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# -*- coding: utf-8 -*-
# Copyright (C) 2017 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., University of Heidelberg, and University of
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2010 - 2016 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., Universit... | jonasfoe/COPASI | copasi/bindings/python/unittests/Test_RunParameterFitting.py | Python | artistic-2.0 | 10,122 | [
"COPASI"
] | 76afea6efa945ede8401333bd0aa25216382c3853425f456f3b2422510f3e1cb |
# MIT License
#
# Copyright (c) 2017 Anders Steen Christensen, Lars Andersen Bratholm and Bing Huang
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without l... | qmlcode/qml | qml/representations.py | Python | mit | 22,846 | [
"Gaussian"
] | 678793d89b612c33af984a8888af28ec416f9e358f6cc44dc523c856aaac8bab |
# ##### BEGIN GPL LICENSE BLOCK #####
#
# 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 distrib... | michielkleinnijenhuis/NeuroBlender | imports/import_surfaces.py | Python | gpl-3.0 | 14,240 | [
"VTK"
] | cb549aa86ea0085b19b5db9510ac483fa459eb76156e75715cd1be286d91efd0 |
import random
import string
import pickle
import cherrypy
import numpy as np
import pandas as pd
from scipy.sparse import csr_matrix
import re
import os
from jinja2 import Environment, FileSystemLoader
path = os.path.abspath(os.path.dirname(__file__))
config = {
'global' : {
'server.socket_host' : '0.0.0.0',
... | dojobo/deepthought_web | deepthought_web.py | Python | bsd-3-clause | 4,592 | [
"Galaxy"
] | a9cbe6e08b928ec35dac3c0c4e38badf9160a14f03053669e58b01363ef0c7ef |
import ast
import os
import sys
if sys.version_info.major == 3:
from configparser import SafeConfigParser
else:
from ConfigParser import SafeConfigParser
from pathlib2 import Path
# Ignore matplotlib deprecation warnings
import warnings
import matplotlib.cbook
warnings.filterwarnings('ignore', category=UserWa... | ritviksahajpal/LUH2 | LUH2/GLM/constants.py | Python | mit | 10,142 | [
"NetCDF"
] | 244f4e2ba3a3eebae42ef137402411bf146fdba1073588765e2e40e2e5d06e37 |
""" ConstantExpressions gathers constant expression. """
from pythran.analyses.aliases import Aliases
from pythran.analyses.globals_analysis import Globals
from pythran.analyses.locals_analysis import Locals
from pythran.analyses.pure_expressions import PureExpressions
from pythran.intrinsic import FunctionIntr
from ... | artas360/pythran | pythran/analyses/constant_expressions.py | Python | bsd-3-clause | 3,550 | [
"VisIt"
] | d792b7a2b1e7e617e8542eb26dcf8b1d0c74a4364ef31a9af391a6c3ccfc4305 |
# Copyright (C) 2016 Arvid Fahlström Myrman
#
# 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 distr... | arvidfm/masters-thesis | src/nn/layers.py | Python | gpl-2.0 | 7,270 | [
"Gaussian"
] | de1d73684e5a7327ae32579f34886bdf646a0b8f554c2b6e481ad591f7ad9e56 |
# Copyright 2015 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... | ageron/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 139,423 | [
"Gaussian"
] | 777900b77a5aed26c57148de7a6860ad0fda1ab0f6dc81639e422e4768625d82 |
"""pyzmq logging handlers.
This mainly defines the PUBHandler object for publishing logging messages over
a zmq.PUB socket.
The PUBHandler can be used with the regular logging module, as in::
>>> import logging
>>> handler = PUBHandler('tcp://127.0.0.1:12345')
>>> handler.root_topic = 'foo'
>>> logge... | IsCoolEntertainment/debpkg_python-pyzmq | zmq/log/handlers.py | Python | lgpl-3.0 | 5,169 | [
"Brian"
] | f828835cee9a12b688438b36f1847da75da32130fb3f578a96b86fc7af0a4988 |
#!/usr/bin/env python
## category General
## desc Postprocesses a BAM file to rename pairs that have an extra /N value
'''
Postprocesses a BAM file to rename pairs that have an extra /N value
Some aligners output paired end reads with names ending in /1 or /2 to signify
where the read came from in a paired end experim... | ngsutils/ngsutils | ngsutils/bam/renamepair.py | Python | bsd-3-clause | 2,243 | [
"pysam"
] | 3c21953fc9b61325db04fd7073f48d460e911beb9b463db234b7bdb4f8eaea17 |
# This is the configuration file for your powerline-shell prompt
# Every time you make a change to this file, run install.py to apply changes
#
# For instructions on how to use the powerline-shell.py script, see the README
# Add, remove or rearrange these segments to customize what you see on the shell
# prompt. Any s... | Menci/powerline-shell | config.py | Python | mit | 1,575 | [
"MOE"
] | 553bc301425778c10888e4dbf009af1d06623bd58ab9d72cc5e8e8cf83a8f515 |
#!/usr/bin/env python
#encoding=utf8
#Copyright [2014] [Wei Zhang]
#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 ... | anthonylife/TaobaoCompetition2014 | src/bpr-1.0/train.py | Python | gpl-2.0 | 4,929 | [
"Gaussian"
] | b1c8fa11a8e09e59f6359a32f98135158c1ecadfceeb681cb7f249b7d51c214f |
import unittest
from pygdbmi import parser
from pygdbmi import visitors
import io
class TestPPrintVisitor(unittest.TestCase):
def setUp(self):
pass
def _test_pprint(self, input_, expected_output, strict):
f = io.StringIO()
ast = parser.parse(input_, strict)
visitor = visit... | simark/pygdbmi | tests/pprint_test.py | Python | mit | 3,875 | [
"VisIt"
] | 619f5f3d9849ed608310a89a4e40a427dd9514d77f6dc6e1c3ce61f624e5c2d3 |
from __future__ import absolute_import, division
import numpy as np
import os
import shutil
import tempfile
import matplotlib
matplotlib.use('Agg', warn=False)
from matplotlib.pyplot import Artist, savefig, clf, cm, get_cmap
from matplotlib.testing.noseclasses import ImageComparisonFailure
from matplotlib.testing.com... | urschrei/geopandas | tests/test_plotting.py | Python | bsd-3-clause | 8,763 | [
"COLUMBUS"
] | f32522457308b3ba445c6dbe1873b084e22d9cccf703ba1caf603c4eca74554b |
# -*- coding:utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011 CERN.
##
## Invenio 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 opti... | kaplun/Invenio-OpenAIRE | modules/bibindex/lib/bibindex_engine_tokenizer_tests.py | Python | gpl-2.0 | 15,529 | [
"Brian"
] | 6862962ff0f1242bf38394871c27eeb65062db417bec7dbe5405b1629ce5beee |
#!/usr/bin/python
# -- Content-Encoding: UTF-8 --
"""
Python modules repository
:author: Thomas Calmant
:license: Apache Software License 2.0
..
Copyright 2014 isandlaTech
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
... | ahmadshahwan/cohorte-runtime | python/cohorte/repositories/python/modules.py | Python | apache-2.0 | 21,225 | [
"VisIt"
] | 681014a76cb8ef4c60e2cb11c8a42c13cc7deef8250bc08532d3e46a5cfa63ec |
from ase.io import write
from gpaw import restart
basename = 'CO'
# load nc binary file and get calculator
atoms, calc = restart(basename + '.gpw')
# write atomic positions to xyz-file
write(basename + '.xyz', atoms)
# loop over all wfs and write their cube files
nbands = calc.get_number_of_bands()
for band in ran... | qsnake/gpaw | doc/tutorials/plotting/CO2plt.py | Python | gpl-3.0 | 512 | [
"ASE",
"GPAW"
] | 4f5d7a1f1e4ff32ac4fb48f5dc27a85a53196bddf2cce2279fe0ee5d22ca69fb |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | dilawar/moose-full | moose-examples/snippets/scaleVolumes.py | Python | gpl-2.0 | 5,431 | [
"MOOSE"
] | 61dd241c02a63e6db5e6c58334912f458d2f51477ce798753f552fb7150ad9d1 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Predict volumes of crystal structures.
"""
import os
import warnings
import numpy as np
from monty.serialization import loadfn
from pymatgen.analysis.bond_valence import BVAnalyzer
from pymatgen.analysis.structure_match... | materialsproject/pymatgen | pymatgen/analysis/structure_prediction/volume_predictor.py | Python | mit | 9,788 | [
"CRYSTAL",
"pymatgen"
] | caf629ff0b95ef94eeec321844b5bc1497555e3d49e83b8b3eeabdbd947846af |
# -*- coding: utf-8 -*-
import functools
import inspyred
import copy
import pyvotune
from pyvotune.log import logger
from pyvotune.util.id_generator import get_id
log = logger()
def crossover(cross):
@functools.wraps(cross)
def validating_crossover(random, mom, dad, args):
max_crossover_attempts =... | aelaguiz/pyvotune | pyvotune/variators/crossovers.py | Python | mit | 21,399 | [
"Gaussian"
] | dd2cd092d250ff5f00c255cd037ee361db86a3ed7debb479c00e59e482bf9ceb |
# 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... | psci2195/espresso-ffans | testsuite/python/lb_interpolation.py | Python | gpl-3.0 | 4,144 | [
"ESPResSo"
] | 30949c2c2d7ee925eb6f3a9be845a915bc1f79350ebc912d8c00add31172620f |
# Too much Tinker
# From http://cseatglance.blogspot.com/2015/08/a-simple-gui-game-with-python-tkinter.html?spref=tw
# Typer: Ginny C Ghezzo
# What I learned:
from tkinter import *
import random
import tkinter.messagebox
root = Tk()
Label(root, text="Find Out the Hidden Position").pack()
def findcurpos(event):
p... | gghezzo/prettypython | PythonEveryDay2015/TooMuchTinker.py | Python | mit | 636 | [
"TINKER"
] | 227f79154b938b83e44860e58fdc9306b889ffdd8f806aa125ed03394598d247 |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('show_job')
@click.argument("job_id", type=str)
@click.option(
"--full_details",
help="when ``True``, the complete list of details for the given job.",
is_flag=True
)
@pa... | galaxy-iuc/parsec | parsec/commands/jobs/show_job.py | Python | apache-2.0 | 1,268 | [
"Galaxy"
] | 0d6dc2d5b316e91c27a7be339e835d4d88899059743ffccfd54ade6a38c3e71a |
# coding=utf-8
"""audio_read reads in a whole audio file with resampling."""
# Equivalent to:
# import librosa
# def audio_read(filename, sr=11025, channels=1):
# """Read a soundfile, return (d, sr)."""
# d, sr = librosa.load(filename, sr=sr, mono=(channels == 1))
# return d, sr
# The code below is adapted f... | dpwe/audfprint | audio_read.py | Python | mit | 12,385 | [
"Brian"
] | a09f1477115560aaf4c9fd85fc19e6d39ace8ad790f2c300759f17ae335f1cfa |
#!/usr/bin/env python
#
# $Id: check_keywords.py 9317 2011-06-10 02:09:04Z nathan_george $
#
# Proprietary and confidential.
# Copyright $Date:: 2011#$ Perfect Search Corporation.
# All rights reserved.
#
import sys, os, re, sandbox, svnwrap, metadata, optparse, xmail
from ioutil import *
parser = optparse.OptionParse... | perfectsearch/sandman | code/buildscripts/codescan/check_keywords.py | Python | mit | 2,960 | [
"VisIt"
] | 4680b0d9c1f0115c5e37bfed7bb7dba749fc57ce78fad4b78f97f7fbb24e56da |
#!/usr/bin/env python
"""
Reconstruction script that implements math algorithm of B0 mass reconstruction
Uses different models for fitting signal and background events
Usage: python reconstruction.py -i [INPUT_FILENAME] [-t [TREE_NAME]] [-n [MAX_EVENTS]] [-b] [-f] [-l] [-q] [-r] [-v]
Run python recons... | semkiv/fcc-reconstruction | reconstruction.py | Python | gpl-3.0 | 15,100 | [
"CRYSTAL",
"Gaussian"
] | c54d4ee276499447bbe90f55d98f40dbe06a5a7de4a166686dfde9b2f7c3d71e |
# Photovoltaics surface
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Djordje Spasic and Jason Sensibaugh <djordjedspasic@gmail.com and sensij@yahoo.com>
# Ladybug is free software; you can redistribute i... | boris-p/ladybug | src/Ladybug_Photovoltaics Surface.py | Python | gpl-3.0 | 35,501 | [
"EPW"
] | 12bfbed5a06bad78b6d579055e9ae465876e0e7e8439d3c5e3d3d5f8d7cbd40c |
# 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 Grads(AutotoolsPackage):
"""The Grid Analysis and Display System (GrADS) is an interactive... | rspavel/spack | var/spack/repos/builtin/packages/grads/package.py | Python | lgpl-2.1 | 2,412 | [
"NetCDF"
] | 30e8700c64bc0842c4b4a2dc9b1bc6f1c94e57d02b606819c1d28bd931b76277 |
"""This module provides functions to format several catalogues
These are:
- eboss_convert_dla
- desi_convert_dla
- desi_from_truth_to_drq
- desi_from_ztarget_to_drq
See the respective docstrings for more details
"""
import os
import numpy as np
import fitsio
from scipy.constants import speed_of_light a... | igmhub/picca | py/picca/converters.py | Python | gpl-3.0 | 12,823 | [
"Gaussian"
] | 275f72e5d8a7dc0055e090b9432e08557fea7dc21ceccf113f26be2e16a424f1 |
"""
Add UUID column to dataset table
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
from galaxy.model.custom_types import UUIDType
import logging
log = logging.getLogger( __name__ )
dataset_uuid_column = Column( "uuid", UUIDType, nullable=True )
def ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py | Python | gpl-3.0 | 1,363 | [
"Galaxy"
] | 4c52aa9e05f392b31ff4bd837090d669460d6540928434e22583d1cb2125e5a0 |
# 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... | jart/tensorflow | tensorflow/contrib/autograph/converters/slices.py | Python | apache-2.0 | 2,760 | [
"VisIt"
] | 0b2c37fcd8817dbf8f372ff46ecde18ebbd1f1df62ecc41899e2ac044076d8ae |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/analysis/test_encore.py | Python | gpl-2.0 | 36,155 | [
"MDAnalysis"
] | 43f9b283ccfff99083c1eb499f0dfddf3f3e37d5384f1530deed9f87e2da108c |
"""
==================================================
Automatic Relevance Determination Regression (ARD)
==================================================
Fit regression model with Bayesian Ridge Regression.
See :ref:`bayesian_ridge_regression` for more information on the regressor.
Compared to the OLS (ordinary l... | depet/scikit-learn | examples/linear_model/plot_ard.py | Python | bsd-3-clause | 2,588 | [
"Gaussian"
] | a9eb60d0848d785c94120c1e03c2ff8411947a6b18fda513dfc3b1a15ea270d4 |
#
# This is a set of functions to browse websites
#
import time
import os
import random
import urllib, urllister
import mapping
from collections import Counter
from random import randint
from datetime import datetime
from selenium import webdriver
from selenium.webdriver.common.keys import Keys
from selenium.common.exc... | nopressurelabs/privacypy | crawl.py | Python | gpl-3.0 | 6,484 | [
"VisIt"
] | cefa80357b3b755e7d89e98b279c70440fdcb863a1a42e0620956da3a6044158 |
from ee.cli.plugins.stack import EEStackController
from ee.core.fileutils import EEFileUtils
from ee.core.mysql import *
from ee.core.shellexec import *
from ee.core.sslutils import SSL
from ee.core.variables import EEVariables
from ee.cli.plugins.sitedb import *
from ee.core.aptget import EEAptGet
from ee.core.git imp... | harshadyeola/easyengine | ee/cli/plugins/site_functions.py | Python | mit | 70,749 | [
"VisIt"
] | d169d735e73808d446fbacf77b25744dfbdae45d66310d0e2d278af53939134a |
# Licensed under GPL version 3 - see LICENSE.rst
'''Sources generate photons with all photon properties: energy, direction, time, polarization.
For objects of type `AstroSource`, the coordinates of the photon
origin on the sky are added to the photon
list. `astropy.coords.SkyCoord` is an object well suited for this
ta... | Chandra-MARX/marxs | marxs/source/source.py | Python | gpl-3.0 | 21,002 | [
"Gaussian"
] | f7dc5c7568e7636fd46c684266c6a66f7b147637dbe4fe758ef437141137ea36 |
"""
Rbf - Radial basis functions for interpolation/smoothing scattered Nd data. A
radial basis function (RBF) is a real-valued function whose value depends only
on the distance from the origin.
Rbf are typically used to build up function approximations of the form:
$ y(x) = \sum_{i=1}^N w_i \, \phi(||x - x_i||) ... | mfouesneau/faststats | faststats/interpolate/bary.py | Python | mit | 7,536 | [
"Gaussian"
] | 71f80531f19dd7c8f49234d41c7becf870d04fbaec881d7d513b71484491a2ec |
import numpy as np
from joblib import Parallel, delayed
from scipy.special import wofz
from scipy.optimize import curve_fit
from protoclass.data_management import RDAModality
from protoclass.preprocessing import MRSIPhaseCorrection
from protoclass.preprocessing import MRSIFrequencyCorrection
from fdasrsf import srs... | I2Cvb/prostate | scratch/water_detection.py | Python | mit | 3,093 | [
"Gaussian"
] | e4a82a50473b6aac0ef0cc9e5d939935eeb950ad08bdf186df39fc1c3fd713cb |
#!/usr/bin/python
import HTSeq
import sys
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
from Bio.Blast import NCBIXML
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio.Blast.Applications import NcbiblastpCommandline
from Counter import Counter # --- Counter.py from python3 is needed to... | mickaelsilva/pythonscripts | AlleleCalling/cluster_versions/callAlleles.py | Python | gpl-2.0 | 18,815 | [
"BLAST",
"HTSeq"
] | d9825302dec1556970bbcc77129c6cf8b621e3ed057acaf75c7b97b2e834725c |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/qcdb/cfour.py | Python | gpl-2.0 | 46,066 | [
"CFOUR",
"Psi4"
] | b80e7f7b29a0097adef7e3f8f6df26c318b216fefd5c48c13547ceb0b83bc78b |
""" SystemAdministrator service is a tool to control and monitor the DIRAC services and agents
"""
import socket
import os
import re
import time
import getpass
import importlib
import shutil
import platform
import psutil
import tempfile
import subprocess
import requests
from packaging.version import Version, InvalidVe... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/Service/SystemAdministratorHandler.py | Python | gpl-3.0 | 26,833 | [
"DIRAC"
] | 479f69e0924849abec0b1d1189725b3de17cecd677fdb876180d9d11dd5bccf3 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkSLCReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkS... | nagyistoce/devide | modules/vtk_basic/vtkSLCReader.py | Python | bsd-3-clause | 464 | [
"VTK"
] | 6fe36824faf327819f59d756d8c256f5b2948f5e8412bc3a1cd6988c82df5d80 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/io/format/tests/test_ordination.py | Python | bsd-3-clause | 11,672 | [
"scikit-bio"
] | dca988630c195191649d234b52223909ddc97316b784f249e7ec39d535f5facb |
"""
perform exon-level counting using DEXSeq
"""
import sys
import os
from bcbio.utils import R_package_path, file_exists, safe_makedir
from bcbio.distributed.transaction import file_transaction
from bcbio.provenance import do
from bcbio import bam
from bcbio.log import logger
import bcbio.pipeline.datadict as dd
de... | hjanime/bcbio-nextgen | bcbio/rnaseq/dexseq.py | Python | mit | 2,919 | [
"BWA"
] | 7d0092966d9c03387d649b6aa09cf159321458ada9597f5803a5d7d238f61209 |
#!/usr/bin/python
# Malwina Prater, mn367@cam.ac.uk, 2017, Copyright
# Centre for Trophoblast Research, University of Cambridge
#
# Script version: v01.
#
# Script to calculate the percent of transcripts mapping to rRNA
#
# INPUTS :
# 1. HTseq_counts file
# 2. Original reference transcriptome alignned to
#
# USAGE ... | CTR-BFX/CambridgeHackathon | rRNA_MT_count.py | Python | gpl-3.0 | 4,956 | [
"HTSeq"
] | 6ce25d5cdf128bfb2cb377dfd6bbb32399f5a2561b23255eb6aaaa0d1779cdcc |
import logging, datetime, tempfile
from time import time
from dirac.lib.base import BaseController, render, c, jsonify, request, response
from dirac.lib.diset import getRPCClient, getTransferClient
from DIRAC import gConfig, gLogger, S_OK
from DIRAC.Core.Utilities.List import sortList, uniqueElements
from DIRAC.Core.U... | DIRACGrid/DIRACWeb | dirac/controllers/jobs/JobMonitor.py | Python | gpl-3.0 | 43,384 | [
"DIRAC"
] | e403f9b7faeee17cbc754b49f19370826982f54a54336edb5909d61f2ddf6f38 |
"""
Tools for reading Ampliconnoise outputs
"""
import itertools
import os.path
import re
import shutil
import tempfile
from Bio.Alphabet import generic_dna
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from anoisetools import sff
class AnoiseRawReader(object):
"""
Reader for AmpliconNoise .ra... | fhcrc/ampliconnoise | anoisetools/anoiseio.py | Python | gpl-3.0 | 4,311 | [
"Biopython"
] | ccd19395c2c83f9864593eb7f8a58e353a6b244afe8637fc5dcc7ab137a5258a |
# ast.py
# Copyright (C) 2006, 2007, 2008, 2009, 2010 Michael Bayer mike_mp@zzzcomputing.com
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""utilities for analyzing expressions and blocks of Python code, as well as generating Python from AS... | kindy61/mako | mako/ast.py | Python | mit | 5,251 | [
"VisIt"
] | 306ca5ed498897e3e02df87027edb8425c5c07011074f0a3835255941cf8756a |
"""
vtkImageExportToArray - a NumPy front-end to vtkImageExport
This class converts a VTK image to a numpy array. The output
array will always have 3 dimensions (or 4, if the image had
multiple scalar components).
To use this class, you must have numpy installed (http://numpy.scipy.org)
Methods
SetInputConnectio... | b3c/VTK-5.8 | Wrapping/Python/vtk/util/vtkImageExportToArray.py | Python | bsd-3-clause | 3,370 | [
"VTK"
] | fb3f37a58462722ad31f274b591abad0e1a189e36252ac237da640018d305f15 |
# Copyright 2017 the GPflow authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writi... | GPflow/GPflow | tests/gpflow/test_kullback_leiblers.py | Python | apache-2.0 | 8,690 | [
"Gaussian"
] | 373dd001ef14fddd9a5287395e78dc04a21aaaeb5406ea9b5a17bc061352a699 |
# -*- coding: utf-8 -*-
import sys
import textwrap
import pytest
from _pytest import fixtures
from _pytest.fixtures import FixtureLookupError
from _pytest.fixtures import FixtureRequest
from _pytest.pathlib import Path
from _pytest.pytester import get_public_names
def test_getfuncargnames():
def f():
pas... | pfctdayelise/pytest | testing/python/fixture.py | Python | mit | 124,369 | [
"VisIt"
] | 40f860ce12a4c736e7650fb45f8dd39cdc82da8488ecd91e92afec33a420e420 |
#!/usr/bin/env python3
########################################################################
# Solves problem 109 from projectEuler.net.
# Counts how many distinct ways can a player checkout with a score
# less than 100 in a game of darts.
# Copyright (C) 2010 Santiago Alessandri
#
# This program is fre... | sanSS/programming-contests | project-euler/problem109.py | Python | gpl-3.0 | 1,969 | [
"VisIt"
] | 6c5f381ecf6006e0fbb41eea7bd492b4495bbf8f1409b34929bbc9b6ff3ac95f |
"""Compiles nodes from the parser into Python code."""
import typing as t
from contextlib import contextmanager
from functools import update_wrapper
from io import StringIO
from itertools import chain
from keyword import iskeyword as is_python_keyword
from markupsafe import escape
from markupsafe import Markup
from .... | pallets/jinja | src/jinja2/compiler.py | Python | bsd-3-clause | 72,172 | [
"VisIt"
] | 1acf8df13849ece58ae3eade2a83bc5a1d595f3f79315a6104a3557fbe6a06bf |
# 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... | tongwang01/tensorflow | tensorflow/contrib/factorization/python/ops/gmm_ops.py | Python | apache-2.0 | 18,611 | [
"Gaussian"
] | f92e27897cb26207749da5a331fbfca247375b144c99ea87240fdeb93391ac4a |
"""
Based upon examples by Scott Daniel (scottvalscott@gmail.com) found here:
https://stash.lsstcorp.org/projects/SIM/repos/sims_catutils/browse/python/lsst/sims/
catUtils/exampleCatalogDefinitions/phoSimCatalogExamples.py
"""
import os
from collections import OrderedDict
import pickle
from lsst.sims.catalogs.g... | rbiswas4/Twinkles | twinkles/InstcatGenerator.py | Python | mit | 5,512 | [
"VisIt"
] | 82409c448762a26ce766e28849f380473c166bef804da8ae48046d2e6ce0b0bc |
#!/usr/bin/env python
#
# Copyright 2006 The Closure Library 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
... | Digaku/closure-library | closure/bin/calcdeps.py | Python | apache-2.0 | 18,506 | [
"VisIt"
] | f02b21e7b3c3ce9efbf9cafa1a2b82e614a6bc3e0dbb984273e0cd3e9570f07b |
"""
subsurface_fracture_model.py
----------------------------
Simulate the evolution of a petroleum fluid transiting a single pathway
through a subsurface fracture.
WARNING!!!
THIS MODULE IS UNDER CONSTRUCTION AND DOES NOT YET REPRESENT AN ACCURATE
SIMULATION OF THE OCEAN SUBSURFACE. PLEASE DO NOT USE THIS FOR ANY P... | socolofs/tamoc | tamoc/subsurface_fracture_model.py | Python | mit | 17,747 | [
"NetCDF"
] | 91e4b9aae654e60616994ada905d0f12cb4cc8c7ae1e25a52d0abffda33776f5 |
"""The PLSOM."""
import logging
from typing import Callable, Dict, Optional, Tuple
import numpy as np
from tqdm import tqdm
from somber.som import BaseSom
from somber.components.initializers import range_initialization
from somber.components.utilities import Scaler
logger = logging.getLogger(__name__)
class PLSom... | stephantul/somber | somber/plsom.py | Python | mit | 5,148 | [
"NEURON"
] | f748307d5df453c2b64c308803268827e007b60ab7ff29b22691b8b56628339d |
import espressomd
import numpy as np
from oif_utils import *
from espressomd.interactions import OifLocalForces
from espressomd.interactions import OifGlobalForces
from espressomd.interactions import OifOutDirection
class FixedPoint(object):
"""
Represents mesh points, not connected to any ESPResSo particle.
... | KonradBreitsprecher/espresso | src/python/object_in_fluid/oif_classes.py | Python | gpl-3.0 | 64,217 | [
"ESPResSo",
"VTK"
] | c09be2ccfa0d95dc73539688337d126f168762a5c24b6da4664d006fb0e6c1e3 |
# Copyright 2002 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import Martel as _M # make sure not imported into client's namespaces
import string as _stri... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/dbdefs/_support.py | Python | apache-2.0 | 591 | [
"Biopython"
] | c7ae94369f22745544fada9dc12b7731d0cea519732363149575dea618b14420 |
from __future__ import absolute_import, division, print_function
import ast
from nose.tools import raises
from jaspyx.context.module import ModuleContext
from jaspyx.visitor import BaseVisitor
class TestBaseVisitor:
def setUp(self):
self.r = {}
self.v = BaseVisitor('test.jpx', self.r, 2)
def ... | ztane/jaspyx | jaspyx/tests/visitor/test_base_visitor.py | Python | mit | 4,341 | [
"VisIt"
] | 40f793854c4831bb5772084d1f2ab665a32d340cfef2769aa3f59789cf8d49e9 |
# -*- coding: utf 8 -*-
from __future__ import division
try:
import cPickle
except ImportError:
import pickle as cPickle
import numpy as np
from scipy import linalg
import theano
import theano.tensor as T
from utils import PickleMixin, minibatch_indices, make_minibatch
from optimizers import rmsprop, sgd_nester... | kastnerkyle/minet | minet/recurrent.py | Python | bsd-3-clause | 40,812 | [
"Gaussian"
] | e99d201dff8aac5e8def5b57bfa420a5d937e3e516d312deb1c78e02c8645f38 |
#
# tsne.py
#
# Implementation of t-SNE in Python. The implementation was tested on Python 2.5.1, and it requires a working
# installation of NumPy. The implementation comes with an example on the MNIST dataset. In order to plot the
# results of this example, a working installation of matplotlib is required.
... | mp-interns/eratosthenes | neigh/tsne.py | Python | bsd-2-clause | 5,731 | [
"Gaussian"
] | 998644c49ca920b0c3229293be939b56bba7297f80be000cb597dff49efc1a3a |
# -*- coding: utf-8 -*-
# Goofy name to avoid collision w/ ../py/test_security.py
from __future__ import absolute_import, division, print_function, unicode_literals
from gratipay.testing import BrowserHarness
from selenium.common.exceptions import NoAlertPresentException
class RejectNullBytesInURI(BrowserHarness):
... | gratipay/gratipay.com | tests/ttw/test_security_ttw.py | Python | mit | 918 | [
"VisIt"
] | 87347336dbb4676ccfa38d62d58e10fd41009b7a6952ef1db1060801f6e2ffed |
from __future__ import division, print_function, absolute_import
import os
import sys
import contextlib
from os.path import join as pjoin
from hashlib import md5
from shutil import copyfileobj
import numpy as np
import nibabel as nib
import tarfile
import zipfile
from dipy.core.gradients import gradient_table
from ... | nilgoyyou/dipy | dipy/data/fetcher.py | Python | bsd-3-clause | 33,864 | [
"Brian",
"VisIt"
] | 5877868e809277abeef3acbbb90637a6c2f4ada9e05b7c6cb162067ee7cb09d4 |
from .galaxies import *
from .galaxy import *
from .simgalaxy import *
from .starpop import *
from .asts import *
| philrosenfield/ResolvedStellarPops | galaxies/__init__.py | Python | bsd-3-clause | 114 | [
"Galaxy"
] | cdb9ca9c9b906b34cf77d95d863469230ee53c6c567307bf4c7b8f868385360c |
# -*- coding: UTF-8 -*-
import numpy as np
from numpy import linspace
from igakit.nurbs import NURBS
from .op_nurbs import opNURBS
from .io import XML, TXT, NML
import sys
from caid.core import bspline as bsplinelib
_bsp = bsplinelib.bsp
from numpy import pi, sqrt, array, zeros
# ... TODO to move from here
def coupl... | ratnania/caid | caid/cad_geometry.py | Python | mit | 142,872 | [
"VTK"
] | c567cf577389a0a8416abe99a5b4fb1d01db3e5381197141a9a7e8a8ed942315 |
"""
Atomic coordinate featurizer.
"""
import logging
import numpy as np
from deepchem.feat.base_classes import Featurizer, ComplexFeaturizer
from deepchem.feat.molecule_featurizers import AtomicCoordinates
from deepchem.utils.data_utils import pad_array
from deepchem.utils.rdkit_utils import MoleculeLoadException, ge... | lilleswing/deepchem | deepchem/feat/complex_featurizers/complex_atomic_coordinates.py | Python | mit | 9,653 | [
"MDTraj",
"RDKit"
] | b1cef1b83fac5825c96fb42ac879f8954c8f0da09cf3515f1837d6e5031effe8 |
# -*- coding: utf-8 -*-
"""
This file contains the logic responsible for coordinating laser scanning.
Qudi 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... | tobiasgehring/qudi | logic/wavemeter_logger_logic.py | Python | gpl-3.0 | 25,790 | [
"Gaussian"
] | bc91c622b317ff92fd1c50899caf767f6164793af69fabd13c99e5bd7c9a52ed |
"""
Library for converting units and creating numpy arrays
with automatic unit conversion.
The conversion factors are taken directly from SIESTA
which means that the number of significant digits are not exact.
"""
import numpy as _np
from copy import copy,deepcopy
_def_L = 'Bohr'
_def_E = 'Ry'
_def_f = 'Ry/Bohr'
_de... | zerothi/siesta-es | sids/helper/units.py | Python | gpl-3.0 | 19,656 | [
"SIESTA"
] | a08dda7d660cb6a8b885a3c2687923977965e69fa2f55c496c645c66be975bf0 |
########################################################################
# $HeadURL$
# File : BuildCloudinitScript.py
# Author : Victor Mendez
########################################################################
"""
This class construct a cloudinit script for a DIRAC image and IaaS endpoint
"""
import os
im... | vmendez/VMDIRAC | WorkloadManagementSystem/Client/BuildCloudinitScript.py | Python | gpl-3.0 | 7,515 | [
"DIRAC"
] | 73ec951ebb2983b278711958ff80f2498cd5c9707ec8413bfe74f04c75653084 |
from math import pi
try:
import openmm.unit as u
except ImportError: # OpenMM < 7.6
import simtk.unit as u
kB = u.BOLTZMANN_CONSTANT_kB * u.AVOGADRO_CONSTANT_NA
# OpenMM constant for Coulomb interactions in OpenMM units
# (openmm/platforms/reference/include/SimTKOpenMMRealType.h)
# TODO: Replace this with an... | choderalab/openmmtools | openmmtools/constants.py | Python | mit | 754 | [
"OpenMM"
] | eee11d88e2fefde2780a6940e6f4ddc94273066fc7117e407e9d16ca6c423dcb |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, division, absolute_import, print_function
from builtins import * # pylint: disable=unused-import, redefined-builtin
from past.builtins import basestring
import logging
import re
import time
from datetime import datetime, timedelta
from dateutil.parser ... | dsemi/Flexget | flexget/plugins/internal/api_trakt.py | Python | mit | 50,434 | [
"VisIt"
] | 53980165927900afc6b6266d9ea404cab9bab8c6e9d991d26de5df2ce646fd19 |
import os
import shutil
import bcbio.bam as bam
import toolz as tz
from bcbio.utils import (file_exists, safe_makedir, append_stem)
from bcbio.pipeline import config_utils
from bcbio.bam import is_paired
from bcbio.provenance import do
from bcbio.distributed.transaction import file_transaction
import bcbio.pipeline.da... | lbeltrame/bcbio-nextgen | bcbio/rnaseq/featureCounts.py | Python | mit | 7,393 | [
"HTSeq"
] | 14f04d6723163a47bfc88f9d2b10c19eb531a2cf6e769f84fcb3a0a75dfe28dd |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides objects describing the basic parameters of the
pseudopotentials used in Abinit, and a parser to instantiate pseudopotential objects..
"""
from __future__ import unicode_literals, divisi... | migueldiascosta/pymatgen | pymatgen/io/abinit/pseudos.py | Python | mit | 100,402 | [
"ABINIT",
"WIEN2k",
"pymatgen"
] | 83751716ea05c5e89c513436e6306c4a0c6fb689c74ccffdd156862e3129a2b3 |
# Copyright (C) 2018 Fulvio Paleari, Henrique Pereira Coutada Miranda
# All rights reserved.
#
# This file is part of yambopy
#
from __future__ import print_function
from builtins import zip
from builtins import map
from builtins import range
from yamboparser import *
from os import *
import argparse
def merge_qp(outp... | alexmoratalla/yambopy | scripts/merge_qp.py | Python | bsd-3-clause | 4,776 | [
"NetCDF"
] | 5d147e78a6559c5e45d57974d1c017b5e5ea4d87c4ff9b4064b84a052fe9fdae |
# (C) British Crown Copyright 2010 - 2018, 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... | dkillick/iris | lib/iris/config.py | Python | lgpl-3.0 | 7,984 | [
"NetCDF"
] | b4216fcdaeec409c01cc4d954d41ccf82552f23bebde27d2bf4eed24f509b199 |
import sys
from flask import Flask, request
import telepot
from telepot.loop import OrderedWebhook
"""
$ python2.7 flask_deeplinking.py <bot_username> <token> <listening_port> https://<domain>/webhook
Webhook path is '/webhook'.
Initial webpage is '/link'.
1. Open browser, visit: `https://<domain>/link`
2. Click on ... | nickoala/telepot | examples/deeplinking/flask_deeplinking.py | Python | mit | 2,073 | [
"VisIt"
] | f8858af2274928a93875779823371949c3300bee1e5d11ec0b6b0739e71d9c9e |
# coding: utf-8
"""
Acceptance tests for Studio's Setting pages
"""
import os
from textwrap import dedent
from bok_choy.promise import EmptyPromise
from mock import patch
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.pages.common.utils import add_enrollment_course_... | cpennington/edx-platform | common/test/acceptance/tests/studio/test_studio_settings.py | Python | agpl-3.0 | 27,998 | [
"VisIt"
] | e326d7cbcc9c37a6daad1c766f78212babad597f98f5d093a99465e26444dd49 |
""" core implementation of testing process: init, session, runtest loop. """
from __future__ import absolute_import, division, print_function
import functools
import os
import sys
import _pytest
from _pytest import nodes
import _pytest._code
import py
try:
from collections import MutableMapping as MappingMixin
ex... | iulian787/spack | lib/spack/external/_pytest/main.py | Python | lgpl-2.1 | 30,081 | [
"VisIt"
] | 143c583ddf10deee9907e9cbe128427e220752e97ab5e8a6994962979a0bf4b0 |
'''
:mod: Utils
Module that collects utility functions.
'''
__RCSID__ = '$Id$'
import fnmatch
from DIRAC import gConfig, S_OK
from DIRAC.Core.Utilities import List
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations... | andresailer/DIRAC | ResourceStatusSystem/Utilities/Utils.py | Python | gpl-3.0 | 2,920 | [
"DIRAC"
] | c5b7f5e4e48d89b566e274ccef3d631a1b08f3750f26f063e58f81a2f81a211b |
import pybullet as p
from time import sleep
physicsClient = p.connect(p.GUI)
p.resetSimulation(p.RESET_USE_DEFORMABLE_WORLD)
p.setGravity(0, 0, -10)
planeOrn = [0,0,0,1]#p.getQuaternionFromEuler([0.3,0,0])
planeId = p.loadURDF("plane.urdf", [0,0,-2],planeOrn)
boxId = p.loadURDF("cube.urdf", [0,3,2],useMaximalCoord... | MadManRises/Madgine | shared/bullet3-2.89/examples/pybullet/examples/deformable_ball.py | Python | mit | 848 | [
"VTK"
] | 7ba1a0b7348abd6fd472e4b6d8f85a6c0a3d4fe9c90a45ed9aaf73640c91a6e4 |
import random
from scipy.stats import norm
class Lattice1D:
"""A class that represents a disordered one dimensional lattice"""
def __init__(self, mean_separation, sigma_separation):
self.mean_separation = mean_separation
self.sigma_separation = sigma_separation
def get_sigma(self):
... | waltervh/BornAgain-tutorial | old/bornagain-python/iff/Lattice1D.py | Python | gpl-3.0 | 2,912 | [
"DIRAC"
] | 2a07ce065d1d51c02c1e33b86920d0516d48fbd17695bad1e4000cffb2634496 |
#!/usr/bin/env python
# -*- Mode: Python -*-
# GObject-Introspection - a framework for introspecting GObject libraries
# Copyright (C) 2010 Zach Goldberg
# Copyright (C) 2011 Johan Dahlin
# Copyright (C) 2011 Shaun McCance
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of ... | anthrotype/gobject-introspection | giscanner/docwriter.py | Python | gpl-2.0 | 33,885 | [
"VisIt"
] | 3c92f4b372aa244ac4e880dd5bfb088d93167502db964c73b712df35cde5c636 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import collections
import errno
import filecmp
import os.path
import re
import tempfile
import sys
# A minimal memoizing decorator. It'll blow up if the args a... | saghul/gyn | gyn/common.py | Python | bsd-3-clause | 19,147 | [
"VisIt"
] | dad8ddf108ac5b0f2545e2aa511ce96670d61549dc02aa596de2a9e5ef25d3c9 |
#!/usr/bin/python
# -*- coding: utf8 -*-
import numpy as np
import math
import time
from scipy.ndimage import correlate1d
def convol1d(array,kernel,scale_factor=None):
"""
The convol1d function convolves an array with a kernel 1D,
and returns the result. Convolution is a general process
that can be used for var... | Hypnus1803/FlowMaps | MainCodes/convol.py | Python | gpl-3.0 | 2,661 | [
"Gaussian"
] | 6113172766cdbe13327672d05bb3f1f085a4ee5e88369389b2a5520ed84a8227 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_virtualservice.py | Python | bsd-3-clause | 24,047 | [
"VisIt"
] | 76abef2446e9df23b92489a4c70073cf6d57ae9cbf9c3079ad80e9f7cdd32605 |
class Grabber:
def __init__(self, baseurl, proxies=none):
self.baseurl = baseurl
self.proxies = proxies
def getPage(projectId):
import requests
response = requests.get(baseurl + '/' + projectId + '/')
# if response.status_code != 200:
# print "Well, that didn't work... | ijjorama/Impact | grabber.py | Python | mit | 1,024 | [
"BLAST"
] | 3cde86fc30c26526569dcc3e9af8580ad529ee7aa59adfb978cbe34189862a8b |
# Copyright 2015 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... | HaebinShin/tensorflow | tensorflow/models/image/cifar10/cifar10.py | Python | apache-2.0 | 14,317 | [
"Gaussian"
] | f0ce503b3f1bee2069d4873f679cf92fdc50e323b9cc3cf21db7d36fa58986a0 |
"""The ants module provides basic functions for interfacing with ants functions.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
>>> os.chdir(... | FCP-INDI/nipype | nipype/interfaces/ants/registration.py | Python | bsd-3-clause | 55,905 | [
"Gaussian",
"VTK"
] | 7bcb0a822d937b588404b32896e7ae511ab83f9e10c06fd9273ad5d46eeb6350 |
from Firefly import logging, scheduler
from Firefly.const import COMMAND_SET_LIGHT
from Firefly.helpers.events import Command
# TODO: Refactor this code.
class CTFade(object):
def __init__(self, firefly, ff_id, start_k, end_k, fade_sec, start_level=100, end_level=100, run=True):
if type(start_level) is not int... | Firefly-Automation/Firefly | Firefly/components/hue/ct_fade.py | Python | apache-2.0 | 4,030 | [
"Firefly"
] | 52fbb743158a2ca62ec04ef6fd9d1d90da7fbd432d453e0029d93398842c0ed3 |
from time import time
from collections import namedtuple
import warnings
from scipy import stats
import numpy as np
from ..base import clone
from ..exceptions import ConvergenceWarning
from ..preprocessing import normalize
from ..utils import (check_array, check_random_state, _safe_indexing,
is_... | anntzer/scikit-learn | sklearn/impute/_iterative.py | Python | bsd-3-clause | 31,090 | [
"Gaussian"
] | 96fce4332d89df66467af6a181114ff067b014f5e8b0d31d991395c7d2269c0e |
"""Small testing script to test biomajmanager functionality"""
from __future__ import print_function
import shutil
import os
import tempfile
import time
import unittest
from nose.plugins.attrib import attr
from pymongo import MongoClient
from datetime import datetime
from biomajmanager.links import Links
from biomajman... | horkko/biomaj-manager | tests/biomaj-manager_tests.py | Python | gpl-2.0 | 190,492 | [
"BLAST"
] | e387f47f36ece342ab1b86c4f480c92f4bc7b50bc31e562eb195937ffc826d63 |
"""
CloudEndpoint is a base class for the clients used to connect to different
cloud providers
"""
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
__RCSID__ = "$Id$"
import os
import ssl
import time
from libcloud import security
from libcloud.comput... | ic-hep/DIRAC | src/DIRAC/Resources/Cloud/CloudEndpoint.py | Python | gpl-3.0 | 18,218 | [
"DIRAC"
] | 2f74e503640f7951cb575d9ac715300f3173c102e0d3440195f7a5121761f06d |
import unittest
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Molecule
from pymatgen.analysis.adsorption import *
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.util.coord import in_coord_list
from pymatgen.util.testing import PymatgenTest
class AdsorbateSiteF... | davidwaroquiers/pymatgen | pymatgen/analysis/tests/test_adsorption.py | Python | mit | 8,755 | [
"pymatgen"
] | 4f5ecac52faa0b5fb5fdb29a003fb0d6d6e7f5054cbb64b75574cb00b9d0a263 |
#!/usr/bin/env python
########################################
# to modify the NetCDF files
########################################
#First import the netcdf4 library
from netCDF4 import Dataset # http://code.google.com/p/netcdf4-python/
import numpy as np
import sys,getopt
import math
import datetime as DT
import net... | CopyChat/Plotting | Python/Psl_correct.py | Python | gpl-3.0 | 14,522 | [
"NetCDF"
] | 1ac697082fd2b3399f1eec098594408ded0cbd2f4b5ed03ff25a8af015281073 |
"""Python to lua translator class"""
import ast
import os
from .config import Config
from .nodevisitor import NodeVisitor
class Translator:
"""Python to lua main class translator"""
def __init__(self, config=None, show_ast=False):
self.config = config if config is not None else Config()
self.... | NeonMercury/python-lua | pythonlua/translator.py | Python | apache-2.0 | 1,804 | [
"VisIt"
] | 06155c9c5629e09aad28ceabd813ead9ee019a883f9d8ffd7322c1efcf65ff83 |
# coding: utf-8
# Copyright 2013 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 ap... | ehiller/CourseBuilderV19-TeacherDashboard | tests/functional/test_classes.py | Python | apache-2.0 | 232,592 | [
"VisIt"
] | 3601d0b1cb70fcfa4b1321a9677f2096984a0541d0213efe6f3282f45b6f3856 |
"""
MultiVolumeVisualizationMix
:Authors:
Berend Klein Haneveld
"""
from MultiVolumeVisualization import MultiVolumeVisualization
from MultiVolumeVisualization import CreateFunctionFromProperties
from MultiVolumeVisualization import CreateEmptyFunctions
from VolumeVisualization import VisualizationTypeSimple
from cor... | berendkleinhaneveld/Registrationshop | ui/visualizations/MultiVolumeVisualizationMix.py | Python | mit | 5,177 | [
"VTK"
] | 2030f69fe9623debbf2431d62d10f5b2e04c28a23fba21dea6ae499979337873 |
"""
Tests for the Course Outline view and supporting views.
"""
from __future__ import absolute_import
import datetime
import json
import re
import six
from completion import waffle
from completion.models import BlockCompletion
from completion.test_utils import CompletionWaffleTestMixin
from django.contrib.sites.mode... | ESOedX/edx-platform | openedx/features/course_experience/tests/views/test_course_outline.py | Python | agpl-3.0 | 27,152 | [
"VisIt"
] | 90438417610fc3f96cc20f70f9f6d7d82eea68c8b04524c8d548923f64c3cf95 |
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