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# Copyright 2016 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... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/tensorflow/contrib/factorization/python/ops/gmm_ops.py | Python | bsd-2-clause | 20,180 | [
"Gaussian"
] | 72f19c53d2df9887848512e93474cbbc6afc727fb9776921baaf619d26c085d6 |
##
# Copyright 2009-2015 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | gppezzi/easybuild-easyblocks | easybuild/easyblocks/n/nwchem.py | Python | gpl-2.0 | 23,893 | [
"Amber",
"NWChem"
] | 1765f26ce6edebba6b6743072e0808faa699f8e3c552b09e3bde786e3e8e37ca |
# 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 RA4classif(RPackage):
"""Automated Affymetrix Array Analysis Classification Package."""
... | iulian787/spack | var/spack/repos/builtin/packages/r-a4classif/package.py | Python | lgpl-2.1 | 1,173 | [
"Bioconductor"
] | 1f047a56bec16e50e8f54c43bf4c28267993e9814631898accc2104b26ee67cb |
# 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)
#
# This is a based largely on the Homebrew science formula:
# https://github.com/Homebrew/homebrew-science/blob/master/bl... | LLNL/spack | var/spack/repos/builtin/packages/blast-plus/package.py | Python | lgpl-2.1 | 7,403 | [
"BLAST"
] | 6bc5a992f17288fe3f5ad549656bb632ef63d4ab5d4aaf3ff68965cb707f7282 |
"""
parser.http.movieParser module (imdb package).
This module provides the classes (and the instances), used to parse the
IMDb pages on the akas.imdb.com server about a movie.
E.g., for Brian De Palma's "The Untouchables", the referred
pages would be:
combined details: http://akas.imdb.com/title/tt0094226/combi... | Thraxis/pymedusa | lib/imdb/parser/http/movieParser.py | Python | gpl-3.0 | 81,173 | [
"Brian"
] | 9439f730a8db89b0d712b12137a55b9e60acbc65c4c433bc3d737c616bd763fd |
import os
import zipfile
import argparse
import numpy as np
import tensorflow as tf
from bigdl.dllib.feature.dataset import base
from sklearn.model_selection import train_test_split
from bigdl.orca import init_orca_context, stop_orca_context
from bigdl.orca import OrcaContext
from bigdl.orca.learn.tf.estimator impor... | intel-analytics/BigDL | ppml/trusted-big-data-ml/python/docker-graphene/examples/ncf_dataframe.py | Python | apache-2.0 | 5,920 | [
"ORCA"
] | c7bb4c2d4ff0229e4cd4d9318a9812b16b573325a3125b9e48d13bb6d2b21b22 |
"""
Copyright 2009-2015 Olivier Belanger
This file is part of pyo, a python module to help digital signal
processing script creation.
pyo is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as
published by the Free Software Foundation, either version 3 o... | belangeo/pyo | pyo/lib/tables.py | Python | lgpl-3.0 | 89,690 | [
"Gaussian"
] | 61e93d4f5bad2073d71aac45ac4c135ccb4f8e39fb15ca5c89404f710f243450 |
"""
Point defects
=============
Identify point defects in the lattice by comparison to a reference lattice.
This filter will identify vacancies, interstitials (including split interstitials) and antisites. A vacancy radius is
used to determine if an atom in the input lattice is associated with a site in the referenc... | chrisdjscott/Atoman | atoman/filtering/filters/pointDefectsFilter.py | Python | mit | 22,273 | [
"CRYSTAL"
] | 4b30885d35b7754e59bb122c01df564285384a60dc1dd1679ed88b651412d7e0 |
"""
Acceptance tests for the teams feature.
"""
import json
import random
import time
from dateutil.parser import parse
import ddt
from nose.plugins.attrib import attr
from selenium.common.exceptions import TimeoutException
from uuid import uuid4
from common.test.acceptance.tests.helpers import get_modal_alert, Event... | Learningtribes/edx-platform | common/test/acceptance/tests/lms/test_teams.py | Python | agpl-3.0 | 83,652 | [
"VisIt"
] | a0246c88e41dfb2540676840e829df9ada558e7905021ed61ae531d51659b167 |
"""
A program to solve the 2D Nonlinear Schrodinger equation using a
second order splitting method
More information on visualization can be found on the Mayavi
website, in particular:
http://github.enthought.com/mayavi/mayavi/mlab.html
which was last checked on 6 April 2012
"""
import math
import numpy
from mayavi ... | openmichigan/PSNM | PythonPrograms/Programs/PythonCode/NLSsplitting2D.py | Python | bsd-2-clause | 2,992 | [
"Mayavi"
] | 17eaf59b67b6e3af525df5ec0f0f12e1488175c2ce0f28aef3976006830ca527 |
#==================================================
# INFO-H-100 - Introduction à l'informatique
#
# Prof. Thierry Massart
# Année académique 2014-2015
#
# Projet: Système Multi-Agent (SMA)
#
#==================================================
import math
import random
import mas as m
import mas_cell as c
import m... | bil-elmoussaoui/MAS | mas_environment.py | Python | gpl-2.0 | 8,447 | [
"Gaussian"
] | 1de69027b13eb4222ab6a2e74cf21d2e047178710d8eb15cd4846c19c5f27122 |
from __future__ import annotations
from collections import namedtuple
from scitbx import matrix, sparse
from dials.algorithms.refinement import DialsRefineConfigError
from dials.array_family import flex
"""The PredictionParameterisation class ties together parameterisations for
individual experimental models: beam,... | dials/dials | algorithms/refinement/parameterisation/prediction_parameters.py | Python | bsd-3-clause | 36,367 | [
"CRYSTAL"
] | b13bd48fbc89c277fc30cf2cac4a9cfeba21f0a4952bf3925a63fb8227236e10 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2005-2012 Julio Sanchez
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Genera... | arunkgupta/gramps | gramps/plugins/rel/rel_es.py | Python | gpl-2.0 | 36,145 | [
"Brian"
] | 862faa2f2a88e94953843ef822dd987d884d90352db1ced491516f1c5a72cdc6 |
"""
Minimal character-level Vanilla RNN model. Written by Andrej Karpathy (@karpathy)
BSD License
"""
## add comments by weixsong
## reference page [The Unreasonable Effectiveness of Recurrent Neural Networks](http://karpathy.github.io/2015/05/21/rnn-effectiveness/)
## this is a 3 layers neuron network.
## input laye... | shunliz/test | python/dl/scratch/rnn-from-scratch/min-char-rnn.py | Python | apache-2.0 | 7,693 | [
"NEURON"
] | d6147e5cec0f74a676c45e82bdf6145b54dde027d3f8dd7c7d91353c4ff28d1c |
#!/usr/bin/env python
"""
download files from storage element
"""
import os
import DIRAC
from COMDIRAC.Interfaces import critical
from COMDIRAC.Interfaces import DSession
from COMDIRAC.Interfaces import DCatalog
from COMDIRAC.Interfaces import pathFromArgument
from DIRAC.Core.Base import Script
Script.setUsageMess... | pigay/COMDIRAC | Interfaces/scripts/dget.py | Python | gpl-3.0 | 2,581 | [
"DIRAC"
] | 4b81cace2d5e6c849dc43abccc1ab4579085435e4348cba0570604ca96e455e2 |
"""
DFO-GN
====================
A derivative-free solver for least squares minimisation with bound constraints.
This version has resampling (not part of main package).
This file is a modified version of DFOGN which allows resampling and restarts,
to better cope with noisy problems.
Lindon Roberts, 2017
Call structur... | numericalalgorithmsgroup/dfogn | dfogn/dfogn_resampling.py | Python | gpl-3.0 | 58,645 | [
"Gaussian"
] | 5a2a86b41ce0e546d39d3dcef5a0497bf9e05816aa577fb393c3f6d7b70ed4b1 |
import os,sys,math,logging
from io import StringIO
from collections import OrderedDict
import numpy as np
import Bio.PDB.Polypeptide as polypeptide
from Bio.PDB import *
from Bio.Seq import Seq
from structure.functions import *
from structure.assign_generic_numbers_gpcr import GenericNumbering
from protein.m... | cmunk/protwis | structure/structural_superposition.py | Python | apache-2.0 | 17,009 | [
"BLAST"
] | a4a5d57494c199cdd3075108c9943a18d8a662b9cd49635a0dd24ed3ff44a7c5 |
"""
=======================================
Localizing multiple objects in an image
=======================================
Extending on the ``plot_localization_tutorial`` example, there are more advanced
ways to search for objects, and draw bounding boxes.
Rather than using the full class label, we can also use the ... | arnabgho/sklearn-theano | examples/plot_multiple_localization.py | Python | bsd-3-clause | 2,637 | [
"Gaussian"
] | fa9129ebadaeca1b5022851a26218885030523e2ae9d5263d099c4142175408b |
import numpy as np
import scipy.linalg
from scipy import special
import matplotlib.pyplot as plt
import fdm
from matplotlib import rc
rc('text', usetex=True)
rc('font', family='serif', size=11)
# rc('axes', titlesize='medium')
rc('legend',fontsize='small')
rc('axes', grid=True)
rc('grid', color='0.9')
rc('lines',... | zrick/tlab | doc/figures.py | Python | gpl-3.0 | 18,697 | [
"Gaussian"
] | 13b227a2c83e49afb79b26d59770a523490f5866a25d5e4daa9dd0996cf0d9ae |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# This test checks netCDF reader. It uses the CF convention.
# Open the file.
reader = vtk.vtkNetCDFCFReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/tos_O1_200... | hlzz/dotfiles | graphics/VTK-7.0.0/IO/NetCDF/Testing/Python/NetCDFCFSphericalCoords.py | Python | bsd-3-clause | 1,729 | [
"NetCDF",
"VTK"
] | 6de86f834f97429f1d923ba6256107404e014cf65b4a6b826100e7271e812526 |
# Lint as: python3
# Copyright 2018 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 ... | tensorflow/lingvo | lingvo/core/quant_test_lib.py | Python | apache-2.0 | 5,906 | [
"Gaussian"
] | a60a0fd9f73a32411ca3f0a33d3eff9a36598102684af437ad7de59f50c3c557 |
#
# CPM modulation and demodulation.
#
#
# Copyright 2005-2007,2011 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# SPDX-License-Identifier: GPL-3.0-or-later
#
#
# See gnuradio-examples/python/digital for examples
from math import pi
import numpy
from gnuradio import gr, filter
from gnuradio ... | sdh11/gnuradio | gr-digital/python/digital/cpm.py | Python | gpl-3.0 | 8,080 | [
"Gaussian"
] | 3bc382c7650eefc1d742d9834f2b06bdafad4f5f84b5c6192e15524af3406c8d |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# Giorgio Patrini <giorgio.patrini@anu.edu.au>
# Lic... | waterponey/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 70,436 | [
"Gaussian"
] | 4d038ec331184bfef0c07ecca30d45fa32e1089cbd8eff444bcf2c8e6efdc408 |
# -*- coding: utf-8 -*-
import models.sxrd_new1 as model
#to make compatible to historical runs
#import models.sxrd_test5_sym_new_test_new66_2_3 as model2
from models.utils import UserVars
import numpy as np
from operator import mul
from numpy.linalg import inv
from geometry_modules import *
"""
functions in classes
#... | jackey-qiu/genx_pc_qiu | models/domain_creator_surface.py | Python | gpl-3.0 | 26,219 | [
"CRYSTAL"
] | 6d3598f55c000863696cb65aa3192245137ce62c107d9016d3f7d8f55b673aaa |
import argparse
import textwrap
import configargparse
class NewlineTextHelpFormatter(argparse.HelpFormatter):
def _fill_text(self, text, width, indent):
return '\n'.join(
textwrap.fill(line, width, initial_indent=indent,
subsequent_indent=indent,
... | bittremieux/ANN-SoLo | src/ann_solo/config.py | Python | apache-2.0 | 10,678 | [
"Dalton"
] | c10ad2083837035cf7bb2c9770b777444cbdd2b191fcf1819931360d609ca631 |
#!/usr/bin/python
# file: webdoc.py
# author: Andrea Vedaldien
# description: Implementation of webdoc.
# Copyright (C) 2007-12 Andrea Vedaldi and Brian Fulkerson.
# All rights reserved.
#
# This file is part of the VLFeat library and is made available under
# the terms of the BSD license (see the COPYING ... | Rachine/VisualPlaceRecognition | urban_release/lib/vlfeat-0.9.17/docsrc/webdoc.py | Python | mit | 42,052 | [
"Brian",
"VisIt"
] | 52fcaaad3edc569857e4ff758d2d9febbc4b938fcb632b26ca88d3ae453089d6 |
# ======================================================================
import sys,os,subprocess,math
import numpy as np
import astropy.io.fits as pyfits
import om10
vb = True
# ======================================================================
# define useful functions for photometry
conv = 1./(np.log(2.)*(2... | mbaumer/OM10 | om10/image.py | Python | mit | 12,635 | [
"Galaxy",
"Gaussian"
] | fe5addacc46640c4ab411d2774837302bac0520ac3b7e6886e4460ab7bc2f276 |
from __future__ import (absolute_import, division, print_function)
import filecmp
import numpy as np
import os
import stresstesting
import tempfile
import mantid.simpleapi as mantid
import mantid.kernel as kernel
from tube_calib_fit_params import TubeCalibFitParams
from tube_calib import getCalibratedPixelPositions, ... | wdzhou/mantid | Testing/SystemTests/tests/analysis/WishCalibrate.py | Python | gpl-3.0 | 8,447 | [
"Gaussian"
] | 4b90657dabe75bc396c8f3b2ec495eaa4aa07fbd4ab13b205c4fd4f815944eab |
# import numpy as np
import os
from setuptools import setup, Extension
from setuptools import find_packages
import numpy as np
VERSION = '0.3.0'
classifiers = [
# How mature is this project? Common values are
# 3 - Alpha
# 4 - Beta
# 5 - Production/Stable
'Development Status :: 3 - Alpha',
... | RivuletStudio/rivuletpy | setup.py | Python | bsd-3-clause | 2,443 | [
"NEURON"
] | b16e79bc7af872e72e8fd88ff00cf45cd65afa19c02a3a5a69a89277d8f12e44 |
"""
==============================================
Generate a left cerebellum volume source space
==============================================
Generate a volume source space of the left cerebellum and plot its vertices
relative to the left cortical surface source space and the freesurfer
segmentation file.
"""
# A... | adykstra/mne-python | examples/forward/plot_left_cerebellum_volume_source.py | Python | bsd-3-clause | 3,203 | [
"Mayavi"
] | 49883cd0f1b5e13d4b65eaa2c6944b6888d8b3f8731d93b6b753178689b43819 |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | andrewcbennett/iris | lib/iris/tests/test_io_init.py | Python | gpl-3.0 | 5,612 | [
"NetCDF"
] | a021f3228acd53d1694831f9c9c5682cbc05ceb4536a7036c930a6f6e4cb2ce5 |
###############################################################################
# Ganga - a computational task management tool for easy access to Grid resources
# http://cern.ch/ganga
#
# $Id: loader.py,v 1.2 2008-11-26 08:31:33 moscicki Exp $
#
# Copyright (C) 2003-2007 The Ganga Project
#
# This file is part of Ganga... | ganga-devs/ganga | ganga/GangaTest/Framework/loader.py | Python | gpl-3.0 | 47,202 | [
"VisIt"
] | 33f55a19af26eb7c66e7a80eb54079ce0f71f785f7720431cc718981990c7137 |
#!/usr/bin/env python
"""
Tarjan's algorithm and topological sorting implementation in Python
by Paul Harrison
Public domain, do with it as you will
"""
def strongly_connected_components(graph):
""" Find the strongly connected components in a graph using
Tarjan's algorithm.
... | nilp0inter/data-is-fun | dataisfun/util/topological_sort.py | Python | gpl-3.0 | 2,505 | [
"VisIt"
] | 66c56272462a6f46b009a974b3d6abddff6731fe5bf3f3173517c5582e7d1efe |
# -*- coding: utf-8 -*-
#
# test_rate_neuron.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 Licens... | lekshmideepu/nest-simulator | testsuite/pytests/test_rate_neuron.py | Python | gpl-2.0 | 5,023 | [
"NEURON"
] | f71145a5de025d9133453f3e7e925616f10171f02f279d66c92fc65cf880a7b1 |
#Import packages that will be used
#GUI generation Packages
import wx
import wx.aui
from wx.lib.buttons import GenBitmapButton,GenBitmapToggleButton
#Operational Packages
import subprocess
import traceback
import types
import os
import sys
import errno
import numpy as np
from xml.dom import minidom
#----------------... | fxb22/BioGUI | plugins/Tools/EXPASYgui.py | Python | gpl-2.0 | 24,520 | [
"BLAST"
] | b26ba00457800ffc2cbef54e77d9a7fd61dabdc2f3426170913dcaa2e51c7700 |
"""
Tools to for cryoscope analysis
Brian Tarasinski
Dec 2017
Edited by Adriaan Rol
"""
from typing import Union
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.ticker
from pycqed.analysis.tools.plotting import (set_xlabel, set_ylabel,
flex_colormesh_plot... | QudevETH/PycQED_py3 | pycqed/analysis/tools/cryoscope_tools.py | Python | mit | 20,428 | [
"Brian"
] | 122451bfa613c9557341444dd4ebbd0eb98908b9e03b8d4dc124d438d4a9c16a |
# Version: 0.15+dev
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
* [![Latest Version]
(https... | clearclaw/plantain | versioneer.py | Python | gpl-3.0 | 66,850 | [
"Brian"
] | 18c7dc7e747ef48b526c9517451dfe41c95b8f6d138071b6b7a183fb58025b4b |
#!/usr/local/bin/python -i
# preceeding line should have path for Python on your machine
# vizplotgui_atomeye.py
# Purpose: viz running LAMMPS simulation via AtomEye with plot and GUI
# Syntax: vizplotgui_atomeye.py in.lammps Nfreq compute-ID
# in.lammps = LAMMPS input script
# Nfreq = plot data poi... | jcarlson23/lammps | python/examples/vizplotgui_atomeye.py | Python | gpl-2.0 | 4,461 | [
"LAMMPS"
] | f6e0f93bcfd9d8b1c8c8fb6e41177a3c426696431a82b990c694352a06ecfc58 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | tests/cluecode/test_holders.py | Python | apache-2.0 | 12,802 | [
"VisIt"
] | 45209270fd1b12adb5169cae359ab14494a7226ebdade1e3cd5ac34e005be2c7 |
#! /usr/bin/env python
import sys
from math import sqrt, pi
import numpy as np
from ase import Atoms
from ase.units import Bohr, Hartree
from ase.parallel import rank
from gpaw import GPAW
from gpaw.external_potential import ConstantElectricField
###
field = 0.01
dx = 2.0
vac = 3.0
nsteps = 3
nbands ... | qsnake/gpaw | gpaw/test/constant_electric_field.py | Python | gpl-3.0 | 1,867 | [
"ASE",
"GPAW"
] | 799d561614ecfaa7c340c9a8a31a02b2b3852f95171e076190b291d13e7a29aa |
# Python package to perform quick analysis on topographic data
# Copyright (C) 2015 Christian Braedstrup
# This file is part of pyTopoTools.
#
# pyTopoTools is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License v2 as published by
# the Free Software Foundation.
#... | LinuxChristian/pyTopoTools | pyTopoTools.py | Python | gpl-2.0 | 23,401 | [
"Gaussian",
"Mayavi"
] | ffce5d2fde97c506c65834b05f898b32c5ef58bbe5a916d3648bd0f65d415f07 |
""" Test class for agents
"""
# imports
import unittest, importlib, datetime
from mock import MagicMock
from DIRAC import gLogger
gLogger.setLevel( 'DEBUG' )
#sut
from DIRAC.TransformationSystem.Agent.TaskManagerAgentBase import TaskManagerAgentBase
from DIRAC.TransformationSystem.Agent.TransformationAgent import Tr... | vmendez/DIRAC | TransformationSystem/Agent/test/Test_Agent.py | Python | gpl-3.0 | 18,144 | [
"DIRAC"
] | c0870cc80723c1bb3bbd5451a5840770b5288032412bc5badebaeb9ad54b0c43 |
r"""
Tree representations (:mod:`skbio.tree`)
========================================
.. currentmodule:: skbio.tree
This module provides functionality for working with trees, including
phylogenetic trees and hierarchies, and prefix trees (i.e., tries).
Functionality is provided for constructing trees, for traversing... | Kleptobismol/scikit-bio | skbio/tree/__init__.py | Python | bsd-3-clause | 7,359 | [
"scikit-bio"
] | e132ec07a3f10ce7c8b38a76e10d1066a854118dc020d1e37610cc9727f48be2 |
""" Basic unit tests for the Job API
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from os.path import dirname, join
import pytest
from io import StringIO
from DIRAC.Interfaces.API.Job import Job
from DIRAC.Core.Utilities.ClassAd.... | ic-hep/DIRAC | src/DIRAC/Interfaces/API/test/Test_JobAPI.py | Python | gpl-3.0 | 3,051 | [
"DIRAC"
] | cbc17a11a521e9daa32fc615a677cc5ec689b004899f374fa9eab9e641a04aeb |
# Copyright (C) 2004-2008 Paul Cochrane
#
# 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 2
# of the License, or (at your option) any later version.
#
# This program is distribut... | paultcochrane/pyvisi | pyvisi/renderers/vtk/scene.py | Python | gpl-2.0 | 11,347 | [
"VTK"
] | 20858db37009f27572c6fc82c6ef25e2053be2d63c2a72264be27ce309abf428 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
'''
Created on Jul 15, 2012
'''
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyue@mit.edu"
__date_... | dongsenfo/pymatgen | pymatgen/apps/battery/tests/test_plotter.py | Python | mit | 1,779 | [
"pymatgen"
] | 5b96dcb7eec8762be8edf6f6508df82bc02232a8bfc5743d16af8489dc5a4e49 |
#
# @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
#... | jH0ward/psi4 | psi4/driver/inputparser.py | Python | lgpl-3.0 | 31,077 | [
"CFOUR",
"Psi4"
] | 873221dc24a85984caacee5f5bebf99a3108b96ac44cf36a5425e759cd525767 |
#!/usr/bin/env python
import os
import sys
from DIRAC.Core.Utilities.DIRACScript import DIRACScript
@DIRACScript()
def main():
# Must be define BEFORE any dirac import.
os.environ["DIRAC_USE_TORNADO_IOLOOP"] = "True"
from DIRAC.ConfigurationSystem.Client.LocalConfiguration import LocalConfiguration
... | DIRACGrid/WebAppDIRAC | src/WebAppDIRAC/scripts/tornado-start-web.py | Python | gpl-3.0 | 1,626 | [
"DIRAC"
] | 10263e87dbc6affa6fd4fe8faa22a1f318ede82cfa266b773545e770254c055e |
# Copyright 2012-2014 Brian May
#
# This file is part of python-tldap.
#
# python-tldap 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.... | brianmay/python-tldap-debian | tldap/backend/fake_transactions.py | Python | gpl-3.0 | 12,883 | [
"Brian"
] | 818fdea70ea6a91a6a15c74cad77a1cb935e33ffc4f6fd18042f8a2da97d5a6b |
#!/usr/bin/env python
"""
refguide_check.py [OPTIONS] [-- ARGS]
Check for a Scipy submodule whether the objects in its __all__ dict
correspond to the objects included in the reference guide.
Example of usage::
$ python refguide_check.py optimize
Note that this is a helper script to be able to check if things ar... | lhilt/scipy | tools/refguide_check.py | Python | bsd-3-clause | 31,478 | [
"Gaussian"
] | ace4521abb86ef7092bc672fa5935883092114c30a999e01f41aca2175cc51ca |
# ---------------------------------------------------------#
# astroNN.apogee.downloader: download apogee files
# ---------------------------------------------------------#
import getpass
import os
import urllib.request, urllib.error
import warnings
import numpy as np
from astroNN.apogee.apogee_shared import apogee... | henrysky/astroNN | astroNN/apogee/downloader.py | Python | mit | 40,175 | [
"VisIt"
] | 95c8bc92269f2e0f9e154b5c4b152e97e4c254982e64ff0a5dbc05af6261999d |
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 27 10:00:55 2016
@author: dcg513
"""
#Imports
from scipy.linalg import solve
from numpy import zeros,linspace,exp,abs
import matplotlib.pyplot as plt
plt.close("all")
#Parameters
length = 1.0 ; nx = 100
xval=linspace(0,length,num=nx)
dx = length/(nx-1)
#Create matrix op... | dcelisgarza/phd_excercises | comp_techniques/problem_class2.py | Python | gpl-3.0 | 1,663 | [
"Gaussian"
] | f20413d0e73030cdca894151e344780c5fb58a240f8f30a76eae6af6b2c04591 |
# -*- coding: utf-8 -*-
__author__ = 'Rainer Arencibia'
"""
The MIT License (MIT)
Copyright (c) 2016 Rainer Arencibia
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, includi... | rainer85ah/VisionViewer | src/__init__.py | Python | mit | 3,608 | [
"Gaussian"
] | 9d3a4861205aa476e9a2c30a9c8653e3d776d27c05ee13b504246ec314f3c4d5 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-proxy-init.py
# Author : Adrian Casajus
########################################################################
__RCSID__ = "$Id$"
import sys
import datetime
import DIRAC
from DIRAC import gLo... | Sbalbp/DIRAC | FrameworkSystem/scripts/dirac-proxy-init.py | Python | gpl-3.0 | 8,646 | [
"DIRAC"
] | a7641185f4cdf55534935d8d7444f84de3e39a6abf4fd35d54be58adb6499529 |
from __future__ import absolute_import, division, print_function
import barnaba as bb
import mdtraj as md
import barnaba.smm as smm
import os
from comp_mine import comp
cwd = os.getcwd()
outdir = "%s/test/tmp" % cwd
refdir = "%s/test/reference/" % cwd
os.system("mkdir -p %s" % (outdir))
def test_smm_1():
fn... | srnas/barnaba | test/test_smm.py | Python | gpl-3.0 | 549 | [
"MDTraj"
] | 4af45675838f565d5c18ad7e06085bc856ad4c66fe4e91b08a59287391170293 |
from uaperrors import StepError
import sys
import os
from logging import getLogger
from abstract_step import AbstractStep
logger = getLogger('uap_logger')
class Bowtie2(AbstractStep):
'''
Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing
reads to long reference sequences. It is pa... | kmpf/uap | include/steps/bowtie2.py | Python | gpl-3.0 | 26,451 | [
"Bowtie"
] | 25df00acb02bc219743dc49247f8fafe33fcc14acacd1935617e448118be68b3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020 Satpy developers
#
# satpy 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 ... | pytroll/satpy | satpy/readers/vii_l2_nc.py | Python | gpl-3.0 | 1,727 | [
"NetCDF"
] | f2ad0d83d7e0c3db18dfef38babe9cdb74df6e1e18097c1302cc697efdcc7e3f |
from __future__ import absolute_import
input_name = '../examples/multi_physics/biot_npbc.py'
output_name = 'test_biot_npbc.vtk'
from tests_basic import TestInput
class Test( TestInput ):
pass
| rc/sfepy | tests/test_input_biot_npbc.py | Python | bsd-3-clause | 197 | [
"VTK"
] | b5277ddb06ef3b43087f2da44a4e8a0b4300a5d725683a4755460a4cb1d24c54 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, 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... | anksp21/Community-Zenpacks | ZenPacks.networking.HPProcurve/setup.py | Python | gpl-2.0 | 3,283 | [
"VisIt"
] | e8932183bef48b4d89ab4b18844262d3ee24d2a867cdabb5cf399900b3466294 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Scour
#
# Copyright 2010 Jeff Schiller
# Copyright 2010 Louis Simard
#
# This file is part of Scour, http://www.codedread.com/scour/
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the Lice... | EtienneOz/WebfontGenerator | scour/scour.py | Python | gpl-2.0 | 109,515 | [
"VisIt"
] | 430c9ab28ecd9bb941cedd0f1e7ee7919ff2bdb7113374d95519ebb0d55a523f |
"""
Browser set up for acceptance tests.
"""
#pylint: disable=E1101
#pylint: disable=W0613
from lettuce import before, after, world
from splinter.browser import Browser
from logging import getLogger
from django.core.management import call_command
from django.conf import settings
from selenium.common.exceptions import... | heran7/edx-platform | common/djangoapps/terrain/browser.py | Python | agpl-3.0 | 7,517 | [
"VisIt"
] | 8bd5236efdb2dd438cfb1a92ff53fea9e6b96f1a2f0b8d7fbcd7f2015d118e70 |
# -*- coding: utf-8 -*-
# Copyright (C) 2014 Canonical
#
# Authors:
# Galileo Sartor
#
# 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; version 3.
#
# This program is distributed in the hope tha... | ubuntu/ubuntu-make | tests/large/test_crystal.py | Python | gpl-3.0 | 2,618 | [
"CRYSTAL"
] | 1ac02f0f9ad6bd89ebe4f6499a18c15eb29ec3e95ce35a259c556262948d0c03 |
# -*- coding: utf-8 -*-
# parts of pygchem (Python interface for GEOS-Chem Chemistry Transport Model)
#
# Copyright (C) 2014 Benoît Bovy
# see license.txt for more details
#
"""
A bunch of utility functions based on the SciTools's Iris package.
"""
import collections
import warnings
from types import StringTypes
i... | benbovy/PyGChem | pygchem/tools/irisutil.py | Python | gpl-3.0 | 47,619 | [
"NetCDF"
] | 29fd5137e9cc1015cafcdda69f1d28dc88c5b4c006bd2beafc1d16a6fe72da94 |
import sys
import os
import re
import io
import traceback
from pybtex.plugin import find_plugin
from pybtex.database import BibliographyData, parse_file
from markdown.preprocessors import Preprocessor
from markdown.util import etree
import logging
log = logging.getLogger(__name__)
class MooseBibtex(Preprocessor):
... | vityurkiv/Ox | python/MooseDocs/extensions/MooseBibtex.py | Python | lgpl-2.1 | 3,958 | [
"MOOSE"
] | 0ade84f11361febe6516a9332904182a10aa68d5526ffffe2f2775865392aa80 |
import calendar
import json
import re
import uuid
import mock
from django.core.cache import cache
from django.test import TestCase
from django.contrib.auth.models import User
from django.core import mail
from funfactory.urlresolvers import reverse
from nose.tools import eq_, ok_
from airmozilla.main.models import E... | Nolski/airmozilla | airmozilla/comments/tests/test_views.py | Python | bsd-3-clause | 21,965 | [
"CASINO",
"VisIt"
] | 46940897faa1a0f0b41e2483affb075f49bee3ab4022a9cc86ba79059a6ca412 |
#
# @file TestRule.py
# @brief Rule unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file ... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestRule.py | Python | gpl-3.0 | 3,175 | [
"VisIt"
] | eaba97af7c622172769880b804116c3a86e4f7154e51ff7301cf61f3637b06a6 |
import sys
import exceptions
import vtk
from vtk.test import Testing
class TestGhostPoints(Testing.vtkTest):
def testLinear(self):
pts = vtk.vtkPoints()
pts.SetNumberOfPoints(4)
pts.InsertPoint(0, (0, 0, 0))
pts.InsertPoint(1, (1, 0, 0))
pts.InsertPoint(2, (0.5, 1, 0))
... | berendkleinhaneveld/VTK | Filters/Geometry/Testing/Python/TestGhostPoints.py | Python | bsd-3-clause | 2,717 | [
"VTK"
] | 3b56cb8ebef520603c1fe4f5309fb26e9201602c8d3ee799128234fffba17c5d |
'''
Created on Aug 4, 2011
@author: sean
'''
from __future__ import print_function
from graphlab.meta.asttools.visitors import Visitor, visit_children
from graphlab.meta.asttools.visitors.symbol_visitor import get_symbols
import ast
from graphlab.meta.utils import py2op
class ConditionalSymbolVisitor(Visitor):
... | ypkang/Dato-Core | src/unity/python/graphlab/meta/asttools/visitors/cond_symbol_visitor.py | Python | agpl-3.0 | 11,320 | [
"VisIt"
] | ef0a9c2b7fe480b3777fae3d7c21f4fb029a71183930c692dbb7e9555159b063 |
# -*- coding: utf-8 -*-
"""This file contains a parser for the Mozilla Firefox history."""
import sqlite3
from plaso.events import time_events
from plaso.lib import eventdata
from plaso.parsers import sqlite
from plaso.parsers.sqlite_plugins import interface
# Check SQlite version, bail out early if too old.
if sql... | 8u1a/plaso | plaso/parsers/sqlite_plugins/firefox.py | Python | apache-2.0 | 15,911 | [
"VisIt"
] | 3c782f3582b4bf96c8047ce0da5d7d06e8914c11eeba56c6e60b822f4872453c |
import os
import os.path as op
from os.path import join as pjoin
import sys
import warnings
import pytest
from mayavi import mlab
import nibabel as nib
import numpy as np
from numpy.testing import assert_array_equal, assert_array_less
from unittest import SkipTest
from surfer import Brain, io, utils
from surfer.util... | mwaskom/PySurfer | surfer/tests/test_viz.py | Python | bsd-3-clause | 17,009 | [
"Mayavi"
] | 9f37d175e29c2ea13f2cebb3306234403266c014fa22ffc36ae76bd229ad020a |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | caio2k/RIDE | src/robotide/lib/robot/reporting/outputwriter.py | Python | apache-2.0 | 1,146 | [
"VisIt"
] | fd61523777c863e66484313a874b3b5358cc36378b060ed1b51980ec8da76cbc |
#!/usr/bin/python
# 04.10.2005
# last revision: 03.09.2007
import sys
import os.path as op
if (len( sys.argv ) == 3):
filename_in = sys.argv[1];
filename_out = sys.argv[2];
else:
print 'Usage: ', sys.argv[0], 'file.mesh file.vtk'
sys.exit()
if (filename_in == '-'):
file_in = sys.stdin
else:
fi... | olivierverdier/sfepy | script/mesh_to_vtk.py | Python | bsd-3-clause | 2,960 | [
"VTK"
] | 18bf54f76a54b7f731a156f67735b2548dc0dc6fe013a35bb889fa2703c9820a |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | mgeplf/NeuroM | neurom/fst/_core.py | Python | bsd-3-clause | 6,298 | [
"NEURON"
] | b092edc6be5f08357abdcb7201e6df35b957db5e0097752ae86b1c952bd9f6b2 |
# -*- coding: utf-8 -*-
# This file is public domain according to its author, Brian Hsu
"""Gist directive for reStructuredText."""
import requests
from docutils.parsers.rst import Directive, directives
from docutils import nodes
from nikola.plugin_categories import RestExtension
class Plugin(RestExtension):
""... | andredias/nikola | nikola/plugins/compile/rest/gist.py | Python | mit | 2,419 | [
"Brian"
] | d52a2058fe90f0fc81796cecb15bb1ded05d55fa1d8a7ef8472f0038eb8f96c8 |
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/main/utils/memcache_lock.py | Python | apache-2.0 | 2,183 | [
"Galaxy"
] | b7e50db74dee6b9e02f8dab5275f917c37d3596168544d333f278e5a6d307a52 |
"""
Generalized linear models currently supports estimation using the one-parameter
exponential families
References
----------
Gill, Jeff. 2000. Generalized Linear Models: A Unified Approach.
SAGE QASS Series.
Green, PJ. 1984. "Iteratively reweighted least squares for maximum
likelihood estimation, and some ... | bert9bert/statsmodels | statsmodels/genmod/generalized_linear_model.py | Python | bsd-3-clause | 64,767 | [
"Gaussian"
] | ee81a513c93ab3a2f96d00c1738066103d640c4a339baf08f5dfcc867c06a966 |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2013 Christopher L. Felton
#
# The myhdl library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License as
# published ... | gw0/myhdl | myhdl/_fixbv.py | Python | lgpl-2.1 | 17,310 | [
"VisIt"
] | ddfed77ebfb81419ce2a9bd25c77a7b31723d5c70428c0570bd3d12dddb5ecb0 |
# -*- coding: utf-8 -*-
# This file is part of Shuup.
#
# Copyright (c) 2012-2016, Shoop Ltd. All rights reserved.
#
# This source code is licensed under the AGPLv3 license found in the
# LICENSE file in the root directory of this source tree.
from __future__ import print_function
import ast
import sys
from itertools ... | hrayr-artunyan/shuup | _misc/ensure_code_style.py | Python | agpl-3.0 | 5,161 | [
"VisIt"
] | 6ab206b7ea842a1e6deaa6e0dc787cc96a8a5ba0468ab928372d4a24b266b51a |
from globals import *
import life as lfe
import references
import factions
import weapons
import chunks
import combat
import groups
import zones
import stats
import brain
import raids
import sight
import camps
import logic
import jobs
import logging
import bad_numbers
import random
import maps
import time
def judge... | flags/Reactor-3 | alife/judgement.py | Python | mit | 29,980 | [
"VisIt"
] | 8e5244c20fd9db7e722bc0920b9efdd0c11af6f093265ee856a61981bd44b528 |
import epw
import core
import skyvector
import os
import json
import subprocess
import sys
class CumulativeSkyMtx(object):
"""Cumulative Sky
Attributes:
epwFileAddress: Path to EPW file.
skyDensity: Density of the sky. 0 generates a Tregenza sky, which will
divide ... | antonszilasi/honeybeex | honeybeex/honeybee/ladybug/sky.py | Python | gpl-3.0 | 17,493 | [
"EPW"
] | bfa67e08492210a8a1beb394daa0f02c654dee7826d6b4b399c4fd9c2462ec59 |
"""
Acceptance tests for Studio related to the container page.
The container page is used both for displaying units, and
for displaying containers within units.
"""
import datetime
import ddt
from nose.plugins.attrib import attr
from unittest import skip
from base_studio_test import ContainerBase
from common.test.acc... | romain-li/edx-platform | common/test/acceptance/tests/studio/test_studio_container.py | Python | agpl-3.0 | 69,269 | [
"VisIt"
] | aa2ce450cb971f12f25760f5c930e56631a205d1dfd9f4a54689087a924e431f |
""" Contains functions used to write specific server packets to byte streams """
from common.constants import privileges
from common.ripple import userUtils
from constants import dataTypes
from constants import packetIDs
from constants import userRanks
from helpers import packetHelper
from objects import glob
""" Logi... | osuripple/pep.py | constants/serverPackets.py | Python | agpl-3.0 | 10,038 | [
"MOE"
] | 4866f91dc47ad98aea10bb3694d3c1342014277c644fa2950f0ca1c8ee53e069 |
# -*- coding: utf-8
#------------------------------------------------------------------#
__author__ = "Xavier MARCELET <xavier@marcelet.com>"
#------------------------------------------------------------------#
import time
import sys
import os
import termcolor
import unittest2 as unittest
from xtd.core.stat.coun... | psycofdj/xtd | xtd/test/core/stat/test_counter.py | Python | gpl-3.0 | 6,670 | [
"VisIt"
] | df3d6eb13d72bf4c85eb557e416a888a58ccdf83f08fb3cabe234b0e343b5aa5 |
#-----------------------------------------------------------------------------
# Copyright (c) 2012 - 2022, Anaconda, Inc., and Bokeh Contributors.
# All rights reserved.
#
# The full license is in the file LICENSE.txt, distributed with this software.
#-------------------------------------------------------------------... | bokeh/bokeh | bokeh/__init__.py | Python | bsd-3-clause | 3,673 | [
"VisIt"
] | 757daf1ef282706444390afed76671d145391043aa6a55c202d97638be6506ce |
#!/usr/bin/env python
"""
Example of a model fitting script.
The user should modify the model
according to the characteristics of
the signal of interest.
Part of the code is taken from the
kmpfit examples:
http://www.astro.rug.nl/software/kapteyn/kmpfittutorial.html#profile-fitting
"""
import numpy as np
import argp... | astrofle/CRRLpy | scripts/makemodel.py | Python | mit | 4,867 | [
"Gaussian"
] | a3316b872c94a972dff65b58b9ee14cf064b4b7e887ccfe1f470904ddc7074f7 |
"""
Logging of tracebacks and L{twisted.python.failure.Failure} instances.
"""
from __future__ import unicode_literals
import types
import traceback
import sys
from warnings import warn
from six import exec_
from ._util import safeunicode
from ._validation import MessageType, Field
TRACEBACK_MESSAGE = MessageType... | iffy/eliot | eliot/_traceback.py | Python | apache-2.0 | 3,403 | [
"exciting"
] | 2e19fbb1f0b169e08201ef15f57bbca283de93c65d90b1e3e3510f6ed5380e62 |
from __future__ import division
import numpy as np
from photutils import centroid_com, centroid_1dg, centroid_2dg
def recenter(image, pos, window_size = 5, method = "1dg"):
"""
Recenter each star in each frame of the image cube before performing
aperture photometry to take care of slight misalignments b... | caltech-chimera/pychimera | chimera/centroid.py | Python | mit | 2,002 | [
"Gaussian"
] | 48355268830e79bcb9556e4a45b28d44fcf74937fadebd8f2ec687c37bd84df0 |
# Copyright (C) 2012, 2013 by Brandon Invergo (b.invergo@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from __future__ import print_function
import os.path
import sys
from Bio._py3k imp... | updownlife/multipleK | dependencies/biopython-1.65/Tests/PAML/gen_results.py | Python | gpl-2.0 | 6,629 | [
"Biopython"
] | 44ec5d915c6e1da56458193121895b56685eb8d248ed72f06605aa0d6b7452ed |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1950-2020/regrid_Monoterp_emissions_n96e_360d.py | Python | gpl-3.0 | 19,130 | [
"NetCDF"
] | 8f35ca241f21ef767ffa6fad3c05e4386dcb073fd4ab19affdf33529628cada3 |
#!/usr/bin/env python
# hgvm-builder chromMatcher.py: match chromosomes from one assembly to another
"""
Takes two assembly FASTAs, a reference and a query, and matches each contig in
the query to one or more contigs in the reference by aligning parts of it.
The reference should have already been indexed with `bwa in... | adamnovak/hgvm-builder | scripts/chromMatcher.py | Python | apache-2.0 | 7,967 | [
"BWA",
"pysam"
] | dbdc0cfc7b2010e5bec091b127d77156fdd447c2b5dedddb19c570245a5c84a0 |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | mhue/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 61,945 | [
"Brian"
] | 8b9d82f86621308e4c84a760997800871ea73b4e7f74e01ddcf355ad7ca21146 |
'''@package docstring
@author: Jyh-Miin Lin (Jimmy), Cambridge University
@address: jyhmiinlin@gmail.com
Initial created date: 2013/1/21
================================================================================
This file is part of pynufft.
pynufft is free software: you can redistribute it and/or modif... | jyhmiinlin/cineFSE | CsTransform/nufft.py | Python | gpl-3.0 | 48,185 | [
"Gaussian"
] | f1cea451226c4b4c242d9253b9d420cdc70e25af7cb3b486e084275094abd160 |
#!/usr/bin/env python
"""
Module that contains classes holding cross-correlations and related
processing, such as frequency-time analysis (FTAN) to measure
dispersion curves.
"""
from seissuite.ant import pserrors, psutils, pstomo
import obspy.signal
try:
import obspy.io.xseed
except:
import obspy.xseed
... | boland1992/seissuite_iran | seissuite/ant/pscrosscorr.py | Python | gpl-3.0 | 152,285 | [
"Gaussian"
] | 1008d30604b1a78b30937a921af50820d65baf921db7dea9ad31f2ed47adaa3c |
"""
General helper functions that don't fit neatly under any given category.
They provide some useful string and conversion methods that might
be of use when designing your own game.
"""
import os, sys, imp, types, math, re
import textwrap, datetime, random, traceback, inspect
from inspect import ismodule
from colle... | YourCyborg/Sun-RPI | src/utils/utils.py | Python | bsd-3-clause | 35,689 | [
"VisIt"
] | ef745f506faecc399216b9ae6a2533bc9a1dbfd98cce32cc8eff31cda5c067ca |
#
# 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... | fweik/espresso | samples/lj_liquid_distribution.py | Python | gpl-3.0 | 5,934 | [
"ESPResSo"
] | 8a2a6e121024fc12e603af6f319cc74a016bc13d614e7ae30371c2b08cd68963 |
from setuptools import setup
setup(
# general meta
name='ebs-deploy',
version='2.0.1',
author='Brian C. Dilley',
author_email='brian.dilley@gmail.com',
description='Python based command line tools for managing '
'Amazon Elastic Beanstalk applications.',
platforms='any',
... | briandilley/ebs-deploy | setup.py | Python | mit | 805 | [
"Brian"
] | fac39541fd41cda73c678176b84177db684c402a4ae311ba5778c15ba1b6a978 |
import random as rand
import matplotlib.pyplot as plt
# import plotly as plt
#
# import numpy as np
# import plotly.plotly as py
#
# # gaussian_numbers = np.random.randn(1000)
# U = []
# for i in range(0, 10 ** 4):
# U.append(rand.random())
#
# # plt.hist(gaussian_numbers)
# plt.figure(1)
# plt.hist(U, cumulative=1... | rch9/stat-modeling-spbstu | lab3/lab1/main_2.py | Python | mit | 892 | [
"Gaussian"
] | 7afa06349489ec04c3cc96f15bb4532f0a0f19f5d1b4d6b26fad767dbd59b40b |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/stats/distance/_mantel.py | Python | bsd-3-clause | 19,512 | [
"scikit-bio"
] | 27b8fe68eed457473015b7669a04bc08bed218992d1efeb80e0b776e5c145468 |
# -*- coding: utf-8 -*-
## @package ivf.core.edge_detection.dog
#
# ivf.core.edge_detection.dog utility package.
# @author tody
# @date 2016/02/15
import cv2
## DoG filter.
# @param img input gray image.
# @param sigma sigma for small Gaussian filter.
# @param k_sigma large/small sigma (Gauss... | tody411/ImageViewerFramework | ivf/core/edge_detection/dog.py | Python | mit | 549 | [
"Gaussian"
] | 32735d4ca6c33ac7c0d8dc3dd98a1cf5fe377e8ed612e2be3ab9f8821b4715a1 |
#!/usr/bin/python
# pidgin_status_change.py
"""
Handy script for changing Pidgin's status with a post from a feed passed as argument.
Usage: ... | raducotescu/pidgin-status-scripts | pidgin_status_change.py | Python | mit | 1,639 | [
"VisIt"
] | 3662f428f1100a8857148208bcb018b543c5dee43e932a6613ae7cb0eb814941 |
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