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# $Id$
#
# Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
""" Defines Naive Baysean classification model
Based on development in: Chapter 6 of "Machine Learning" by Tom Mitchell
"""
import numpy
from rdkit.ML.Data import Quantize
def _getBinId(val, qBounds) :
bid = ... | rdkit/rdkit-orig | rdkit/ML/NaiveBayes/ClassificationModel.py | Python | bsd-3-clause | 8,744 | [
"RDKit"
] | 80a7d2f8272bc24e6fb86ee9c4ff9ed8c4cfd0c3f75004795dd1512e98ae11c3 |
from __future__ import division
import numpy as np
import copy
import inspect
import types as python_types
import marshal
import sys
import warnings
from keras import activations, initializations, regularizers, constraints
from keras import backend as K
from keras.engine import InputSpec, Layer
from ke... | bnsnapper/keras_extensions | keras_extensions/rbm.py | Python | mit | 21,081 | [
"Gaussian"
] | d17273b8229d057e1b08f32e3b9dab00e48f600720c12d0f316de6c292dcab62 |
#!/usr/bin/python
# coding=utf-8
__author__ = 'Didier Walliang'
import math
import numpy as np
import matplotlib.pyplot as plt
import os.path
from matplotlib import dates
from astropy.io import fits
from astropy.modeling import models, fitting
from astropy.convolution import Gaussian2DKernel
from astropy.stats import ... | astrochoupe/seeing-measurement | measure.py | Python | gpl-2.0 | 14,551 | [
"Gaussian"
] | 92cca9e8a1d6e4c458de293050a0882e50f2c2d6000c835fc1bbfa04c48aabd3 |
# -*- coding: utf-8 *-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foun... | andrebellafronte/stoq | stoq/gui/shell/shell.py | Python | gpl-2.0 | 19,092 | [
"VisIt"
] | 6f78883062f843da37aecf11834dbc411b9411fd942c9af9644dee384b0b2479 |
"""
Pijaz client application settings.
Visit http://developer.pijaz.com/#manage-apps to create and edit client
applications.
"""
# App ID.
APP_ID = ''
# API key.
API_KEY = ''
"""
Product settings.
Visit http://developer.pijaz.com/#theme-designer to create and edit platform
products.
"""
# Workflow ID.... | pijaz/pijaz-sdk | examples/python/config.sample.py | Python | mit | 860 | [
"VisIt"
] | 4ce49c1d2ce838a157c21ea5169584bf519a8a2e3707e8503834d23ac4f0e37d |
from sfepy.base.base import *
from sfepy.solvers.solvers import NonlinearSolver
import sfepy.base.plotutils as plu
##
# 13.12.2005, c
# 14.12.2005
# 02.10.2007
def check_tangent_matrix( conf, vec_x0, mtx_a0, evaluator ):
vec_x = vec_x0.copy()
delta = conf.delta
vec_r, status = evaluator.eval_residual( vec... | certik/sfepy | sfepy/solvers/nls.py | Python | bsd-3-clause | 9,028 | [
"VTK"
] | 6ed47d6d78b53d84ef1c8c9b2ae8bfac75a77bd09445369e214d59ae94531314 |
""" JobStateUpdateHandler is the implementation of the Job State updating
service in the DISET framework
The following methods are available in the Service interface
setJobStatus()
"""
from __future__ import absolute_import
import six
from six.moves import range
__RCSID__ = "$Id$"
import time
from DI... | fstagni/DIRAC | WorkloadManagementSystem/Service/JobStateUpdateHandler.py | Python | gpl-3.0 | 13,370 | [
"DIRAC"
] | 61b3bd66857cb601a7a8c6a677691638e2c9315a136bbacabfc2ca4bb48b425c |
from distutils.version import StrictVersion
import numpy as np
import scipy
import nose.tools as nt
from unittest import mock
from nose.plugins.skip import SkipTest
import hyperspy.api as hs
from hyperspy.misc.utils import slugify
class TestModelJacobians:
def setUp(self):
s = hs.signals.Signal1D(np.ze... | vidartf/hyperspy | hyperspy/tests/model/test_model.py | Python | gpl-3.0 | 41,020 | [
"Gaussian"
] | bd043695b02915ad46e48f95c308290b76549e42a62a088df11f9188e236b0cd |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Feature_Comparison/multiple_features/results/test10_cross_validate_objects_1200ms_scaled_method_v_force_motion.py | Python | mit | 4,600 | [
"Mayavi"
] | a9c398d1595ca9a5e30ad94fd707717794b8368064154a63da5c08d696c644b8 |
# -*- coding: utf-8 -*-
u"""SILAS execution template.
:copyright: Copyright (c) 2020 RadiaSoft LLC. All Rights Reserved.
:license: http://www.apache.org/licenses/LICENSE-2.0.html
"""
from __future__ import absolute_import, division, print_function
from pykern import pkio
from pykern import pkjson
from pykern.pkcollec... | mkeilman/sirepo | sirepo/template/silas.py | Python | apache-2.0 | 11,600 | [
"CRYSTAL"
] | f72f762ca571c8497c07321ff6fbeacbfaae36deed5482dacdff760e08d17cef |
from distutils.core import setup
from Cython.Build import cythonize
from distutils.extension import Extension
import numpy as np
import mpi4py as mpi4py
import sys
import platform
import subprocess as sp
import os.path
import string
# Now get include paths from relevant python modules
include_path = [mpi4py.get_inclu... | pressel/pycles | setup.py | Python | gpl-3.0 | 14,188 | [
"NetCDF"
] | 5ba63f45798cfe627dceaa4860a83f73edc167dd94713c91fdcfbb3a3b6f66bd |
# This script reads the carrier database
# and display it along a path in histogram form
# along with a representation of the carriers in energy space
from __future__ import print_function
from __future__ import division
from builtins import range
from past.utils import old_div
from yambopy import *
import matplotlib.... | henriquemiranda/yambo-py | scripts/realtime/plot_occ2.py | Python | bsd-3-clause | 7,697 | [
"DIRAC"
] | b67e3f6b1be8891b7b9f8e8fa70d303b240a2e69341affc813b3ede175ca6716 |
##############################################################################
# Copyright (c) 2017-2018 Mark Olesen, OpenCFD Ltd.
#
# This file was authored by Mark Olesen <mark.olesen@esi-group.com>
# and is released as part of spack under the LGPL license.
# LLNL-CODE-647188
#
# For details, see https://github.com/s... | matthiasdiener/spack | var/spack/repos/builtin/packages/openfoam-com/package.py | Python | lgpl-2.1 | 34,061 | [
"ParaView",
"VTK"
] | 601a4c3f2eaa263d6a49efa80807c5a48af7edb3402abc3f54f862827a9afb27 |
# -*- coding: utf-8 -*-
"""Color constants and a getter function."""
def get(color_name):
"""Return specified color if exists, else return white."""
color = _COLORS.get(color_name)
return color if color else 'white'
# converting color name to color code here couldn't change the color
# converting in ren... | kuraha4/roguelike-tutorial-python | src/colors.py | Python | mit | 1,464 | [
"Amber"
] | e0a8576a7dd8744caa48a2226a42b72dd4fbd04537eaa8001f92d7b3ddf490e9 |
"""
=================
:mod:`crossovers`
=================
.. Copyright 2012 Inspired Intelligence Initiative
.. 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 Fou... | saulshanabrook/pushgp.py | thirdparty/inspyred-1.0/inspyred/ec/variators/crossovers.py | Python | bsd-3-clause | 18,632 | [
"Gaussian"
] | 460e28e396410cde671e38d3c38bd283363b12d980c3b39036062a330a9eeaf1 |
## Copyright (c) 2015 Ryan Koesterer GNU General Public License v3
##
## This program is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any l... | rmkoesterer/uga | uga/RunTools.py | Python | gpl-3.0 | 5,404 | [
"pysam"
] | 3f3eff5c39b8de1771ab3fa3cff6aee7a58b81fe3a7c97f0d48fbd82df5e9b7a |
# -*- encoding: utf-8 -*-
"""
Gaussian optics.
The module implements:
- Ray transfer matrices for geometrical and gaussian optics.
See RayTransferMatrix, GeometricRay and BeamParameter
- Conjugation relations for geometrical and gaussian optics.
See geometric_conj*, gauss_conj and conjugate_gauss_beams
The co... | flacjacket/sympy | sympy/physics/gaussopt.py | Python | bsd-3-clause | 19,362 | [
"Gaussian"
] | e94939d7ae72d8d02d6b609d7029aa08557c2f35953b832b405a775c7caf1ffc |
"""
Module to set up run time parameters for Clawpack -- AMRClaw code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
t_shelf = 3.2*3600 # time approaching continental slope
t_harbor = 3.5*3600 # time approachi... | clawpack/adjoint | paper1_examples/tsunami_Alaska/compare/setrun_sflag_lowtol.py | Python | bsd-2-clause | 16,061 | [
"NetCDF"
] | e2ebf51f70089a6c7017e00be3f7a99e9239f3b04b97342c3e971c1e0794c060 |
"""Utilities used in the Kadenze Academy Course on Deep Learning w/ Tensorflow.
Creative Applications of Deep Learning w/ Tensorflow.
Kadenze, Inc.
Parag K. Mital
Copyright Parag K. Mital, June 2016.
"""
import matplotlib.pyplot as plt
import tensorflow as tf
import urllib
import numpy as np
import zipfile
import os
... | niazangels/CADL | session-5/libs/utils.py | Python | apache-2.0 | 21,027 | [
"Gaussian"
] | e54985b4885462a6e89e117fc67d79afcb8309f20b87ab57ade4a1bd646955e0 |
import datetime
import re
import smtplib
import time
import urllib
from typing import Any, List, Optional, Sequence
from unittest.mock import MagicMock, patch
import ujson
from django.conf import settings
from django.contrib.auth.views import INTERNAL_RESET_URL_TOKEN
from django.contrib.contenttypes.models import Cont... | timabbott/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 198,704 | [
"VisIt"
] | dad9f124078b596f77d2c2ab2f59581b3d488bec7e51c07ae8566d9f4976a8d7 |
import re
from copy import deepcopy
import numpy as np
import tatsu
from mdt.component_templates.base import ComponentBuilder, ComponentTemplate
from mdt.lib.components import get_component
from mdt.model_building.parameters import FreeParameter, ProtocolParameter
from mdt.models.composite import DMRICompositeModel
fr... | cbclab/MDT | mdt/component_templates/composite_models.py | Python | lgpl-3.0 | 21,871 | [
"Gaussian"
] | 513f0e7babcfaea9739fb6ecb7532476bbcec981a58fcd916a53cd22eae970f9 |
#!/usr/bin/env python
import os
import logging
class DataFace(object):
""" Some data IFace bowtie can work with.
"""
def size(self):
raise NotImplementedError("size() needs to be implemented!")
class SamFile(DataFace):
def __init__(self,sam_desc):
self.file_desc = sam_... | iml/bowtie2 | scripts/test/dataface.py | Python | gpl-3.0 | 1,769 | [
"Bowtie"
] | 31ee5da6abe27dd437fded11357a9a3b1a19e0f9a84d31e008f2712b93256c69 |
#!/usr/bin/python
# backpage_sitekey_to_marketid
backpage_sitekey_to_marketid = {
"abbotsford": "YXX",
"aberdeen": "ABZ",
"abilene": "ABI",
"acapulco": "ACA",
... | usc-isi-i2/dig-alignment | versions/1.0/datasets/istr/market/sourcemarket.py | Python | apache-2.0 | 249,792 | [
"COLUMBUS"
] | 6d3567468c987f1369893fff957ad0294f28956b40e6d9cfdfd272c1a11aaa7a |
import re
from nxtools import *
from .common import *
def shorten(instr, nlen):
line = instr.split("\n")[0]
if len(line) < 100:
return line
return line[:nlen] + "..."
def filter_match(f, r):
"""OR"""
if type(f) in [list, tuple]:
res = False
for fl in f:
if re.m... | immstudios/nebula-core | nebulacore/meta_utils.py | Python | gpl-3.0 | 1,789 | [
"Firefly"
] | 5a2aeecdac7ae3aba2a96ecbaf89f95ced9dcb283ff3fe568177f1285e6e1e85 |
#!/usr/bin/env python
import time
import math
import numpy
from appionlib import apDisplay
from appionlib.apCtf import ctftools
debug = False
#===================
def generateCTF1d(radii=None, focus=1.0e-6, cs=2e-3, volts=120000, ampconst=0.07,
failParams=False, overfocus=False):
"""
calculates a CTF function b... | vossman/ctfeval | appionlib/apCtf/genctf.py | Python | apache-2.0 | 9,912 | [
"Gaussian"
] | 4b916085627df98592713c7ac508b56d11b8d76334dd27513496955b863b5637 |
#!/usr/bin/python
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 oau... | stu1992/Melbourne-Clouds | upload.py | Python | gpl-3.0 | 6,656 | [
"VisIt"
] | a36404025f01c6920f0cc756422ddcc1066e5cbffad774cc6b23a61c3e49c189 |
# -*- coding: utf-8 -*-
# creates: surface.png
from ase.io import read, write
exec(compile(open('N2Cu.py').read(), 'N2Cu.py', 'exec'))
image = read('N2Cu.traj@-1')
write('surface.pov', image, transparent=False, display=False, run_povray=True)
| misdoro/python-ase | doc/tutorials/surface.py | Python | gpl-2.0 | 243 | [
"ASE"
] | 97fa8f1bd83ec08d8a39bb4aa101d026f118cb054127e3951b8d2502863df81c |
# $Id$
#
# 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.
#
from __future__ impor... | strets123/rdkit | rdkit/Dbase/DbInfo.py | Python | bsd-3-clause | 5,347 | [
"RDKit"
] | cb2d1ce09305456af88f274c86e0c46dec552fdb918817b6a2485a47b245df05 |
"""
Views for user API
"""
from django.shortcuts import redirect
from django.utils import dateparse
from rest_framework import generics, views
from rest_framework.decorators import api_view
from rest_framework.response import Response
from opaque_keys.edx.keys import UsageKey
from opaque_keys import InvalidKeyError
... | vismartltd/edx-platform | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 9,321 | [
"VisIt"
] | 4d82c2e36d913be394c1ca3c9c75e72220b115b8f7e1051c1685faab4176d586 |
#
# Copyright 2018 Analytics Zoo 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... | intel-analytics/analytics-zoo | pyzoo/test/zoo/orca/automl/test_metrics.py | Python | apache-2.0 | 8,596 | [
"ORCA"
] | 62014fbb78143cf55e729bb05115fa502dfcf3ddf97c35d1ceb03ea79ff0ed19 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2009-2014:
# Gabes Jean, naparuba@gmail.com
# Gerhard Lausser, Gerhard.Lausser@consol.de
# Gregory Starck, g.starck@gmail.com
# Hartmut Goebel, h.goebel@goebel-consult.de
#
# This file is part of Shinken.
#
# Shinken is free software: you c... | kaji-project/shinken | shinken/stats.py | Python | agpl-3.0 | 6,828 | [
"CRYSTAL"
] | 44946b6544d084fd514b1582dfcdd1dc6a989bd853a43ecd92e42a10d7f79305 |
import LFPy
import numpy as np
import matplotlib.pylab as pl
import sys
import os
import random as random
#setting a random seed to get the same result all the time
np.random.seed(1988)
#what this program need fro running
#where is and will be the data
f2 = open('cellname', 'r')
celln = [line.strip() for line in f2]
c... | csdori/skCSD | simulation/LFP_calc_sine.py | Python | bsd-3-clause | 8,494 | [
"NEURON"
] | 783422a9033b7d86f08649752917bc22e34b396826c7461561c9493fe3fbd626 |
# Name: mapper_metno_hfr
# Purpose: Mapper for CODAR SeaSonde High-Frequency radar data provided by MET Norway
# For data see: https://thredds.met.no/thredds/catalog/remotesensinghfradar/catalog.html
# Authors: Artem Moiseev
# Licence: This file is part of NANSAT. You can redistribute it... | nansencenter/nansat | nansat/mappers/mapper_metno_hfr.py | Python | gpl-3.0 | 6,968 | [
"NetCDF"
] | a08bf80b8aab9b70eecbc05e74b89b9f962ca468ea00934329b80993e647baba |
from typing import List
import pytest
from find import search
from find.search import InvalidValueException
from magic import seasons
from magic.database import db
# Some of these tests only work hooked up to a cards db, and are thus marked functional. They are fast, though, and you should run them if editing card s... | PennyDreadfulMTG/Penny-Dreadful-Tools | find/find_test.py | Python | gpl-3.0 | 23,978 | [
"Amber",
"BLAST"
] | 66df5a92a5a3951c75dce557c2865aac3896b02062b3caf2923b6910877248e5 |
# Include the Dropbox SDK libraries
from dropbox import session
# Onitu has a unique set of App key and secret to identify it.
ONITU_APP_KEY = "6towoytqygvexx3"
ONITU_APP_SECRET = "90hsd4z4d8eu3pp"
# ACCESS_TYPE should be 'dropbox' or 'app_folder' as configured for your app
ACCESS_TYPE = 'dropbox'
sess = session.Dro... | onitu/onitu | drivers/dropbox/get_access_token.py | Python | mit | 1,017 | [
"VisIt"
] | aa189e37eec31ce5b968c9e970c577f8a1e7327be531ca6fc707deab0aedd629 |
#!/usr/bin/env python
# Copyright 2014-2018 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... | gkc1000/pyscf | pyscf/cc/gccsd_t_slow.py | Python | apache-2.0 | 2,817 | [
"PySCF"
] | f903317330d7725a1274d371ff6f31df0000054635263b6a0f602379475cc8cd |
NAME = "Minbias1PV"
#from tempfile import mkstemp
#from shutil import move
#from os import remove, close
#
#def replace(file_path, pattern, subst):
# #Create temp file
# fh, abs_path = mkstemp()
# with open(abs_path,'w') as new_file:
# with open(file_path) as old_file:
# for line in old_file... | saschastahl/ridge-analysis | scripts/GangaData2015.py | Python | mit | 1,323 | [
"DIRAC"
] | bc0bcd7083081e765293605e6429f8ce26f6d508ffa30cd1c8ac646d84b446de |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | modules/tensor_mechanics/test/tests/capped_mohr_coulomb/small_deform_hard_22.py | Python | lgpl-2.1 | 1,644 | [
"MOOSE"
] | 689eee2e7e0a5cf95f154e1d557a39187b0a8ce2eef264bba8f6f933e16dced3 |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | python/mooseutils/sqa_check.py | Python | lgpl-2.1 | 4,229 | [
"MOOSE"
] | 837c5326bc91b46cbd72f421e6ea4520ffd052c37344cecb9f30b0f48075bda2 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | juanchopanza/NeuroM | neurom/core/_neuron.py | Python | bsd-3-clause | 9,124 | [
"NEURON"
] | cc6a0399aab3b4ceb23d79bb169224317b28c3505148b96d3e7088cf10e166ef |
"""
The B{0install select} command-line interface.
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import os, sys
import logging
from zeroinstall import _
from zeroinstall.cmd import UsageError
from zeroinstall.injector import model, selections, requirements
... | pombredanne/zero-install | zeroinstall/cmd/select.py | Python | lgpl-2.1 | 6,751 | [
"VisIt"
] | 6979fb741acaeef3fb2d4f86c0a1a22571733e7462e107e430bb43bdc4e5f77e |
'''Module with classes and methods to analyse and process exported geomodel grids
Created on 21/03/2014
@author: Florian Wellmann (some parts originally developed by Erik Schaeffer)
'''
import numpy as np
try:
import matplotlib.pyplot as plt
except ImportError:
print("\n\n\tMatplotlib not installed - plotting... | flohorovicic/pygeomod | pygeomod/geogrid.py | Python | mit | 38,875 | [
"VTK"
] | dee58c68c7d6c6f6db378df693eda6bf33203b195158641ec88a897376a140d7 |
#!/usr/bin/python
"""
This script is an HTSeq alternatives.
It is count reads in regions, but if there
are overlapping regions the read is counted in both
regions. Read also counted if partially overlap
"""
import sys
import gzip
class Exon:
def __init__(self, fields):
self.chrx = fields[0]
self.... | TravisCG/SI_scripts | exonreadcount.py | Python | gpl-3.0 | 1,804 | [
"HTSeq"
] | a9f9480574f70bdfc9902b7cd6517135c9663f9d260982c1722af4ced83ad0e9 |
from django.conf.urls import url
from . import views
urlpatterns = [
url(r'^(?P<domain>.{1,36})/downlad.js/?$', views.downloadJS, name='downloadJS'),
url(r'^(?P<domain>.{1,36})/visit.js/?$', views.trackerJS, name='trackerJS'),
url(r'^(?P<domain>.{1,36})/visit.js/(?P<visitor>.{1,36})/?$', views.track... | hicinformatic/DJANGO-Tracker | urls.py | Python | gpl-3.0 | 2,604 | [
"VisIt"
] | 1f7f0c215d5671fee10e8e5d4895c16b48b1a10b05b4e1708794fbd43745ed5f |
""" This tests only need the JobDB, and connects directly to it
Suggestion: for local testing, run this with::
python -m pytest -c ../pytest.ini -vv tests/Integration/WorkloadManagementSystem/Test_JobDB.py
"""
# pylint: disable=wrong-import-position
from DIRAC.Core.Base.Script import parseCommandLine
pa... | petricm/DIRAC | tests/Integration/WorkloadManagementSystem/Test_JobDB.py | Python | gpl-3.0 | 2,640 | [
"DIRAC"
] | a2b19376ccb2877b6f1f0b50ca8998c99be0da8450bcc2c73fd4154c1a018366 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/BMED_8813_HAP/Features/multiple_features/best_kNN_PC/cross_validate_categories_kNN_PC_BMED_8813_HAP_scaled_method_II_area_force.py | Python | mit | 4,444 | [
"Mayavi"
] | 9392fb83504fac97e6d320223066d699570659222da5d174f53bc1249b0d5cc7 |
# Module wordnet.py
#
# Original author: Oliver Steele <steele@osteele.com>
# Project Page: http://sourceforge.net/projects/pywordnet
#
# Copyright (c) 1998-2004 by Oliver Steele. Use is permitted under
# the Artistic License
# <http://www.opensource.org/licenses/artistic-license.html>
"""Utility functions to use wit... | PennNLP/SLURP | semantics/wntools.py | Python | gpl-3.0 | 12,392 | [
"Amber"
] | f8534cdff38ef2721093e07f4e5e63e92773dde8252b28c3acd32894975b27b5 |
def get_versions():
return versions[0]["number"]
versions = [
{
"number": "1.7.5.3",
"features": [
"1. get_organelle_from_reads.py: fix a bug when no qualified reads found (issue 123)",
"2. get_organelle_from_reads.py: pass --spades-options to pre-assembly for Mac M1 ... | Kinggerm/GetOrganelle | GetOrganelleLib/versions.py | Python | gpl-3.0 | 31,892 | [
"BLAST"
] | 93f859fb4d5191267d79c9baec1852b5ab55c681829c791244a104daf8f8dc3b |
#!/usr/bin/python3
import numpy as np # For array operations.
import sys
nx = 0 # number of points in Ox; if 0, then search dns.ini
ny = 0 # number of points in Oy; if 0, then search dns.ini
nz = 0 # number of points in Oz; if 0, then search dns.ini
sizeofmask = 6
# do not edit below this line
# getting grid siz... | zrick/tlab | scripts/python/xdmf.py | Python | gpl-3.0 | 9,712 | [
"ParaView"
] | 0a8a91d2b5f11be4e296a10dd041cbec3e2d6c0fa365b736c22086c6129d9818 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkStreamPoints(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.v... | nagyistoce/devide | modules/vtk_basic/vtkStreamPoints.py | Python | bsd-3-clause | 497 | [
"VTK"
] | 795e630317ede4a8f8259c245d546e6a68c9687a7da880fec83846ae27ec0ae8 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | beernarrd/gramps | gramps/gen/filters/rules/family/__init__.py | Python | gpl-2.0 | 2,993 | [
"Brian"
] | f9c8cb1af93c6b8cdf4399af5389be62a5bc2385dbab7ec961eccb0b813e1aaf |
import param
import topo.pattern
import topo.pattern.random
import __main__
import os
import contrib
import topo
from topo.transferfn.misc import PatternCombine
from topo.transferfn.misc import HalfRectify
from topo import numbergen
from topo.pattern import Gaussian
from topo.numbergen import UniformRandom, BoundedNum... | ioam/svn-history | contrib/JanA/surround_model_design.py | Python | bsd-3-clause | 33,000 | [
"Gaussian"
] | f7dcc8699ef1f02cd1aad40988dc5d8a630f42433ded329c046aee3d5311885f |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/utils/Platform/generic/generic_RegisterSoundProvider.py | Python | gpl-3.0 | 966 | [
"ORCA"
] | 029286931b27d409f8875b9ee7d7c9b479db0dfff20872872e4218d62e15b789 |
from __future__ import generators
from pygr.leelabdb import *
import pygr.coordinator
def map_clusters(server,**kwargs):
"map clusters one by one"
hg17=BlastDB(ifile=server.open_resource('hg17','r')) # CONSTRUCT RESOURCE FOR US IF NEEDED
# LOAD DB SCHEMA
(clusters,exons,splices,genomic_seq,spliceGraph... | ctb/pygr | tests/oldtests/old/mapclusters3.py | Python | bsd-3-clause | 1,250 | [
"BLAST"
] | 251b13365140b653ba5d06bec421580aa333a9cd92f53f43af45cb5b07f72035 |
#!/usr/bin/python
"""Test of navigation to same page links."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
#sequence.append(WaitForDocLoad())
sequence.append(PauseAction(5000))
sequence.append(utils.StartRecordingAction())
sequence.append(KeyComboAction("<Control>Home"))
sequence.append... | GNOME/orca | test/keystrokes/firefox/line_nav_follow_same_page_link.py | Python | lgpl-2.1 | 2,088 | [
"ORCA"
] | 0e85631c96f15745f8d7028709b8f0b01b678337e9ae9ee271cad70a4f43cc00 |
# -*- coding: utf-8 -*-
import os
from click import Argument
from groundwork.patterns import GwCommandsPattern, GwRecipesPattern
class GwRecipesBuilder(GwCommandsPattern, GwRecipesPattern):
"""
Provides commands for listing and building recipes via command line interface.
Provided commands:
* reci... | useblocks/groundwork | groundwork/plugins/gw_recipes_builder.py | Python | mit | 3,282 | [
"VisIt"
] | 0047221d0bf48bad3cd49ef99d64a54109372613b98c8982c84b25ff1ac6b0a7 |
"""
Unit tests for basic CDL constructs.
"""
import os
import tempfile
import unittest
import cdlparser
import numpy as np
#---------------------------------------------------------------------------------------------------
class TestBasics(unittest.TestCase) :
#--------------------------------------------------------... | ocehugo/cdlparser | test/test_basics.py | Python | bsd-3-clause | 2,901 | [
"NetCDF"
] | 16cc26fae77b858742665a1bf535e9b6314309c4b0dd4d98f72c132839824d8e |
import numpy as np
from ase.units import Bohr
"""This module defines different external potentials to be used in
time-independent and time-dependent calculations."""
class ExternalPotential:
""" External potential
"""
def __init__(self, vext_g=None, gd=None):
"""Initialize with a grid and the c... | qsnake/gpaw | gpaw/external_potential.py | Python | gpl-3.0 | 13,131 | [
"ASE"
] | f887b35263eb4b4cb5f00887f242bb18067c40b9004955c3c70b5220d03a871e |
from sqlalchemy.types import *
import json
import pickle
import copy
import uuid
import binascii
from galaxy.util.bunch import Bunch
from galaxy.util.aliaspickler import AliasPickleModule
# For monkeypatching BIGINT
import sqlalchemy.dialects.sqlite
import sqlalchemy.dialects.postgresql
import sqlalchemy.dialects.mys... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/custom_types.py | Python | gpl-3.0 | 4,279 | [
"Galaxy"
] | 4977ce6b363d3f14b6b3be7186cfafbc828be19c64b0adedb1936e4dea3e62dd |
"""Pylons middleware initialization"""
import types
from beaker.middleware import CacheMiddleware, SessionMiddleware
from routes.middleware import RoutesMiddleware
from paste.cascade import Cascade
from paste.registry import RegistryManager
from paste.urlparser import StaticURLParser
from paste.deploy.converters impo... | DIRACGrid/DIRACWeb | dirac/config/middleware.py | Python | gpl-3.0 | 2,564 | [
"DIRAC"
] | 2ea85ba099bc7803d0a3ac4a7f90bb4b3be5ec3dfc30cb92b464058f512e5542 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | alexlo03/ansible | lib/ansible/modules/network/avi/avi_cloudconnectoruser.py | Python | gpl-3.0 | 4,187 | [
"VisIt"
] | 7011fb21fd659ebf76eb8773fa4688a9e1d796e2e594d3aede2226716513f72d |
"""A Chaco file reader.
"""
# Author: Suyog Dutt Jain <suyog.jain@aero.iitb.ac.in>
# Copyright (c) 2009, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Instance, Str
from traitsui.api import View, Group, Item
from tvtk.api import tvtk
# Local imports.
from mayavi.core.source... | dmsurti/mayavi | mayavi/sources/chaco_reader.py | Python | bsd-3-clause | 2,647 | [
"Mayavi",
"VTK"
] | 55b6088d116a6eeae75101c2156221760942f4fda3a27333cb1d2d8e068e96f8 |
from __future__ import nested_scopes
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# Christopher Blunck (blunck... | nzsquirrell/p2pool-myriad | oldstuff/SOAPpy/NS.py | Python | gpl-3.0 | 3,724 | [
"Brian"
] | 7187143df3653840e54c01ca340fee44ebd029814e1bdbd3b69317a710bbcdc1 |
#
# Copyright (C) 2013,2014 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... | sehrhardt/espresso | testsuite/python/nonBondedInteractions.py | Python | gpl-3.0 | 5,205 | [
"ESPResSo"
] | 6f8f1b95a9d9423902777dd5704601f4cf7fc023bb314c49e1f299a29f1e2d45 |
#Chip.py
#Implements a casino chip, which is used for betting on games.
#Created by: Andrew Davis
#Created on: 1/9/2016
#Open source (MIT license)
#import statements
from Utilities import get_chip_color
#class declaration for Chip superclass
class Chip(object):
"""A Chip is a representation of money in fixed
... | techgineer/casino-sim | src/Chip.py | Python | mit | 2,552 | [
"CASINO"
] | d60f11f990653d8277c9ca89f2ce32e34a92857cfa35e8e931e679f038c464ca |
#! /bin/env python
# Python Distutils setup script for SPARX
# VERSION_NUMBER of SPARX
VERSION_NUMBER = '3.1.3'
# number of Thread using in per job
ENABLE_MULTITREADING = 1
if ENABLE_MULTITREADING:
import multiprocessing
NumberOfThread = 2 * multiprocessing.cpu_count()
else:
NumberOfThread = ... | itahsieh/sparx-alpha | setup.py | Python | gpl-3.0 | 7,096 | [
"VTK"
] | 4d6ba870b8e3f1a578169782604ffbb405cd91c7a5e4ac0d9bf52c8cd438db96 |
# Copyright (C) 2016
# Max Planck Institute for Polymer Research & JGU Mainz
# 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 ... | espressopp/espressopp | src/io/DumpXYZ.py | Python | gpl-3.0 | 4,709 | [
"ESPResSo"
] | 91b669149e0084691c70a29c6d1072afa40cdbdc607c4fc7f4440a88ef92ac18 |
# -*- coding: utf-8 -*-
import os, json
import flannelfox.tools
from collections import OrderedDict
if os.environ.get('FF_ROOT', False):
HOME_DIR = os.environ.get('FF_ROOT')
else:
HOME_DIR = os.path.expanduser('~')
# #############################################################################
# Special variables t... | FlannelFox/FlannelFox | flannelfox/settings.py | Python | mit | 5,166 | [
"Galaxy"
] | 35c49bc9c2452851ffb615eec50b81e0af72516212f56acb88fa8353fa50c545 |
"""Get dependencies from packages on the Python Package Index (PyPI)
Adapted from Olivier Girardot's notebook:
https://github.com/ogirardot/meta-deps/blob/master/PyPi%20Metadata.ipynb
licensed under the Creative Commons Attribution 3.0 Unported License.
To view a copy of that license, visit
http://creativecommons.o... | hdashnow/python-dependencies | dependencies.py | Python | mit | 5,312 | [
"VisIt"
] | c7170bef28fb2ecf9effe57226ce83138f9cf1e3df6d7af68dbcd66bdea16ef5 |
# -*- coding: utf-8 -*-
# Copyright(C) 2008-2011 Romain Bignon
#
# This file is part of a weboob module.
#
# This weboob module 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 ... | laurentb/weboob | modules/aum/contact.py | Python | lgpl-3.0 | 11,860 | [
"exciting"
] | cad69e175186897a6eed8fe3522325de7ffbd6774bc0766740f1b28672cb0d2b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License, V... | sparkslabs/kamaelia | Sketches/MPS/VideoRecorder/VideoRecord.py | Python | apache-2.0 | 3,283 | [
"DIRAC"
] | 3d0a03726f8d421049b2f6e982f8ac520ef130a965c36c7f9ee9f5444bfb7cd8 |
# -*- coding: utf-8 -*-
#
# brunel_delta_nest.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Licen... | espenhgn/nest-simulator | pynest/examples/brunel_delta_nest.py | Python | gpl-2.0 | 12,068 | [
"NEURON"
] | 4ce930317ac307bce4fb23f8d4f52bc34c9052f5fc1f3b20c95121ac26caa8e3 |
from Firefly import logging
from Firefly.components.zwave.device_types.switch import ZwaveSwitch
from Firefly.const import ACTION_OFF, ACTION_ON, SWITCH
from Firefly.services.alexa.alexa_const import ALEXA_SMARTPLUG
TITLE = 'Aeotec Smart Switch 6'
BATTERY = 'battery'
ALARM = 'alarm'
POWER_METER = 'power_meter'
VOLTAG... | Firefly-Automation/Firefly | Firefly/components/zwave/aeotec/zw096_smart_switch_6.py | Python | apache-2.0 | 2,215 | [
"Firefly"
] | 404335b3b164d45c3aba92924918eabc328971cc2c586dfb3ed766854dc8914d |
import sys
if sys.version_info < (3,0):
from urllib import urlopen
fileHeader = "/user/schafer/web/outreach/dojo/"
else:
from urllib.request import urlopen
fileHeader = "../"
exclusionList = ["CVCoderDojo","jbschafer","uniscratch"]
approvalList = ["CVCoderDojo","jbschafer","uniscratch","crogersaea267"]... | jbschafer/LearningLabServer | scripts/updateProgress.py | Python | gpl-2.0 | 14,443 | [
"VisIt"
] | 932fac06616a82b2bd744f7a214870e0c214f46860600d12dd504d7745715a3c |
#!/usr/bin/env python
# L. Brodeau, 2015
# Potential temperature to conservative temperature (TEOS 10)
import sys
import os
import numpy as nmp
from netCDF4 import Dataset
from string import replace
import gsw
if len(sys.argv) != 5:
print 'Usage: '+sys.argv[0]+' <Temperature_file_to_convert> <temperature_nam... | brodeau/barakuda | python/exec/convert_pt_to_CT.py | Python | gpl-2.0 | 2,140 | [
"NetCDF"
] | ccac1e465c24bc090c0d62cc97691b01d7e9ead8da2761d3bb3d85ee7b7d620b |
class Module:
def __init__(self, mainMenu, params=[]):
# metadata info about the module, not modified during runtime
self.info = {
# name for the module that will appear in module menus
'Name': 'Linux PillageUser',
# list of one or more authors for the module
... | EmpireProject/EmPyre | lib/modules/collection/linux/pillage_user.py | Python | bsd-3-clause | 4,805 | [
"BLAST"
] | 2a8f6a7780a625f58bceef04d1bd8ce68828c44ca559e99ed08eaed8577b8c4f |
import base64
import traceback
import pyglet
from geoplotlib.core import GeoplotlibApp
from core import FONT_NAME
class AppConfig:
def __init__(self):
self.reset()
def reset(self):
self.layers = []
self.bbox = None
self.savefig = None
self.tiles_provider = 'positron'... | andrea-cuttone/geoplotlib | geoplotlib/__init__.py | Python | mit | 12,232 | [
"Gaussian"
] | f1b40f2f66b22c3e06cc57bb82a9a8371a57ea39215ff22920c6d71d9a8fab95 |
import unittest
from uptide.netcdf_reader import NetCDFInterpolator, CoordinateError, NetCDFFile
import itertools
import os
from numpy import arange, array, ones
# function used to fill the netcdf field, has to be linear
def f(lat, lon):
return lat*10 + lon
test_file_name1 = 'tests/test_netcdf_reader1.nc'
test_... | stephankramer/uptide | tests/test_netcdf_reader.py | Python | lgpl-3.0 | 6,525 | [
"NetCDF"
] | 847418e65ffe0805c3ff5fca756b67664f450fdd2b7318183b33c0bcb64a26dc |
# Copyright (c) 2015-2016, 2018 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2016 Ceridwen <ceridwenv@gmail.com>
# Copyright (c) 2018 Nick Drozd <nicholasdrozd@gmail.com>
# Licensed under the LGPL: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html
# For details: https://github.com/PyCQA/astroid/blob/m... | ekwoodrich/python-dvrip | env/lib/python3.5/site-packages/astroid/transforms.py | Python | mit | 3,377 | [
"VisIt"
] | d67a70256710512223729716775a5cf9d261b473b289ba101ec11300841de5ca |
"""
Functions to visualize an Experiment.
"""
__authors__ = "James Bergstra"
__license__ = "3-clause BSD License"
__contact__ = "James Bergstra <pylearn-dev@googlegroups.com>"
import math
import sys
# -- don't import this here because it locks in the backend
# and we want the unittests to be able to set th... | CVML/hyperopt | hyperopt/plotting.py | Python | bsd-3-clause | 19,940 | [
"Gaussian"
] | be6b7e65009b3a022833e7c43f664ead2d567d6074aa355e411da774930df3dc |
import numpy as np
from ase.units import Bohr
from gpaw import Calculator
from gpaw.localized_functions import create_localized_functions as clf
class STM:
def __init__(self, surfacecalc, tipcalc):
self.scalc = surfacecalc
self.tcalc = tipcalc
self.surface = surfacecalc.get_atoms()
... | qsnake/gpaw | gpaw/stm/__init__.py | Python | gpl-3.0 | 1,977 | [
"ASE",
"GPAW"
] | 3dd55e08a88cf4207b1fd6cec3a6f8fe33679330d5c7b8af13239b1efc09d26e |
import numpy as np
import argparse
from time import time
from builder.args import addLoggingParams, addDebuggingParams, \
addEarlyStop, addSupDataParams
from builder.profiler import setupLogging
from ae.net import TrainerSAENetwork
from ae.contiguousAE import ContiguousAutoEncoder
from ae.con... | mbojrab/playbox | trunk/projects/supervised/semiSupervisedTrainer.py | Python | mit | 6,842 | [
"NEURON"
] | aadfb04c709208d87300ffb9a39e027bdf6b453596bfe6491b1d75971e1b66ad |
# -*- coding: utf-8 -*-
## Description: class MorphML for loading MorphML from file or xml element into MOOSE
## Version 1.0 by Aditya Gilra, NCBS, Bangalore, India, 2011 for serial MOOSE
## Version 1.5 by Niraj Dudani, NCBS, Bangalore, India, 2012, ported to parallel MOOSE
## Version 1.6 by Aditya Gilra, NCBS, Bangalo... | upibhalla/moose-core | python/moose/neuroml/MorphML.py | Python | gpl-3.0 | 40,773 | [
"MOOSE",
"NEURON"
] | 11fa136505fe0c251b2c49924a7383cf067e3769e39aa184adf0be21a7dec604 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | mol_dqn/chemgraph/dqn/run_dqn.py | Python | apache-2.0 | 15,386 | [
"RDKit"
] | e96467655a139cfeb2f320fe14095f7e40d48673a46bd402141d19bd9fa45c23 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Defines classes and methods used for recurrent neuronal networks.
Copyright (C) 2012 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Fr... | espenhgn/LFPy | LFPy/network.py | Python | gpl-3.0 | 66,722 | [
"NEURON"
] | 251efcb3f8b938cce3430c9c326bca016f337ccd897964a62e43d0c3ad39cb78 |
import sys
import json
import random
import numpy as np
def sigmoid(z):
"""
Return the sigmoid function evaluated at the given input.
:param z: Vector or scalar input.
:return: Sigmoid of the given input.
"""
return 1.0 / (1.0 + np.exp(-z))
def sigmoid_prime(z):
"""
... | mrbell/connectfour | tdc4bot.py | Python | gpl-3.0 | 6,309 | [
"Gaussian"
] | 1ae0dbf119c1890f5cc19ea0a1802873f824159f84555ae491d2aea1cbea607c |
"""Probit regression class and diagnostics."""
__author__ = "Luc Anselin luc.anselin@asu.edu, Pedro V. Amaral pedro.amaral@asu.edu"
import numpy as np
import numpy.linalg as la
import scipy.optimize as op
from scipy.stats import norm, chisqprob
import scipy.sparse as SP
import user_output as USER
import sum... | spreg-git/pysal | pysal/spreg/probit.py | Python | bsd-3-clause | 26,765 | [
"COLUMBUS"
] | 84bb201c23f9372d91133546df1791aac7722b66dd6fb7034efcad505c07cb5d |
# The MIT License (MIT)
#
# Copyright (c) 2018, TU Wien
#
# 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,... | wpreimes/gldas | src/gldas/interface.py | Python | bsd-3-clause | 16,937 | [
"NetCDF"
] | 19c6e282d87ce9b6cdd59b621f42196e8b3761e7b8bee98ae6dfa7049770316e |
#!/usr/bin/env python -i
# preceding line should have path for Python on your machine
# demo.py
# Purpose: illustrate use of many library interface commands
# Syntax: demo.py
# uses in.demo as LAMMPS input script
from __future__ import print_function
import sys
# parse command line
argv = sys.argv
if len(... | Pakketeretet2/lammps | python/examples/demo.py | Python | gpl-2.0 | 1,302 | [
"LAMMPS"
] | feffb91a1dccc757f712af376a4bfe7aacded9e2fcbab355ab24f64c1a0f97b5 |
"""A simple wrapper for `tvtk.Cutter`.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2008, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Instance, Property
from traitsui.api import View, Group, Item
from tvtk.api import tvtk
# Local imports... | dmsurti/mayavi | mayavi/components/cutter.py | Python | bsd-3-clause | 2,478 | [
"Mayavi"
] | bfd4bdecd4445d0a5e03e69aed198b155d4953efa89258d96d74b3e8c66bc7ad |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
import numpy as np
import os
import os.path as op
from scipy import sparse, linalg
from copy import deepcopy
from .io.constants import FIFF
from .io.tree import dir... | rajegannathan/grasp-lift-eeg-cat-dog-solution-updated | python-packages/mne-python-0.10/mne/source_space.py | Python | bsd-3-clause | 101,801 | [
"Mayavi"
] | adf97e9266371011a3b81f597a3fc6ae7df64cde7630ebd729a25cd8586ca995 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/lib/NeighborSearch.py | Python | gpl-2.0 | 4,718 | [
"MDAnalysis"
] | 8fb118bb51186202d879fbea2d1e4485c71ff33342424106f4fa8c45279ba1c7 |
# coding: utf-8
"""
This module defines the events signaled by abinit during the execution. It also
provides a parser to extract these events form the main output file and the log file.
"""
from __future__ import unicode_literals, division, print_function
import sys
import os.path
import datetime
import collections
im... | rousseab/pymatgen | pymatgen/io/abinitio/events.py | Python | mit | 28,120 | [
"ABINIT",
"NetCDF",
"pymatgen"
] | 5cb0e594a51daee1c551e16f31460119a28a9b434a508296385c8daeaae164b3 |
################################################################################
# SCFGP: Sparsely Correlated Fourier Features Based Gaussian Process
# Github: https://github.com/MaxInGaussian/SCFGP
# Author: Max W. Y. Lam (maxingaussian@gmail.com)
####################################################################... | MaxInGaussian/SCFGP | experiments/kin8nm/test_regression.py | Python | bsd-3-clause | 1,832 | [
"Gaussian"
] | 6473d03bd0e211e062c20947aa33f75679b501033eeab4b1ad16ddb0bdd55a7f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
'''General routines shared between decoders
'''
# Copyright © 2013 Kevin Thibedeau
# This file is part of Ripyl.
# Ripyl 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... | kevinpt/ripyl | ripyl/decode.py | Python | lgpl-3.0 | 48,118 | [
"Gaussian"
] | fc2994fc570f73cee242ccaf758b84bb0e9c6f1348e41b988f780cd92d48963a |
# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is... | eddiejessup/pizza | src/data.py | Python | gpl-2.0 | 12,483 | [
"LAMMPS"
] | f48dd58365b09edef1a3b80e3cf02489368804009fd03f70defbb151b5b6f17d |
"""
@name: Modules/Core/Utilities/_test/test_coordinate_tools.py
@author: D. Brian Kimmel
@contact: d.briankimmel@gmail.com
@copyright: 2016-2019 by D. Brian Kimmel
@date: Created on Jun 21, 2016
@licencse: MIT License
@summary:
Passed all 5 tests - DBK 2016-11-22
"""
__updated__ = '2019-09-07'... | DBrianKimmel/PyHouse | Project/src/Modules/Core/Utilities/_test/test_coordinate_tools.py | Python | mit | 1,987 | [
"Brian"
] | a34f575f3da7907305262bf5fb8af7cf744ff17fe648f3e3ac2c2ccdfa2b1961 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_clocksyn_lodens_0004/brian2_benchmark_COBAHH_clocksyn_lodens_0004.py | Python | gpl-3.0 | 3,772 | [
"Brian"
] | 0e60a10162104b807e8efc284dd5f1ae1d6c8ebf566ea5504c8484f879d47057 |
#!/usr/bin/env python
from subprocess import call
import shutil
import simplejson
from collections import OrderedDict
import os
from GitBoil import Boil
### TODO
# make README.md blank
# update key words
# https://github.com/jamesrhaley/es2015-babel-gulp-jasmine.git
new_name = raw_input("what should the project be c... | jamesrhaley/boilJS | boil_JS.py | Python | mit | 1,987 | [
"GULP"
] | 18467e4bb4ca661a10e125dc9dea12db1d06426080aedf1c27adc81a1b68b315 |
import rdkit.Chem.GraphDescriptors as RDKit
from ._base import Descriptor
from ._graph_matrix import DistanceMatrix
__all__ = ("BalabanJ",)
class BalabanJ(Descriptor):
r"""Balaban's J index descriptor(rdkit wrapper)."""
since = "1.0.0"
__slots__ = ()
def description(self):
return "Balaban'... | mordred-descriptor/mordred | mordred/BalabanJ.py | Python | bsd-3-clause | 733 | [
"RDKit"
] | ab2f287bbdb154553547cbf770b682b1367078e250b22e082ada5d7577ba906d |
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