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# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
import os
from logging import getLogger
from django.conf import settings
from lettuce import step, world
from nose.tools import assert_in, assert_true
from selenium.webdriver.common.keys import Keys
from student import auth
from student.model... | BehavioralInsightsTeam/edx-platform | cms/djangoapps/contentstore/features/common.py | Python | agpl-3.0 | 12,703 | [
"VisIt"
] | 0ce7e37eb701f89c8d76a01a0d20efe1b1511f61436441fb7ae9c99d1a65aff3 |
# -*- coding: utf-8 -*-
#
# Firefly documentation build configuration file, created by
# sphinx-quickstart on Tue Feb 16 13:22:41 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# A... | Firefly-Automation/Firefly | docs/conf.py | Python | apache-2.0 | 9,258 | [
"Firefly"
] | a7f85df5e77fd1268b3b587630ca3d0825ae8320b12720d193fc6132c137bd92 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | src/commoncode/codec.py | Python | apache-2.0 | 5,524 | [
"VisIt"
] | 2b33272d27c55cee42d2e5cbc1b14c6d9612109dd6d7a8d7966dd57aeebee277 |
import residue_sidechains as res_scs
import read_amber_prmtop as amber
import chirality as chir
import networkx as nx
def res_atom_graph(molecule_graph, residues):
"""returns the graph of atoms in residues
:param molecule: molecule containing residue and atom graphs
:type molecule: amber.Molecule
:pa... | khs26/rotamer_library | rotamer/topology/identify_residue.py | Python | mit | 3,770 | [
"Amber"
] | 9dc41c6a45fe9758884fee5bd124aa5b7582f58a258bbf71715d1e7480dce1f2 |
# -*- coding: utf-8 -*-
#
# Ray documentation build configuration file, created by
# sphinx-quickstart on Fri Jul 1 13:19:58 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... | robertnishihara/ray | doc/source/conf.py | Python | apache-2.0 | 14,389 | [
"VisIt"
] | 1f074ae5992e707ffa797aecafd6b9be1e8325a9f618fadd1795c5a4cc99950e |
# $Id$
#
# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" unit testing code f... | rdkit/rdkit-orig | rdkit/DataStructs/UnitTestcBitVect.py | Python | bsd-3-clause | 10,915 | [
"RDKit"
] | 6269788acdb9d38d87b221a21c9d68226c44c4bfdef00fa14ec5a0ca8a42eef2 |
#!/usr/bin/env python
"""
This is a simple installation script for casual users of pymatgen who simply
plan to use pymatgen as a basic analysis library and is not planning to
develop on it. This script should work on most Linux and Mac systems that
have Python 2.7+ installed and setuptools installed. These are the onl... | migueldiascosta/pymatgen | docs/_static/pmg_install.py | Python | mit | 6,875 | [
"ASE",
"pymatgen"
] | 7b302ec03a2f66aa43c0301e1ce8f4189aee9204d4062889a9d6589a9f3b9800 |
# Language translations
text = {
# Main menu
'Select a mod': {
'en': 'Select a mod',
'fr': 'Sélectionnez un mod',
'es': 'Selecciona un mod',
'ru': 'Выбрать мод',
},
'Miscellaneous Stuff': {
'en': 'Miscellaneous Stuff',
'fr': 'Divers',
'es': 'Opcion... | Zamiell/isaac-racing-mods | program/languages.py | Python | gpl-3.0 | 9,254 | [
"VisIt"
] | b050f09bdadd177cae076c710772bf0fd56a66d500495d721e1df544156d6bfe |
import numpy
def acg(N):
""" approximated confined gaussian window of support N;
https://en.wikipedia.org/wiki/Window_function#Confined_Gaussian_window
"""
# sigma = 1.0
s = 1.0
# edge
A = (N - 1) / 2.0
x = numpy.linspace(0, N * 0.5, 8192, endpoint=True)
y = x + A
def G(y... | rainwoodman/pypm | makeacg.py | Python | gpl-3.0 | 2,115 | [
"Gaussian"
] | 7fdb69b83ea533bd783a624037fdb714794eddf85f83f2b33a75fd85c7f4a6d5 |
#!/usr/bin/env python
import sys
sys.path.append( '.' )
from optparse import OptionParser
from sfepy.mesh.mesh_generators import gen_cylinder_mesh
from sfepy.discrete.fem.meshio import MeshIO
usage = """%prog [options]
Cylinder mesh generator.
"""
help = {
'filename' :
'output file name [default: %default]',
... | RexFuzzle/sfepy | script/cylindergen.py | Python | bsd-3-clause | 4,144 | [
"VTK"
] | 02abf592717e8053098b392442f9b2b405e1cfe8c16179a3d30405a01b5d5bfd |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string, optparse, subprocess
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 = ['name','version','moduleid','desc... | dbankier/TiLogCatcher | ios/build.py | Python | mit | 8,766 | [
"VisIt"
] | 5d79b35623eae140b28fbfd78e0f2655e1bd5272ee91cee86752c5e71a494ab1 |
from ase.constraints import FixAtoms
from ase.io import read
from ase.thermochemistry import HarmonicThermo
from ase.vibrations import Vibrations
from espresso import espresso
from espresso.vibespresso import vibespresso
##################################################################################################... | brohr/brohr.github.io | ASE/Transition_States/run_freq.py | Python | gpl-2.0 | 3,757 | [
"ASE",
"ESPResSo"
] | ae5f0e9e19e98341069dae943987bb675dc9eece7a46fe7b06a4404c2aab0b0a |
# -----------------------------------------------------------------------------
# User configuration
# -----------------------------------------------------------------------------
outputDir = '/Volumes/KSW-Data/tonic/mpas-contours-sorted-composite/'
inputFile = '/Volumes/KSW-Data/Data/DataExploration/Data/MPAS/data/x... | Kitware/tonic-data-generator | scripts/paraview/mpas/earth-contours-sorted-composite.py | Python | bsd-3-clause | 5,301 | [
"ParaView",
"VTK"
] | ff4eb976361f7a33641d69ad3d3feafa83c1635d57e8d3ea3bfc5820c906f81b |
import cv2
import numpy as np
from matplotlib import pyplot as plt
# inpired by: http://opencv-python-tutroals.readthedocs.io/en/latest/py_tutorials/py_imgproc/py_canny/py_canny.html
def show_colour_transforms():
for flag in [i for i in dir(cv2) if i.startswith('COLOR_')]:
if flag.startswith('COLOR_BGR')... | EC-software/EC_stuff | imagine/opencv_fun.py | Python | gpl-2.0 | 6,098 | [
"Gaussian"
] | ffe2686272d2f5f064e329a75db98b1c5bef5ac14740f172bf44fffc14278dd9 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-parameters
# Author : Stuart Paterson
########################################################################
"""
Retrieve parameters associated to the given DIRAC job
Example:
$ dirac-wms-job-p... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_job_parameters.py | Python | gpl-3.0 | 1,972 | [
"DIRAC"
] | a1807d4e070a3e6c7d7ad7442aacf038af7148eadec8cdf3032b7652cb2da19c |
# -*- coding: utf8 -*-
# LaTeX math to Unicode symbols translation dictionaries.
# Generated with ``write_tex2unichar.py`` from the data in
# http://milde.users.sourceforge.net/LUCR/Math/
# Includes commands from: wasysym, stmaryrd, mathdots, mathabx, esint, bbold, amsxtra, amsmath, amssymb, standard LaTeX
mathaccen... | superdesk/Live-Blog | documentor/libraries/docutils-0.9.1-py3.2/docutils/math/tex2unichar.py | Python | agpl-3.0 | 34,480 | [
"Bowtie"
] | 804a16f261c0f9a63d8839405cdd299bc1fe792ecdd20dcf2a0d93a247bf63e2 |
# Copyright 2015 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 a... | 4Quant/tensorflow | tensorflow/models/image/cifar10/cifar10.py | Python | apache-2.0 | 13,637 | [
"Gaussian"
] | dec283074eb411598ddd81ec8a4bca6fec0c2c18871a84224224311579a6293e |
import logging
import httplib
import httplib2
import os
import random
import sys
import time
from apiclient.discovery import build
from apiclient.errors import HttpError
from apiclient.http import MediaFileUpload
from oauth2client.client import flow_from_clientsecrets
from oauth2client.file import Storage
from oauth2... | sandeepraju/git-talk | gittalk/upload.py | Python | bsd-3-clause | 7,092 | [
"VisIt"
] | 05b27898be6a93f68829c6a4b55c11f5af077367ca0fcf34c09441d1d5b67625 |
#generic python modules
import argparse
import operator
from operator import itemgetter
import sys, os, shutil
import os.path
##########################################################################################
# RETRIEVE USER INPUTS
###############################################################################... | jhelie/ff_contacts_sizes | ff_contacts_sizes.py | Python | gpl-2.0 | 39,696 | [
"MDAnalysis"
] | e4a88dc93f889b69150c14aca90665c9fb5ac56c8969bfdd9de6ebde22f9d66c |
#! /usr/bin/env python3
from vasppy.summary import potcar_spec
import argparse
def parse_command_line_arguments():
parser = argparse.ArgumentParser( description='Generate POTCAR specification based on hashing individual pseudopotential strings' )
parser.add_argument('potcar', help="filename of the VASP POTCAR... | bjmorgan/vasppy | vasppy/scripts/potcar_spec.py | Python | mit | 953 | [
"VASP"
] | 425fb62750c867384a122e41586c52d9d73c197b313fa7f6adbb4c2a81be24a4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010 Radim Rehurek <radimrehurek@seznam.cz>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Module for Latent Semantic Analysis (aka Latent Semantic Indexing) in Python.
Implements fast truncated SVD (Singular Value Decomp... | zachmayer/gensim | gensim/models/lsimodel.py | Python | lgpl-2.1 | 34,983 | [
"Gaussian"
] | 24dd8507419b6384b2d49840fbee588d5168f0ac2c0f17727778d0fc58da360b |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/web/movietags.py | Python | gpl-2.0 | 5,108 | [
"VisIt"
] | a92b4f99e0c1a419e70419480bad5aabc5556bc519e0659ed3b34bcc2b6dfefe |
import libtcodpy as libtcod
import random
class RoomAddition:
'''
What I'm calling the Room Addition algorithm is an attempt to
recreate the dungeon generation algorithm used in Brogue, as
discussed at https://www.rockpapershotgun.com/2015/07/28/how-do-roguelikes-generate-levels/
I don't think Brian Walker has e... | AtTheMatinee/Roguelike-Core | dungeonGeneration.py | Python | mit | 18,166 | [
"Brian"
] | 01b9d69e0dd59d57b9d69391c2d988a561ffd2d5fac9aa0114c4741c48ae7767 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
"""Classes that deal with macromolecular crystal structures.
Includes: PDB and mmCIF pars... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/PDB/__init__.py | Python | gpl-2.0 | 2,126 | [
"Biopython",
"CRYSTAL"
] | 230f8be6943c511ef85009d60b2d2c51eb14f4c6ab6cf6687a1a7cca7d7e0a52 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. 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
#
# U... | sunqm/pyscf | pyscf/mcscf/mc1step_symm.py | Python | apache-2.0 | 6,498 | [
"PySCF"
] | ec4c7d098057d05836e81ed1c477d092ead54266b6223cb767d5d02535de8cf9 |
# -*- coding:utf-8 -*-
# @author xupingmao
# @since 2016/12
# @modified 2022/02/07 13:04:50
import profile
import math
import re
import web
import xauth
import xutils
import xconfig
import xtables
import xtemplate
import xmanager
import os
from web import HTTPError
from xconfig import Storage
from xutils import History... | xupingmao/xnote | handlers/note/note_view.py | Python | gpl-3.0 | 14,848 | [
"VisIt"
] | dfc66b763524feb67060f35d4c07ea946de137e8b02811a7cc4400210808f810 |
"""The suite of window functions."""
from __future__ import division, print_function, absolute_import
import warnings
import numpy as np
from scipy import fftpack, linalg, special
from scipy._lib.six import string_types
__all__ = ['boxcar', 'triang', 'parzen', 'bohman', 'blackman', 'nuttall',
'blackmanhar... | yuanagain/seniorthesis | venv/lib/python2.7/site-packages/scipy/signal/windows.py | Python | mit | 54,134 | [
"Gaussian"
] | c11d8ff6d985498cea08d72975a356642cd2238052536833b0ecc02d522dcfaa |
"""
Records who we trust to sign feeds.
Trust is divided up into domains, so that it is possible to trust a key
in some cases and not others.
@var trust_db: Singleton trust database instance.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall i... | afb/0install | zeroinstall/injector/trust.py | Python | lgpl-2.1 | 3,217 | [
"VisIt"
] | cdc356ac7fe65cecb5570035e93cce28389723600c1f75a71f5d4bd864349ae5 |
""" Tools for using spherical harmonic models to fit diffusion data
References
----------
Aganj, I., et. al. 2009. ODF Reconstruction in Q-Ball Imaging With Solid
Angle Consideration.
Descoteaux, M., et. al. 2007. Regularized, fast, and robust analytical
Q-ball imaging.
Tristan-Vega, A., et. al. 2010. A new me... | samuelstjean/dipy | dipy/reconst/shm.py | Python | bsd-3-clause | 29,921 | [
"DIRAC"
] | b8e6544456dbbd32d7718ac408d6316d72c8aad021bd98e0ea8395c802a28060 |
# Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![Latest Version]
(h... | olof/svtplay-dl | versioneer.py | Python | mit | 67,775 | [
"Brian"
] | 17dddbb4d1f5149fbc3b552bb5bd2328e9cf8661e04154d8ed37e0b48a2002af |
'''
python module for ASE2-free and Numeric-free dacapo
U{John Kitchin<mailto:jkitchin@andrew.cmu.edu>} December 25, 2008
This module supports numpy directly.
* ScientificPython2.8 is required
- this is the first version to use numpy by default.
see https://wiki.fysik.dtu.dk/stuff/nc/ for dacapo netcdf variable
d... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/calculators/jacapo/jacapo.py | Python | gpl-2.0 | 152,002 | [
"ASE",
"Gaussian",
"NetCDF"
] | 0d3fdbd26f988fda2d553befb65a95bcbbfe06a74dc45f5fe75e84f533aeaf4d |
"""Cluster based on RMSD between conformations
{{header}}
Meta
----
depends:
- meta.pandas.pickl
- trajs
- top.pdb
"""
import mdtraj as md
from msmbuilder.io import load_meta, itertrajs, save_trajs, preload_top
## Load
meta = load_meta()
centroids = md.load("centroids.xtc", top=preload_top(meta))
## Kernel
S... | mpharrigan/mixtape | msmbuilder/project_templates/landmarks/featurize.py | Python | lgpl-2.1 | 646 | [
"MDTraj"
] | 4ab328bf627a061ce95799a94a1bbe1387cd4327eac0c6d499e29f4028cdc386 |
# -*- coding: utf-8 -*-
#
# This file is part of INSPIRE.
# Copyright (C) 2014-2017 CERN.
#
# INSPIRE 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 ... | inspirehep/inspire-schemas | tests/unit/test_reference_builder.py | Python | gpl-2.0 | 33,261 | [
"Brian"
] | 7974e9035281a32631caf6ea446f4d2d1efdd783b119fc607df13ba0a41a45f5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import os
from numbers import Number
from pymatgen.core.composition import Composition
from pymatgen.core.periodic_table import Element
from pymatgen.p... | migueldiascosta/pymatgen | pymatgen/phasediagram/tests/test_pdanalyzer.py | Python | mit | 5,104 | [
"pymatgen"
] | 4640f8da089df7bbb9c4c7d7e157620ba31a079e6ca3d94421127a3c2c270ab7 |
#
# Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" lazy generator of 2D pharm... | greglandrum/rdkit | rdkit/Chem/Pharm2D/LazyGenerator.py | Python | bsd-3-clause | 4,270 | [
"RDKit"
] | 720d6987d92a094702d73334115e251617aeaefb1990591c8e3a013bd172d59a |
# This class provides access to selected data from a trajectory
# via an interface that can be accessed remotely by Pyro. It
# can be used by programs that wish to inspect a trajectory that
# resides on a different machine.
#
# Written by Konrad Hinsen
# last revision: 2000-8-3
#
from Scientific.IO.NetCDF import NetCD... | fxia22/ASM_xf | PythonD/site_python/MMTK/Tools/TrajectoryViewer/TrajectoryInspector.py | Python | gpl-2.0 | 2,663 | [
"NetCDF"
] | 2ac8a06037fb749ab5c155b837ff58f2b6d21e83d958e36422f0466a1e4bd33b |
# Copyright (c) 2014 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""
This script is intended for use as a GYP_GENERATOR. It takes as input (by way of
the generator flag config_path) the path of a json file that dictates the file... | dreamllq/node | tools/gyp/pylib/gyp/generator/analyzer.py | Python | apache-2.0 | 23,439 | [
"VisIt"
] | 188d528ce5318e5d039f235b76dccc1f42ac5125301b2dadfcb7a047beb073de |
import os
import copy
import cPickle
import numpy as np
seed = np.random.randint(2**16)
# seed = 2958
seed = 60017
print "Seed: ", seed
if "DISPLAY" not in os.environ:
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from optofit.cneuron.compartment import Compartment, SquidCompartmen... | HIPS/optofit | examples/my_two_gp_demo.py | Python | gpl-2.0 | 20,290 | [
"Gaussian",
"NEURON"
] | fcc489bf07abffe31a4702fcd67f934d622051188462cb505d92ff0220933440 |
#!/usr/bin/env python
""" Enable using one or more Storage Elements
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base import Script
read = False
write = False
check = False
remove = False
site = ''
mute = False
Script.setUsageMessage("""
Enable using one or more Storage Elements
Usage:
%s SE1 [SE2 ...]
""... | andresailer/DIRAC | DataManagementSystem/scripts/dirac-admin-allow-se.py | Python | gpl-3.0 | 6,499 | [
"DIRAC"
] | 037e8fb63c03c24e80fb62eb11c8dafa8cb7050ae558e22a5639ac7ad512cf0e |
from __future__ import division
import numpy as np
from pyhsmm.internals.hmm_states import HMMStatesPython, HMMStatesEigen
from pyhsmm.internals.hsmm_states import HSMMStatesPython, HSMMStatesEigen, \
GeoHSMMStates
from autoregressive.util import AR_striding
from pylds.lds_messages_interface import filter_and_sam... | fivejjs/pyhsmm-slds | pyslds/states.py | Python | mit | 3,637 | [
"Gaussian"
] | 27e7319ac33d7e32743d002de316708839e349e5d44658bd3e67006874fc1f1d |
########################################################################
# $Id$
# File : TorqueComputingElement.py
# Author : Stuart Paterson, Paul Szczypka
########################################################################
""" The simplest Computing Element instance that submits jobs locally.
"""
__RCSID__ =... | calancha/DIRAC | Resources/Computing/TorqueComputingElement.py | Python | gpl-3.0 | 11,733 | [
"DIRAC"
] | 1a2fda22a4cfdd7404e28c7b3ae62e2f676822c56689919dee9ec7959fd73fdb |
from ..utils import floor_threshold, Timing
from ..utils import shuffle as shuffle_data
from multiprocessing import cpu_count
import pandas as pd
import numpy as np
from msmbuilder.featurizer import (AlphaAngleFeaturizer, ContactFeaturizer,
DihedralFeaturizer)
class BaseMetric(ob... | msmbuilder/mdentropy | mdentropy/metrics/base.py | Python | mit | 5,007 | [
"MDTraj"
] | 58bb85d06caf1f85a5987ca179a0b228015b6ead78bdd1fab0fcaf2f88a2ccce |
#!/usr/bin/python
# Copyright (C) 2012-2015 ASTRON (Netherlands Institute for Radio Astronomy)
# P.O. Box 2, 7990 AA Dwingeloo, The Netherlands
#
# This file is part of the LOFAR software suite.
# The LOFAR software suite is free software: you can redistribute it and/or
# modify it under the terms of the GNU Genera... | jjdmol/LOFAR | LTA/ltastorageoverview/lib/scraper.py | Python | gpl-3.0 | 16,943 | [
"VisIt"
] | afa8e14cde7e1b5aec3457a1bd807c707f00042e2b91cb73fe134b795e5eb182 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | testsuite/python/lb_boundary_velocity.py | Python | gpl-3.0 | 2,102 | [
"ESPResSo"
] | 9e2a6bccaea12ae1465ee7a874d1e0d93caa1ca92cfe7d90a0fbf5704174d474 |
# -*- coding: utf-8 -*-
"""testowyl -- some tests for owyl.
Copyright 2008 David Eyk. All rights reserved.
$Author$\n
$Rev$\n
$Date$
"""
__author__ = "$Author$"[9:-2]
__revision__ = "$Rev$"[6:-2]
__date__ = "$Date$"[7:-2]
import unittest
import owyl
from owyl import blackboard
class OwylTests(unittest.TestCase):... | Gaboose/owyl | tests/testowyl.py | Python | bsd-3-clause | 17,101 | [
"VisIt"
] | e2f1a3b0311e45804652d202bc7f251dff2b6592b2cd0d85356d051883546ec1 |
import numpy as np
import unittest
import datetime
import pytest
from laserchicken import utils, test_tools, keys
from laserchicken.utils import fit_plane
from time import time
class TestUtils(unittest.TestCase):
def test_GetPointCloudPoint(self):
""" Should not raise exception. """
pc = test_tools... | eEcoLiDAR/eEcoLiDAR | laserchicken/test_utils.py | Python | apache-2.0 | 11,259 | [
"Gaussian"
] | 314efbbcb5042e5166a28dd742f07293c43dffc9734ddbae0a79e6c12146ad88 |
"""Test PAC methods."""
import numpy as np
from tensorpac.methods.meth_switch import get_pac_fcn, pacstr
from tensorpac.methods.meth_surrogates import compute_surrogates, normalize
from tensorpac.methods.meth_pp import preferred_phase
from tensorpac.methods.meth_erpac import erpac, ergcpac, _ergcpac_perm
n_pac_range =... | EtienneCmb/tensorpac | tensorpac/methods/tests/test_pac_methods.py | Python | bsd-3-clause | 4,223 | [
"Gaussian"
] | 494b145dd13a8409482439a3baffa1cc3d1ec9d5b12019b2cc21c9012bb93134 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2007 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Softw... | tiagocardosos/stoq | stoqlib/gui/editors/tilleditor.py | Python | gpl-2.0 | 16,970 | [
"VisIt"
] | 17726217b4ada8c65e98badba0b053269f7f85ff048992808fe344f69755f7f3 |
# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Robert Layton <robertlayton@gmail.com>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Philippe Gervais <philippe.gervais@inria.fr>
# Lars Buitinck
... | bnaul/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 68,070 | [
"Gaussian"
] | ff09781c14ce5e0be22a237253f674d6b29524211c733b9450c602492b3a34b3 |
#!/usr/bin/env python
from setuptools import setup, find_packages
def get_install_reqs():
install_reqs = []
with open('requirements.txt') as f:
install_reqs.append(f.read().splitlines())
return install_reqs
def get_long_description():
with open('README.rst') as f:
desc = f.read()
... | lucaskolstad/rBCM | setup.py | Python | bsd-3-clause | 1,370 | [
"Gaussian"
] | c92845ad1e56ffbbc33f5c6a10499e17c05767b5cc8d832639d2810d1630dd9f |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import unittest
import pbtest
class ServiceWorkersTest(pbtest.PBSeleniumTest):
"""Verifies interaction with sites that use Service Worker caches"""
def get_tab_data_domains(self):
domains = self.js(
"let tabData = chrome.extension.getBackgro... | EFForg/privacybadgerchrome | tests/selenium/service_workers_test.py | Python | gpl-3.0 | 1,827 | [
"VisIt"
] | 2794caa15d4140e8cd3d1cf2e7b041302eb4ce95ad03c2ac8cd38c0a01b3b09d |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2014 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permission to us... | SystemsBioinformatics/stochpy | stochpy/core2/PyscesCore2.py | Python | gpl-3.0 | 50,226 | [
"PySCeS"
] | 2b951edbe9ea3ca160a051123d03d6f820d9edc4055b2103c7d6fedd79807b36 |
#!/usr/bin/python
import os,random
from math import pi,sqrt
def crossprod(vec1,vec2):
vector = [vec1[1]*vec2[2]-vec1[2]*vec2[1],-(vec1[0]*vec2[2]-vec1[2]*vec2[0]),vec1[0]*vec2[1]-vec1[1]*vec2[0]]
return vector
def dotprod(vec1,vec2):
vector = vec1[0]*vec2[0]+vec1[1]*vec2[1]+vec1[2]*vec2[2]
r... | msg-byu/enumlib | support/unclefuncs.py | Python | mit | 26,160 | [
"VASP"
] | 9a83b0179acf704cc88cceec2353d31db19d0393aff2290e820640d27b2d17b4 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
]
operations = [
migrations.CreateModel(
name='ProductPurchase',
fields=[
('id', models.AutoFi... | dogukantufekci/supersalon | supersalon/purchases/migrations/0001_initial.py | Python | bsd-3-clause | 1,157 | [
"VisIt"
] | 89ffa7cba3784f3f73083c6972c1a9c3c30f2a08be603704393b9244060a18a7 |
"""rbf - Radial basis functions for interpolation/smoothing scattered Nd data.
Written by John Travers <jtravs@gmail.com>, February 2007
Based closely on Matlab code by Alex Chirokov
Additional, large, improvements by Robert Hetland
Some additional alterations by Travis Oliphant
Permission to use, modify, and distrib... | teoliphant/scipy | scipy/interpolate/rbf.py | Python | bsd-3-clause | 8,919 | [
"Gaussian"
] | c5ab68b7f9b25e063a8f123cd0bbe93a880a9d504a0bc7b0bcef41965b802319 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2010 Nick Hall
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of th... | beernarrd/gramps | gramps/plugins/tool/ownereditor.py | Python | gpl-2.0 | 7,196 | [
"Brian"
] | 502b85647ff8def3dadb88a9fe3afa644f68a94e48381bae8fbeae24f714ab7b |
'''
Compiler.py
Translate AST to Mara Bytecode.
'''
import node
import scope
import special
import constant
from util.dispatch import method_store, multimethod
from util.functions import unique_id
from util.reflection import deriving
class CompileError(Exception, deriving('eq', 'show')):
def __init__(self, msg,... | dacjames/mara-lang | bootstrap/mara/compiler.py | Python | mit | 9,149 | [
"VisIt"
] | 8688f5cecc43cac5375ff46f873671d9db461f1c6f22cbaaef9bc8ab98b912e4 |
#!/usr/bin/env jython
# copyright 2002 the Brothers Wilcox
# <mailto:zooko@zooko.com>
#
# This file is part of OvP.
#
# OvP is open source 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 Lic... | zooko/ogresvpixies | CAvCAPieces.py | Python | gpl-2.0 | 10,331 | [
"VisIt"
] | 5bb386c5de09ad16c95002502840fdf8b8e7a77e0edb154e9ab5c8bcbbe4a8a8 |
""" InfoGetter
Module used to map the policies with the CS.
"""
import copy
from DIRAC import S_OK, S_ERROR, gConfig, gLogger
from DIRAC.ResourceStatusSystem.Utilities import RssConfiguration, Utils
__RCSID__ = '$Id: $'
def getPoliciesThatApply( decisionParams ):
"""
Method... | Andrew-McNab-UK/DIRAC | ResourceStatusSystem/Utilities/InfoGetter.py | Python | gpl-3.0 | 9,530 | [
"DIRAC"
] | a002041374ca5ab9c8bb038abd7561552bd7e369b832abadccaab6e27c34ba71 |
__author__ = 'AndriiLab'
""" Script calculates ratio between two channels ch1/ch2 from image series.
Next it compares two group of series (e.g. two proteins) and
out xls file with results of comparison and graphs with plotted data"""
import cv2
import glob
from matplotlib import pyplot
import numpy
from openpyxl imp... | AndriiLab/ImageAnalysisScripts | ratioBetweenTwoChannelsBetweenTwoProteins.py | Python | gpl-2.0 | 6,715 | [
"Gaussian"
] | cde94eb394d05305f490d3d5e890b850c70c4d19e387eaaa11826c85aa9bcff8 |
import random
import string
from django.db import transaction
from django.shortcuts import render, redirect
import haikunator
from .models import Room
def about(request):
return render(request, "chat/about.html")
def new_room(request):
"""
Randomly create a new room, and redirect to it.
"""
new_ro... | cloud-fire/signalnews | chat/views.py | Python | bsd-3-clause | 1,271 | [
"VisIt"
] | 8209cc99bb920d64c51cd57640c5984cd2b942ddd2e2f744b6fa3150b6937fed |
#!/usr/bin/env python
'''
CREATED:2014-01-17 16:30:07 by Brian McFee <brm2132@columbia.edu>
Compute hierarchical segmentation evaluation metrics
Usage:
./segment_hier_eval.py -r TRUTH_LEVEL1.TXT [TRUTH_LEVEL2.TXT ...] \
-e PREDICTION_LEVEL1.TXT [PREDICTION_LEVEL2.TXT ...] \
... | bmcfee/mir_eval | evaluators/segment_hier_eval.py | Python | mit | 3,231 | [
"Brian"
] | 8a469f67db325651acc2d085c9f4c33d616b33119efd6d2433d97e6006364fba |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('visits', '0002_auto_20151112_1103'),
]
operations = [
migrations.RemoveField(
model_name='visit',
na... | dogukantufekci/supersalon | supersalon/visits/migrations/0003_auto_20151112_1121.py | Python | bsd-3-clause | 701 | [
"VisIt"
] | 7d9e2d5d8ac8da7a152bfbfb2aaab6a2fac246f1cec79ed69f806484fe7b02a4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import urllib2
import random
from flask import Flask, request, redirect
import combos
app = Flask(__name__)
def valid_link_from(dirty_link):
link = urllib2.unquote(dirty_link)
if urllib2.urlparse.urlparse(link).scheme is '':
link = 'http://' + link
... | weeezes/ComboURL | main.py | Python | mit | 1,139 | [
"VisIt"
] | 3dec046da5ed8a5e4a7705df5cdd667959a77840c09022ddeb43b4d1239e46b0 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
lttree_check.py
The original template file format supports any... | CFDEMproject/LAMMPS | tools/moltemplate/src/lttree_check.py | Python | gpl-2.0 | 126,637 | [
"LAMMPS"
] | 29710d144a53c6745f48ff59a04697ee14fee5628c12b24659d2927fa8608867 |
"""
Core visualization operations based on PyVista.
Actual implementation of _Renderer and _Projection classes.
"""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
# Joan Massich <mailsik... | Teekuningas/mne-python | mne/viz/backends/_pyvista.py | Python | bsd-3-clause | 33,533 | [
"Mayavi",
"VTK"
] | d8b55e2c19afe5932d3187bbb0c20f53d152bb01fa65acb8f80d11e884f86339 |
#!/usr/bin/env python
"""
manipulate meteadata in the FileCatalog
"""
import os
import DIRAC
from DIRAC import S_OK, S_ERROR
from COMDIRAC.Interfaces import critical
from COMDIRAC.Interfaces import DSession
from COMDIRAC.Interfaces import DCatalog
from COMDIRAC.Interfaces import pathFromArgument
class DMetaCommand... | pigay/COMDIRAC | Interfaces/scripts/dmeta.py | Python | gpl-3.0 | 5,307 | [
"DIRAC"
] | f0d320941e86a282c2f7a35e5a5b5728f4ffbc1d10adf263371cde1db315f827 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
# Copyright (c) 2016 Mikkel Schubert <MikkelSch@gmail.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without ... | MikkelSchubert/paleomix | paleomix/pipelines/zonkey/database.py | Python | mit | 23,270 | [
"pysam"
] | 3dd42581e396a987de384202bed36725cb385c8439e7560dcc666016500ffd6e |
# coding=utf-8
from ._commandbase import RadianceCommand
from ..parameters.gendaymtx import GendaymtxParameters
import os
class Gendaymtx(RadianceCommand):
u"""
gendaymtx - Generate an annual Perez sky matrix from a weather tape.
Attributes:
output_name: An optional name for output file name. If... | ladybug-analysis-tools/honeybee | honeybee_plus/radiance/command/gendaymtx.py | Python | gpl-3.0 | 4,211 | [
"EPW"
] | 5724472c8469d4d455c805316fb2387c14ef8f0aaab5fff47447ba162a613cee |
#
# QAPI command marshaller generator
#
# Copyright IBM, Corp. 2011
# Copyright (C) 2014-2015 Red Hat, Inc.
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
# Michael Roth <mdroth@linux.vnet.ibm.com>
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
#... | mtottenh/QEMU-TPM | scripts/qapi-commands.py | Python | gpl-2.0 | 7,801 | [
"VisIt"
] | 921cebd0b42f664a5800c927e4131fe76cdd4b79d1094c5cf74854c40a31115d |
"""Experimental code for cleaner support of IPython syntax with unittest.
In IPython up until 0.10, we've used very hacked up nose machinery for running
tests with IPython special syntax, and this has proved to be extremely slow.
This module provides decorators to try a different approach, stemming from a
conversation... | Foxfanmedium/python_training | OnlineCoursera/mail_ru/Python_1/env/Lib/site-packages/IPython/testing/ipunittest.py | Python | apache-2.0 | 6,429 | [
"Brian"
] | 26cd16be2358f0bff5e24ee07e4b564e656670e6582b0d9518164c6cd9581d8f |
# see http://blog.sigfpe.com/2012/03/overloading-python-list-comprehension.html
from ast import *
import sys
class RewriteComp(NodeTransformer):
def visit_func(self, node):
print dump(node)
return node
def visit_Str(self, node):
print dump(node)
namenode = Name(id="FreeString"... | pipcet/py-antistring | antistring.py | Python | gpl-2.0 | 746 | [
"VisIt"
] | b248d3518887abbd72e7ac5e89ebab4a5264c16efb6d4910432011b6197e41c4 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the gating feature.
"""
from __future__ import absolute_import
from textwrap import dedent
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.accepta... | jolyonb/edx-platform | common/test/acceptance/tests/lms/test_lms_gating.py | Python | agpl-3.0 | 12,079 | [
"VisIt"
] | 445e914ef3b2e3c38f7ba94f47f490368a66673ef97667a00b1354a373f8309d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import pickle
import collections
from pymatgen.core.periodic_table import Element, Specie, DummySpecie, \
PeriodicTable, get_el_sp
from py... | sonium0/pymatgen | pymatgen/core/tests/test_periodic_table.py | Python | mit | 12,650 | [
"pymatgen"
] | 5ee556c63ac24c99f480b173abc61fad6954ef69c94a0df0a69c74998000f563 |
# -*- coding: utf-8 -*-
"""
Models used to implement SAML SSO support in third_party_auth
(inlcuding Shibboleth support)
"""
from __future__ import absolute_import
import json
import logging
import re
import os
from config_models.models import ConfigurationModel, cache
from django.conf import settings
from django.con... | CredoReference/edx-platform | common/djangoapps/third_party_auth/models.py | Python | agpl-3.0 | 37,332 | [
"VisIt"
] | ac4d60a3eaa4e833391008aefa41feb67267dc3c15a3b3e9812d8324b064dd31 |
# This script will use the output from find_raster_path.py
# to generate a mosaic dataset.
# To run the gdal commands you first have to set the path and GDAL_DATA variable in environments.
# C:\Python27\Lib\site-packages\osgeo
# GDAL_DATA C:\Python27\Lib\site-packages\osgeo\data\gdal
from __future__ import print_func... | rmichie/PyScripts | Warp_Rasters.py | Python | apache-2.0 | 7,235 | [
"ADF"
] | bd296d945c7055d02daeec1d8c68764dbd526d59e56a916b45283b82bd839576 |
print("""
FEM simulation using getfem++ and siconos.
""")
import siconos.kernel as kernel
import getfemtosiconos as gts
import numpy as np
import getfem as gf
from matplotlib.pyplot import *
t0 = 0.0 # start time
T = 10.0 # end time
h = 0.005 # time step
g = 9.81 # gravity
e = 0.1 # restitution coef... | siconos/siconos-deb | examples/Mechanics/FEM/python/block_multi_inter.py | Python | apache-2.0 | 5,665 | [
"VTK"
] | a0672db77d9bfbcc17fb4a10386a320af04a5557e7e46d38f492e25641411e9f |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/topology/test_top.py | Python | gpl-2.0 | 2,633 | [
"MDAnalysis"
] | 2cfd846056ffe5dcc8ddbd9ceac917ca95ee15f1083f218a3b4e708b8d22418a |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2017 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | FarnazH/horton | horton/espfit/cost.py | Python | gpl-3.0 | 7,399 | [
"CRYSTAL"
] | e060b27ae802ed528f6af6f19a10eb60dc0acbfb4f6d5fc6a5736efa6e156440 |
nomes_list = [
"Aaren"
,
"Aarika"
,
"Abagael"
,
"Abagail"
,
"Abbe"
,
"Abbey"
,
"Abbi"
,
"Abbie"
,
"Abby"
,
"Abbye"
,
"Abigael"
,
"Abigail"
,
"Abigale"
,
"Abra"
,
"Ada"
,
"Adah"
,
"Adaline"
,
"Adan"
,
"Adara"
,
"Adda"
,
"Addi"
,
"Addia"
,
"Addie"
,
"Addy"
,
"Adel"
,
"Adela"
,
"Adelaida"
,
"Adelaide"
,
"Adele"
,
"Adelhei... | Pharaoh00/Pharaoh-Toolkit | 0.0.6/modulos/listas/nomesLista_First.py | Python | mit | 54,952 | [
"Amber",
"CRYSTAL",
"FLEUR"
] | 84c7cb3766ab30a22e849f5aef3aaa0a153047c6e26514c73cf4a7ea077400a4 |
"""Minimum mode follower for finding saddle points in an unbiased way.
There is, currently, only one implemented method: The Dimer method.
"""
import sys
import time
import warnings
import numpy as np
from ase.optimize.optimize import Optimizer
from math import cos, sin, atan, tan, degrees, pi, sqrt
from ase.paral... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/dimer.py | Python | gpl-2.0 | 45,632 | [
"ASE"
] | 6b40260669064c9fa61512e26cb57d087be79ca9cd5575ef7cf9a96373abbfff |
#!/usr/bin/python
#
# Copyright 2015 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... | cctaylor/googleads-python-lib | examples/adwords/v201506/campaign_management/validate_text_ad.py | Python | apache-2.0 | 2,880 | [
"VisIt"
] | 4442fa5ee2de8580cd44dcc8718a5c7aba599abedd4ea040de024b1c2407ad40 |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
"""
Miscellaneous tools used by OpenERP.
"""
from functools import wraps
import cProfile
from contextlib import contextmanager
import subprocess
import logging
import os
import passlib.utils
import socket
import sys
im... | allenp/odoo | openerp/tools/misc.py | Python | gpl-3.0 | 38,315 | [
"VisIt"
] | b0e65f3bfe9ed7afa1931b41d2bb118da5dbf6f8e39bd1d207a017d0c75e66f3 |
#!/usr/bin/env python3
# This Python file uses the following encoding: utf-8
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
from collections import Counter, OrderedDict
from pprint import pprint
from scipy.optimize import curve_fit
from kural import Thirukkural
from tamil.utf8 import get_letters,... | Ezhil-Language-Foundation/open-tamil | examples/kural_mathirai.py | Python | mit | 2,246 | [
"Gaussian"
] | 2a7ee0e94975108ab8dcb2b6909dcd623f73ec2f43f2eb8f2516174e0af429d0 |
__author__ = 'dalton'
_world = {}
starting_position = (0, 0)
def load_tiles():
"""Parses a file that describes the world space into the _world object"""
with open('resources/map.txt', 'r') as f:
rows = f.readlines()
x_max = len(rows[0].split('\t')) # Assumes all rows contain the same number of t... | dalrrard/text-adventure-tut | adventuretutorial/world.py | Python | mit | 758 | [
"Dalton"
] | a7e4162fb9c3f7695947d68a2ce66fd2ee4b61adc5844604f053af342ad502d7 |
# -*- coding: utf-8 -*-
"""
A VTK RenderWindowInteractor widget for wxPython.
Find wxPython info at http://wxPython.org
Created by Prabhu Ramachandran, April 2002
Based on wxVTKRenderWindow.py
Fixes and updates by Charl P. Botha 2003-2008
Updated to new wx namespace and some cleaning up by Andrea Gavana,
December 2... | florian-wagner/gimli | python/pygimli/gui/vtk/wxVTKRenderWindowInteractor.py | Python | gpl-3.0 | 24,830 | [
"VTK"
] | ea8805bb463b794bd7c28385379e1b49f46ef1264cb33a9227d9802f6b8deb9a |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/tree/tests/test_tree.py | Python | bsd-3-clause | 59,271 | [
"scikit-bio"
] | aed1df4471c79b018864933f5dc496f61f31c879bea7b511be6f65b5822022fc |
from brian import *
N = 300
v0 = 5 * mV
tau = 20 * ms
sigma = 5 * mV
vt = 10 * mV
vr = 0 * mV
g_gap = 1. / N
beta = 60 * mV * 2 * ms
delta = vt - vr
eqs = '''
dv/dt=(v0-v)/tau+g_gap*(u-N*v)/tau : volt
du/dt=(N*v0-u)/tau : volt # input from other neurons
'''
def myreset(P, spikes):
P.v[spikes] = vr # reset
P.... | mac389/gap-junctions | network.py | Python | apache-2.0 | 908 | [
"Brian"
] | 740ccd3b423ae7728040d84966a20d062b5ed948482ce510b9e868468f9a7523 |
from astn import AstToGAst, GAstToAst
import ast
import gast
class Ast2ToGAst(AstToGAst):
# stmt
def visit_FunctionDef(self, node):
new_node = gast.FunctionDef(
self._visit(node.name),
self._visit(node.args),
self._visit(node.body),
self._visit(node.dec... | ryfeus/lambda-packs | Tensorflow_Pandas_Numpy/source3.6/gast/ast2.py | Python | mit | 7,224 | [
"VisIt"
] | 436c7c69ab2d4a49c79b9c43fd0ed20ef7a6a1f55f05c2a01691c084f40ed329 |
# -*- coding: utf-8 -*-
"""Algorithms for spectral clustering"""
# Author: Gael Varoquaux gael.varoquaux@normalesup.org
# Brian Cheung
# Wei LI <kuantkid@gmail.com>
# License: BSD
import warnings
import numpy as np
from ..base import BaseEstimator, ClusterMixin
from ..utils import check_random_state,... | kmike/scikit-learn | sklearn/cluster/spectral.py | Python | bsd-3-clause | 19,078 | [
"Brian",
"Gaussian"
] | 2660862e4b45a388570837ed95ed72f6c5689b20f8c08a7206260fa234334b48 |
#!/usr/local/sci/bin/python
# PYTHON3
#
# Author: Kate Willett
# Created: 8 January 2016
# Last update: 6 April 2020
# Location: /data/local/hadkw/HADCRUH2/UPDATE2014/PROGS/PYTHON/
# GitHub: https://github.com/Kate-Willett/Climate_Explorer/PYTHON/
# -----------------------
# CODE PURPOSE AND OUTPUT
# ----------------... | Kate-Willett/Climate_Explorer | PYTHON/WriteNetCDF_CEDAESGF_JAN2016.py | Python | cc0-1.0 | 17,298 | [
"NetCDF"
] | df6ad994bcdaedba41b6bc42ed18a013cccb7b9d26089379ef2e40152b81534b |
"""Pre-processing module.
This module contains several pre-processing routines that can help
detect more patterns with PatternMatcher.
Classes included in this module are:
- ShiftToMult: transforms all left shifts of a constant in
multiplications
- SubToMult: transforms subs operator into + (-1)*
- NotToInv(): ... | quarkslab/sspam | sspam/pre_processing.py | Python | bsd-3-clause | 4,842 | [
"VisIt"
] | 4e26684b4383cba72d2741610a9609302976a04bc50be69c3febece11cff7dc6 |
#!/usr/bin/env python3
# Copyright (C) 2021
# Max Planck Institute for Polymer Research & JGU Mainz
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | espressopp/espressopp | testsuite/storage/testAddParticlesArray.py | Python | gpl-3.0 | 4,284 | [
"ESPResSo",
"Gaussian"
] | d872177800f15ecf2f5db612bb5f94e702f357ffa85d230bd81a47aedbe447f9 |
# BSD 3-Clause License
#
# Copyright (c) 2016-19, University of Liverpool
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notic... | fsimkovic/cptbx | conkit/io/a3m.py | Python | gpl-3.0 | 6,265 | [
"Biopython"
] | a3f54d386c72fa78c3bb8b879eea8eba09949fe93fe2cd36ac8ede76f927e95e |
from os import getcwd
from unittest import TestCase
from galaxy.jobs.command_factory import build_command
from galaxy.util.bunch import Bunch
MOCK_COMMAND_LINE = "/opt/galaxy/tools/bowtie /mnt/galaxyData/files/000/input000.dat"
TEST_METADATA_LINE = "set_metadata_and_stuff.sh"
TEST_FILES_PATH = "file_path"
class Tes... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/unit/jobs/test_command_factory.py | Python | gpl-3.0 | 6,344 | [
"Bowtie",
"Galaxy"
] | 03bf27c23d9f2b00cc7a4b3e1d1be27a457b36805a909fed849619268c7c8d8c |
import ocl
import pyocl
import camvtk
import time
import vtk
import datetime
import math
if __name__ == "__main__":
print(ocl.version())
myscreen = camvtk.VTKScreen()
#stl = camvtk.STLSurf("../stl/gnu_tux_mod.stl")
stl = camvtk.STLSurf("../stl/mount_rush.stl")
#stl = camvtk.STLSurf("../stl/... | aewallin/opencamlib | examples/python/drop-cutter/batchdropcutter_mtrush.py | Python | lgpl-2.1 | 2,392 | [
"VTK"
] | 74889aa453e7703557c641a1f4cb64aff046ca351f1709cc50ce122d08ee8d96 |
# (C) British Crown Copyright 2010 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | jswanljung/iris | lib/iris/tests/__init__.py | Python | lgpl-3.0 | 39,426 | [
"NetCDF"
] | 0d896e731f1874c8519fd8a0e4a99fe410b1c3d7e98fdd16ee04b53a8577ece3 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Created on Apr 28, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Apr 28, 2012"
import unittest
impo... | rousseab/pymatgen | pymatgen/io/tests/test_babelio.py | Python | mit | 2,167 | [
"Pybel",
"pymatgen"
] | e7ec0cb1fa8f15aef191a230292464b8ad8cd0005d107631efadfde60e2dd849 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import factory
reload(factory)
from factory import *
osVersions = [
'macosx',
# 'linux-arm',
'linux32',
'linux64',
'win32',
'win64'
]
@properties.renderer
def get_short_revision_mist(props):
if 'got_revision' in props:
return props['go... | ethereum/ethereum-buildbot | factories/mist.py | Python | mit | 6,168 | [
"GULP"
] | 9de4d5693eb6ea4223bf185783d0ad2496ae12e3262a149aec149292bff55795 |
# For details on how netCDF4 builds on HDF5:
# http://www.unidata.ucar.edu/software/netcdf/docs/file_format_specifications.html#netcdf_4_spec
import os.path
import warnings
import weakref
from collections import ChainMap, Counter, OrderedDict, defaultdict
from collections.abc import Mapping
import h5py
import numpy as... | shoyer/h5netcdf | h5netcdf/core.py | Python | bsd-3-clause | 40,898 | [
"NetCDF"
] | 4ad17e209b1f85a70eb973b2683e6b5d721d69ad30e11f7d536fb20daaf9d364 |
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