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#!/usr/bin/env python
"""
Copyright 2001 Pearu Peterson all rights reserved,
Pearu Peterson <pearu@ioc.ee>
Permission to use, modify, and distribute this software is given under the
terms of the LGPL. See http://www.fsf.org
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK.
$Revision: 1.1 $
$Date:... | chunshen1987/iSS | utilities/for_paraview/lib152/LookupTable.py | Python | mit | 1,505 | [
"VTK"
] | 53e39e330dde4ace5fa3162eae5144bd971f17cd384ece396b092b48cc1033c9 |
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #
# (c) 2010... | Chuban/moose | python/chigger/graphs/__init__.py | Python | lgpl-2.1 | 939 | [
"MOOSE"
] | 5345abb086cebd0f2fc3bb7135f71c785a72cb40264ad4d5205a4a3a58a990ef |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from __future__ import absolute_import
import json
from datetime import datetime, timedelta
import ddt
import six
from six.moves import range
from openedx.core.lib.tests import attr
from ...fixtures.course import CourseFixture, XBlockFixtureDesc
from ..... | ESOedX/edx-platform | common/test/acceptance/tests/lms/test_lms_courseware.py | Python | agpl-3.0 | 39,021 | [
"VisIt"
] | 5daf77d76957da320145b2787220f3411d6f4053becd464934376c4ff9a985fb |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
import biplist
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description... | apptentive/apptentive-titanium | ApptentiveModule/build.py | Python | bsd-3-clause | 7,344 | [
"VisIt"
] | 8d859d5fcdea185f156f9e0de7528d867bb6153e98d8e7b29306f06e93985960 |
import copy, utils.log, random
from utils.utils import randGaussBounds
from logic.smbool import SMBool, smboolFalse
from logic.smboolmanager import SMBoolManager
from logic.helpers import Bosses
from graph.graph_utils import getAccessPoint, GraphUtils
from rando.Filler import FrontFiller
from rando.FillerRandom import... | theonlydude/RandomMetroidSolver | rando/RandoSetup.py | Python | mit | 25,990 | [
"Gaussian"
] | b5c48463c137ecef64882ec84c696da389cd37e7cb758e8827e4f3b02ba81c66 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Complete pipeline for online processing using OnACID.
@author: Andrea Giovannucci @agiovann and Eftychios Pnevmatikakis @epnev
Special thanks to Andreas Tolias and his lab at Baylor College of Medicine
for sharing their data used in this demo.
KERAS_BACKEND=tensorflow... | simonsfoundation/CaImAn | use_cases/CaImAnpaper/create_movie_zebra.py | Python | gpl-2.0 | 15,113 | [
"NEURON"
] | 8573624ddff42a77be23a2694a48eb91de31da1712ae26623676743fe89e5531 |
"""
This a nonuniform sampler with jittered sampling (JS) sampling scheme. |br|
The modules samples the given signals nonuniformly. |br|
The sampling aptterns are generated using JS scheme.
The used JS patterns generator is described further in
"Generation and Analysis of Constrained Random Sampling Patterns",
availa... | JacekPierzchlewski/RxCS | rxcs/acq/nonuniJS.py | Python | bsd-2-clause | 19,801 | [
"Gaussian"
] | 91a3bace50c77a27bfacdcc2deb6fb6dee0ee918e6a5b9c095c31b222e9b265a |
../../../../../../../../share/pyshared/orca/scripts/apps/yelp/yelp_v2/script_settings.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/yelp/yelp_v2/script_settings.py | Python | gpl-3.0 | 88 | [
"ORCA"
] | 343eb2670c6f17ae2a5ca05aeed1785f20c21bbeeeaa019aa4063f6b4582a72d |
##############################################################################
# Copyright (c) 2013-2018, 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... | EmreAtes/spack | var/spack/repos/builtin/packages/r-kegggraph/package.py | Python | lgpl-2.1 | 2,078 | [
"Bioconductor"
] | d410ec1f76fb9e87919bd9584fb402e991184daf2d06576f896fcace73cb75d9 |
# -*- coding: UTF-8 -*-
"""
Based on ``behave tutorial``
Feature: Step Parameters
Scenario: Blenders
Given I put "apples" in a blender
When I switch the blender on
Then it should transform into "apple juice".
Feature: Scenario Outline
Scenario Outline: Blenders
Given I put <thing> in a blende... | raulpush/monitorizare-site | bin/features/steps/step_tutorial03.py | Python | apache-2.0 | 1,424 | [
"Galaxy"
] | 25ee353227a3553b952a94bb0f911096c5a526a605f7aab139ef768adec94f7f |
"""Test of BLACS Redistributor.
Requires at least 8 MPI tasks.
"""
import sys
import numpy as np
from gpaw.band_descriptor import BandDescriptor
from gpaw.grid_descriptor import GridDescriptor
from gpaw.mpi import world, distribute_cpus
from gpaw.utilities import compiled_with_sl
from gpaw.utilities.scalapack impor... | robwarm/gpaw-symm | gpaw/test/parallel/realspace_blacs.py | Python | gpl-3.0 | 3,818 | [
"GPAW"
] | 6a0b2a92055e278c39e10df6c875549ad7a3548e86b8d54dc299d48492562c1a |
# Copyright 2012 by Eric Talevich. 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.
"""Command-line wrapper for the tree inference program RAxML.
Derived from the help page for RA... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Phylo/Applications/_Raxml.py | Python | gpl-2.0 | 19,858 | [
"Biopython"
] | e9b599c470deb93a70f9d7ae7f5a47daa20862c02102f9b37cf53a30979d6128 |
# -*- coding: utf-8 -*-
#
# brunel2000_classes.py
#
# This file is part of cynest.
#
# Copyright (C) 2004 The cynest Initiative
#
# cynest 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 th... | gewaltig/cython-neuron | cynest/nest/tests/test_graphics.py | Python | gpl-2.0 | 5,928 | [
"NEURON"
] | 68e901e24257476b24c0226962617610029cdcb337bdf1173eb56659599989b2 |
# -*- coding: utf-8 -*-
"""
Created on Fri Feb 19 17:55:55 2016
@author: nblago
"""
import numpy as np
from matplotlib import pylab as plt
import scipy.optimize as opt
def twoD_Gaussian(xdata_tuple, amplitude, xo, yo, sigma_x, sigma_y, theta, offset):
'''
Produces a 2D gaussian centered in xo, yo with the pa... | scizen9/kpy | SEDMrph/fit_utils.py | Python | gpl-2.0 | 3,020 | [
"Gaussian"
] | 4daaf51885379c618ccb64e2fd502b4f7413981f82695623b47157d3db8d0f5e |
#!/usr/bin/python
# EPG Simulation code, based off of Matlab scripts from Brian Hargreaves <bah@stanford.edu>
# 2015 Jonathan Tamir <jtamir@eecs.berkeley.edu>
from __future__ import division
import numpy as np
from numpy import pi, cos, sin, exp, conj
from warnings import warn
def rf(FpFmZ, alpha, phi):
"Same as... | jtamir/mri-sim-py | epg/epg.py | Python | mit | 9,067 | [
"Brian"
] | efee6f2749798b01694ae0f06de9af4f88c4cb8311df6e28fb2435bcec19eb62 |
'''
Copyright (c) 2017 Yogesh Khatri
This file is part of mac_apt (macOS Artifact Parsing Tool).
Usage or distribution of this software/code is subject to the
terms of the MIT License.
'''
import binascii
import collections
import csv
import logging
import os
import sqlite3
import sys
import xlsxwri... | ydkhatri/mac_apt | plugins/helpers/writer.py | Python | mit | 36,470 | [
"MOE"
] | bf7c13d13902ed8fee68844bc93e95f066c5a73d89a748be14ce2cfe3ae3c2dc |
import oauth2 as oauth
import json
import urllib
import unittest
import random
# Stashboard application id
app_id = "stashboard-hrd"
# These keys can be found at /admin/credentials
consumer_key = 'anonymous'
consumer_secret = 'anonymous'
oauth_key = 'ACCESS_TOKEN'
oauth_secret = 'ACCESS_SECRET'
# Create your consume... | Mfellner77/stashboard | docs/_static/examples/example.py | Python | mit | 1,850 | [
"exciting"
] | 54d7b5ceca09f9b8856d4dcbe04c2938700d6053a75362b92747354ca8187011 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
# Copyright 2010-2013 The Orca Team
#
# 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... | h4ck3rm1k3/orca-sonar | src/orca/structural_navigation.py | Python | lgpl-2.1 | 136,541 | [
"ORCA"
] | d6532e61e2ec7dd0bacc0f125c221d16a6947a369cabd17248403dda86550f0f |
# coding: utf-8
"""A tornado based Jupyter notebook server."""
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
from __future__ import absolute_import, print_function
import notebook
import binascii
import datetime
import errno
import importlib
import io
import jso... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/notebook/notebookapp.py | Python | bsd-2-clause | 55,293 | [
"VisIt"
] | a5957d23037fbed55ab200775473cc8471bbebe6f9d0ab5a833bddabb59bde7f |
#!/usr/bin/env python
"""
Adapted from bx/scripts/axt_to_fasta.py
"""
from galaxy import eggs
import pkg_resources
pkg_resources.require( "bx-python" )
import sys
import bx.align.axt
def usage(s=None):
message = """
axt_to_fasta species1 species2 < axt_file > fasta_file
"""
if (s == None): sys.exit (message)
else:... | volpino/Yeps-EURAC | tools/filters/axt_to_fasta.py | Python | mit | 1,082 | [
"Galaxy"
] | 8c066bbe3f405f62c0c3dc7b4f0c9ee89b366eb01316e064a0141bb2623438b8 |
class person:
population = 0;
def __init__(self,name):
self.name = name;
self.__class__.population+=1;
# or person.population +=1;
def sayHi(self):
print 'my name is ',self.name
@classmethod #how_many = classmethod(how_many)
def how_many(self):
print 'population: {}'.format(self.population)
def sayhi(... | dramaticlly/Python4Interview | pyclass.py | Python | mit | 1,258 | [
"CFOUR"
] | 64ee18b419ff2b93a2374781f59f22b298afcea7ea347101239725f79397c835 |
"""
This module provides GOCDB2CSAgent code.
The agent is used to synchronize information between GOCDB and DIRAC configuration System (CS)
Right now it only adds perfosonar endpoints
The following options can be set for the GOCDB2CSAgent.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN GOCDB2CSAge... | DIRACGrid/DIRAC | src/DIRAC/ConfigurationSystem/Agent/GOCDB2CSAgent.py | Python | gpl-3.0 | 11,417 | [
"DIRAC"
] | c55fa6e82fecf4193b35a364937e7465a68412c73810c1c603fb32c8c79a7a44 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/crystal/defects/__init__.py | Python | gpl-3.0 | 45,250 | [
"CRYSTAL",
"VASP"
] | e10b389c2304cef8e71aa68367c5b0f04e84cec4ab8a90714baf95c79acbb209 |
import numpy as np
import pyarrow as pa
import vaex
from ..expression import _binary_ops, _unary_ops, reversable
class NumpyDispatch:
def __init__(self, arrow_array):
self.arrow_array = arrow_array
self._numpy_array = None
@property
def numpy_array(self):
# convert lazily, since no... | maartenbreddels/vaex | packages/vaex-core/vaex/arrow/numpy_dispatch.py | Python | mit | 2,184 | [
"VisIt"
] | d338fa2bcbc144ab635013a15fb4431e80876ca640e4abdb5345fb15606f9fd9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
TODO: Modify module doc.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "... | sonium0/pymatgen | pymatgen/io/tests/test_nwchem.py | Python | mit | 12,100 | [
"NWChem",
"pymatgen"
] | ec8da46808f0ed863a0930cdfe29ad6bb8876b32351f8e8c2d44761fbd61d11d |
# Copyright (c) 2015-2016 Cisco Systems, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge... | cimarron-pistoncloud/molecule | test/unit/core/test_core.py | Python | mit | 4,639 | [
"Galaxy"
] | 03ffcf90749afb54be7cdf1bd282251febdb3641b2885d371c184de1a328fd7a |
"""Some test functions for bivariate interpolation.
Most of these have been yoinked from ACM TOMS 792.
http://netlib.org/toms/792
"""
import numpy as np
from triangulate import Triangulation
class TestData(dict):
def __init__(self, *args, **kwds):
dict.__init__(self, *args, **kwds)
self.__dict__ ... | runt18/nupic | external/linux32/lib/python2.6/site-packages/matplotlib/delaunay/testfuncs.py | Python | agpl-3.0 | 20,963 | [
"Gaussian"
] | 19876a9eadc9491df00f0717300df741005a806c8fa1deee7309ed2bc99aa911 |
#############################################################################
# $HeadURL$
#############################################################################
""" ..mod: FTSRequest
=================
Helper class to perform FTS job submission and monitoring.
:deprecated:
"""
# # imports
import sys... | calancha/DIRAC | DataManagementSystem/Client/FTSRequest.py | Python | gpl-3.0 | 38,242 | [
"DIRAC"
] | f96516926ababca93f7736bd74e62f8396a35d599f846f0f137eb35f92ec4004 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# @Author: Brian Cherinka, José Sánchez-Gallego, and Brett Andrews
# @Filename: test_cube.py
# @License: BSD 3-clause (http://www.opensource.org/licenses/BSD-3-Clause)
#
# @Last modified by: José Sánchez-Gallego (gallegoj@uw.edu)
# @Last modified time: 2018-07-25 18:06:38... | albireox/marvin | python/marvin/tests/tools/test_cube.py | Python | bsd-3-clause | 11,015 | [
"Brian",
"Galaxy"
] | fc72cce3b2a19f5efe8306ace358b30e0c7b2c3d13f22aa9e4bfde3d53d0a4dc |
##########################################################################################
#
# run_parallel_xml_parser
#
#
# Copyright (c) 06/08/2013 Davit Bzhalava
#
##########################################################################################
"""
./run_parallel_xml_parser.py -i xml.out -f query... | NIASC/VirusMeta | blast_module/run_parallel_xml_parser.py | Python | gpl-3.0 | 13,517 | [
"BLAST"
] | 5f79c398cb6439104dae93694f340dd1f17a586d886af347f65ac531dfbb3c96 |
# -*- coding: utf8 -*-
#
# Module MESH
#
# Part of Nutils: open source numerical utilities for Python. Jointly developed
# by HvZ Computational Engineering, TU/e Multiscale Engineering Fluid Dynamics,
# and others. More info at http://nutils.org <info@nutils.org>. (c) 2014
"""
The mesh module provides mesh generators:... | timovanopstal/nutils | nutils/mesh.py | Python | mit | 16,422 | [
"VTK"
] | eb132064579e7b1d9dc4ec2ccab341509e7a7811367341e3666b2e997d03835d |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkTIFFWriter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtk... | nagyistoce/devide | modules/vtk_basic/vtkTIFFWriter.py | Python | bsd-3-clause | 468 | [
"VTK"
] | 2659550e152ecc3fefe08e053df524c44be1a781094b18755cbab0dbcf88b672 |
import numpy, mlpy, time, scipy, os
import audioFeatureExtraction as aF
import audioTrainTest as aT
import audioBasicIO
import matplotlib.pyplot as plt
from scipy.spatial import distance
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from sklearn.lda import LDA
import csv, os.path, sklearn, sklearn.hmm, cPi... | lehinevych/smrs | project/lib/audio/audioSegmentation.py | Python | mit | 33,347 | [
"Gaussian"
] | 2ea6dd250b09a8fc4c574af5dae8937c620778f28bc036770ecec80a2eca078e |
# Copyright 2014 PerfKitBenchmarker Authors. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... | AdamIsrael/PerfKitBenchmarker | perfkitbenchmarker/linux_benchmarks/speccpu2006_benchmark.py | Python | apache-2.0 | 19,410 | [
"GAMESS",
"Gromacs",
"NAMD",
"VisIt"
] | d73bd9bbf5d7659c375844cdf4a4fb5a0065f88c797d16a43aee515cc742b5ac |
from django.core.validators import MinValueValidator, MaxValueValidator
from django.db import models, IntegrityError
from datetime import datetime
from edc.core.crypto_fields.fields import EncryptedFirstnameField
from edc.subject.appointment.models import Appointment
from edc.subject.appointment_helper.models import ... | botswana-harvard/edc-bhp074 | bhp074/apps/eit_infant/models/infant_birth.py | Python | gpl-2.0 | 3,774 | [
"VisIt"
] | 7c4b0c705f5c9b01fe92f9a00b83c542bf77755a3114ce721d5142f0d47fbf12 |
import unittest
from MooseDocs.testing import MarkdownTestCase
class TestSlider(MarkdownTestCase):
"""
Test to make sure that "moose/python/MooseDocs/extensions/MooseSlider.py"
parses a test block correctly.
"""
def testSlider(self):
self.assertConvert('test_slider.html', 'test_slider.md')
| stimpsonsg/moose | docs/tests/slider/test_slider.py | Python | lgpl-2.1 | 320 | [
"MOOSE"
] | c36983ffd23e3951f8438e914e1bbbc5eb633a172142254164c2baa2b316cde2 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test single point, unrestricted time-dependent logfiles in cclib"""
import os
import unittest
import numpy
from skip... | cclib/cclib | test/data/testTDun.py | Python | bsd-3-clause | 2,804 | [
"MOLCAS",
"TURBOMOLE",
"cclib"
] | f54a3b07a7956596850a080f8de9ec1266e500521ec0cf2986df159211783b03 |
#!/usr/bin/env python
from instagram.client import InstagramAPI
from ConfigParser import SafeConfigParser
import argparse
import datetime
import logging
config_parser = SafeConfigParser()
config_parser.read('config')
arg_parser = argparse.ArgumentParser(description='Auto-like my GF\'s Instagram')
arg_parser.add_argu... | VirenMohindra/InstaGF | insta_gf.py | Python | mit | 3,064 | [
"VisIt"
] | e4b5d642ad2119f8decc5122cb4ce56e9e21628528f1e107018fcfb1d094668d |
from typing import Text
def is_reserved_subdomain(subdomain):
# type: (Text) -> bool
if subdomain in ZULIP_RESERVED_SUBDOMAINS:
return True
if subdomain[-1] == 's' and subdomain[:-1] in ZULIP_RESERVED_SUBDOMAINS:
return True
if subdomain in GENERIC_RESERVED_SUBDOMAINS:
return Tr... | vaidap/zulip | zerver/lib/name_restrictions.py | Python | apache-2.0 | 26,777 | [
"Octopus"
] | 5003441185351e1d82b93a22214f1ec27ba13781c00d3dbc728ade7eeb56f164 |
# Copyright 2022 The Scenic 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 w... | google-research/scenic | scenic/train_lib/optimizers.py | Python | apache-2.0 | 8,623 | [
"VisIt"
] | 5f8384a9d8b63b34e8fb815f2acff832a044bf19d2c7deaf201cbcc8b7d2bdeb |
"""
DataFrame
---------
An efficient 2D container for potentially mixed-type time series or other
labeled data series.
Similar to its R counterpart, data.frame, except providing automatic data
alignment and a host of useful data manipulation methods having to do with the
labeling information
"""
from __future__ import... | rs2/pandas | pandas/core/frame.py | Python | bsd-3-clause | 372,297 | [
"Elk"
] | 57d037c6725cf8805fffef310708f3738a46537948ca798bba3f80c19800a1e1 |
import numpy as np
from unittest import TestCase
from exatomic.va import GenInput as gi, gen_delta
from exatomic.gaussian import Fchk
from exatomic.adf import Output
from exatomic.base import resource
class TestGenInput(TestCase):
def setUp(self):
self.h2o2 = Fchk(resource('g16-h2o2-def2tzvp-freq.fchk'))
... | exa-analytics/atomic | exatomic/va/tests/test_inputs.py | Python | apache-2.0 | 3,564 | [
"ADF",
"Gaussian"
] | 3c83f484d5c2b4b785e9f94beead1b1f6a3249e560bc1aead3722fbdf1347502 |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=1) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=1) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfiles --... | ktan2020/legacy-automation | win/Lib/mimetypes.py | Python | mit | 21,200 | [
"NetCDF"
] | e04d7655e9452cd8bb9020ef20caa2e11b3f60bdb8cbfb7edb19f995ed4961d4 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | testsuite/python/dawaanr-and-bh-gpu.py | Python | gpl-3.0 | 6,480 | [
"ESPResSo"
] | eaa9c902028ec512e138e63be40f45e30d4fa46815ca33cd5efd91826823e46e |
#!/usr/bin/env python
########################################################################
# :file: dirac-dms-directory-sync
# :author: Marko Petric
########################################################################
"""
Provides basic rsync functionality for DIRAC
Syncs the source destination folder recu... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_directory_sync.py | Python | gpl-3.0 | 18,385 | [
"DIRAC"
] | 8f97a9c30c761c43e2fb36a6d775e5683e6342a2eb9e36218109eb93bf1c51cc |
''' Tests for netcdf '''
from __future__ import division, print_function, absolute_import
import os
from os.path import join as pjoin, dirname
import shutil
import tempfile
import warnings
from io import BytesIO
from glob import glob
from contextlib import contextmanager
import numpy as np
from numpy.testing import (... | arokem/scipy | scipy/io/tests/test_netcdf.py | Python | bsd-3-clause | 19,268 | [
"NetCDF"
] | 3791fd7db8d5f94fb0e232efddb6bbd4e827192a0201600476f86ce6a2ab17b4 |
"""\
DFunctionals.py Exchange and Correlation Density Functionals
This program is part of the PyQuante quantum chemistry program suite.
Copyright (c) 2004, Richard P. Muller. All Rights Reserved.
PyQuante version 1.2 and later is covered by the modified BSD
license. Please see the file LICENSE that is part of ... | berquist/PyQuante | PyQuante/DFunctionals.py | Python | bsd-3-clause | 29,043 | [
"DIRAC"
] | cb22006ba365a4182a3f316ee8b673ea8bb8437f33a748728e734ea6765e30b5 |
# (C) British Crown Copyright 2014 - 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/unit/fileformats/pyke_rules/compiled_krb/fc_rules_cf_fc/test_build_auxiliary_coordinate.py | Python | gpl-3.0 | 7,457 | [
"NetCDF"
] | e3d1b18a10b12c67d5dab51c8cd72c5b44f544732ca74299d75086323eeff9c2 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import pickle
import os
import numpy as np
import warnings
import scipy.constants as const
from pathlib import Path
from monty.tempfile import ScratchDir
from pymatgen.util.testing import Pymat... | dongsenfo/pymatgen | pymatgen/io/vasp/tests/test_inputs.py | Python | mit | 32,263 | [
"VASP",
"pymatgen"
] | e6822784a4aa7a2dee27c19b5135239306282f9dea2cd580054760b90681b69f |
#!/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 | modules/geochemistry/python/tests/test_readerutils.py | Python | lgpl-2.1 | 2,809 | [
"MOOSE"
] | ff51c23bee149a7c27bd4a5188002d1d2c80057aa725f019cacfeef426683090 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | Garrett-R/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 25,170 | [
"Gaussian"
] | f2844bca96c34729bbf24e7ca5b45a78eccae5909aef829e196f636df86ac6da |
#! /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-os-config | scripts/fixup_osconfig_v1_keywords.py | Python | apache-2.0 | 7,591 | [
"VisIt"
] | 47293a7b8182a9dac9539882acaa28bb348cff70d6d2e013f472c7d7b5a876db |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Import csv library; Part of python standard libs
import csv
# Import 3rd party packages. Check if installed and die with error message
# if not.
try:
import matplotlib as mpl
import mpl_toolkits.axes_grid1
mpl.use('Qt5Agg')
mpl.interactive(True)
im... | Athemis/PyDSF | pydsf.py | Python | mit | 26,410 | [
"Gaussian"
] | 4eda55d6384fc042d61e7148b300a442f04ba9c031e7a7ea2e3bb00952b0fd49 |
from tensor import tensor, new, lorentz_key
from c_variable import c_variable
from itertools import permutations
type_dict = {
1 : "CScalar",
2 : "CSpinor",
3 : "CVec4",
5 : "CTensor"
}
vect_gauge_dict = {
0 : "0",
1 : "ATOOLS::Spinor<SType>::R1()",
2 : "ATOOLS::Spinor<SType>::R2()",
3... | cms-externals/sherpa | MODEL/UFO/lorentz_structures.py | Python | gpl-3.0 | 8,060 | [
"DIRAC"
] | c23e00a1ffdf92195688af87d6d8a10cd8f022eddcdaa1f32fd7c5e95a97080d |
"""
roi_fitting.py
Part of the CsPyController experiment control software
author = Martin Lichtman
housekeeper = Y.S.@AQuA
created = 2014.07.01
modified >= 2015.10.19
This file contains an analysis which tries to fit 121 gaussians to the atom
array.
"""
from __future__ import division
import logging
import numpy a... | QuantumQuadrate/CsPyController | python/roi_fitting.py | Python | lgpl-3.0 | 16,886 | [
"Gaussian"
] | 33e53d93787b0b1a2d5b78cd07fd20e015a8bcb23f90dfa2b8bbf82408d0a9ac |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
'''
Created on Jun 27, 2012
'''
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "S... | sonium0/pymatgen | pymatgen/entries/tests/test_exp_entries.py | Python | mit | 1,282 | [
"pymatgen"
] | 8292bffb69047bb1b1dc86aef24be7fda4cba1376c4b996d57e3b83ede91cb9b |
# -*- coding: utf-8 -*-
"""Van der Waals density functional.
This module implements the Dion-Rydberg-Schröder-Langreth-Lundqvist
XC-functional. There are two implementations:
1. A simlpe real-space double sum.
2. A more efficient FFT implementation based on the Román-Péres-Soler paper.
"""
import os
import sys
i... | ajylee/gpaw-rtxs | gpaw/xc/vdw.py | Python | gpl-3.0 | 26,614 | [
"GPAW"
] | 30da5b2e3958c917aba1f7c5be9614a78539a0f1c94453feb585ee560319ff6d |
#!/usr/bin/env python
import logging
import sys
import argparse
import vcf
import pysam
from metasv.breakdancer_reader import BreakDancerReader
from metasv.pindel_reader import PindelReader
from metasv.cnvnator_reader import CNVnatorReader
from metasv.breakseq_reader import BreakSeqReader
from metasv.vcf_utils import... | msahraeian/metasv | scripts/svtool_to_vcf.py | Python | bsd-2-clause | 3,201 | [
"pysam"
] | 3a96a97180c702a28d98efbda664d888463db9280d37dd902a5f177d617ad788 |
import unittest
import netCDF4
from numpy.testing import assert_array_equal
import numpy as np
class Test_Unsigned(unittest.TestCase):
"""
Test autoconversion to unsigned ints when _Unsigned attribute is True.
This attribute is is set by netcdf-java to designate unsigned
integer data stored with a sign... | Unidata/netcdf4-python | test/tst_Unsigned.py | Python | mit | 1,618 | [
"NetCDF"
] | 33c44abd4f73cf4d9e38c46ae377d1a26c3ac713357daffd97e40fa97f1db77d |
# -*- coding: utf-8 -*-
'''
Copyright (C) 2016 Rafael Picanço.
The present file is distributed under the terms of the GNU General Public License (GPL v3.0).
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
'''
import os
impo... | cpicanco/player_plugins | self_contained/gaze_categories.py | Python | gpl-3.0 | 11,632 | [
"Gaussian"
] | 0f94c06e4f015d348a5d0a7a5d20e530f5207af64b0252de937f46670bf57e12 |
#!/usr/bin/env python
## Program: VMTK
## Module: $RCSfile: vmtkfebiowytet10.py,v $
## Language: Python
## Date: $Date: 2016/08/19 09:49:59 $
## Version: $Revision: 1.6 $
## Copyright (c) Jingfeng Jiang, Yu Wang. All rights reserved.
## See LICENCE file for details.
## This software is di... | jjiang-mtu/virtual-breast-project | dynamic_SWE/write_FEBio_format_quadratic/vmtkfebiowytet10.py | Python | gpl-2.0 | 1,844 | [
"VTK"
] | b849a7f384c1a0e8d29c1ec98e817a9fd760087dacd3715c980570dd429a49ab |
# $Id: nodes.py 8592 2020-12-15 23:06:26Z milde $
# Author: David Goodger <goodger@python.org>
# Maintainer: docutils-develop@lists.sourceforge.net
# Copyright: This module has been placed in the public domain.
"""
Docutils document tree element class library.
Classes in CamelCase are abstract base classes or auxilia... | sonntagsgesicht/regtest | .aux/venv/lib/python3.9/site-packages/docutils/nodes.py | Python | apache-2.0 | 81,942 | [
"VisIt"
] | 04cf6c2b389348c6a5d602b9b56fbc4010577880ea9517897530767856865a6a |
from psi4 import *
import sys; sys.path.append('.so INSTALL DIRECTORY GOES HERE')
from molutil import *
from driver import *
class _options(object):
def __getattr__(self, obj):
return get_global_option(obj)
def __setattr__(self, obj, val):
set_global_option(obj, val)
options = _options()
| spring01/libPSI | lib/psi4/__init__.py | Python | gpl-2.0 | 319 | [
"Psi4"
] | ecf12c5e212bb9c27bedcd911385e296269cc9f304489cc9bf5b5522afc90415 |
from chemopt import export
from chemopt.configuration import (conf_defaults, fixed_defaults,
substitute_docstr)
from chemopt.interface import molpro, molcas
@export
@substitute_docstr
def calculate(molecule, hamiltonian, basis,
el_calc_input=None, backend=None,
... | mcocdawc/chemopt | src/chemopt/interface/generic.py | Python | lgpl-3.0 | 1,947 | [
"MOLCAS",
"Molpro"
] | 6214240070139eb695acd5e6be5d344baf7cb477ec5bcff79ecf90d6ed973473 |
# Copyright (c) 2013, GlaxoSmithKline Research & Development Ltd.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# ... | rdkit/rdkit | Contrib/fraggle/fraggle.py | Python | bsd-3-clause | 2,638 | [
"RDKit"
] | 0f11d1e1854df35c333f3f21827aa3f7eed4f6be1adecea3dced699cba02d9c1 |
##############################################################################
# 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-biocgenerics/package.py | Python | lgpl-2.1 | 1,731 | [
"Bioconductor"
] | 31b5428c8ab93fe2ec08c3067499e6cb2ea523a784077b04fa743c2516934bbb |
__author__ = "Bruno Fosso"
__version__ = 2.0
__mail__ = "b.fosso@ibbe.cnr.it"
import getopt
import os
import shutil
import sys
import time
from string import strip
try:
import psutil
except:
sys.exit("psutil module not found")
try:
import numpy
except:
sys.exit("numpy module not found")
try:
from ... | bfosso/MetaShot | PE_extraction.py | Python | gpl-3.0 | 6,930 | [
"Biopython"
] | 2764a41a8546105a100d6df648b94899830d15787c4c19b53e9ca544d0757c70 |
"""
Generic module for managing manual data transfer jobs using Galaxy's built-in file browser.
This module can be used by various external services that are configured to transfer data manually.
"""
import logging, urllib2, re, shutil
from data_transfer import *
log = logging.getLogger( __name__ )
__all__ = [ 'Manua... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/jobs/deferred/manual_data_transfer.py | Python | gpl-3.0 | 6,607 | [
"Galaxy"
] | d495f1cf31d6bfe6f50a1cf66c19b81cfcf05259b22fa2b97daa24b6a4ce639f |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS that utilize the
progress page.
"""
from contextlib import contextmanager
import ddt
from six.moves import range
from ...fixtures.course import CourseFixture, XBlockFixtureDesc
from ...pages.common.logout import LogoutPage
from ...pages.lms.courseware import ... | cpennington/edx-platform | common/test/acceptance/tests/lms/test_progress_page.py | Python | agpl-3.0 | 16,757 | [
"VisIt"
] | 766e9d8ba63e396f1bf4a5e8e85a74bd2d28cfdf542e6f424cc55d7f534b89ef |
"""The suite of window functions."""
from __future__ import division, print_function, absolute_import
import warnings
import numpy as np
from scipy import fftpack, linalg, special
from scipy._lib.six import string_types
__all__ = ['boxcar', 'triang', 'parzen', 'bohman', 'blackman', 'nuttall',
'blackmanhar... | sriki18/scipy | scipy/signal/windows.py | Python | bsd-3-clause | 58,296 | [
"Gaussian"
] | a74b25bf170692a5018e3daebaff075770f7129b0f80a8a120872870e0339cd8 |
#!/usr/bin/python2.6
import os, sqlite3
from pygooglechart import SimpleLineChart, XYLineChart, Axis
db = sqlite3.connect("/tmp/moe-data-traffic.db", isolation_level=None)
period = 900
def get_times():
cursor = db.cursor()
cursor.execute("SELECT DISTINCT time FROM bandwidth ORDER BY time ASC")
prev = None
# Don't ... | nanaya/moebooru | public/test/make_stats.py | Python | isc | 6,862 | [
"MOE"
] | d0094e4c8e52926e21c2b2f26ab72c9984322548101f3a076938dcc9a3a30692 |
##
# Copyright 2009-2017 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | ULHPC/easybuild-easyblocks | easybuild/easyblocks/g/gamess_us.py | Python | gpl-2.0 | 14,251 | [
"GAMESS"
] | b27e1a77a199eb632f830b5946d1693f0119eab225fa0da8efb05e978e45f02b |
# -*- coding: utf-8 -*-
""" Sahana Eden Incident Reporting Model
@copyright: 2009-2012 (c) Sahana Software Foundation
@license: MIT
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Sof... | ashwyn/eden-message_parser | modules/eden/irs.py | Python | mit | 58,442 | [
"VisIt"
] | 4282fe959394fd3bcfe3b2d45d734757d0b5a5ecb92716e55caad5571a56a52b |
#!/usr/bin/python
'''*
* Copyright (c) 2013 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... | godofgrunts/Potassium-OBS-Controller | lib/upload_video.py | Python | gpl-3.0 | 5,540 | [
"VisIt"
] | 5d19fe205f526f9144affcd6eeafe01f0231e75a40fc567f97ae2fc2702e8ca6 |
import suspect
import numpy
def test_null_transform():
fid = numpy.ones(128, 'complex')
data = suspect.MRSData(fid, 1.0 / 128, 123)
transformed_data = suspect.processing.frequency_correction.transform_fid(data, 0, 0)
assert type(transformed_data) == suspect.MRSData
def test_water_peak_alignment_mis... | bennyrowland/suspect | tests/test_mrs/test_processing.py | Python | mit | 4,033 | [
"Gaussian"
] | 35e1ef7f5cc269449d400eee2a5f92d8ade273654d29c323a3f004253cb2e549 |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# 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;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | src/rmock/core/data.py | Python | lgpl-3.0 | 6,945 | [
"VisIt"
] | 4e5f370d154f1a161d0902c0a9e5a5bd2a149d5ef701b9e8001da75f157a645a |
"""
This file demonstrates the creation of a directed graph using the
Python interface to VTK.
"""
from vtk import *
#------------------------------------------------------------------------------
# Script Entry Point
#------------------------------------------------------------------------------
if __name__ == "__ma... | berendkleinhaneveld/VTK | Examples/Infovis/Python/graph1.py | Python | bsd-3-clause | 1,552 | [
"VTK"
] | 69b2e5c6dfad8093b528d39e270e434034537187ca4dc393386ba76cddda893a |
# Copyright 2004 by Cymon J. Cox and Frank Kauff. All rights reserved.
# Copyright 2008 by Michiel de Hoon. All rights reserved.
# Revisions copyright 2009 by Cymon J. Cox. All rights reserved.
# Revisions copyright 2009 by Peter Cock. All rights reserved.
#
# This code is part of the Biopython distribution and go... | bryback/quickseq | genescript/Bio/Sequencing/Phd.py | Python | mit | 4,723 | [
"Biopython"
] | a8e44ec558e8bffe69715070a3852ecb9ad17c81dddecf04d18526921dfc10aa |
# coding=utf-8
'''Define Schema'''
from __future__ import absolute_import
from datetime import datetime
from flask import url_for, g
from firefly.ext import db
from firefly.views.utils import timesince
from firefly.models.consts import CATEGORY_COLORS
from .user import User
__all__ = ["Category", "Post", "Video", "... | mozillazg/firefly | firefly/models/topic.py | Python | mit | 3,010 | [
"Firefly"
] | 378b03b9d5295f90db53530800767c7cfcf4d7eb26cb9f83031f31e930826771 |
import sys
import time
import pyaml
try:
from blessed import Terminal
except ImportError:
Terminal = None
from lacore.adf.util import creation
def format_size(bytes):
size = ""
if bytes:
kib = bytes // 1024
mib = kib // 1024
gib = mib // 1024
if not kib:
siz... | longaccess/longaccess-client | lacli/richtext.py | Python | apache-2.0 | 5,760 | [
"ADF"
] | e6dcf2343050188b97c83ee565997051f576c56a378d10befd2b1f2e10c455af |
#
# Copyright (C) 2013 Sean Poyser
#
# 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, or (at your option)
# any later version.
#
# This Program is distributed in the ... | kodibear/plugin.video.watchcartoononline2 | resolve.py | Python | gpl-2.0 | 3,083 | [
"BLAST"
] | fdb6104e2c83009720e926569125ccbb14d4d252e8fcc3ce202f147fbda59f84 |
"""Provide JIDT estimators."""
from pkg_resources import resource_filename
import numpy as np
from abc import abstractmethod
from idtxl.estimator import Estimator
from . import idtxl_exceptions as ex
from . import idtxl_utils as utils
try:
import jpype as jp
except ImportError as err:
ex.package_missing(err, 'J... | pwollstadt/trentoolxl | idtxl/estimators_jidt.py | Python | gpl-3.0 | 81,085 | [
"Gaussian"
] | 3bc3d69a9e4301874ac0d46af5a7bdb3cf34b1d46d3b50dc90c703b79820c130 |
#!/usr/bin/python
# -- Content-Encoding: UTF-8 --
"""
iPOPO component factories repository
:author: Thomas Calmant
:license: Apache Software License 2.0
..
Copyright 2014 isandlaTech
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the L... | ahmadshahwan/cohorte-runtime | python/cohorte/repositories/python/ipopo.py | Python | apache-2.0 | 12,551 | [
"VisIt"
] | 35478d6cbfab9fc2736726ec119c579d6937a5b3423c145128e786c8a23e4161 |
#! /usr/bin/python
import numpy as np
# Transfer sigmoid function
#
# @param x Numeric value to transform
# @param derivative Flag to use an alternative formula
# @return float Transformed value to use as a mean to update weights
def sgm(x, derivative=False):
if not derivative:
return 1 / (1+np.exp(-x))... | joeyinbox/pointing-gesture-recognition | src/classes/BackPropagationNetwork.py | Python | gpl-2.0 | 5,874 | [
"Gaussian"
] | 038be5f10de7c36ccc88896b038482522bc717c4aca9f807cdc8b697ffe07101 |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from os.path import isabs, dirname
import os
import collections
from zeroinstall import SafeException
def ensure_dir(path):
if not os.path.isdir(path):
os.makedirs(path)
def group_by_target_url_dir(archives):
r... | bastianeicher/0repo | repo/paths.py | Python | lgpl-2.1 | 2,173 | [
"VisIt"
] | a9cca54043e45083349256a6caa045cc5f6cd677adccbddec1be1c7dcad09fed |
# Dual Annealing implementation.
# Copyright (c) 2018 Sylvain Gubian <sylvain.gubian@pmi.com>,
# Yang Xiang <yang.xiang@pmi.com>
# Author: Sylvain Gubian, Yang Xiang, PMP S.A.
"""
A Dual Annealing global optimization algorithm
"""
import numpy as np
from scipy.optimize import OptimizeResult
from scipy.optimize import... | nmayorov/scipy | scipy/optimize/_dual_annealing.py | Python | bsd-3-clause | 29,699 | [
"VisIt"
] | 32237ced33871d8a94208c03ef188467ef22eb29c114e6d62c1a0a9474ec90f7 |
from __future__ import print_function
import argparse
import sys
__author__ = 'Sean M. Ryno'
__copyright__ = 'Copyright 2017, Sean M. Ryno'
__credits__ = 'Sean M. Ryno'
__license__ = 'GPL v3.0'
__version__ = '0.1'
__maintainer__ = 'Sean M. Ryno'
__email__ = 'sean.m.ryno@gmail.com'
__status__ = 'Development'
def par... | sryno/rynosm | makeGRO/convertToGromacs.py | Python | gpl-3.0 | 7,723 | [
"Gromacs"
] | eab4840f39bd44613a5c95261b2c2bee57b41a0fc7d8924cb65db2b4d772bbcc |
"""
DIRAC.DataManagementSystem.Service package
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
| yujikato/DIRAC | src/DIRAC/DataManagementSystem/Service/__init__.py | Python | gpl-3.0 | 163 | [
"DIRAC"
] | fa7ab9db4f0790302c0ab10c5c4114dda203678dd1b471ea5a02d71068222b5d |
# Copyright 2017 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 required by applicable law or agreed to in writing, ... | google/decoupled_gaussian_process | bases_manager.py | Python | apache-2.0 | 18,831 | [
"Gaussian"
] | f972cae767776888051fb1629470de24685c67f372725e9d25d7c8feb8c01abd |
from PyGMO.problem._problem import tsp, tsp_cs, tsp_vrplc, _tsp_encoding
from PyGMO import __extensions__
if __extensions__["gtop"] is True:
from PyGMO.problem._problem import tsp_ds
tsp_ds.encoding_type = _tsp_encoding
# Renaming and placing the enums
tsp.encoding_type = _tsp_encoding
tsp_vrplc.encoding_type ... | jdiez17/pagmo | PyGMO/problem/_tsp.py | Python | gpl-3.0 | 16,108 | [
"VisIt"
] | 9aab9c428c48d1eed832f46592fa2f76ac1d0ef16de5eea42ef3a2e647cf4050 |
from __future__ import division, print_function, absolute_import
import time
import GPy
import matplotlib.pyplot as plt
import numpy as np
from safemdp.grid_world import (compute_true_safe_set, compute_S_hat0,
compute_true_S_hat, draw_gp_sample, GridWorld)
# Define world
world_shape ... | befelix/SafeMDP | examples/sample.py | Python | mit | 2,859 | [
"Gaussian"
] | 69f1f64ae54f0436540036be7d9ebb3127a08685aec6f97f65517b1b4f7c2148 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes Authors All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unle... | caesarxuchao/contrib | hack/boilerplate/boilerplate.py | Python | apache-2.0 | 4,753 | [
"VisIt"
] | 0a0b490c97d735de536dc56bb4935e03ca76d37e47a7206d44baebf3b04e0744 |
from collections import OrderedDict
import logging
import os
import shutil
import subprocess
import parmed.unit as units
from intermol.desmond.desmond_parser import load, save
DES_PATH = ''
logger = logging.getLogger('InterMolLog')
to_canonical = {
'stretch': ['bond'],
'angle': ['angle'],
'dihedral'... | shirtsgroup/InterMol | intermol/desmond/__init__.py | Python | mit | 3,641 | [
"Desmond"
] | e7933a879d4d0189267b2f671dfbd30a574e4f8eaadd5f8f47aa0c9c9c5ce8ea |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/tools/input/keywords.py | Python | gpl-3.0 | 26,451 | [
"CRYSTAL",
"VASP"
] | e2c9f689681da68de64421a5c726eff5f43a36649d74e4dc18955619cf32dfc6 |
#!/usr/bin/env python
traindat = '../data/fm_train_real.dat'
testdat = '../data/fm_test_real.dat'
parameter_list=[[traindat,testdat, 1.3],[traindat,testdat, 1.4]]
def kernel_gaussian_modular (train_fname=traindat,test_fname=testdat, width=1.3):
from modshogun import RealFeatures, GaussianKernel, CSVFile
feats_trai... | AzamYahya/shogun | examples/undocumented/python_modular/kernel_gaussian_modular.py | Python | gpl-3.0 | 695 | [
"Gaussian"
] | 2dd719e9e16e887a761e06d29d79eb1183d0cec48b5aac9bb0ae31214835d271 |
from numpy import *
import scipy.optimize as opt
from scipy.special import erf
def load_data(h5file, inst, iteration, measurements, shots, roi=None):
"""
Loads data from h5file into the array hist_dat
:param h5file: reference to an hdf5 data file
:param inst: instrument sourcing of data, (so far only... | QuantumQuadrate/CsPyController | python/costs_hybrid.py | Python | lgpl-3.0 | 8,292 | [
"Gaussian"
] | 5fbad47b6098e89dd942ff3f99b970f9eb4e0c983679e1d69e2002648d374d3f |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Changing field 'Visit.reason'
db.alter_column('visits_visit', 'reason', self.gf('django.db.models.fields... | mariajosefrancolugo/osp | osp/visits/migrations/0002_auto__chg_field_visit_reason.py | Python | lgpl-3.0 | 5,001 | [
"VisIt"
] | b648fcfd571e2b7eea9bd162ed1a1da3d38afc751f564fed53043f25f7b7b0e9 |
# $Id$
#
# Copyright (C) 2015 Novartis Institute of BioMedical Research
# All Rights Reserved
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above co... | jandom/rdkit | Code/GraphMol/FilterCatalog/Wrap/rough_test.py | Python | bsd-3-clause | 18,869 | [
"RDKit"
] | aba7f469dd5a2e130dfd8f90b33a4965d3ca997d68e41982e27575061b4f8ddb |
#!/usr/bin/env python2
desc="""Generate nice graph with coverage for multiple samples.
Tracks are in colors and merged track is added if less than 13 samples.
First generate cov.bed files is:
for f in bowtie2/*.bam; do echo `date` $f; bedtools coverage -counts -abam $f -b ../ensembl/Fusarium_oxysporum.FO2.15.dna.topl... | lpryszcz/bin | genome_track.py | Python | gpl-3.0 | 12,889 | [
"pysam"
] | f4951399cfd054d73c01e4397592f4520e0a56bc2303cde4a7b2334815d48bd6 |
import datetime
import itertools
import logging
import os
import time
from collections import defaultdict
from operator import itemgetter
from typing import (
AbstractSet,
Any,
Callable,
Dict,
Iterable,
List,
Mapping,
Optional,
Sequence,
Set,
Tuple,
Union,
)
import djang... | kou/zulip | zerver/lib/actions.py | Python | apache-2.0 | 263,517 | [
"Octopus"
] | 08e8e6a8db641bd9feca5cfa50344859640a918dd4f1795be90f9eb6de5a28cf |
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