text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
# -*- coding: utf-8 -*-
#
# coral documentation build configuration file, created by
# sphinx-quickstart on Tue Sep 24 18:33:33 2013.
#
# 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... | klavinslab/coral | docs/conf.py | Python | mit | 8,577 | [
"Biopython"
] | e84a204c78ab504024dfe90c15183898c7b9dc48366d11cdc3b0cc481e05aac1 |
"""
Model construction from parse trees and the model API.
"""
import sys
import codecs
import traceback
from collections import OrderedDict
from arpeggio import Parser, Sequence, NoMatch, EOF, Terminal
from textx.exceptions import TextXSyntaxError, TextXSemanticError
from textx.const import MULT_OPTIONAL, MULT_ONE, M... | igordejanovic/textX | textx/model.py | Python | mit | 43,346 | [
"VisIt"
] | 35bf6e9197b5228058d9caaebd5fd62e1343a83f7a41763666a89287bf6197a9 |
#########################################################
# YAM(BO)PY(THON) Library
#
# Generation of Yambo input files using python
#
# Authors: A Molina-Sanchez, HPC Miranda
#
# January 2016
#########################################################
# Bethe-Salpeter spectra calculations at given times
# of a Real-... | alexmoratalla/yambopy | scripts/realtime/rt-bse.py | Python | bsd-3-clause | 4,179 | [
"Yambo"
] | 9797b04548ea5c05e206430966903686a7f765b34d6f39559944e481fdab1eab |
'''
Created on 02.03.2014
@author: bluesbreaker
'''
import re
import numpy
from lxml import etree
from CSUStAn.astng.inspector import ClassIRLinker
from CSUStAn.cross.duck_typing import DuckTypeHandler
from logilab.common.configuration import ConfigurationMixIn
from logilab.astng.inspector import IdGeneratorMixIn
fr... | exbluesbreaker/csu-code-analysis | logilab-astng XML Generator/src/CSUStAn/ucr/builder.py | Python | gpl-2.0 | 15,656 | [
"VisIt"
] | dffb345d97532690655949cd01afff439e7ad8b7bc7724f7c5e0a0a984c70af1 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/p4util/optproc.py | Python | gpl-2.0 | 4,749 | [
"Psi4"
] | 5b8d82d15699a3eb23c7b81bd7b609d6d7460689b21cff77a90021b9c59791e7 |
## Author: Christopher Bull.
## Affiliation: Climate Change Research Centre and ARC Centre of Excellence for Climate System Science.
## Level 4, Mathews Building
## University of New South Wales
## Sydney, NSW, Australia, 2052
## Contact: z3457920@student.unsw.edu.au
... | chrisb13/mkmov | commands/_twodbm.py | Python | gpl-3.0 | 3,231 | [
"NetCDF"
] | 5fc62aad586e22970f3c927a67cfa4625ddc7f93a3799e4e32e0d1f18e160f46 |
from numpy import *
import numpy as np
import itertools
import time
import sys
import cPickle as pickle
# Import NN utils
from nn.base import NNBase
from nn.math import softmax, sigmoid, sigmoidGrad,make_onehot
from nn.math import MultinomialSampler, multinomial_sample
from misc import random_weight_matrix
class RNN... | PDFangeltop1/cs224d | assignment2/assignment2/rnnlm.py | Python | mit | 14,285 | [
"Gaussian"
] | 87e9786a5bcd94f97d624b751736449ce3bfbb8da8ca83ded391a77e984fa19e |
#!/usr/bin/env python
import io
import netCDF4
import numpy
import m6plot
import m6toolbox
import matplotlib.pyplot as plt
import os
try: import argparse
except: raise Exception('This version of python is not new enough. python 2.7 or newer is required.')
def run():
parser = argparse.ArgumentParser(description='''... | nicjhan/MOM6-examples | tools/analysis/section_transports.py | Python | gpl-3.0 | 9,699 | [
"NetCDF"
] | 15684dd66b39d3bb1690173207e79541c8ab0c5ffac68ea6851b76fd7f967ec6 |
'''
Created on 2012-09-30
A simple script that reads a WRF netcdf-4 file and displays a 2D field in a proper geographic projection;
application here is plotting terrain height in the inner WRF domain.
@author: Andre R. Erler
'''
## includes
# matplotlib config: size etc.
import numpy as np
import matplotlib.pylab as... | aerler/WRF-Projects | src/archive/plotInnerDomain.py | Python | gpl-3.0 | 5,404 | [
"NetCDF"
] | 080b781315cd53d11f5eed34b301e422d3b863d4c17cd4276c6591e883844bdd |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-fix-mysql-script
# Author : Ricardo Graciani
########################################################################
"""
Fixes the mysql.server script, it requires a proper /LocalInstallation s... | Sbalbp/DIRAC | Core/scripts/dirac-fix-mysql-script.py | Python | gpl-3.0 | 957 | [
"DIRAC"
] | 4bc46c7c33b7c80053c75aa1e7f94fa172fbc242899942f3c83c1467b318af0d |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import plat... | nuclear-wizard/moose | python/TestHarness/util.py | Python | lgpl-2.1 | 29,229 | [
"MOOSE",
"VTK"
] | 6040348037b58ae8b1c4fbe4b9bc49c9dd695c0fb52fac35fb0415ae3338e706 |
# -*- coding: utf-8 -*-
#
# test_stdp_triplet_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 t... | SepehrMN/nest-simulator | pynest/nest/tests/test_stdp_triplet_synapse.py | Python | gpl-2.0 | 12,801 | [
"NEURON"
] | e8fd5eb30fc1a2e4af32cbc130ae8496761fbd1e47df8dbc178137418e7fbadb |
# script to use BioPython to parse taxonomy annotations for genbank file
from Bio import SeqIO
gbk_filename = "NC_005213.gbk"
faa_filename = "NC_005213_converted.fna"
input_handle = open(gbk_filename, "r")
output_handle = open(faa_filename, "w")
# Short version:
# SeqIO.write(SeqIO.parse(input_handle, "g... | jrherr/bioinformatics_scripts | python_scripts/gbk_to_fna.py | Python | mit | 819 | [
"Biopython"
] | f775471ea3827c4f64829d25d18ef4a155b8429311a257b9a403e2e98774153a |
"""Utilities for handling PDBQT files."""
from typing import Dict, List, Optional, Set, Tuple
from deepchem.utils.typing import RDKitMol
def pdbqt_to_pdb(filename: Optional[str] = None,
pdbqt_data: Optional[List[str]] = None) -> str:
"""Extracts the PDB part of a pdbqt file as a string.
Either ... | deepchem/deepchem | deepchem/utils/pdbqt_utils.py | Python | mit | 10,945 | [
"RDKit"
] | b89662d1360673ee42c1c45fc7981b8232f9510da58bcd280d20f6f8dd287147 |
import os
import tempfile
import unittest
from pyepw.epw import {{ obj.class_name }},{% for field in obj.fields %}{% if field.is_list %}{{field.object_name}} ,{% endif %}{% endfor %}EPW
class Test{{ obj.class_name }}(unittest.TestCase):
def setUp(self):
self.fd, self.path = tempfile.mkstemp()
def te... | rbuffat/pyepw | generator/templates/test_class.py | Python | apache-2.0 | 6,965 | [
"EPW"
] | 8d897d4ba78a956cb877a2da590a14590f04f4a343e8467157ad818190aa1fa6 |
########################################################################
# $HeadURL $
# File: OperationHandlerBaseTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/25 08:09:08
########################################################################
""" :mod: OperationHandlerBaseTests
==============... | avedaee/DIRAC | RequestManagementSystem/test/OperationHandlerBaseTests.py | Python | gpl-3.0 | 2,762 | [
"DIRAC"
] | 0e10c5793d61a4dcbc4d808d28f18ffc73c56dc03a79cecb164437898e3a57a5 |
# encoding: utf-8
# module PyKDE4.kio
# from /usr/lib/python2.7/dist-packages/PyKDE4/kio.so
# by generator 1.135
# no doc
# imports
import PyKDE4.kdeui as __PyKDE4_kdeui
import PyQt4.QtCore as __PyQt4_QtCore
import PyQt4.QtGui as __PyQt4_QtGui
from KBookmarkImporterBase import KBookmarkImporterBase
from KBookmarkGr... | ProfessorX/Config | .PyCharm30/system/python_stubs/-1247972723/PyKDE4/kio/KXBELBookmarkImporterImpl.py | Python | gpl-2.0 | 949 | [
"VisIt"
] | 5af4f59a9403d718e1668989824f2df9fad1655f2accde78a071dbd9bedcad6b |
"""Utilities
The module contains some commonly functions and classes.
"""
from __future__ import division
from functools import wraps
from bisect import bisect_right
from distutils.spawn import find_executable
from numpy import floor, ceil, round, arcsin, sin, pi, sqrt
from scipy.stats import norm
from progressbar ... | tomkooij/sapphire | sapphire/utils.py | Python | gpl-3.0 | 4,976 | [
"Gaussian"
] | 24c82bff14037c93d02d8f855979d0b5841157ec23a121a8fe40b8e6f87ecf31 |
"""
Helper functions for mlab. These combine creation of the data sources,
and applying the modules to them to make standard visualization
operation. They should always return the module object created, for
consistency, and because retrieving the vtk data source from a module object
is possible via tools.get_vtk_src
E... | dmsurti/mayavi | mayavi/tools/helper_functions.py | Python | bsd-3-clause | 40,264 | [
"Mayavi",
"VTK"
] | 0a76e8146d1871d0eebe12e69e15f60cae22bb1be80b5fb53810e2dc8550eccc |
# -*- coding: utf-8 -*-
# Copyright 2014-2016 The HyperSpyUI developers
#
# This file is part of HyperSpyUI.
#
# HyperSpyUI 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
#... | hyperspy/hyperspyUI | hyperspyui/_tools/gaussiantool.py | Python | gpl-3.0 | 6,376 | [
"Gaussian"
] | c7340d8603548a459a74926a47b23eabe81881d8f2dc6566d78666e2bd611e4f |
#!/usr/bin/env python
from brian import *
import neurotools as nt
duration = 1*second
N_sims = 3
lif_eq = ['dV/dt = (V_rest-V)/tau_mem : volt']
V_rest = 0*mV
V_reset = 0*mV
V_th = 10*volt # to study "threshold-free" potential
t_refr = 2*ms
tau_mem = 10*ms
N_in = [100, 100, 100]
f_in = [10*Hz, 10*Hz, 10*Hz]
DV_s = [0... | achilleas-k/brian-scripts | lif_mean_variance.py | Python | apache-2.0 | 2,070 | [
"Brian"
] | bc477fada51506954fdfaa431b4fb2c2292d48338090d12d43f3ba851e5093ff |
#!/usr/bin/env python
import os, datetime, sys
import nesoni
from nesoni import config
def cleanup(text):
lines = text.split('\n')
lines[0] = '<b style="font-size: 125%">'+lines[0].strip()+'</b>'
del lines[1]
return '\n'.join(lines)
VERSION = nesoni.VERSION
README = open('README','rb').read().... | Victorian-Bioinformatics-Consortium/nesoni | release.py | Python | gpl-2.0 | 15,318 | [
"Biopython"
] | 36d8da2e81da210d3d89b1f5a4d216c1f8721fbe834da0fece51b25e0d66b91f |
"""This file contains code used in "Think Stats",
by Allen B. Downey, available from greenteapress.com
Copyright 2010 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
import urllib
import myplot
import Pmf
results = 'http://www.coolrunning.com/results/10/ma/Apr25_27thAn_set1.shtml'
"""
S... | tjctw/PythonNote | thinkstat/relay.py | Python | cc0-1.0 | 2,054 | [
"Brian"
] | fe2d1631efcb0962206bb1870483d9dbf7ede29c7a80d5dcc5cf4a20e3178364 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# shell - advanced shell
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published ... | heromod/migrid | mig/shared/functionality/shell.py | Python | gpl-2.0 | 4,006 | [
"Brian"
] | b3a3a410be11b2b8cd7128343fed967bffab81dc4ee4e9238df5d0423949cb64 |
"""
Robust location and covariance estimators.
Here are implemented estimators that are resistant to outliers.
"""
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import warnings
import numbers
import numpy as np
from scipy import linalg
from scipy.stats import chi2
from . import empir... | shikhardb/scikit-learn | sklearn/covariance/robust_covariance.py | Python | bsd-3-clause | 29,613 | [
"Gaussian"
] | 2b03b116cb269a1233efb4d064baa0691aae2ae639bec73f8c6103fd6f5435af |
"""
Created on Sun Sep 10 22:06:46 2017
Converting from GSFLOW_print_controlfile4_gcng_melt30yr.m
Creates inputs files to run GSFLOW, based on the "Sagehen" example but
modified for Chimborazo's Gavilan Machay watershed. Crystal's AGU2016
poster.
GSFLOW Input files:
- control file (generate with GSFLOW_print_... | UMN-Hydro/GSFLOW_pre-processor | python_scripts/GSFLOW_print_controlfile4_gcng_melt30yr.py | Python | gpl-3.0 | 23,365 | [
"CRYSTAL"
] | c303b923b92716452c3f6ec390ca42d9a6445e85e35be501759486589c0bf973 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/py-espresso/package.py | Python | lgpl-2.1 | 2,351 | [
"ESPResSo"
] | 390b2b53c6045908f3244c8ed9f4d7752e683456217443f97983eef8de3c6baf |
"""Support for building and spinnaker releases."""
# pylint: disable=wrong-import-position
# These would be required if running from source code
SPINNAKER_RUNNABLE_REPOSITORY_NAMES = [
'clouddriver',
'deck',
'echo', 'fiat', 'front50',
'gate', 'igor', 'kayenta', 'orca', 'rosco']
# For building and val... | ewiseblatt/spinnaker | dev/buildtool/__init__.py | Python | apache-2.0 | 2,340 | [
"ORCA"
] | ed5ce5a35c6320639799988a78edc419724f983509c77e366ff0e97aef9ad543 |
########################################################################
# $HeadURL $
# File: LcgFileCatalogProxyHandler.py
########################################################################
"""
:mod: LcgFileCatalogProxyHandler
.. module: LcgFileCatalogProxyHandler
:synopsis: This is a service which repres... | Sbalbp/DIRAC | DataManagementSystem/Service/LcgFileCatalogProxyHandler.py | Python | gpl-3.0 | 3,518 | [
"DIRAC"
] | fca985bfff323aeeaefe2b1daa669c64fe414678d0e6bffe0d1643a9234c39b5 |
# 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... | kkreis/espressopp | src/interaction/AngularHarmonic.py | Python | gpl-3.0 | 3,358 | [
"ESPResSo"
] | 32d176518b7e50d9ece97abb329e5047f67d14504359c0000748ea619771cfc9 |
# Copyright (C) 2019 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 versio... | espressomd/espresso | testsuite/scripts/samples/test_electrophoresis.py | Python | gpl-3.0 | 2,243 | [
"ESPResSo"
] | 64635752c3b59604d9a98c30983c00e76273c1a58e6427e819763282b8f92307 |
"""Contains the hardware interface and drivers for the FAST Pinball platform
hardware, including the FAST Core and WPC controllers as well as FAST I/O
boards.
"""
# fast.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
... | qcapen/mpf | fast2.py | Python | mit | 50,693 | [
"Brian"
] | 33322093f07974bd2d50ea817cb4d1c67a92d6865a418305396c142fde64400b |
""" Functions and Classes used to fit an estimate of an unabsorbed
continuum to a QSO spectrum.
"""
# p2.6+ compatibility
from __future__ import division, print_function, unicode_literals
try:
unicode
except NameError:
unicode = basestring = str
import numpy as np
import matplotlib.pyplot as pl
import matplot... | nhmc/LAE | python_modules/barak/fitcont.py | Python | mit | 19,020 | [
"Gaussian"
] | f8ce2cc49d9e27f4dcda44138a238f0613caeb3b3817ed4c727f7a40a16dd105 |
"""
Acceptance tests for Content Libraries in Studio
"""
from ddt import ddt, data
from flaky import flaky
from nose.plugins.attrib import attr
from .base_studio_test import StudioLibraryTest
from ...fixtures.course import XBlockFixtureDesc
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.utils ... | dkarakats/edx-platform | common/test/acceptance/tests/studio/test_studio_library.py | Python | agpl-3.0 | 27,333 | [
"VisIt"
] | a676bf7dc8cb49ea6568e066f9fb8b9b8165bddacd8bfb8973e46fb465c510b1 |
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 12 15:50:15 2014
@author: svfilhol
Geometry, morphology of surface
"""
import numpy as np
import cv2
def slope(Z, dx, neighbor=None):
"""
**S = slope(Z)**\n
Function to calculate the slope of a 2D matrix
Parameters
==========
**Z** - 2D matri... | ArcticSnow/dempy | dempy/morphometry.py | Python | mit | 4,143 | [
"Gaussian"
] | 831392310e6320c914aa9ad10365e6c25061fd3a818010d5e60a7cc1e2038476 |
# -*- 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... | minhphung171093/GreenERP_V9 | openerp/tools/misc.py | Python | gpl-3.0 | 38,199 | [
"VisIt"
] | 65f0c92bf37c7d847849c1d93a7ea96eea5b35d711b7e8f9c2b16f5fcc6269e7 |
# -*- coding: utf-8 -*-
# this file is released under public domain and you can use without limitations
#########################################################################
## Customize your APP title, subtitle and menus here
#########################################################################
response.logo... | orbnauticus/metabase | models/menu.py | Python | bsd-2-clause | 3,159 | [
"ASE"
] | b333a1e2f4ee9a61c09d8a6328a9dd223ab19dc174518ac4cbc9f36a1e8800a3 |
import shogun as sg
import data
import numpy as np
# load data
feature_matrix = data.swissroll()
# create features instance
features = sg.RealFeatures(feature_matrix)
# create Diffusion Maps converter instance
converter = sg.DiffusionMaps()
# set target dimensionality
converter.set_target_dim(2)
# set number of time... | MikeLing/shogun | applications/tapkee/samples/dm.py | Python | gpl-3.0 | 952 | [
"Gaussian"
] | 9fd4e7693f63e84e5e4c7c489c72d65a8eb64c552713159624a79d2f6168b2ed |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | galsim/bounds.py | Python | gpl-3.0 | 6,507 | [
"Galaxy"
] | ad267c90573219bfb13d016ce20ecac6fff6793a117ad8cc83d22a812d2b6fb6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Copyright (C) 2011-2015 German Aerospace Center DLR
(Deutsches Zentrum fuer Luft- und Raumfahrt e.V.),
Institute of System Dynamics and Control
All rights reserved.
This file is part of PySimulator.
PySimulator is free software: you can redistribute it and/or modify... | PySimulator/PySimulator | PySimulator/Plugins/Simulator/Dymola/Dymola.py | Python | lgpl-3.0 | 19,454 | [
"MOE"
] | 9a0eeff376521a95b99379af5b1d5b73769f73fbe2714f4f4a0345868888c655 |
#!/usr/bin/env python
# This example demonstrates how to extract "computational planes" from
# a structured dataset. Structured data has a natural, logical
# coordinate system based on i-j-k indices. Specifying imin,imax,
# jmin,jmax, kmin,kmax pairs can indicate a point, line, plane, or
# volume of data.
#
# In this ... | hjanime/VisTrails | examples/vtk_examples/VisualizationAlgorithms/warpComb.py | Python | bsd-3-clause | 3,241 | [
"VTK"
] | 118793d4c74a0202ccbe0d42cf2550de8c78708b98bcce0cd5bc6e489de67f39 |
#!/usr/bin/python
#
#####################################################################################
# Scriptname : sat6-register.py
# Scriptauthor : Frank Reimer
# Creation date : 2016-01-05
# License : GPL v. 3
#
# This script was inspired by https://github.com/sideangleside/sat6-bootstrap
#
####################... | hambuergaer/sat6_client_configuration | sat6-register.py | Python | gpl-3.0 | 20,789 | [
"VisIt"
] | 81907fe0f8fb241aa4b2d70af3dac82098c9fe6eb93adbe8a85f7cc9e5c0d85b |
import logging
import urllib
from collections import defaultdict
from lxml import html
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions import PermissionDenied
from django.core.urlresolvers import reverse
from django.contrib.auth.models import User, Anonymo... | altsen/diandiyun-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 38,079 | [
"VisIt"
] | 0fb15d331fa69b5d94fbd18044fc41212ab7d3d04de82d9a974c1dc50b097a16 |
# -*- coding: utf-8 -*-
# @Author: twankim
# @Date: 2017-02-24 17:46:51
# @Last Modified by: twankim
# @Last Modified time: 2018-03-09 22:15:30
import numpy as np
import time
import sys
import os
import argparse
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from ssac import weakSSAC
from... | twankim/weaksemi | compare_random.py | Python | mit | 10,209 | [
"Gaussian"
] | 9a2fe2d77491c2a5418e06fba2778bdb0a78ed86bffde8cb10bf1681003d9286 |
#!/usr/bin/python
#
# ice - web frontend for SeaIce, based on the Python-Flask framework.
#
# Copyright (c) 2013, Christopher Patton, all rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistrib... | nassar/yamz | ice.py | Python | bsd-3-clause | 31,923 | [
"VisIt"
] | eb88f5ce510d5385c16f6d8d245e9039200e54874642095cc6796d29669b46ea |
# Copyright (c) 2017 Jon Cooper
#
# This file is part of pygame-xbox360controller.
# Documentation, related files, and licensing can be found at
#
# <https://github.com/joncoop/pygame-xbox360controller>.
import pygame
import xbox360_controller
BLACK = (0, 0, 0)
WHITE = (255, 255, 255)
RED = (255... | joncoop/pygame-xbox360controller | visualizer.py | Python | mit | 6,684 | [
"Amber"
] | 6f4dbc7fc9632d2ff21e54a12bbe89f67584fd75ea98524423b8e7beba76abb1 |
from django.conf import settings
from django.contrib.sites.models import Site
# The URL that users get sent back to after visiting spreedly
SPREEDLY_RETURN_URL = getattr(settings, 'SPREEDLY_RETURN_URL', '/thanks/')
# The base URL for all spreedly related pages
SPREEDLY_URL = getattr(settings, 'SPREEDLY_URL', '/subscr... | robot-republic/django-spreedly | spreedly/settings.py | Python | mit | 1,733 | [
"VisIt"
] | c706249183256f63f228fc76181969b735db2d53277ed44c2a19681279e99122 |
import os
from vmtk import vmtkscripts
import vtk
import pickle
import json
main_dir = "/home/sansomk/caseFiles/mri/VWI_proj"
store_name = "step1_normalization"
normalization_dir ="normalization"
case_list = [1,3,4,5,7,8,11,12,13,14]
completed_cases = [1,3]
image_vols_dir = "image_vols"
registration_dir = "registra... | kayarre/Tools | vmtk/segment_ventricles.py | Python | bsd-2-clause | 4,024 | [
"VTK"
] | ccb55b8d5184187046786c2c7ab5592cc9497b2c102d6404cf34e9d8c8da7993 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import datetime
import re
from HTMLParser import HTMLParser
from sqlalchemy import or_, orm
from sqlalchemy.dialects.postgresql import JSONB
from app import db
from app import logger
import page
from util import NoDoiException
from util import clean_doi
from util import is_d... | Impactstory/sherlockoa | pmh_record.py | Python | mit | 20,955 | [
"MOOSE"
] | c8018751f10f03ac83e79dfed655508e639e02c788952a4d4030d94073826455 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function, unicode_literals
from builtins import object, dict, str
import os
import json
import logging
import networkx as nx
from indra.statements import Influence
# Python 2
try:
basestring
# Python 3
except:
basestring = str
logger = logg... | johnbachman/belpy | indra/assemblers/cag/assembler.py | Python | mit | 12,338 | [
"Cytoscape"
] | a42e710c5167c6e39c774eb41f516781772fec9dba00ceba611117427712aa7b |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2015 Jan Decaluwe
#
# The myhdl library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License as
# published by t... | hgomersall/myhdl | myhdl/_intbv.py | Python | lgpl-2.1 | 17,082 | [
"VisIt"
] | 3bc6b87a5f23db5a80db11c75fa378a23f078e5306260edb3aba360288792926 |
#!/usr/bin/env python
#-*- coding: utf-8 -*
#
# Copyright (c) 2009 Antonio Barbuzzi <antonio.barbuzzi@gmail.com>,
# Telematics Lab, DEE, Politecnico di Bari, Italy. All rights reserved.
#
#
# This file is part of DeSRTO.
#
# DeSRTO is free software: you can redistribute it and/or modify
# it under the terms ... | antoniobarbuzzi/desrto | tcpcapreader.py | Python | gpl-2.0 | 18,428 | [
"VisIt"
] | ff235a8d5fec5ed77fd4ff4280c40d4a8c5a5df4eb10ae97f2294bcc289da094 |
import hashlib, warnings
import numpy as np
import pandas as pd
from scipy.stats import norm as normal_dbn
from ..algorithms.lasso import ROSI, lasso
from .core import (infer_full_target,
infer_general_target,
repeat_selection,
gbm_fit_sk)
from .learners impor... | selective-inference/selective-inference | selectinf/learning/utils.py | Python | bsd-3-clause | 24,890 | [
"Gaussian"
] | e5a6792a42dd68c82650e94c55a40889bf6b88d5a620d746543f0ebcdf70c5f3 |
import os
import time
import DIRAC
import threading
from DIRAC import gConfig, gLogger, S_OK, S_ERROR, gMonitor
from DIRAC.Core.Utilities import List, Time, MemStat
from DIRAC.Core.DISET.private.LockManager import LockManager
from DIRAC.FrameworkSystem.Client.MonitoringClient import MonitoringClient
from DIRAC.Core.DI... | sposs/DIRAC | Core/DISET/private/Service.py | Python | gpl-3.0 | 23,465 | [
"DIRAC"
] | 59a1439afe73b39a3711b65361276d135da750c62ef8937f3203936e397a6723 |
execfile("./config.py")
import skysim_sources
import skysim_images
import variousfct
# Matrix of PSF stars
psfstars = skysim_sources.build_array_stars((900, 900), matrix_x = 6, matrix_y = 6, distance=120)
psfmags = [17, 17.5, 18, 18.5, 19, 19.5]
psfnames = ["a", "b", "c", "d", "e", "f"]
for i in range(6): # x = m... | COSMOGRAIL/COSMOULINE | skysim/pipe/build_sourcelist_default.py | Python | gpl-3.0 | 1,379 | [
"Galaxy"
] | 0ec7b69d2533d9bb56c294a994b5513d69acefdf558cca18eabff16773379512 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/data/tf/data.py | Python | apache-2.0 | 8,922 | [
"ORCA"
] | c319f35119e8e93db685726f5647ebb6a716e5730852cf22feec4caa770f5fb7 |
# !/usr/bin/env python
# -*- coding: utf-8 -*-
import vtk
def main():
colors = vtk.vtkNamedColors()
colors.SetColor("BkgColor", [26, 51, 102, 255])
surface = vtk.vtkParametricSuperToroid()
source = vtk.vtkParametricFunctionSource()
renderer = vtk.vtkRenderer()
mapper = vtk.vtkPolyDataMapper... | lorensen/VTKExamples | src/Python/GeometricObjects/ParametricSuperToroidDemo.py | Python | apache-2.0 | 5,175 | [
"VTK"
] | b817da7c480c2ff44eb9e28b56fc298e0e70444be300aa45e2564c60f88bb826 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def CLPointGrid(minx,dx,maxx,miny,dy,maxy,z):
plist = []
xvalues = [round(minx+n*dx,2) for n in range(int(round((maxx-minx)/dx))+1) ]
yvalues = [round(miny+n*dy,2) for n in range(int(round((maxy-miny)/dy))+1) ]
for y in yvalues... | aewallin/opencamlib | examples/python/offsetCutter_test_2.py | Python | lgpl-2.1 | 3,521 | [
"VTK"
] | 425e8425c3a5116fbc9d19254bad299cb96ea442c774c2720639b51b9af867e3 |
"""
@name: /home/briank/workspace/PyHouse/Project/src/Modules/House/Family/insteon/_test/test_insteon_buttons.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2013-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Dec 10, 2019
@summary:
"""
# ## END DBK
| DBrianKimmel/PyHouse | Project/src/Modules/House/Family/Insteon/_test/test_insteon_buttons.py | Python | mit | 316 | [
"Brian"
] | 794442c230381b45328b52425fbeb6ac04c3ae32c35e31469b6b11c86262effd |
from __future__ import unicode_literals
from flask.ext.babel import gettext as _
# a pack of commons size for fast testing and javascript shortcut
frequent = (
(240, 320),
(320, 480),
(360, 640),
(640, 480),
(800, 600),
(1024, 768),
(1280, 960),
(1680, 1050),
(1920, 1080),
)
# def... | EliotBerriot/screen-sizer | sizes.py | Python | gpl-3.0 | 1,957 | [
"Galaxy"
] | 9c6b0448ae630022266b1bc61d9419484cfaa1b0ddba2ecfccf813958a85b9db |
"""
Abstract syntax tree visitor that performs evaluation on the nodes.
"""
import math
from ..parser import ast
from ..parser.visitor import NodeVisitor
from .types import (
Undefined, Null, NumberType, StringType, ObjectType, BooleanType,
get_primitive_type, check_object_coercible, NaN
)
from .exceptions impo... | jeffkistler/BigRig | bigrig/interpreter/visitor.py | Python | bsd-3-clause | 32,585 | [
"VisIt"
] | 5c46bd7fdfc98f5a522b2a7654e70d9d5ee35340f05b7941d35273a7dd38cec4 |
import scipy.stats.distributions as sd
import numpy as np
import itertools
class TickerSampling():
################################# Main
def sample(self, i_click_distr, i_letter, i_return_labels=False, i_n_rejection_samples=1E6, i_display=False):
"""
Input:
* Draw one sampl... | singleswitch/ticker | experiments/simulations/ticker_sampling.py | Python | mit | 7,239 | [
"Gaussian"
] | 223ef1fab593a7e27968ea26105399ad59b304c7660f99e4fcd8ce1669a6de57 |
import logging
import numpy as np
import os
import time
import configparser
import netCDF4
# Python script generated by netCDF kickstarter
# at 2016-04-12T07:31Z
# http://publicwiki.deltares.nl/display/OET/netCDF%20kickstarter
logging.basicConfig()
logger = logging.getLogger()
logger.setLevel(logging.DEBUG)
# CREA... | openearth/delft3d-gt-backend | roles/worker_dummy/files/dummy_netcdf_output.py | Python | gpl-3.0 | 5,311 | [
"NetCDF"
] | 4d606ff1f5c17ce7e619d9cf27471127b955f0aada214a8a90bee36a616384ab |
#
# @file TestL3Unit.py
# @brief L3 Unit unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file located at
# sr... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestL3Unit.py | Python | bsd-3-clause | 5,851 | [
"VisIt"
] | eccbc483bab18a87244f407fb28062b7c0760db262c63af35adfd566248ae10d |
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 13 19:56:19 2013
@author: Nicholas Léonard
"""
import time, sys
from pylearn2.utils import serial
from itertools import izip
from pylearn2.utils import safe_zip
from collections import OrderedDict
from pylearn2.utils import safe_union
import numpy as np
import theano.s... | jfsantos/ift6266h14 | stochastic_gater.py | Python | mit | 58,597 | [
"NEURON"
] | 068d82e87c79535c80a5516f5979f015500e6698f09bd31e77c01eae9574e20c |
import sys
import pdb
import logging
from time import sleep, time
from datetime import datetime, timedelta
from splinter import Browser
from Parser import Parser, ParseChildIdError, ParseAvailableDatesError
from Utils import poll_on_method
class AppointmentError(Exception):
pass
class LoginError(AppointmentEr... | NickBayard/mlh | Appointment.py | Python | mit | 8,364 | [
"VisIt"
] | c0f5ba8addd633530335de18c86d05116a27b737e24b71cc9d0b1c2794596d73 |
import numpy as np
from collections import OrderedDict
from lammps import PyLammps
from PolyLibScan.Analysis.sim_run import AtomFilter
class LmpController(object):
"""Initialize and control a lammps instance"""
def __init__(self, Id, parameters, paths, parameterisation, fifos, previous_instance=''):
... | luminescence/PolyLibScan | Tools/lmp_control.py | Python | mit | 12,554 | [
"Gaussian",
"LAMMPS"
] | 1517b77381e5ae5c9747ac575404f3732438b244fde52e6e56569fdef4a9125a |
import os
from DIRAC import S_OK, S_ERROR, gConfig, gLogger
from DIRAC.Core.Utilities import List
from DIRAC.ConfigurationSystem.Client.Helpers import Registry
from DIRAC.ConfigurationSystem.Client.Helpers import CSGlobals
from DIRAC.Core.DISET.AuthManager import AuthManager
from DIRAC.Core.DISET.ThreadConfig import Th... | zmathe/WebAppDIRAC | Lib/SessionData.py | Python | gpl-3.0 | 4,726 | [
"DIRAC"
] | bbe4dbb33f7a290750c480863c0cff3899555832a2990a72c321857ba5143d40 |
# -*- coding: utf-8 -*-
'''
Created on 28 Nov 2013
@author: Kimon Tsitsikas
Copyright © 2012-2013 Kimon Tsitsikas, Delmic
This file is part of Odemis.
Odemis is free software: you can redistribute it and/or modify it under the terms
of the GNU General Public License version 2 as published by the Free Software
Fou... | gstiebler/odemis | src/odemis/acq/align/test/coordinates_test.py | Python | gpl-2.0 | 20,137 | [
"Gaussian"
] | 4c093fee8f68188bc0f8209559ff040bff2309b05cef749789f7f783d0f6115e |
import os
import sys
import types
import re
from numpy.core.numerictypes import issubclass_, issubsctype, issubdtype
from numpy.core import product, ndarray, ufunc
__all__ = ['issubclass_', 'get_numpy_include', 'issubsctype', 'issubdtype',
'deprecate', 'deprecate_with_doc', 'get_numarray_include',
'ge... | qsnake/numpy | numpy/lib/utils.py | Python | bsd-3-clause | 36,175 | [
"VisIt"
] | 6ecbf63523c1ae307b1eb39a15310e24881b57b0a7de5530bafd798ffa6cb5e5 |
# Orca
#
# Copyright 2004-2009 Sun Microsystems Inc.
# Copyright 2010 Joanmarie Diggs
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your op... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/default.py | Python | gpl-3.0 | 179,480 | [
"ORCA"
] | f396fd1b206ca224c8fec992189e9964ad91e58c2a54ff40c9de8fe2ad5e9eda |
import sys
import psycopg2
from ase.db.sqlite import init_statements, index_statements, VERSION
from ase.db.sqlite import all_tables, SQLite3Database
class Connection:
def __init__(self, con):
self.con = con
def cursor(self):
return Cursor(self.con.cursor())
def commit(self):
... | suttond/MODOI | ase/db/postgresql.py | Python | lgpl-3.0 | 3,508 | [
"ASE"
] | 06e5a25b88cc24c927de137b916b5656eac2eb7601ec42f9e8b831b9365d3be4 |
#!/usr/bin/env python
######################################################################
# Alchemical Analysis: An open tool implementing some recommended practices for analyzing alchemical free energy calculations
# Copyright 2011-2015 UC Irvine and the Authors
#
# Authors: Pavel Klimovich, Michael Shirts and Dav... | hainm/alchemical-analysis | alchemical_analysis/alchemical_analysis.py | Python | lgpl-2.1 | 56,374 | [
"Amber",
"Gaussian",
"Gromacs"
] | 55ef1a6d2fc90ea323b0e499d68a441fc091b59962f0b84c67060d6319ce1986 |
#!/usr/bin/env python
#
# $File: migrateByProb.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistrib... | BoPeng/simuPOP | docs/migrateByProb.py | Python | gpl-2.0 | 1,503 | [
"VisIt"
] | 7d3061274d975bd12c32f13f71ae2a961264601e364e894f4866ff921c155f48 |
"""DBF fields definitions.
TODO:
- make memos work
"""
"""History (most recent first):
26-may-2009 [als] DbfNumericFieldDef.decodeValue: strip zero bytes
05-feb-2009 [als] DbfDateFieldDef.encodeValue: empty arg produces empty date
16-sep-2008 [als] DbfNumericFieldDef decoding looks for decimal point
... | chadspratt/AveryDB | filetypes/libraries/dbfpy/fields.py | Python | apache-2.0 | 15,272 | [
"VisIt"
] | ef62737c9ec965e711559bb4a1debf4221abee1c3dbdd599269b35e20f0954f8 |
# -*- coding: utf-8 -*-
"""
Created on Sat Feb 7 16:02:16 2015
@author: nick
"""
from copy import deepcopy
import math
from skgraph import graph
from scipy.spatial.distance import pdist
import numpy as np
import sys
from numpy.linalg import norm
def gaussianKernel(X,Y,beta):
Z=[X,Y]
return np.exp(-beta * pd... | nickgentoo/scikit-learn-graph | skgraph/tree/tree_kernel_PTCL_new.py | Python | gpl-3.0 | 13,712 | [
"Gaussian"
] | 1df68831de4983165b904c1bc68a0cc35b3c1c67da34a3730f77e3001344c343 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | fevangelista/psi4 | psi4/extras.py | Python | lgpl-3.0 | 6,885 | [
"CFOUR",
"Psi4"
] | a8bd161719b761a595001f8613969f20d8d170be3e6f63b9d1d57b8977fbddf4 |
"""
# (C) Copyright 2016 SLU Global Bioinformatics Centre, SLU
# (http://sgbc.slu.se) and the B3Africa Project (http://www.b3africa.org/).
#
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Lesser General Public License
# (LGPL) version 3 which accompani... | fikipollo/b3galaxy | server/server.py | Python | gpl-3.0 | 14,336 | [
"Galaxy"
] | f19369f031bd5d91900ffa2668c58ca1d343014a63d8bfc2300fcafa735ed4f8 |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy,... | alexholcombe/dot-jump | dataRaw/test_dot-jump16Feb2017_15-36.py | Python | gpl-3.0 | 29,526 | [
"Gaussian"
] | 73d5b369bfc9ac8c995fd6c1f7e747bfff725c3b792a26f42f43f78d21f871c6 |
from galaxy.util import asbool, mask_password_from_url
from pulsar.client import amqp_exchange_factory
from pulsar import manager_endpoint_util
import functools
import threading
import logging
log = logging.getLogger(__name__)
TYPED_PARAMS = {
"amqp_consumer_timeout": lambda val: None if str(val) == "None" else ... | ssorgatem/pulsar | pulsar/messaging/bind_amqp.py | Python | apache-2.0 | 4,902 | [
"Galaxy"
] | f8196cedeae236030b5dc20897106e729e1643cd174a94934eda47529c9ee912 |
# -*- encoding: utf-8 -*-
"""
General helper functions that don't fit neatly under any given category.
They provide some useful string and conversion methods that might
be of use when designing your own game.
"""
import os
import gc
import sys
import copy
import types
import math
import re
import textwrap
import rand... | jamesbeebop/evennia | evennia/utils/utils.py | Python | bsd-3-clause | 69,374 | [
"VisIt"
] | 2296738924f70f0928cdf81667add693385d8ef32ec39e4a840f73917f9bcd5c |
import sys
import numpy as np
from numpy import array as npa
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection, CircleCollection
from matplotlib.gridspec import GridSpec
from matplotlib.collections import PatchCollection
from matplotlib.patches import Circle... | neelravi/vasp | circles.py | Python | gpl-3.0 | 1,330 | [
"VASP",
"pymatgen"
] | cf28bdf5dc7f89734d17d086555883851580a2cc1dfd52730cef1b374a684389 |
# Generated by Haxe 3.4.4
# coding: utf-8
from datetime import datetime as python_lib_datetime_Datetime
from datetime import timezone as python_lib_datetime_Timezone
import math as python_lib_Math
import math as Math
from os import path as python_lib_os_Path
import inspect as python_lib_Inspect
import os as python_lib... | gameduell/duell | duell.py | Python | bsd-2-clause | 519,491 | [
"VisIt"
] | e16d2ff702c6b393c34511705e9954f45d2b367d7c4e96248e3e90ee87770129 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | casawa/mdtraj | mdtraj/tests/test_netcdf.py | Python | lgpl-2.1 | 7,087 | [
"Amber",
"MDTraj",
"NetCDF"
] | 14e330410881d1d061fd3d22d48becd1ffbb68d438ad3b23deaf03fd5c2d9b74 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/p4util/numpy_helper.py | Python | lgpl-3.0 | 17,628 | [
"Psi4"
] | 089b8cad4b79ea4fa25efbdf629751bbb128d6da0069211d87542f9590302448 |
# -*- Mode:Python; indent-tabs-mode:nil; tab-width:4 -*-
#
# Copyright (C) 2016 Canonical Ltd
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 3 as
# published by the Free Software Foundation.
#
# This program is distributed in the h... | sergiusens/snapcraft | snapcraft/storeapi/constants.py | Python | gpl-3.0 | 2,415 | [
"VisIt"
] | 1d29f1593ab32d80b1c94e7189c81c20153ca9ebc6839e85e88f47e2213ee05b |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | fabio-otsuka/invesalius3 | invesalius/data/volume_widgets.py | Python | gpl-2.0 | 4,868 | [
"VTK"
] | 1dc1d40ef006e37cf4a9528c10bc262a4c6c924079fe36a51675c2beb8d0b2db |
# -*- coding: utf-8 -*-
# Nemubot is a smart and modulable IM bot.
# Copyright (C) 2012-2014 nemunaire
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License,... | Bobobol/nemubot-1 | message/visitor.py | Python | agpl-3.0 | 970 | [
"VisIt"
] | 5e5aaad45f09c3ccc832c2945c82ca4ba446cd4c874e7b5cadf3403aac5b2ec1 |
# -*- coding: utf-8 -*-
"""Define pRF finding parameters here."""
# Part of py_pRF_motion library
# Copyright (C) 2016 Marian Schneider, Ingo Marquardt
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Fo... | MSchnei/py_pRF_motion | pyprf_feature/simulation/configs/pRF_sim_config_circle1.py | Python | gpl-3.0 | 4,233 | [
"Gaussian"
] | 9fc587137e7a4c76c07d79a29fce78bfdd237b4c7884633148718fa72a08c71f |
from __future__ import print_function
import mdtraj as md
from mdtraj.testing import get_fn, eq, DocStringFormatTester, skipif
from mdtraj.nmr.shift_wrappers import find_executable, SPARTA_PLUS, PPM, SHIFTX2
from mdtraj.utils import six
@skipif(not find_executable(SPARTA_PLUS), 'SPARTA+ binary not found')
def test_spa... | kyleabeauchamp/mdtraj | mdtraj/tests/test_nmr.py | Python | lgpl-2.1 | 2,784 | [
"MDTraj"
] | fcdc06ed06fddd0cbf2d5b58bd5efe38b130699454278a976b4bccfa59ef8459 |
# Copyright (C) 2019 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 versio... | KaiSzuttor/espresso | testsuite/scripts/tutorials/test_html_runner.py | Python | gpl-3.0 | 9,173 | [
"ESPResSo"
] | 9513c344e32e5cda6b46b127e43f7228194f6b6172c6390a957a55415cd76921 |
# Copyright 2004-2017 Tom Rothamel <pytom@bishoujo.us>
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, m... | kfcpaladin/sze-the-game | renpy/pyanalysis.py | Python | mit | 21,001 | [
"VisIt"
] | 3f2fc6ab943bad4eed1e05d76cf5809d93f361319fd50d6400b9e51c7800e9ec |
# Graph Algorithms using basic python Constructs.
# Narayana Chikkam, Dec, 22, 2015.
from __future__ import print_function
from collections import defaultdict
from heapq import *
import itertools
import copy
from lib.unionfind import UnionFind
from lib.prioritydict import PriorityDict
class Vertex:
def __init__(s... | arssivka/naomech | behavior/graph.py | Python | isc | 28,215 | [
"VisIt"
] | a09d1ad7ebe82e13649d40b250d0f36ccdca0301c79c6d294b1f9fcd3c28b18f |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def GetRGBColor(colorName):
'''
Return the red, green and blue components for a
color as doubles.
'''
rgb = [0.0, 0.0, 0.0] # black
vtk.vt... | hlzz/dotfiles | graphics/VTK-7.0.0/Common/ComputationalGeometry/Testing/Python/closedSplines.py | Python | bsd-3-clause | 6,614 | [
"VTK"
] | 1e10a5a67fe27a9062f6a88113a55ad34b803cea57c11df8f0b407d7ebecd63b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2005 onwards University of Deusto
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution.
#
# This software consists of contributions made by many individuals,
# list... | ganeshgore/myremolab | server/src/test/unit/weblab/login/test_user_auth.py | Python | bsd-2-clause | 8,289 | [
"CDK"
] | 3b3e3af88cf81ea6cfc1e23c1a326ff8747309c734a8d98afe3df210b1956ff2 |
#!/usr/bin/env python
try:
import gi
gi.require_version('NumCosmo', '1.0')
gi.require_version('NumCosmoMath', '1.0')
except:
pass
import matplotlib as mpl
import matplotlib.pyplot as plot
from scipy.stats import norm
from scipy.stats import beta
import numpy as np
import math
from gi.repository import NumCosm... | NumCosmo/NumCosmo | examples/example_epdf1d.py | Python | gpl-3.0 | 4,399 | [
"Gaussian"
] | 7f4aaac3a922eabd3a5fbe2ea8ac549c093c7945f2ec82152a4e007f74d8335f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# showvgridprivatefile - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under t... | heromod/migrid | mig/cgi-bin/showvgridprivatefile.py | Python | gpl-2.0 | 1,128 | [
"Brian"
] | 88e09244de9305ef31ce464ae6d593148238c44bcea461e4bff53cf33c5bb095 |
#!/cluster/home2/mglerner/anaconda3/bin/python
#!/usr/bin/env python
import sys
if __name__ == '__main__':
from pypat.hbond import pymol_hbond_analysis
from optparse import OptionParser
usage = """
Run this like:
pymol -qcr collect_water_bridges.py -- --name=myprotein --dist-cutoff=3.5
... | LernerLabs/PyPAT | drivers/collect_water_bridges.py | Python | apache-2.0 | 2,681 | [
"PyMOL"
] | 2c9554263b744b4c8b7f32b222a2f0b84df7c5b242cf248494e6464a1c24e3fb |
#!/usr/bin/env python
# coding: utf-8
"""Test suite for autopep8.
Unit tests go in "UnitTests". System tests go in "SystemTests".
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import os
import re
import sys
... | SG345/autopep8 | test/test_autopep8.py | Python | mit | 198,367 | [
"Psi4"
] | 6b48b28d2ce5af4121775f1512b95a54b8c40a326699995990fd3e8e15d5324a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements input and output processing from PWSCF.
"""
import re
from collections import defaultdict
from monty.io import zopen
from monty.re import regrep
from pymatgen.core.lattice import ... | davidwaroquiers/pymatgen | pymatgen/io/pwscf.py | Python | mit | 19,639 | [
"CRYSTAL",
"pymatgen"
] | 6c68963cc2f14a3b5a3d9cf697f5384dfce28416145624024d21541444ae65a8 |
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