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# Copyright (c) 2014-2015 Bruno Daniel <bruno.daniel@blue-yonder.com>
# Copyright (c) 2015-2017 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2016-2018 Ashley Whetter <ashley@awhetter.co.uk>
# Copyright (c) 2016 Derek Gustafson <degustaf@gmail.com>
# Copyright (c) 2016 Glenn Matthews <glenn@e-dad.net>
# Copyrigh... | kczapla/pylint | pylint/test/extensions/test_check_docs.py | Python | gpl-2.0 | 65,618 | [
"VisIt"
] | 38abe07a82553711634032b5ac140eb941654013e4bb5aea328aeb75a858cf7a |
from mock import Mock
from unittest import TestCase
from bok_choy.page_object import PageObject, PageLoadError, unguarded, WrongPageError
from bok_choy.promise import BrokenPromise
from tests.pages import SitePage
class InvalidURLPage(SitePage):
"""
Create a page that will return a malformed URL.
"""
... | drptbl/bok-choy | tests/test_page_object.py | Python | apache-2.0 | 2,902 | [
"VisIt"
] | 1b9393a92499d77cc8965a42151576f9359a77aa0481f0fc3ca96800764798b7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.periodic_table import Element, Specie
from pymatgen.core.composition import C... | xhqu1981/pymatgen | pymatgen/core/tests/test_structure.py | Python | mit | 50,711 | [
"pymatgen"
] | 4e56c9e7800ad6553c1961fcfdcf536cecdd5c692bddd7ade49f84951d363f37 |
#!/usr/bin/python
"""
This module specifically deals with the dynamical quantities
related to Multi Gaussian Expansion models (Monnet et al. 1992, Emsellem et al. 1994).
It includes the derivation of projected and deprojected photometry, and
the derivation of velocity moments via the Jeans Equations.
"""
"""
Importi... | emsellem/pygme | pygme/dynMGE.py | Python | bsd-3-clause | 32,859 | [
"Gaussian"
] | a8c32e78573b445b1d72ae65a188ace37e44bde1a522cde1f497f036ed8fb460 |
#encoding:utf-8
from __future__ import division
from Sequencer import Sequence, Note
from itertools import cycle
from Synth import BaseSynth, ClassicSynth, ChorusSynth, PianoSynth
from pyo import *
from AudioEngine import WalkingBass, Melody
from Chordbook import durations, changeOctave
class AudioPlayer():
def __in... | poifra/Creamuspython2 | AudioManager.py | Python | mit | 4,550 | [
"Gaussian"
] | 6d779a09e3fa8f840319f00a4788c859eef65ada1711219397f66eec0a75887c |
"""Smolyak sparse grid constructor."""
from collections import defaultdict
from itertools import product
import numpy
from scipy.special import comb
import numpoly
import chaospy
def sparse_grid(
order,
dist,
growth=None,
recurrence_algorithm="stieltjes",
rule="gaussian",
... | jonathf/chaospy | chaospy/quadrature/sparse_grid.py | Python | mit | 5,495 | [
"Gaussian"
] | 1f349e99a866b380a297235b86e53f53f55d879b6412f3bb5b8c633ad0620fb9 |
# -------------------------------------------------------------------
# Switch Class
# -------------------------------------------------------------------
# source: Brian Beck, PSF License, ActiveState Code
# http://code.activestate.com/recipes/410692/
class switch(object):
""" Readable switch construct... | AmritaLonkar/trunk | SU2_PY/SU2/util/switch.py | Python | gpl-2.0 | 1,518 | [
"Brian"
] | d59032c698d5fbf32564e97529406af1676550b322ffcd097d46617c62ed829d |
import numpy as np
from growth_procs import direction_to,\
normalize_length,\
get_entity,\
prepare_next_front
L_NORM=3.0
def extend_front(front,seed,constellation) :
# attract by a different neuron, get information
other_entities = get_entity("cell_type_2",constellation)
if not len(other_e... | btorboist/neuromac | examples/simultaneous_runs/TestF_Left_Distant.py | Python | gpl-3.0 | 745 | [
"NEURON"
] | 6dae1aac120c477c17d4e3a23bd3ea4819c99fb67cdf7f40dc5d80a96a33f3b0 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/ao2mo/addons.py | Python | apache-2.0 | 7,717 | [
"PySCF"
] | 1afffd50a3a404b23fed79564caedd16dda491c2de2b67e15bdf830609d985a5 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/web/epgsimilar.py | Python | gpl-2.0 | 7,545 | [
"VisIt"
] | 66712a0e5c8706fe7eb26d7ddb186ac14e3159adac55d7b4478782b8298339d3 |
"""
Contains a variety of sensory models, specifically models for the
visual pathway.
"""
import topo
import param
import numbergen
import lancet
import numpy
import imagen
from imagen.patterncoordinator import PatternCoordinator, PatternCoordinatorImages
from topo.base.arrayutil import DivideWithConstant
from topo.... | Tasignotas/topographica_mirror | topo/submodel/earlyvision.py | Python | bsd-3-clause | 15,028 | [
"Gaussian"
] | cad47e5f0be6fc64b25fea2dbe2398464d962725d4fd69f537551d0a6c946ec8 |
import warnings
from collections import Counter, defaultdict, deque, abc
from collections.abc import Sequence
from concurrent.futures import ThreadPoolExecutor
from functools import partial, reduce, wraps
from heapq import merge, heapify, heapreplace, heappop
from itertools import (
chain,
compress,
count,... | erikrose/more-itertools | more_itertools/more.py | Python | mit | 133,020 | [
"ADF"
] | 470d74f0ad8ca52c66cd420bd741e59c0b3f35f79abb8100ebb0eeccc89259d7 |
from __future__ import print_function
from __future__ import division
from sklearn.decomposition import PCA
from scipy import stats
from copy import deepcopy
import vtk
import numpy as np
import pickle
import json
import os,sys
class BoundError(Exception):
def __init__(self, value):
self.value = value
class ... | pdedumast/ShapeVariationAnalyzer | ShapeVariationAnalyzer/shapepcalib.py | Python | apache-2.0 | 33,570 | [
"VTK"
] | e0224a5c9c4878ebbea7c1ad72ec0bbc75b82e1fadfd084452fbb738e7df82ec |
'''
Arthur Glowacki
APS ANL
10/26/2014
'''
from vtk import *
import math, time
import h5py
import numpy as np
from PyQt4 import QtCore
class Volumizer(QtCore.QThread):
notifyProgress = QtCore.pyqtSignal(int)
notifyFinish = QtCore.pyqtSignal()
def __init__(self):
QtCore.QObject.__init__(self)
self.filename = '... | aglowacki/ScanSimulator | Volumizer.py | Python | gpl-2.0 | 3,464 | [
"VTK"
] | cab2573f50e82ae0cdbea43d92338be27b32bd32e828deee757a5f1681ff64f2 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""A simple little tool which watches GTK+'s global recent files list and
removes anything that matches a hashed blacklist of URI prefixes.
--snip--
@note: The config file is stored in XDG_DATA_DIR for two reasons:
1. It's probably a good idea to have it roaming.
... | ssokolow/gtk-recent-scrubber | gtk_cleanup.py | Python | gpl-3.0 | 12,641 | [
"VisIt"
] | 45a31639c62db19beeb15a98eb8483d63d12e0eacf90cedcb7828afdd84efaa6 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import gobject
import gtk, os, pango, sys
from zeroinstall import _
from zeroinstall.injector import model, writer
from zeroinstall import support
from zeroinstall.gtkui import gtkutils
import utils
... | res2k/0install | zeroinstall/0launch-gui/impl_list.py | Python | lgpl-2.1 | 7,503 | [
"VisIt"
] | 8b535c33ebe5825016efe7e9e99a7484a786a4d0c688de5d9b9300612bd50c57 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import numpy as np
import math
import itertools
import collections
import warnings
from pymatgen.core.periodic_table import get_el_sp
from pymatgen.core.structure impor... | aykol/pymatgen | pymatgen/electronic_structure/bandstructure.py | Python | mit | 37,898 | [
"CRYSTAL",
"pymatgen"
] | 4feb4b943534383cb7665f73fdf7d0bad7b434d062982617d711164fb1f2c667 |
"""
Defining some constants for plots. Colors and
general styles.
"""
import matplotlib as mpl
import numpy as np
mpl.use('Agg')
mpl.rcParams['hatch.linewidth'] = 8
from matplotlib import rc, cm
viridis = cm.get_cmap('viridis')
magma = cm.get_cmap('magma')
plasma = cm.get_cmap('plasma')
fsize = 17
rc('text', ... | aemerick/galaxy_analysis | plot/plot_styles.py | Python | mit | 2,117 | [
"Galaxy"
] | 56355f5ca9199fafbf83ea426c0d9e8e2d27ac8de2555dfa6bcdc3b9919a74dc |
#!/usr/bin/env python
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# Written (W) 2012 Heiko Strathmann
# Copyrigh... | cfjhallgren/shogun | examples/undocumented/python/modelselection_grid_search_krr.py | Python | gpl-3.0 | 5,007 | [
"Gaussian"
] | 0f81e3588856bf1a1ac3cb6ed1769632ac9158809d7302dec33413c355400a1c |
# Copyright 2013-2020 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 RInteractivedisplaybase(RPackage):
"""Base package for enabling powerful shiny web display... | iulian787/spack | var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py | Python | lgpl-2.1 | 1,208 | [
"Bioconductor"
] | 3630866c0652b69fb2784cfc9a442e76c4ed8cb951e076b431f104a396db32dd |
import numpy as np
import types
from downsample import downsample as downsample_2d
from convolve_nd import convolvend as convolve
def smooth(image, kernelwidth=3, kerneltype='gaussian', trapslope=None,
silent=True, psf_pad=True, interp_nan=False, nwidths='max',
min_nwidths=6, return_kernel=False, norma... | dattalab/d_code | imaging/alignment/image_registration/image_registration/fft_tools/smooth_tools.py | Python | mit | 8,382 | [
"Gaussian"
] | 291417ddc0fa75913c7ea9c4aff89c0562fe788df24ce59f71f25b01a0c516a1 |
#coding:utf-8
# Author: mozman
# Purpose: svg container classes
# Created: 15.09.2010
# Copyright (C) 2010, Manfred Moitzi
# License: MIT License
"""
The **container** module provides following structural objects:
* :class:`svgwrite.Group`
* :class:`svgwrite.SVG`
* :class:`svgwrite.Defs`
* :class:`svgwrit... | meshulam/sly | deps/svgwrite/container.py | Python | mit | 9,024 | [
"VisIt"
] | f68a75314279952100f5d37722e24005d5e8f94ecf6014e9d6ef7f12b2ed2cb7 |
from __future__ import absolute_import
from enum import Enum
from itertools import izip
import operator
import numpy as np
from scipy import signal
from scipy.ndimage import binary_closing, generic_filter, label
from scanomatic.models.phases_models import SegmentationModel
__EMPTY_FILT = np.array([]).astype(bool)
... | Scan-o-Matic/scanomatic | scanomatic/data_processing/phases/segmentation.py | Python | gpl-3.0 | 31,924 | [
"Gaussian"
] | f3c9196e8838ac4e01eb267796c317d801aca5a1a2b9b2f2a9f0524456a14b1f |
# Copyright (C) 2010-2019 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 v... | espressomd/espresso | testsuite/python/observable_cylindrical.py | Python | gpl-3.0 | 10,895 | [
"ESPResSo"
] | 1b528b71ce82f4e7f828468b5dc90581506101c16a4f712e1c02e2ea22fc1b3c |
# GenData.py
import sys
import numpy as np
import cv2
import os
import argparse
# module level variables ##########################################################################
###################################################################################################
def main():
ap = argparse.Argume... | muchlisinadi/ALPR-Indonesian-plate | invert_imageData.py | Python | mit | 2,316 | [
"Gaussian"
] | e838b9dfddde9e3640fe3438e55380f0d5755855a46b897699cf17aa6979bcdb |
import static
import debug
from mpi4py import MPI
import data
import dirac
import logging
import socket
import os.path as op
import os
import boto
import bisect
import itertools
import pandas
import numpy as np
"""
def initLogging():
comm = MPI.COMM_WORLD
logfile = "/scratch/sgeadmin/log_mpi_r%i.txt"%comm.Get_r... | JohnCEarls/tcDirac | tcdirac/master.py | Python | gpl-2.0 | 5,986 | [
"DIRAC"
] | 588bfaf7033d0ac110331976f945f7b74bf1050fb6de9412a3e06d9938568a87 |
# Dropbox Auto Directory Sync Script
import os
import webbrowser
import urllib2
import json
import hashlib
import sys
import subprocess
import time
import datetime
import multiprocessing
import re
from InstallModule import InstallModule
from Dialog import Dialog
from InterfaceServer import *
from Updater import Update... | StephanHeijl/PortableDevSync | PortableDevSync.py | Python | apache-2.0 | 10,163 | [
"VisIt"
] | e9c29d8ea85c56028465a7596651a60daf92df28d720b823b7e3d3f897365fa3 |
""" Storage Factory Class - creates instances of various Storage plugins from the Core DIRAC or extensions
This Class has three public methods:
getStorageName(): Resolves links in the CS to the target SE name.
getStorage(): This creates a single storage stub based on the parameters passed in a dict... | fibbo/DIRAC | Resources/Storage/StorageFactory.py | Python | gpl-3.0 | 11,109 | [
"DIRAC"
] | 1d40fe9cc9578a4a77d37e1068ac88acfa9d7d48d2fbc7488bb64faae818f43d |
import numpy as np
import netCDF4 as netCDF
import matplotlib.pyplot as plt
from mpl_toolkits.basemap import Basemap
from datetime import datetime
from scipy.signal import medfilt2d
import pyroms
import pyroms_toolbox
from bathy_smoother import *
# get horizontal grid from v1
grd_v1 = pyroms.grid.get_ROMS_grid('YELLO... | kshedstrom/pyroms | examples/Yellow_Sea/make_YELLOW_grd_v2.py | Python | bsd-3-clause | 5,212 | [
"NetCDF"
] | 4d74e0c3b2f0ae9a660e85da51314b007256ade57e35a972ee7348164e2c3109 |
import plotly
import os
import shutil
import pytest
# Fixtures
# --------
@pytest.fixture()
def setup():
# Reset orca state
plotly.io.orca.config.restore_defaults(reset_server=False)
here = os.path.dirname(os.path.abspath(__file__))
# Run setup before every test function in this file
pytestmark = pytest.m... | plotly/plotly.py | packages/python/plotly/plotly/tests/test_orca/test_sg_scraper.py | Python | mit | 1,549 | [
"ORCA"
] | f14a6f03d17943fee7b4a0dc7950a3b95df21824af9557ee2fcd844512b2a020 |
# -*- coding: utf-8 -*-
# Copyright 2007-2020 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | dnjohnstone/hyperspy | hyperspy/signal_tools.py | Python | gpl-3.0 | 67,918 | [
"Gaussian"
] | 974ffaa30a479491fef8753e9b5e1758b3e258b46d6cf9e3c9fe1c86871adfd7 |
#!/usr/bin/env python
# encoding: utf-8
# Carlos Rafael Giani, 2007 (dv)
# Thomas Nagy, 2007-2008 (ita)
import os, sys, re, optparse
import ccroot # <- leave this
import TaskGen, Utils, Task, Configure, Logs, Build
from Logs import debug, error
from TaskGen import taskgen, feature, after, before, extension
from Config... | oneman/xmms2-oneman-old | wafadmin/Tools/d.py | Python | lgpl-2.1 | 14,276 | [
"VisIt"
] | 0f8af7232c9c2087fd2a050a7f7a60d18afc2ccc48c7d9192a80ff46cabfdb04 |
# -*- coding: utf-8 -*-
"""Internal DSL functions for edges."""
import warnings
from typing import Dict, Optional, Union
from ..constants import (
ACTIVITY,
CELL_SURFACE,
DEGRADATION,
EFFECT,
EXTRACELLULAR,
FROM_LOC,
INTRACELLULAR,
LOCATION,
MODIFIER,
NAME,
NAMESPACE,
... | pybel/pybel | src/pybel/dsl/edges.py | Python | mit | 4,929 | [
"Pybel"
] | f245f5759feb1d593f1d3b303d1bcc1474c81ac6825c9ba1e1879d8e4e791e31 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Package for analyzing elastic tensors and properties.
"""
from .elastic import (
ComplianceTensor,
ElasticTensor,
ElasticTensorExpansion,
NthOrderElasticTensor,
diff_fit,
find_eq_stress,
genera... | materialsproject/pymatgen | pymatgen/analysis/elasticity/__init__.py | Python | mit | 531 | [
"pymatgen"
] | 2b8802cbc0a7d96ece598e138fea49876bf3c474b7f5967729ae3857edef023d |
# -*- coding: utf-8 -*-
#------------------------------------------------------------
# pelisalacarta - XBMC Plugin
# Canal para somosmovies
# http://blog.tvalacarta.info/plugin-xbmc/pelisalacarta/
#------------------------------------------------------------
import urlparse,urllib2,urllib,re
import os, sys
from core ... | Zanzibar82/pelisalacarta | python/main-classic/channels/somosmovies.py | Python | gpl-3.0 | 19,043 | [
"ADF"
] | e086fd1f78763e8f6ee4b386b2224072cbdde49b91c8fcab95a1351464047822 |
"""
Pyinvoke tasks.py file for automating releases and admin stuff.
Author: Shyue Ping Ong
"""
import datetime
import glob
import json
import os
import re
import subprocess
import webbrowser
import requests
from invoke import task
from monty.os import cd
from pymatgen import __version__ as CURRENT_VER
NEW_VER = da... | davidwaroquiers/pymatgen | tasks.py | Python | mit | 9,157 | [
"pymatgen"
] | 0d53682768852bf0f783ab300e63d7d2dbc1437021a0e7da93d6535fde805d67 |
"""The WaveBlocks Project
This file contains the class which represents a homogeneous Hagedorn wavepacket.
@author: R. Bourquin
@copyright: Copyright (C) 2016 R. Bourquin
@license: Modified BSD License
"""
from numpy import zeros, complexfloating, array, eye, atleast_2d, angle, squeeze
from numpy.linalg import det
... | WaveBlocks/WaveBlocksND | WaveBlocksND/HagedornWavepacketPsi.py | Python | bsd-3-clause | 7,340 | [
"Gaussian"
] | bad7f1a72a5b4e1e0e2e1b80c0779908b348e361773d844c5495cd16ddc05d78 |
#!/usr/bin/env python
# Phil.py
# Copyright (C) 2012 Diamond Light Source, Graeme Winter
#
# This code is distributed under the BSD license, a copy of which is
# included in the root directory of this package.
#
# Phil parameter setting - to get a single place where complex parameters to
# set for individual prog... | xia2/xia2 | src/xia2/Handlers/Phil.py | Python | bsd-3-clause | 36,352 | [
"CRYSTAL"
] | 9aedd8307b020a1c449664c85d6c0b9785e80fe9ed027f9aa697b95bd366b3fb |
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | Cartman0/roboto | scripts/lib/fontbuild/italics.py | Python | apache-2.0 | 9,272 | [
"Gaussian"
] | 3a8a5727f164e7d9cca057bcdccdb2fea5fc5213012aba9b2c1ee79aaebb3cc1 |
import nash.parser as parser
import nash.interpreter as interpret
nash_parser = parser.Parser()
interpreter = interpret.Interpreter()
def test_parsing_multiple_lines():
program = "x -> x + 1"
ast = nash_parser.parse(program)
assert ast == ('BLOCK', [('FUNCTION', [('IDENTIFIER', 'x')], ('BLOCK', [('ADD', (... | mightymoose/nash | tests/test_parsing_unary_function.py | Python | bsd-3-clause | 589 | [
"VisIt"
] | 14e69bbeeca1e8f25bbff2170b26d3c7393bc9edc3d8c341d42a6fc5c77d0ce2 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2020-2021, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
"""Dependency structs."""
# FIXME: add caching all over the place
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
imp... | renard/ansible | lib/ansible/galaxy/dependency_resolution/dataclasses.py | Python | gpl-3.0 | 20,327 | [
"Galaxy"
] | 93652f2e64afb7c337dac46e5fcf74c0f4da804639348d867d5faeae82ceb497 |
# Copyright (c) 2010 Howard Hughes Medical Institute.
# All rights reserved.
# Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
# http://license.janelia.org/license/jfrc_copyright_1_1.html
"""
This script creates a simple network that includes each type of network component.
""... | JaneliaSciComp/Neuroptikon | Source/Scripts/Synapses.py | Python | bsd-3-clause | 1,601 | [
"NEURON"
] | 0308124c26b14cc78d054be5b10536b6d1f7e3ee0f94463f3df1ccb3cc18e806 |
########################################################################
# $HeadURL $
# File: FTSStrategy.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/12 13:12:07
########################################################################
""" :mod: FTSStrategy
=================
.. module: FTSStrat... | andresailer/DIRAC | DataManagementSystem/private/FTS2/FTS2Strategy.py | Python | gpl-3.0 | 18,645 | [
"DIRAC"
] | 0aaf23df80b71cf08cecaa5225ca132017600a870aa8dbd4ad174e9943342af3 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure that all files contain proper licensing information."""
import json
import optparse
import os.path
import subproces... | hujiajie/chromium-crosswalk | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 22,227 | [
"Galaxy"
] | 8168fdf2cced97bffb5897eab5f146786039cb6566403ee7145f12e0b6f504a2 |
# This file is part of Merlin/Arthur.
# Merlin/Arthur is the Copyright (C)2009,2010 of Elliot Rosemarine.
# 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; you can redistribute it an... | ellonweb/merlin | Arthur/views/lookup.py | Python | gpl-2.0 | 3,660 | [
"Galaxy"
] | 14cb6cf5efac5e4a1d33315a4f9d15b69c85d25d6acd36eeeed9e65e2174fb97 |
import string
import requests
import urllib
import urllib.request
import urllib.error
import socket
import zlib
import random
class YikYakAPI:
endPointIP = "107.170.53.122"
endPointURL = "http://yikyakapp.com/YikYakFiles/"
def __init__(self, proxyIP, proxyPort):
self.proxyIP = proxyIP
... | deveyNull/YikYakTerminal | hackyak.py | Python | gpl-2.0 | 6,572 | [
"Galaxy"
] | 4f6563bcd6e80fc9cc7a9d66bea1b4812e41ec82fb11a7aaee550b3aafb4ba3d |
# -*- coding: utf-8 -*-
r"""
.. _disc-filtering:
===================================
Background information on filtering
===================================
Here we give some background information on filtering in general,
and how it is done in MNE-Python in particular.
Recommended reading for practical applications ... | mne-tools/mne-tools.github.io | 0.19/_downloads/68dbe405ac02c372b6167f7e86b7e3e0/plot_background_filtering.py | Python | bsd-3-clause | 49,896 | [
"Gaussian"
] | 10a284722616ef7a8bf5b3a608c44fcb9958cacb8ecff31e59b5416a9d0e5489 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-bamsignals/package.py | Python | lgpl-2.1 | 2,155 | [
"Bioconductor"
] | eed4fbf4d6b13dabff8ae6a9315400dac70eec56ba7931ae0f9b21b3efe00f0f |
"""Transform a string with Python-like source code into Diofant expression."""
import ast
import unicodedata
from io import BytesIO
from keyword import iskeyword
from tokenize import (ENDMARKER, NAME, NEWLINE, NUMBER, OP, STRING, TokenError,
tokenize, untokenize)
from ..core import Basic, Symbol... | skirpichev/omg | diofant/parsing/sympy_parser.py | Python | bsd-3-clause | 27,584 | [
"VisIt"
] | 92d6e6992b203172c46f7eea322e70c7603e02a698196bab5c611fb66f476dde |
"""Configuration class for redmapper.
This file contains the generic redmapper configuration class and associated classes.
"""
import yaml
import fitsio
import copy
from esutil.cosmology import Cosmo
import numpy as np
import re
import os
import logging
from .cluster import cluster_dtype_base, member_dtype_base
from ... | erykoff/redmapper | redmapper/configuration.py | Python | apache-2.0 | 36,615 | [
"Galaxy"
] | 6895968f322424d182e6f92e7881211e35122c6969470b86e9c9999927ae8a3b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# vncstop - Stop a running VNC session
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License... | heromod/migrid | mig/shared/functionality/vncstop.py | Python | gpl-2.0 | 2,740 | [
"Brian"
] | 18220d6eef5af9f58ce933a3a98050c9acc4537076512e4bad5202cac84d0fbe |
#!/usr/bin/python
#- * -coding: utf - 8 - * -
import os
import MySQLdb
import pymol
import urllib
import subprocess
db = MySQLdb.connect('localhost','root', '54321', 'Pymoldata')# your host, #your username# your password# name of the data base
cur = db.cursor()
def addData():
print 'Enter Details:'
pdbid =... | rishiraj824/PymolDSA | main.py | Python | gpl-3.0 | 2,414 | [
"PyMOL"
] | 314b91f19e07351f9cd942ab30d0f53c71383868e81929b044746d266e7d4162 |
# el.po
val = {" days." : " ημέρες.",
"(all)" : "(όλα)",
"(any)" : "(οποιοδήποτε)",
"(anyone)" : "(Κανένα)",
"(available)" : "(διαθέσιμο)",
"(blank)" : "(κενό)",
"(both)" : "(και τα δύο)",
"(everyone)" : "(οποιοσδήποτε)",
"(master user, not editable)" : "(υπέρχρήστης, μη επεξεργάσιμο)",
"(no change)" : "(καμία αλλαγή)... | bobintetley/asm3 | src/asm3/locales/locale_el.py | Python | gpl-3.0 | 214,413 | [
"Amber",
"VisIt"
] | 8d21b6b9c7b16994a70e48f84c0fbe8be47884167fe8b4cbb5e7000a9ef161e7 |
"""
Job runner plugin for executing jobs on the local system via the command line.
"""
import os
import errno
import logging
import datetime
import tempfile
import subprocess
from time import sleep
from galaxy import model
from ..runners import BaseJobRunner
from ..runners import JobState
from galaxy.util import DATA... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/jobs/runners/local.py | Python | gpl-3.0 | 8,777 | [
"Galaxy"
] | bb882017f66623e251b5fe081cdc0bd61fbd1b47b853066a45e7a5fcfd03ef50 |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 3: Deep Learning and Neural Networks
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2015 by Jeff Heaton
Licensed under the Apache License, V... | PeterLauris/aifh | vol3/vol3-python-examples/examples/example_iris.py | Python | apache-2.0 | 4,131 | [
"VisIt"
] | f66de9d77ea5f2cab5c21dbccb60a5b8cae05f55b67b6a697764da837c9b8f95 |
import unittest
from owlapy import CollectionContainer
from owlapy import CollectionContainerVisitor
from owlapy import OWLEntityCollectionContainerCollector
from owlapy.model import IRI
from owlapy.model import NodeID
from owlapy.model import OWLAnonymousIndividual
from owlapy.model import OWLClass
class TestCollec... | patrickwestphal/owlapy | tests/collectioncontainervisitor_tests.py | Python | gpl-3.0 | 1,244 | [
"VisIt"
] | 5df1bd30ddb4701ec07299d80eaf1309b4509df2d8c2458d7e29d23b829439a7 |
#!/usr/bin/python
'''
N-body backends
'''
TEST = False
TEST = True
work_dir = './playground/'
galaxy_progs_path = '/dgalex2/qinyj/galaxy/progs/'
galaxy_runid = 999
galaxy_dump_time = 1
import os, sys, glob, shutil, time
import subprocess as spc
import numpy as np
import pcs_snap
r_tx = lambda s: '\... | shiaki/iterative-modelling | src/nbody.py | Python | bsd-3-clause | 3,391 | [
"Galaxy"
] | f9d1ebab7d4a786f08afd1ea166ab9ff84ee8bd209075507fbada5f32b6c9b47 |
"""
simple, elegant templating
(part of web.py)
Template design:
Template string is split into tokens and the tokens are combined into nodes.
Parse tree is a nodelist. TextNode and ExpressionNode are simple nodes and
for-loop, if-loop etc are block nodes, which contain multiple child nodes.
Each node can emit som... | nurv/BicaVM | webserver/web/template.py | Python | gpl-3.0 | 43,918 | [
"VisIt"
] | b8af3d78f6d8d39b7e916e10cc7fe97bc79db1deab7057ba3b6edca950f46140 |
"""
tests for has_terminated.
"""
import datetime
from bok_choy.web_app_test import WebAppTest
from ..helpers import UniqueCourseTest
from ..ga_helpers import GaccoTestMixin, GA_GLOBAL_COURSE_CREATOR_USER_INFO, GA_OLD_COURSE_VIEWER_USER_INFO
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.common.logout i... | nttks/edx-platform | common/test/acceptance/tests/lms/test_ga_terminated.py | Python | agpl-3.0 | 6,143 | [
"VisIt"
] | 5f31fa0ce8680e5605a97ee667350b625e41d94c27d15726131db3e015441142 |
# -*- coding: utf-8 -*-
# These tests don't work at the moment, due to the security_groups multi select not working
# in selenium (the group is selected then immediately reset)
from textwrap import dedent
import fauxfactory
import pytest
from riggerlib import recursive_update
from widgetastic_patternfly import Checkab... | anurag03/integration_tests | cfme/tests/cloud_infra_common/test_provisioning.py | Python | gpl-2.0 | 21,665 | [
"VisIt"
] | 3f342c60ede1ab328815b2a3e3054481029b5d5599c26d10b5dca715c2f0f845 |
"""
Tarjan's strongly connected components algorithm is recursive. Python doesn't do well with deep recursion, so
ultimately this code will need to be implemented on a more grown-up language. For now, however, the recursion
limit test that ships with python reported a segfault at a recursion limit exceeding 19100 -- ... | bkuczenski/lca-tools | antelope_background/engine/background_engine.py | Python | gpl-2.0 | 28,343 | [
"VisIt"
] | bc01ad1fc930b687e6ab9e0b2c20bd22bdf7d734c1ae75f6ccc9797fab2af0e9 |
import numpy as np
import vtk
def WrapNPAsVTKImageData(nparr,
spacing=[1.0,1.0,1.0],
origin=[1.0,1.0,1.0],
AutoCopy=False):
vtkArr = vtk.vtkFloatArray()
# the SetVoidArray function uses the python 'buffer object'
# interface, whi... | rkwitt/quicksilver | 3rd_party_software/pyca/Code/Python/VTK/PyCAVTK.py | Python | apache-2.0 | 1,592 | [
"VTK"
] | 4714ad8bfb2f1ceb964cf48cdb81786c3f85c65bd775e8dfa2c609b96d6142b4 |
#!/usr/bin/env python
from aiida import load_dbenv
load_dbenv()
from aiida.orm import load_node, load_workflow
import numpy as np
from phonopy.structure.atoms import Atoms as PhonopyAtoms
from phonopy import Phonopy
# Set WorkflowPhonon PK number
#######################
wf = load_workflow(437)
#####################... | abelcarreras/aiida_extensions | workflows/tools/get_data_phonon.py | Python | mit | 2,436 | [
"phonopy"
] | bc427681229566b22b6d84883724679f080478bb174adb6b080ebcdeaa5623e0 |
#!/usr/bin/python
#
# Copyright 2015 John Kendrick
#
# This file is part of PDielec
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the MIT License
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied wa... | JohnKendrick/PDielec | PDielec/GenericOutputReader.py | Python | mit | 23,036 | [
"CRYSTAL"
] | c8e6801c2e937508eb13b15b821ca602d391178cc0d30f9c20526e70d114ab66 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.community.AIX | ZenPacks/community/AIX/modeler/plugins/community/snmp/AIXSWInstalledMap.py | Python | gpl-2.0 | 1,728 | [
"VisIt"
] | 017c7ec128f45b9c508f25aedcf6525151d83565501a16e73a425132865ab663 |
""" DIRAC.TransformationSystem.DB package """
| DIRACGrid/DIRAC | src/DIRAC/TransformationSystem/DB/__init__.py | Python | gpl-3.0 | 46 | [
"DIRAC"
] | 119ee16abc2be3523fddbf1afc3ee3e2d1c616b1d06145987d9a9f0fab4011be |
# -*- Python -*-
# Configuration file for the 'lit' test runner.
import os
import sys
import re
import platform
import subprocess
import lit.util
import lit.formats
from lit.llvm import llvm_config
from lit.llvm.subst import FindTool
from lit.llvm.subst import ToolSubst
# name: The name of this test suite.
config.n... | llvm-mirror/llvm | test/lit.cfg.py | Python | apache-2.0 | 12,306 | [
"cclib"
] | bf4ff44a915beb769988e40f0f0566a24339f48e8ba46e51cb3c8c066df750a4 |
import numpy as np
from .dtype import img_as_float
__all__ = ['random_noise']
def random_noise(image, mode='gaussian', seed=None, clip=True, **kwargs):
"""
Function to add random noise of various types to a floating-point image.
Parameters
----------
image : ndarray
Input image data. Wi... | chintak/scikit-image | skimage/util/noise.py | Python | bsd-3-clause | 7,610 | [
"Gaussian"
] | 0a841b783a39c8fcf73f3d339a5bacf4ad57f9d17f6fc6ab8015e67fb50945c0 |
# Author: Suyog Dutt Jain <suyog.jain@aero.iitb.ac.in>
# Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2008-2015, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import abspath
from io import BytesIO
import copy
import numpy
import unittest
# Local imports.
from m... | dmsurti/mayavi | mayavi/tests/test_contour.py | Python | bsd-3-clause | 6,044 | [
"Mayavi"
] | e83c969fcc3b064874ffe43b2c5e498c253078c21a754c0dce45713f2e76ca6c |
#By /u/TachyonNZ
# Van Doorn by /u/net_goblin
#TEXT-COM, V0.1
import random as rd
import time as tm
########################################################################
# constants #
########################################################################... | TachyonNZ/textcom | textcom.py | Python | mit | 55,198 | [
"CASINO",
"MOOSE"
] | 1baa1d4bdc7bf8be7214425448fe05b4836b3b23fc58b6ca99ce06ae80f20eb9 |
# -*- coding: utf-8 -*-
""" Tests for student account views. """
import re
from unittest import skipUnless
from urllib import urlencode
import json
import mock
import ddt
import markupsafe
from django.conf import settings
from django.core.urlresolvers import reverse
from django.core import mail
from django.contrib im... | jbassen/edx-platform | lms/djangoapps/student_account/test/test_views.py | Python | agpl-3.0 | 20,224 | [
"VisIt"
] | de9c5b38b9870167ce4066ddbdd89d340df20d99adfa46473fb68f20a1b77389 |
# ##WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING #
# Under development #
# ##WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING#... | coberger/DIRAC | Workflow/Modules/UploadOutputs.py | Python | gpl-3.0 | 3,457 | [
"DIRAC"
] | d98d81f25215a45078da4af478a054a701fc0396b9b25f6867b82c8dc15289ee |
#!/usr/bin/env python3
# ver 0.1 - coding python by Hyuntae Jung on 2/11/2017
# ver 0.2 - support pdb and dcd files for openmm on 5/8/2017
# ver 0.3 - support xtc trajectory files for Monte Carlo using "reduce_unitcells_3d_to_1d" on 6/6/2017
import argparse
parser = argparse.ArgumentParser(
formatter_class=ar... | jht0664/Utility_python_gromacs | python/dn-auto.py | Python | mit | 6,685 | [
"MDAnalysis",
"OpenMM"
] | cca099aa9458372b1ef68e66ba3fa5b137639d43ed88e7e94c6a9088da91f439 |
from argparse import ArgumentParser,FileType
from sys import stdout
def argparser():
"""Returns an argument parser that handles CLI."""
parser = ArgumentParser(prog="python massage.py", description="kernel-weighted time series density.", epilog="Andy's free (as in beer) software.")
parser.add_argument("in... | triposorbust/masseuse | masseuse/cli.py | Python | mit | 1,407 | [
"Gaussian"
] | 4f1bcdbde8a12e78d93341647064fdc1204152405132adca24a7782e2157985f |
"""
Generalized additive models
Requirements for smoothers
--------------------------
smooth(y, weights=xxx) : ? no return ? alias for fit
predict(x=None) : smoothed values, fittedvalues or for new exog
df_fit() : degress of freedom of fit ?
Notes
-----
- using PolySmoother works for AdditiveModel, and GAM with P... | pprett/statsmodels | statsmodels/sandbox/gam.py | Python | bsd-3-clause | 15,251 | [
"Gaussian"
] | b36ae76a1a1237e244b14822de84730f83e6b854e8a79785f41f1a27698611be |
'''
Created on Mar 23, 2015
@author: ayan
'''
from __future__ import (absolute_import, division, print_function)
from collections import namedtuple
import numpy as np
GridPadding = namedtuple('GridPadding',
['mesh_topology_var', # Padding information.
'face_dim'... | NOAA-ORR-ERD/gridded | gridded/pysgrid/utils.py | Python | unlicense | 8,777 | [
"NetCDF"
] | 3ce2db503c8f1534005fdcf954120fa089365c0a4a74bee52d6070316fa16d13 |
"""
Implementations of Restricted Boltzmann Machines and associated sampling
strategies.
"""
# Standard library imports
from itertools import izip
import logging
# Third-party imports
import numpy
N = numpy
np = numpy
import theano
from theano import tensor
T = tensor
from theano.tensor import nnet
from pylearn2.costs... | skearnes/pylearn2 | pylearn2/models/rbm.py | Python | bsd-3-clause | 58,312 | [
"Gaussian"
] | 803e79aeed2c8affe7396dd8bb16af273c78a6cf4f4e6e0ac15c953f7077f55f |
# -*- coding: utf-8 -*-
from django.contrib import admin
from website.models import *
############## ATOMS ######################
class AtomIsotopeAdminInline(admin.TabularInline):
model = AtomIsotope
extra = 1
class AtomAdmin(admin.ModelAdmin):
list_display = ("name","slug","per_id")
search_fields =... | Krozark/Harpe-Website | Harpe-website/website/admin.py | Python | bsd-2-clause | 3,627 | [
"BLAST"
] | a36ed58eacdae50fc7daeea1510742920f2fca4a31d18df8ec6ee99cf26b6bcf |
"""Show how various parameters affect logNlogS."""
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import lines
from copy import deepcopy
from frbpoppy import CosmicPopulation, Survey, SurveyPopulation, hist
# from frbpoppy.population import unpickle
from tests.convenience import plot_aa_style, rel... | davidgardenier/frbpoppy | tests/lognlogs/flattening.py | Python | mit | 7,989 | [
"Gaussian"
] | cfaec0b80ad2b77af93729cacea444d8f92d27e2e628321b22d1bde2891a3971 |
import luigi
from luigi.contrib.kubernetes import KubernetesJobTask
from os.path import basename
import glob
class PeakPickerTask(KubernetesJobTask):
sampleFile = luigi.Parameter()
posOrNeg = luigi.Parameter()
endSuffix = luigi.Parameter()
paramFile = "PPparam"
name = "peak-pick... | phnmnl/MTBLS233-Jupyter | preprocessing_workflow.py | Python | apache-2.0 | 9,290 | [
"Galaxy",
"OpenMS"
] | a2f2cc116f6cc340e02117da2b685000cce37abbb6c0d57bd9bab69974da8590 |
'''
Created on 14 Jul 2015
@author: navjotkukreja
'''
import os
from scipy import misc
from matplotlib import pyplot as plt
from skimage import data
from skimage.feature import blob_dog, blob_log, blob_doh
from math import sqrt
from skimage.color import rgb2gray
image = misc.imread('16_right.jpeg')
image_gray = ima... | navjotk/diabetic-dissert | load.py | Python | apache-2.0 | 1,214 | [
"Gaussian"
] | 4285244e40c51c51feb811cec802f5069fdc5ff5860dd93dc27cb708dca6a9fc |
"""
Test derivatives typed up in dials_regression/doc/notes/prediction/stills_prediction_nave3.pdf
"""
from __future__ import annotations
import pytest
from cctbx.sgtbx import space_group, space_group_symbols
from dxtbx.model.experiment_list import Experiment, ExperimentList
from libtbx.phil import parse
from scitb... | dials/dials | tests/algorithms/refinement/test_stills_spherical_relp_derivatives.py | Python | bsd-3-clause | 12,635 | [
"CRYSTAL"
] | 3c86c451defa36ba3fd2e5930044f915bef89408dff78e34bdd2f000d8b4ca31 |
# -*- coding: utf-8 -*-
"""Tests for edge predicates"""
import unittest
from pybel import BELGraph
from pybel.dsl import pathology, protein
from pybel.struct.filters.edge_predicates import has_pathology_causal
from pybel.testing.utils import n
class TestEdgePredicates(unittest.TestCase):
"""Tests for edge pred... | pybel/pybel | tests/test_struct/test_filters/test_edge_predicates.py | Python | mit | 1,077 | [
"Pybel"
] | bee01089a12915387bf73608db97f7b0a060630d002670a6bb68f8ae641227e2 |
import sys
from django.apps.config import AppConfig as DjangoAppConfig
from django.conf import settings
from django.core.management.color import color_style
from django.core.checks import register
from .site_visit_schedules import site_visit_schedules
from .system_checks import visit_schedule_check
style = color_styl... | botswana-harvard/edc-visit-schedule | edc_visit_schedule/apps.py | Python | gpl-2.0 | 1,911 | [
"VisIt"
] | 045f8ae4093fbf22a45b2343ba8af7befeea4fd3e0d47452b7a2d668d9d801e5 |
from itertools import tee
try:
from future_builtins import zip
except ImportError: # not 2.6+ or is 3.x
try:
from itertools import izip as zip
except ImportError:
pass
import requests
# Requires bx python
from bx.intervals.intersection import Intersecter, Interval
from .diffevent import Diff... | jeffhsu3/genda | genda/transcripts/transcripts_utils.py | Python | bsd-3-clause | 13,102 | [
"pysam"
] | 25fef9cc8788f78e0b1309489d870c0e2b72a83b4f396ee7cf96d164040d2d05 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2014, 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 s... | andersx/cclib | src/cclib/writer/xyzwriter.py | Python | lgpl-2.1 | 4,078 | [
"VMD",
"cclib"
] | 4248fb60db0035bd12e7bb1f59ead7ef80e24ecb65b6d9232ef9c985a9b6b635 |
# Authors : Denis A. Engemann <denis.engemann@gmail.com>
# Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License : BSD-3-Clause
from copy import deepcopy
import numpy as np
from ..fixes import _import_fft
from ..io.pick import _pick_data_channels, pick_info
from ..utils import verbose, warn, fill_do... | bloyl/mne-python | mne/time_frequency/_stockwell.py | Python | bsd-3-clause | 9,692 | [
"Gaussian"
] | acd9e5cccb4ede60f9d18943c979e1f084ad2c6b4c432a3c93fb8422ed69ee01 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# by Panos Mavrogiorgos, email : pmav99 >a< gmail
import vtk
def get_program_parameters():
import argparse
description = 'Scalar bar widget.'
epilogue = '''
'''
parser = argparse.ArgumentParser(description=description, epilog=epilogue,
... | lorensen/VTKExamples | src/Python/Widgets/ScalarBarWidget.py | Python | apache-2.0 | 2,261 | [
"VTK"
] | 0449d895e010ec1778e3cfea84283e4fd009360b88faec06186e696a9a139f2d |
# 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/analysis/CenterOfMass.py | Python | gpl-3.0 | 1,695 | [
"ESPResSo"
] | 0750baab3dcd5626e161a3026fb506aa52cf3ac7d37724e4f00231e327369794 |
"""
CBMPy: CBMultiCore module
=========================
PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
Copyright (C) 2009-2022 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Gener... | SystemsBioinformatics/cbmpy | cbmpy/CBMultiCore.py | Python | gpl-3.0 | 5,327 | [
"PySCeS"
] | 47641ea6b7d67abf5c23146f4c932c2255094a2c37c8b3e1d2281f1b3063d80d |
#!/usr/bin/python
import os, sys
ncs_lib_path = ('../../../')
sys.path.append(ncs_lib_path)
import ncs
def run(argv):
sim = ncs.Simulation()
ib_parameters = sim.addNeuron("ib","izhikevich",
{
"a": 0.02,
"b": 0.2,
"c": -55.0,
"d": 4.0,
"u": -13.0,
"v": -6... | BrainComputationLab/ncs | python/samples/models/izh/intrinsically_bursting_izh.py | Python | bsd-2-clause | 821 | [
"NEURON"
] | 55887cf3d970cffff57393468e52451bfbc59979e06502509e7fb0d7564d0daa |
# -*- 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 pytest
import ... | k0ste/ansible | test/units/galaxy/test_collection.py | Python | gpl-3.0 | 54,635 | [
"Galaxy"
] | f9698e3e879fcdccd4f00712fb820156c26a027b28d8aa0020c130bfa0749ca8 |
"""Generalized Linear Models
"""
import numpy as np
import statsmodels.api as sm
from scipy import stats
from matplotlib import pyplot as plt
#GLM: Binomial response data
#---------------------------
#Load data
#^^^^^^^^^
# In this example, we use the Star98 dataset which was taken with permission
# from Jeff Gill (2... | yarikoptic/pystatsmodels | examples/example_glm.py | Python | bsd-3-clause | 4,209 | [
"Gaussian"
] | 9e5c5cbd5bd01d7269f8181be804c196090dc53f9e73024c5071e337e3c41361 |
import os
import errno
import socket
import time
import eventlet
import unittest
httplib2 = eventlet.import_patched("httplib2")
from eventlet.timeout import Timeout
from ..loadbalancer import Balancer
from ..actions import Empty, Static, Unknown, NoHosts, Redirect, Proxy, Spin
class MockBalancer(object):
"Fake Ba... | futuresimple/mantrid | mantrid/tests/actions.py | Python | bsd-3-clause | 8,111 | [
"Firefly"
] | 6396633f8544f8f2f6b9d1d8ae0ef3a801d72b44f9ee40a95bae19d0a1869374 |
#!/usr/bin/python
### select_specific_sequences.py ################################################################
### By Geoffrey Thomson
### This script I modified from the online tutorial
### (http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec11).
### It takes a fasta file and txt file of fasta IDs as i... | G-Thomson/GPyS | select_specific_sequeces.py | Python | mit | 1,312 | [
"Biopython"
] | 711ed9788acefbdc6fc302bf7c6e7cdfcc206aca7e937dbccac40f91ffab6432 |
#!/usr/bin/env python
# Copyright 2016 Daniel Nunes
#
# 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... | GandaG/fomod-editor | src/exceptions.py | Python | apache-2.0 | 3,384 | [
"VisIt"
] | 0085e213e6b2e07142e82d8b7f99d8433236145b7a74d09c97d7765a011a06f0 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
sphere = vtk.vtkSphereSource()
# make two copies of the shape and distort them a little
transform1 = vtk.vtkTransform()
transform1.Translate(0.2, 0.1, 0.3)
transform1.Scale(1.3, 1.1,... | ashray/VTK-EVM | Filters/Hybrid/Testing/Python/TestProcrustesRigidCentroid.py | Python | bsd-3-clause | 4,587 | [
"VTK"
] | 503d6674b5ea77a21507a10f656222b0388c9325394574e019e7a76a8bab64f6 |
"""
Module containing the available algorithms
"""
from abc import ABCMeta, abstractmethod
import random
import six
from deap import base, creator, tools, algorithms
import numpy as np
@six.add_metaclass(ABCMeta)
class AlgorithmBase():
"""
Base class for algorithms
"""
def __init__(self, in_data, out_... | Hofsmo/PyPiW | pypiw/algorithms.py | Python | gpl-3.0 | 5,775 | [
"Gaussian"
] | a5d6a6b5713dc0ffd85d1d8c38832bc0b86cf70b8c6c9692365010d9b7c81860 |
# ===============================================================================
# Copyright (C) 2014 Ryan Holmes
#
# This file is part of eos.
#
# eos 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... | DarkFenX/Pyfa | eos/saveddata/targetProfile.py | Python | gpl-3.0 | 20,115 | [
"Jaguar"
] | 0fc1dc3e96ab03860a194f073ef5e80ebb9e1fbdd5c4435258be7d394d68903e |
''' Copyright (c) 2013 Potential Ventures Ltd
Copyright (c) 2013 SolarFlare Communications Inc
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above c... | stuarthodgson/cocotb | cocotb/generators/bit.py | Python | bsd-3-clause | 3,426 | [
"Gaussian"
] | 29f4d758428c93767aa6ab45ad2b3305491db45ab3f29e50b249f2039501d29c |
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