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#!/usr/bin/env python3
"""
This program computes oligonucleotide profiles (microcomposition) for sequences given as arguments.
Depending on the set of parameters used, the program guess what is possible to do and will perform accordingly. Use the proper (and minimal) parameter set you need to achieve what you want.
Luc... | itsmeludo/ContaLocate | Kount.py | Python | gpl-3.0 | 23,261 | [
"Biopython"
] | 4e89a51ef31b35aac90ecb3f2bbf574fa0e0fd0f7ca95b8d1c9c2506c520ebfb |
import random
import math
import numpy as np
import scipy.interpolate as si
class Path:
"""
Represents a state of system in the lagrangian space (path
configurations X constraint).
"""
_maxVlambdaPert = 100.
_maxVertexPert = 0.01
_initialVlambda = 0.
_changeVlambdaProbability = 0.05
... | trianam/dissertation | plotters/voronoiPath/path.py | Python | cc0-1.0 | 16,259 | [
"Gaussian"
] | 68034feafff1729e3bc8cf8141bc31144d817b74434a4298ae6e5b637aa8b77a |
import dataclasses
import typing
from random import Random
from typing import Dict, Iterator
import randovania
from randovania.game_description import default_database
from randovania.game_description.assignment import NodeConfigurationAssignment, PickupTarget
from randovania.game_description.default_database import d... | henriquegemignani/randovania | randovania/games/prime2/patcher/claris_patcher_file.py | Python | gpl-3.0 | 29,348 | [
"Amber",
"CRYSTAL"
] | e3f5cfb4592934ace9bacba80460408ad6f01d41ff5bc160c585653387a636d1 |
from .. import lbx
from .. import savegame
from space_object import SpaceObject
__author__ = "peterman"
__date__ = "$May 15, 2010 9:12:05 AM$"
class Star(SpaceObject):
def __init__(self, star_id):
self.set_id(star_id)
# /__init__
def set_size(self, size):
self.__size = size
def get_... | mimi1vx/openmoo2 | oldmess/universe/star.py | Python | gpl-2.0 | 10,080 | [
"VisIt"
] | 60a71c67c380ac4d9c1c495dd5acb7a0450795f1705a4fe078e9bd3844fa318b |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. 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
#
# U... | sunqm/pyscf | pyscf/ci/addons.py | Python | apache-2.0 | 1,311 | [
"PySCF"
] | 7f9350ffa4687eb27d46ef99db63ff11b313416f62e6a4f957702d1777755727 |
from __future__ import division, unicode_literals
import inspect
import time
import serial
from .util import to_two_bytes, two_byte_iter_to_str, pin_list_to_board_dict
# Message command bytes (0x80(128) to 0xFF(255)) - straight from Firmata.h
DIGITAL_MESSAGE = 0x90 # send data for a digital pin
ANALOG_MESSAGE ... | andyclymer/ControlBoard | lib/modules/pyFirmata-master/pyfirmata/pyfirmata.py | Python | mit | 19,932 | [
"CRYSTAL"
] | bf1abf0095b4d6a4aa774d50215e310257c2fcaa691d73c9a019993f4ef506d4 |
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems 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.o... | coufon/neon-distributed | tests/test_initializers.py | Python | apache-2.0 | 2,974 | [
"Gaussian"
] | 6703b6b794c737b5708d7c99fd292fc7a91d70d144dcaab1d65b90258d1fe77d |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2018, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Löwdin population analysis."""
import random
import numpy
from cclib.method.population import Populatio... | cclib/cclib | cclib/method/lpa.py | Python | bsd-3-clause | 4,317 | [
"cclib"
] | 9fadadaad15e779a329788b9cdd51a8b9fc08e860ec738b1e2f2408751a0ff72 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/tools/init_cfg/lattice.py | Python | gpl-3.0 | 3,714 | [
"ESPResSo"
] | 717878a19175f2566947abec90694f1427c3f32318876ba482e9463d48169e4a |
import os
from itertools import product
import csv
from django.test import SimpleTestCase
from django.conf import settings
from django.core.management import call_command
import numpy
import mock
import gjfwriter
import utils
import constants
import mol_name
import ml
import structure
import fileparser
import graph
i... | crcollins/chemtools-webapp | chemtools/tests.py | Python | mit | 52,884 | [
"ADF"
] | e8edfc8732bb7c8fe1a5dedb34249f43b0518d09f5c0e8a356aa05a09a5ebc31 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
#pylint: disable=invalid-name
#! /usr/bin/pyt... | mganeva/mantid | tools/VTKConverter/VTKConvert.py | Python | gpl-3.0 | 5,381 | [
"VTK"
] | e061414d0a35af040ee4f18ff50ec3a207b8fa20511abd8cc70eae1f9f0974ea |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2013, 2014, 2015 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 optio... | switowski/invenio | invenio/ext/script/__init__.py | Python | gpl-2.0 | 12,359 | [
"VisIt"
] | 1e0a79b3b00d3e956e8d40aa8c07644fa5bbbf1a63963367927e5cde26642b3f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import os
import shutil
import subprocess
import numpy as np
from vasp.incar import Incar
from vasp.chgcar import Chgcar
from vasp.kpoints import Kpoints
from ph_ana... | yuzie007/ph_analysis | ph_analysis/finite_displacer.py | Python | mit | 4,797 | [
"VASP",
"phonopy"
] | d3d059114d2dd271ad7aee9071512ac7745dbb2a91138b37e255fcef7d58544b |
# -*- coding: utf-8 -*-
"""Functions to make 3D plots with M/EEG data."""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <lar... | jaeilepp/mne-python | mne/viz/_3d.py | Python | bsd-3-clause | 81,443 | [
"Mayavi",
"VTK"
] | e5e79e3e6d419f64fe8dd712c83895d90dc98c560a9a69dc58fc9c54fb667841 |
"""cpassdb - Storage
This module contains all code regarding reading from and writing to disk, as
well as directory structuring.
"""
__author__ = "Brian Wiborg <baccenfutter@c-base.org>"
__license__ = "GNU/GPLv2"
import os
import sys
import json
import glob
import arrow
import commands
from .config import STORAGE_ROO... | baccenfutter/cpassdb | cpassdb/storage.py | Python | gpl-2.0 | 12,362 | [
"Brian"
] | 9990971b2df4a940891574af736e24718a57518ad5ba6de7ec15e65494310e42 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | annarev/tensorflow | tensorflow/python/autograph/pyct/cfg.py | Python | apache-2.0 | 32,331 | [
"VisIt"
] | 3fc8ad7f3e26b67119487a9cc12414d153131e0bb137ae92ad8520750182dbb0 |
"""
################################################################################
# Copyright (c) 2003, Pfizer
# Copyright (c) 2001, Cayce Ullman.
# Copyright (c) 2001, Brian Matthews.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provid... | burzillibus/RobHome | venv/lib/python2.7/site-packages/SOAPpy/Utilities.py | Python | mit | 5,112 | [
"Brian"
] | 5d454b3f53e6b6f6c16a84493ad7b5361dbad0de4b9e520b9750412dea0d47e1 |
"""
Copyright (c) 2014 Brian Muller
Copyright (c) 2015 OpenBazaar
"""
import abc
import random
from base64 import b64encode
from config import PROTOCOL_VERSION
from dht.node import Node
from dht.utils import digest
from hashlib import sha1
from log import Logger
from protos.message import Message, Command, NOT_FOUND, ... | OpenBazaar/OpenBazaar-Server | net/rpcudp.py | Python | mit | 8,063 | [
"Brian"
] | 52a9f775e4ad8310751200bb657ec9bbf20f3183f640c39b176de9d8f8ae1a77 |
from __future__ import division, print_function
import numpy as np
from dipy.denoise.denspeed import nlmeans_3d
# from warnings import warn
# import warnings
# warnings.simplefilter('always', DeprecationWarning)
# warn(DeprecationWarning("Module 'dipy.denoise.nlmeans' is deprecated,"
# " use m... | nilgoyyou/dipy | dipy/denoise/nlmeans.py | Python | bsd-3-clause | 2,956 | [
"Gaussian"
] | ea6f596759223b66f16be6fc3caa4c7d377e95edc91e3cefc0a184281056712c |
import numpy as np
from collections import Iterable
from menpo.image import Image
from menpofit.visualize import view_image_multiple_landmarks
from menpofit.error import euclidean_bb_normalised_error
def _rescale_shapes_to_reference(shapes, affine_transform, scale_transform):
rescaled_shapes = []
for shape ... | yuxiang-zhou/menpofit | menpofit/result.py | Python | bsd-3-clause | 118,801 | [
"Gaussian"
] | 41b9bff1dc708d3e29418d411cebaeaf4d1632579ceb35170a9860e077d5be6d |
# Copyright 2000-2001 by Andrew Dalke.
# Revisions copyright 2008 by Peter Cock.
# 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.
"""Standard nucleotide and protein alphabets de... | bryback/quickseq | genescript/Bio/Alphabet/IUPAC.py | Python | mit | 3,110 | [
"Biopython"
] | 85af8fce9ab62e81e169277a79fd3b0419727b47d9a8f55dac89f533fb5bc9a9 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2004-2007 Donald N. Allingham
# Copyright (C) 2010 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either ve... | sam-m888/gprime | gprime/display/__init__.py | Python | gpl-2.0 | 844 | [
"Brian"
] | baaf690ec3fbbcd715ab97e58019941f0ef1c58a56650bf315638dcfc51f14fe |
../../../../share/pyshared/orca/phonnames.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/phonnames.py | Python | gpl-3.0 | 44 | [
"ORCA"
] | cc90824c2df6dd5b9de33913ae5365c44d8a5908ae450eae21acaf3641412102 |
"""
Views for user API
"""
import json
from django.shortcuts import redirect
from django.utils import dateparse
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import UsageKey
from rest_framework import generics, views
from rest_framework.decorators import api_view
from rest_framework.response import... | teltek/edx-platform | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 13,242 | [
"VisIt"
] | c74e5d3a359814958d405b628ef50ab698515aee87f4ab664f62674c1cd47c12 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# care_edit_mopac_results.py
#
# Copyright 2016 Carlos Eduardo Sequeiros Borja <casebor@gmail.com>
#
# 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 ... | casebor/labioscripts | python/care_edit_mopac_results.py | Python | gpl-3.0 | 2,541 | [
"MOPAC"
] | 4691b8f1ebdbd89ad26f22c2727053136bb16d65031f010a1e1782fa8ec4895f |
# -----------------------------------------------------------------------------
# Milky Way - Turn based strategy game from Milky Way galaxy
#
# URL: https://github.com/FedericoRessi/milkyway/
# License: GPL3
#
# pylint: disable=invalid-name
# ------------------------------------------------------------------... | FedericoRessi/milkyway | conftest.py | Python | gpl-3.0 | 421 | [
"Galaxy"
] | 283070352034d9a3fed4c89dd537b49b0605732fe3c4c1a586dbda0709bb00ff |
from math import pi
from itertools import izip
import numpy as np
from ase.units import Hartree
from gpaw.xc import XC
from gpaw.xc.sic import SIC
from gpaw.atom.generator import Generator
from gpaw.atom.configurations import parameters
from gpaw.utilities import hartree
class NSCFSIC:
def __init__(self, paw):
... | qsnake/gpaw | gpaw/utilities/sic.py | Python | gpl-3.0 | 3,324 | [
"ASE",
"GPAW"
] | 303581f01f0bc7bb54d7624db00bb75469ba784f247b6c8f72adc899ab76c271 |
from pycparser import parse_file
from minic.c_ast_to_minic import *
from minic.minic_ast import *
from minic.mutils import *
import sys
'''
WSTool extracts the set of written variables from each 'for' or 'while' loop
in a C program.
From the command line in the directory of WSTool.py, execute:
python WSTool.py <name ... | martylee/Python | CSC410-Project-1-master/WSTool.py | Python | gpl-2.0 | 5,193 | [
"VisIt"
] | 0fe339afe86763b902d028a84e7e9b387877e1e3c4f55c37529f3420aaa9e446 |
#!/usr/bin/env python
#########################################################################################
#
# Resample data.
#
# ---------------------------------------------------------------------------------------
# Copyright (c) 2014 Polytechnique Montreal <www.neuro.polymtl.ca>
# Authors: Julien Cohen-Adad
#... | 3324fr/spinalcordtoolbox | dev/sct_resample/sct_resample_old.py | Python | mit | 9,124 | [
"Gaussian"
] | 0f09e4ea0a220395322d0b47620b58c64efb8f69c59315f0cccc5c8b097e7a22 |
#
# 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 t... | mozts2005/OuterSpace | client-pygame/libsrvr/ige/ospace/IGalaxy.py | Python | gpl-2.0 | 16,124 | [
"Galaxy"
] | dd549826166779c80604033e33544bfa1b4bf3e2622d6b195718cb168713f187 |
# -*- coding: utf-8 -*-
"""
Tests for the text processor.
"""
from __future__ import unicode_literals
import json
from unittest import TestCase, main
from datetime import datetime
import mock
from nose.tools import * # noqa (PEP8 asserts)
from nose.plugins.attrib import attr
import nltk
from textblob.compat import P... | sloria/TextBlob | tests/test_blob.py | Python | mit | 41,699 | [
"Octopus"
] | 0eef10ba4c2c10d598d5ac987c1907cd53ca03a724b7e863062cb78b3c82dee1 |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
# pylint: disable=E1111
import unittest
import json
import requests
import datetime
from urllib import quote
from django.test import TestCase
from nose.tools import raises
from mock import Mock, patch
from django.conf import settings
from django.tes... | echanna/EdxNotAFork | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 88,197 | [
"VisIt"
] | 8cf72e8cfb7d33ca637322eb8e5284f5897a2fdcb6900c605471c8b6415421bc |
########################################################################
# $Id$
# File : ProcessMonitor.py
# Author : Stuart Paterson
########################################################################
""" The Process Monitor utility allows to calculate cumulative CPU time and memory
for a given PID and it... | calancha/DIRAC | Core/Utilities/ProcessMonitor.py | Python | gpl-3.0 | 18,404 | [
"DIRAC"
] | 9fe7ff32957a1dc756fa1e6b7f104682be4b1518705066620865154a73f68efa |
#!/usr/bin/env python3
import os
from functions import auto_snapshot
from functions import enable_compression
from functions import validation
#
# Interactive ZFS on Linux setup
#
#
# Print Description
#
os.system("clear")
print("This script will provide a guided setup for ZFS on Linux. Feel free to modify and di... | jsirianni/zfs-auto-deploy | install.py | Python | gpl-3.0 | 7,650 | [
"VisIt"
] | 55c77cd218e0d5a41cce9d6e3d2896d6053892d84e6c6ca6c9c81618b42f36f0 |
from optparse import OptionParser
import os
import time
import sys
from Bio.Blast import NCBIXML
formats = ['fastq', 'fasta', 'fa', 'fas']
class AlignmentBase:
""" Data structure to store alignment object. """
def __init__(self, subject_base, query_base, position_subject, position_query, position_query_loca... | molecol/targeted-resequencing-with-mips | exon_boundaries_on_transcript/map_seq_on_exons_by_blast.py | Python | mit | 17,633 | [
"BLAST"
] | 136f06e6df7fcfcb215cb43998a3b4874e4d25a250b1aaf587c471474594f00a |
##
# Copyright 2009-2016 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... | hpcleuven/easybuild-easyblocks | easybuild/easyblocks/g/gamess_us.py | Python | gpl-2.0 | 14,039 | [
"GAMESS"
] | 2a4e57825d7a878c7bebf6d18564b066dd05f9567626806564ee16175230c172 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# main.py
#
# Copyright 2015 Eusebio Aguilera <eusebio.aguilera@gmail.com>
#
# 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... | eusebioaguilera/cvsamples | handwriting_recognition/main.py | Python | lgpl-3.0 | 5,553 | [
"Gaussian"
] | 025203632dc1d6cd78b1d085d7d23662e4aa3760bbf592d288a92ee89d18e8ad |
import numpy
import numpy.linalg
import scipy.linalg
import scipy.interpolate
from scipy.signal import wiener, filtfilt, butter, gaussian
from scipy.ndimage import filters
from matplotlib import pyplot as plt
plt.style.use('classic')
from assimulo.solvers import IDA
from assimulo.problem import Implicit_Problem
from... | matthewpklein/battsimpy | tests/dae_genPart_noJ.py | Python | gpl-3.0 | 37,032 | [
"Gaussian"
] | 9405810524de695c4fe10c5bf2e2703335cae5f31747af4a74a2aeba6d59936c |
# proxy module
from __future__ import absolute_import
from mayavi.sources.three_ds_importer import *
| enthought/etsproxy | enthought/mayavi/sources/three_ds_importer.py | Python | bsd-3-clause | 101 | [
"Mayavi"
] | 362aa13c6ea925472f525b21d968fba4fbaadec428d74d39ec98e82b9e40820a |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
#"""
#PSLibrary Job File
######################
#Job files (extension '.job') are used inside the `pslibrary`_ package to house
#input data for pseudopotential generation using the a... | exa-analytics/exatomic | exatomic/qe/psp/jobfile.py | Python | apache-2.0 | 3,549 | [
"ESPResSo",
"Quantum ESPRESSO"
] | ac7c2213ad40c046889eb8762ff1bb7049846b31c95df424b3e12da20498a086 |
#!/usr/bin/env python3
try:
import netCDF4 as netCDF
except:
print("netCDF4 is not installed!")
sys.exit(1)
class PISMDataset(netCDF.Dataset):
def create_time(self, use_bounds=False, length=None, units=None):
self.createDimension('time', size=length)
t_var = self.createVariable('time... | pism/pism | examples/preprocessing/PISMNC.py | Python | gpl-3.0 | 5,381 | [
"NetCDF"
] | ccdf2640633efc9270873552962b267def0a14ec51fddb84cf74fdc4ba0bc30c |
# Copyright 2016 Curtis Sand
#
# 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 writi... | fretboardfreak/potty_oh | potty_oh/signal_generator.py | Python | apache-2.0 | 19,082 | [
"Gaussian"
] | fa386c29865352546d4afed7bf9a6f99372a4fcc10857a898233a03efbcef3ec |
# -*- coding: utf-8 -*-
"""QGIS Unit tests for edit widgets.
.. note:: This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
"""
__au... | geopython/QGIS | tests/src/python/test_qgsrelationeditwidget.py | Python | gpl-2.0 | 12,569 | [
"Galaxy"
] | b3d6c414ee0556409ea28fac9ac3e078a834e2e2f8cb53f2c8041b645271e43e |
__author__ = 'Mike McCann'
__copyright__ = '2012'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
__doc__ = '''
STOQS Query manager for building ajax responses to selections made for QueryUI
@undocumented: __doc__ parser
@status: production
@license: GPL
'''
from collections import defaultdict, Ma... | MBARIMike/stoqs | stoqs/utils/STOQSQManager.py | Python | gpl-3.0 | 136,368 | [
"NetCDF"
] | 2cd93c9285e606d1e292bcd2cdc2c9467cb95f126048383c9f839df83d1e2d95 |
import ast
import weakref
import sys
import collections
from greentype.utils import is_collection
def decorated_with(node, name):
if not isinstance(node, (ast.ClassDef, ast.FunctionDef)):
raise ValueError('Illegal node type "{}". Should be either class '
'or function definition.'.... | east825/green-type | greentype/ast_utils.py | Python | mit | 5,055 | [
"VisIt"
] | f96ed75c590246aa9f97c3afe30166838bde65479522372f7b6521cbda448c5e |
#! /usr/bin/env python
########################################################################
# $HeadURL: $
########################################################################
__RCSID__ = "$Id: $"
from DIRAC import exit as DIRACExit
from DIRAC.Core.Base import Script
Script.setUsageMessage("""
Cl... | sposs/DIRAC | DataManagementSystem/scripts/dirac-dms-clean-directory.py | Python | gpl-3.0 | 1,311 | [
"DIRAC"
] | f0b43774e1f07d51f65e1c729ec4104029eea3785968268555893c3b1325e7d1 |
# Copyright (c) 2010 The Chromium OS Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Command to extract the dependancy tree for a given package."""
from __future__ import print_function
import json
import portage # pylint: disabl... | guorendong/iridium-browser-ubuntu | third_party/chromite/scripts/cros_extract_deps.py | Python | bsd-3-clause | 6,727 | [
"VisIt"
] | 9dfd84f6a6c4326630434e276ca8c488425b3d52f84c2cd45ca09e5f02cf6da1 |
# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import os
from Bio.PopGen import GenePop
from Bio.PopGen.GenePop import ... | bryback/quickseq | genescript/Bio/PopGen/FDist/Utils.py | Python | mit | 7,053 | [
"Biopython"
] | 580f7c17a2a0e091f103b96423d5f7999f6c930f1f80173f3c6e0bba99bd31c1 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008) - although it uses the... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_nosyn_32000/brian2_benchmark_COBAHH_nosyn_32000.py | Python | gpl-3.0 | 3,353 | [
"Brian"
] | 8a38da863d067a51432cb76e82fe60cddaf57d1b20aa2679e5e5eb05c266d356 |
# 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/function.py | Python | lgpl-3.0 | 4,624 | [
"VisIt"
] | 9213dada4adf5d6b9c93c9d0cc8e40c07690aed1ec172ce3d3fece620e83974a |
'''
Created on Sept 22, 2017
Convert IPW TOPO files to netCDF
@author: Micah prime
'''
import pandas as pd
import numpy as np
from smrf import ipw
import netCDF4 as nc
from datetime import datetime
from matplotlib import pyplot as plt
fp_output = '/home/micahsandusky/Code/workdir/test_ipw_convert/tuol_topo.nc'
dem =... | USDA-ARS-NWRC/AWSF | examples/make_topo_ncdf.py | Python | gpl-3.0 | 4,185 | [
"NetCDF"
] | c3d1643b0b9768f0c578d711909b8c7b85b2c2d009116bd8849ee962deda37c3 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure that all files contain proper licensing information."""
import json
import optparse
import os.path
import subproces... | boundarydevices/android_external_chromium_org | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 15,039 | [
"Galaxy"
] | 27890a2594cc82937e5ce9804d9b1cc4f6a276857fc518479afd6a7d55c564b4 |
# coding: utf-8
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..compat import compat_urllib_parse_urlparse
from ..utils import (
ExtractorError,
parse_iso8601,
qualities,
)
class SRGSSRIE(InfoExtractor):
_VALID_URL = r'(?:https?://tp\.srgssr\.ch/p(?:/[^/]+)... | israeltobias/DownMedia | youtube-dl/youtube_dl/extractor/srgssr.py | Python | gpl-3.0 | 7,163 | [
"Jaguar"
] | da822ae8639441cbd453fede5d6257d24b728373c22eecf82ff1cb870750c955 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from Method import *
from RombergIterate import *
import sys, time, datetime, os
if __name__ == "__main__":
rangeOut = False
sair = False
while( not sair):
firstTime = False
os.system('clear')
print bcolors.HEADER + '============================= Romberg =======... | glaucomunsberg/romberg | Principal.py | Python | gpl-2.0 | 3,458 | [
"Gaussian"
] | 1def182dc5ddcdeecc4b3bc710b32e6a49adc5f714790a8ce92ef03f060fe6a0 |
#!/usr/bin/env python
#
# Copyright (C) 2015, the ximpol team.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU GengReral Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# T... | lucabaldini/ximpol | ximpol/config/gaussian_disk.py | Python | gpl-3.0 | 1,308 | [
"Gaussian"
] | f62c33bf1ebfef772ff253c03cc0ea611003c883c73185d9671be516edd35e60 |
class TreeNode:
def __init__(self, **kwargs):
self.children = dict()
def get(self, key):
return self.children.get(key, None)
def get_children(self, sort=False):
if sort:
return sorted(self.children.values())
return self.children.values()
def add(self, key, ... | mhozza/string_algorithms | string_algorithms/tree.py | Python | mit | 2,185 | [
"VisIt"
] | 8f9b57a35f108602642c0e4eee07a1c287eea7322e44e719214927b09d8fa95b |
import sys
sys.path.insert(1, "../../../")
import h2o, tests
def distribution_behaviorGBM():
#Log.info("==============================")
#Log.info("Default Behavior - Gaussian")
#Log.info("==============================")
eco = h2o.import_file(path=h2o.locate("smalldata/gbm_test/ecology_model.csv"))
#... | brightchen/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_loss_behaviorGBM.py | Python | apache-2.0 | 2,967 | [
"Gaussian"
] | 068531ad020fe6a44bc02dde4a6129db5a89f23b672aa19f637760c8fb64349e |
# pylint: disable=C0111
# pylint: disable=W0621
# Disable the "wildcard import" warning so we can bring in all methods from
# course helpers and ui helpers
# pylint: disable=W0401
# Disable the "Unused import %s from wildcard import" warning
# pylint: disable=W0614
# Disable the "unused argument" warning because let... | nanolearning/edx-platform | common/djangoapps/terrain/steps.py | Python | agpl-3.0 | 6,853 | [
"VisIt"
] | aa52693767cb897c9ba7aa0d680ff07f8281d5de054ff6596e55624807ace776 |
__author__ = 'Deniz'
from bs4 import BeautifulSoup
from splinter import Browser
import argparse, os, re, time
mmr_filepath_Dict = {}
def main():
global mmr_filepath_Dict
BASE_URL = "http://na.op.gg/"
parser = argparse.ArgumentParser(description='Attempt to search op.gg with the summoner names in every fi... | Murkantilism/LoL_API_Research | Summoner_Data_Retrieval/Scrape_mmr_opgg.py | Python | mit | 5,728 | [
"VisIt"
] | 8c2ac75b6f292add326e8f98fa52b9f340e7058feab45935fd9670c81b66c288 |
global astrom
global tmpdir
import traceback, tempfile
tmpdir = '/usr/work/pkelly/'
astrom='solve-field'
def length_swarp(SUPA,FLAT_TYPE,CHIPS):
import os, re, utilities, bashreader, sys, string
from copy import copy
from glob import glob
dict = get_files(SUPA,FLAT_TYPE)
search_params = initialize... | deapplegate/wtgpipeline | non_essentials/calc_test/calc_tmpsave.save.py | Python | mit | 206,007 | [
"Galaxy"
] | f5f413f26d90cfb8e58991e33da24fc1ff1715694a640b2640fb2d9f2e3a1fa9 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
# pylint: disable=no-init,invalid-name,too-ma... | mganeva/mantid | Testing/SystemTests/tests/analysis/POLDICreatePeaksFromCellTest.py | Python | gpl-3.0 | 6,042 | [
"CRYSTAL"
] | ad37aaf5b423170b9b734efbb330e35299544a98dba690fa663ec2c6a810b1f2 |
# -*- coding: utf-8 -*-
import datetime
from time import sleep
from lettuce import *
from django.utils.datastructures import SortedDict
from rapidsms.contrib.locations.models import *
from survey.features.page_objects.aggregates import AggregateStatusPage, DownloadExcelPage, InvestigatorReportPage
from survey.features... | antsmc2/mics | survey/features/aggregates-steps.py | Python | bsd-3-clause | 12,809 | [
"VisIt"
] | 068ff9a38d28392f75097894ebca695025a9a1ffe901e0a090a05a260b4bab62 |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Reiko Michisaki'
__copyright__ = '2013'
__license__ = 'GPL v3'
__contact__ = 'duane at mbari.org'
__doc__ = '''
loader for ESP CANON activities in September 2013
Mike McCann; Modified by Duane Edgington and Reiko Michisaki
MBARI 02 September 2013... | josephmfaulkner/stoqs | stoqs/loaders/CANON/esp_loadsep2013.py | Python | gpl-3.0 | 2,775 | [
"NetCDF"
] | 9101d62a0e2108c407237da9cf40693f296ccb642471de8b97a8b678dba82df6 |
"""
Module simplifying manipulation of XML described at
http://libvirt.org/formatdomain.html
"""
import logging
from autotest.client.shared import error
from virttest import xml_utils
from virttest.libvirt_xml import base, accessors, xcepts
from virttest.libvirt_xml.devices import librarian
class VMXMLDevices(list):... | chuanchang/tp-libvirt | virttest/libvirt_xml/vm_xml.py | Python | gpl-2.0 | 73,245 | [
"VisIt"
] | 8b15a95381c0c8e48d1348d097248ac31ec169c48772364d1937e3396e3b83ff |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/integrator/Adress.py | Python | gpl-3.0 | 2,463 | [
"ESPResSo"
] | e7d4d81c236d932547a973f3b4bb8af2e6720f4544a212bf9b46ea6b4cfcb64a |
#!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from parlai.core.teachers import Teacher
from .build import build
from parlai.utils.io import PathManager
import json
im... | facebookresearch/ParlAI | parlai/tasks/casino/agents.py | Python | mit | 14,045 | [
"CASINO"
] | 138bbc0f9f2afa792248f26eb6e41a0b312358cf7f5ae16f7eb8404f9186ae4a |
import numpy as np
import pdb
from scipy.interpolate import interp1d
from scipy.stats import pearsonr
from scipy.stats import norm
import scipy.signal as signal
from matplotlib import gridspec
import matplotlib
matplotlib.use('Qt4Agg')
import matplotlib.pyplot as plt
from matplotlib.widgets import RadioButtons, Button,... | giffordw/zpy | zpy/__init__.py | Python | mit | 17,230 | [
"Galaxy"
] | a5c6dad6520436069e8026796ada24ca507c5781e113594f6382c1bf3cd60690 |
# Copyright 1999 by Jeffrey Chang. 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.
from __future__ import print_function
import os.path
import unittest
import shutil
from Bio._... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_File.py | Python | gpl-2.0 | 2,588 | [
"Biopython"
] | e125af4b2929ffa2224e06f13fa4c14cda25d7b16cb1af04ab1348ababbfabe1 |
# -*- coding: utf-8 -*-
"""
pygments.lexers.compiled
~~~~~~~~~~~~~~~~~~~~~~~~
Just export lexer classes previously contained in this module.
:copyright: Copyright 2006-2017 by the Pygments team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
from pygments.lexers.jvm import JavaLexer, Sc... | wandb/client | wandb/vendor/pygments/lexers/compiled.py | Python | mit | 1,385 | [
"CRYSTAL"
] | f5dfd70d5ef9162fc49ebb153c07b17ecf0b440cac7e2c6964336a5448631945 |
#
# 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 http://mozilla.org/MPL/2.0/.
#
# Copyright (c) 2015 Digi International Inc., All Rights Reserved.
#
from hamcrest import assert_that, ends_with, is... | brucetsao/XBeeZigBeeCloudKit | splinter_tests/test_add_widget_page.py | Python | mpl-2.0 | 7,121 | [
"VisIt"
] | 78cf56d981d33f81a56c8bf6326c9dc808d1ba88608b28355558e589fb34355c |
import moogli
import moose
from moose import neuroml
from PyQt4 import Qt, QtCore, QtGui
import sys
import os
app = QtGui.QApplication(sys.argv)
filename = os.path.join( os.path.split(os.path.realpath(__file__))[0]
, "../neuroml/PurkinjeCellPassivePulseInput/PurkinjePassive.net.xml"
... | dilawar/moose-full | moose-examples/moogli/simple_viewing.py | Python | gpl-2.0 | 1,196 | [
"MOOSE"
] | e2172471b41b6647ad377a0075c5cc1b74391910f9dfafe32ab9ea18a643bbc0 |
"""
climatology.py
Compute a multi-epoch (multi-day) climatology from daily SST Level-3 grids.
Simple code to be run on Spark cluster, or using multi-core parallelism on single machine.
"""
import sys, os, calendar, urlparse, urllib
from datetime import datetime
import numpy as N
from variables import getVariables,... | dataplumber/nexus | climatology/clim/climatology1.py | Python | apache-2.0 | 10,033 | [
"Gaussian"
] | 4d27966852158a5b1d13b15304b006c6a676ab190f22b276979c6e57dd6889df |
# -*- coding: utf-8 -*-
#
# Copyright (c), 2015-2016, Quantum Espresso Foundation and SISSA (Scuola
# Internazionale Superiore di Studi Avanzati). All rights reserved.
# This file is distributed under the terms of the MIT License. See the
# file 'LICENSE' in the root directory of the present distribution, or
# http://o... | afonari/q-e_schrodinger | bin/qexsd/qespresso/__init__.py | Python | gpl-2.0 | 938 | [
"Quantum ESPRESSO"
] | f11348f7497e6e21202ddfc3f4a69907509be48de5dd7f551ddbac539aec6c6d |
import tkSimpleDialog
import tkMessageBox
#import p3d.protein
#import p3d.geo
from pymol.wizard import Wizard
from pymol import cmd, util
from pymol.controlling import mode_dict
class Bond(object):
def __init__(self,bond1,bond2,resid1,resid2):
if bond2 > bond1:
self.bond1=bond1
self... | tmorrell/SamStruct | inputs/selector_prot.py | Python | gpl-2.0 | 14,462 | [
"PyMOL"
] | f53a1bdd45a1790ce5b7103c12b7b0c33cc235c08891231a06d67d8d9cd84324 |
#!/usr/bin/env python3
# -*- coding: utf8 -*- #
#
#
# Copyright (C) by p.oseidon@datec.at, 1998 - 2017
#
# This file is part of tau4.
#
# tau4 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... | p-o-seidon/tau4 | src/tau4/test__tau4sensors.py | Python | gpl-3.0 | 17,045 | [
"VisIt"
] | 1c5fd688a33950c341a038d14e81f1a40919d60aff57b2ecd446b9322442b933 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | junghans/espressopp | src/interaction/DihedralHarmonicCos.py | Python | gpl-3.0 | 3,583 | [
"ESPResSo"
] | 872e5714bf07849d299106d84e27c3a0619ea4dae95cf33246271c7f36b5f800 |
import logging
import time
import traceback
import numpy as np
from ..conventions import cf_encoder
from ..core import indexing
from ..core.pycompat import dask_array_type
from ..core.utils import FrozenDict, NdimSizeLenMixin
# Create a logger object, but don't add any handlers. Leave that to user code.
logger = log... | xray/xray | xarray/backends/common.py | Python | apache-2.0 | 10,715 | [
"NetCDF"
] | cd7f6e8a7990fe173d4bd0c8ea48eb9513c99c25cc8db1cf25ad760d1e2eb434 |
# -*- coding: utf-8 -*-
"""
<DefineSource>
@Date : Fri Nov 14 13:20:38 2014 \n
@Author : Erwan Ledoux \n\n
</DefineSource>
The Doer defines instances that are going to decorate a big family of classes in this framework.
Staying on the idea, that one module should associate
one class, now a decorated class by a Doe... | Ledoux/ShareYourSystem | Pythonlogy/ShareYourSystem/Standards/Classors/Doer/Drafts/__init__ copy 3.py | Python | mit | 19,047 | [
"Brian",
"VisIt"
] | cb0d8b0407be862cc0aced62f931f15696f92ca7a2dffd08d5b0e379c4c6b48e |
"""
the diags_file contains the hits that dagchainer found, the all_file is the full list of blast hits.
this script goes through all of the hits in the dag file and adds any hit from the all_file that is within 'dist' of
any hit in the diag.
"""
from rtree import Rtree
import sys
import os
import psyco; psyco.full(... | LyonsLab/coge | bin/dagchainer/find_nearby.py | Python | bsd-2-clause | 3,684 | [
"BLAST"
] | b5272fc21177503fcc1626d8e94a47320c97c16a4371cddc2647aa449dbd645f |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pymatgen.analysis.elasticity.elastic import ElasticTensor
from pymatgen.analysis.interfaces.substrate_analyzer import SubstrateAnalyzer
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymat... | vorwerkc/pymatgen | pymatgen/analysis/interfaces/tests/test_substrate_analyzer.py | Python | mit | 1,474 | [
"pymatgen"
] | 583f89faf1c018a17a2a14cdeaee669e4afe17fefbfd85a94949ea9e04520090 |
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import poisson, norm, uniform
from scipy.integrate import trapz
from am_bda import get_pdf_quantiles
NPTS = 100
NSIM = 1000
year = np.arange(10)+1976
accid = np.array([24, 25, 31, 31, 22, 21, 26, 20, 16, 22])
deaths = np.array([734, 516, 754, 877, 81... | amaggi/bda | chapter_02/ex_12.py | Python | gpl-2.0 | 2,104 | [
"Gaussian"
] | 85e5f80be9a5a4e615dfd996e2f2c4cdc670202dbb045fc790dad54d08af4088 |
import os
from setuptools import setup
os.chdir(os.path.abspath(os.path.dirname(__file__)))
packages = []
for rootdir, dirs, files in os.walk('vistrails'):
if '__init__.py' in files:
packages.append(rootdir.replace('\\', '.').replace('/', '.'))
def list_files(d, root):
files = []
for e in os.l... | Nikea/VisTrails | setup.py | Python | bsd-3-clause | 3,886 | [
"VTK"
] | be6c4ace14fda3fceb8c0402cbef720d4a4e3af5e4fa85233dac9b82eccf19f7 |
"""
Core visualization operations based on PyVista.
Actual implementation of _Renderer and _Projection classes.
"""
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
#
# License: Simplif... | adykstra/mne-python | mne/viz/backends/_pyvista.py | Python | bsd-3-clause | 12,256 | [
"VTK"
] | 62f24652211294a567b2c7a3b679a4899f659c1c6c354dde59b422915b35814c |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
def cars_checkpoint():
cars = h2o.upload_file(pyunit_utils.locate("smalldata/junit/cars_20mpg.csv"))
predictors = ["displacement","power","weight","acceleration","year"]
response_col = "economy"
distribution = "gaussi... | h2oai/h2o-dev | h2o-py/tests/testdir_algos/gbm/pyunit_NOPASS_error_checkpointGBM.py | Python | apache-2.0 | 4,184 | [
"Gaussian"
] | afc82821d7de007143616de0eac42b43f55cd0675947fc69c60f468148ec19d3 |
#!/usr/bin/env python
# import os
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create pipeline - rectilinear grid
#
rgridReader = vtk.vtkRectilinearGridReader()
rgridReader.SetFileName(VTK_DATA_ROOT + "/Data/RectGrid2.vtk")
outline = vtk.vtkOutlin... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Extraction/Testing/Python/extractRectGrid.py | Python | gpl-3.0 | 1,492 | [
"VTK"
] | 79cbdcb976db10f37292059948d74ad5144f4b8ca0ab934af62f0d599e13b511 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | wizmer/NeuroM | neurom/geom/tests/test_transform.py | Python | bsd-3-clause | 11,389 | [
"NEURON"
] | a4d834abda583de8a9a023981aaa1ac9443812dc0bb335d8dc8d1b885785b362 |
# Copyright (C) 2012,2013,2015
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms... | capoe/espressopp.soap | src/interaction/CoulombTruncated.py | Python | gpl-3.0 | 5,450 | [
"ESPResSo"
] | db724a7a4f2932499156f3b31ac1c5b89e337ceab7abee5b67ebd63f94e8bd49 |
# -*- coding: utf-8 -*-
""" *==LICENSE==*
CyanWorlds.com Engine - MMOG client, server and tools
Copyright (C) 2011 Cyan Worlds, Inc.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3... | TOC-Shard/moul-scripts | Python/Personal.py | Python | gpl-3.0 | 10,450 | [
"VisIt"
] | 5eb61f2732e0bfbbbd09001a615c84740d42e68bba05375d8e719c0c707036b8 |
# 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/.
""" Global sisl fixtures """
import contextlib
import os
import numpy as np
from pathlib import Path
import pytest
fro... | zerothi/sisl | sisl/conftest.py | Python | mpl-2.0 | 7,718 | [
"GULP",
"SIESTA",
"VASP",
"Wannier90"
] | 67f51956f10c606d8407b1d05f097785ef6669516ac0fa1a2b4b7942145e21de |
""" Pyflation - Cosmological simulations in Python
Pyflation is a python package to simulate cosmological perturbations in the early universe.
Using the Klein-Gordon equations for both first and second order perturbations,
the evolution and behaviour of these perturbations can be studied.
The main entry point to thi... | ihuston/pyflation | pyflation/__init__.py | Python | bsd-3-clause | 712 | [
"VisIt"
] | 199b097956c5a2bf453c2ebf3e2d486d7f530916ae7bc75f851efc1830e4d216 |
""" SQLAlchemyDB:
This module provides the BaseRSSDB class for providing standard DB interactions.
Uses sqlalchemy
"""
__RCSID__ = "$Id$"
import datetime
from sqlalchemy import create_engine, desc, exc
from sqlalchemy.engine.reflection import Inspector
from sqlalchemy.orm import sessionmaker
from sqlalchemy.... | chaen/DIRAC | Core/Base/SQLAlchemyDB.py | Python | gpl-3.0 | 10,709 | [
"DIRAC"
] | f39e8958f413808121ea6f55e02058d74a2e63775d99e992ad375d4538c8277f |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
import time
m = 1000
n = 2000
display = True
... | sg0/Elemental | examples/interface/BPDense.py | Python | bsd-3-clause | 1,231 | [
"Gaussian"
] | 8cdc3e6405de84d01334a0d6a80fbbec140fb1497ed26fe624b2ed9ead428d79 |
"""Pretty-printing (pprint()), the 'Print' Op, debugprint() and pydotprint().
They all allow different way to print a graph or the result of an Op
in a graph(Print Op)
"""
from __future__ import print_function
from copy import copy
import logging
import os
import sys
import warnings
import hashlib
import numpy as np
... | rizar/attention-lvcsr | libs/Theano/theano/printing.py | Python | mit | 52,435 | [
"Amber"
] | 921847b78e36177d8685e1ba54fcbc78346e50f6ffcd2c7ee4965c95c440b175 |
"""
#This software was developed by the University of Tennessee as part of the
#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
#project funded by the US National Science Foundation.
#See the license text in license.txt
"""
from __future__ import division
import numpy as np # type: ignore
from num... | SasView/sasmodels | sasmodels/resolution2d.py | Python | bsd-3-clause | 9,437 | [
"Gaussian"
] | 36eb954b9971fe7949e6cf800b98934847c7ff606017a97869bbabec01f5fddf |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008-2009 Gary Burton
# Copyright (C) 2008 Robert Cheramy <robert@cheramy.net>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2010 Nick Ha... | Forage/Gramps | gramps/plugins/export/exportgedcom.py | Python | gpl-2.0 | 54,688 | [
"Brian"
] | 14f94dae93c20f7ed8d7692545b90ce7ae58b2c58716cbf47be0e7fdb2bbbabb |
"""
Uniweb validator project
wave.py : Checks URL against WAVE validator in various ways
Copyright (c) 2009 Brian Shumate
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, inc... | brianshumate/uniweb | surfbot/utils/wave.py | Python | bsd-2-clause | 2,287 | [
"Brian"
] | 6f1a57bc573e09cf7158663ed1b2357649466776ffaf14d3fb69e97f8756dfcb |
# coding=utf-8
import asyncio
import webbrowser
import logging
import os
import sys
import time
from random import randint
from flask import Flask, render_template_string, send_from_directory, request
from amber.web_modules.sockets import Socket
from amber.web_modules.web_utils import threaded
MODULE_DIR = os.path.a... | DefaltSimon/Amber | amber/web_modules/web_core.py | Python | mit | 2,425 | [
"Amber"
] | f2af18f26e73fcb582db24e7cd8238d679a4876917bf23640eecd4d26dd930a4 |
import pytest
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR, convertToReturnValue, returnValueOrRaise
def test_Ok():
retVal = S_OK("Hello world")
assert retVal["OK"] is True
assert retVal["Value"] == "Hello world"
def test_Error():
retVal = S_ERROR("This is bad")
assert retVal["OK... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/test/Test_ReturnValues.py | Python | gpl-3.0 | 1,392 | [
"DIRAC"
] | 0383d02f07aa19714c50a36c7c61aaa2c8152faffede30308572b1ccb29275a9 |
import cairo
import pango
import pangocairo as pc
import gtk
import math
from .structures import Size, Position, Rectangle, Color, BorderRadius, Padding, Gradient, RadialGradient
from ..events.events import WindowEventSource
from ..logger import log
from datetime import datetime
from jgui.settings import DEBUG as debug... | jyapayne/JGUI | jgui/surface/surface.py | Python | mit | 45,131 | [
"Gaussian"
] | 48484bcf24043a739bd4e915bc43de85ef04e08ec29ae7faabd1552f9132d21c |
#! /usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-set-site-protocols
# Author : Stuart Paterson
########################################################################
"""
Defined protocols for each SE for a given site.
"""
from __fut... | fstagni/DIRAC | Interfaces/scripts/dirac-admin-set-site-protocols.py | Python | gpl-3.0 | 1,389 | [
"DIRAC"
] | 8dfeeea27986f495b24aef0b574eb87edef619519803c76e8048caf661a109b9 |
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