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# -*- test-case-name: twisted.web.test.test_util -*-
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
"""
An assortment of web server-related utilities.
"""
from __future__ import division, absolute_import
import linecache
from twisted.python import urlpath
from twisted.python.compat import _... | lowitty/server | libsLinux/twisted/web/util.py | Python | mit | 10,856 | [
"VisIt"
] | 1a2345fa0323f30b73a71fad47726bbee4ec6ef3f984d21869e0a041f4787b2a |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Ncio(CMakePackage):
"""This is a library used by NCEP GSI system to read the GFS forecast
... | LLNL/spack | var/spack/repos/builtin/packages/ncio/package.py | Python | lgpl-2.1 | 1,051 | [
"NetCDF"
] | 6941aae0d54ef59748a58451a0a304adb514c0189e11b9dbb4d9a7e705778e81 |
#!/usr/bin/env python
"""
This file is part of RAPD
Copyright (C) 2009-2018, Cornell University
All rights reserved.
RAPD 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, version 3.
RAPD is distributed i... | RAPD/RAPD | src/sites/gatherers/necat_e.py | Python | agpl-3.0 | 48,185 | [
"CRYSTAL"
] | 283f3e3eb8675951fa322acf43367c26fe6f12091dd836e4b1c111387b53ab78 |
import unittest
from paegan.transport.models.behaviors.capability import Capability
import os
import json
class CapabilityTest(unittest.TestCase):
def test_from_json(self):
data = open(os.path.normpath(os.path.join(os.path.dirname(__file__),"./resources/files/capability_behavior.json"))).read()
d ... | asascience-open/paegan-transport | tests/test_capability.py | Python | gpl-3.0 | 1,856 | [
"Gaussian"
] | fc11c01e4f21bd563357bf0f5536d07b8349e50b7e099b54394b72eaf6445bdc |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import itertools
import os
from django.contrib.auth.models import User
from django.contrib.auth.signals import user_logged_in, user_logged_out
from django.http... | yephper/django | tests/test_client_regress/tests.py | Python | bsd-3-clause | 68,159 | [
"VisIt"
] | 2a30bcc310653888616f9e4729e5af74bf8348fbb322c30a0af1a69415838d6d |
import subprocess
import os
try:
import rdkit
except ImportError:
print >> sys.stderr, 'rdkit not installed...'
print >> sys.stderr, 'build rdkit...'
subprocess.call(['git', 'clone', 'https://github.com/rdkit/conda-rdkit.git'])
os.chdir('conda-rdkit')
subprocess.call(['conda', 'build', 'boost']... | cdmbi/PCM | install.py | Python | gpl-2.0 | 371 | [
"RDKit"
] | f170ae40c848bea887724460321e36c2a3c1e46df69daf98e6411aef8411feb9 |
# PyVision License
#
# Copyright (c) 2006-2008 David S. Bolme
# 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. Redistributions of source code must retain the above copyright
# notice, thi... | tigerking/pyvision | src/pyvision/features/v1like.py | Python | bsd-3-clause | 23,660 | [
"Gaussian"
] | e8eaf28c0d3b63c4a08ef27fa7685153fc26a97e71119da5ab2bf874677ab646 |
"""
Simple two-dimensional mathematical or geometrical pattern generators.
$Id$
"""
from __future__ import with_statement
__version__='$Revision: 10131 $'
from math import pi, sin, cos, sqrt
import numpy
from numpy.oldnumeric import around,bitwise_and,sin,add,Float,bitwise_or
from numpy import alltrue
from .. imp... | ioam/svn-history | contrib/basic.py | Python | bsd-3-clause | 38,948 | [
"Gaussian"
] | c6f088881fee9b44e35c6177860cd87a980bf1193dbd118c990e2318d324ca93 |
"""
Binned Regression: Poisson vs Gaussian
--------------------------------------
Figure 5.15
The left panels show data sets with 50 points, binned in 5 bins (upper panels)
and 40 bins (lower panels). The curves show the input distribution (solid), the
Poisson solution (dashed), and the Gaussian solution (dotted). The... | nhuntwalker/astroML | book_figures/chapter5/fig_poisson_likelihood.py | Python | bsd-2-clause | 4,970 | [
"Gaussian"
] | 8595cb805171060ec93b6081958a05767a885bddb160c74ff5b374e783588260 |
'''
'''
import time
import h5py
import numpy as np
from scipy import interpolate
#from scipy.integrate import odeint
# --- local ---
import util as UT
import sfrs
import observables as obvs
class Evolver(object):
def __init__(self, cms, evol_dict=None):
''' Class object that evolves the input Cent... | changhoonhahn/centralMS | centralms/tests/centralms.py | Python | mit | 29,528 | [
"Galaxy"
] | 2303a60a43c1bdd0aab6d5c4d51ef5c12debcaad92c2c0073ead8cdea3b6f131 |
# Time-stamp: <2015-06-03 00:50:50 Tao Liu>
"""Description: Filter duplicate reads depending on sequencing depth.
Copyright (c) 2011 Tao Liu <taoliu@jimmy.harvard.edu>
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file COPYING included
with the distr... | vd4mmind/MACS | MACS2/refinepeak_cmd.py | Python | bsd-3-clause | 6,920 | [
"pysam"
] | 8c5ba65947e8cebf0b9564475d7dece8a14be76514072dd328176ece5e55e5df |
#!/usr/bin/env python3
"""
Title: wav player
Author: James Cooper <james@coopercs.ca>
Copyright: Rylan Grayston
License: GPLv2
This program takes a wav file and its accompanying cue file (both converted from gcode with the gcode-to-wav converter)
and plays back each layer.
"""
## Parameters for debugging
USE_VIRTUAL_... | PeachyPrinter/peachytoolchain | src/wav_player.py | Python | gpl-3.0 | 10,090 | [
"VisIt"
] | 972044d015438c9fdf3c40c9246052222e8da24fdba939be048ccbb49f38f30a |
__script__.title = 'KKB Overview'
__script__.version = '1.1'
# 2018-07-12 include deadtimes
# 2021-05-16 Temperatures are missing
__FOLDER_PATH__ = 'V:/shared/KKB Logbook/Temp Plot Data Repository/'
if not os.path.exists(__FOLDER_PATH__):
os.makedirs(__FOLDER_PATH__)
#__savefile__ = 'overview... | Gumtree/Kookaburra_scripts | Internal/KKB_overview_vs1.py | Python | epl-1.0 | 26,477 | [
"CRYSTAL"
] | 29f1a59b7e9a2dae93ee543a85a37c2bd720342c28013226e53d82b8eaf9f96f |
import vtk
import numpy as np
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName('slice.vtp')
reader.Update()
data = reader.GetOutput()
data.GetLines().InitTraversal()
idList = vtk.vtkIdList()
aPolygon = vtk.vtkPolygon()
aPolygon.GetPointIds().SetNumberOfIds(data.GetNumberOfPoints())
for i in range(data.GetNumb... | kayarre/Tools | vtk/slice_area.py | Python | bsd-2-clause | 1,672 | [
"VTK"
] | 6239d7140c0adf71ec513a28af3de4fa479e257f4ff78c6e912f5e85c0f48043 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/interaction/StillingerWeberPairTermCapped.py | Python | gpl-3.0 | 11,299 | [
"ESPResSo"
] | f4bbba2f36e6b6715a23b51651b182d8528f6ef69fb4ed942d014282068e50ec |
from __future__ import print_function
import copy
from .helpers import SkipThisVertex,def_from_model
from .converter import py2cpp
import string,re
from string import Template
epsValue=[[[[0,0,0,0],[0,0,0,0],[0,0,0,0],[0,0,0,0]],[[0,0,0,0],[0,0,0,0],[0,0,0,0],[0,0,0,0]],
[[0,0,0,0],[0,0,0,0],[0,0,0,0],[0,0,... | hep-mirrors/herwig | Models/Feynrules/python/ufo2peg/general_lorentz.py | Python | gpl-3.0 | 172,316 | [
"DIRAC"
] | 315a5f8d47b09fac22f63975c573f25ae960183130a3ee4d53bfc1d1be487fad |
#!/usr/bin/env python
"""
Base neuron class used by LPU.
"""
import warnings
from abc import ABCMeta, abstractmethod
import os.path
import numpy as np
import pycuda.gpuarray as garray
from pycuda.compiler import SourceModule
from neurokernel.LPU.utils.simpleio import *
class BaseNeuron(object):
__metaclass__ =... | neurokernel/lamina | lamina/neurons/baseneuron.py | Python | bsd-3-clause | 14,564 | [
"NEURON"
] | 54216a946e66427bc93d0954ad813c2263a06955cae446c7987cc1c1b96a7d72 |
# coding=utf-8
# 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 app... | corona10/grumpy | grumpy-tools-src/grumpy_tools/compiler/block_test.py | Python | apache-2.0 | 9,932 | [
"VisIt"
] | 6e689a282e060c3c00ed3592dcd3e3adf34f6078565fba80ebf77478a3fb6138 |
import pandas as pd
import numpy as np
import time
import seaborn as sns
import matplotlib.pyplot as plt
from IPython.display import display
from sklearn.preprocessing import LabelEncoder
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.ensemble import RandomForestClassifier
from sklearn.linear_m... | taspinar/siml | siml/sk_utils.py | Python | mit | 5,104 | [
"Gaussian"
] | ca4454b374fec51523f05ab822f9e62471aecf901662be5e0b5ef45a95addaea |
#!/usr/bin/env python
import glob
import os
import defopt
import pandas as pd
import seawater
import xarray as xr
import data.observational
from data.observational import DataType, Platform, Sample, Station
VARIABLES = ["TEMP", "PSAL"]
META_FIELDS = {
"PLATFORM_NUMBER": None,
"PROJECT_NAME": None,
"PI_... | DFO-Ocean-Navigator/Ocean-Data-Map-Project | scripts/data_importers/argo.py | Python | gpl-3.0 | 4,772 | [
"NetCDF"
] | fb1efecb2ebb2b3fe6619a7e6cb6d8fa45ab5f6e17e5d672e634204c64b9ba1f |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2004-today OpenERP SA (<http://www.openerp.com>)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms o... | ClearCorp-dev/odoo | addons/project/project.py | Python | agpl-3.0 | 69,026 | [
"VisIt"
] | 5a01f728261d58934be9014b9f7978bddcd62a6961a6d7ad1c7bad7b6dd5a88f |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | kubeflow/katib | examples/v1beta1/trial-images/mxnet-mnist/common/fit.py | Python | apache-2.0 | 14,998 | [
"Gaussian"
] | 63d8af5bff5a795f7a2b97b510e4f43cbb0878cf42d2b2859915529870a6a11c |
import sys
sys.path.append("../")
import mpl_header
import matplotlib.pyplot as plt
import numpy as np
np.random.seed(500)
def gaussian(x, y, a=1.0, sigma_x=1.5, sigma_y=1.0, x_0=0.0, y_0=0.0):
""" Gaussian Function
http://en.wikipedia.org/wiki/Gaussian_function
"""
return a*np.exp(-((x-x_0)**2/(... | charnley/matplotlib-header | examples/plot_mesh.py | Python | bsd-2-clause | 1,004 | [
"Gaussian"
] | a7a2ec73fc24098be78947d27d6e4f6e494ee080dcf7112b8bc9a0e58c813cb9 |
"""
A robot exclusion rules parser for Python by Philip Semanchuk
Full documentation, examples and a comparison to Python's robotparser module
reside here:
http://NikitaTheSpider.com/python/rerp/
Comments, bug reports, etc. are most welcome via email to:
philip@semanchuk.com
Simple usage examples:
import ro... | petterw/crawler | robotexclusionrulesparser.py | Python | gpl-3.0 | 29,337 | [
"VisIt"
] | a797e9eea0855311353bb066d0af41027b13966f21c2dad4c28b70827f48d247 |
"""
Created on 18 Feb 2013
@author: jmht
Query the octopus server http://octopus.cbr.su.se to get transmembrane predictions
"""
import logging
import os
import sys
import urllib
if sys.version_info.major < 3:
from HTMLParser import HTMLParser
from urllib2 import urlopen, HTTPError
else:
from html.parser... | rigdenlab/ample | ample/modelling/octopus_predict.py | Python | bsd-3-clause | 4,964 | [
"Octopus"
] | 67079fada8ef9b7ddd51f68ba6961f52a8de56e8b0c846db6859d836046fb00a |
"""
The annotationmodel module contains the classes for the AnnotationModel.
"""
import os.path
import time
import logging
import copy
from collections import MutableMapping
from PyQt4.QtGui import QTreeView, QItemSelection, QItemSelectionModel, QSortFilterProxyModel, QBrush
from PyQt4.QtCore import QModelIndex, QAbstr... | bitmingw/FindYourSister | sloth/sloth/annotations/model.py | Python | bsd-2-clause | 27,345 | [
"VisIt"
] | 3a8a1c79276078afd67532889f3743ffd63d3ec04ddf26aa9837f380944e5955 |
import logging
import os
import tempfile
import urllib
import zipfile
from galaxy import datatypes, eggs, model, util, web
from galaxy.datatypes.display_applications.util import decode_dataset_user, encode_dataset_user
from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
from galaxy.util import inflect... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py | Python | gpl-3.0 | 63,598 | [
"Galaxy"
] | 013e7806692d0985b84f515f8fcb2a73335dfcaab79e572b91ed8e81a824e6a6 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | tiagocardosos/stoq | stoqlib/gui/dialogs/labeldialog.py | Python | gpl-2.0 | 3,204 | [
"VisIt"
] | 28d103b9b6db4150ca9fb3787ab8eae4e572db2823db680c7d64f796486e5cfb |
"""
GPoFM: Gaussian Process Training with
Optimized Feature Maps for Shift-Invariant Kernels
Github: https://github.com/MaxInGaussian/GPoFM
Author: Max W. Y. Lam [maxingaussian@gmail.com]
"""
import os, sys
import numpy as np
import numpy.random as npr
import matplotlib.pyplot as plt
from GPoFM import *
BEST_... | MaxInGaussian/GPoFM | examples/boston_housing/boston_housing.py | Python | bsd-3-clause | 6,175 | [
"Gaussian"
] | 72ec6868daa0d8d09cb01163581733cbe91acc3a48f960bf28eb70a2a00adaf8 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Long-range potentials for molecular dynamics."""
from . import pppm
| joaander/hoomd-blue | hoomd/md/long_range/__init__.py | Python | bsd-3-clause | 231 | [
"HOOMD-blue"
] | 3a1bbd7fcf333de8a8ce58cb875e1603e9221cc539922180a52ce98f725b1d5e |
import unittest
import numpy as np
import os
import rdkit
import tensorflow as tf
from nose.tools import assert_true
from tensorflow.python.framework import test_util
from deepchem.feat.mol_graphs import ConvMol
from deepchem.feat.mol_graphs import MultiConvMol
from deepchem.feat.graph_features import ConvMolFeaturize... | rbharath/deepchem | deepchem/models/tensorgraph/tests/test_layers.py | Python | mit | 21,475 | [
"RDKit"
] | 4f061c8f025ccdf19f274e588d96939fad7e62be5ad11b75c766f9bcd1d65299 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
"""
Creates... | nuclear-wizard/moose | test/tests/mesh/patterned_mesh/pattern_mesh.py | Python | lgpl-2.1 | 1,186 | [
"MOOSE",
"VTK"
] | f7908b1b7f507b694bfbadf79b196d440e28133b2f4519467a42382689d3a0a8 |
"""
Atomic coordinate featurizer.
"""
import logging
import numpy as np
from deepchem.feat import Featurizer
from deepchem.feat import ComplexFeaturizer
from deepchem.utils import pad_array
from deepchem.utils.rdkit_utils import MoleculeLoadException, get_xyz_from_mol, \
load_molecule, merge_molecules_xyz, merge_mole... | miaecle/deepchem | deepchem/feat/atomic_coordinates.py | Python | mit | 10,840 | [
"MDTraj",
"RDKit"
] | 0dc3a6dd6f8409962567034778459f876ae60a309507c2cadbc4a44dc76dbd03 |
'''
Post Processing
===============
'''
def GetMesh(odb,instance,dti='I'):
'''Retrieves mesh on an instance in an Abaqus Output Database.
:param odb: output database
:type odb: odb object
:param instance: instance name declared in the Abaqus inp file.
:type instance: string
:param dti: int data type... | lcharleux/abapy | abapy/postproc.py | Python | gpl-2.0 | 108,824 | [
"ParaView",
"VTK"
] | 7040cdc573fd3d5808f79c6308fecd5b78d2a0da625a1cb58d8edafb5084343d |
from __future__ import print_function
from symfit.api import Parameter, Variable, Fit, exp
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
palette = sns.color_palette()
x = Variable()
A = Parameter()
sig = Parameter(name='sig', value=1.4, min=1.0, max=2.0)
x0 = Parameter(name='x0', value=15.... | Eljee/symfit | examples/gaussian.py | Python | gpl-2.0 | 841 | [
"Gaussian"
] | 9f25f4028b9fbd378a92944021c0d1b02f903e30a179c5050b30f82178840de3 |
# Copyright (c) 2012 - N.P. de Klein
#
# This file is part of Python Mass Spec Analyzer (PyMSA).
#
# Python Mass Spec Analyzer (PyMSA) 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 ver... | davidmam/pyMSA | pyMSA/test/test_plots.py | Python | gpl-3.0 | 3,501 | [
"OpenMS"
] | a699a2f93fa68491cf88945b1a1359305af5aef6115c8ccf03ba649315f469ca |
# -*- coding: utf-8 -*-
""" Tests for student account views. """
import logging
import re
from unittest import skipUnless
from urllib import urlencode
import ddt
import mock
import pytest
from django.conf import settings
from django.contrib import messages
from django.contrib.auth import get_user_model
from django.co... | Edraak/edraak-platform | lms/djangoapps/student_account/test/test_views.py | Python | agpl-3.0 | 48,791 | [
"VisIt"
] | d6b5b63c6cd819bb92076b5e08e9dfff90830700dd82e5c2da8ef62ebe6362a1 |
##### NEED TO FIX DIVISION OPERATOR!!!!!
from __future__ import division
#http://docs.python.org/release/2.2.3/whatsnew/node7.html
#The most controversial change in Python 2.2 heralds the start of an effort to fix an old design flaw that's been in Python from the beginning. Currently Python's division operator, /,... | andreasbastian/pyControl | laserPowerRanging.py | Python | gpl-3.0 | 4,798 | [
"BLAST"
] | ef166e812524f7598e3f3aa849b39cb2e726875d64e626b03dea6bc1488b06af |
#!/usr/bin/env python
# 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 fo... | wizmer/NeuroM | examples/soma_radius_fit.py | Python | bsd-3-clause | 3,139 | [
"NEURON"
] | 183fe459ad67771ae5fc0f76c86ec5fd0bc32a0b3463e88ae8ec83ec92e11624 |
'''
Created on Jul 8, 2013
@author: ajju
'''
from BeautifulSoup import BeautifulStoneSoup
from TurtleContainer import Container, AddonContext
from common import HttpUtils, Logger, EnkDekoder, XBMCInterfaceUtils, AddonUtils
from common.DataObjects import ListItem
from moves import SnapVideo
from snapvideo import Google... | noba3/KoTos | addons/plugin.video.filmibynaturex-2.5.7/mymoves/sominaltv/Sominal.py | Python | gpl-2.0 | 16,231 | [
"ADF"
] | 53e19141536f9b0744a8c4bf9c2fb1e479ffa7e9d722b5685d04e8adb059bdb4 |
# This file is part of Merlin.
# Merlin is the Copyright (C)2008,2009,2010 of Robin K. Hansen, Elliot Rosemarine, Andreas Jacobsen.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; ... | d7415/merlin | Hooks/ships/prod.py | Python | gpl-2.0 | 3,578 | [
"CRYSTAL"
] | f682622a962359db16393aba69a2deb856c88ec2eb214ea2f85ced713d9b5f09 |
#!/usr/bin/env python3
"""
Creates a netcdf file from a list of dictionaries containing name and 2-D data
create_cdf - new and neater
createCDF - deprecated
"""
#N18 from datetime import datetime
#N18 import dateutil.parser
import netCDF4 as nc
import numpy as np
import time # Just for creation date
... | mifads/pyscripts | emxcdf/makecdf.py | Python | gpl-3.0 | 18,009 | [
"NetCDF"
] | e7be8327ac2c0f6386f0c65ab385ecdcdf3511fb0baf7036a28327efd107cbb2 |
from textwrap import dedent
import py.test
from kinko.refs import ArgRef
from kinko.nodes import Tuple, Symbol, Number, Keyword, List, Placeholder
from kinko.nodes import String
from kinko.types import Func, IntType, StringType, NamedArg, TypeVar, Markup
from kinko.types import Record, ListType, Union, DictType, Opti... | vmagamedov/kinko | tests/test_checker.py | Python | bsd-3-clause | 23,044 | [
"VisIt"
] | ca1a24ae11e69223162978f95005e48f5cc2ff1da2f0169afa54790ee65b90cb |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
gama
----
Access to GAMA (Galaxy And Mass Assembly) data, via the DR2 SQL query form.
http://www.gama-survey.org/dr3/query/
:author: James T. Allen <james.thomas.allen@gmail.com>
"""
from .core import GAMA, GAMAClass
| ceb8/astroquery | astroquery/gama/__init__.py | Python | bsd-3-clause | 287 | [
"Galaxy"
] | 4d5e5da6ce6f0cada2bdae8b5f393335c58ed34c01c45312db241836cf5c627e |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageMapToColors(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
v... | nagyistoce/devide | modules/vtk_basic/vtkImageMapToColors.py | Python | bsd-3-clause | 495 | [
"VTK"
] | 99bd7013f3f0800c9ec3706ba689b1fd3f8f706393327af7eb87cdda5737b055 |
# -*- coding: utf-8 -*-
#
# Pyplis is a Python library for the analysis of UV SO2 camera data
# Copyright (C) 2017 Jonas Gliss (jonasgliss@gmail.com)
#
# This program is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License a
# published by the Free Software Foundat... | jgliss/pyplis | pyplis/plumespeed.py | Python | gpl-3.0 | 143,069 | [
"Gaussian"
] | a3a4aed75ef0a299f0b483e9e9d9e594b1931c26de3af58485e4924b0f54d3b0 |
"""
Binary Tree implementations, recursive and iterative traversals
@author: Lia Nemeth
"""
import weakref
from forest.utils import Queue, Stack
def copy_node(origin, destination):
if not (origin is None or destination is None):
destination.key = origin.key
destination.item = origin.item
... | lucasnemeth/forest | forest/BinaryTree.py | Python | bsd-3-clause | 12,861 | [
"VisIt"
] | 54a1cbe2312d1d43c62073b96ae45b5c91d6861f696f4144f9054e3bc9cd1112 |
# Sample module in the public domain. Feel free to use this as a template
# for your modules (and you can remove this header and take complete credit
# and liability)
#
# Contact: Brian Carrier [carrier <at> sleuthkit [dot] org]
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is f... | sidheshenator/autopsy | pythonExamples/dataSourceIngestModule.py | Python | apache-2.0 | 7,511 | [
"Brian"
] | 8fb514e96a0d6e51e2508ed622e16ed5e446462b9b710a9d0303c3521482e529 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | SNoiraud/gramps | gramps/plugins/webreport/citation.py | Python | gpl-2.0 | 2,965 | [
"Brian"
] | dd5ad769438b983a030231f1fc9c0d1e27cf66b2026d6f0bccb7818ded180672 |
"""
Shogun demo
Fernando J. Iglesias Garcia
"""
import numpy as np
import matplotlib as mpl
import pylab
import util
from scipy import linalg
from modshogun import QDA
from modshogun import RealFeatures, MulticlassLabels
# colormap
cmap = mpl.colors.LinearSegmentedColormap('color_classes',
{'red': [(0, 1, 1),
... | sanuj/shogun | examples/undocumented/python_modular/graphical/multiclass_qda.py | Python | gpl-3.0 | 3,294 | [
"Gaussian"
] | 59ff362400b844b713be8f015fd02fb416aebf7a5bb264375813f2aa7ad76800 |
"""
Calculate MUV descriptors with the RDKit.
"""
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__license__ = "3-clause BSD"
import numpy as np
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import ChiralType
class MUVDescriptors(object):
"""
Cal... | skearnes/muv | muv/descriptors.py | Python | bsd-3-clause | 3,160 | [
"RDKit"
] | 4a7903ad5c5820274995a202896b9132ee987af1a555a93cd8fd3c5414ddfffe |
from datetime import datetime, time
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.db import models
from django.db.models import Count
from django.db.models import Q
from django.shortcuts import render_to_response
from django.template import RequestContext
from ... | botswana-harvard/edc-describe | edc_describe/views/base_model_group_describer.py | Python | gpl-2.0 | 7,416 | [
"VisIt"
] | 058693c775e0664254c83e379543cfb3c9dbf8b22e976b8083407a4ad2add851 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import json
import os
from pymatgen.entries.computed_entries import ComputedEntry
from pymatgen.apps.battery.insertion_battery import InsertionElectrode
from pymatgen.apps.battery.conversion_b... | gVallverdu/pymatgen | pymatgen/apps/battery/tests/test_plotter.py | Python | mit | 1,501 | [
"pymatgen"
] | 6d7f9171eae15d32990bd7428f7b5ab45af242b180ff787c54da410cae89e5d5 |
# -*- coding: utf-8 -*-
# Download Status Module by: Blazetamer (2014)
import os
import xbmc
import xbmcaddon
from libs import addonwindow as pyxbmct
import kodi
from libs import message
addon_id=kodi.addon_id
_addon = xbmcaddon.Addon()
_addon_path = _addon.getAddonInfo('path')
file_name = "http://trakt.... | odicraig/kodi2odi | addons/plugin.video.velocity/libs/window_box.py | Python | gpl-3.0 | 4,516 | [
"VisIt"
] | f0ec0b582a1c6a7e5475b2b9389f0edfbbf59e0526f5202a14b2ab612fdb38b8 |
#
# co_co_illegal_expression.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 License, or
# (at your... | kperun/nestml | pynestml/cocos/co_co_illegal_expression.py | Python | gpl-2.0 | 12,099 | [
"NEURON"
] | 8f51e4e3cfbdc59b3ad44fb8c0bddac7af72d2b9372f122459f11e9bf2c05eb0 |
#
# 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/chronos/autots/model/test_auto_prophet.py | Python | apache-2.0 | 4,460 | [
"ORCA"
] | 52ac5d171d60678d9997e33744c0493ec46fdc12d49544dfeb66027cf4d3c135 |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# 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 requ... | mguzdial3/MineCode | python-codec/examples/Example Gridworld/sample_sarsa_agent.py | Python | apache-2.0 | 9,131 | [
"Brian"
] | 194a04ff1fc893ad1710563b57478d4565bc43a30df5a43b8a65573796474a97 |
#
# QAPI visitor generator
#
# Copyright IBM, Corp. 2011
# Copyright (C) 2014-2015 Red Hat, Inc.
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
# Michael Roth <mdroth@linux.vnet.ibm.com>
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See the CO... | lunixbochs/qemu | scripts/qapi-visit.py | Python | gpl-2.0 | 12,592 | [
"VisIt"
] | e7c5ce1756690c837a40a6456da01ebbcc5e2c1827eb215bbf4f78aad7068aa5 |
# 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 as scp
import scipy.ndimage as ni
import scipy.io
import roslib; roslib.load_manifes... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/simulation_results/comparision_with_kNN_PCA/Combined/object_training/k_PC_categories_generalized_force_motion.py | Python | mit | 8,128 | [
"Mayavi"
] | c75fb929aaf6f8e3ea8a084bd75164eb550aa466f9f00ef6583d7699c41a40ee |
from model_mommy import mommy
from kb.tests import test
class LiveTestArticleDetailView(test.BaseLiveServer):
def test_upvote_and_downvote_article(self):
article = mommy.make_recipe('kb.tests.published_article', slug='eggs')
url = '/article/eggs/'
self.visit(url)
self.assertEqu... | eliostvs/django-kb | kb/tests/article/integration_tests.py | Python | bsd-3-clause | 1,323 | [
"VisIt"
] | aaba1ae35d5135a2839bf45686405a5295bb5b9a945378ffc6e512d9371820fe |
"""Scrape data from MDN pages into API format."""
from __future__ import unicode_literals
from collections import OrderedDict
from itertools import chain
from django.utils.six import text_type
from parsimonious import IncompleteParseError
from webplatformcompat.models import (
Browser, Feature, Reference, Section,... | jwhitlock/web-platform-compat | mdn/scrape.py | Python | mpl-2.0 | 29,184 | [
"VisIt"
] | 499e488091b07934b3d872d194468cf69e575f82725f9d5a061ede5e081dc309 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | annarev/tensorflow | tensorflow/python/data/experimental/kernel_tests/sql_dataset_test.py | Python | apache-2.0 | 24,970 | [
"MOE"
] | 4cf086e2dc23586f6eddad777a01da6bee074643e6e4fb2e502035e1fd2da8ce |
"""
Model Share
===========
Provides functions that are common to all models in the TAMOC suite
This module defines functions that perform standard tasks for the modeling
modules in the TAMOC suite. These include standard authoring of output
files and reading ambient data from output files.
Notes
-----
These c... | socolofs/tamoc | tamoc/model_share.py | Python | mit | 4,642 | [
"NetCDF"
] | 1668c6276ae08437996d0996573c1b5efb7959c640f19a75d369eee4151dfbe6 |
#
# Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 The SCons Foundation
#
# 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 limitati... | cournape/numscons | numscons/scons-local/scons-local-1.2.0/SCons/Taskmaster.py | Python | bsd-3-clause | 39,532 | [
"VisIt"
] | 470aa5b90a6495dbdaec4f393f89ddd431ab86514e9d2af23c8ccd85cd87edca |
#!/usr/bin/env python
# This example shows how to align a set of objects together using the
# Procrustes algorithm. We make three ellipsoids by distorting and
# translating a sphere and then align them together, using the
# different modes of Procrustes alignment: rigid-body, similarity and
# affine.
import vtk
sph... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/Modelling/Python/procrustesAlignment.py | Python | gpl-3.0 | 5,728 | [
"VTK"
] | 19e57dd37a3cff558b2fd3596d089e5dde253fcb0a483982530cc12a6ce09ad7 |
"""
Module for grid search parameter optimization and exploration
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
from __future__ import absolute_import
from builtins import zip
from builtins import range
from builtins import open
from builtins impor... | Neurosim-lab/netpyne | netpyne/batch/grid.py | Python | mit | 15,588 | [
"NEURON"
] | a46ef1cc304898b0e3b15a6f554bd3aebbe900fdda5ae33d0b05e8e10e1fd30e |
#!/usr/bin/env python3
import itertools
from collections import defaultdict
import logging
from operator import mul
import networkx as nx
import numpy as np
import pandas as pd
from pgmpy.base import DirectedGraph
from pgmpy.factors.discrete import TabularCPD, JointProbabilityDistribution, DiscreteFactor
from pgmpy.... | abinashpanda/pgmpy | pgmpy/models/BayesianModel.py | Python | mit | 28,954 | [
"VisIt"
] | d37a1a71cb576aebd4ba2d6e22967caa0b5714c59f23e1bf37d990d751ee2d4f |
"""
Restricted Boltzmann Machines (RBM) Implementation in Tensorflow
"""
from __future__ import division, print_function, absolute_import
import tensorflow as tf
import numpy as np
from xrbm.utils import tfutils
class RBM():
'Restricted Boltzmann Machines (RBM)'
def __init__(self, num_vis, num_hid, vis_type=... | omimo/xRBM | xrbm/models/rbm.py | Python | mit | 7,929 | [
"Gaussian"
] | 95c7af8ed7c40b4f418efe2ddde23373b43c820136ddb4a58a8de46ae40e1f23 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# cell scalars to point scalars
# get the interactor ui
# Create the RenderWindow, Renderer and RenderWindowInteractor
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.A... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Core/Testing/Python/CellDataToPointData.py | Python | gpl-3.0 | 1,548 | [
"VTK"
] | c56b647c24df7de51cb3b3398eaeff78ab754f2fbc785f44b7bec97996622d11 |
# 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.
"""Bio.SearchIO parser for BLAT output formats.
This module adds support for parsing BLAT... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/SearchIO/BlatIO.py | Python | gpl-2.0 | 30,382 | [
"BLAST",
"Biopython"
] | 539a9e464b0694b22a0c43a0800ec4e8bbcce3afce76046b5bae5366b2cbedec |
"""Calculator for General Energy-based Fragmentation"""
from sys import stdout
from os import system
from ase.units import Ha, Bohr
import ase.units as u
#from future import printf
from copy import deepcopy
from ase.calculators.nwchem import NWChem
from numpy import zeros, append, array, transpose, savetxt, abs, pi
#... | PHOTOX/fuase | ase/ase/calculators/monofragment-gebf.py | Python | gpl-2.0 | 10,120 | [
"ASE",
"NWChem"
] | e943e55eccc793ece4cc033bedaf696a293b4922bc3166955b2505dbea8f9f68 |
#!/usr/bin/env python
r"""
Tree representations (:mod:`skbio.core.tree`)
=============================================
.. currentmodule:: skbio.core.tree
This module provides functionality for working with trees, including
phylogenetic trees and hierarchies. Functionality is provided for
constructing the trees, for t... | Jorge-C/bipy | skbio/core/tree.py | Python | bsd-3-clause | 76,608 | [
"VisIt",
"scikit-bio"
] | c4fd871d7cbb8428994bc8f44e8bb1afa5101a4f5667ee6ca01324ddac95349f |
import logging
import os
import sys
import StringIO
import stat
import yaml
import zookeeper
from twisted.internet.defer import inlineCallbacks, Deferred, fail, returnValue
from juju.unit.lifecycle import (
UnitLifecycle, UnitRelationLifecycle, RelationInvoker)
from juju.unit.workflow import RelationWorkflowSta... | mcclurmc/juju | juju/unit/tests/test_lifecycle.py | Python | agpl-3.0 | 37,560 | [
"SIESTA"
] | 82e5205de1fac5d2c5899f9a558e3f328d0a48a6beb722ca8470c836159106e9 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (t... | apache/allura | Allura/allura/tests/functional/test_site_admin.py | Python | apache-2.0 | 37,987 | [
"VisIt"
] | d14dc0fbbf76515e502f69be33be2b8962b3e5515c8c309515ab0a09b980db16 |
"""
NetCDF reader/writer module.
This module is used to read and create NetCDF files. NetCDF files are
accessed through the `netcdf_file` object. Data written to and from NetCDF
files are contained in `netcdf_variable` objects. Attributes are given
as member variables of the `netcdf_file` and `netcdf_variable` objects... | nmayorov/scipy | scipy/io/netcdf.py | Python | bsd-3-clause | 39,266 | [
"NetCDF"
] | d8ccedc293f7b13588490aab7a3756c37d01731a680304a41c4527c8925454df |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | gunan/tensorflow | tensorflow/python/autograph/pyct/transpiler_test.py | Python | apache-2.0 | 6,134 | [
"VisIt"
] | 0f88c0890f08547e09e035f70d61c1426b244abf83ae597b1882a2184cf4371c |
########################################################################
# File : ComputingElement.py
# Author : Stuart Paterson, A.T.
########################################################################
""" The Computing Element class is a base class for all the various
types CEs. It serves several purpos... | vmendez/DIRAC | Resources/Computing/ComputingElement.py | Python | gpl-3.0 | 18,516 | [
"DIRAC"
] | 59057d175bd92120c667b5e34c6cc99286e2334e9a6ef943febafef9bf6e3898 |
# ----------------------------------------------------------------------------
# Copyright 2015-2016 Nervana Systems Inc.
# 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.apa... | Jokeren/neon | tests/test_optimizer.py | Python | apache-2.0 | 8,211 | [
"Gaussian"
] | 6d2e62fde15e035b668294ef4a562dce9ac21e5dc60313fff67acf08f997ec7f |
import bs4
import copy
import datetime
import functools
import time
from django.conf import settings as django_settings
from django.core import management
from django.core import serializers
import django.core.mail
from django.core.urlresolvers import reverse
from django.test import TestCase
from django.test.client imp... | openpgh/askpgh | askbot/tests/email_alert_tests.py | Python | gpl-3.0 | 46,273 | [
"VisIt"
] | dd649c1d2120f0a73de837dc2e475b2a10e792f6e681733bfa41dece976abdc9 |
"""
Contains GUI forms for the displacement filter.
"""
from __future__ import absolute_import
from __future__ import unicode_literals
from . import base
from ...filtering.filters import displacementFilter
################################################################################
class DisplacementSettingsDi... | chrisdjscott/Atoman | atoman/gui/filterSettings/displacementSettingsDialog.py | Python | mit | 3,599 | [
"VTK"
] | 3a659b5ff69ebee0d6536317192a536fcd446c6a67812d34742b8b4376175e19 |
# -*- coding: utf-8 -*-
"""
BeamBlock.py - Class for Beam Blockage calculations
Author::
Nick Guy - OU CIMMS/Univ of Miami
This program was ported from code written in IDL used at Colorado State University.
It is believed that the original code at CSU was written by Steven Nesbitt.
Timothy Lang also contributed to ... | nguy/PyRadarMet | pyradarmet/BeamBlock.py | Python | gpl-2.0 | 35,446 | [
"NetCDF"
] | a301f216cbe11493febfc4b3d02aba5fe3d5b7ffd5b444f6e5a12902a8bbe745 |
# -*- coding: utf-8 -*-
"""
数值函数.
@author: zhoujiagen
Created on 02/11/2018 7:12 PM
"""
import math
# ---------------------------------------------------------------------------
# 距离(Distance)函数
# ---------------------------------------------------------------------------
def euclidean(vec1, vec2):
"""
距离函... | zhoujiagen/giant-data-analysis | data-computing-giants/python-computing/src/gda/tools/numeric_function.py | Python | mit | 2,848 | [
"Gaussian"
] | 5c370f65b3f48bc4f0748801c2a31e3a823cee6775ec7d2eb4976801498001d9 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforge/morphology/visitor/visitorbaseclasses.py | Python | bsd-2-clause | 6,321 | [
"VisIt"
] | 54aa06decd16adb71906b893e8b5209feb6df262d23164fb176d537a4de7d3ec |
# -*- coding: utf-8 -*-
r"""Define a Time Of Flight instrument for resolution calculations
"""
import numpy as np
from ..constants import e, hbar, neutron_mass
from ..crystal.sample import Sample
from ..energy import Energy
from .chopper import Chopper
from .detector import Detector
from .exceptions import DetectorEr... | granrothge/neutronpy | neutronpy/instrument/tof_instrument.py | Python | mit | 14,795 | [
"CRYSTAL"
] | f90e989c386f13651a9bc3e4ed6ffcc11c6eb836d6d9d8f795270d54cd3e4104 |
# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. 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.
'''
Support for asynchronous execution.
'''
import os
import thread
... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/PopGen/Async/__init__.py | Python | gpl-2.0 | 3,522 | [
"Biopython"
] | d9f717ffea02cfb1c5e5604ff287324488ae0cb7ada032aea75007b2556ff05c |
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg
##
## 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
... | ostrokach/biskit | Biskit/amberResidueLibrary.py | Python | gpl-3.0 | 8,488 | [
"Amber"
] | 2114e5df449792ea7dbb625405cffba5a87e1fa02f574bae6420ab2e479646c4 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | maintainer/benchmarks/ferrofluid.py | Python | gpl-3.0 | 7,635 | [
"ESPResSo"
] | efa8939d0c25a09bee5f080ad54bd73c0d358b5d265b7fe53d39f6ad660147f0 |
########################################################################
# $Id$
########################################################################
""" DIRAC FileCatalog Database """
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.... | miloszz/DIRAC | DataManagementSystem/DB/FileCatalogDB.py | Python | gpl-3.0 | 36,419 | [
"DIRAC"
] | 05f3014e64a40e7549e52d01d0336320b5996cedaf3105540d7f2a82f4db00a8 |
import cgi
from itertools import chain, groupby
from operator import itemgetter
import re
from parsimonious import Grammar, NodeVisitor
from dxr.filters import LINE, FILE
from dxr.mime import icon
from dxr.utils import append_update, cached
@cached
def direct_searchers(plugins):
"""Return a list of all direct s... | pelmers/dxr | dxr/query.py | Python | mit | 17,262 | [
"VisIt"
] | ac7c09bbefb415047181a45334d62e0207d8f3af902ff6c296e07066f3a0075c |
import numpy as np
import networkx as nx
from collections import defaultdict
from models import ( ClassInstance, ClassInstanceClassInstance, Relation,
Review, Treenode, TreenodeConnector, TreenodeClassInstance )
class Neuron(object):
def __init__(self, neuron_id, project_id):
self.neuron = Cla... | htem/CATMAID | django/applications/catmaid/objects.py | Python | agpl-3.0 | 17,884 | [
"NEURON"
] | fe8df5f45b24ef1abe22be3a5ec0f0bb0512bcc3ba95f9b41fc883589327baee |
tests = [("python", "UnitTestTrainer.py", {}),
("python", "UnitTestOther.py", {}), ]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))
| ptosco/rdkit | rdkit/ML/Neural/test_list.py | Python | bsd-3-clause | 266 | [
"RDKit"
] | 590c2fb4e3eb678f7c1da27e418abc8e58078d76f14c997a8a29dfff178b93e6 |
import os
import HTSeq
from .utils import infer_extension
class Window(object):
"""Representation of the windows"""
def __init__(self, name, filepath, filetype=None, window_length=100, pseudocount=1, func=None):
"""Initialization of Window
:param name: str -- name of the signal
:para... | guma44/MetaProfile | MetaProfile/Window.py | Python | isc | 4,673 | [
"HTSeq"
] | bbb0110f4341b1f5da5957620bb2bf737558779a3f4746e189807ed33d022cca |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/qcdb/libmintsmolecule.py | Python | lgpl-3.0 | 124,644 | [
"Elk",
"Psi4"
] | 94792b7b454c2855b8fc4f7fcccb9f3b72eaadd1374fa82e5b3c956dd6752057 |
from SimPEG import Utils, Survey, np
from SimPEG.Survey import BaseSurvey
from simpegEM.Utils import SrcUtils
from BaseTDEM import FieldsTDEM
class RxTDEM(Survey.BaseTimeRx):
knownRxTypes = {
'ex':['e', 'Ex', 'N'],
'ey':['e', 'Ey', 'N'],
'ez':['e', 'Ez'... | lheagy/simpegem | simpegEM/TDEM/SurveyTDEM.py | Python | mit | 5,303 | [
"VMD"
] | 6dbb777f45fa857c4f6cafdb72a2fa489c5b697e56eac6f1389b747c6b87bf1c |
#! /usr/bin/env python
# Example of use of pyem toolbox. Feel free to change parameters
# such as dimension, number of components, mode of covariance.
#
# You can also try less trivial things such as adding outliers, sampling
# a mixture with full covariance and estimating it with a mixture with diagonal
# gaussians (... | jhmadhav/pynopticon | src/em/doc/examples/demo1.py | Python | gpl-3.0 | 3,164 | [
"Gaussian"
] | 34dd44f3b7f59e204865f075effe003fd2a7beea4c5b3585e569cab29eb03a19 |
#!/usr/bin/env python
# Dan Blankenberg
"""
Reads a list of intervals and a maf. Outputs a new set of intervals with statistics appended.
"""
from __future__ import print_function
import sys
import bx.intervals.io
from bx.bitset import BitSet
from galaxy.tools.util import maf_utilities
def __main__():
maf_sourc... | ieguinoa/tools-iuc | tools/maf_stats/maf_stats.py | Python | mit | 4,982 | [
"Galaxy"
] | 5c7c65165b2d219f748d129ff3e34c9fd04dece72845414da3b5cf03db056519 |
# $HeadURL$
""" SystemAdministrator service is a tool to control and monitor the DIRAC services and agents
"""
__RCSID__ = "$Id$"
from types import *
import os, re, commands, getpass
from datetime import timedelta
from DIRAC import S_OK, S_ERROR, gConfig, shellCall, systemCall, rootPath, gLogger
from DIRAC.Core.DISE... | calancha/DIRAC | FrameworkSystem/Service/SystemAdministratorHandler.py | Python | gpl-3.0 | 20,753 | [
"DIRAC"
] | c1964b723e9f255706f456951a8ec9386fbae63d69eb0786b72ce2819214a2ac |
from __future__ import print_function
import numpy as np
from ase.utils.bee import get_ensemble_energies
from ase.parallel import paropen as open
from gpaw import GPAW
atom = GPAW('H.gpw', txt=None).get_atoms()
molecule = GPAW('H2.gpw', txt=None).get_atoms()
e1 = atom.get_potential_energy()
e2 = molecule.get_potenti... | robwarm/gpaw-symm | doc/tutorials/H2/ensembles.py | Python | gpl-3.0 | 736 | [
"ASE",
"GPAW"
] | 96d8c56480b362f136685a8261444e04fc704abb1c1255cf7307e103fe794b11 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/endorsed_plugins.py | Python | lgpl-3.0 | 1,048 | [
"Psi4"
] | 23aaa1489445c10bfadf73a2ba3fcddd0964182ad9264fb68f025d2f169a0368 |
# Copyright 2004-2012 Tom Rothamel <pytom@bishoujo.us>
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, m... | MSEMJEJME/Get-Dumped | renpy/display/core.py | Python | gpl-2.0 | 76,399 | [
"VisIt"
] | 4e71f31319a8f7586759b07f9c7f10228658b7eeb5eb2867a5b7a2cc8f1c19c4 |
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