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import logging
from Bio.GenBank.Scanner import GenBankScanner
logger = logging.getLogger(__name__)
def parse_seq_rec(gbkfile, do_features=False):
"Parse the gbkfile into a Bio.SeqRecord.SeqRecord"
with open(gbkfile, 'r') as handle:
# this is pretty much the exact code of Bio.Seq.read, except
... | victor-lin/npact | pynpact/pynpact/genbank.py | Python | bsd-3-clause | 3,959 | [
"Biopython"
] | 5cec3f952f4873fb915732fbf11db50d6585cb2a2eb68ac251ec4c45f74531cc |
# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
import re
from lxml.cssselect import CSSSelector
from zope.testbrowser.browser import Browser, ListControl, SubmitControl
from splinter... | bmcculley/splinter | splinter/driver/zopetestbrowser.py | Python | bsd-3-clause | 12,991 | [
"VisIt"
] | 486755051ad08ea998de83aa1d32547bf666b91a2f7e8c621e3e9f6b17b81dcb |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2012 Doug Blank
# Copyright (C) 2013 John Ralls <jralls@ceridwen.us>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the... | Fedik/gramps | gramps/gen/const.py | Python | gpl-2.0 | 11,791 | [
"Brian"
] | 23d674afb94300d98da4e0f565619af28d023c793bfca1756bd2cfe5f3c9cac5 |
"""Authentication out of the box.
References
----------
https://stackoverflow.com/questions/13428708/best-way-to-make-flask-logins-login-required-the-default
https://stackoverflow.com/questions/14367991/flask-before-request-add-exception-for-specific-route
"""
from typing import Dict, Optional
from abc import ABC, a... | jwkvam/bowtie | bowtie/auth.py | Python | mit | 3,073 | [
"Bowtie"
] | c7b5b62fe4a9a57aa179507bae95420a608d96bf7377c8925d9c9e19d7d9fbd8 |
"""A host of different cross-correlation peak interpolation methods."""
import numpy as np
import scipy.optimize
def _time_shift(samples, shift):
"""Shift samples by shift samples."""
freqs = np.fft.fftfreq(len(samples))
fft_shift = np.exp(-2j * np.pi * shift * freqs)
fft = np.fft.fft(samples)
re... | swkrueger/Thrifty | thrifty/experimental/xcorr_interpolators.py | Python | gpl-3.0 | 5,741 | [
"Gaussian"
] | 98c2a82855ede2266e4840aea84b83929578b44c17ae4a66b7a67a21ba4a5019 |
# Copyright (C) 2012,2013,2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms... | kkreis/espressopp | src/esutil/unittest/PTestCollectives.py | Python | gpl-3.0 | 1,920 | [
"ESPResSo"
] | f264bb747d1b625e5c69b0db531b767404a4a58c5dec48db8177a9877695edae |
class TelegramTokenError(Exception):
msg = 'Missing Telegram token, ' \
'visit:https://core.telegram.org/ ' \
'to obtain a token'
def __str__(self):
return self.msg
class TotalCornerTokenError(Exception):
msg = 'Missing TotalCorner token, ' \
'visit:http://www.totalc... | nik849/Odds | odds/errors.py | Python | mit | 648 | [
"VisIt"
] | 5d0df28c67fb324388c7f40715668a7f8403768da88c1406186772517cc64f7c |
# FIXME: to bring back to life
# ########################################################################
# # File: DataLoggingDBTests.py
# # Author: Krzysztof.Ciba@NOSPAMgmail.com
# # Date: 2012/07/12 13:01:10
# ########################################################################
#
# """ :mod: DataLoggingDBTests
... | ic-hep/DIRAC | tests/Integration/DataManagementSystem/FIXME_DataLoggingDBTests.py | Python | gpl-3.0 | 4,116 | [
"DIRAC"
] | aa36dc6fd2689541ccbc1edef3b45867473e175df352ecdc2f4df379365fb176 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | RyanSkraba/beam | sdks/python/apache_beam/runners/interactive/pipeline_instrument_test.py | Python | apache-2.0 | 12,148 | [
"VisIt"
] | 297c7ff12cc9b4fe46957e5fbb6ea3f9d6d5653ed2330a5e9a47c000f11db2d9 |
# At the 64-bit Anaconda prompt, "activate my-rdkit-env" first.
import sys
from rdkit import Chem
from io import StringIO
import common
class MyAromaticSmilesWriter(common.AromaticSmilesWriter):
def getoutput(self, smi):
m = Chem.MolFromSmiles(smi)
if m is None:
return ""
... | nextmovesoftware/smilesreading | scripts/RDKit.py | Python | bsd-2-clause | 1,948 | [
"RDKit"
] | 2613f8be148215ff4c4afb3549757db7e55bb5e078f3ebe7cbc986c7738e73e6 |
''' Fvtk module implements simple visualization functions using VTK.
The main idea is the following:
A window can have one or more renderers. A renderer can have none, one or more actors. Examples of actors are a sphere, line, point etc.
You basically add actors in a renderer and in that way you can visualize the fore... | jyeatman/dipy | dipy/viz/fvtk.py | Python | bsd-3-clause | 53,175 | [
"Mayavi",
"VTK"
] | 803dbe689dc7eee1bc27dfee1a752b307fa4384af1f325dd07937d69087d6d17 |
# -*- coding: utf-8 -*-
""" Sahana Eden Common Alerting Protocol (CAP) Model
@copyright: 2009-2014 (c) Sahana Software Foundation
@license: MIT
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to dea... | gnarula/eden_deployment | modules/s3db/cap.py | Python | mit | 78,715 | [
"VisIt"
] | 69c5170b95dfe04e89d564694abb40ecd2178898b4afc813554f163004fe7893 |
from copy import deepcopy, copy
from math import sqrt
import math
import os
import subprocess
import time
import vtk
from vtk import vtkTransform
from ddapp import objectmodel as om
from ddapp import ikplanner
from ddapp import ik
import bot_frames
from PythonQt import QtCore, QtGui
from ddapp import filterUtils
from... | gizatt/director | src/python/ddapp/pfgrasp.py | Python | bsd-3-clause | 21,185 | [
"VTK"
] | 428b5552c9ea8cf286d79cdfc7337e759b66719ad094d2c3431d9cc68c6cf602 |
# -*- coding: utf-8 -*-
#
# This file is part of INSPIRE.
# Copyright (C) 2014-2017 CERN.
#
# INSPIRE 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 ... | chris-asl/inspire-query-parser | inspire_query_parser/visitors/visitor_impl.py | Python | gpl-3.0 | 1,550 | [
"VisIt"
] | ffeabe889a2f01f588dd0a428a16638ae337a7395caa6a0435dc5f0b1f0d344e |
"""
Test the about xblock
"""
from __future__ import absolute_import
import datetime
import ddt
import mock
import pytz
import six
from ccx_keys.locator import CCXLocator
from django.conf import settings
from django.test.utils import override_settings
from django.urls import reverse
from milestones.tests.utils import... | ESOedX/edx-platform | lms/djangoapps/courseware/tests/test_about.py | Python | agpl-3.0 | 28,959 | [
"VisIt"
] | cb3fdd0b2d19b5451fd72710db6f65dbc6c6108685150d1fc78596eb35986bc8 |
from jasp import *
JASPRC['mode'] = 'run'
from nose import *
import shutil
from ase.lattice.cubic import BodyCenteredCubic
def setup_func():
"set up test fixtures"
pass
def teardown_func():
"tear down test fixtures"
if os.path.isdir('Fe-magmom'):
print('deleting the Fe-magmom dir')
s... | jboes/jasp | jasp/tests/test-magmom.py | Python | gpl-2.0 | 3,620 | [
"ASE"
] | f714f2b596e23b260c865f371a0c19caa284196f70e83a7eee0770c68b3deea1 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import sys
import numpy as np
import matplotlib.pyplot as plt
from sklearn import datasets
from sklearn import cross_validation
from matplotlib import colors
def gen_data(dim=2, size=100):
return datasets.make_classification(n_samples=size, n_features=dim,
... | pjhades/coursera | ml1/pla.py | Python | mit | 6,062 | [
"VisIt"
] | 102fef7731b616e18cc916b1e90b363f984b99793b0eda8cac2322a82f3ecece |
# Standard Library
import re
import textwrap as twrap
from pathlib import Path
from pkg_resources import resource_filename
# OrthoEvol
from OrthoEvol.Manager.config import references
# Based off of https://github.com/etetoolkit/ete/blob/master/ete3/citation.py
class Webster(object):
archive_options... | datasnakes/Datasnakes-Scripts | OrthoEvol/Manager/webster.py | Python | mit | 3,930 | [
"BLAST"
] | ceed90f6f6a3f390701a4fe00cc2720c4a3f1e5166bfc29782863b2e7d361812 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/machines/urls/__init__.py | Python | gpl-3.0 | 925 | [
"Brian"
] | 870d4ca2628ddabef5462d6a8c2558bc7cead7a1c9fa5d5914b4e0806842e486 |
#
# This program is free software you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation either version 3 of the License, or
# (at your option) any later version.
#
# Written (W) 2013 Roman Votyakov
#
from pylab import *
from numpy im... | cfjhallgren/shogun | examples/undocumented/python/graphical/classifier_gaussian_process_binary_classification.py | Python | gpl-3.0 | 3,740 | [
"Gaussian"
] | dbaa5cd40859ee8debaa303e568b93528e62acc055f9ed3a65289603371490a7 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/songs/forms/editverseform.py | Python | gpl-2.0 | 6,770 | [
"Brian"
] | 9bcbfc11eeccdc2f88764969c67f866806f1b20f4c597118cf0878ec6ed895fa |
# python 3.0
from rdkit import Chem
import jchem
from SA_Score import sascorer
from NP_Score import npscorer
class SANP():
"""
NP: Natural likeness point
SA: Sythetic accesbility
"""
def __init__(self, disp = False, graph = False):
self.fscore = npscorer.readNPModel()
self.disp = disp
self.graph = graph
... | jskDr/jamespy_py3 | jrdkit_scores.py | Python | mit | 707 | [
"RDKit"
] | ef40ab89443368616aef349f1233a36c83e1a6679b1821646987b227f67dcda2 |
# -*- coding: utf-8 -*-
"""Module providing parser definitions
(c) The James Hutton Institute 2017-2019
Author: Leighton Pritchard
Contact: leighton.pritchard@hutton.ac.uk
Leighton Pritchard,
Information and Computing Sciences,
James Hutton Institute,
Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
Scotland,
UK
The MIT L... | widdowquinn/find_differential_primers | diagnostic_primers/scripts/parsers/__init__.py | Python | mit | 3,902 | [
"BLAST"
] | 371bc19b15d9a6d66522fe7ee71fed0b411985e804d54fa25c7df7cfa528f75f |
""" Unit tests for pipelines with mpi
"""
import logging
import sys
import unittest
import numpy
from astropy import units as u
from astropy.coordinates import SkyCoord
from data_models.polarisation import PolarisationFrame
from wrappers.serial.image.operations import export_image_to_fits, smooth_image
from wrappe... | SKA-ScienceDataProcessor/algorithm-reference-library | deprecated_code/workflows/mpi/unitests/test_imaging_mpi.py | Python | apache-2.0 | 13,594 | [
"Gaussian"
] | 6b1831e97e2a547f067a8ac8e4882d6ecb40f9aed5b2ba04c49a54492ebf5ac1 |
# NOTE: This example uses the next generation Twilio helper library - for more
# information on how to download and install this version, visit
# https://www.twilio.com/docs/libraries/python
import os
from twilio.rest import Client
# Your Account Sid and Auth Token from twilio.com/user/account
# To set up environmenta... | TwilioDevEd/api-snippets | notifications/rest/services/update-service/update-service.7.x.py | Python | mit | 740 | [
"VisIt"
] | 33c0aa2c96f6fdd5d67c1fd2155aef8bcc219146acb2bb975812d3cf645656b8 |
"""
Defines a common implementation of the built-in PyNN Connector classes.
Simulator modules may use these directly, or may implement their own versions
for improved performance.
:copyright: Copyright 2006-2016 by the PyNN team, see AUTHORS.
:license: CeCILL, see LICENSE for details.
"""
from __future__ import divi... | anupkdas-nus/global_synapses | pyNN-dispackgaes/connectors.py | Python | gpl-3.0 | 46,376 | [
"NEURON"
] | eb335290931d9a489bef33e49e54e96cb6a5998c2ea0eee10f396a4196e14d3a |
'''
Spatial Two Stages Least Squares with Regimes
'''
__author__ = "Luc Anselin luc.anselin@asu.edu, Pedro V. Amaral pedro.amaral@asu.edu, David C. Folch david.folch@asu.edu"
import numpy as np
import pysal
import regimes as REGI
import user_output as USER
import summary_output as SUMMARY
import multiprocessing as mp... | lanselin/pysal | pysal/spreg/twosls_sp_regimes.py | Python | bsd-3-clause | 33,675 | [
"COLUMBUS"
] | 6aed622b2602057148080690c9b4492c4243e5b007c9f1e277e4eab175d94fa9 |
# encoding: utf-8
"""colors.py - select how to color the atoms in the GUI."""
import gtk
from ase.gui.widgets import pack, cancel_apply_ok, oops, help
import ase
from ase.data.colors import jmol_colors
import numpy as np
import colorsys
named_colors = ('green', 'yellow', 'blue', 'red', 'orange', 'cyan',
... | slabanja/ase | ase/gui/colors.py | Python | gpl-2.0 | 19,544 | [
"ASE",
"Jmol"
] | c7bdd6793e5516c09debc4e59d84acf8e1c51b0b1c6d01fdfe5250f88d2d61aa |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/test/zoo/orca/data/test_ray_xshards.py | Python | apache-2.0 | 3,600 | [
"ORCA"
] | a56b8b3814a32d5b9a459e2d21d570a5aa84a0370cdf98a998a806683b702d08 |
#
# plots.py -- Utility functions for plotting.
#
# This is open-source software licensed under a BSD license.
# Please see the file LICENSE.txt for details.
#
import numpy as np
import matplotlib as mpl
from matplotlib.figure import Figure
from ginga.util import iqcalc as _iqcalc # Prevent namespace confusion below... | pllim/ginga | ginga/util/plots.py | Python | bsd-3-clause | 22,907 | [
"Gaussian"
] | 2ee191612fff30613002207c673139588456b52ebaf30fb2014361ff60c9c211 |
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 12 15:47:32 2014
@author: Andrew
"""
from automatedAFManalysis.afm_sql_code.afmsqlcode import SQLConnection, SQLData, FeatureInfo
from scipy import signal
import numpy as np
from PyQt4 import QtCore, QtGui
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg ... | ajmorss/automatedAFManalysis | Single_Bond_Automatic_Analysis_App.py | Python | cc0-1.0 | 46,447 | [
"Gaussian"
] | 235ecf70bdd2c43f9708fb7b7726da5c7ecfbc7085e12ab3cb807399522e353c |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""A library for parsing and interpreting results from computational chemistry packages.
The goals of cclib are centered ... | gaursagar/cclib | src/cclib/__init__.py | Python | bsd-3-clause | 1,634 | [
"ADF",
"Firefly",
"GAMESS",
"Gaussian",
"Jaguar",
"MOPAC",
"Molpro",
"NWChem",
"ORCA",
"Q-Chem",
"cclib"
] | 36da10358c3019d9576988aa5fc00910ea74280499a04ce5733163e7c9f39968 |
#!/usr/bin/python
from datetime import datetime, timedelta
import httplib2
import os
import sys
from apiclient.discovery import build
from oauth2client.file import Storage
from oauth2client.client import flow_from_clientsecrets
from oauth2client.tools import run
from optparse import OptionParser
# CLIENT_SECRETS_FI... | lhongskie/yt-samples-python | yt_analytics_report.py | Python | apache-2.0 | 4,235 | [
"VisIt"
] | 4e73103b0f201793c6035ead4de4709c79b1db12c89e374d9c935316c9af4a48 |
# 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 writing, software
# distributed under t... | openstack/rally | tests/hacking/checks.py | Python | apache-2.0 | 21,689 | [
"VisIt"
] | ee0874c453c608e216c07e1a7d6c57e956c8d0eaf6f403b7547a30749a5e341e |
# 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... | frreiss/tensorflow-fred | tensorflow/python/ops/image_ops_test.py | Python | apache-2.0 | 241,604 | [
"Gaussian"
] | 16cb8e6cc807248c90037054dc819b0af67d9b7371616100eda057e490a8f5af |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_backupconfiguration.py | Python | gpl-3.0 | 5,304 | [
"VisIt"
] | d6a2a75717eb6b528384758865e1fd0c244ee885e2cd0e7a1a33fcf2c4c6572e |
from keras.models import Sequential, Model
from keras.layers import Flatten, Dense, Dropout, Reshape, Permute, Activation, Input #, merge
from keras.layers.convolutional import Convolution2D, MaxPooling2D, ZeroPadding2D
from keras.layers.normalization import LRN2D
from keras.optimizers import SGD
import numpy as np
fro... | babraham123/deepdriving | alexnet_lrn.py | Python | mit | 3,836 | [
"Gaussian"
] | 1a5490a876e5a332f7ce86a46ac9a6f3526263a98b6121def4a1aa3de47c87cc |
# convcmd - convert extension commands definition
#
# Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from common import NoRepo, MissingTool, SKIPREV, mapfile
from cvs import conv... | joewalnes/idea-community | plugins/hg4idea/testData/bin/hgext/convert/convcmd.py | Python | apache-2.0 | 14,056 | [
"VisIt"
] | c710d0e78526237e546231b4ec1e4cce636883f658588839de83eb822f4e6ff6 |
#This file does three things:
#1. calculate the frequency of mutations, insertions, and deletions at each position in an
#NGS read.
#2. find the degree of coverage of the reference genome
#3. find the fraction of each subject read that was aligned to a corresponding sequence
#in the refenece genome.
# @author ... | annashcherbina/FASTQSim | src/getBlastStats.py | Python | gpl-3.0 | 21,042 | [
"BLAST"
] | 8a1c130dac94cec7f207cd279eebba471969435e0bcf3d1f0e4035119529cfa2 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Run writer unit tests for cclib."""
import sys
import unittest
sys.path.insert(1, 'io')
from .io.testccio import *
f... | langner/cclib | test/test_io.py | Python | bsd-3-clause | 629 | [
"cclib"
] | f4175818e2d060fceedb772ea9c9af019d8b31a2afb93f0fdcc1f292077ffb8d |
"""
@name: Modules/House/Entertainment/Pandora/__init__.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c)2014-2020 by D. Brian Kimmel
@note: Created on Feb 27, 2014
@license: MIT License
"""
__updated__ = '2020-02-10'
__version_info__ = (20, 1, 28)
__version__ = '.'.j... | DBrianKimmel/PyHouse | Project/src/Modules/House/Entertainment/Pandora/__init__.py | Python | mit | 3,164 | [
"Brian"
] | 456edd293fb9937a6f34dd11df6dc03fb49006b27734d3d59e4bbd0fd8401578 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | WindCanDie/spark | python/pyspark/ml/tests/test_training_summary.py | Python | apache-2.0 | 13,137 | [
"Gaussian"
] | 8cbbb051b8797c53f83bc2423b0d781050796242ac3f7a0d7a1bffeabb7585fd |
#
# @file TestL3SpeciesReference.py
# @brief L3 SpeciesReference unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automati... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestL3SpeciesReference.py | Python | gpl-3.0 | 6,791 | [
"VisIt"
] | e12fc09c70af2b913543145b2b23371b705201cb111aa2937ec8dbf9e34b4380 |
# Copyright (C) 2016 Google Inc.
# Licensed under http://www.apache.org/licenses/LICENSE-2.0 <see LICENSE file>
import textwrap
from integration.ggrc import TestCase
from freezegun import freeze_time
from datetime import date, datetime
from ggrc import db
from ggrc.notifications import common
from ggrc.models import ... | NejcZupec/ggrc-core | test/integration/ggrc_workflows/notifications/test_middle_level_one_time_wf.py | Python | apache-2.0 | 5,693 | [
"NAMD"
] | 20e6380a5451a8cf55757454e91c80a73fa8c65227d2a01ed6b66e080f637ea9 |
'''Peak detection algorithms.'''
import numpy as np
from scipy import optimize
from scipy.integrate import simps
def indexes(y, thres=0.3, min_dist=1):
'''Peak detection routine.
Finds the peaks in *y* by taking its first order difference. By using
*thres* and *min_dist* parameters, it is possible to red... | atjacobs/PeakUtils | peakutils/peak.py | Python | mit | 4,579 | [
"Gaussian"
] | f04bf2321364bef2821e9ae77e5069c9c7c62d154a6eb10fc6cafb3be7912a38 |
"""Metrics to assess performance on classification task given class prediction.
Functions named as ``*_score`` return a scalar value to maximize: the higher
the better.
Function named as ``*_error`` or ``*_loss`` return a scalar value to minimize:
the lower the better.
"""
# Authors: Alexandre Gramfort <alexandre.gr... | manhhomienbienthuy/scikit-learn | sklearn/metrics/_classification.py | Python | bsd-3-clause | 99,712 | [
"Brian"
] | 696c0c27c725ff34b50632e3fed4088aed6821886d7e6aa0b9c4a9f5b754ff39 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Created on Apr 17, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "S... | aykol/pymatgen | pymatgen/io/tests/test_gaussian.py | Python | mit | 12,133 | [
"Gaussian",
"pymatgen"
] | a2a130ca77ac7105ec74bd7a52d9dd390f5e0b4b6b942a2af318bff16b10f608 |
import numpy as np
import matplotlib.pyplot as plt
class STRF(object):
'''Allows the estimation of spatiotemporal receptive fields
Args:
patch_size (int): Dimension of the square patch spanned by the
spatial basis.
sigma (float): Standard deviation of the Gaussian distribution.
... | codekansas/spykes | spykes/ml/strf.py | Python | mit | 10,722 | [
"Gaussian"
] | 1dcb92e8a6a300b37c0563636a6eb9f8550205ecf5363113c77db4c12c27a0c6 |
###############################################################################
# #
# 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 #
... | Ecogenomics/mingle | mingle/blast_workflow.py | Python | gpl-3.0 | 21,547 | [
"BLAST"
] | 321460e7e0c71563daf15ffacb51420b938672ad43dd465bbde4d684d6ef6372 |
"""RabbitMQAdmin module serves for the management of the internal RabbitMQ
users database. It uses rabbitmqctl command. Only the user with the right
permissions can execute those commands.
"""
from __future__ import print_function
import re
from DIRAC import S_OK , S_ERROR
import errno
from DIRAC.Core.Utilities i... | chaen/DIRAC | Core/Utilities/RabbitMQAdmin.py | Python | gpl-3.0 | 4,699 | [
"DIRAC"
] | 486f366cc95c83061d956f3feadc7108dd5a1aedbe28365dd05f58429da40065 |
# coding: utf-8
from __future__ import division, unicode_literals
import unittest
import pickle
import collections
from pymatgen.core.periodic_table import Element, Specie, DummySpecie, \
PeriodicTable, get_el_sp
from copy import deepcopy
class ElementTestCase(unittest.TestCase):
def test_init(self):
... | yanikou19/pymatgen | pymatgen/core/tests/test_periodic_table.py | Python | mit | 12,207 | [
"pymatgen"
] | 56a5ad2f89de1e2cea8860294d7386cf6dea66152ac910f7123eaf7f65a4a836 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkTableWriter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vt... | nagyistoce/devide | modules/vtk_basic/vtkTableWriter.py | Python | bsd-3-clause | 472 | [
"VTK"
] | 9110bd0bbefd7242bf5f66f8dce72067a7a0f814d4672dd9d69a8224d306c17d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2013 The Plaso Project Authors.
# Please see the AUTHORS file for details on individual 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 L... | iwm911/plaso | plaso/formatters/safari.py | Python | apache-2.0 | 1,120 | [
"VisIt"
] | b6f7666a18985957fba52909ba906213e18f52b00feb3a4e9973fa2bd21cd577 |
# -*- coding: utf-8 -*-
#
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as pu... | thica/ORCA-Remote | src/ORCA/scripttemplates/Template_Discover_Scan.py | Python | gpl-3.0 | 8,118 | [
"ORCA"
] | 6437d5bdf31afb8dc26411542d4a586c6dbf99c747e7f3ac4fb42ec47288ed51 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2011 by Paweł T. Jochym <pawel.jochym@ifj.edu.pl>
#
# This file is part of Elastic.
# Elastic 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... | jochym/Elastic | examples/example1.py | Python | gpl-3.0 | 2,896 | [
"ASE",
"CRYSTAL",
"VASP"
] | 61e7bd801b999f7e8679b7c30daa6f76d5b03ed51bd7e7ce6331edb7c0aecd07 |
# -*- coding: utf-8 -*-
##############################################################################
#
# Copyright (C) 2019 Compassion CH (http://www.compassion.ch)
# @author: Emanuel Cino <ecino@compassion.ch>
#
# The licence is in the file __manifest__.py
#
#################################################... | ecino/compassion-switzerland | website_event_compassion/models/privacy_statement.py | Python | agpl-3.0 | 636 | [
"VisIt"
] | 24432d677bbebe64cf8a3d967854ef9784c322e00bd698657cdc806aaf2b87b2 |
def load_data(input_path, n):
"""TODO: Docstring for load_data.
:returns: TODO
"""
X, y = [], []
all_files = [x for x in os.listdir(input_path) if x[0] != '.']
temp = set([re.sub('(^\.h$)|(^\.cc$)|(^\.c$)', '.cpp', os.path.splitext(x)[1]) \
for x in... | ShiehShieh/Code_Identifier | draft.py | Python | mit | 2,173 | [
"NEURON"
] | 3f903b19e997ae3e1d444acc6747db4289a562f8b80429f33e7ee31c780a800c |
# -*- Mode:Python; indent-tabs-mode:nil; tab-width:4 -*-
#
# Copyright (C) 2019-2020 Canonical Ltd
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 3 as
# published by the Free Software Foundation.
#
# This program is distributed in ... | snapcore/snapcraft | tests/unit/plugins/v1/test_colcon.py | Python | gpl-3.0 | 47,510 | [
"CRYSTAL"
] | 09686c87c115fd875fcf233397ebcc5e5eaf0f7637a0999613e1f836487bb911 |
"""
brownian() implements two-dimensional Brownian motion (i.e. the Wiener process).
"""
import numpy as np
from ddm.core._numba import numba
import inspect
from ddm.video.base_reader import IterReader
from ddm.video.util import Video
import math
# @numba.vectorize(["float64(float64,float64,float64)"])
# def bounce(x... | andrej5elin/ddm | ddm/sim/brownian.py | Python | gpl-3.0 | 6,999 | [
"Gaussian"
] | 34e11bcaffb9bdb051fbeeefe19d00e8a6b38634d73c734a1f98c58c986d61cd |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/qcdb/interface_dftd3.py | Python | lgpl-3.0 | 12,114 | [
"Psi4",
"TURBOMOLE"
] | f603a43ec511a6f8c2ea2f3c5c2668317bbdd6af8e070c95ab15c4b77bc370d9 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2008 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Softw... | andrebellafronte/stoq | stoqlib/importers/stoqlibexamples.py | Python | gpl-2.0 | 3,414 | [
"VisIt"
] | bca78c025a6a1057483d115824546b8f934061f825527bf2dd493ec59474ad8a |
# coding: utf-8
import logging
import re
import urllib
from urlparse import urljoin
from django.conf import settings
from django.contrib.syndication.views import Feed
from django.http import HttpResponse, Http404, HttpResponseRedirect, HttpResponsePermanentRedirect
from django.template import loader
from django.utils... | rhymeswithcycle/openparliament | parliament/search/views.py | Python | agpl-3.0 | 7,510 | [
"VisIt"
] | 48ee7a2422202db797a7afa4a31f9278f1762a67e96f07eec9661d6e4b240f55 |
'''
simple middleware and context processor for session-based messaging with types
Heavily inspired by patches on ticket 4604. Differs in that in this a notification
has type.
Installation:
add notifications.Notification to MIDDLEWARE_CLASSES
and notifications.notifications to TEMPLATE_CONTEXT_PROCESSORS
That assumes... | brew/fruitynutters | webapps/fruitynutters/notifications.py | Python | mit | 4,841 | [
"exciting"
] | d5c26abf443c3fe1ee06e3bd64a80a0fdc9809c5d5bd2063e3df5b0760f6a1a8 |
#! /usr/bin/env python
#Protein amino acid composition analysis = Paacman
#Version 1.0 (released 5/22/2017 by Patrick Erickson)
#Please visit the Paacman Github repository to view the legal license before using
#Paacman: https://github.com/kay-lab/Paacman
#This python script will analyze the .txt files containing de... | kay-lab/Paacman | Paacman.py | Python | mit | 40,947 | [
"VisIt"
] | f82a0b81b53c4296163399407ac2f157fb6ba5767bcde3623deab39b799a0526 |
#!/usr/bin/env python
# $Id$
# -*- coding: utf-8
'''
test libcint
'''
__author__ = "Qiming Sun <osirpt.sun@gmail.com>"
import sys
import os
import ctypes
import numpy
_cint = numpy.ctypeslib.load_library('libcint', os.path.abspath(os.path.join(__file__, '../../build')))
PTR_LIGHT_SPEED = 0
PTR_COMMON_ORIG =... | sunqm/libcint | testsuite/test_cint4c1e.py | Python | bsd-2-clause | 7,040 | [
"PySCF"
] | ddcc89088f76e25b7bb8304db0dd5ea331bdeb74c3f11f9cb19496a255991df7 |
"""Testing for kernels for Gaussian processes."""
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# License: BSD 3 clause
import pytest
import numpy as np
from sklearn.utils.fixes import signature
from sklearn.gaussian_process.kernels import _approx_fprime
from sklearn.metrics.pairwise \
import PAIR... | vortex-ape/scikit-learn | sklearn/gaussian_process/tests/test_kernels.py | Python | bsd-3-clause | 12,610 | [
"Gaussian"
] | 9fedb2726961c11f92901dbf329e799b65e7206f580b9c0f1e09e42c70829338 |
"""
Migration script to modify the 'notify' field in the 'request' table from a boolean
to a JSONType
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
from sqlalchemy.exc import *
from galaxy.model.custom_types import *
from galaxy.util.json import loads,... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0057_request_notify.py | Python | gpl-3.0 | 2,080 | [
"Galaxy"
] | bc8d702b2235182143913b3d330393720f76aeb1452a7cd18d50e0ba2bcb45f4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import json
from pymatgen.core.structure import Molecule
from pymatgen.io.nwchem import NwTask, NwInput, NwInputError, NwOutput
"""... | nisse3000/pymatgen | pymatgen/io/tests/test_nwchem.py | Python | mit | 13,939 | [
"NWChem",
"pymatgen"
] | 097640faa5ef4e80a7108f4f0b538e7ce53d0f224597f3e8fc3798a908472f50 |
#!/usr/bin/env python
from unittest import TestCase
from bson import dumps, loads
class TestBinary(TestCase):
def setUp(self):
lyrics = b"""
I've Had Enough - Earth Wind and Fire
Getting down, there's
a party in motion
Everybody's on the scene
And I can hear the s... | martinkou/bson | bson/tests/test_binary.py | Python | bsd-3-clause | 1,820 | [
"CRYSTAL"
] | 8f819cbb4d00c23e063dae037a0f3fd307260a7f354d9cfc24202a10213975b2 |
from abc import ABCMeta, abstractmethod
import logging
import traceback
from cis.exceptions import FileFormatError
from cis.data_io.aeronet import get_aeronet_file_variables
from cis.data_io.hdf import get_hdf4_file_variables
from cis.data_io.netcdf import get_netcdf_file_variables, remove_variables_with_non_spatiotemp... | zak-k/cis | cis/data_io/products/AProduct.py | Python | gpl-3.0 | 13,762 | [
"NetCDF"
] | 38f09e509bc821b45f8169f33c585195ec9a09a1540ac81e78c9c48738c79575 |
"""A component to manage an implicit plane widget.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Instance, Bool, Property
from traitsui.api import View, Group, Item, InstanceEditor
from tvtk.api ... | dmsurti/mayavi | mayavi/components/implicit_plane.py | Python | bsd-3-clause | 6,933 | [
"Mayavi",
"VTK"
] | ccb3929fb80ed2511f1b41b678188015a09a76e15e76b0769bf436a438ba3f36 |
#!/usr/bin/env python
"""
SYNOPSIS
wrf2icar.py [-h] [--verbose] [-v, --version] <filename>
DESCRIPTION
Convert a WRF output file into a slightly smaller ICAR input file
assumes a common set of variable names. If these need to be changed
e.g. for a new version of WRF, edit the list of names ... | NCAR/icar | helpers/wrf/wrf2icar.py | Python | mit | 6,786 | [
"NetCDF"
] | 7f26c6b3526f704c2f4c16305d998ccd2c537f3a4de83b9f02db565b878fe492 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2012 Doug Blank
# Copyright (C) 2013 John Ralls <jralls@ceridwen.us>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the... | pmghalvorsen/gramps_branch | gramps/gen/const.py | Python | gpl-2.0 | 10,384 | [
"Brian"
] | fecdf91cce391b6d1ddfec25e535b81e513722301a40d28c0a005f20994aea70 |
"""
Tests for ConvMolFeaturizer.
"""
import unittest
import os
import numpy as np
import pytest
from deepchem.feat.graph_features import ConvMolFeaturizer, AtomicConvFeaturizer
class TestConvMolFeaturizer(unittest.TestCase):
"""
Test ConvMolFeaturizer featurizes properly.
"""
def test_carbon_nitrogen(self):... | lilleswing/deepchem | deepchem/feat/tests/test_graph_features.py | Python | mit | 4,816 | [
"RDKit"
] | 55a1efd50b960b0ca47d201eb302d3ad9b1c8d5973c94eedd81cb969453eba57 |
# -*- coding: utf-8 -*-
"""
Create an initial ATP Profile for an ECs Mesh and write it out as .vtp.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Import path for the GenerateATPMap script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__... | BlueFern/DBiharMesher | meshes/c4080ang/syn/Generate4080ATPMapV2.py | Python | gpl-2.0 | 1,273 | [
"VTK"
] | 1d420d9d945515a0cfbdfe2be7c29a1cf3b1bd233df5f140f1c3b5fffb31a95c |
import os
import sys
import json
import random
from random import randint
from time import sleep
from crawler import *
# These constants are used by the application to randomily pick a number
# in between on of these ranges.
MIN_PAGE_VIEW_SLEEP = 1
MAX_PAGE_VIEW_SLEEP = 240
AVG_PAGE_VIEW_SLEEP = 120
class Simulated... | bartmika/py-autobrowserbot | simulatedbrowser.py | Python | mit | 3,673 | [
"VisIt"
] | b4583ece2fbac6007a607941cc90a0e968c13a1bf32fd029acf013222c605ed4 |
import sys
from py._code.code import FormattedExcinfo
import py
import pytest
import warnings
import inspect
import _pytest
from _pytest._code.code import TerminalRepr
from _pytest.compat import (
NOTSET, exc_clear, _format_args,
getfslineno, get_real_func,
is_generator, isclass, getimfunc,
getlocati... | razvanc-r/godot-python | tests/bindings/lib/_pytest/fixtures.py | Python | mit | 44,841 | [
"VisIt"
] | 5055f898031fd10b919aabca5c8d215ee3faf388fdb493faa7d8fc12a5b210fc |
#!/usr/bin/env python2
import numpy as np
import pandas as pd
from mdtraj import Trajectory
from mdtraj import Topology
from mdtraj import element
from mdtraj.geometry import distance
from top_manip import typed_elementwise_rep
mapping_options = {}
def mode_rows(a):
"""Efficiently returns the most common row of a... | uchicago-voth/cgmap | src/cgmap.py | Python | apache-2.0 | 27,837 | [
"MDTraj"
] | e9d07677a2f61e9f8b62e4a1f87afad0e3ba61f76d4864222ffd1cdf3cae8949 |
#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2009-2011 by the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of thi... | faribas/RMG-Py | rmgpy/constants.py | Python | mit | 6,433 | [
"Avogadro"
] | f47c2c145affebe1367e6f0ff09b0c53c4b1eb65a6e79394cc56ab939949434f |
""" ResourceStatusHandler
Module that allows users to access the ResourceStatusDB remotely.
"""
from DIRAC import gLogger, S_OK
from DIRAC.Core.DISET.RequestHandler import RequestHandler, getServiceOption
from DIRAC.Core.Utilities.ObjectLoader import ObjectLoader
def convert(table, params):
"""Conversion util... | ic-hep/DIRAC | src/DIRAC/ResourceStatusSystem/Service/ResourceStatusHandler.py | Python | gpl-3.0 | 8,543 | [
"DIRAC"
] | 0ec2a745fc9e2f9cb81c9f5c778b14128ce2ebd4f10335b656270acddccff40a |
from ovito import *
from ovito.io import *
from ovito.modifiers import *
import numpy as np
node = import_file("../../files/CFG/shear.void.120.cfg")
node.add_to_scene()
node.modifiers.append(SliceModifier(
distance = -12,
inverse = True,
slice_width = 18.0
))
node.modifiers.append(SliceModifier(
dist... | srinath-chakravarthy/ovito | tests/scripts/test_suite/cluster_analysis_modifier.py | Python | gpl-3.0 | 1,067 | [
"OVITO"
] | 993df3dc81a7937065113999607014b047454df48b2274fd15716b04abb040fa |
#!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# 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,... | govarguz/espressopp | bench/polymer_melt/espressopp/espressopp_polymer_melt.py | Python | gpl-3.0 | 6,057 | [
"ESPResSo",
"Gromacs",
"LAMMPS"
] | 03bcd643db1702ec5e42323d481f4c77b6271d9c2f0386b91495470ddb800739 |
""" SingularityCE is a type of "inner" CEs
(meaning it's used by a jobAgent inside a pilot).
A computing element class using singularity containers,
where Singularity is supposed to be found on the WN.
The goal of this CE is to start the job in the container set by
the "ContainerRoot" config option... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/SingularityComputingElement.py | Python | gpl-3.0 | 18,099 | [
"DIRAC"
] | 93fd81fdb03c92fc7b4855cc6e1749916000cdcc34288475fdf2192b5d6f0440 |
#!/usr/bin/env python
################################################################################
##
## substructure_molecular_attributes.py
## Author: Satoshi Takahama (satoshi.takahama@epfl.ch)
## Nov. 2014
##
## -----------------------------------------------------------------------------
##
## This file is pa... | stakahama/aprl-ssp | substructure_molecular_attributes.py | Python | gpl-3.0 | 3,010 | [
"Pybel"
] | 25e5bf471fb5f66739c7574545f8d91d6a644b29b104fee5614ce0ef4958adf0 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-show-task-queues
# Author : Ricardo Graciani
########################################################################
"""
Show details of currently active Task Queues
"""
from __future__ import pri... | fstagni/DIRAC | WorkloadManagementSystem/scripts/dirac-admin-show-task-queues.py | Python | gpl-3.0 | 2,817 | [
"DIRAC"
] | 368cb8c8141c62a8064e6fad381493ac0e98a45976809c5fd5e0919e8b7162c6 |
# Author: Artem Pulkin
"""
This and other `_slow` modules implement the time-dependent Hartree-Fock procedure. The primary performance drawback is
that, unlike other 'fast' routines with an implicit construction of the eigenvalue problem, these modules construct
TDHF matrices explicitly via an AO-MO transformation, i.... | gkc1000/pyscf | pyscf/pbc/tdscf/krhf_slow.py | Python | apache-2.0 | 13,478 | [
"PySCF"
] | d4926316639410522dce0d7b298d97cd72f8ed6cb2d68ac09f78ad3fc0885b40 |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser Gen... | jchodera/cclib | src/cclib/method/population.py | Python | lgpl-2.1 | 3,285 | [
"cclib"
] | ce923dae799d6d69f0fa927de8113b1f2fa3dcc5245e7ac58cd6cf310cb90fbd |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
# Copyright (C) 2014 Free and Open Source Software Learning Centre
# http://fosslc.org
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published b... | Freeseer/freeseer | src/freeseer/frontend/configtool/PluginWidget.py | Python | gpl-3.0 | 4,750 | [
"VisIt"
] | c19fccea6d09ff9e5abc8502e83cc082082e9dd79dd55f3cc632ea315717a183 |
# Copyright (c) 2009-2010 Six Apart Ltd.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice,
# this list of conditions an... | saymedia/batchhttp | tests/client_with.py | Python | bsd-3-clause | 3,423 | [
"MOOSE"
] | 110cae26bc4af80a76e7a98074c7c90731e7cc076cc1a7e7dc01f866bedf5cea |
# python3
# Copyright 2018 DeepMind Technologies Limited. 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 re... | deepmind/acme | acme/agents/tf/d4pg/agent.py | Python | apache-2.0 | 13,956 | [
"Gaussian"
] | 6f11eeead49c7671457a05b7415a1a5ecda13a8dd1a0fc16ad109630476a82aa |
#
# co_co_equations_only_for_init_values.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, o... | kperun/nestml | pynestml/cocos/co_co_equations_only_for_init_values.py | Python | gpl-2.0 | 2,654 | [
"NEURON"
] | 641f314766ac96c73ced02cddcd78235f082f4d26ba1e7ffbc6d98b58ae4a2a2 |
# 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... | theflofly/tensorflow | tensorflow/python/autograph/converters/control_flow.py | Python | apache-2.0 | 18,448 | [
"VisIt"
] | 5f55a8b6e443aeadae5b80cdbe3370466603bab3ac2d7f9a2600aa84bb0c8abd |
#!/usr/bin/env python
# -*- c-file-style: "sourcery" -*-
#
# Use and distribution of this software and its source code is governed
# by the terms and conditions defined in the "LICENSE" file that is part
# of this source code package.
#
"""
UNDER CONSTRUCTION: Driver for training the covariate shift detector on the com... | paolodedios/shift-detect | src/main/python/shift_detect/driver.py | Python | mpl-2.0 | 4,737 | [
"Gaussian"
] | 08c2efb270136f40c3492b83bb588d73345fe2f617584eeb4bfc891802f1be22 |
from __future__ import unicode_literals
from .. import Provider as PersonProvider
class Provider(PersonProvider):
formats_female = (
'{{first_name_female}} {{last_name}}',
'{{first_name_female}} {{last_name}}',
'{{first_name_female}} {{last_name}}',
'{{first_name_female}} {{last_na... | thedrow/faker | faker/providers/person/en/__init__.py | Python | mit | 86,768 | [
"Amber",
"Brian",
"COLUMBUS",
"CRYSTAL",
"Dalton",
"Desmond",
"MOE"
] | c032da144a6035235b4b2d67d9c5ea05cae013ae9b27ce2e2a89ec0cbb2821a1 |
"""PyMorph [Py MOrphological Parameters' Hunter], is a pipeline to find the Morphological parameters of galaxy. Authors: Vinu Vikram , Yogesh Wadadekar, Ajit K. Kembhavi. 2008 Feb, Alan Meert 2010"""
import os
import sys
import time
import csv
import traceback
import argparse
import fitsio
import numpy as np
import r... | vvinuv/pymorph | pymorph/pymorph.py | Python | gpl-2.0 | 32,954 | [
"Galaxy"
] | a76dbc01ad8ab935cc0561cf0d48b3040f2c3bb63edb0a516125ffecb51fd0e1 |
# 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... | DCSaunders/tensorflow | tensorflow/contrib/factorization/python/ops/gmm_ops.py | Python | apache-2.0 | 18,624 | [
"Gaussian"
] | 0b65a83d1222b409723be659c71b3316bea3d5c4ae281a84375a91d417c1555b |
# Run Bowtie on cells
import multiprocessing as mp
import numpy as np
import os
import sys
import getopt
import itertools
index=''
fldir=''
num_proc=1
out_base=''
try:
opts, args = getopt.getopt(sys.argv[1:],"i:o:n:r:",["idir=","odir=","njobs=","ref-index-path="])
except getopt.GetoptError:
print ("getopterr... | govinda-kamath/clustering_on_transcript_compatibility_counts | Zeisel_pipeline/run_bowtie.py | Python | mit | 1,651 | [
"Bowtie"
] | d8af31e20f5840b52966ee860f8ac63ac4c1cf54084925daa70b63986117d8cd |
# -*- coding: utf-8 -*-
"""
Provides classes for parsing exported data of Hatena diary.
This module has two classes.
One is support for Movable Type format,
the other is support XML a.k.a. Hatena Diary format.
Developed for MovableType format, but it has many bugs of convering
hyperlink and footnote and more. Then re... | mkouhei/hatena2rest | src/hatena2rest/processing.py | Python | gpl-3.0 | 3,215 | [
"TINKER"
] | 86bde2a9a5647aa4d4c70803e3fd20c20ccfd0cd3fc9bffcd5252aca6baa1be0 |
__author__ = "Rick Sherman, Nitin Kumar"
__credits__ = "Jeremy Schulman"
import unittest2 as unittest
from nose.plugins.attrib import attr
from mock import MagicMock, patch, mock_open
import os
from lxml import etree
import sys
import json
from ncclient.manager import Manager, make_device_handler
from ncclient.transp... | spidercensus/py-junos-eznc | tests/unit/test_device.py | Python | apache-2.0 | 29,022 | [
"Firefly"
] | 6a189fd119ea2eb6206e208240968c401fa52329419ba7ab890f954e1c4d2740 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2006, 2007, 2008, 2009, 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,... | CERNDocumentServer/invenio | modules/websubmit/lib/websubmitadmin_templates.py | Python | gpl-2.0 | 182,328 | [
"VisIt"
] | cba5c5be5c0d0b52a018fab2ed5bc404258c1e6afc4d79cd81cca4e7f4ee4bf1 |
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