepsen/OpenTran | v2.0/framework/lan_ast_unused.py | Python | mit | 10,877 | [
"VisIt"
] | d3ee10473d9c0fa226187c6212846d73768e0d24cbc85d9f86ba9e800b58f95e |
import pandas as pd
import data
import dtools
from pybrain.datasets import SupervisedDataSet
from pybrain.tools.shortcuts import buildNetwork
from pybrain.supervised.trainers import RPropMinusTrainer
from pybrain.structure import RecurrentNetwork, FullConnection
from pybrain.structure.modules ... | ABcDexter/BitcoinTradingAlgorithmToolkit | src/example.py | Python | gpl-3.0 | 4,587 | [
"Gaussian"
] | 1485c0ab0fafeeee5ee438bb0e96bb19ba4020546ad5df5e912582d99e839be6 |
#! /usr/bin/python3
#
# SCANIT - Control A spectrometer and collect data
#
# LICENSE:
# This work is licensed under the Creative Commons Zero License
# Creative Commons CC0.
# To view a copy of this license, visit
# http://directory.fsf.org/wiki/License:CC0
# or send a letter to:
# Creative Commons, PO Box 1866, Mount... | jluscher/SCANIT | scanit_v031.py | Python | cc0-1.0 | 67,771 | [
"VisIt"
] | d81390a50195967bec6fc8d6d0cf14df767bcef9de08951a0e82cff0d2abb520 |
from Sire.IO import *
from Sire.Move import *
from Sire.Mol import *
from Sire.MM import *
from Sire.System import *
from Sire.Units import *
from nose.tools import assert_almost_equal
(mols, space) = Amber().readCrdTop("../io/ala.crd", "../io/ala.top")
coul_cutoff = 10 * angstrom
lj_cutoff = 10 * angstrom
rf_diel... | chryswoods/SireTests | unittests/OpenMM/test_setup.py | Python | gpl-2.0 | 2,444 | [
"Amber",
"OpenMM"
] | 09c2e2493c61ee5735d9774ae922fbb9b8afd880fa6c5dcff6bd73fd42f76b00 |
"""
################################################################################
# Copyright (c) 2003, Pfizer
# Copyright (c) 2001, Cayce Ullman.
# Copyright (c) 2001, Brian Matthews.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provid... | 2ndy/RaspIM | usr/share/python-support/python-soappy/SOAPpy/Utilities.py | Python | gpl-2.0 | 5,145 | [
"Brian"
] | eb9b04a083c3e0ab15e4bde87a1defe46c4341f7c92b09b7fc519014dacf8601 |
import unittest
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.core.tensors import Tensor
from pymatgen.analysis.elasticity.strain import Strain, Deformation, \
convert_strain_to_deformation, DeformedStructureSet
from pymatgen.util.testing import PymatgenTest
... | gVallverdu/pymatgen | pymatgen/analysis/elasticity/tests/test_strain.py | Python | mit | 8,456 | [
"pymatgen"
] | 786539a6fb4dfc28e107574cbc7d86f29e499f4beb1d0927d5c2e53149c933ab |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | beernarrd/gramps | gramps/gen/filters/rules/person/_hasnote.py | Python | gpl-2.0 | 1,754 | [
"Brian"
] | 0306be59cd2f4fa5c43c37d0c024d9450c2617a87246acc4b74d40e750a8efcb |
import os
import pytest
from six import StringIO
from eppy.modeleditor import IDF
from eppy.iddcurrent import iddcurrent
from eppy import modeleditor
from eppy.tests.test_runner import versiontuple
THIS_DIR = os.path.dirname(os.path.abspath(__file__))
RESOURCES_DIR = os.path.join(THIS_DIR, os.pardir, 'resources')
... | jamiebull1/eppy | eppy/tests/conftest.py | Python | mit | 1,478 | [
"EPW"
] | aa7c9583baa00b8832cbe7fa488ec14b40893b226978b5e1435a62b9bed902ab |
#!/usr/bin/env python
# -*- coding: utf-8 -*
# Copyright 2018 Actian Corporation
# 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
#... | ActianCorp/dbmv | bin/typesMapping.py | Python | apache-2.0 | 100,523 | [
"ASE"
] | 473460c32aac7ec4a4788d6c2ef6981dabf34bc9d741d5641c3289c7b232da97 |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import functools
import glob
import itertools
import jinja2
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import sys
import time
import urllib2
import zlib
from xml.etree import ElementTree
from cStringIO ... | atuljain/odoo | addons/web/controllers/main.py | Python | agpl-3.0 | 68,892 | [
"VisIt"
] | c0aa175e73fe3a83e648b9de094aa8702bd038cf452895d855d8ed3f19a772bc |
from unittest import TestCase
import unittest
import ezyrb.online as on
import numpy as np
import filecmp
import os
class TestOnline(TestCase):
def test_online_attributes_01(self):
mu_value = np.array([.0, .0])
output_name = 'Pressure'
online_handler = on.Online(mu_value, output_name)
np.testing.assert_ar... | fsalmoir/EZyRB | tests/test_online.py | Python | mit | 4,630 | [
"VTK"
] | 7128468dccb87cc3ba4fe5b390d951ae84a4a217c585f788a10ea81fd544509c |
PRIORITY = (
('normal', 'Normal'),
('urgent', 'Urgent'),
)
REASON_NOT_DRAWN = (
('collection_failed', 'Tried, but unable obtaining sample from patient'),
('absent', 'Patient did not attend visit'),
('refused', 'Patient refused'),
('no_supplies', 'No supplies'),
)
ITEM_TYPE = (
('tube', '... | botswana-harvard/lab-requisition | lab_requisition/choices.py | Python | gpl-2.0 | 401 | [
"VisIt"
] | 00f2721cc3afa1e3200f6f1984ddd0db3389811b633801ad75c17000768526c3 |
#!/usr/bin/python
#
# Regression test driver for cmd-line tools
#
# Usage: test_cmdline_tool.py [<options>] <tool> <arguments>
#
# If the -g option is given or the TEST_GENERATE environment variable is set to 1,
# *-expected.<suffix> files will be generated instead of running the tests.
#
# Any generated output is wri... | MatthiasWM/openscad | tests/test_cmdline_tool.py | Python | gpl-2.0 | 13,362 | [
"Gaussian"
] | 911f695cd5bf9188be217989a0253074f898e7225d8dbad850fb7f5ab3c3e672 |
#!/usr/bin/env python3
import os
import argparse
import statistics
import sys
import gzip
def main():
args = get_arguments()
print('\nLoading reads from: ' + args.input_fastq, file=sys.stderr)
input_reads = load_fastq(args.input_fastq)
print(' Found ' + int_to_str(len(input_reads)) + ' reads (' +
... | rrwick/Fast5-to-Fastq | fastq_to_fastq.py | Python | gpl-3.0 | 8,709 | [
"VisIt"
] | 89652cb0a8f6e77cd63008324647d81303a7dd675bfcc213d5fc85991d4dc3b2 |
from __future__ import division
import sys
import numpy as np
import pdb
class Cluster(object):
def __init__(self, data, reads=None, samples=None):
self.chrA = data[0]
self.startA = int(data[1])
self.endA = int(data[2])
self.chrB = data[3]
self.startB = int(data[4])
... | talkowski-lab/Holmes | pycluster/cluster.py | Python | mit | 9,036 | [
"pysam"
] | e9b8c3f8d5d93f7351ae6e34a16f937af8a417ceb8fa99bd857882e1a5569511 |
#!/usr/bin/env python
# Part of BP discovery pipeline
# Given a bam file (reads are mapped to putative lariats), this script figures out the
# the mismatch at the branchpoint position.
import pysam
import sys
import argparse
DEBUG=False
parser = argparse.ArgumentParser(description='A script to collect stats on the e... | yfu/tools | parse_bam/bp_err.py | Python | gpl-3.0 | 2,027 | [
"pysam"
] | 84ff4f731605f5831c29b8bcfcfd143dd1a1a9ea2ac5332dd3c3f54edb3b7772 |
#### PATTERN | WEB ###################################################################################
# Copyright (c) 2010 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
# http://www.clips.ua.ac.be/pages/pattern
##################################... | agermanidis/Pattern | web/__init__.py | Python | bsd-3-clause | 80,882 | [
"VisIt"
] | fda3ff6c32eab5ef26c9e24905983de4947a87ac60c38bb1b7b0b7b847daf053 |
import cv2
import numpy as np,sys
A = cv2.imread('zoro2.png')
B = cv2.imread('sharingan.jpg')
# generate Gaussian pyramid for A
G = A.copy()
gpA = [G]
for i in xrange(6):
G = cv2.pyrDown(G)
gpA.append(G)
# generate Gaussian pyramid for B
G = B.copy()
gpB = [G]
for i in xrange(6):
G = cv2.pyrDown(G)
g... | HDLynx/sharingan | Blending.py | Python | gpl-2.0 | 1,199 | [
"Gaussian"
] | a1e2b635abd2d8279cb56b9eb45ef8516907304cd47f26f241f0fea0e6cac7b4 |
""" PublisherHandler
This service has been built to provide the RSS web views with all the information
they need. NO OTHER COMPONENT THAN Web controllers should make use of it.
"""
from datetime import datetime, timedelta
from types import NoneType
# DIRAC
from DIRAC ... | Andrew-McNab-UK/DIRAC | ResourceStatusSystem/Service/PublisherHandler.py | Python | gpl-3.0 | 12,431 | [
"DIRAC"
] | 078137f15a1272273ca06fdf81994fd2430d519959f93d09074ea7a6408d21c9 |
import subprocess
from .exceptions import PyperclipException
EXCEPT_MSG = """
Pyperclip could not find a copy/paste mechanism for your system.
For more information, please visit https://pyperclip.readthedocs.org """
def init_osx_clipboard():
def copy_osx(text):
p = subprocess.Popen(["pbcopy", "w... | toobaz/pandas | pandas/io/clipboard/clipboards.py | Python | bsd-3-clause | 3,678 | [
"VisIt"
] | 4a3094f3fc7237e77429404b394b3f864f0f3f6b21e35445afb32e5ffda73f72 |
#!/usr/bin/python
class Lineprinter:
def __init__ (self):
self.value = 0
def incr(self):
self.value = self.value + 1
def section(self):
print "\n\n=== %d ===" % self.value
self.incr()
lp = Lineprinter()
###
lp.section()
#we use the juniper version of ncclient v0.1a from https://github.com/Junipe... | francisluong/python-netdev | scratch/nc002_swinfo.py | Python | mit | 3,685 | [
"Firefly"
] | 0a1227aba9dd532282b84a5f45d5e1fa91af4653053819e0c73af319f59ffceb |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_clocksyn_hidens_compiled_0016.py | Python | gpl-3.0 | 3,910 | [
"Brian"
] | b35a8619a9b7371c81c2756ce6ae01b11a3774d28e5058e7b4e9c74b942f2a18 |
#
# Copyright (C) 2000 greg Landrum
#
""" unit testing code for trees and decision trees (not learning/xvalidation) """
import unittest
from rdkit.ML.DecTree import TreeUtils
from rdkit.ML.DecTree.DecTree import DecTreeNode as Node
class TestTreeUtils(unittest.TestCase):
def test_TreeUtils(self):
# Tree i... | bp-kelley/rdkit | rdkit/ML/DecTree/UnitTestTreeUtils.py | Python | bsd-3-clause | 1,321 | [
"RDKit"
] | 6a1b709f5e3ab39fb5555d2ff925d89fb1915cdab134cdc5bd036bac423c6558 |
# -*- coding: utf-8 -*-
'''
Copyright (c) 2015 by Tobias Houska
This file is part of Statistical Parameter Estimation Tool (SPOTPY).
:author: Tobias Houska and Alejandro Chamorro-Chavez
This class holds the Simulated Annealing (SA) algorithm based on Kirkpatrick et al. (1983):
Kirkpatrick, S., Gelatt, C. D., Vecchi... | gitporst/spotpy | spotpy/algorithms/sa.py | Python | mit | 7,216 | [
"Gaussian"
] | 7e722d7026117245930ece6e0e65e9bfe50e8ce6d46c47075a4087e2609e7987 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Base classes representing defects.
"""
import logging
from abc import ABCMeta, abstractmethod
from functools import lru_cache
import numpy as np
from monty.json import MontyDecoder, MSONable
from pymatgen.core.composit... | vorwerkc/pymatgen | pymatgen/analysis/defects/core.py | Python | mit | 25,022 | [
"VASP",
"pymatgen"
] | ebc8cb2e38eb0495993344925cbaf6a23ea3bd7247af8f1d52e95ceb1a537464 |
import os
import pickle
from sklearn import tree
import torch
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import norm
from sklearn.neighbors import KernelDensity
import matplotlib.pyplot as plt
if os.path.isfile("god.file"):
outputs,coeffs=pickle.load(open("god.file","rb"))
else:
raise... | Fuchai/Philosophy-Machine | amne_binding/binding_tree_analysis.py | Python | apache-2.0 | 2,395 | [
"Gaussian"
] | 6e975dd12ef1b8439ea55f60529833c6f5a635fb218af507eb25c8b3c38b695c |
# proxy module
from __future__ import absolute_import
from mayavi.filters.extract_grid import *
| enthought/etsproxy | enthought/mayavi/filters/extract_grid.py | Python | bsd-3-clause | 96 | [
"Mayavi"
] | a18122667865e5104a57a10224421fb01db37bbfae2c9f8ade7386d9cb502e49 |
# -*- coding: utf-8 -*-
from math import *
from mumax2_geom import *
Nx = 64
Ny = 64
Nz = 4
sX = 320e-9
sY = 320e-9
sZ = 20e-9
hsX = 0.5 * sX
hsY = 0.5 * sY
hsZ = 0.5 * sZ
csX = sX/Nx
csY = sY/Ny
csZ = sZ/Nz
setgridsize(Nx, Ny, Nz)
setcellsize(csX, csY, csZ)
# setperiodic(8,8,0)
# LLB R
load('exchange6')
load('... | mumax/2 | examples/heat-demag-simple.py | Python | gpl-3.0 | 2,600 | [
"Gaussian"
] | 783aa6d379c8804ab1fae3d4df423274f9f58e111d0fddc127ee85ea868288e4 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_clocksyn_lodens_0016/brian2_benchmark_COBAHH_clocksyn_lodens_0016.py | Python | gpl-3.0 | 3,775 | [
"Brian"
] | 412743c7aed7c8ebee02ba77a3741cbf25d6f3404248178164a0fe4002f3d47d |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/integrator/VelocityVerletOnGroup.py | Python | gpl-3.0 | 1,906 | [
"ESPResSo"
] | 895e39d6e2fe8e617f41ee6e0bfc0fade03bac1e5f2009f47191c3fe6b338540 |
'''
All generic pulse shapes are defined here.
'''
import numpy as np
from math import pi, sin, cos, acos, sqrt
def gaussian(amp=1, length=0, cutoff=2, sampling_rate=1e9, **params):
'''
A simple gaussian shaped pulse.
cutoff is how many sigma the pulse goes out
'''
if length == 0:
raise V... | BBN-Q/QGL | QGL/PulseShapes.py | Python | apache-2.0 | 9,532 | [
"Gaussian"
] | a41188b579bb62729f6d61faba4ef34fb6cf9481027b08548c3362ad294a83c9 |
import operator
import numpy as np
from skimage import measure
from collections import defaultdict
import itertools
from StringIO import StringIO
import tempfile
#To fix normnals
from trimesh import Trimesh
from mayavi import mlab
from tvtk.api import tvtk
def marche_cubes( ids , volume):
"""
Given a se... | tartavull/tigertrace | tigertrace/util/mesh/mesh.py | Python | mit | 15,151 | [
"Mayavi"
] | 7c0b57f7f857e0667be096bcc9763ab851e2131bf2f93982e64f12b5818076c1 |
#!/usr/bin/env python
import vtk
import numpy as np
from vmtk import vmtkscripts
from scipy.stats import skew
import argparse
import copy
# evaluate the inlet of the each case
def Execute(args):
print("get average along line probes")
cell_type = "point"
if(cell_type == "cell"):
vtk_process... | kayarre/Tools | vmtk/inlet_calculation.py | Python | bsd-2-clause | 3,775 | [
"VTK"
] | 9ad152d83201714f8b083754c772ce56b596b4250c566ac27cda9298eaa5461f |
# -*- coding: utf-8 -*-
"""The check functions."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD-3-Clause
import importlib
from builtins import input # no-op here but facilitates testing
from difflib import get_close_matches
from distutils.version import LooseVersion
import operator
imp... | pravsripad/mne-python | mne/utils/check.py | Python | bsd-3-clause | 29,299 | [
"Mayavi"
] | 46c935058e180baf50ffa39abfc91dfef5944524cffb21c10ebf1bcbdf6a503e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains classes to wrap Python VTK to make nice molecular plots.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "0.1"
__maintainer__ =... | mbkumar/pymatgen | pymatgen/vis/structure_vtk.py | Python | mit | 50,109 | [
"Jmol",
"VTK",
"pymatgen"
] | 5d76d8e063227906925e3dd4141bf4f1d4915c96e4eea50da420dc23d5ea1558 |
# Copyright (C) Brian Kelley 2021
#
# @@ 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.
#
"""
Free Wilson Analysis
A Mathematical Contribution to Struct... | ptosco/rdkit | Contrib/FreeWilson/freewilson.py | Python | bsd-3-clause | 21,559 | [
"Brian",
"RDKit"
] | d61c067ae75d78efc38b0b385fb19ac8e9314cb1755d6a236c2702e803e199ad |
from __future__ import division
from __future__ import print_function
from builtins import str
from builtins import range
from scipy import signal
from scipy.stats import uniform, norm
import numpy as np
import seaborn as sns
import matplotlib.mlab as ml
import matplotlib.pyplot as plt
from sima import spikes
######... | jzaremba/sima | examples/spikeinference.py | Python | gpl-2.0 | 4,351 | [
"Gaussian"
] | e98828b4ab2bb044afc2ae6929df8e77f44a16a1ef458bf02e21caf0cc34f784 |
# (c) 2014, Brian Coca, Josh Drake, et al
#
# 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 version.
... | hfinucane/ansible | lib/ansible/plugins/cache/jsonfile.py | Python | gpl-3.0 | 5,314 | [
"Brian"
] | a963f30a1da1daa125d7a73c60456e2984d7e4e06aa137f58d6ca69c57d80cf4 |
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