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# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines the VaspInputSet abstract base class and a concrete
implementation for the parameters developed and tested by the core team
of pymatgen, including the Materials Virtual Lab, Materials Pr... | gmatteo/pymatgen | pymatgen/io/vasp/sets.py | Python | mit | 118,728 | [
"BoltzTrap",
"VASP",
"pymatgen"
] | b5015cceff2c01db0a9bf653f731bf7607cf06cddb697af97bc3995e946b2cc0 |
# First we need to import the libraries that
# we need
# Import the time library so that we can make
# the program pause for a fixed amount of time
import time
# Import the Raspberry Pi GPIO libraries that
# allow us to connect the Raspberry Pi to
# other physical devices via the General
# Purpose Input-Output (GPIO) p... | bobrathbone/pischools | traffic_led/PedestrianCrossing.py | Python | gpl-3.0 | 1,970 | [
"Amber"
] | 2bf367fe985af7ec62becf77c07122dec9546856754fe0cd0be0596f86f7fa86 |
# -*- coding: utf-8 -*-
import cv2
import numpy as np
# import matplotlib.pyplot as plt
from PIL import Image
from difflib import SequenceMatcher
from PIL import *
from PIL import ImageEnhance
import time
from pytesseract import image_to_string, image_to_boxes
import os
def getNameArea(imageFolderPath):
"""
... | Hubert51/AutoGrading | learning/Ruijie/handwriting_recognization/main.py | Python | mit | 9,146 | [
"Gaussian"
] | 6b0f7796f9b38c88c61d62b8015686cd50f4653a13841e0bcd9358d05d20f339 |
"""
Acceptance tests for Studio related to the textbooks.
"""
from common.test.acceptance.tests.studio.base_studio_test import StudioCourseTest
from ...pages.studio.textbook_upload import TextbookUploadPage
from ...pages.lms.textbook_view import TextbookViewPage
from ...tests.helpers import disable_animations
from nose... | shabab12/edx-platform | common/test/acceptance/tests/studio/test_studio_textbooks.py | Python | agpl-3.0 | 3,445 | [
"VisIt"
] | d0ae586c7bc2aeb9107886e1042415fec4ed5b1c1029757a20f5b6a4af4a5f2f |
###
### This script can be run with pvpython rather than pvbatch, as it does not
### need mpi.
###
### Purpose:
###
### Read all timesteps of the halos point files (vtu) which have fewer
### halo points and the raw-particles (vtu) which have many more halo points.
### For the few halo points, we create a glyph fil... | Kitware/cinema | scripts/data_generation/cosmology/hacc_composite_time.py | Python | bsd-3-clause | 11,672 | [
"ParaView"
] | bde61b01933e131b2eacffb8721e7882a54b3c865aa62d73ccae2be711137880 |
#!/usr/bin/env python
import sys
lines_gaff = sys.stdin.readlines()
improper_style_name = 'cvff'
sys.stdout.write(' write_once("In Settings") {\n')
for i in range(0, len(lines_gaff)):
line = lines_gaff[i]
atypes = line[:11].split('-')
atype1 = atypes[0].strip()
atype2 = atypes[1].strip()
atype3... | yidongxiainl/lammps | tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_improper_to_lt.py | Python | gpl-2.0 | 3,681 | [
"Amber",
"LAMMPS"
] | 32b11a134a5fb43ed01b10259228bf125a05432211d96037bf78f9d049c24745 |
#-*-coding:utf-8-*-
"""
@package butility.base
@brief Most fundamental base types
@author Sebastian Thiel
@copyright [GNU Lesser General Public License](https://www.gnu.org/licenses/lgpl.html)
"""
from __future__ import unicode_literals
from __future__ import division
from butility.future import (with_metaclass,
... | Byron/bcore | src/python/butility/base.py | Python | lgpl-3.0 | 30,451 | [
"VisIt"
] | 8c318a284f6b979d4e2097dddc77eba79204e4fa787d6e1e609e7662fbbe23f9 |
"""
SliceCompareViewerWidget
:Authors:
Berend Klein Haneveld
"""
from vtk import vtkRenderer
from vtk import vtkInteractorStyleUser
from vtk import vtkCellPicker
from vtk import vtkImageMapToColors
from vtk import vtkColorTransferFunction
from vtk import vtkDataSetMapper
from vtk import vtkActor
from vtk import vtkI... | berendkleinhaneveld/Registrationshop | ui/widgets/SliceCompareViewerWidget.py | Python | mit | 7,860 | [
"VTK"
] | 1216a66d2c7699bd61d6c41c5338103a2f20d6701e679c304dd80fca48636f9b |
import tempfile
import os
import subprocess
import shutil
from boto.s3.connection import S3Connection, Bucket, Key
def test_bwa():
work_dir = tempfile.mkdtemp()
create_config(work_dir)
create_manifest(work_dir)
# Call Pipeline
try:
subprocess.check_call(['toil-bwa', 'run',
... | jpfeil/toil-scripts | src/toil_scripts/bwa_alignment/test/test_bwa_alignment.py | Python | apache-2.0 | 2,209 | [
"BWA"
] | 0da8642e5dcd6b94a86d19ccfd31a01fe8ef3c6f9b6e8ee83006ceee1db1ebc0 |
#!/usr/bin/env python
#
#
# This file is part of do_x3dna
#
# Author: Rajendra Kumar
# Copyright (C) 2014-2018 Rajendra Kumar
#
# do_x3dna uses 3DNA package (http://x3dna.org).
# Please cite the original publication of the 3DNA package:
# Xiang-Jun Lu & Wilma K. Olson (2003)
# 3DNA: a software package for the analysis... | rjdkmr/do_x3dna | dnaMD/dnaMD/commands/globalEnergy.py | Python | gpl-3.0 | 14,043 | [
"Gromacs"
] | aaebc0a0368259f62f49e4c48d1073291d1f47078242c3fe6c667dc8e4ea2c92 |
# Copyright (c) 2018 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""
xarray with MetPy Tutorial
==========================
`xarray <http://xarray.pydata.org/>`_ is a powerful Python package that provides N-dimensional
labeled arrays and datasets ... | ahaberlie/MetPy | tutorials/xarray_tutorial.py | Python | bsd-3-clause | 15,531 | [
"NetCDF"
] | 67c589af4c21b66812b824a38143557c95adf4fe9bf681499454195ea23ca1be |
# Copyright 2004 by Harry Zuzan. 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.
"""
Classes for accessing the information in Affymetrix cel files.
Functions:
read Read a ... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Affy/CelFile.py | Python | gpl-2.0 | 6,587 | [
"Biopython"
] | e76fc9bfd9a0fcb4adfad3c956272e595fac5d547b99e9d0558b68a24c3db109 |
"""
DIRAC.WorkloadManagementSystem.JobWrapper package
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
| yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/JobWrapper/__init__.py | Python | gpl-3.0 | 190 | [
"DIRAC"
] | 2dde212d336616d0d299c58a856e731303b74e89f6586b597d4ddd7ce72caaf4 |
#!/usr/bin/env python
import pysam
import argparse, sys
import math, time, re
from collections import Counter
from argparse import RawTextHelpFormatter
__author__ = "Colby Chiang (cc2qe@virginia.edu)"
__version__ = "$Revision: 0.0.1 $"
__date__ = "$Date: 2015-04-22 09:31 $"
# --------------------------------------
#... | abelhj/svtools | svtools/bin/svtyper/scripts/vcf_group_multiline.py | Python | mit | 27,563 | [
"pysam"
] | 0b0e0b4d9fa2fb61002abcd1e529e84daef249e8d6fc481c574c41ad1dbac7f7 |
#! /usr/env/python
"""
Python implementation of VoronoiDelaunayGrid, a class used to create and manage
unstructured, irregular grids for 2D numerical models.
Do NOT add new documentation here. Grid documentation is now built in a semi-
automated fashion. To modify the text seen on the web, edit the files
`docs/text_fo... | csherwood-usgs/landlab | landlab/grid/voronoi.py | Python | mit | 34,968 | [
"NetCDF"
] | 7a0763d37180aa2ac8443157f5f75df3e49603788cc1f6314ac55586b0947516 |
"""
This module supports simple linear one-port networks based on the
following ideal components:
V independent voltage source
I independent current source
R resistor
C capacitor
L inductor
These components are converted to s-domain models and so capacitor and
inductor components can be specified with initial voltage... | mph-/lcapy | lcapy/oneport.py | Python | lgpl-2.1 | 41,294 | [
"CRYSTAL"
] | ca3cdf0ae8127a7065cf80b8189255c466b1ae2d94bea02a31f64ddab47be579 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# expand - emulate shell wild card expansion
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public L... | heromod/migrid | mig/shared/functionality/expand.py | Python | gpl-2.0 | 19,186 | [
"Brian"
] | 0d1d078ebf9c6a319bddf26ba852d3b1b4dcb17706f40f7f780cc3ae8e570c3a |
# Copyright (c) 2012 OpenStack Foundation
# 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 ... | srajag/nova | nova/tests/compute/test_resource_tracker.py | Python | apache-2.0 | 49,365 | [
"exciting"
] | 9c0a156dab6766c605e8d1958b7086997130ff6b26e82cb6b8aa5a5a9afd0193 |
"""
Acceptance tests for Home Page (My Courses / My Libraries).
"""
from __future__ import absolute_import
import datetime
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.account_settings import AccountSettingsPage
from common.test.acceptance.pages.studio.i... | ESOedX/edx-platform | common/test/acceptance/tests/studio/test_studio_home.py | Python | agpl-3.0 | 3,149 | [
"VisIt"
] | 4a0a4e92fec10efcfd06ae2b4956efe4d987ef52b6c941c8ff0a117006da549e |
"""
This is an example for an MD simulation of a simple Lennard-Jones fluid
with ESPResSo++. We will start with particles at random positions within
the simulation box interacting via a shifted Lennard-Jones type potential
with an interaction cutoff at 2.5.
Newtons equations of motion are integrated with a Velocity-Ver... | cgchemlab/chemlab | examples/chain_growth_catalytic/prepare_sample_system.py | Python | gpl-3.0 | 11,964 | [
"ESPResSo"
] | cfe70260e3f1c953c680f5b62db409f8e60659394caeef0a9996d6681e210af2 |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your opt... | Markus-Goetz/CDS-Invenio-Authorlist | modules/bibupload/lib/batchuploader_engine.py | Python | gpl-2.0 | 26,870 | [
"VisIt"
] | 2367e528665cf59ab18d40f5954356e9d57ce2de9123d2a3e3899dc9d83418bc |
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University
# Berlin, 14195 Berlin, Germany.
# 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 ... | trendelkampschroer/PyEMMA | pyemma/coordinates/data/frames_from_file.py | Python | bsd-2-clause | 7,557 | [
"MDTraj"
] | f3d47b75f0de73b1149bf0ff42be505b3f985dc9246743ec43a923b96ffb072e |
#* 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/lgpl-2.1.html
import plat... | harterj/moose | python/TestHarness/util.py | Python | lgpl-2.1 | 30,177 | [
"MOOSE",
"VTK"
] | 4489d18301fdf4fd913a8b1c93ba7fae05694dd80333085b37f91185b0baf72f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains classes to wrap Python VTK to make nice molecular plots.
"""
import itertools
import math
import os
import subprocess
import time
import numpy as np
try:
import vtk
from vtk... | gmatteo/pymatgen | pymatgen/vis/structure_vtk.py | Python | mit | 48,211 | [
"Jmol",
"VTK",
"pymatgen"
] | 291be964d8a81b0b0158fe3a671f0e1ad9fd8548cf5b7bbf84df534114d3766a |
# Copyright (c) 2012 - 2014 the GPy Austhors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core import GP
from .. import likelihoods
from .. import kern
from .. import util
class GPCoregionalizedRegression(GP):
"""
Gaussian Process model for heterosced... | gusmaogabriels/GPy | GPy/models/gp_coregionalized_regression.py | Python | bsd-3-clause | 1,876 | [
"Gaussian"
] | f940612c60aaac54afee42abff3191d2e5c5aa799e5ba13fa983ab7745f2ba7e |
#!/usr/bin/python
import _mysql as mysql
import _mysql_exceptions as mysql_exceptions
import MySQLdb.cursors
import os
import pickle
import numpy as np
import sys
import StringIO
from scipy.misc import comb
import getopt
import csv
import re
import subprocess
import random
import glob
def usage():
print "\n-------... | juliandev/SIFTER | src/scripts/sifter_prepare.py | Python | gpl-3.0 | 35,833 | [
"VisIt"
] | 78ae62a352e71114a3bd39000a9dd474aa3f5696df0b3d46dab5da85110d8400 |
#
# iqcalc.py -- image quality calculations on FITS data
#
# Eric Jeschke (eric@naoj.org)
#
# Copyright (c) 2011-2012, Eric R. Jeschke. All rights reserved.
# This is open-source software licensed under a BSD license.
# Please see the file LICENSE.txt for details.
#
import math
import logging
import numpy
import thre... | bsipocz/ginga | ginga/util/iqcalc.py | Python | bsd-3-clause | 14,707 | [
"Gaussian"
] | bdcf289f899fcc3d6a553c8beed9040fcc7ab7203436d52bad8e529e3f76557c |
#!/usr/bin/env python
from Bio import SeqIO
import tempfile
import subprocess
import shutil
import os
import re
"""
FASTA statting tool. Usable from the shell or imported as a module.
"""
entrez_CFSAN_genera = '("Campylobacter"[Organism]) OR ("Erwinia"[Organism]) OR ("Listeria"[Organism]) OR ("Escherichia"[Organ... | crashfrog/Dispatch | fasta_statter.py | Python | unlicense | 16,556 | [
"BLAST",
"Bowtie"
] | 2e5a907f75b147d1cf4365f7e3015bb3a047344c3655548692077c382964f506 |
#!/usr/bin/env python
''' Example use :
cat file.fq | ./fastq2wm33.py > ./bwa pssm ... -
Significant speedup can be achieved with using the pypy interpreter: http://pypy.org/
After installation, change interpreter from python to pypy in first line or run
cat file.fq | pypy fastq2wm33.py > ./bwa pssm ... - '''
import... | pkerpedjiev/bwa-pssm | scripts/fastq2wm.py | Python | gpl-3.0 | 8,621 | [
"BWA"
] | 91431afda2dda1506cb3f4339430d1f70a7aed2774e03e7895c21e72b8f52db6 |
# -*- coding: utf-8 -*-
#
# Pyplis is a Python library for the analysis of UV SO2 camera data
# Copyright (C) 2017 Jonas Gliss (jonasgliss@gmail.com)
#
# This program is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License a
# published by the Free Software Foundat... | jgliss/pyplis | pyplis/doascalib.py | Python | gpl-3.0 | 65,370 | [
"Gaussian"
] | a4484d90b88f33ff8cf7ba76b9ba9bfed6b95d52c8c8a2a90101ea7f30a72f39 |
'''
Authors: Ivan E. Cao-Berg (icaoberg@scs.cmu.edu)
Created: April 24, 2012
Copyright (C) 2012 Murphy Lab
Lane Center for Computational Biology
School of Computer Science
Carnegie Mellon University
April 24, 2012
* I. Cao-Berg Added getNominalMagnification method that queries OMERO and
tries to retrieve the nomi... | icaoberg/pyslid | pyslid/image.py | Python | gpl-3.0 | 6,345 | [
"VisIt"
] | 93225dbcfb8d4241b74c1fbeeefba3aa9e389fa123e1151b78b7dd35be780387 |
'''@package docstring
@author: Jyh-Miin Lin (Jimmy), Cambridge University
@address: jyhmiinlin@gmail.com
Created on 2013/1/21
================================================================================
This file is part of pynufft.
pynufft is free software: you can redistribute it and/or modify
it u... | jyhmiinlin/cineFSE | CsTransform/good_3d_pynufft.py | Python | gpl-3.0 | 59,360 | [
"Mayavi"
] | 8f78a9d9a481b9ed115a6978b99d977a3bf75a98828d12d9a6af30afa8214b78 |
from setuptools import setup, find_packages
setup(
name = 'fqn',
version = '0.7.1',
description = 'Functions that can retrieve objects using Fully Qualified Names',
author = 'Brian Lauber',
author_email = 'constructible.truth@gmail.com',
packages = find_packages(exclude = ["tests", "tests.*"]),... | briandamaged/fqn | setup.py | Python | mit | 386 | [
"Brian"
] | 1b33df633c30444c5e31ff76db7da05071775d147f2d5f3726f4e8210cba8463 |
# Created by DrLecter, based on DraX' scripts
# This script is part of the L2J Official Datapack Project
# Visit us at http://www.l2jdp.com/
# See readme-dp.txt and gpl.txt for license and distribution details
# Let us know if you did not receive a copy of such files.
import sys
from com.l2scoria.gameserver.model.ques... | zenn1989/scoria-interlude | L2Jscoria-Game/data/scripts/village_master/elven_human_buffers_2/__init__.py | Python | gpl-3.0 | 3,935 | [
"VisIt"
] | fbd4ce6b2ed8d8112e993b90c97beb7706a1271c42e207c6fb002d4d281ca77a |
""" DIRAC.Resources.Catalog package """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
| yujikato/DIRAC | src/DIRAC/Resources/Catalog/__init__.py | Python | gpl-3.0 | 149 | [
"DIRAC"
] | 7d1cf88bf28f4a52dcdd801bac73b8e04983cdc6afbe47440de4abff07344d43 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2018, Chris Houseknecht <@chouseknecht>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | caphrim007/ansible | lib/ansible/modules/clustering/k8s/k8s.py | Python | gpl-3.0 | 4,928 | [
"Galaxy"
] | 50cc0c9eef3931b255b33106242adcff4b1bc563409f084f9e7c03ea48b4373a |
# -*- coding: utf-8 -*-
# Nemubot is a smart and modulable IM bot.
# Copyright (C) 2012-2014 nemunaire
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License,... | Bobobol/nemubot-1 | modules/more.py | Python | agpl-3.0 | 8,516 | [
"VisIt"
] | 2f27f7b334fba49ee178e3c014f9d21540fa52f9b8c8f9b57fa8bba581a2c2e5 |
##########################################################################
# This illustrates some of the capabilities for spine placement.
# It has spines whose size increase with distance from the soma.
# Further, the angular direction of the spines spirals around the dendrite.
#######################################... | BhallaLab/moose-examples | tutorials/Rdesigneur/ex9.3_spiral_spines.py | Python | gpl-2.0 | 838 | [
"MOOSE"
] | 99089720df5e69449881ae004840a31a7b7418d3fd213a447b44e811d02e503f |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/data/ray_xshards.py | Python | apache-2.0 | 18,454 | [
"ORCA"
] | 30ac2d54ddeac51eb25938d3d330d4254ad794b7ea8d0c592dae27117aeea33d |
import sys
from collections import namedtuple
from ua_parser import user_agent_parser
PY2 = sys.version_info[0] == 2
PY3 = sys.version_info[0] == 3
if PY3:
string_types = str
else:
string_types = basestring
MOBILE_DEVICE_FAMILIES = (
'iPhone',
'iPod',
'Generic Smartphone',
'Generic Feature... | natewinck/surfstat | user_agents/parsers.py | Python | gpl-2.0 | 6,000 | [
"Galaxy"
] | ec3b42af7701922819b2732a8aedc28368115352314838a71d945c110fcc3ab5 |
"""
Missing module doc.
"""
import subprocess
import os
import numpy as np
from pymatgen.io import atat
def run_mcsqs(structure, clusters, supercell=None, total_atoms=None, search_time=0.01):
"""
Helper function for calling mcsqs with different arguments
Args:
clusters (dict): dictionary of clus... | fraricci/pymatgen | pymatgen/command_line/mcsqs_caller.py | Python | mit | 3,925 | [
"pymatgen"
] | f4ab6c858698b1ef9ec1fabad199f1a6b2705b6cf16b6e91516bfa8ab9c8bcad |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
from vtk.test import Testing
class TestCommand(Testing.vtkTest):
def _test(self, fname):
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName... | hlzz/dotfiles | graphics/VTK-7.0.0/Common/DataModel/Testing/Python/quadraticQuadDeriv.py | Python | bsd-3-clause | 1,642 | [
"VTK"
] | f2c3c873635955cfc95718580594c2580321d5b33ce7f94bdcd26a29f0b4da88 |
#!/usr/bin/env python
import sys, argparse
import numpy as np
def print_line(items):
print(items)
def read_profiles(inputfile, outputfile, params, dimension,depth1,depth2, reverse=False, format="%g"):
from netCDF4 import Dataset, num2date, date2num
rootgrp = Dataset(inputfile, 'r', format='NETCDF4')
... | OpenDA-Association/OpenDA | model_gotm/tests/gotm_simple_kalman/stochModel/bin/profilemean.py | Python | lgpl-3.0 | 4,485 | [
"NetCDF"
] | aa34c0b1f4f917ca40ed111d0809fc654addf419a8077322823ed68a61df09f0 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
#
# Test butterfly subdivision of point data
#
sphere = vtk.vtkSphereSource()
sphere.SetPhiResolution(11)
sphere.SetThetaResolution(11)
colorIt = vtk.vtkElevationFilter()
colorIt.SetI... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Modeling/Testing/Python/subdividePointData.py | Python | gpl-3.0 | 2,598 | [
"VTK"
] | 336d3b338831d25796c9f9a64f275248db733cf4972bfba9753f3a2d3379f6ac |
import numpy as np
from scipy.special import erf
#--> The lnlikes
#-> The lnlike calculated with generalized chi square
#------------------------------------------------------------------------------#
# Note:
# When I compare the two different methods to compare the upperlimits, the
# results are surprisingly consiste... | darkbear9494/LinFit | linfit/likelihoods.py | Python | mit | 13,199 | [
"Gaussian"
] | 1a477b8949b49e822ebb5f99a6c4718c8d108a2178d7e6b53641f5c1075fd33b |
import sys
import argparse
import methylpy
def parse_args():
# create the top-level parser
parser = argparse.ArgumentParser(
description = "You are using methylpy "
+ methylpy.__version__
+ " version ("
+ methylpy.__file__[:methylpy.__file__.rfind("/")]+"/"
... | yupenghe/methylpy | methylpy/parser.py | Python | apache-2.0 | 97,419 | [
"BWA",
"Bowtie"
] | 83b1f5299b8cc4f81f939b483b2dfa1f39956072c7fcda8443765faf3acf7264 |
import sys
import argparse
import numpy as np
import math
import matplotlib.pyplot as plt
import matplotlib as mp
import os
from scipy import interpolate
import xes_energies
import pdb
from scipy.ndimage.filters import gaussian_filter as filt
data_extractor = np.genfromtxt
# backsatter energy for graphite 002
e0 = ... | hoidn/LCLS | xes/xes/xes_process.py | Python | gpl-3.0 | 12,428 | [
"CRYSTAL",
"Gaussian"
] | 5179bec7ba93cee141a616be2b4b20e89dda2d735b0b3df4a57750fc95416196 |
r"""OS routines for Mac, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, or ce, e.g. unlink, stat, etc.
- os.path is one of the modules posixpath, or ntpath
- os.name is 'posix', 'nt', 'os2', 'ce' or 'riscos'
- os.curdir is a string representing the current di... | rzabini/gradle-sphinx | src/main/jython/os.py | Python | apache-2.0 | 25,197 | [
"VisIt"
] | 634207e03c5735a58c20ef702d206d0b5efac98090b6a4f0e1cd2867dc1eb65f |
#!/usr/bin/env python
#######################
# Script to take center RA/DEC location & generate dithered offsets
# for baseline project exposures
########################
### History:
## 2014/07/21 rgm: take out "coordinates": "absolute",
## which we are told is invalid.
## 2014/07/25 rgm: fix --disableout... | deapplegate/wtgpipeline | dithermaker.py | Python | mit | 11,793 | [
"VisIt"
] | c3b3f96bd21a985c136ac68271db25abc822bc8a59ea28cef7814d36cd437dc8 |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008-2011 Daniel Moisset, Ricardo Quesada, Rayentray Tappa,
# Lucio Torre
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the... | eevee/cocos2d-mirror | cocos/layer/scrolling.py | Python | bsd-3-clause | 16,009 | [
"VisIt"
] | fe6493ca83325b3dce64e4499d59a540c9574f72a6cfb85e1dc5491199f17d94 |
# Copyright 2018 Google Inc.
#
# 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,... | google/differentiable-atomistic-potentials | dap/tf/neighborlist.py | Python | apache-2.0 | 11,919 | [
"ASE",
"pymatgen"
] | ca256bfdec4ae846b45231dc4fbc978b563ce9e56728e1d0732bcf0c31fdca73 |
#!/usr/bin/env python
"""
Converter to generate 3 (or 4) column base-pair coverage from an interval file.
usage: %prog bed_file out_file
-1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in interval file
-2, --cols2=N,N,N,N: Columns for chrom, start, end, strand in coverage file
"""
import sys
from ga... | volpino/Yeps-EURAC | lib/galaxy/datatypes/converters/interval_to_coverage.py | Python | mit | 6,336 | [
"Galaxy"
] | 7a8ce0b05847149a68a95d5bcc6bf727b3188e8986cdc2a0025d3cb54418627a |
from __future__ import print_function
import numpy as np
import pylab as plt
import fitsio
from legacypipe.survey import *
from astrometry.util.util import Tan
from astrometry.util.fits import *
from astrometry.util.resample import *
from astrometry.util.plotutils import *
from wise.forcedphot import unwise_tiles_touch... | legacysurvey/pipeline | py/legacyanalysis/wise-cutouts.py | Python | gpl-2.0 | 17,422 | [
"Gaussian"
] | 43e8477810b84f4654f43d735e8622b9a4e665cb61c4a189d387e01d55ed4493 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | govarguz/espressopp | testsuite/unittest/TestReal3D.py | Python | gpl-3.0 | 4,531 | [
"ESPResSo"
] | 740996c799a6732c60a933c183ed183d6699f95f23242d2d2f683bbee2f5fd3f |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD (3-clause)
import sys
import os
import os.path as op
import shutil
import numpy as np
from scipy import linalg
from .fixes imp... | lorenzo-desantis/mne-python | mne/bem.py | Python | bsd-3-clause | 49,041 | [
"Mayavi"
] | 6dbb78e6831dae757a4c7f1171610569005fa095f1796db94554b0d0870a3746 |
from django.db import models
from edc_base.model.fields import OtherCharField
from edc_constants.choices import YES_NO_UNKNOWN
from edc_base.model.models import BaseUuidModel
from edc_base.model.validators import date_not_future
from edc_visit_tracking.models import CrfInlineModelMixin
from edc_sync.models import Sync... | TshepangRas/tshilo-dikotla | td_infant/models/infant_fu_immunizations.py | Python | gpl-2.0 | 3,416 | [
"VisIt"
] | 4c34ff20a03789bd1114f2853958dd27f5be7b6e26cae2adc8496e2ed108e09d |
# coding: utf-8
"""
Acceptance tests for Studio's Setting pages
"""
from __future__ import unicode_literals
from nose.plugins.attrib import attr
from unittest import skip
from base_studio_test import StudioCourseTest
from bok_choy.promise import EmptyPromise
from ...fixtures.course import XBlockFixtureDesc
from ..help... | playm2mboy/edx-platform | common/test/acceptance/tests/studio/test_studio_settings.py | Python | agpl-3.0 | 19,808 | [
"VisIt"
] | c63a50573d227cc82705269ed90bd14338f47b14abd2679b88dd6bfc0cc12825 |
"""
This code generates the path required for a knight's tour
around a chessboard with user-specified dimensions
Written by Sophie Li, 2016, modified for use with SenseHat by Stuart Weenig
http://blog.justsophie.com/algorithm-for-knights-tour-in-python/
"""
import sys
from time import sleep
if raw_input('Use real sen... | sweenig/piwars | knightstour/sophie.py | Python | gpl-3.0 | 5,585 | [
"VisIt"
] | 52da4568f9a9745b37a0416e273027115403d3a0e65690b56556e53aa661cbd9 |
# Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.
#
# This work is licensed under the Creative Commons Attribution-NonCommercial
# 4.0 International License. To view a copy of this license, visit
# http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to
# Creative Commons, PO Box 1866, Mountain ... | microsoft/DiscoFaceGAN | metrics/metric_base.py | Python | mit | 6,479 | [
"VisIt"
] | c9013c84af79bc60cfca7025781fef8d124ac26a6fef5ca23ce59b891ba5a93f |
import os.path as op
from sfepy.base.base import *
from sfepy.base.conf import transform_variables, transform_fields
from sfepy.base.testing import TestCommon
variables = {
'u' : ('unknown field', 'f', 0),
'v' : ('test field', 'f', 'u'),
}
def in_dir(adir):
return lambda x: op.join(adir, x... | olivierverdier/sfepy | tests/test_mesh_interp.py | Python | bsd-3-clause | 5,360 | [
"VTK"
] | aaa41468b18cee229194e9fea7145167d5ad82004187bfc19f250774e034eae7 |
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# 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 library ... | FedoraScientific/salome-hexablock | src/TEST_PY/test_v6/makeSphere.py | Python | lgpl-2.1 | 1,306 | [
"VTK"
] | 188438c49d379dc8c02066408bde606bcfc3db21f592a8c0707c89c26f6115c7 |
import os, sys
import constants as C
def count_keys(hash):
return len([x for x in hash])
def trim_distal_primer(primers_list, seq, trim_type, begin, end):
"""Doc string here.."""
d_primer_found = ""
trimmedPortion = ""
loc = 0
# chage this to find the primer within C.dista... | avoorhis/mbl_sequencing_pipeline | pipeline/primer_utils20120211.py | Python | gpl-2.0 | 17,584 | [
"BLAST"
] | 4a4a04c6dbc2ba2b5d8201601ace6dc7bcda6b0c840e989ddc00cacd7d04d84c |
# -*- coding: UTF-8 -*-
"""
Routines to visualize the DA White Dwarf model atmosphere fit
"""
from __future__ import absolute_import
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
from scipy.stats import norm
from itertools import cycle
import matplotlib
matplotlib.use... | gnarayan/WDmodel | WDmodel/viz.py | Python | gpl-3.0 | 36,265 | [
"Gaussian"
] | fc4c6bf6b32daeb12380b30897ddd6fce376c19e739a566cf87a2454674c9d28 |
#Robot Framework JMeter Library
#
#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 Software Foundation, either version 3 of the License, or
#any later version.
#
#This program is distributed in the hope that it w... | kowalpy/Robot-Framework-JMeter-Library | JMeterLib.py | Python | lgpl-3.0 | 2,485 | [
"VisIt"
] | 222762a0bd66afbba3f7a2cf8f05656a0cdde038f3392eeb772a30cd5e0898ec |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2018, 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.
"""Calculation of electric multipole moments based on data parsed by cclib."""
import sys
from collections.abc import Ite... | langner/cclib | cclib/method/moments.py | Python | bsd-3-clause | 5,571 | [
"cclib"
] | 08bcb2997ea9550489cdcfc7cda805779f0209eeb8577cf8550de3c87d13ee5d |
def update_param(name, param):
if name == 'distribution':
param['values'].remove('ordinal')
return param
return None # param untouched
extensions = dict(
extra_params=[('verbose', 'FALSE')],
validate_params="""
# Required maps for different names params, including deprecated params
.g... | michalkurka/h2o-3 | h2o-bindings/bin/custom/R/gen_gbm.py | Python | apache-2.0 | 1,504 | [
"Gaussian"
] | 67082deef2457ef7f8abfdf16eefd4ba01c89642700df204e79078801a896de0 |
"""An Image file reader object.
"""
# Author: KK Rai (kk.rai [at] iitb.ac.in)
# R. Ambareesha (ambareesha [at] iitb.ac.in)
# Chandrashekhar Kaushik
# Suyog Dutt Jain <suyog.jain [at] aero.iitb.ac.in>
# Prabhu Ramachandran <prabhu [at] aero.iitb.ac.in>
# Copyright (c) 2007, Enthough... | liulion/mayavi | mayavi/sources/image_reader.py | Python | bsd-3-clause | 4,931 | [
"Mayavi",
"VTK"
] | b2c59313c4eea0026c1aeee39b5d44f0af7315e56391a6392cef8342a969be7a |
#!/usr/bin/env python
import os.path
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--lammps', type=str, nargs='+',
help='directories containing LAMMPS simulation files', default=[])
parser.add_argument('--espp', type=str, nargs='+',
help='directories c... | pdebuyl/cg_md_polymerization | code/analyse_epoxy.py | Python | bsd-3-clause | 2,007 | [
"ESPResSo",
"LAMMPS"
] | 07a7b7d8f538ce76765a798067d8a9f83c1046464d1a11ae649bf5c3e53d432d |
from __future__ import print_function
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import collections
import os
import gyp
import gyp.common
import gyp.msvs_emulation
import json
import sys
generator_support... | giovannic/giovannic.github.com | node_modules/npm/node_modules/node-gyp/gyp/pylib/gyp/generator/dump_dependency_json.py | Python | mit | 3,465 | [
"VisIt"
] | 5ff428825ee76a0ba3001a12c737ae25213f2d80d5482ed8d6ef227af6e1a2fb |
"""Fast Attention Models utilities."""
import abc
import enum
import functools
from typing import Any, Callable, Dict, Optional, Tuple, Iterable
from absl import logging
from flax import linen as nn
import jax
from jax import lax
from jax import random
import jax.numpy as jnp
import numpy as np
from scenic.model_lib.... | google-research/scenic | scenic/projects/fast_vit/model_utils.py | Python | apache-2.0 | 52,572 | [
"Gaussian"
] | b8ac9542e8fdc6d1e11fc5ead8a82d76429958ca1a0593825c26e5d892f274be |
'''
Copyright (c) 2018 by Tobias Houska
This file is part of Statistical Parameter Optimization Tool for Python(SPOTPY).
:author: Tobias Houska
This file holds the standards for every algorithm.
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __futu... | bees4ever/spotpy | spotpy/algorithms/_algorithm.py | Python | mit | 20,835 | [
"Gaussian"
] | b2944632eca9b9ccb3842ee3d0b103b96d2c1a46399682233a5557bdde899a09 |
# .. py:currentmodule:: dolfin_adjoint
#
# Topology optimisation of fluids in Stokes flow
# ==============================================
#
# .. sectionauthor:: Patrick E. Farrell <patrick.farrell@maths.ox.ac.uk>
#
# This demo solves example 4 of :cite:`borrvall2003`.
#
# Problem definition
# ******************
#
# Th... | live-clones/dolfin-adjoint | examples/stokes-topology/stokes-topology.py | Python | lgpl-3.0 | 13,406 | [
"ParaView"
] | 93fe9ef2396494845c61e7197a8ac8e7932a5b78c166e42559fba642dfb23c24 |
#
# _____ _____ _______ __ _ _______ ______ _______ _____
# | | |_____] |______ | \ | | |_____/ |_____| | |
# |_____| | |______ | \_| | | \_ | | __|__ |_____
#
# _______ _____ __ _ _ _ _______ ______ _______ _____ _____ __ _
# | | | | \ | ... | trailheadlabs/RLIS_Trails_to_OT | RLISTrails2OT.py | Python | mit | 17,351 | [
"ORCA"
] | 874f914518ab6e5a09627a033c8477b5d6dd1779f2398c151b6ab66abd3b2a80 |
#!/usr/bin/env python
"""
Sentry
======
Sentry is a realtime event logging and aggregation platform. It specializes
in monitoring errors and extracting all the information needed to do a proper
post-mortem without any of the hassle of the standard user feedback loop.
Sentry is a Server
------------------
The Sentry ... | ngonzalvez/sentry | setup.py | Python | bsd-3-clause | 6,988 | [
"GULP"
] | 534e1a28d9742220910e85f014234fe0902582361018332aea453d1d15a14c55 |
"""Validate dependencies."""
import ast
from pathlib import Path
from typing import Dict, Set
from homeassistant.requirements import DISCOVERY_INTEGRATIONS
from .model import Integration
class ImportCollector(ast.NodeVisitor):
"""Collect all integrations referenced."""
def __init__(self, integration: Integ... | nkgilley/home-assistant | script/hassfest/dependencies.py | Python | apache-2.0 | 8,331 | [
"VisIt"
] | 566f1ffbf6435c89d8fba22b19a0b16e95c91100b8ac9d8bb8f7deb9abff71cf |
import numpy as np
import scipy.sparse as ss
from tomviz import utils
import tomviz.operators
import time
class ReconARTOperator(tomviz.operators.CancelableOperator):
def transform_scalars(self, dataset, Niter=1):
"""
3D Reconstruction using Algebraic Reconstruction Technique (ART)
"""
... | cryos/tomviz | tomviz/python/Recon_ART.py | Python | bsd-3-clause | 7,960 | [
"VTK"
] | 1ab2b4d663051c72b1f168a9de05667def5352a1cbfa772891a0ec4ee5a7de5a |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | pierrelapointe/scancode-toolkit | src/licensedcode/__init__.py | Python | apache-2.0 | 1,570 | [
"VisIt"
] | 44b5bd252594c5857d42c3710ab50f9c507b9cdd59e91e15eff7026b26b347fe |
from __future__ import absolute_import, division
from django.conf import settings
from django.core import urlresolvers
from django.db import connection
from django.db.models import Sum
from django.db.models.query import QuerySet
from django.http import HttpResponseNotFound, HttpRequest, HttpResponse
from django.templa... | vaidap/zulip | analytics/views.py | Python | apache-2.0 | 36,396 | [
"VisIt"
] | 96ab6d693523945d48d48a5e43a0e11a1695f69ee341175ccdf3b7c44a60a9db |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/analysis/test_nuclinfo.py | Python | gpl-2.0 | 5,976 | [
"MDAnalysis"
] | dd3720c3941242df81e5990c077e131f4601c044e0f90aec32ae7436431a6cc8 |
#Copyright ReportLab Europe Ltd. 2000-2012
#see license.txt for license details
__version__ = '$Id$'
from tools.docco.rl_doc_utils import *
from reportlab.platypus.tableofcontents import TableOfContents
from datetime import datetime
import reportlab
from reportlab.rl_config import invariant
title("ReportLab PDF Librar... | Distrotech/reportlab | docs/userguide/ch1_intro.py | Python | bsd-3-clause | 16,512 | [
"VisIt"
] | d23e51ceadce8cd513f3c5c067a740fdc4d3d83cc096a7d6000b72e279ea11ae |
import datetime as dt
import re
import pytest
from marshmallow import fields, validate
from .schemas import CategorySchema, CustomList, CustomStringField, CustomIntegerField
from .utils import build_ref, get_schemas
def test_field2choices_preserving_order(openapi):
choices = ["a", "b", "c", "aa", "0", "cc"]
... | marshmallow-code/apispec | tests/test_ext_marshmallow_field.py | Python | mit | 14,507 | [
"Brian"
] | 322638d21641fb6092f0ac640cd0dc172c6fa65b2d2a5aa16890414906b50579 |
import os, sys, re, inspect, types, errno, pprint, subprocess, io, shutil
import ParseGetPot
import copy
from socket import gethostname
#from options import *
from util import *
from time import sleep
from RunParallel import RunParallel
from CSVDiffer import CSVDiffer
from XMLDiffer import XMLDiffer
from Tester import ... | amburan/moose | framework/scripts/TestHarness/TestHarness.py | Python | lgpl-2.1 | 34,926 | [
"MOOSE",
"VTK"
] | 49229dab8125b7354aa271575553947b5fd456a052a84eece748b9f4a86b2010 |
"""
:mod: Utils
Module that collects utility functions.
"""
import fnmatch
from DIRAC import gConfig, S_OK
from DIRAC.Core.Utilities import List
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
def voimport(base_mod):
"""
Function to import from extensions, if not found, tries fro... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Utilities/Utils.py | Python | gpl-3.0 | 2,883 | [
"DIRAC"
] | 4ec8cf94f4860802f803c108bfee1a0402a6dbfb75aacfa8ddb6c3c5b18fcfaa |
# Copyright 2017 Canonical Ltd.
# Licensed under the LGPLv3, see LICENCE file for details.
import base64
from datetime import datetime, timedelta
import json
import os
import tempfile
from unittest import TestCase
import nacl.encoding
import requests.cookies
import six
from six.moves.urllib.parse import parse_qs
from ... | fabricematrat/py-macaroon-bakery | macaroonbakery/tests/test_agent.py | Python | lgpl-3.0 | 17,234 | [
"VisIt"
] | 9e7286780a9c8579bedc44e3a764a45a41fc92875b412ae7ef8795d95d4e4485 |
import MDAnalysis
import matplotlib.pyplot as plt
import numpy as np
from MDAnalysis.analysis.align import *
from MDAnalysis.analysis.rms import rmsd
def proRMSD(u,ref):
"""
This function produces RMSD data and plots for Protein.
:input
1) Universe of Trajectory
2) reference universe
... | mktumbi/SimAnaRep | SimAnaRepproRMSD.py | Python | gpl-2.0 | 2,516 | [
"MDAnalysis"
] | b3bde7bda0c9c3cb34cdf6dc9b87fff7806e44d7e6f05e330df4ffedf54c47f5 |
#!/usr/bin/env python
################################################################################
# Copyright (C) 2014, 2015 GenAP, McGill University and Genome Quebec Innovation Centre
#
# This file is part of MUGQIC Pipelines.
#
# MUGQIC Pipelines is free software: you can redistribute it and/or modify
# it und... | ccmbioinfo/mugqic_pipelines | pipelines/rnaseq_denovo_assembly/rnaseq_denovo_assembly.py | Python | lgpl-3.0 | 50,453 | [
"BLAST",
"Bioconductor"
] | 66e5df6cd3431fa82268e87d7fcea033e3b5e254804297ff8aa04a2c8f32197f |
from .tabular_utils import parse_tab_blast, get_queries, get_targets
from ...configuration import DaijinConfiguration, MikadoConfiguration
import functools
def _serialise_tabular(self):
if isinstance(self.xml, str):
self.xml = [self.xml]
else:
assert isinstance(self.xml, (list, set))
asse... | lucventurini/mikado | Mikado/serializers/blast_serializer/tab_serialiser.py | Python | lgpl-3.0 | 1,954 | [
"BLAST"
] | 19620dafdf269b1c3f565e511eef786d42f5aadc16b760cb9332cd67e81a7cfe |
"""PHENICX-Anechoic Dataset Loader
.. admonition:: Dataset Info
:class: dropdown
This dataset includes audio and annotations useful for tasks as score-informed source separation, score following, multi-pitch estimation, transcription or instrument detection, in the context of symphonic music:
M. Miron, J.... | mir-dataset-loaders/mirdata | mirdata/datasets/phenicx_anechoic.py | Python | bsd-3-clause | 13,876 | [
"VisIt"
] | c36ddc46f34334eb63cbf818d9198f63e46e02361e6334acc71ea9863de758b3 |
""" Compares the run-time of the Python and the libmaxdiv implementation of the MDI algorithm on time-series of varying length. """
import sys
sys.path.append('..')
import numpy as np
from time import time
import csv
from maxdiv import maxdiv, maxdiv_util, libmaxdiv_wrapper
# ensure reproducable results
np.random.s... | cvjena/libmaxdiv | tools/timing.py | Python | lgpl-3.0 | 3,848 | [
"Gaussian"
] | 7d35e5063f652e41bc9ad877349d40e32aa57db51fba66e23fdabc30ca9174ff |
# Author: Travis Oliphant
# 1999 -- 2002
from __future__ import division, print_function, absolute_import
import warnings
import threading
from . import sigtools
from scipy._lib.six import callable
from scipy._lib._version import NumpyVersion
from scipy import linalg
from scipy.fftpack import (fft, ifft, ifftshift, ... | felipebetancur/scipy | scipy/signal/signaltools.py | Python | bsd-3-clause | 87,587 | [
"Gaussian"
] | 0c9b57c8e83ab0593b452516ea3de6566363dd9abf659eaf2026c4d524e68195 |
#!/usr/bin/env python
#
# $File: PyMutator.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute ... | BoPeng/simuPOP | docs/PyMutator.py | Python | gpl-2.0 | 1,744 | [
"VisIt"
] | b28da68cb3f5b74acac5bb0220f924579191b03c972ce324a884d0f23820c8b0 |
# -*- 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/analysis/waterdynamics.py | Python | gpl-2.0 | 41,156 | [
"MDAnalysis"
] | f2f0fb9427e50748ac578103b9301159f60a2772c31c267118d1f9cfd30db75a |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Provides an interface to manage URI scheme support in iris.
"""
import collections
from collections import OrderedDict
im... | SciTools/iris | lib/iris/io/__init__.py | Python | lgpl-3.0 | 15,009 | [
"NetCDF"
] | 502aa2cec08784ebe6a76ff2e13cfa314ace3eae235e3f89fa9298a63cb870d1 |
# hdfutil.py ---
#
# Filename: hdfutil.py
# Description:
# Author:
# Maintainer:
# Created: Thu Aug 23 17:34:55 2012 (+0530)
# Version:
# Last-Updated: Mon Sep 3 17:55:03 2012 (+0530)
# By: subha
# Update #: 618
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# Utility function to s... | dilawar/moose-full | moose-core/python/moose/hdfutil.py | Python | gpl-2.0 | 13,698 | [
"MOOSE"
] | b433a2d8cd8c76fd47698e4b954b4c920c56d2166b81833695d4babeb78be06d |
import unittest
from test import support
from itertools import *
from weakref import proxy
from decimal import Decimal
from fractions import Fraction
import sys
import operator
import random
import copy
import pickle
from functools import reduce
maxsize = support.MAX_Py_ssize_t
minsize = -maxsize-1
def ... | theheros/kbengine | kbe/res/scripts/common/Lib/test/test_itertools.py | Python | lgpl-3.0 | 71,090 | [
"GULP"
] | 428e9737858a5ec2d42ebbfc60e811c93fc11aa9f5c2b6276a3d434c435c2e1f |
#!/usr/bin/env python
# -*- coding: utf-8 -*- #
from __future__ import unicode_literals
AUTHOR = 'Adrian Torrie'
SITENAME = 'adriantorrie.github.io'
SITESUBTITLE = 'Python Data Science and Machine Learning portfolio.'
SITEURL = 'https://adriantorrie.github.io'
RELATIVE_URLS = True
CATEGORY_URL = 'category/{slug}.html'... | adriantorrie/adriantorrie.github.io_src | pelicanconf.py | Python | mit | 1,942 | [
"VisIt"
] | 09093445a7e91ec1eb74ec7d783c0f4f0f393eb5329258aa57c37f5d117f9755 |
import unittest
import numpy as np
from numpy.testing import assert_allclose
from doubly_stochastic_dgp.layers import GPMC_Layer, GPR_Layer
from gpflow import settings as _settings
from gpflow import session_manager as _session_manager
custom_config = _settings.get_settings()
custom_config.numerics.jitter_level = 1... | ICL-SML/Doubly-Stochastic-DGP | tests/test_zoo_models.py | Python | apache-2.0 | 5,700 | [
"Gaussian"
] | 66a38e3487a02a1cc20ef214e845fb25a73026c67470b9f0f1fe86508b56c36c |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | fweik/espresso | testsuite/python/mmm1d.py | Python | gpl-3.0 | 4,601 | [
"ESPResSo"
] | 5bb31972b4c2deb7706b13c73db6a1bc246f65158b30179d1248181dbe781380 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | espressopp/espressopp | src/external/__init__.py | Python | gpl-3.0 | 978 | [
"ESPResSo"
] | 63d59a4f4155a9efa5ad2a5a30f8a50dad82a81634487dca20764767e14970fe |
# ============================================================================
#
# 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/view/templates/__init__.py | Python | gpl-2.0 | 1,286 | [
"VisIt"
] | b6f8ea405b3a938559cb002fbc9024390d323512eb455b74689380029d8e381b |
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