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import os
import logging
import time
import traceback
from datetime import timedelta
from galaxy import model
from galaxy import util
from galaxy.util.bunch import Bunch
from galaxy.util import DATABASE_MAX_STRING_SIZE, shrink_stream_by_size
from galaxy.jobs import JobDestination
from galaxy.jobs.runners import Asynch... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/jobs/runners/pbs.py | Python | gpl-3.0 | 27,609 | [
"Galaxy"
] | bb0fc56f1fcbff02a89a30abbb2202e437bd3e0c08cad5f7d8778c7fb5453943 |
# Version: 0.19
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/python-versioneer/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible with: Python 3.6, 3.7, 3.8, 3.9 and pypy3
* [![Latest Version][pypi... | bbfrederick/rapidtide | versioneer.py | Python | apache-2.0 | 69,935 | [
"Brian"
] | fc4389c49522d969908498bc09cdf41c3bcfc570a361758c736fbfba8393b28e |
#
# Copyright (C) 2017-2019 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... | pkreissl/espresso | testsuite/python/auto_exclusions.py | Python | gpl-3.0 | 2,335 | [
"ESPResSo"
] | 3dc4b98ef6e52f3f25fcb943fb10ca1f1018963e52289dac9a374c64ed2f56dc |
# Functions to implement several important functions for
# various Continous and Discrete Probability Distributions
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
import math
import warnings
from copy import copy
from scipy.misc import comb, derivative
from s... | teoliphant/scipy | scipy/stats/distributions.py | Python | bsd-3-clause | 215,895 | [
"Gaussian"
] | 8c2d290a338b0e1b673cc9ff6d2fc52dd586c29aa001e4845f0f368e99e65be8 |
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# License: BSD 3 clause
from __future__ import print_function
import numpy as np
from scipy import linalg, optimize
from ..base import BaseEstimator, RegressorMixin
from ..metrics... | giorgiop/scikit-learn | sklearn/gaussian_process/gaussian_process.py | Python | bsd-3-clause | 35,051 | [
"Gaussian"
] | 118d1cc5e50de8f9159aa2b9ad4f00315a896338b6914b4b4fd8e686e777b770 |
"""**Utilities for storage module**
"""
import os
import re
import copy
import numpy
import math
from ast import literal_eval
from osgeo import ogr
from safe.common.numerics import ensure_numeric
from safe.common.utilities import verify
from safe.common.exceptions import BoundingBoxError
# Default attribute to assi... | takmid/inasafe | safe/storage/utilities.py | Python | gpl-3.0 | 29,624 | [
"NetCDF"
] | e4f0198089a98b0753048d0d3be0cea08a969e5109caed5a18ea7c6112a10fde |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
3D visualization of activation maps using Mayavi
"""
from __future__ import absolute_import
# Author: Gael Varoquaux <gael dot varoquaux at normalesup dot org>
# License: BSD
import os
import tempfil... | alexis-roche/nipy | nipy/labs/viz_tools/maps_3d.py | Python | bsd-3-clause | 14,555 | [
"Mayavi",
"VTK"
] | 00374a6123b4787523bb9acf4717681d8d3cd9bbdc2b30f9058f4af52ca34aba |
"""Constants used by ansible-test. Imports should not be used in this file (other than to import the target common constants)."""
from __future__ import annotations
from .._util.target.common.constants import (
CONTROLLER_PYTHON_VERSIONS,
REMOTE_ONLY_PYTHON_VERSIONS,
)
# Setting a low soft RLIMIT_NOFILE value... | ansible/ansible | test/lib/ansible_test/_internal/constants.py | Python | gpl-3.0 | 1,985 | [
"Galaxy"
] | e9c5e3ae269ce550e4fd796697c1e25e123c4b3c459c1b3aa71aefa1b056706e |
import logging, threading, sys, os, time, subprocess, string, tempfile, re, traceback, shutil
from galaxy import util, model, config
from galaxy.model import mapping
from galaxy.model.orm import lazyload
from galaxy.datatypes.tabular import *
from galaxy.datatypes.interval import *
from galaxy.datatypes import metadat... | volpino/Yeps-EURAC | lib/galaxy/cloud/__init__.py | Python | mit | 29,970 | [
"Galaxy"
] | a2aa00d25aa53594ada493cdd43966417a0a9914e89563ecdd91420dbee56092 |
# -*- coding: utf-8 -*-
from __future__ import division
from __future__ import print_function
import numpy as np
from fancytools.os.PathStr import PathStr
from imgProcessor.imgIO import imread
from imgProcessor.equations.gaussian import gaussian
class FitHistogramPeaks(object):
'''
try to fit the... | radjkarl/imgProcessor | imgProcessor/measure/_BACKUP_FitHistogramPeaks.py | Python | gpl-3.0 | 8,848 | [
"Gaussian"
] | a37832e15c921d5d1cfc44251e4ac5f15557c938ec131346900486013e2a02a8 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import glob
class Redundans(Package):
"""Redundans pipeline assists an assembly of heterozygous ... | rspavel/spack | var/spack/repos/builtin/packages/redundans/package.py | Python | lgpl-2.1 | 1,801 | [
"BWA"
] | 8ce30f75a4205d709a55c65d1ca2dcc9abe843f78d52cdabdd75c1b235c08172 |
# -*- coding: utf-8 -*-
"""Tests for the PyBEL assembler."""
import json
import networkx as nx
import pybel.constants as pc
from pybel.dsl import abundance, activity, bioprocess, \
complex_abundance, hgvs, pmod, protein, reaction
from indra.assemblers.pybel import assembler as pa
from indra.databases import hgn... | sorgerlab/belpy | indra/tests/test_pybel_assembler.py | Python | mit | 25,932 | [
"Pybel"
] | b4720ea28a62bd4c7db84843e87dc241dfa8cfd46aaec3082ee7666668735ba0 |
# Generated from antlr4-python3-runtime-4.7.2/src/autogen/Grammar.g4 by ANTLR 4.7.2
from antlr4 import *
if __name__ is not None and "." in __name__:
from .GrammarParser import GrammarParser
else:
from GrammarParser import GrammarParser
import sys
err = sys.stderr.write
def printf(string, *args):
sys.stdo... | damorim/compilers-cin | 2020_3/projeto4/GrammarCheckerVisitor.py | Python | mit | 20,808 | [
"VisIt"
] | ce0e9cf7baa79cc9afc910686d673fda083fb0139361e326cbed6352226267c9 |
from __future__ import print_function
from future import standard_library
standard_library.install_aliases()
from builtins import range
from past.builtins import basestring
import sys, os
sys.path.insert(1, "../../")
import h2o
import imp
import random
import re
import subprocess
from subprocess import STDOUT,PIPE
from... | YzPaul3/h2o-3 | h2o-py/tests/pyunit_utils/utilsPY.py | Python | apache-2.0 | 128,719 | [
"Gaussian"
] | c9e97df9348da0f063c976c125ebfe48db6a1ce7f61781973806d27e0eaf8111 |
""" This integration test only need the TaskQueueDB
(which should of course be properly defined also in the configuration),
and connects directly to it
"""
import unittest
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
from DIRAC import gLogger
from DIRAC.WorkloadManagementSystem.DB.T... | arrabito/DIRAC | tests/Integration/WorkloadManagementSystem/Test_TaskQueueDB.py | Python | gpl-3.0 | 5,660 | [
"DIRAC"
] | ce18be3291d6f6a1351c378832aa87ee7d700f12c8e9ce340e87980644b857e9 |
# -*- coding: utf-8 -*-
import pytest
import time
import sys
from .test_base_class import TestBaseClass
try:
from collections import Counter
except ImportError:
from counter26 import Counter
aerospike = pytest.importorskip("aerospike")
try:
import aerospike
from aerospike import exception as e
except... | aerospike/aerospike-client-python | test/new_tests/test_exists_many.py | Python | apache-2.0 | 10,509 | [
"ASE"
] | 3d3eca4f13bf9e7fb1861ea8ce37fce1019ee3da80465fd398be8b19c66019a2 |
#!/usr/bin/python2.7
#-*- encoding: utf-8 -*-
__author__ = "Tomáš Beluský"
__date__ = "05.03. 2013"
import os
import re
import sys
import pysam
import optparse
from src.interface.Logger import Logger
from src.interface.interface import parseRegion
from src.interface.Settings import Settings
from src.resources.Sample... | tomasbelusky/gataca | gataca.py | Python | gpl-3.0 | 7,428 | [
"pysam"
] | 8844ecdacaa0d929e032d03b2f915a2221d61b2f287afece2d92518293216d5c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# settingskeywords - keywords for basic user settings
# Copyright (C) 2003-2015 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... | heromod/migrid | mig/shared/settingskeywords.py | Python | gpl-2.0 | 4,959 | [
"Brian"
] | 061950ebc99ca9d8f2757cbac894fa2a87e69aeee859649b95a0fde78a31652b |
#!/usr/bin/python
import sys
from ctypes import *
from functions import *
from math import sqrt
import numpy as np
import multiprocessing
import pyfits
import signal
# Load the library for the CFitsio routines
overseer = CDLL("/home/steven/Projects/galaxy_icd/libraries/liboverseer.so.0")
def main(sample):
naxes ... | boada/ICD | parallel_main_gs_VJ.py | Python | mit | 5,457 | [
"Galaxy"
] | 0cd8897233653609c6dfb9c514d2bca02c2493b72a07f09344794ff25258bb5e |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
# Create a rendering window and renderer.
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.SetWindowName("Cube")
renWin.AddRenderer(ren)
# Create a renderwindowinteractor.
iren = vtk.vtkRenderWin... | lorensen/VTKExamples | src/Python/GeometricObjects/Cube1.py | Python | apache-2.0 | 1,078 | [
"VTK"
] | 5181753d84034460d8019b9a11121d489c716fb3f19e60d2620fed2ec126718d |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from datetime import datetime, timedelta
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
import pytz
import urllib
from bok_choy.promise import EmptyPromise
from common.test.acceptance.tests... | jjmiranda/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 53,428 | [
"VisIt"
] | 105555400269d2e418ffb575c91b705472b5e85a2f7f3c80a7e8f3af347a5c88 |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy,... | alexholcombe/dot-jump | dataRaw/test_dot-jump10Feb2017_10-32.py | Python | gpl-3.0 | 29,423 | [
"Gaussian"
] | 51e39983c6be930a9bca21dbf906e5718e5cb88b22fa200caf3a538bf48d857a |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# LAMMPS documentation build configuration file, created by
# sphinx-quickstart on Sat Sep 6 14:20:08 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# aut... | Pakketeretet2/lammps | doc/utils/sphinx-config/conf.py | Python | gpl-2.0 | 10,097 | [
"LAMMPS"
] | fdfe5c599118ca9bfdb9eba4a8f22cd33f83a0152c5636b337294c067aa81454 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | dgasmith/psi4 | psi4/driver/qcdb/align.py | Python | lgpl-3.0 | 6,553 | [
"Psi4"
] | 08f0f610e554a7c6ad87501aea1d2ae8214a3af2493ae17dc8959f0a71289210 |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# 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 requ... | steckdenis/rlglue-py3 | tests/test_sanity_experiment.py | Python | apache-2.0 | 1,095 | [
"Brian"
] | 0d98b2e9cd38abbf7d4d4164c9fede31117dcab05c9b5911dc502207a6132291 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# volume render a medical data set
# renderer and interactor
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren... | sumedhasingla/VTK | Rendering/Volume/Testing/Python/VolumePickerCrop.py | Python | bsd-3-clause | 7,111 | [
"VTK"
] | 8ead75782533564f0c02511c316ddc0a6ac12aeca13dc3629b1ec9d6a7dd92d3 |
from setuptools import setup, find_packages
setup(
name = 'calculator_service',
packages=find_packages(),
version = '1.0',
description = 'Example application with Servant',
author='Brian Zambrano',
author_email='brianz@gmail.com',
classifiers=[
'Programming Language :: Python',
... | clearcare/servant | examples/calculator_service/setup.py | Python | lgpl-3.0 | 663 | [
"Brian"
] | 1d8f7329c50dfa78e7f6eabcc5f83c26f1bdc1d0a2b5f886658c56c4f60ea7bd |
# 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.
from Bio._py3k import range
from Bio._py3k import basestring
from Bio.Seq import UnknownSeq
from Bio.SeqUtils.CheckSum import seguid
from Bio.SeqFeatu... | updownlife/multipleK | dependencies/biopython-1.65/Tests/seq_tests_common.py | Python | gpl-2.0 | 15,350 | [
"BioPerl",
"Biopython"
] | 950c9025b82c1648a559057bc79f3237c4078bfe4a94ae8b0c555b5db035152f |
import gzip
import json
import os
import warnings
from collections import OrderedDict
from astropy import units as un
from astropy.coordinates import SkyCoord as coord
from astroquery.simbad import Simbad
from tqdm import tqdm
from astrocats.supernovae.scripts.repos import repo_file_list
from ...catalog.utils impor... | astrocatalogs/supernovae | scripts/hostcandidatecat.py | Python | mit | 2,606 | [
"Galaxy"
] | 73639b386684a2efc3e62c4194c3ac1aa7eca54ae1f93de59d87c2dfaf49a23b |
# (C) British Crown Copyright 2010 - 2017, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | zak-k/iris | lib/iris/tests/test_analysis.py | Python | gpl-3.0 | 46,744 | [
"NetCDF"
] | 6c32c3a0927338f5605c815da2c0aca8ea0ea42f48bcabd55fbd807152cb562c |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2013 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 option) a... | MSusik/invenio | modules/bibcheck/lib/plugins/dates.py | Python | gpl-2.0 | 2,853 | [
"VisIt"
] | 70b5bc8b8da729410c011e6d51521e591aeb51b8e7424544b7c3486fa4f6bfce |
#!/usr/bin/env python
# This document is part of CrowdProjects
# https://github.com/skytruth/CrowdProjects
# =========================================================================== #
#
# Copyright (c) 2014, SkyTruth
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without... | SkyTruth/CrowdProjects | Data/FrackFinder/PA/2013/Transformations_and_QAQC/Digitizer/bin/finalizeInputTasks.py | Python | bsd-3-clause | 14,474 | [
"Elk"
] | df2a9a30462a50ea95907d0113bb95efcdfc834e08453a93272e5a291858259c |
def BFS(adj,start):
while len(Q)>0:
current=Q.pop(0)-1
for i in xrange(1,N+1):
if visit[i-1]==False and adj[current][i-1]==1:
level[i-1]=level[current]+1
Q.append(i)
visit[i-1]=True
root=1
s=raw_input().split()
N=int(s[0])
M=int(s[1])
adj=... | shree-shubham/Unitype | Even Tree.py | Python | gpl-3.0 | 965 | [
"VisIt"
] | df53b52f0233f34f683d84ec74bba2cfc20735f8c931274acd139fd8b1294d29 |
################################################################################
# Copyright (C) 2015 Hannu Hartikainen, Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
"""
Tests for the module bayespy.plot.
This file m... | jluttine/bayespy | bayespy/tests/test_plot.py | Python | mit | 5,543 | [
"Gaussian"
] | 148949bad5da6b375843fc126f5fcd92f9c61c2b118f08b84b5bc12f404f21a4 |
# -*- coding: utf-8 -*-
"""
Default Django settings. Override these with settings in the module pointed to
by the DJANGO_SETTINGS_MODULE environment variable.
"""
from __future__ import unicode_literals
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module d... | himleyb85/django | django/conf/global_settings.py | Python | bsd-3-clause | 21,531 | [
"VisIt"
] | e157effa19cee9f8a06e0a368026430eecec0bf834c584649447c243a3f65e43 |
# Takes in two words and returns the edit distance
def levenshtein_distance(first,second):
columns = len(first) + 1
rows = len(second) + 1
current_row = [0]
# Constructs first row
for column in xrange(1,columns):
current_row.append( current_row[column - 1] + 1 )
... | ridwanmsharif/fzysearch | fzysearch/__init__.py | Python | mit | 8,707 | [
"VisIt"
] | f4783ac48d14bac15423213c55cac30a682b38e8bf7a460f1b2f9d8df7becb9b |
#!/usr/bin/env python
"""
Dispersion analysis of a heterogeneous finite scale periodic cell.
The periodic cell mesh has to contain two subdomains Y1 (with the cell ids 1),
Y2 (with the cell ids 2), so that different material properties can be defined
in each of the subdomains (see ``--pars`` option). The command line ... | sfepy/sfepy | examples/linear_elasticity/dispersion_analysis.py | Python | bsd-3-clause | 34,986 | [
"VTK"
] | db86dd1fa664fdb4189face3b6df6fbf625226470475a0d5a6577e3a5e940c28 |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
datatypes_repository_name = 'emboss_datatypes_0020'
datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This reposit... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_0020_basic_repository_dependencies.py | Python | gpl-3.0 | 7,193 | [
"Galaxy"
] | 24bf58ff5e35940bbe45a205adac4384aa82f7e98db718ba1d9ad2da3886ace1 |
# -*- 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... | shyamalschandra/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 52,396 | [
"Gaussian"
] | f436a4e5472ab7c43fcfcb6f93c35b7391c0a458332b32f8445d834a92cd71bf |
# Copyright (c) 2017, Zhenwen Dai
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core.sparse_gp_mpi import SparseGP_MPI
from .. import likelihoods
from .. import kern
from ..inference.latent_function_inference.vardtc_md import VarDTC_MD
from GPy.core.parameterization.variational... | befelix/GPy | GPy/models/sparse_gp_regression_md.py | Python | bsd-3-clause | 4,089 | [
"Gaussian"
] | e0189a4fb2c25f848b0ea4dcf1535e4b47decc0c04e4caf608ed2c15d12a8728 |
import galaxy.model
from galaxy.model.orm import *
from galaxy.model.mapping import context as sa_session
from base.twilltestcase import TwillTestCase
class TestMetadataEdit( TwillTestCase ):
def test_00_metadata_edit( self ):
"""test_metadata_edit: Testing metadata editing"""
self.logout()
... | volpino/Yeps-EURAC | test/functional/test_metadata_editing.py | Python | mit | 3,175 | [
"Galaxy"
] | 328aee7982d48cda628638d5777aa3db4a128a720fdcb91437ec70025934e6a3 |
"""
=========================================================
Gaussian Processes regression: basic introductory example
=========================================================
A simple one-dimensional regression example computed in two different ways:
1. A noise-free case
2. A noisy case with known noise-level per ... | sanketloke/scikit-learn | examples/gaussian_process/plot_gpr_noisy_targets.py | Python | bsd-3-clause | 3,706 | [
"Gaussian"
] | d17f03cafa80049d91004c2d2be67892b2d9bf1c58f3c5bb007c84038d71d14e |
# -*- coding: utf-8 -*-
# TODO: Port to pytest
# PEP8 asserts
from copy import deepcopy
import httplib as http
import time
import mock
import pytest
import pytz
import datetime
from nose.tools import * # noqa
from tests.base import OsfTestCase, fake
from osf_tests.factories import (
UserFactory, NodeFactory, Pr... | pattisdr/osf.io | addons/wiki/tests/test_wiki.py | Python | apache-2.0 | 62,008 | [
"VisIt"
] | 10f10c1fbc01c3554e5277bbd67cf2efe9add08ab3be0295bd62e8c4ecabb516 |
#!/usr/bin/env python
traindat = '../data/fm_train_real.dat'
testdat = '../data/fm_test_real.dat'
parameter_list=[[traindat,testdat,1.0],[traindat,testdat,1.2]]
def kernel_io (train_fname=traindat,test_fname=testdat,width=1.9):
from tempfile import NamedTemporaryFile
import shogun as sg
feats_train=sg.create_feat... | shogun-toolbox/shogun | examples/undocumented/python/kernel_io.py | Python | bsd-3-clause | 960 | [
"Gaussian"
] | cfb0a48e9a31e2bc658dd1136bf9ef7eb619d960c824687978722d8b5aaed105 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/diatomic.py | Python | gpl-2.0 | 11,013 | [
"Psi4"
] | 078e007247bc36232fc818675037bf66e4b36beed57a9758bff05f5382369b99 |
import os
from brian import pA, second, nS, Hz, ms
import h5py
import numpy as np
import matplotlib.pyplot as plt
from perceptchoice.model.monitor import SessionMonitor
from perceptchoice.model.network import default_params, pyr_params, simulation_params, AccumulatorNetwork
from perceptchoice.model.virtual_subject im... | jbonaiuto/perceptual-choice-hysteresis | src/python/perceptchoice/model/run.py | Python | gpl-3.0 | 19,418 | [
"Brian"
] | 07afaab13da77e2135869e5f57fe90076c615a2f210670ca8fe6b610dfddd2ed |
# -*- coding: utf-8 -*-
"""
lantz.processors
~~~~~~~~~~~~~~~~
:copyright: 2015 by Lantz Authors, see AUTHORS for more details.
:license: BSD, see LICENSE for more details.
"""
import warnings
from . import Q_
from .log import LOGGER as _LOG
from stringparser import Parser
class DimensionalityWarnin... | LabPy/lantz | lantz/processors.py | Python | bsd-3-clause | 12,354 | [
"Brian"
] | f34ef6e7d2e7f3279ab5fce3a5362d599568c948a5ca1c5bbc75f33d3b68018d |
__author__ = 'Michael Isik'
from pybrain.supervised.evolino.variate import UniformVariate, GaussianVariate
class Filter(object):
""" Base class for all kinds of operators on the population during the
evolutionary process like mutation, selection or evaluation.
"""
def __init__(self):
pass... | arabenjamin/pybrain | pybrain/supervised/evolino/gfilter.py | Python | bsd-3-clause | 3,909 | [
"Gaussian"
] | 5c05521d7bcdc377b454284e62dda206b116905e46623a5ac3605e1d6142421d |
# -*- coding: utf-8 -*-
"""
Generate centreline and write it out as .vtk legacy format.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Import path for the CentrelineGenerator script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__), '../... | BlueFern/DBiharMesher | meshes/c4080ang/Generate4080Centreline_90.py | Python | gpl-2.0 | 1,015 | [
"VTK"
] | 6e2617026075a43f2bf3a84c477117a2d84d3eb8b11a9e230b79fa03fab5970f |
# -*- coding: utf-8 -*-
#
# Copyright 2009-2011, Simon Kennedy, python@sffjunkie.co.uk
#
# 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
#
# Unl... | aman-thakral/astral | astral/astral.py | Python | apache-2.0 | 63,633 | [
"COLUMBUS"
] | 0cd6e3cf39459ba334ebe365c230a709a6c75495cd769ccc9dc335457636d6e0 |
"""
Covariance estimators using shrinkage.
Shrinkage corresponds to regularising `cov` using a convex combination:
shrunk_cov = (1-shrinkage)*cov + shrinkage*structured_estimate.
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Gael Varoquaux <gael.varoquaux@normalesup.org>
# Virgile ... | sergeyf/scikit-learn | sklearn/covariance/_shrunk_covariance.py | Python | bsd-3-clause | 22,957 | [
"Gaussian"
] | 617883086030f214683b3f4ab5b7f81dd1019b1289e1466a5a4e3335f64b0a5c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
================================================================================
mingus - Music theory Python package, Instrument module
Copyright (C) 2008-2009, Bart Spaans
This program is free software: you can redistribute it and/or modify
it under the... | edudobay/mingus | mingus/containers/Instrument.py | Python | gpl-3.0 | 7,067 | [
"CRYSTAL"
] | 7c0700b5fa91a4561c70384ceb7673c5d47e06984ed9a56da0623929197612f9 |
# Copyright (C) 2016, Craig Warren
#
# This module is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License.
# To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/.
#
# Please use the attribution at http://dx.doi.org/10.1016/j.sigpro.2016.04.010
import arg... | gprMax/gprMax | user_libs/antenna_patterns/initial_save.py | Python | gpl-3.0 | 7,687 | [
"VisIt"
] | b9f69adc0426afbd6e6466ce13198fd158e5c14dc8d95c02262a3c8ec40c8500 |
../../../../share/pyshared/orca/espeechfactory.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/espeechfactory.py | Python | gpl-3.0 | 49 | [
"ORCA"
] | 8ed12c78fc1baade993fe9e8dd9f132190a883d225e6014f7f84a3b535145b6f |
"""
Module to generate tims from coadds, to allow Tractor fitting to the coadds
rather than to the individual CCDs.
"""
import numpy as np
class Duck(object):
pass
def _build_objmask(img, ivar, skypix, boxcar=5, boxsize=1024):
"""
Build an object mask by doing a quick estimate of the sky background on a
... | legacysurvey/pipeline | py/legacypipe/fit_on_coadds.py | Python | gpl-2.0 | 31,634 | [
"Gaussian"
] | 9a9b37391b1d563e2e0b1268bf65e3862ee2784179fd3a00e327fc3f2b1a2ebb |
# Copyright 2015 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
import ast
import re
import unittest
from dataclasses import dataclass
from enum import Enum
from pathlib import Path
from textwrap import dedent
from typing import Callable, List, Optiona... | benjyw/pants | src/python/pants/engine/rules_test.py | Python | apache-2.0 | 36,309 | [
"VisIt"
] | 432515958530ead1580b19e98df579a541635ecbb413125980c7259aa451c1b2 |
import pyimgur
import time
import os
import win32gui, win32ui, win32con, win32api
from PIL import Image
import winsound
import sys
import pythoncom, pyHook
import threading
import urllib2
import random
import copy
#settings:
cid = "5976c17ac696c9b" #client id
sound = True #beep if error
skey = 'F9' #screenshot key
l... | ricsoncheng/PyImg | pyimg.py | Python | gpl-2.0 | 3,259 | [
"VisIt"
] | 2971db27fc18702d0eb3d714830da3d984f4410ee9bc99b988be668e8864ce48 |
from __future__ import absolute_import
# coding=utf-8
import os
import sys
from setuptools import find_packages
from setuptools import setup
here = os.path.abspath(os.path.dirname(__file__))
PY3 = sys.version_info[0] == 3
install_requires = []
dependency_links = []
req_files = ['requirements.txt']
if not PY3:
req... | ruitian/firefly | setup.py | Python | mit | 1,526 | [
"Firefly"
] | 921ebaded75e817465e4917bf7959dbd6dd34d9a351a8476f98c22991b1144e9 |
from galaxy.web.base.controller import *
from galaxy.web.framework.helpers import time_ago, iff, grids
from galaxy.model.orm import *
from galaxy.datatypes import sniff
from galaxy import util
from galaxy.util.streamball import StreamBall
from galaxy.util.odict import odict
import logging, tempfile, zipfile, tarfile, o... | volpino/Yeps-EURAC | lib/galaxy/web/controllers/requests.py | Python | mit | 57,189 | [
"Galaxy"
] | 5ef0117070e37ae316c8e01dff6aa36890c78dde3a3ffc72ee40655bb46c7cef |
from numpy import zeros
from os import fstat
from re import compile
from ase.io.fortranfile import FortranFile
def read_rho(fname):
"Read unformatted Siesta charge density file"
# TODO:
#
# Handle formatted and NetCDF files.
#
# Siesta source code (at least 2.0.2) can possibly also
# s... | slabanja/ase | ase/io/siesta.py | Python | gpl-2.0 | 7,443 | [
"ASE",
"NetCDF",
"SIESTA"
] | 2b6b06eae1792d6a68109f17a359efc073e98216d0c2d1b9cb717033b0828cd6 |
from veros import runtime_settings
class Variable:
def __init__(
self,
name,
dims,
units="",
long_description="",
dtype=None,
time_dependent=True,
scale=1.0,
write_to_restart=False,
extra_attributes=None,
mask=None,
ac... | dionhaefner/veros | veros/variables.py | Python | mit | 28,529 | [
"NetCDF"
] | 50a84d8260e14e66911b7c064fb6a37c01db501ce0e11f7a14fefa2785671686 |
"""
denclue.py
@author: mgarrett
"""
import numpy as np
from sklearn.base import BaseEstimator, ClusterMixin
import networkx as nx
def _hill_climb(x_t, X, W=None, h=0.1, eps=1e-7):
"""
This function climbs the 'hill' of the kernel density function
and finds the 'peak', which represents the density attract... | mgarrett57/DENCLUE | denclue.py | Python | mit | 8,997 | [
"Gaussian"
] | 930464df5bcde8fec2ffc59c7e988907ab516218c293cbcb152d2c26b89a6ee5 |
"""
This file is part of Giswater 3
The program is free software: you can redistribute it and/or modify it under the terms of the GNU
General Public License as published by the Free Software Foundation, either version 3 of the License,
or (at your option) any later version.
"""
# -*- coding: utf-8 -*-
import csv
import... | Giswater/giswater_qgis_plugin | core/shared/search.py | Python | gpl-3.0 | 42,496 | [
"VisIt"
] | 5c534b47f383ce08e69a31a5bfab4a65676a88fa35c6f4afd7e8dfcdfdfacedb |
# -*- coding: utf-8 -*-
"""Provides all the data related to the internet."""
from typing import List
HTTP_METHODS = [
"GET",
"POST",
"PUT",
"DELETE",
"OPTIONS",
"CONNECT",
"HEAD",
]
HTTP_STATUS_CODES = [
100,
101,
102,
103,
200,
201,
202,
203,
204,
... | lk-geimfari/church | mimesis/data/int/internet.py | Python | mit | 41,174 | [
"Bowtie",
"CASINO",
"Octopus"
] | 8084164c79a90081d05e3745b87450769ba17752242906a6e0030a06e771416d |
"""
Statistical tools for time series analysis
"""
import numpy as np
from scipy import stats, signal
import scikits.statsmodels as sm
from scikits.statsmodels.sandbox.tsa.tsatools import lagmat, lagmat2ds
from adfvalues import *
#from scikits.statsmodels.sandbox.rls import RLS
#NOTE: now in two places to avoid circu... | matthew-brett/draft-statsmodels | scikits/statsmodels/sandbox/tsa/stattools.py | Python | bsd-3-clause | 25,570 | [
"ADF"
] | 5766ac83000ff2ab0da3f41e6efe4a09e8e865685266b45ab9819bd9a06844ab |
#!/usr/bin/env python
# Copyright 2009-2015 Jasper Poppe <jgpoppe@gmail.com>
#
# 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 requ... | martinseener/seedBank | seedbank/seedbank.py | Python | apache-2.0 | 11,013 | [
"VisIt"
] | 8d7fe7b43af0fe952cf2fd8015374c3f2d65ccd137d6d14e996c150e1a3db1e5 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Input Generator and Parser
#############################
Every attempt is made to follow the Documentation on the
NWChem `website`_ with a general theme of the input Generator
ac... | exa-analytics/exatomic | exatomic/nwchem/inputs.py | Python | apache-2.0 | 9,914 | [
"NWChem"
] | ba535b3ed868bf084f8474145fbe66ba8160c3f123290f2931cee54afcfb8997 |
'''
This tutorial demonstrates reading and writing files to remote archives using
on-disk I/O operations.
To demonstrate this, we make use of the :py:mod:`xarray` module, which cannot
read from a streaming object.
Set up the workspace
--------------------
.. code-block:: python
>>> from datafs import DataAPI
... | ClimateImpactLab/DataFS | examples/ondisk.py | Python | mit | 4,893 | [
"NetCDF"
] | 034d8bc7f797a6f39fe19cd3928c39200f34eb4fd910e7a8e39e0fc3020903c2 |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software ... | tux-00/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 32,411 | [
"Galaxy"
] | 9d81e8f5aa7557e2af75af496421cd90062e94639c87c7decb19656f99b3d6ce |
'''Classes and methods for segmentation of reticular objects within cells.'''
## IMPORT DEPENDENCIES ##
import matplotlib
matplotlib.use('Agg')
import os
import sys
import pickle
import time
from operator import itemgetter
import numpy as np
import pandas as pd
from skimage import io
from skimage.morphology import wa... | nrweir/pyto_segmenter | MitoSegment.py | Python | gpl-3.0 | 45,810 | [
"Gaussian"
] | ea435644c61059969718fbd3e0feb6d7ad6b2aab2d36a350e385ad92fd27de37 |
#!/usr/bin/env python
"""
This program is used to compress the netcdf history data files in the CESM L1
output. I.e. the raw output files stored under short-term archive.
By "compression", I mean it converts the format of the netCDF file from the classic
format, which does not support compression, to the netCDF4 form... | aerler/WRF-Tools | Python/compress/netCDFcompressor.py | Python | gpl-3.0 | 19,343 | [
"NetCDF"
] | b053e3692ead49e3842d768807e621a993afe1b71855b33b3cc91316ae8e6730 |
# -*- coding: utf-8 -*-
"""
/***************************************************************************
QAD Quantum Aided Design plugin
classe per gestire il map tool di richiesta di un punto
-------------------
begin : 2013-05-22
copyright :... | geosim/QAD | qad_getpoint.py | Python | gpl-3.0 | 56,260 | [
"CASINO"
] | 0333ca630fd98fffcc9ef0bc844310d7851524ade7781721ebde587c5df9f8f7 |
#!/usr/bin/env python
"""
Modification of `python -m SimpleHTTPServer` with a fallback to /index.html
on requests for non-existing files.
This is useful when serving a static single page application using the HTML5
history API.
# taken from http://www.piware.de/2011/01/creating-an-https-server-in-python/
# generate s... | less-xx/tile-map-editor | server.py | Python | mit | 1,431 | [
"VisIt"
] | 11a327048fc92775bac30212121eb0d802b3585a426088964083f88627d3d1a7 |
"""
Single page performance tests for Studio.
"""
from nose.plugins.attrib import attr
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.studio.overview import CourseOutlinePage
from ..tests.helpers import AcceptanceTest
@attr(har_mode='explicit')
class StudioP... | Stanford-Online/edx-platform | common/test/acceptance/performance/test_studio_performance.py | Python | agpl-3.0 | 3,277 | [
"VisIt"
] | 21feefec7a7f31e789a49159c260af13ca9637d4e97cfc1365c865949243ee5e |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2004-today OpenERP SA (<http://www.openerp.com>)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms o... | deKupini/erp | addons/project/project.py | Python | agpl-3.0 | 73,270 | [
"VisIt"
] | bcc8b61123e5711145477f0797b4b97c5b12feb5acfad1718ce10e2cdc9a2b43 |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# @author: Li Li (lili@bnl.g... | ericdill/scikit-xray | skbeam/core/fitting/xrf_model.py | Python | bsd-3-clause | 54,231 | [
"Gaussian"
] | 6364f51c37351d75c2ed0e476db762ff3216fd2c80b8d7b76f1cd768e252ae00 |
from sympy.core import S, C, sympify
from sympy.core.function import Function, ArgumentIndexError
from sympy.ntheory import sieve
from math import sqrt as _sqrt
from sympy.core.compatibility import reduce
class CombinatorialFunction(Function):
"""Base class for combinatorial functions. """
######################... | ichuang/sympy | sympy/functions/combinatorial/factorials.py | Python | bsd-3-clause | 14,216 | [
"VisIt"
] | dd2e569ec83443924e6495b8a516cdf0d6c794fb59b965e3f6e31c09ca1b09d0 |
"""
Tools to download and process SDSS fits files.
More information can be found at
http://www.sdss.org/dr7/products/spectra/index.html
"""
import gc # garbage collection
import pylab as pl
import numpy as np
from scipy.ndimage.filters import gaussian_filter1d, uniform_filter1d
from scipy import interpolate
from . i... | bsipocz/astroML | astroML/datasets/tools/sdss_fits.py | Python | bsd-2-clause | 12,338 | [
"Galaxy"
] | 9f0bdb57f339bfad323c8babc5856b166159e5764abfe68f2fbf3f7bad862e52 |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or ... | HackFisher/depot_tools | third_party/pylint/checkers/exceptions.py | Python | bsd-3-clause | 13,796 | [
"VisIt"
] | ac37c1cdfd86c3d22271ea608df1ad296585084b3c97dfcc8d9ff28addde339e |
# Copyright (C) 2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, o... | espressopp/espressopp | src/integrator/VelocityVerletRESPA.py | Python | gpl-3.0 | 4,029 | [
"ESPResSo"
] | 7b83b15d8b8b4c461adf57726d0d68ee2bae6ed571b979b9fae1e0fe6420b8b2 |
import Neuron
import pandas
import matplotlib as plt
'''
NILA algorithm (Networked Intelligent Learning Android) v1.0
Warnings:
1: Humanist People: This is a high logical and rational place. Be careful.
2: Religious Pepole: There's evolution down here. Be careful.
'''
TrainingSet = [[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0... | abreufernandof/NeuralNets | RNE.py | Python | gpl-3.0 | 10,392 | [
"NEURON"
] | 9f44d21f43d7311f8b51a54c0ef520e8803e359edd7d827c9d633210cf1c085a |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | lukecwik/incubator-beam | sdks/python/apache_beam/runners/direct/consumer_tracking_pipeline_visitor_test.py | Python | apache-2.0 | 5,827 | [
"VisIt"
] | c344d3070d11a8c2f380617b5a399fef3e4d1e6be06891c1e8bc7bdc7914f21f |
# encoding: utf-8
# ---------------------------------------------------------------------------
# Copyright (C) 2008-2014, IPython Development Team and Enthought, Inc.
# Distributed under the terms of the BSD License. See COPYING.rst.
# ---------------------------------------------------------------------------
""... | RaoUmer/distarray | distarray/globalapi/random.py | Python | bsd-3-clause | 6,860 | [
"Gaussian"
] | a7de28a573a4d18973454a75813890c0fcbf0cd2ee72b2981ad280228b6ba31f |
import sys
import requests
from ..request import request
from ..request_class import Request
from ..habanero_utils import sub_str, check_kwargs
from .filters import (
works_filter_details,
members_filter_details,
funders_filter_details,
)
class Crossref(object):
"""
Crossref: Class for Crossref se... | sckott/habanero | habanero/crossref/crossref.py | Python | mit | 51,659 | [
"Octopus"
] | 31923813d3b3620b3b9ff185e20e71279266cbd57a29dc0479b030f9e933e3a7 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | tiagocardosos/stoq | stoqlib/domain/payment/card.py | Python | gpl-2.0 | 14,652 | [
"VisIt"
] | 1621cf50a35edf038f3cecf1cf2dae5f51a0c126a33d13aac75b937940440966 |
"""
Gridding: Cut a section from a grid
"""
from fatiando import gridder, utils
from fatiando.vis import mpl
# Generate some synthetic data on a regular grid
x, y = gridder.regular((-10, 10, -10, 10), (100,100))
# Using a 2D Gaussian
z = utils.gaussian2d(x, y, 1, 1)
subarea = [-2, 2, -3, 3]
subx, suby, subscalar = gri... | seancug/python-example | fatiando-0.2/cookbook/grid_cut.py | Python | gpl-2.0 | 697 | [
"Gaussian"
] | a335af581555aaa9ec3633bea3cb208bcd9d5d7c36ee2f3c8c6a5ff50a91c450 |
"""
module for generating and serializing xml and html structures
by using simple python objects.
(c) holger krekel, holger at merlinux eu. 2009
"""
import sys, re
if sys.version_info >= (3,0):
def u(s):
return s
def unicode(x):
if hasattr(x, '__unicode__'):
return x.__unicode__()
... | lamby/pkg-codespeak-lib | py/_xmlgen.py | Python | mit | 8,023 | [
"VisIt"
] | b2a7e61925a1f9d951fb5ebfb69a5357f97c7be6ef47a3d0fdec1b1425068544 |
# -*- coding: utf-8 -*-
import sys, os
project = u'Partisci'
copyright = u'2012, Brian Dorsey'
# The short X.Y version.
version = '0.1'
# The full version, including alpha/beta/rc tags.
release = '0.1'
templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
extensions = ["sphinxcontrib.programout... | briandorsey/partisci | doc/conf.py | Python | bsd-2-clause | 1,190 | [
"Brian"
] | cdb254105401a9ce0af3410101a06a505177501a3870edc4a2022f9d0542b4e2 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2016, Brian Coca <bcoca@ansible.com>
# 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
DOCUMENTATION = '''
module: systemd
autho... | computersalat/ansible | lib/ansible/modules/systemd.py | Python | gpl-3.0 | 21,313 | [
"Brian"
] | 45b806d5d3fe758096d1c5ba4cfabc823a7c07ebcd50be61cf4611e4d46db78a |
# -*- encoding: utf-8 -*-
# Yuuno - IPython + VapourSynth
# Copyright (C) 2017 StuxCrystal (Roland Netzsch <stuxcrystal@encode.moe>)
#
# 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, eit... | stuxcrystal/yuuno | yuuno_ipython/ipy_vs/runvpy.py | Python | lgpl-3.0 | 2,570 | [
"MOE"
] | fcf71d1c2ccef853cbd6d6cd8a1b996e4fbb74fa5b96d2b5c8c685e9706948a6 |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011, 2013 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 yo... | Panos512/invenio | modules/docextract/lib/refextract_regression_tests.py | Python | gpl-2.0 | 135,097 | [
"DIRAC"
] | dcae293f2a08e8929f336ed7bc1a342c731d3d0c5ec67438bedb74fd682bec06 |
#!/usr/bin/env python
"""
Gaussian process classification using mean-field variational inference.
Probability model:
Gaussian process classification
Prior: Gaussian process
Likelihood: Bernoulli-Logit
Variational model
Likelihood: Mean-field Normal
"""
from __future__ import absolute_import
from __future__ imp... | ruohoruotsi/Wavelet-Tree-Synth | edward-examples/gp_classification.py | Python | gpl-2.0 | 2,315 | [
"Gaussian"
] | cfe7e9678d4513a1af64532770befcbbf4f2fdebb76c6f3e0219ecaa92ada0ea |
from __future__ import print_function
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
import matplotlib as mpl
from ase.io import read
from pyqstem.util import atoms_plot
from pyqstem import PyQSTEM
from pyqstem.potentials import poisson_solver,create_potential... | jacobjma/PyQSTEM | test/test_tem_dft.py | Python | gpl-3.0 | 1,270 | [
"ASE",
"GPAW"
] | 503b414ce3a10b3053e26aed0ed6437d39b4fd064792c9796ec7b7dceef8af01 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/analysis/diffusionmap.py | Python | gpl-2.0 | 15,136 | [
"MDAnalysis"
] | c95194e712bcf4fb524266087050775dbd88265065d079965609db5cede5bba0 |
from Bio.Blast import NCBIWWW
from core.utils import BLAST
class BLASTNcbi(BLAST):
"""Handles duties related to blast against sequences in NCBI GenBank."""
def do_blast(self) -> None:
"""Blasts against NCBI and saves returned XML file to local disk."""
with open(self.query_file) as handle:
... | carlosp420/VoSeq | blast_ncbi/utils.py | Python | bsd-3-clause | 559 | [
"BLAST"
] | bf499c035b4044e7595229521d3bec2ab9a52f97f4b458cc71d91402bcee70fe |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | ravibhure/ansible | lib/ansible/modules/network/avi/avi_dnspolicy.py | Python | gpl-3.0 | 3,787 | [
"VisIt"
] | 5baf84191c4072402e9ff85112f5c11914555b2910a654aca0ebd4118a50f990 |
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# Copyright 2013 IBM Corp.
# 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
#
# ... | shakamunyi/nova | nova/tests/unit/network/test_manager.py | Python | apache-2.0 | 160,707 | [
"FEFF"
] | bc2b6b658437e5a5933c9b1e0cc78c3005055636bbfef7ed24d68f253faa145c |
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space 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 Lice... | Lukc/ospace-lukc | server/lib/ige/ospace/GalaxyGenerator.py | Python | gpl-2.0 | 24,944 | [
"Galaxy"
] | a48857229f38831bffa87517463da9db3094aece9701bf146366de9d2273f708 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
import os.path as osp
import numpy as np
from sisl.unit import units
import sisl._array as _a
from sisl.messages import... | zerothi/sisl | sisl/io/openmx/omx.py | Python | mpl-2.0 | 13,616 | [
"OpenMX"
] | deadf81c57db1089adde3ea7139609335449a6da9f2092016e900b14ec1bb3e3 |
#!/usr/bin/python
# LICENSE: GPL2
# (c) 2014 Kamil Wartanowicz
import sys,os.path
sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
import logging
from lxml import etree
import shutil
from util import types
from util import hextools
PIN_1 = "1111"
PIN_1_ATTEMPTS = "3"
PIN_1_UNBLOCK = "11111111"
PIN_1_UN... | kamwar/simLAB | sim_soft/sim_xml.py | Python | gpl-2.0 | 17,800 | [
"ADF"
] | c1f2f80f86d5a07cf74d34b127e7609d1d599adcfb1dc85b9a30083a811a2d01 |
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