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#!/usr/bin/env python
'''
Republish a single object selected based on persistance.
Use standard ROS message types (Float32MultiArray for now)
'''
from __future__ import division
from optparse import OptionParser
import roslib
import rospy
import numpy as np
from std_msgs.msg import Float32MultiArray
from multi_tracker... | florisvb/multi_tracker | nodes/republish_pref_obj_data.py | Python | mit | 5,548 | [
"Firefly"
] | 9a896ae0c84ebd6e1b2e8d5b0dd86ec22edea95b9afecf2711b90841038a61bb |
#
# 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... | shaneknapp/spark | python/pyspark/pandas/generic.py | Python | apache-2.0 | 105,985 | [
"Elk"
] | 2e35da6df574016536d8deebcfc895f37338b3b3c9d135b81caae11da0c03bbf |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/transformations/positionaveraging.py | Python | gpl-2.0 | 7,900 | [
"MDAnalysis"
] | 623634579c65b25641ffb9c81b292664887a15f643e1334f50dc372ff49e4d2b |
"""
===========
gaussfitter
===========
.. codeauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com> 3/17/08
Latest version available at <https://github.com/keflavich/gaussfitter>, where
it was moved from google code on January 30, 2014
"""
from __future__ import print_function, division, absolute_import
import numpy a... | scienceopen/gaussfitter | gaussfitter/gaussfitter.py | Python | bsd-3-clause | 25,442 | [
"Gaussian"
] | b626913502c0b4f5d018c61a43635f0b3b9c6ba4526f2adc9d0fae69de5c642b |
r"""
Description: Generates 2-D data maps from OpenFoam data saved by paraview
as a CSV file. The data has to be saved as point data and the following fields
are expected p, points:0->2, u:0->2. An aperture map is the second main input
and is used to generate the interpolation coordinates as well as convert
the flow ve... | stadelmanma/netl-AP_MAP_FLOW | apmapflow/scripts/apm_process_paraview_data.py | Python | gpl-3.0 | 6,758 | [
"ParaView"
] | e08209f7d386c82cf08d5eac1bf08b8c946fb549450e088b4d0e533551b729a5 |
# 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
from twilio.rest import Client
# Your Account Sid and Auth Token from twilio.com/user/account
account = "ACXXXXXXXXXXXXXXXXXXXXX... | teoreteetik/api-snippets | notifications/rest/services/retrieve-service/retrieve-service.6.x.py | Python | mit | 491 | [
"VisIt"
] | a338c971ea4e68f8ec2e105cfe422e4d9aa75e6f846e962eb3f0f6a082fde0be |
# Copyright 2004 by Frank Kauff and Cymon J. Cox. 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.
"""
Parser for ACE files output by PHRAP.
Written by Frank Kauff (fkauff@duke.e... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/Sequencing/Ace.py | Python | mit | 17,793 | [
"Biopython"
] | ccdffa4ede639cb784903746616a6d0e597a3942a73cc033bcc602ebaf4df237 |
# coding: utf-8
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..utils import (
ExtractorError,
float_or_none,
int_or_none,
parse_duration,
parse_iso8601,
remove_end,
unescapeHTML,
)
from ..compat import (
compat_etree_fromstring,
compat_HT... | lzambella/Qyoutube-dl | youtube_dl/extractor/bbc.py | Python | gpl-3.0 | 41,565 | [
"VisIt"
] | 87e49b62bdb022601ec8c2241abf9bdfd9487f39e5a92753285e919cc1c8650d |
"""PyBdEcho.py
The PyBoard 'Echo' audio capture/playback demonstration code.
https://github.com/alanbchristie/PyBdEcho
Refer to project's LICENCE.txt for licence restrictions.
v1.0.1 was presented at EuroPython, Rimini, July 2017.
This application is designed to run on the MicroPython PyBoard and
was developed usi... | alanbchristie/PyBdEcho | PyBdEcho.py | Python | mit | 42,973 | [
"Amber"
] | 47a1297264a4d23ef1f2253cd5337ed749140a9cf309d5b2e9179aca0cb8f854 |
# Copyright (c) 2021 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""
Custom flake8 plugin to catch MetPy-specific bad style/practice.
Currently this only looks for multiplication or division by units, since that can break
masked arrays and is slo... | dopplershift/MetPy | tools/flake8-metpy/flake8_metpy.py | Python | bsd-3-clause | 2,533 | [
"VisIt"
] | 843a2600c85a7dba4f6dbf0e3e3053f208e403def353e0f20c49676109d14f42 |
# (C) British Crown Copyright 2014 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | mo-g/iris | docs/iris/example_tests/test_orca_projection.py | Python | gpl-3.0 | 1,349 | [
"ORCA"
] | 1a39c4e76454937a6d6ccc87e059677a86f71b065e962d319007e751fe7775ee |
"""
Module for gradients of the cost function in parameter estimation
See https://www.dropbox.com/s/k9qlgn0pd6wtqlw/LSE_Gradient.pdf?dl=0
for a bunch of equations that summarize most of the functions below
@author Siddharth Reddy <sgr45@cornell.edu>
"""
from __future__ import division
import logging
import numpy a... | rddy/lentil | lentil/grad.py | Python | apache-2.0 | 129,711 | [
"Gaussian"
] | 6d8d01fd30d27522c5e14912c777ba5135d911eb7f18089b9343fe924c43efca |
# -*- coding: utf-8 -*-
@auth.requires_membership('lekarz')
def index():
redirect('wizyty')
@auth.requires_membership('lekarz')
def wizyty():
# |
db.visit.id_patient.writable = db.visit.id_doctor.writable = db.visit.visit_day.writable = db.visit.visit_hour.writable = False
grid = SQLFORM.grid(
... | alatar-/iwm-project | controllers/lekarz.py | Python | mit | 2,076 | [
"VisIt"
] | 9a2157b5865b5becc17edb7a817e4a44f5b647ea6e77bd5e68c99f9d810c08f4 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | TheTimmy/spack | var/spack/repos/builtin/packages/openbabel/package.py | Python | lgpl-2.1 | 3,329 | [
"Open Babel",
"Pybel"
] | 30335ac02efbaa233587c19847390adecfb4784e33718db975737c5304ccb4cc |
from __future__ import print_function
import unittest
from os import path
from shyft import shyftdata_dir
from shyft import api
from shyft.repository.netcdf.concat_data_repository import ConcatDataRepository
#from shyft.repository.netcdf.concant_data_repository import ConcatDataRepositoryError
from shapely.geometry im... | jfburkhart/shyft | shyft/tests/test_concat_data_repository.py | Python | lgpl-3.0 | 7,312 | [
"NetCDF"
] | 61759fa4278ee54548d4c1d9cc931beab7bf3a206c3c003118b209f8f705d435 |
"""
End-to-end tests for w2ui of biz feature
"""
from datetime import datetime
import pytz
from bok_choy.web_app_test import WebAppTest
from nose.plugins.attrib import attr
from common.test.acceptance.pages.biz.ga_contract import BizContractDetailPage, BizContractPage
from . import AGGREGATOR_USER_INFO, GaccoBizTest... | nttks/edx-platform | common/test/acceptance/tests/biz/test_ga_w2ui.py | Python | agpl-3.0 | 15,111 | [
"VisIt"
] | c0f215e337acfdeb705cccfb4bf75dd4cd10144bb2cb754ee4b95766434b59bb |
"""Identify program versions used for analysis, reporting in structured table.
Catalogs the full list of programs used in analysis, enabling reproduction of
results and tracking of provenance in output files.
"""
from __future__ import print_function
import os
import contextlib
import subprocess
import sys
import yaml... | lbeltrame/bcbio-nextgen | bcbio/provenance/programs.py | Python | mit | 11,876 | [
"BWA",
"Bioconductor",
"Galaxy",
"HTSeq"
] | 962033358b1bdad78ca6c9d9d42b0c04e4657fd2be2f31433070f0fbd2d0dba0 |
from .location import Location
from .syntax_tree import Node
class Terminal(Node):
__slots__ = ('value', 'location', 'annotations')
def __init__(self, value, *location):
self.location = Location(*location)
self.value = value
self.annotations = []
def __repr__(self):
return "<{0.__class__.__name__} '{0.value... | jdavidls/uScript | uscript/model/source/lexicon.py | Python | cc0-1.0 | 1,939 | [
"VisIt"
] | 1a55352fa008e070f294f24b2e4224b5a1e1e6f886c9689b8672fab407e256ab |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import logging
import numpy as np
import scipy
from scipy import stats
from pymatgen.analysis.defects.core import DefectCorrection
from pymatgen.analysis.defects.utils import ang_to_bohr, hart_to_ev, eV_to_k, \... | dongsenfo/pymatgen | pymatgen/analysis/defects/corrections.py | Python | mit | 37,740 | [
"VASP",
"pymatgen"
] | 495509387ce92a578dec9e11c24df67fbdb770595d83a3e5fad82bbae9e0695c |
#-------------------------------------------------------------------------------
# Copyright (c) 2013 Gael Honorez.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0
# which accompanies this distribution, and is available at
# htt... | IDragonfire/modular-client | src/galacticWar/options/options.py | Python | gpl-3.0 | 7,180 | [
"Galaxy"
] | 8cc29cff6656d68877bd17560be12bbaf1f204f0d5e3d9d1ea77827294bc7c4d |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth import logout, authen... | jbzdak/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 95,668 | [
"VisIt"
] | 4b844d0b6b315aac99d17de248c885f3d921517e8eeaf952f4b9705693416a48 |
#!/usr/bin/env python
# Testing the new parallel scanner class
import os
backupdir = os.getcwd()
import numpy as np
import pysces
tbox = pysces.PyscesUtils.TimerBox()
import time
m = pysces.model('isola2a')
ser = pysces.Scanner(m)
print("Serial execution...")
print("Start: ", tbox.normal_timer('SER'))
print(next... | bgoli/pysces | pysces/examples/testparscanner.py | Python | bsd-3-clause | 2,904 | [
"PySCeS"
] | f6750aeecc5171c7016852bf5b22e1c88c93ce26d0d97d8102c4f041e08e0731 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/admin/object_admin.py | Python | gpl-2.0 | 29,892 | [
"VisIt"
] | 5b76789966dca9f0fa23b25426a83835f096d04b83a32fa1d8a5cbb21c04aa61 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/peacock_app/PeacockApp/test_PeacockApp.py | Python | lgpl-2.1 | 11,579 | [
"MOOSE"
] | 4794c6b69dd200093487d87b5c185e737357e0f40c528543eae5ce784c314028 |
"""
Copyright (c) 2012-2013, Nicolas Kuttler.
All rights reserved.
License: BSD, see LICENSE for details
Source and development at https://github.com/piwik/piwik-python-api
"""
from piwikapi.analytics import PiwikAnalytics
class PiwikGoals(PiwikAnalytics):
def __init__(self, api_url):
"""
Initi... | piwik/piwik-python-api | piwikapi/plugins/goals.py | Python | bsd-3-clause | 2,312 | [
"VisIt"
] | 428961f2fb37b8fa1e8a840630ffc3deeeb8b4e588cfc9d1d2a7d8d766b0d744 |
#! /usr/bin/env python
"""
This programs performs a geometry optimization on the anion of a closed-shell
molecule with cp2k using generic settings: DFT/PBE.
Note that is mandatory to define a cell_parameter, and a xyz structure.
If you have a restart file, a basis set and you can also define it in the command line.
I... | felipeZ/nonAdiabaticCoupling | scripts/qmflows/opt_anion_cp2k.py | Python | mit | 2,754 | [
"CP2K"
] | 3e248dc1917256438baa1edd5fa26c65f4c01453ff214cbe3bbf8b12c492326c |
"""
============================================
K-fold cross-validation for model comparison
============================================
Different models of diffusion MRI can be compared based on their accuracy in
fitting the diffusion signal. Here, we demonstrate this by comparing two
models: the diffusion tensor ... | nilgoyyou/dipy | doc/examples/kfold_xval.py | Python | bsd-3-clause | 5,622 | [
"Gaussian"
] | 89a60e0656272335bc8389b09444b758edd7f4f48d39f153f952c037683b9526 |
#!/usr/bin/env python3
"""
This script is a python version of TimingAccuracyGLQ. We use numpy functions to
simplify the creation of random coefficients.
"""
import time
import numpy as np
from pyshtools import expand
from pyshtools import spectralanalysis
# ==== MAIN FUNCTION ====
def main():
TimingAccuracyGLQ()... | SHTOOLS/SHTOOLS | examples/python/TimingAccuracy/TimingAccuracyGLQ.py | Python | bsd-3-clause | 2,851 | [
"Gaussian"
] | aea262f3e94f64c17a7c77d040c0440109604ee183bf7b75c4896f918447650e |
# -----------------------------------------------------------------------
# Copyright: 2010-2022, imec Vision Lab, University of Antwerp
# 2013-2022, CWI, Amsterdam
#
# Contact: astra@astra-toolbox.com
# Website: http://www.astra-toolbox.com/
#
# This file is part of the ASTRA Toolbox.
#
#
# The ASTRA Toolbo... | astra-toolbox/astra-toolbox | samples/python/s014_FBP.py | Python | gpl-3.0 | 2,476 | [
"Gaussian"
] | cdda6bd4089cf60b75127120370cc55c2221b4e50925ff2d3a55fd2313d924ae |
import serial
import inspect
import time
import itertools
from util import two_byte_iter_to_str, to_two_bytes
# Message command bytes - straight from Firmata.h
DIGITAL_MESSAGE = 0x90 # send data for a digital pin
ANALOG_MESSAGE = 0xE0 # send data for an analog pin (or PWM)
DIGITAL_PULSE = 0x91 # SysE... | e430doug/SoilProject | pyfirmata/pyfirmata.py | Python | bsd-2-clause | 18,750 | [
"CRYSTAL"
] | 1406c7a96f7a19f14523808c0b089a53e6e9eec5e7a2602330a033b8ec3b288f |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2011 ~ 2012 Deepin, Inc.
# 2011 ~ 2012 Wang Yong
#
# Author: Wang Yong <lazycat.manatee@gmail.com>
# Maintainer: Wang Yong <lazycat.manatee@gmail.com>
# Zhai Xiang <zhaixiang@linuxdeepin.com>
#
# This program is free software:... | linuxdeepin/deepin-ui | dtk/ui/titlebar.py | Python | gpl-3.0 | 9,037 | [
"Gaussian"
] | e2860ba287a7458a56cf0cddc897511ed2e09bf26f18e3d5f3dcc6dc6bec92ae |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2005-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
#
# 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; ... | beernarrd/gramps | gramps/gui/dbloader.py | Python | gpl-2.0 | 21,742 | [
"Brian"
] | 6165cacf7b7b1f9b324797df4dd5c38183712e7b19be2c73b8fc4bdcc3b7e5af |
'''
This module contains database routines that may be accessed with or without using a web framework. All use SQLObject; this
adds a bit of overhead, but provides nice exception management.
The connection object is set locally based on parameters in the projectSpecs import. We're using MySQL. The database
schema i... | pbarton666/buzz_bot | djangoproj/djangoapp/crawler/b_dbRoutines.py | Python | mit | 31,285 | [
"VisIt"
] | ea3f3d1b9e97636985f5cc261685d0d7550a4f4fb3dcdc0334388bfbce013248 |
#!/usr/bin/env python
import tables as tb
import numpy as np
import argparse
import sys
def find_multichain_terms(ids, chain_starts):
assert len(ids.shape) == 2
chain_starts = np.array(chain_starts, dtype='i')
assert len(chain_starts.shape) == 1
chain_num = (ids[:][:,:,None] >= chain_starts[None,None,:... | John-Jumper/Upside-MD | py/ugly_hack_break_chain.py | Python | gpl-2.0 | 7,803 | [
"Gaussian"
] | f657604598e4548b484dba7733021211123267ad94a1f7cc9899cdb58715673b |
"""
this pipeline quantify expression level of both host and virus
"""
#============= import required packages =================
import sys,os
sys.path.append('/home/shangzhong/Codes/Pipeline')
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0) # disable buffer
from Modules.f00_Message import Message
from Modules.p0... | shl198/Pipeline | DetectVirus/01_DetectVirus.py | Python | mit | 10,474 | [
"BLAST"
] | d9f517767fdf8a8f736fa754cd8ce8a8bf4fc0656e44ef87ee945fb88fca00fc |
#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina"]
__license__ = "GPL"
__version__ = "1.8.0-dev"
__maintainer__ = "Greg Caporaso"
__email__ = "g... | wasade/qiime | scripts/parallel_align_seqs_pynast.py | Python | gpl-2.0 | 5,080 | [
"BLAST"
] | d2ccbb0dd1d9964745d943754b16ba834e47b88f6d5fa6a66f5d31ad023ab3f0 |
#!/usr/bin/python
# vim: et sw=4 ts=4:
# -*- coding: utf-8 -*-
#
# Piwik - free/libre analytics platform
#
# @link http://piwik.org
# @license http://www.gnu.org/licenses/gpl-3.0.html GPL v3 or later
# @version $Id$
#
# For more info see: http://piwik.org/log-analytics/ and http://piwik.org/docs/log-analytics-tool-how-... | sunwooz/blogcog-piwik | vendor/piwik/piwik/misc/log-analytics/import_logs.py | Python | mit | 85,429 | [
"VisIt"
] | e60836606f92a55b102492342700c3c4b754580174cb22ec8c0ad0d57df9df35 |
#!/usr/bin/env python
# Small python wrapper that passes the xml commands to the HTS-barcode-checker script
# This requires the HTS-barcode-checker script to be present in the $PATH variable
# import the used modules
import sys, os
from subprocess import call
# set the directory for a new CITES database file if the ... | naturalis/HTS-barcode-checker | galaxy/HTS-barcode-checker.py | Python | bsd-3-clause | 835 | [
"Galaxy"
] | fe429a3648ef76fbf7215f44671519c5ba36abc1639a78c30188ad8a9e915893 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
from monty.serialization import loadfn, dumpfn
from monty.os.path import which
from pymatgen.core.structure import Molecule
from pymatgen.io.qchem.outputs import QCOutput, check_for... | gVallverdu/pymatgen | pymatgen/io/qchem/tests/test_outputs.py | Python | mit | 10,645 | [
"pymatgen"
] | 9b90d7e2eabbfc24aa53ddd308f6a104c7e30873c06f3cc6f0be3dcfd693b009 |
import tensorflow as tf
import matplotlib
import numpy as np
import matplotlib.pyplot as plt
import random
import math
import scipy.stats as stats
np.random.seed(1234)
random.seed(1234)
plt.switch_backend("TkAgg")
def plotScatter(points, color):
xs = [x[0] for x in points]
ys = [y[1] for y in points]
... | garibaldu/boundary-seekers | Boundary Hunter Ideas/TensorFlow/GN-KMeans.py | Python | mit | 9,064 | [
"MOE"
] | cebea54129e8e7d6759be716433260d62eb7e0b47c4c69c0f82e575dd151f91d |
from bs4 import BeautifulSoup
import urllib2
import re
import os
import shutil
import glob
from astroquery.utils import download_list_of_fitsfiles
'''
When you want the THINGS data, but don't want to click on every link
(and wait...)
'''
# base = ("https://bulk.cv.nrao.edu/littlethings/")
base = "http://www.mpia.de... | e-koch/ewky_scripts | get_THINGS.py | Python | mit | 2,083 | [
"Galaxy"
] | bad5594269571a6fe2978d81cf1aed9849d97e26f950e8af23effbf9f32b57d7 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# settings - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of ... | heromod/migrid | mig/cgi-bin/settings.py | Python | gpl-2.0 | 1,104 | [
"Brian"
] | 5e73e438a1b4363bcf3c49ba33382749c98ab9a9e31e3c0f58f6f68507cb05ed |
#!/usr/bin/env python
# -*- coding:utf-8 mode:python; tab-width:4; indent-tabs-mode:nil; py-indent-offset:4 -*-
##
"""
test_gamess
~~~~~~~~~~~~~~
Test GAMESS-US specific functionality that is not handled elsewhere.
"""
import sys
import unittest
import geoprep
from adapters import gamess_us
from tests imp... | mattbernst/polyhartree | tests/test_gamess_us.py | Python | gpl-3.0 | 4,019 | [
"GAMESS"
] | c8cec19f6fbf5ed3642ccc734c342ad013e748843a0f01b510ccb5984bc331e5 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | demis001/scikit-bio | skbio/sequence/tests/test_base.py | Python | bsd-3-clause | 1,423 | [
"scikit-bio"
] | 629ef34754ff5cc810bf72c8976778631a635f2b1b493cdf8d409362dfd3d848 |
""" This is a test of the PublisherHandler
It supposes that the RSS DBs are present, and that the service is running
"""
# pylint: disable=invalid-name,wrong-import-position
import unittest
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
from DIRAC.Core.DISET.RPCClient import RPCClient
f... | arrabito/DIRAC | tests/Integration/ResourceStatusSystem/Test_Publisher.py | Python | gpl-3.0 | 1,465 | [
"DIRAC"
] | 678384ea3f535bf1d7112ccfeadafc234580a5319d96946cb457d68b6b8b6bf3 |
import os
import sys
import subprocess
from contextlib import contextmanager
import argparse
import glob
ENV_ROOT = 'test_ambertools'
AMBER_VERSION = 'amber17'
def is_conda_package(package_dir):
basename = os.path.basename(package_dir)
return not (basename.startswith('osx') or basename.startswith('linux'))
... | Amber-MD/ambertools-conda-build | conda_tools/validate_ambertools_build.py | Python | mit | 5,502 | [
"Amber"
] | b34466d3b454c775c06d9821f43d14178bccdf7ac4dc92b0b45c994cf047f9e9 |
#!/usr/local/sci/bin/python
#***************************************
# 27 April 2015 KMW - v1
# For TEMPERATURE ONLY
# Plots a time series for any or all regions
# Option to overplot the same region from another source too
# Option to add trends of each source
# Option to add correlation of each source
#
#***********... | Kate-Willett/Climate_Explorer | PYTHON/PlotAllRegionsTimeSeries_APR2015.py | Python | cc0-1.0 | 27,217 | [
"NetCDF"
] | 124507a77c638d12ff4106b77c082814c8d935ceb7aadfbc9508b46e8d4d1ab4 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# License: MIT License (See LICENSE.md)
# Copyright (c) 2017, California Institute of Technology
# All rights reserved.
"""
Generate a moltemplate (.lt) file containing a definition of a polymer
molecule whose monomers are located at the posi... | jewettaij/moltemplate | moltemplate/genpoly_lt.py | Python | mit | 52,963 | [
"LAMMPS"
] | 31ae52ab942b62f06cd8da2e5f324d96084c2ba3c5e5d85fddc28711eb6f131d |
#!/usr/bin/env python
import os
import pychemia
import tempfile
import shutil
from pychemia.utils.computing import hashfile
from pychemia.db import has_connection
def test_queue():
"""
Test (pychemia.db.PyChemiaQueue) :
"""
if not has_connection():
return
print... | MaterialsDiscovery/PyChemia | tests/test_db_queue.py | Python | mit | 1,530 | [
"VASP"
] | b33d5a271ffd1be31adfe5aa57153cd78f70755efe44f9d5d6e06a87d334fa8f |
import time
import numpy as np
import multiprocessing as multiprocess
import click
from scipy.stats import logistic as log
from scipy.stats import norm as norm
import scipy.linalg
from scipy.optimize import minimize, fsolve, root, brentq, ridder, newton, bisect
from spikes_activity_generator import generate_spikes, sp... | noashin/kinetic_ising_model_neurons | EP_coupling_linear_regression.py | Python | mit | 17,626 | [
"Gaussian",
"NEURON"
] | 2ab010082c4e96d855e502388df1a329f28acd53d0dee3a223613d75524082e3 |
tests=[
("python","testMolDescriptors.py",{}),
]
longTests=[]
if __name__=='__main__':
import sys
from rdkit import TestRunner
failed,tests = TestRunner.RunScript('test_list.py',0,1)
sys.exit(len(failed))
| soerendip42/rdkit | Code/GraphMol/Descriptors/Wrap/test_list.py | Python | bsd-3-clause | 224 | [
"RDKit"
] | d0ade8c15260016a9131ce8a44bc45330cd23f8fca1ce23a3bfe3dae6d800d12 |
# (C) British Crown Copyright 2010 - 2017, 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... | QuLogic/iris | lib/iris/tests/integration/test_trajectory.py | Python | gpl-3.0 | 11,465 | [
"NetCDF"
] | 653eb04589ead770ff4f5b2cd890153910dd1fe91251f9bc4aa66c1dd03ee517 |
# Copyright 2021 The TensorFlow Probability 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 o... | tensorflow/probability | tensorflow_probability/python/sts/components/autoregressive_integrated_moving_average.py | Python | apache-2.0 | 17,691 | [
"Gaussian"
] | 02cf2936b74dc8373e59a33cf02bbaa003a369362f4ae2f20d4c21aced8dd464 |
# -*- coding: utf-8 -*-
# ------------------------------------------------------------
# pelisalacarta 4
# Copyright 2015 tvalacarta@gmail.com
# http://blog.tvalacarta.info/plugin-xbmc/pelisalacarta/
#
# Distributed under the terms of GNU General Public License v3 (GPLv3)
# http://www.gnu.org/licenses/gpl-3.0.html
# --... | neno1978/pelisalacarta | python/main-classic/platformcode/mct.py | Python | gpl-3.0 | 30,470 | [
"ADF"
] | 02c19eea5e709df8f2d9869135143b79c9cb1f7607685c70a5fc48a3cb74b563 |
import numpy as np
from mayavi import mlab
from BDSpace.Coordinates import Cartesian
from BDSpace.Curve.Parametric import Helix
from BDSpace.Pathfinder import line_between_two_points, helix_between_two_points, arc_between_two_points
import BDSpaceVis as Visual
coordinate_system = Cartesian()
coordinate_system.rotate_... | bond-anton/Space | demo/04_pathfinder_demo.py | Python | apache-2.0 | 2,158 | [
"Mayavi"
] | 960053cd2134e01f27ff87abb55f028b3bf52dd123b7c5a57614ca30f5f2855d |
from WebAppDIRAC.Lib.WebHandler import WebSocketHandler, asyncGen
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC import gConfig, gLogger
from DIRAC.Core.Utilities.CFG import CFG
from DIRAC.ConfigurationSystem.private.Modificator import Modificator
import json
class RegistryManagerHandler(WebSocketHandle... | zmathe/WebAppDIRAC | WebApp/handler/RegistryManagerHandler.py | Python | gpl-3.0 | 13,994 | [
"DIRAC"
] | fb7a11633cb5ccb6276ea12c577428219bb42679db4388c247429216a4c65f70 |
import pandas as pd
from obspy import UTCDateTime
import numpy as np
import argparse
from obspy.clients.fdsn import Client
# from netCDF4 import Dataset
import sys
def _cat2df(cat):
cols = ['date', 'evla', 'evlo', 'evdp', 'mag', 'magtype']
data = [[evt.origins[0].time, evt.origins[0].latitude, evt.origins[0].... | xumi1993/seispy | seispy/io.py | Python | gpl-3.0 | 2,809 | [
"NetCDF"
] | af7dddbad4061617382473cfa9b4d5ae8c3c04f31ecb7d22c08b64f53d060cfc |
#
# ImageViewPg.py -- classes for the display of FITS files in web browsers
# using javascript/HTML5 canvas/websockets
#
# Eric Jeschke (eric@naoj.org)
#
# Copyright (c) Eric R. Jeschke. All rights reserved.
# This is open-source software licensed under a BSD license.
# Please see the file LICEN... | eteq/ginga | ginga/web/pgw/ImageViewPg.py | Python | bsd-3-clause | 16,507 | [
"FLEUR"
] | cc08167695c35612f11873af33d68f9cfdb4755b0f3235b6decbca8531879315 |
import pybullet as p
import time
import pybullet_data
p.connect(p.DIRECT)
p.setAdditionalSearchPath(pybullet_data.getDataPath())
p.setGravity(0, 0, -10)
p.setPhysicsEngineParameter(numSolverIterations=5)
p.setPhysicsEngineParameter(fixedTimeStep=1. / 240.)
p.setPhysicsEngineParameter(numSubSteps=1)
p.loadURDF("plane.... | nrz/ylikuutio | external/bullet3/examples/pybullet/examples/humanoid_benchmark.py | Python | agpl-3.0 | 1,459 | [
"VisIt"
] | d992a4c1534a2d2c96d00bef8facea9dd151ec2ad67e928e20519460c078fc39 |
# Copyright 2014 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""This file contains printing-related functionality of the bisect."""
import datetime
import re
from bisect_results import BisectResults
import bisect_uti... | guorendong/iridium-browser-ubuntu | tools/auto_bisect/bisect_printer.py | Python | bsd-3-clause | 15,228 | [
"VisIt"
] | 00a5782be646447156ae027a123e28770982a99f71857faf2a26b85177298696 |
#! /usr/bin/env python
# ==========================================================================
# Generate residuals of COMPTEL observations
#
# Copyright (C) 2019-2022 Juergen Knoedlseder
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License... | ctools/ctools | modules/comscripts/comobsres.py | Python | gpl-3.0 | 24,626 | [
"Gaussian"
] | 4ab372aa2dd1a9bcef926964d842bd6a31f94ae021da5698fb86d0f20d76275f |
#!/usr/bin/env python3
#
# Copyright (c) 2012 Brian Yi ZHANG <brianlions at gmail dot com>
#
# This file is part of pynebula.
#
# pynebula 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 th... | brianlions/python-nebula | tests/add_nebula_path.py | Python | gpl-3.0 | 841 | [
"Brian"
] | 7e4a0c04d341963fec14128a95cff15b1da2bf1f50c514eced7b5777c26ad314 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/r-genomeinfodb/package.py | Python | lgpl-2.1 | 2,206 | [
"Bioconductor"
] | 37333d5bd4a12be3a1a5c7bf9a18a04412fc49eac95076551c3f8ee1e7916eae |
#!/usr/bin/env python
'''
Use "scanner" function to compute the molecule dissociation curve and the
force on the curve. Note the force is based on the atomic unit.
'''
import numpy as np
import matplotlib.pyplot as plt
from pyscf import gto, scf
bond = np.arange(0.8, 5.0, .1)
energy = []
force = []
mol = gto.Mole(... | gkc1000/pyscf | examples/grad/16-scan_force.py | Python | apache-2.0 | 1,722 | [
"PySCF"
] | 95317ea441059ee29c1728f9a6da9bc50f68c5dc60f79047226401f2dec6cf50 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2020 Google LLC
#
# 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 requi... | googleapis/python-bigquery-migration | scripts/fixup_migration_v2alpha_keywords.py | Python | apache-2.0 | 6,383 | [
"VisIt"
] | 6fa1878df70a9c52154e91e23b51e8a95fda040447a14e3e20c72b177b85b09d |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | lewismc/climate | ocw/tests/test_dataset_loader.py | Python | apache-2.0 | 6,290 | [
"NetCDF"
] | bc862c9eb343080120eb762a574677f199e9ae8bfa824574907193a9f2cc7d8f |
'''
This file contains the main algorithms
used to train the hmms, namely forward,backward,viterbi and baum-welch
TODO: tests
'''
try:
import psyco
psyco.full()
except:
pass
# Usually we use nicknames for the states and links
#
# B = {Begin}, E= {all emitting states}, N={all null States}
# S ={ all states} = B U E... | arthurfait/HMM-3 | hmm/algo_HMM.py | Python | gpl-3.0 | 86,654 | [
"Gaussian"
] | 50dcb8ab886a31f58b4565544bf322b849923d6ca0583c8e29eca96f12efe4e5 |
import numpy
from pmesh.pm import RealField, ComplexField
from nbodykit.utils.meshtools import SlabIterator
def gaussian_complex_fields(pm, linear_power, compute_displacement=False):
r"""
Make a Gaussian realization of a overdensity field, :math:`\delta(x)`
If specified, also compute the corresponding... | mschmittfull/nbodykit | nbodykit/mockmaker.py | Python | gpl-3.0 | 9,538 | [
"Gaussian"
] | a887e398d46c80f6d24221ac4868ea34dbfcb2140a0425161f2f2404cbf66ab6 |
""" Module containing a front-end to the ElasticSearch-based ElasticJobParametersDB.
This module interacts with one ES index: "ElasticJobParametersDB",
which is a drop-in replacement for MySQL-based table JobDB.JobParameters.
While JobDB.JobParameters in MySQL is defined as::
CREATE TABLE `JobParamet... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/DB/ElasticJobParametersDB.py | Python | gpl-3.0 | 7,315 | [
"DIRAC"
] | f4a0c7cf2e65a2fb500a92db6620ffbc2c43070c7913981677cc5982502267e6 |
import numpy as np
import spec
import Gnuplot
def Get_TPC_Spec(tpc, dt, applywindow = True, window = 'gaussian',
window_var=0.01, returnwin=False):
"""
Calculates a windowed bispectrum of a three point correlation matrix.
Returns the bispectrum, the frequency axis, and optionally the time and
w... | Smattacus/data-analysis | python/modules/tpanalaze.py | Python | gpl-2.0 | 2,661 | [
"Gaussian"
] | e3b73f62e2947b5c50b0540dff3fbf260286432c60b1aab101dc08269f3eb3fe |
# Orca
#
# Copyright 2004-2008 Sun Microsystems Inc.
#
# This library 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 2.1 of the License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/Thunderbird/__init__.py | Python | gpl-3.0 | 1,016 | [
"ORCA"
] | c34ed661a3dfc1a2affc92b4abaaead7bdd801bbb9fcdb6f0e9c8565f9751e62 |
import os
import numpy as np
from . import get_data_home
from .tools import download_with_progress_bar
DATA_URL = ("https://github.com/astroML/astroML-data/raw/main/datasets/"
"spec4000.npz")
def reconstruct_spectra(data):
"""Compute the reconstructed spectra.
Parameters
----------
data:... | astroML/astroML | astroML/datasets/sdss_corrected_spectra.py | Python | bsd-2-clause | 2,718 | [
"Galaxy"
] | 6a4034daf64281fa09dccc592f9cc2739a8fc187ac443fe4aa9895503135f17e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2014 The ProteinDF development team.
# see also AUTHORS and README if provided.
#
# This file is a part of the ProteinDF software package.
#
# The ProteinDF is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Publ... | ProteinDF/ProteinDF_bridge | proteindf_bridge/modeling.py | Python | gpl-3.0 | 24,765 | [
"Amber"
] | b684dfaf0d919b94e96311e582ba912b165dcb28d3faf2ec5bc266358b3c33dd |
""" Encapsulate here the logic for matching jobs
Utilities and classes here are used by MatcherHandler
"""
import time
from DIRAC import gLogger
from DIRAC.FrameworkSystem.Client.MonitoringClient import gMonitor
from DIRAC.Core.Utilities.PrettyPrint import printDict
from DIRAC.Core.Security import Properties
fr... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/Client/Matcher.py | Python | gpl-3.0 | 15,203 | [
"DIRAC"
] | 569e1051ac38068c54b59e643a0b2caa5102892139889a256d9faf391fb13100 |
# -*- coding: utf-8 -*-
#
# Copyright 2012 - 2013 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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 Foundati... | dursobr/Pythics | pythics/examples/waves.py | Python | gpl-3.0 | 5,371 | [
"Brian"
] | 1c064a1905af323e959ee2123ac3e3a1e4251f5c0b42ee18ca9fe152e4c4a05f |
"""SCons.Util
Various utility functions go here.
"""
#
# Copyright (c) 2001 - 2019 The SCons Foundation
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# wit... | loonycyborg/scons-plusplus | python_modules/Util.py | Python | lgpl-3.0 | 53,803 | [
"VisIt"
] | e8c487292a6b252bd079651f24bfffa8b12694328fd3d5033803e8adbf5a7a6e |
#!/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/flow_maps | flows/convol.py | Python | bsd-2-clause | 2,415 | [
"Gaussian"
] | 9b344eec98dcec1cb9580eb0eb78c67cec17705c89a273dae7e82f6a6810a3a2 |
# coding=utf-8
"""
Unit Tests for sickbeard/numdict.py
"""
# pylint: disable=line-too-long
import os.path
import sys
import unittest
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), '../lib')))
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
from sickbea... | pedro2d10/SickRage-FR | tests/numdict_tests.py | Python | gpl-3.0 | 19,808 | [
"Octopus"
] | 6f504262998cc518d07495e43c7aa72d7d6b91132d2266bfff2123288eed0c16 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from future import standard_library
standard_library.install_aliases()
from builtins import *
import sys
from genestack_client import Application... | genestack/python-client | genestack_client/cla.py | Python | mit | 10,971 | [
"Bowtie"
] | 2f46ba378be1003dbee4ea83ed44d01eeca257580805968c89fb4c81ee66d893 |
# description: GUI application to interactively segment and register
# ECoG electrodes with post-implant CT and pre-implant MRI
#
# Copyright (C) 2014 Zhongtian Dai
#
# 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... | towle-lab/electrode-registration-app | app/app.py | Python | gpl-2.0 | 64,694 | [
"Mayavi",
"VTK"
] | 06b55054810ade623d2e68633cd3e74c013f268b6be300bfa2a440aa7bc66343 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# TestCurl - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of ... | heromod/migrid | mig/server/TestCurl.py | Python | gpl-2.0 | 7,171 | [
"Brian"
] | c7cf5a66b76851c57f44b3e9f5639c4a0190da097661a583a1270ef7e3abb7f7 |
"""Visits factories."""
import random
from datetime import datetime
import factory
import factory.django
from django.contrib.auth import get_user_model
from django.utils import timezone
from core.factory import AddressFactory
from . import models
User = get_user_model()
class PlaceFactory(factory.DjangoModelFact... | oser-cs/oser-website | visits/factory.py | Python | gpl-3.0 | 3,278 | [
"VisIt"
] | f237d647449036354b68bf19566ca7520f2c551dcb4f59157e7d74426aa483c8 |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# 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 ver... | spring01/libPSI | src/lib/libfunctional/matlab/mfiles/install.py | Python | gpl-2.0 | 2,973 | [
"Psi4"
] | 7f372e4a201d563b2d8ff5e062f1e9d013fb6a1621b1c634ee51fe0d33e92e2a |
"""
Copyright (C) 2014, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Maintainer: Rudolf Streif (rstreif@jaguarlandrover.com)
"""
"""
Initialize server package... | dvthiriez/rvi_backend | server/__init__.py | Python | mpl-2.0 | 1,044 | [
"Jaguar"
] | b68487893c99d2bbef477b84a681c4654d4fbae10ea3c5cd32b69e74e746c9b7 |
# Copyright 2009 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
This module allows to control GenePop.
"""
import os
import re
im... | bryback/quickseq | genescript/Bio/PopGen/GenePop/Controller.py | Python | mit | 32,431 | [
"Biopython"
] | aecea7ad7e0cb95fda5f1a35a5bb1268e11190088a2b7a2f74a5cbd2f2961e68 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to interface with the Materials Project REST
API v2 to enable the creation of data structures and pymatgen objects using
Materials Project data.
To make use of the Materials AP... | richardtran415/pymatgen | pymatgen/ext/matproj.py | Python | mit | 67,460 | [
"ABINIT",
"VASP",
"pymatgen"
] | 891b49fd75f3b6872479a38c71963aee4fb5a26e21e4e238527eaa153c74ed19 |
from __future__ import absolute_import
import abc
import sys
import threading
import typing as tp # NOQA
import warnings
import numpy
import chainer
from chainer import backend
from chainer.backends import _cpu
from chainer.backends import cuda
from chainer.backends import intel64
from chainer import types # NOQA
f... | wkentaro/chainer | chainer/device_resident.py | Python | mit | 13,742 | [
"VisIt"
] | 71b1c56974de89fad5da2d7fc0d6b65167f34d3a4cc4fdf7eef0fbdaf8434a5b |
#!/usr/bin/env python
from numpy import (
asfortranarray,
atleast_3d,
exp,
sinc,
pi,
zeros,
outer,
isnan,
log,
logspace,
arange,
allclose,
diff,
atleast_1d,
isfinite,
repeat,
append,
)
import h5py
from scipy.interpolate import interp1d
import logging
f... | scienceopen/histfeas | histfeas/transcararc.py | Python | gpl-3.0 | 8,836 | [
"Gaussian"
] | 632637e51bac639f3790cdfc3e50267adfb81d63f95fd75e3d5bb0398c4cb857 |
#!/usr/bin/env python
# ==========================================================================
#
# Copyright NumFOCUS
#
# 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
#
# ... | InsightSoftwareConsortium/ITK | Utilities/Maintenance/BuildHeaderTest.py | Python | apache-2.0 | 5,499 | [
"VTK"
] | ed28b1d224fc085205a0d146b24eeeaf081c85adfbdf1f378696624d45c6607e |
"""
Copyright (c) 2004-Present Pivotal Software, Inc.
This program and the accompanying materials are made available under
the terms of the 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.... | edespino/gpdb | src/test/tinc/tincrepo/mpp/models/test/sql_related/test_sql_concurrency_test_case.py | Python | apache-2.0 | 2,505 | [
"ORCA"
] | 4127716e40e49bedbb7f7cf65608f80347a47a10ffca66c2de6b9fb2728308f8 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function, division
import unittest
import tempfile
import atexit
import shutil
import textwrap
import os
import pickle
import warnings
import numpy as np
from numpy.testing import assert_array_equal
import pytest
try:
import azure.storage.blob... | alimanfoo/zarr | zarr/tests/test_hierarchy.py | Python | mit | 38,032 | [
"VisIt"
] | 65b0f96a0d37ccb9e3d61424aa3ac28d46f1a0e79a7c55409b943a5f01d79f59 |
#!/usr/bin/env python3
from __future__ import print_function
import argparse
import io
import os
import subprocess
import sys
import tempfile
import time
from contextlib import ExitStack
from functools import partial
from threading import Thread
import pysam
class VariantCallingError (RuntimeError):
"""Exceptio... | bimbam23/tools-iuc | tools/varscan/varscan.py | Python | mit | 53,097 | [
"ADF",
"pysam"
] | db473c2d863bea3123998d944447ff46ecd729b457fc2915cb446b41f831d073 |
"""
Converting the colour table on the Wikipedia CPK article to JSON format
=======================================================================
The Wikipedia article on `CPK colouring`_ contains a nice table for the colours
for each element in various colouring schemes. This script aims to convert that
table into ... | tschijnmo/ccpoviz | ccpoviz/data/wikicolour2json.py | Python | mit | 3,359 | [
"Jmol",
"RasMol"
] | 8c5fd0162d1af59199cc2f0b40874b360bf24d407b8a1be96149cc66c0e893a6 |
#!/usr/bin/python
#
# Open SoundControl for Python
# Copyright (C) 2002 Daniel Holth, Clinton McChesney
#
# This library 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 2.1 of the Licen... | shouldmakemusic/yaas | LiveOSC/CallbackManager.py | Python | gpl-2.0 | 2,717 | [
"VisIt"
] | da7958e992ddb3eb3874d49b48e2be9278c0e861ed47515d10a886b45de6aa5d |
"""
Module of kernels that are able to handle continuous as well as categorical
variables (both ordered and unordered).
This is a slight deviation from the current approach in
statsmodels.nonparametric.kernels where each kernel is a class object.
Having kernel functions rather than classes makes extension to a multiv... | bert9bert/statsmodels | statsmodels/nonparametric/kernels.py | Python | bsd-3-clause | 6,399 | [
"Gaussian"
] | 093dbd2e26bd514e7002b371290a18b3c951fc981502a524edc454ad24fe5731 |
"""
Utilities to score protein-ligand poses using DeepChem.
"""
import numpy as np
def pairwise_distances(coords1: np.ndarray, coords2: np.ndarray) -> np.ndarray:
"""Returns matrix of pairwise Euclidean distances.
Parameters
----------
coords1: np.ndarray
A numpy array of shape `(N, 3)`
coords2: np.nda... | miaecle/deepchem | deepchem/dock/pose_scoring.py | Python | mit | 6,263 | [
"Gaussian"
] | fce4333d401309025c579622861dd40eac2fe0218edab4d5e2ede551e351ce2b |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | xialonglee/contrib | hack/boilerplate/boilerplate.py | Python | apache-2.0 | 6,289 | [
"VisIt"
] | 08004dc4e82850e9d7af0ad9e3f95764ba0bf0a6dad0562f02ccaf6035426676 |
"""This script generates Slicer Interfaces based on the CLI modules XML. CLI
modules are selected from the hardcoded list below and generated code is placed
in the cli_modules.py file (and imported in __init__.py). For this to work
correctly you must have your CLI executabes in $PATH"""
import xml.dom.minidom
import s... | blakedewey/nipype | nipype/interfaces/slicer/generate_classes.py | Python | bsd-3-clause | 21,625 | [
"VTK"
] | 45e2cf15b6f683b67ed7899bb2bc1c895e627c99673cce2d690f1ec3d0dfa12e |
import functools
from typing import List, Any
import numpy as np
import scipy.sparse as sp
import pytest
from sklearn.metrics import euclidean_distances
from sklearn.random_projection import johnson_lindenstrauss_min_dim
from sklearn.random_projection import _gaussian_random_matrix
from sklearn.random_projection imp... | manhhomienbienthuy/scikit-learn | sklearn/tests/test_random_projection.py | Python | bsd-3-clause | 15,196 | [
"Gaussian"
] | 416fa87a3c181f2c020a044c1932cc8f1367ab1d94a679c8698b805c3512191c |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# 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 requi... | googleapis/python-vpc-access | scripts/fixup_vpcaccess_v1_keywords.py | Python | apache-2.0 | 6,123 | [
"VisIt"
] | 1c454c768c45b896c77bba30cdf15481aafe02a533f64591806278006501799d |
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