text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
# -*- coding: utf-8 -*-
#
# brette_gerstner_fig_3d.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 ... | tammoippen/nest-simulator | pynest/examples/brette_gerstner_fig_3d.py | Python | gpl-2.0 | 3,030 | [
"NEURON"
] | 3b34cc586834d01009181576829badc46c51ecedc32bfb62a21186e13ddb7261 |
#
# Copyright 2020 Johannes Hoermann (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software F... | libAtoms/matscipy | matscipy/electrochemistry/poisson_nernst_planck_solver_fenics.py | Python | lgpl-2.1 | 15,708 | [
"Matscipy"
] | 7eba04a8d3e182d1efa9427d5424fe378a9c1fa71745299a1da58aa01ceac1f7 |
# -*- coding: utf-8 -*-
"""
Author: Ang Ming Liang
Please run the following command before running the script
wget -q https://raw.githubusercontent.com/sayantanauddy/vae_lightning/main/data.py
or curl https://raw.githubusercontent.com/sayantanauddy/vae_lightning/main/data.py > data.py
Then, make sure to get your kag... | probml/pyprobml | vae/standalone/vae_info_celeba_lightning.py | Python | mit | 10,476 | [
"Gaussian"
] | d3917bdc7c65231b9e5379ec3927130e0e06e681f0444dab8cfc01a374c57a78 |
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | peterbraden/tensorflow | tensorflow/contrib/distributions/__init__.py | Python | apache-2.0 | 1,265 | [
"Gaussian"
] | 0fce756326733ac3cbebbbf4fdd82d5fff7a889d9c8dc778e872175b0eba319d |
from ase.atoms import Atoms
from ase.units import Bohr
def read_turbomole(filename='coord'):
"""Method to read turbomole coord file
coords in bohr, atom types in lowercase, format:
$coord
x y z atomtype
x y z atomtype f
$end
Above 'f' means a fixed atom.
"""
from ase import A... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/io/turbomole.py | Python | gpl-2.0 | 5,680 | [
"ASE",
"TURBOMOLE"
] | 42f54f01f3356fdd92b6e736ac3098b6e600e4191d5accce4811227da4ac9697 |
from galaxy.util.bunch import Bunch
from pulsar.client.action_mapper import (
FileActionMapper,
)
def test_endpoint_validation():
client = _min_client("remote_transfer")
mapper = FileActionMapper(client)
exception_found = False
try:
mapper.action('/opt/galaxy/tools/filters/catWrapper.py', ... | ssorgatem/pulsar | test/action_mapper_test.py | Python | apache-2.0 | 1,536 | [
"Galaxy"
] | fcb611ff3c2519b4f01d8428415f695c0a6150a61c3ca3cfe3cec3fff299800c |
# coding=utf-8
"""A converter for USGS shakemap grid.xml files."""
import codecs
import logging
import os
import shutil
import sys
from datetime import datetime
from subprocess import call, CalledProcessError
from xml.dom import minidom
import numpy as np
import pytz
# This import is required to enable PyQt API v2
#... | Charlotte-Morgan/inasafe | safe/gui/tools/shake_grid/shake_grid.py | Python | gpl-3.0 | 40,680 | [
"Gaussian"
] | f01833c34522e918cab43949f5a838dc3975c6cff2f3067d1d1290eacfcc45db |
# -*- coding: utf-8 -*
###############################################################################
# rkr.py
# Rydberg-Klein-Rees potential energy curve from spectroscopic constants
# Gv Bv
# Stephen.Gibson@anu.edu.au - May 2016
###############################################################################
import ... | stggh/PyDiatomic | cse/tools/RKR.py | Python | gpl-3.0 | 8,127 | [
"Gaussian"
] | a46cd8fe34bf499c93686f9b3770f2799ce2fe3448f8456a771debc9d3713bfb |
#previous record: 84
import random
import matplotlib.pyplot as plt
def summation(result,first):
array = [0,0,0,0,0,0,0,0,0,0]
second = result - first
array[first] = 1
array[second] = 1
return array
class neuron(object):
def __init__(self):
self.value = 0
def sum(sel... | LorenzoM1997/math-neural-network | math_neural_network_0.0.6.py | Python | mit | 4,576 | [
"NEURON"
] | ed57b19d9bb9e750355921ee5e09d90a95b0117858ade638530c3a78a09d75fb |
from galaxy.web.base.controller import *
import pkg_resources
pkg_resources.require( "simplejson" )
import simplejson
from galaxy.tools.parameters import *
from galaxy.tools import DefaultToolState
from galaxy.tools.parameters.grouping import Repeat, Conditional
from galaxy.datatypes.data import Data
from galaxy.util... | volpino/Yeps-EURAC | lib/galaxy/web/controllers/workflow.py | Python | mit | 37,430 | [
"Galaxy"
] | e11d637736b5de654b6f0caab090d2098a3ed2c95fa7c5d98c4cb64739b9aea3 |
import sys
sys.path.insert(1, "../../../")
import h2o
import random
def cv_carsGBM(ip,port):
# read in the dataset and construct training set (and validation set)
cars = h2o.import_file(path=h2o.locate("smalldata/junit/cars_20mpg.csv"))
# choose the type model-building exercise (multinomial classificati... | mrgloom/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_cv_carsGBM.py | Python | apache-2.0 | 7,230 | [
"Gaussian"
] | 9fc82836d983f710b7dca765d6a9540df86c6dee5554b85f131338ab8a2f3979 |
#! /usr/bin/env python
from MDAnalysis import *
#from MDAnalysis.analysis.align import *
import numpy
import math
u = Universe("init.pdb","sampled.pos.pdb")
v = Universe("init.pdb")
# residues
a1 = u.selectAtoms("segid A and resid 50") # beginning of helixA1
b1 = u.selectAtoms("segid A and resid 176")
a2 = u.selectA... | demharters/git_scripts | dist_1mi5.py | Python | apache-2.0 | 1,627 | [
"MDAnalysis"
] | f87d7d376fed5ee2dfba5f60f732688db1eb500ba3daf0f63a4e4905462e3f3c |
import pathlib
from math import fsum
import numpy as np
import pytest
import meshplex
from .helpers import is_near_equal, run
this_dir = pathlib.Path(__file__).resolve().parent
@pytest.mark.parametrize("a", [0.5, 1.0, 1.33]) # edge length
def test_regular_tet0(a):
points = (
a
* np.array(
... | nschloe/voropy | tests/test_mesh_tetra.py | Python | mit | 13,502 | [
"VTK"
] | 4cb43a8915070b6f2909480f1d3604210eb0a251e7b7ea24d85ea1adfc25e4cf |
# -*- coding: utf-8 -*-
# Copyright (c) 2008, 2010, 2013 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2014-2017 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 Google, Inc.
# Copyright (c) 2014 Arun Persaud <arun@nubati.net>
# Copyright (c) 2015 Ionel Cristian Maries <contact@ionelmc.ro>
... | kczapla/pylint | pylint/test/unittest_pyreverse_writer.py | Python | gpl-2.0 | 3,991 | [
"VisIt"
] | f7b826f99ab800990872c579fe3b1f13f7b0ac56f6b8c21d839ec9b52ea7fae3 |
import pandas as pd
import itertools
from sys import argv
script, strain_name = argv
edges_final = pd.read_csv('%s_edges_best_itineration.txt'%strain_name, sep='\t')
while True:
try:
per_genes = int(raw_input("\n What minimum percentage of matching genes would you like [from 0 to 100]? "))
blast... | NP-Omix/BioCompass | BioCompass/filter_edges.py | Python | bsd-3-clause | 2,462 | [
"BLAST"
] | 92f701961a14c22bc6fafeaa218994c5a6607f47b50c02170564e979a9c72829 |
from django.core.management.base import BaseCommand, CommandError
from optparse import make_option
import os
import sys
def null_technical_500_response(request, exc_type, exc_value, tb):
raise exc_type, exc_value, tb
class Command(BaseCommand):
option_list = BaseCommand.option_list + (
make_option('--... | genova/rapidsms-senegal | apps/django_extensions/management/commands/runserver_plus.py | Python | bsd-3-clause | 2,969 | [
"VisIt"
] | edf2fbfb35ebd119bd11d4d3ce1fb02207e3845535d02ea7d18029e2bbe4dc7b |
# Version: 0.17
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, and pypy
* [![Latest Version]
(http... | has2k1/onelib | versioneer.py | Python | bsd-3-clause | 68,878 | [
"Brian"
] | 6a602fb241586b6a1e1dba9dda0e84ccdb8c08a528d4b153a3ed68ba1bdb107e |
"""Module Description
Copyright (c) 2014, Ying Jin <yjin@cshl.edu >
This code is free software; you can redistribute it and/or modify it
under the terms of the Artistic License (see the file COPYING included
with the distribution).
@author: Ying Jin
@contact: yjin@cshl.edu
"""
import sy... | mhammell-laboratory/tetoolkit | TEToolkit/GeneFeatures.py | Python | gpl-3.0 | 7,064 | [
"HTSeq"
] | 63c7469430f4c7fc23b711b470042f173b0dbdd19da51d64b121524d7dec4e9e |
# Copyright (C) 2015
# Jakub Krajniak (jkrajniak at gmail.com)
# 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:... | espressopp/espressopp | src/tools/topology_helper.py | Python | gpl-3.0 | 12,520 | [
"ESPResSo",
"Gromacs"
] | afd348d802700c61fb778413f9811d3b2feca6d6defe9cce9288c941ff053516 |
# 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/lib/parameters.py | Python | apache-2.0 | 2,769 | [
"PySCF"
] | 91e4cad805fccb455f427aeba5df7282e59f917d347e0cc5d10541daa660594e |
import parser
import compiler
import phpbuiltins
import prepr
from phpbuiltins.primitives import primitives
import phpbuiltins.constants as constants
import phpclass
import phpfunction
import phparray
import coerce
from varref import VarRef, VarDef
from errors import ExecuteError, ReturnError, StopExecutionError
import... | g-i-o-/pyphp | pyphp/executer.py | Python | mit | 19,104 | [
"VisIt"
] | deb286fd8a3e0d8cac1b953a50021b1fe34f8f4cd77bea943a5d622f458d9224 |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | gptech/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 100,278 | [
"VisIt"
] | edac78340117cf8bafec51eb3fb3d4eb073374208bcbf0181cb3c8a34b9836fb |
# -*- coding: utf-8 -*-
import copy
import json
import os
from email.utils import formataddr
from django.conf import settings
from django.core import mail
from unittest import mock
import pytest
from waffle.testutils import override_switch
from olympia import amo
from olympia.access.models import Group, GroupUser
... | eviljeff/olympia | src/olympia/activity/tests/test_utils.py | Python | bsd-3-clause | 27,303 | [
"VisIt"
] | 2e2dfe1b0e04d1cdf0ce6cbc4032d86398190efbd050f109272d32acf8d84a56 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | lach76/scancode-toolkit | src/commoncode/ignore.py | Python | apache-2.0 | 12,787 | [
"VisIt"
] | 6dbbec8463b310a5e65e0ee3f0bca07bd1ebd220c2848ce7eb202fab3ffc439a |
#!/usr/bin/env python
"""Test out HMMs using the Occasionally Dishonest Casino.
This uses the ocassionally dishonest casino example from Biological
Sequence Analysis by Durbin et al.
In this example, we are dealing with a casino that has two types of
dice, a fair dice that has 1/6 probability of rolling any number an... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_HMMCasino.py | Python | gpl-2.0 | 6,551 | [
"Biopython",
"CASINO"
] | 4fa0213e1d1aad508efbdfc61a8cf34d6993ebc257e7364e723ab87a5c8f4519 |
#!/usr/bin/env python
import os
import re
import urllib
import csv
import datetime
import time
from string import Template
from optparse import OptionParser
last_tag_pattern = 'EMPATHY_3_8*'
upload_server = 'master.gnome.org'
template = '''\
$name $version is now available for download from:
$download
$md5sums
What... | mssurajkaiga/empathy | release.py | Python | gpl-2.0 | 8,188 | [
"VisIt"
] | b62224701e96d34a89ed761e8e9fc99c73ef89027492df676a28f7d1cc59a21a |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import numpy as np
from scipy.spatial.distance import cdist
import matplotlib.pyplot as plt
from math import sqrt
import matplotlib.animation as animation
from brian import *
''' Spikes model in computational neuroscience with Brian library. '''
# -----------... | Aurelien1609/Computational-model | spikes_model.py | Python | bsd-3-clause | 12,338 | [
"Brian"
] | 1225a5f4ab83c4145003c04f3a8dd44625ec9a28a71c05720c34f49e1e94a5fb |
#!/usr/bin/env python
# Copyright (C) 2016 by Ali Baharev <ali.baharev@gmail.com>
# All rights reserved.
# BSD license.
from os import walk
from os.path import normpath, join
from sys import argv, exit
from PyPDF2 import PdfFileMerger
def main():
root = normpath(argv[1])
pdfs_merged = argv[2]
merger = PdfF... | baharev/SG2PS_Qt_GUI | pdf_concat/pdf_concat.py | Python | lgpl-3.0 | 751 | [
"VisIt"
] | 99cd180994f2d7c0c6dd2dfd605ae9d318becab7be73ed235d838a722d59725c |
"""
Unit tests for utils
"""
import textwrap
import unittest
from ddt import data, ddt, unpack
from regression.pages.common.utils import (
convert_date_format,
extract_mmm_dd_yyyy_date_string_from_text,
extract_numerical_value_from_price_string,
get_target_url_from_text,
read_enrollment_codes_fro... | edx/edx-e2e-tests | regression/pages/common/tests/test_utils.py | Python | agpl-3.0 | 13,873 | [
"VisIt"
] | e5cd20085feb1dc4690037de3857e99c17e78bb8ee27f15191786bacf207d735 |
#!/usr/bin/env python
import os, sys, time
path = os.path.split(os.path.realpath(__file__))[0]; os.chdir(path); sys.path.insert(0, path)
import util
while True:
try:
print("Visit https://cocalc.com" + util.base_url() + '/app/\n')
except Exception as mesg:
print(mesg)
print("wai... | tscholl2/smc | src/dev/project/info.py | Python | agpl-3.0 | 349 | [
"VisIt"
] | 56edb236de708e3069baab6bae1ee63c2d4579a75f4d58226eb767e745f9b249 |
# -*- coding: utf-8 -*-
# @Author: patrick
# @Date: 2016-09-01 17:04:53
# @Last Modified by: Patrick Bos
# @Last Modified time: 2016-10-06 07:30:16
# as per tensorflow styleguide
# https://www.tensorflow.org/versions/r0.11/how_tos/style_guide.html
from __future__ import absolute_import
from __future__ import divis... | roofit-dev/parallel-roofit-scripts | tensorflow_testing/tensorflow_roofit_demo_2-stripped.py | Python | apache-2.0 | 11,328 | [
"Gaussian"
] | ea8349c328c0eac8edcea801e876de3513abb8ec87a7cf7fa40c265c807f30ff |
# -*- coding: utf-8 -*-
'''
Random Forest classifier
'''
from sklearn.cluster import DBSCAN
from sklearn import metrics
from sklearn.preprocessing import StandardScaler
from ...core.routes import register
from .base import BaseMl, BaseMlSk
from sklearn.naive_bayes import GaussianNB
from sklearn.ensemble import AdaBoo... | Succeed-Together/bakfu | classify/ml/ml_sklearn.py | Python | bsd-3-clause | 2,016 | [
"Gaussian"
] | 44f6c04c8a06b560a35b8e697535c7d3474d5e1d318af62aeb0dc288a01763e7 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/tdscf/test/test_tdrks.py | Python | apache-2.0 | 15,918 | [
"PySCF"
] | 1cc84c02cd3ff52ff02b178116d331dce4bc5b35bdd9348b17b6a7972131af2a |
""" This module loads all the classes from the VTK Geovis library into
its namespace. This is an optional module."""
from vtkGeovisPython import *
| spthaolt/VTK | Wrapping/Python/vtk/geovis.py | Python | bsd-3-clause | 149 | [
"VTK"
] | e6cab0baf7b09a77d46f382c8c0cf582cd286fc5481af654a8f80226fe240b3e |
# -*- coding: utf-8 -*-
#########################################################################
## rdesigneur0_5.py ---
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of th... | dilawar/moose-core | python/rdesigneur/rdesigneur.py | Python | gpl-3.0 | 73,863 | [
"MOOSE",
"NEURON"
] | 2af67e41d4c611a7c5b67d3e1bd6fa76acd6ead0ec2dfdc0dda82bececb5c009 |
#!/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/MooseDocs/test/extensions/test_comment.py | Python | lgpl-2.1 | 2,834 | [
"MOOSE"
] | 99e664d1719b0ef1773a3e15be949b94cc121d2a15c66c87941c7b6b966a55bc |
# Copyright (c) 2018, Henrique Miranda
# All rights reserved.
#
# This file is part of the yambopy project
#
from yambopy import *
from netCDF4 import Dataset
from math import sqrt
import numpy as np
from cmath import exp
from yambopy.units import ha2ev, ev2cm1, I
class YamboElectronPhononDB():
"""
Python clas... | alexmoratalla/yambopy | yambopy/dbs/OLD_elphondb.py | Python | bsd-3-clause | 8,788 | [
"Yambo"
] | a5dee1bd43c7469102577177a00bccbd4c267f7322dcda88e2e0ee83aa33f17e |
"""
=================
Lorentzian Fitter
=================
"""
import numpy
from numpy.ma import median
from numpy import pi
from pyspeckit.mpfit import mpfit
from . import fitter
class LorentzianFitter(fitter.SimpleFitter):
def __init__():
self.npars = 3
self.npeaks = 1
self.onepeaklorentz... | bsipocz/pyspeckit | pyspeckit/spectrum/models/lorentzian.py | Python | mit | 1,865 | [
"Gaussian"
] | 62960172d7a3359a2a9c22e789ee5efa8b3f9979e3b4c4bc40d1e148c67276b5 |
# This file is part of cclib (http://cclib.sf.net), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2007, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You shou... | Clyde-fare/cclib_bak | src/cclib/method/cda.py | Python | lgpl-2.1 | 4,729 | [
"cclib"
] | bcae16244d8d910f4522a3792b870cc817355d48f66d1c1370c63ee0427d4385 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2015, Adrián Gómez Pueyo and Alberto Castro
# This file is part of maxdft.
# maxdft 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 ... | albertocbarrigon/maxdft | src/ga.py | Python | gpl-3.0 | 3,657 | [
"Octopus"
] | 9cea886f15479ee023e7fe9d2024a45d246deaac4eb9eebe7ebd199754111855 |
"""Tornado handlers for the tree view.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distributed as part ... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/IPython/html/tree/handlers.py | Python | bsd-3-clause | 3,597 | [
"Brian"
] | a0e4f1a9f2069a2b807d0b5feda0e66d92ecd1d19c03acf34a067e62b3ec8301 |
import pdb
import numpy as np
import math
import time
import chainer
import chainer.functions as F
import chainer.links as L
from chainer import cuda
from util import gaussian_logp
from util import gaussian_logp0
class VAE(chainer.Chain):
def __init__(self, dim_in, dim_hidden, dim_latent, num_layers, temperatur... | ashwindcruz/dgm | sdgm_pose/model.py | Python | mit | 7,234 | [
"Gaussian"
] | 939105655dbba67284e22eb0c78616977d44b7e67676bda216f1c976301ce9dd |
"""
Views for the verification flow
"""
import datetime
import decimal
import json
import logging
import six
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.contrib.staticfiles.storage import staticfiles_storage
from django.core.mail import send_mail
from django... | edx-solutions/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 62,323 | [
"VisIt"
] | f359286ea1d2dc94c6610b8220ce8502157abb1490dea3bcba973aa1555e79d6 |
#!/usr/bin/python
"""
Copyright 2016 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | druss316/G-Harvestor | html/resetPassword.py | Python | gpl-3.0 | 2,752 | [
"Galaxy"
] | ef0f0d8e6145ec81f2b5d70556cb3cac48a54bd0db3703a8244716cd16a258c3 |
import math
class QuadratureRule(object):
"""
Quadrature rules are implemented using this class, in order to
simplify the code and provide a common infrastructure
for tasks such as error estimation and node caching.
You can implement a custom quadrature rule by subclassing
:class:`QuadratureRu... | fperez/sympy | sympy/mpmath/quadrature.py | Python | bsd-3-clause | 37,720 | [
"Gaussian"
] | d472879830ebbe83f1beaefbac9dbf1ae866e995020c5bd47d9b274cc7937f90 |
# Orca
#
# Copyright (C) 2010-2011 The Orca Team
# Copyright (C) 2011-2012 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# 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; e... | h4ck3rm1k3/orca-sonar | src/orca/scripts/toolkits/WebKitGtk/script.py | Python | lgpl-2.1 | 25,694 | [
"ORCA"
] | 0d631b8c7951106f44943f8f3e3e18d5a073e895a77b4e6e922672340f16ed9f |
# 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 the G... | espressopp/espressopp | src/integrator/ExtForce.py | Python | gpl-3.0 | 2,172 | [
"ESPResSo"
] | c21e7abc2fc42ad1f595fd848711fd1e514dc3e0589f8895e028887fa453a6b1 |
from robot import Robot
class TheRobot(Robot):
def initialize(self):
self.health = 100
self._movefor = 0
self._moveforce = 0
self._turnto = 0
def respond(self):
self.turnto()
self.scan_and_fire()
# Move away if damaged
health = self.sensors['HEA... | CodingRobots/CodingRobots | robots/examples/Zombie.py | Python | gpl-3.0 | 1,251 | [
"BLAST"
] | 8d31e2cefca496a7f964f6e4ca20de9bd4d41972a22f3005b9b42fe9f865964c |
from behave import when, given, then
@when(u'I visit the user registration page')
def step_impl(context):
context.browser.get(context.server_url + '/user/register')
| libretees/libreshop | libreshop/tests/steps/customer.py | Python | gpl-3.0 | 170 | [
"VisIt"
] | 6885df13e833114f706745589aa05d911a429bc159cc94a1d793524907a4ca84 |
"""
Integration routines
====================
Methods for Integrating Functions given function object.
quad -- General purpose integration.
dblquad -- General purpose double integration.
tplquad -- General purpose triple integration.
fixed_quad -- Integrate func(x) using Gaussian ... | lesserwhirls/scipy-cwt | scipy/integrate/info.py | Python | bsd-3-clause | 1,259 | [
"Gaussian"
] | 179f9cfcd3fc5abd9bc3e9d13adf50bd9e707931c32a023e978ea9656e8f6d06 |
import unittest
import scipy
import pysal
import numpy as np
from pysal.spreg import error_sp as SP
class TestBaseGMError(unittest.TestCase):
def setUp(self):
db=pysal.open(pysal.examples.get_path("columbus.dbf"),"r")
y = np.array(db.by_col("HOVAL"))
self.y = np.reshape(y, (49,1))
X... | chhao91/pysal | pysal/spreg/tests/test_error_sp.py | Python | bsd-3-clause | 14,241 | [
"COLUMBUS"
] | 4e428a700929579de4a86f29e91db864d3f63a45a0e9c50223db6c528e5a7caa |
"""Bayesian Gaussian Mixture Model."""
# Author: Wei Xue <xuewei4d@gmail.com>
# Thierry Guillemot <thierry.guillemot.work@gmail.com>
# License: BSD 3 clause
import math
import numpy as np
from scipy.special import betaln, digamma, gammaln
from .base import BaseMixture, _check_shape
from .gaussian_mixture impo... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/sklearn/mixture/bayesian_mixture.py | Python | mit | 32,991 | [
"Gaussian"
] | 104289e192d06d54c06f54d6190a08cba58cdc056c2b175e90ffdb23780a0e4a |
# 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 ... | BlueBrain/NeuroM | neurom/core/morphology.py | Python | bsd-3-clause | 18,223 | [
"NEURON"
] | 4a1ddb95726d36d66a016a3631476d1cc369f721872626bf7d5e77a406c541e6 |
#!/usr/bin/env python
"""
means.py
"""
import os
import multiprocessing
from itertools import groupby
from ..calendar import dpm, next_month, next_day, prev_month, prev_day
from ..utils import chunks
from .share import MACH_OPTS
from nco import Nco
nco = Nco(**MACH_OPTS)
global results_list
results_list = []
# Sort ... | jhamman/rasmlib | rasmlib/post_processing/means.py | Python | gpl-3.0 | 18,243 | [
"NetCDF"
] | b667f093ca714f1422a976c340c32483d1ee835ab1ee2a5dcf6a77b9ca93f0db |
import types
import rdflib
from ontquery.terms import OntId
from pyontutils.utils_extra import check_value
from pyontutils.namespaces import TEMP
from pyontutils.closed_namespaces import rdf, rdfs, owl
try:
breakpoint
except NameError:
from IPython import embed as breakpoint
def flattenTriples(triples):
f... | tgbugs/pyontutils | pyontutils/combinators.py | Python | mit | 34,410 | [
"NEURON"
] | 9d3cd2d052e250f337c49d3c828e358cb2ceabbf6e99519a9435b218eb7c8d4e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Unit tests for StructureNL (SNL) format
"""
__author__ = "Anubhav Jain"
__credits__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Pro... | tallakahath/pymatgen | pymatgen/matproj/tests/test_snl.py | Python | mit | 9,885 | [
"pymatgen"
] | 57ab769f85b4e31b23780dc1c7091a516e39a6a29d1135728fe8a5dde0adc3d3 |
#from smfret import distances
from odin.smfret.distances import residue_residue, atom_atom
from odin.exptdata import SingleMolecExperiment
import numpy as np
class smFRET(SingleMolecExperiment):
"""
Class for working with a single molecule FRET (Forster
Resonance Energy Transfer) experiment. This is a si... | tjlane/odin | src/python/smfret/smfret.py | Python | gpl-2.0 | 5,774 | [
"MDTraj"
] | df4336cc7c912d209d4f5878d6cfb660b21e09bacacfd508528c88e633430120 |
# (c) 2013-2016, Michael DeHaan <michael.dehaan@gmail.com>
# Stephen Fromm <sfromm@gmail.com>
# Brian Coca <briancoca+dev@gmail.com>
# Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under t... | alxgu/ansible | lib/ansible/plugins/action/assemble.py | Python | gpl-3.0 | 6,409 | [
"Brian"
] | 22e02ca5d04a939ed7949819949df9487ae1b22ddecda8ba45356094d123ceb2 |
import math
import operator
import six
from rdkit import Chem
from nose.tools import eq_
from .. import ABCIndex
binary = [
operator.add,
operator.sub,
operator.mul,
operator.truediv,
operator.floordiv,
operator.mod,
operator.pow,
]
unary = [operator.neg, operator.pos, operator.abs, mat... | mordred-descriptor/mordred | mordred/tests/test_compose_descriptor.py | Python | bsd-3-clause | 646 | [
"RDKit"
] | 382f6767373411c0a68181d60056dc43885dbbd825dfaef3823751780c34b9b0 |
#!/usr/bin/env python
#
# $File: infiniteSites.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/infiniteSites.py | Python | gpl-2.0 | 2,880 | [
"VisIt"
] | f2949ae940a4d0ddc6de8e292fa9add33f38a3abf284b922123a7f2e0d327d01 |
# -*- coding: utf-8 -*-
# Generated by Django 1.9.4 on 2017-12-06 18:43
from __future__ import unicode_literals
import current_user
from django.conf import settings
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
initial = True
dependencies =... | linea-it/dri | api/activity_statistic/migrations/0001_initial.py | Python | gpl-3.0 | 1,652 | [
"VisIt"
] | 2f97f1f8c7730352635a380deb45cfc45081ec05f4d32e297a2364fece957489 |
#
# ENVISIoN
#
# Copyright (c) 2019 Linda Le, Gabriel Anderberg, Didrik Axén,
# Adam Engman, Kristoffer Gubberud Maras, Joakim Stenborg
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1... | rartino/ENVISIoN | envisionpy/hdf5parser/vasp/PCF.py | Python | bsd-2-clause | 8,482 | [
"VASP"
] | 64d27ff5204ccbd490b627eafbf77ab652fa2d30a730be391663c75b08aed2a1 |
# BEGIN_COPYRIGHT
# END_COPYRIGHT
"""
Build dbSNP index database from Galaxy genome segment extractor output
in interval format.
Before using this tool, you should perform the following steps. Given
a SNP defined as lflank[alleles]rflank, a reference genome DB and a
requested flanking size L::
1. align [lflankArf... | crs4/omero.biobank | bl/vl/app/snp_manager/build_index.py | Python | gpl-2.0 | 3,080 | [
"Galaxy"
] | 7bd7050e54e6ec92bc38153c28bedaae6e6574e4c73c2e0ccd047453fa219b04 |
from distutils.core import setup
setup(
name='nmrex',
version='1.0.0',
description='Exploratory data science for NMR and structural biology',
author='Leonid Vlasenkov MIPT & IBCh',
url='https://github.com/vlasenkov/nmrex',
license='MIT',
packages=['nmrex'],
install_requires=[
'... | vlasenkov/nmrex | setup.py | Python | mit | 680 | [
"Biopython"
] | a872f289e36a2e8f8f12b20cf5ba7dc4f23e69d633ead30d6d1d8559ce752492 |
#__Author = 'Jongmin Yu' @ Ph.D Candidate @ GIST-MLV
#__Laboratory of Machine Learning and Computer Vision
#
#--Title.Gaussian probability density function for image file
#__data format = numpy
#
from math import sqrt
from parser import st2list
import matplotlib
__author__ = 'Schmitz'
from matplotlib import pyplot a... | jminyu/PatternRecognition_library | Pattern_Recognition_lib.py | Python | gpl-3.0 | 2,816 | [
"Gaussian"
] | 211ad67a3769af9cf40ced36eb74377defa3f6d22ee3bac1ecc8bfb0aee0c157 |
# Copyright 2011-2013 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# SPDX-License-Identifier: GPL-3.0-or-later
#
#
'''
Blocks and utilities for digital modulation and demodulation.
'''
# The presence of this file turns this directory into a Python package
import os
try:
from .digital_pyt... | sdh11/gnuradio | gr-digital/python/digital/__init__.py | Python | gpl-3.0 | 1,150 | [
"Gaussian"
] | 7cdd4d082edba77a1289295175a57a46a6498f741a805efd694bd303f8d8d944 |
"""
An abstract representation of NetCDF data for manipulation purposes.
The purpose of this is to allow arbitrary manipulation of NetCDF data,
decoupled from the netCDF4 file-based API.
For example::
import ncobj.nc_dataset as ncds
with netCDF4.Dataset(file_in_path) as ds_in:
in_group = ncds.read(ds... | pp-mo/ncobj | lib/ncobj/__init__.py | Python | gpl-3.0 | 19,019 | [
"NetCDF"
] | 7e84c6bad714a524fef9a55ec6ebfc1d678d5bba76d2c004d7b491dccf2374db |
""" MoveReplica operation handler
This handler moves replicas from source SEs to target SEs. Replicas are first replicated to target SEs and then removed from the source SEs
"""
# # imports
import os
# # from DIRAC
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.FrameworkSystem.Client.MonitoringClient import ... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/Agent/RequestOperations/MoveReplica.py | Python | gpl-3.0 | 20,628 | [
"DIRAC"
] | 95b758354604b47999ddf3e696907d9fc2adbbafe10879d9045d45a0c5eff061 |
import ovito
from ovito.vis import PythonViewportOverlay
# Define a function that paints on top of the rendered image.
def render_overlay(painter, **args):
painter.drawText(10, 10, "Hello world")
# Create the overlay.
overlay = PythonViewportOverlay(function = render_overlay)
# Attach overlay to the active viewp... | srinath-chakravarthy/ovito | doc/python/example_snippets/python_viewport_overlay.py | Python | gpl-3.0 | 404 | [
"OVITO"
] | 5b2d6d9e662cc18a4da302160cec3fbdb9b237840f010c2ac8f8e2ecccae2b6c |
"""
.. module:: pdf
:synopsis: This module implements Probability Density Functions (PDFs)."
.. moduleauthor:: Martin Hunt <mmh@Purdue.edu>
This file is part of PUQ
Copyright (c) 2013 PUQ Authors
See LICENSE file for terms.
"""
from __future__ import absolute_import, division, print_function
import numpy as np
i... | c-PRIMED/puq | puq/pdf.py | Python | mit | 25,544 | [
"Gaussian"
] | f07593a29644c95ec6793299594e71702fccb363ef15fcb22d0664fce2047c86 |
from flask import Flask
from flask import jsonify
import psycopg2 as pg
import simplejson as json
# from flask import json
# from typing import List
# app = Flask(__name__)
top_js_repos = [
"d3/d3",
"facebook/react",
"angular/angular.js",
"jquery/jquery",
"facebook/react-native",
"meteo... | CodeOneTwo/oss-study | paper.py | Python | gpl-3.0 | 1,855 | [
"GULP"
] | bf5aa2b9442015c57e2f5055e72b96955cfbf959ee6264be261cc38a3b4fdc88 |
import numpy as np
from robosuite.environments.robot_env import RobotEnv
from robosuite.models.base import MujocoModel
from robosuite.models.grippers import GripperModel
from robosuite.robots import ROBOT_CLASS_MAPPING, Manipulator
class ManipulationEnv(RobotEnv):
"""
Initializes a manipulation-specific robo... | ARISE-Initiative/robosuite | robosuite/environments/manipulation/manipulation_env.py | Python | mit | 16,122 | [
"Gaussian"
] | bd92d62729ddfaee5bef6748cc341f1ea65ef4119272357f2ed851ee2af037dc |
"""
Extreme deconvolution solver
This follows Bovy et al.
http://arxiv.org/pdf/0905.2979v2.pdf
Arbitrary mixing matrices R are not yet implemented: currently, this only
works with R = I.
"""
from time import time
import numpy as np
from scipy import linalg
from sklearn.mixture import GMM
from astroML.utils import l... | drphilmarshall/Bananas | xdeconv.py | Python | mit | 9,541 | [
"Gaussian"
] | 2c1d443640eaaa651cd100d985895ea94f687deff326d5a31f8802c2b0546b85 |
import atompos
from django.core.cache import cache
import json
import logging
import os
import re
import socket
from subprocess import Popen, PIPE
from tempfile import NamedTemporaryFile
from urllib2 import urlopen, HTTPError
# TODO: expand
SUPPORTED_FORMATS = [
'smiles',
'inchi',
'pdb',
'atb' # used for ATB I... | jimivdw/OAPoC | atompos/atompos/main/util.py | Python | mit | 12,079 | [
"GROMOS"
] | 78641f7fdeacec34f017b71ebf0993a0da0c2a251fffaf22252b7e0ca068e870 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
#
# This file is part of the NNGT project to generate and analyze
# neuronal networks and their activity.
# Copyright (C) 2015-2019 Tanguy Fardet
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | Silmathoron/NNGT | nngt/plot/animations.py | Python | gpl-3.0 | 35,919 | [
"NEURON"
] | 92fa2d357d0724adf664362a9184539bbe7573b8e73d99e3421be2161bc7f07c |
import os
import sys
import distutils.util
import numpy
build_dir = "build/lib.%s-%s" % (distutils.util.get_platform(), sys.version[0:3])
sys.path.insert(0, os.path.join(os.getcwd(), build_dir))
import HTSeq
os.chdir("example_data")
print("TSS test, scheme 1")
exec(compile(open(os.path.join("..", "doc", "tss1.py")).... | simon-anders/htseq | python3/test/tss_test.py | Python | gpl-3.0 | 1,101 | [
"HTSeq"
] | 27da2a642cf6b7dc1cb3b95f65fbeadaf574b50c64ad3084d21ac960a051d3f6 |
"""
homeassistant.components.isy994
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Connects to an ISY-994 controller and loads relevant components to control its
devices. Also contains the base classes for ISY Sensors, Lights, and Switches.
For configuration details please visit the documentation for this component at
https://home-a... | nnic/home-assistant | homeassistant/components/isy994.py | Python | mit | 7,099 | [
"VisIt"
] | 48c2b073d97803d6e50cd4e4ef3220d809e99eebf3a83546e81d5a629204fb04 |
import logging
from datetime import datetime
import couchdb
from couchdb.client import ResourceNotFound, ResourceConflict
from couchdb.schema import Document, Schema, BooleanField, DateTimeField, \
IntegerField, TextField, DictField, ListField, View
import gearshift
from gearshift import id... | dbrattli/python-gearshift | gearshift/identity/cdprovider.py | Python | mit | 14,779 | [
"VisIt"
] | edd37814180ec448915a42baaabde21011bf33f54dd5f4c6bedb3e62927be014 |
"""
Acceptance tests for Studio related to the container page.
The container page is used both for displaying units, and
for displaying containers within units.
"""
import datetime
import ddt
from base_studio_test import ContainerBase
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.te... | philanthropy-u/edx-platform | common/test/acceptance/tests/studio/test_studio_container.py | Python | agpl-3.0 | 68,679 | [
"VisIt"
] | d5a0594c7b033b2c682e371312806f739a296da15418507ba7c08fdd48752111 |
# -*- coding: utf-8 -*-
# Ping
"""
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 ... | thica/ORCA-Remote | src/interfaces/ping/interface.py | Python | gpl-3.0 | 2,699 | [
"ORCA"
] | 07f38f916be1406d881f576853650a601bbc7ade256f630ea81e6a424bec260b |
#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2009-2011 by the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of thi... | chatelak/RMG-Py | rmgpy/molecule/draw.py | Python | mit | 69,068 | [
"RDKit"
] | f4c0b68f3662ff5cc541db80e0bde02170032e7af26ea065730b8469841c76ca |
# Copyright (C) 2011 by Brandon Invergo (b.invergo@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import re
line_floats_re = re.compile("-*\d+\.\d+")
def parse_basics(lines, results):
... | bryback/quickseq | genescript/Bio/Phylo/PAML/_parse_baseml.py | Python | mit | 11,443 | [
"Biopython"
] | 0841e808a8755a82e9b8fa7582e296f78f8ccc92794e96fc46906d085f0320ea |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Andrew I Baznikin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Ge... | arunkgupta/gramps | gramps/plugins/rel/rel_da.py | Python | gpl-2.0 | 7,411 | [
"Brian"
] | c0c50f2d01c46e0fbe41c960cc4fbe748be007e1bcc68620a1b39e0ed9e043c2 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import warnings
from io import StringIO, BytesIO
from astropy.table import Table
from astropy.io import fits
from astropy import coordinates
from astropy import units as u
from ..query import BaseQuery
from ..utils import commons
from ..utils import async... | ceb8/astroquery | astroquery/heasarc/core.py | Python | bsd-3-clause | 14,765 | [
"VisIt"
] | 5f5024577b4b65d615854232bb43ce24be237613c97b202e8d95ae5e2981fe31 |
"""
This file contains view functions for wrapping the django-wiki.
"""
import cgi
import logging
import re
from django.conf import settings
from django.shortcuts import redirect
from django.utils.translation import ugettext as _
from opaque_keys.edx.keys import CourseKey
from wiki.core.exceptions import NoRootURL
fro... | proversity-org/edx-platform | lms/djangoapps/course_wiki/views.py | Python | agpl-3.0 | 4,319 | [
"VisIt"
] | e64b779362546eca623f194922dbebd6345a56e65aa0c3852bd7c7eca41b4202 |
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Abstract base classes for the SearchIO object model."""
import sys
# Add path to Bio
sy... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/SearchIO/_model/_base.py | Python | gpl-2.0 | 2,621 | [
"Biopython"
] | 20045511a4fe95a10d48a394e74e054977ed26d7bb8a9d7fb2b70a9cd8ef74c7 |
"""aospy DataLoader objects"""
import logging
import os
import pprint
import numpy as np
import xarray as xr
from .internal_names import (
ETA_STR,
GRID_ATTRS,
TIME_STR,
)
from .utils import times, io
def _preprocess_and_rename_grid_attrs(func, grid_attrs=None, **kwargs):
"""Call a custom preprocess... | spencerahill/aospy | aospy/data_loader.py | Python | apache-2.0 | 25,915 | [
"NetCDF"
] | b53ac4ec1ea8a5ae1952202dd0723e775f9ed3580f5f3b25c5dbe161f9a80761 |
# (c) 2014, Brian Coca, Josh Drake, et al
# (c) 2017 Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
DOCUMENTATION = '''
cache: memcached
short_description: Use ... | roadmapper/ansible | lib/ansible/plugins/cache/memcached.py | Python | gpl-3.0 | 7,520 | [
"Brian"
] | 1c33a99ab2c49ed15e0d1ca473cbc9ca6bb183a881de692d1de2821811324c69 |
#!/usr/bin/env python
"""
Dense Optical Flow
==================
Runs dense optical flow algorithm on image sequence and displays output
"""
import numpy as np
import cv2
def dense_optical_flow(imgs, display_image=True, display_type='hsv', write_video=False, video_name='D_OF.avi'):
"""
Runs and displays dense... | amarschn/VOT_2014_Tracking_Challenge | dense_optical_flow.py | Python | mit | 4,163 | [
"Gaussian"
] | 024959f76bee7c70b07549b12a77fcd475d20d159f15e7436b64f543a6110fdd |
#!/usr/bin/python
# Filename: grids.py
#
# Code by Martin Jucker, distributed under an MIT License
# Any publication benefitting from this piece of code should cite
# Jucker, M 2014. Scientific Visualisation of Atmospheric Data with ParaView.
# Journal of Open Research Software 2(1):e4, DOI: http://dx.doi.org/10.5334/j... | mjucker/pv_atmos | grids.py | Python | mit | 28,543 | [
"ParaView"
] | 8fcbb9cdc04e27de37ef917586be9989b2ba89b9b9b6f49908513735d1ad7183 |
#!/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 | test/tests/time_integrators/convergence/implicit_convergence.py | Python | lgpl-2.1 | 2,169 | [
"MOOSE"
] | acc546c06931150608c797679b2bc8a7f3f70317fd084d4993d4305f2cf7bb8d |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd.
# License: GNU General Public License v3. See license.txt
#!/usr/bin/python
# This script is for cleaning up of all data from system including
# all transactions and masters (excludes default masters).
# Basically after running this file, system will reset to i... | gangadhar-kadam/sapphire_app | utilities/cleanup_data.py | Python | agpl-3.0 | 6,486 | [
"VisIt"
] | 883958fbcd344063ac53628d6c006c8c795e4df42e7ee133f083eaaf00844e3d |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import json
import os
import re
import pyte... | anryko/ansible | test/units/galaxy/test_api.py | Python | gpl-3.0 | 37,761 | [
"Galaxy"
] | 3bcf5b64962560c1e6837dc704cbbd545ed1e7577daeca6cfb543c518d153128 |
# -*- coding: utf-8 -*-
"""Functions to make 3D plots with M/EEG data."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Mainak Jas <maina... | larsoner/mne-python | mne/viz/_3d.py | Python | bsd-3-clause | 137,590 | [
"VTK"
] | 2cb80e36b4303291dcf77b27b59b80fbb809c2589a19816737ff7c52366ac7ad |
import numpy as np
from scipy.spatial import distance
from scipy.optimize import curve_fit
import csv
import math
def get_rows(fname, nheader):
counter = 0
rows = []
with open(fname, 'rU') as f:
csvrows = csv.reader(f, delimiter=',',quotechar='|')
for row in csvrows:
if counter > nheader - 1:
... | maggiemaes/Methods-for-BAX-recruitment-analysis | analysis_tools.py | Python | mit | 8,838 | [
"Gaussian"
] | 1dc1142da36f0ec1c9193faae99316130a594b04896a76381d3fe81ca28687fb |
# $Id$
#-----------------------------------------------------------------------
# Copyright (C) 2004-2019
# Associated Universities, Inc. Washington DC, USA.
#
# 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 So... | kernsuite-debian/obit | python/UVImager.py | Python | gpl-2.0 | 26,654 | [
"Gaussian"
] | 532e2ec5ea6c169cbc667cea1b489928105736161611faa98ef06a5abcb759ab |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2013 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the Licens... | tiagocardosos/stoq | stoqlib/gui/search/searchdialog.py | Python | gpl-2.0 | 19,684 | [
"VisIt"
] | 4e04e273e068d307a34fbf8217a3d682143bade9c606d71ddb96db24213fa2cf |
# -*- 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/win/win_Ping.py | Python | gpl-3.0 | 1,450 | [
"ORCA"
] | 186c45fcc8e28a0a401a1ac4c731c34a05c429e86ac4b5cb6a7e72c99d4b928d |
from pylab import *
from scipy.spatial.distance import pdist, squareform, cdist
class Current :
"""
Encodes a Current as a sum of weighted vector diracs.
\omega(v) = \sum_i (Omega_i, v(x_i))
"""
def __init__(self, points, normals) :
assert (points.shape[1] == 2), "3D currents have not been implemented yet !"
... | jeanfeydy/lddmm-ot | LDDMM_Python/lddmm_python/modules/data_attachment/currents.py | Python | mit | 2,772 | [
"DIRAC",
"Gaussian"
] | c8102492db2f77ebf41852b6c184850f519ecc8685490a1ac9ea65e05d434f12 |
#!/usr/bin/env python
from distutils.core import setup
import bdist_mpkg
setup(name='PyXG',
version='0.3.0',
description='A Python interface to Xgrid',
license='BSD',
author='Brian Granger/Barry Wark/Beat Rupp',
author_email='ellisonbg@gmail.com',
url='http://launchpad.net/pyxg',
py_module... | pyxg/pyxg | setup.py | Python | bsd-3-clause | 852 | [
"Brian"
] | 6eb5391270ca46e2811c4887584e9d07558a583652892a26d4da5f273965cf60 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.