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##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/py-pyani/package.py | Python | lgpl-2.1 | 2,432 | [
"BLAST",
"Biopython"
] | 6f87049b083258b9e3698712e210802b53b5d113956db2685f9620497d508eae |
# 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 sys
# Add path to Bio
sys.path.append('../../..')
"""Perform two-point crossovers between the genomes of two organisms.
This module performs... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/GA/Crossover/TwoPoint.py | Python | gpl-2.0 | 1,311 | [
"Biopython"
] | 0cfc8fcc9008bf06f71a7307ac3b0546528c48defd75e9f13cfb8dc99a1d9ffc |
#
# 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 | server/setup.py | Python | gpl-2.0 | 1,803 | [
"Galaxy"
] | 074cee8dee53ac2ad81ebc4510a876ab508242e68b2389584f421f2f1e91fded |
import numpy as np
import os
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import matplotlib.pyplot as plt
import time
from datetime import datetime
from matplotlib.dates import date2num, num2date
import pyroms
import pyroms_toolbox
import _remapping
class nctime(object):
pass
def remap_bio_... | kshedstrom/pyroms | examples/cobalt-preproc/Initial_bio/remap_bio_woa.py | Python | bsd-3-clause | 4,602 | [
"NetCDF"
] | c1f854967b07855a8c377a15269003ec11943466d1396c62d6c78a977126ab26 |
# c: 07.05.2007, r: 08.07.2008
filename_mesh = 'database/phono/mesh_circ21.mesh'
dim = 2
field_1 = {
'name' : 'a_harmonic_field',
'dim' : (1,1),
'domain' : 'Omega',
'bases' : {'Omega' : '2_3_P1'}
}
variables = {
't': ('unknown field', 'a_harmonic_field', 0),
's': ('test field', 'a_harmonic... | certik/sfepy | tests/test_msm_symbolic.py | Python | bsd-3-clause | 8,704 | [
"VTK"
] | 3c13964b452837c4f36b4c2013cbaae1f872d6d0f56a5944d9c8c4de0f07610f |
#!/usr/bin/env python
#
# Author: Mike McKerns (mmckerns @caltech and @uqfoundation)
# Copyright (c) 1997-2015 California Institute of Technology.
# License: 3-clause BSD. The full license text is available at:
# - http://trac.mystic.cacr.caltech.edu/project/pathos/browser/pathos/LICENSE
"""
example of using the 'raw... | mathieudesro/pathos | examples/pp_map.py | Python | bsd-3-clause | 2,528 | [
"exciting"
] | 8d13441ebefe049c83aa8254f6132c23b9e78f051a11b1a6bf97ea5cd2e91367 |
#!/opt/local/bin/python2.5
#=============================================================================================
# Render a replica trajectory in PyMOL
#=============================================================================================
#=============================================================... | jchodera/yank | examples/mhc-peptide-tcr/render_trajectory.py | Python | lgpl-3.0 | 12,046 | [
"Amber",
"NetCDF",
"PyMOL"
] | f85f1c50d8572ef4a59d3640fcac7fe25817ac950c21a4586968384853a87623 |
# -*- coding: utf-8 -*-
#
# This file is part of pysenslog.
# Copyright 2015 Leonardo Rossi <leonardo.rossi@studenti.unipr.it>.
#
# pysenslog 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 versi... | hachreak/pylocating | src/pylocating/benchmarks/simple_pso.py | Python | gpl-2.0 | 2,977 | [
"Gaussian"
] | d669860634cb7ec5d02c9cd3b75d84795a38d64eae5ae84c8b77f0f57bba9fc1 |
import sys
from ase.build import molecule, fcc111, add_adsorbate
from ase.optimize import QuasiNewton
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.vibrations import Vibrations
sys.path.append("..")
from __init__ import AnharmonicModes
slab = fcc111('Au', size=(2, 2, 2), vacuum=4... | keldLundgaard/ase-anharmonics | tests/test_all_modes_anharmonic.py | Python | lgpl-2.1 | 1,029 | [
"ASE"
] | ec071bdc25e7a1409259f8f77969445c232ff8fcd9c3b866e6d92aba76680614 |
import unittest
from test import support
import sys
import random
import math
import array
# SHIFT should match the value in longintrepr.h for best testing.
SHIFT = 30 if sys.implementation.name == "ironpython" else sys.int_info.bits_per_digit # https://github.com/IronLanguages/ironpython3/issues/974
BASE = 2 ** SHI... | IronLanguages/ironpython3 | Src/StdLib/Lib/test/test_long.py | Python | apache-2.0 | 49,274 | [
"Brian"
] | a72b781e9932dc45a2dc77f39622bf72c92b92966aa89bacd5a4e6643136efbd |
'''
This __init__ file is for a PySCeS "eXtension module" (pysx), the following variables can be set for each module
'''
pysx_name = 'Pysces module template'
pysx_oscompat = ['posix','nt']
pysx_base_class = 'CONTRIB_demo'
pysx_author = 'Brett G. Olivier'
pysx_email = 'bgoli@users.sourceforge.net'
pysx_affiliation = 'T... | bgoli/pysces | pysces/contrib/demo/__init__.py | Python | bsd-3-clause | 449 | [
"PySCeS"
] | 16892d5b37002f091adf8b5d341ab2daaad2c9a6825fdb32a3dcb5cddf0635bc |
from pattern import Pattern
import time
import math
class SimplePattern(Pattern):
def next_frame(self, octopus, data):
intensity = 127 + 127*math.cos(time.time())
color = (intensity, intensity, intensity)
for pixel in octopus.pixels():
pixel.color = color | TheGentlemanOctopus/thegentlemanoctopus | octopus_code/core/octopus/patterns/simplePattern.py | Python | gpl-3.0 | 298 | [
"Octopus"
] | e5a09c2a3f7368b7983640fe4301c5f4f8e35600bc7102ec99cc26de19c1e0ad |
import os
import errno
import socket
import time
import eventlet
from eventlet.timeout import Timeout
from unittest import TestCase
from ..actions import Empty, Static, Unknown, NoHosts, Redirect, Proxy, Spin
class MockBalancer(object):
"Fake Balancer class for testing."
def __init__(self, fixed_action=None)... | alex/mantrid | mantrid/tests/actions.py | Python | bsd-3-clause | 6,516 | [
"Firefly"
] | 029b9a20982d97c34dd9359764c97f5bb67338270906b5960685907d56444977 |
# 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/interaction/DihedralHarmonicUniqueCos.py | Python | gpl-3.0 | 3,198 | [
"ESPResSo"
] | f86d5a75321b0cbe5dc8d1d4343355de05097cb62cb836c619fb072b3b88466e |
#! /usr/bin/env python3
'''
\section{solution\_structures.py}
\\hyperlink{content}{Content}
Program is intended for making of the solid solution from some initial lattice
Requirements: python3
Program uses following moduli:
random, os, subprocess, copy, shutil, read_write_i
Input file - solution_structures.in wit... | DarthFeiwante/solution_structures | solution_structures.py | Python | gpl-2.0 | 52,640 | [
"CRYSTAL"
] | e0faa21966a5a4cc0fa09cc2edcb5c0d641ca663298d5143b5939ce7cbc78870 |
"""
Code for managing the implementation cache.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, logger
import os
from zeroinstall.support import basedir
from zeroinstall import SafeException, support
class BadDigest(SafeException):... | michel-slm/0install | zeroinstall/zerostore/__init__.py | Python | lgpl-2.1 | 11,560 | [
"VisIt"
] | 1e2238a20e22f09017dd76521625affb96c6ddcf2bdddb887283f13df444542c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import pickle
import unittest
import warnings
from pathlib import Path
import numpy as np
import pytest # type: ignore
import scipy.constants as const
from monty.io import zopen
from monty.tempfile ... | davidwaroquiers/pymatgen | pymatgen/io/vasp/tests/test_inputs.py | Python | mit | 36,646 | [
"VASP",
"pymatgen"
] | aae71cbfff547eb002c5111681e4c8c39b5055ab08bf8e3ecf3466cd93a849de |
from partsdb.partsdb import PartsDB
from tables import *
from partsdb.tools.Exporters import GenBankExporter
from flask import Flask, session, redirect, url_for, escape, request, render_template, make_response, flash, abort
from flask.ext.sqlalchemy import SQLAlchemy
from flask_user import UserMixin, SQLAlchemyAdapte... | HaseloffLab/MarpoDB | server/server.py | Python | mit | 17,580 | [
"BLAST"
] | 178e6ca5ee44cc018f46abfa95cfc8b7a5a37fbe26df1c8a65df5bfe919f0770 |
#!/usr/bin/env python
"""Module cma implements the CMA-ES (Covariance Matrix Adaptation Evolution Strategy).
CMA-ES is a stochastic optimizer for robust non-linear non-convex
derivative- and function-value-free numerical optimization.
This implementation can be used with Python versions 2.6, 2.7, 3.x.
CMA-ES... | raphaelvalentin/qtlayout | syntax/optimize/cma/cma-1.0.04/cma-1.0.04.py | Python | gpl-2.0 | 334,924 | [
"exciting"
] | f4a95113ba44d9874d92e5dca5f83c5fad32850bec9ba9a77c85205751c5d4e0 |
"""
@name: Modules/House/_test/test_rooms.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2013-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Apr 10, 2013
@summary: Test handling the rooms information for a house.
Passed all 10 tests - DBK 2019-10-16
"... | DBrianKimmel/PyHouse | Project/src/Modules/House/_test/test_rooms.py | Python | mit | 4,905 | [
"Brian"
] | 40d1395cc2c74c8a60b0826efe9e6e09ad2bf7eacef7930321279be97a4040a4 |
""" ConanFile user tools, as download, etc
"""
from __future__ import print_function
import sys
import os
from conans.errors import ConanException
from conans.util.files import _generic_algorithm_sum, load
from patch import fromfile, fromstring
from conans.client.rest.uploader_downloader import Downloader
import reques... | dragly/conan | conans/tools.py | Python | mit | 13,706 | [
"Jaguar"
] | cfd6ced6948061870c87136d3583310e3b26359cced862152966413ff35004b7 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | casawa/mdtraj | mdtraj/tests/test_binpos.py | Python | lgpl-2.1 | 5,236 | [
"MDTraj",
"VMD"
] | 06bceb3d6f9a5ff087222f8e0a823a8e6879e02c6c0e6ebc3b347ba26cbd7703 |
################################################################################
# Peach - Computational Intelligence for Python
# Jose Alexandre Nalon
#
# This file: tutorial/polynomial-regression.py
# Using neural networks to approximate functions by polynomials.
######################################################... | bobquest33/peach | tutorial/neural-networks/polynomial-regression.py | Python | lgpl-2.1 | 3,346 | [
"NEURON"
] | 1996a3eb13a18e73b09b6af9e6ae39f04ed659ea1e761befce65e4b53718f6fa |
'''
SASSIE Copyright (C) 2011 Joseph E. Curtis
This program comes with ABSOLUTELY NO WARRANTY;
This is free software, and you are welcome to redistribute it under certain
conditions; see http://www.gnu.org/licenses/gpl-3.0.html for details.
'''
import sys,numpy,time
sys.path.append('./')
import dcdio
... | StevenCHowell/zazmol | src/python/extensions/dcdio/test_dcdio.py | Python | gpl-3.0 | 2,739 | [
"CHARMM"
] | 17c37321c08f8250ed193547ae79e6897cfbca111a80046883c63a2b9a6540e4 |
#!/usr/bin/env python
#Aim: Using the variants file generated from the parental control (in case you are dealing with an outcross in a reference background and you have sequenced the polimorfic parental as a control.) and
# using the gnm_ref file, the variants located in the control will be replaced in the refere... | sergioSEa/Developed_scripts | change_snp.py | Python | gpl-3.0 | 3,112 | [
"Biopython"
] | 9ac6b0d7f86b52bbcc8d11029393d4b2d60d0f7a46445790f7ac2b2b1aebef9c |
# coding: utf-8
from __future__ import division, print_function, unicode_literals, \
absolute_import
import unittest
import os
import json
import numpy as np
import pandas as pd
from pymatgen import Structure
from veidt.describer.general import FuncGenerator, MultiDescriber
from veidt.describer.structural_descr... | materialsvirtuallab/veidt | veidt/describer/tests/test_general_describer.py | Python | bsd-3-clause | 2,379 | [
"pymatgen"
] | d08a1e8e40b39cf1bc0d95d900c6c073b43a2503fd7d55007e5bcf529798a954 |
# Copyright 2011-2017, Damian Johnson and The Tor Project
# See LICENSE for licensing information
"""
Basic enumeration, providing ordered types for collections. These can be
constructed as simple type listings...
::
>>> from stem.util import enum
>>> insects = enum.Enum('ANT', 'WASP', 'LADYBUG', 'FIREFLY')
>>... | tparks5/tor-stem | stem/util/enum.py | Python | lgpl-3.0 | 4,390 | [
"Firefly"
] | 56c6221c4f30f05c581fef872f131d8ee745941c0f13a8c6eb3f8e487e8d69d8 |
# -*- coding: utf-8 -*-
"""
pysteps.cascade.bandpass_filters
================================
Bandpass filters for separating different spatial scales from two-dimensional
images in the frequency domain.
The methods in this module implement the following interface::
filter_xxx(shape, n, optional arguments)
wher... | pySTEPS/pysteps | pysteps/cascade/bandpass_filters.py | Python | bsd-3-clause | 7,085 | [
"Gaussian"
] | e2914e131cd29cbdaada62af76003c82d421d6ff26993e185a264f7bb2841262 |
from __future__ import with_statement
from test import test_support
import unittest
import codecs
import sys, StringIO, _testcapi
class Queue(object):
"""
queue: write bytes at one end, read bytes from the other end
"""
def __init__(self):
self._buffer = ""
def write(self, chars):
... | mancoast/CPythonPyc_test | cpython/251_test_codecs.py | Python | gpl-3.0 | 45,271 | [
"FEFF"
] | 9be4a2e4bf5b79632768042f4b272d6592c203e336b07d8c25bbba92022bddb5 |
# This file is part of the Frescobaldi project, http://www.frescobaldi.org/
#
# Copyright (c) 2008 - 2014 by Wilbert Berendsen
#
# 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
... | wbsoft/frescobaldi | frescobaldi_app/scorewiz/parts/plucked_strings.py | Python | gpl-2.0 | 14,133 | [
"ADF"
] | edc55a6c7ae9f1f464c783cd33f233c71f5b4d67612462bed1689ad97d48e3f0 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from datetime import datetime
import os
from unittest import TestCase
from django.test import ignore_warnings
from django.utils import html, safestring
from django.utils._os import upath
from django.utils.deprecation import RemovedInDjango20Warning
from ... | iambibhas/django | tests/utils_tests/test_html.py | Python | bsd-3-clause | 8,173 | [
"ADF"
] | d6d2fab153d58dfc1195d8ae37e3b65796c82761db9cdc10a104ac091280b06a |
#! /usr/bin/env python
"""
Utility functions for spectral fitting.
"""
__author__ = 'Valentin Christiaens'
__all__ = ['akaike',
'blackbody',
'combine_spec_corrs',
'convert_F_units',
'convert_F_vs_mag',
'extinction',
'find_nearest',
'inject_e... | carlgogo/vip_exoplanets | vip_hci/specfit/utils_spec.py | Python | bsd-3-clause | 15,847 | [
"Gaussian"
] | 0f147550cc427d4a4a932011a17699a96204368936284a22f4aff484023d9157 |
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 25 13:08:19 2015
@author: jgimenez
"""
from PyQt4 import QtGui, QtCore
from reset_ui import resetUI
import os
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
def _fromUtf8(s):
return s
try:
_encoding = QtGui.QApplication.UnicodeUTF8
... | jmarcelogimenez/petroFoam | reset.py | Python | gpl-2.0 | 1,458 | [
"VTK"
] | b915e0e6892add7632c69e6ee23752d07f280ccd6972f08134865f2bd6774d28 |
"""
Extended math utilities.
"""
# Authors: Gael Varoquaux
# Alexandre Gramfort
# Alexandre T. Passos
# Olivier Grisel
# Lars Buitinck
# Stefan van der Walt
# Kyle Kastner
# License: BSD 3 clause
from __future__ import division
from functools import partial
import ... | mblondel/scikit-learn | sklearn/utils/extmath.py | Python | bsd-3-clause | 21,403 | [
"Gaussian"
] | 3c0ebdfb4efa5267738a194ef6af72571f244db82a9b7019474bfc91c4268187 |
# -*- coding: utf-8 -*-
#########################################################################
### Jesus Garcia Manday
### gauus.py
### @Descripcion: script to remove noise and apply blur the images
#########################################################################
import numpy as np
import cv2
import os
im... | jmanday/Master | TFM/scripts/gauss.py | Python | apache-2.0 | 3,420 | [
"Gaussian"
] | 88f1bbb32a8dd580fd6d3b60aeaa4a75329be16eef700ddbeb349fee765b0dd3 |
# -*- coding: utf-8 -*-
'''
This module defines :class:`ChannelIndex`, a container for multiple
data channels.
:class:`ChannelIndex` derives from :class:`Container`,
from :module:`neo.core.container`.
'''
# needed for Python 3 compatibility
from __future__ import absolute_import, division, print_function
import nump... | SummitKwan/python-neo | neo/core/channelindex.py | Python | bsd-3-clause | 5,671 | [
"NEURON"
] | badf1da2cb45865c7cf948a7e3b3aaa15dbc24b3470b72b8c468a14d985a45ae |
# coding=utf-8
# (The line above is necessary so that I can use 世界 in the
# *comment* below without Python getting all bent out of shape.)
# Copyright 2007-2009 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may o... | lekkas/livegrep | src/vendor/re2/lib/codereview/codereview.py | Python | bsd-2-clause | 108,228 | [
"VisIt"
] | c9fd434a9052e18e50c2b7861cec883bf9a3a9138eef8ff152a8674f9c6bcda2 |
""" :mod: SRM2Storage
=================
.. module: python
:synopsis: SRM v2 interface to StorageElement
"""
# # imports
import os
import re
import time
import errno
from types import StringType, StringTypes, ListType, IntType
from stat import S_ISREG, S_ISDIR, S_IMODE, ST_MODE, ST_SIZE
# # from DIRAC
from ... | fibbo/DIRAC | Resources/Storage/SRM2Storage.py | Python | gpl-3.0 | 83,209 | [
"DIRAC"
] | 52d00e66ae714efaba63fe99d9f159e3e800ffb2eb386f51e1d478eb315d9438 |
#!/usr/bin/env python
# encoding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2017 Prof. William H. Green (whgreen@mit.edu),
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)
#
... | Molecular-Image-Recognition/Molecular-Image-Recognition | code/rmgpy/cantherm/gaussianTest.py | Python | mit | 6,909 | [
"ChemPy",
"Gaussian"
] | a8011500547004efe7de5f4bb9cc5bc94f76a228018ae51ebc9f46edaacc5baa |
#!usr/bin/env python
import matplotlib
matplotlib.use('Agg')
import pysam
import numpy as np
import scipy.stats as st
import matplotlib.pyplot as plt
import sys
import csv
import argparse
import operator
import random
import time
import string
#from multiprocessing.dummy import Pool as TP
__author__ = "Kathrin Trappe... | ESeiler/daisy | hgt_eval.py | Python | gpl-3.0 | 18,887 | [
"pysam"
] | 99ae112d5cb1c79913f861639502b34e3db52cb5ec55ab781842452a5d04d4ad |
#!/usr/bin/env python
# megamapper executer
# by Nikolaus Obholzer, Jan 2012
import sys, re, tempfile, subprocess
import os, shutil
from galaxy import eggs
def stop_err(msg):
sys.stderr.write(msg)
sys.exit()
def main():
# Handle input params
in_fname = sys.argv[1]
out_file1 = sys.argv[2]
ou... | maxplanck-ie/Megamapper | hmfseq_megamapper.py | Python | bsd-3-clause | 1,162 | [
"Galaxy"
] | 04aebf60b2b02b584ef5170730e06678ef444dc7f054fbb9cb1d853c8f54b115 |
import templet
import json
import os
import re
import time
import locale
import math
import collections
import Bio.Blast.NCBIWWW
import Bio.Blast.NCBIXML
import assembly
import ab1
import contig
def blast_seq(seq, save_path, ncbi_db='nr', json_path=None, json_limit=None):
"""Submit *seq* to NCBI BLAST.
*seq*... | madhadron/seqlabd | seqlab/sequence_report.py | Python | gpl-3.0 | 20,796 | [
"BLAST"
] | c434d6732887c10b636f57942879fa8212be8a170cb7df358f63642d1b930416 |
"""
Test for MlabSource and its subclasses.
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
import unittest
import numpy as N
from mayavi.tools import sources
################################################################################
# `Tes... | liulion/mayavi | mayavi/tests/test_mlab_source.py | Python | bsd-3-clause | 28,371 | [
"Mayavi"
] | c0076f4e9674f85b98df254da1015a0f2ee1e4db90ddd8683e99678c54a8a85d |
# $Id: module_index.py 1894 2006-02-23 08:55:45Z cpbotha $
class MyGaussian:
kits = ['vtk_kit']
cats = ['User','Optic Flow']
keywords = ['gaussian', 'source']
| nagyistoce/devide | modules/user/opticflow/module_index.py | Python | bsd-3-clause | 174 | [
"Gaussian"
] | 5895d1d9e04da23eeb6be02f5c5041cb2d039b6cbe41291b303727ad311bfa95 |
########################################################################
# $HeadURL$
# File : Watchdog.py
# Author: Stuart Paterson
########################################################################
""" The Watchdog class is used by the Job Wrapper to resolve and monitor
the system resource consumption. ... | sposs/DIRAC | WorkloadManagementSystem/JobWrapper/Watchdog.py | Python | gpl-3.0 | 34,695 | [
"DIRAC"
] | ac5eb1db8f396f0608ed84e78d5c9fca9737db6d2ac1f1ed2ae387b44415c0fc |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from unittest import expectedFailure
from common.test.acceptance.tests.helpers import UniqueCourseTest
from common.test.acceptance.pages.lms.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.courseware import CoursewarePage
from common.te... | romain-li/edx-platform | common/test/acceptance/tests/lms/test_lms_acid_xblock.py | Python | agpl-3.0 | 5,706 | [
"VisIt"
] | cd5be01e644d4674e3c3a5cb5cb1c18a016aa12b2df75bec956d778faa64f5bc |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.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 Foundation, either version 3 of the License, or
# (at your option) an... | sharifmamun/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 16,352 | [
"Galaxy"
] | f9cc465f1170c37f712a312782d14b017c113c16cbffd3dee705c264a8ed2ee8 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-compute | tests/unit/gapic/compute_v1/test_target_vpn_gateways.py | Python | apache-2.0 | 93,215 | [
"Octopus"
] | dc1fd7a21ff4e69131de3e93c9d2aa1a6cb49ab4cab43f4a8ff03ade0a2ac99b |
PE_INDEPENDENT_PKGS = {
'cuda': {
'buildable' : False,
'modules' : 'cudatoolkit',
},
'cosma': {
'variants': "+ipo+scalapack+cuda cuda_arch=60 build_type=Release"
},
'fftw': {
'variants': "+mpi +openmp precision=long_double,double,float"
},
'gromacs': {
... | eth-cscs/production | spack/reframe/src/spack_util/spack_config.py | Python | gpl-3.0 | 8,824 | [
"Gromacs",
"NetCDF"
] | 6535ee1eea31b77422a69c25060903219976712299926a50bc040c48101713f5 |
#!/usr/bin/env python
"""
This script cannot be run directly, because it needs to have test/functional/test_toolbox.py in sys.argv in
order to run functional tests on repository tools after installation. The install_and_test_tool_shed_repositories.sh
will execute this script with the appropriate parameters.
"""
import ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py | Python | gpl-3.0 | 56,349 | [
"Galaxy"
] | f7dbef52e522f375475bf7b451622fafad05114eeced281631966193ceb912fb |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import itertools
import pytest
import numpy as np
from numpy.testing import assert_allclose
from ..utils import discretize_model
from ...modelin... | kelle/astropy | astropy/convolution/tests/test_discretize.py | Python | bsd-3-clause | 6,190 | [
"Gaussian"
] | a2200d33f72238e26592d2d85c14b9a3409a2e30bd95d88248c846117ed05793 |
# $Id$
#
# Copyright (C) 2001-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Interface to the C... | rvianello/rdkit | rdkit/ML/Cluster/Murtagh.py | Python | bsd-3-clause | 2,982 | [
"RDKit"
] | 8ec8c936ed0bad9cf5984354f58071a55050c66a6dd41d8bf236acc99788b24c |
#!/usr/bin/env python
########################################################################
# $HeadURL$
########################################################################
""" Ban one or more Storage Elements for usage
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base im... | Sbalbp/DIRAC | DataManagementSystem/scripts/dirac-admin-ban-se.py | Python | gpl-3.0 | 7,087 | [
"DIRAC"
] | b6accd1a36100ea748ae8c964278e5bfdc79df631489c1026d02a60ac4190efa |
"""
===========================
Formaldehyde mm-line fitter
===========================
This is a formaldehyde 3_03-2_02 / 3_22-221 and 3_03-2_02/3_21-2_20 fitter.
It is based entirely on RADEX models.
This is the EWR fork of the fitter in pyspeckit.
Module API
^^^^^^^^^^
"""
from __future__ import print_function
im... | e-koch/pyspeckit | pyspeckit/spectrum/models/h2co_mm.py | Python | mit | 7,074 | [
"Gaussian"
] | ba3cc3339fe2e012cfdf7243f73a0bfe4cb0bf25e470eae00d3b261258d26d1a |
"""
Utilities for interacting with dflow and casimir models via the virtual
watershed.
"""
import copy
import json
import os
from datetime import datetime
from numpy import fromstring, reshape, meshgrid, array, flipud
from pandas import Series, read_excel
from scipy.interpolate import griddata
from uuid import uuid4
f... | tri-state-epscor/wcwave_adaptors | vwpy/dflow_casimir.py | Python | bsd-2-clause | 11,749 | [
"NetCDF"
] | ff262547f64abed0f227cb68914cfa59f0f4b91647ea9ae50f60fdb494ea5d8c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
################################################################################
#
# qooxdoo - the new era of web development
#
# http://qooxdoo.org
#
# Copyright:
# 2006-2012 1&1 Internet AG, Germany, http://www.1und1.de
#
# License:
# LGPL: http://www.gnu.org/li... | sebastienhupin/qxrad | qooxdoo/tool/pylib/ecmascript/transform/check/lint.py | Python | lgpl-3.0 | 23,924 | [
"VisIt"
] | e85ee9f80e8aab086458fe78a7202e686870be5b04a97583cc411865f2ca8358 |
# Copyright 2013-2018 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 *
from sys import stdout
import glob
from os import O_NONBLOCK, rename
from os.path import basename
fro... | iulian787/spack | var/spack/repos/builtin/packages/wrf/package.py | Python | lgpl-2.1 | 12,344 | [
"NetCDF"
] | 050c7f5d766894bd532e09c750b06b247733e20012cbba4901c239ffc5dd09ae |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2009 Zuza Software Foundation
#
# This file is part of Pootle.
#
# 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 t... | lehmannro/pootle | local_apps/pootle_app/management/commands/initdb.py | Python | gpl-2.0 | 6,666 | [
"VisIt"
] | 14ffc46e410a2b6ba63822a3080e7218b5ab1ebd74e61a5cc91a2d6c2ad29314 |
r"""
Util functions (:mod: `qiita_db.util`)
======================================
..currentmodule:: qiita_db.util
This module provides different util functions.
Methods
-------
..autosummary::
:toctree: generated/
quote_data_value
scrub_data
exists_table
get_db_files_base_dir
compute_check... | josenavas/QiiTa | qiita_db/util.py | Python | bsd-3-clause | 63,332 | [
"scikit-bio"
] | 95156843f8f3b6c02d0753e8090313a5d4c83a8090a8aac60f1da6d60e8a26d7 |
"""Common functions. """
import pysam
import logging
import subprocess
from contextlib import contextmanager
# create logger for the entire program
log = logging.getLogger('riboplot')
log.setLevel(logging.DEBUG)
# create console handler with a higher log level
ch = logging.StreamHandler()
ch.setLevel(logging.INFO)
... | vimalkumarvelayudhan/riboplot | riboplot/ribocore.py | Python | bsd-3-clause | 12,920 | [
"pysam"
] | 4ad1160bad21ccfe3ebab9b039d454db69a815ebbd31318725c31baa2fc19a3f |
# Copyright 2018 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... | asimshankar/tensorflow | tensorflow/contrib/tpu/python/tpu/tensor_tracer.py | Python | apache-2.0 | 36,120 | [
"VisIt"
] | 7e9ae718e9e88758e8d17abcedb7384386fd9c88556d77f0662d1c7cf060a936 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | testsuite/python/thermalized_bond.py | Python | gpl-3.0 | 5,150 | [
"ESPResSo"
] | c0a872cd7320e02f4e2a088aa107e4b7339295b13f0649d7cf012a7c4b48bdf3 |
__author__="Ning Guo, ceguo@connect.ust.hk; Hongyang Cheng, d132535@hiroshima-u.ac.jp"
__supervisor__="Jidong Zhao, jzhao@ust.hk"
__institution__="The Hong Kong University of Science and Technology"
""" 2D model for Hierachical/Concurrent multiscale simulation
which implements explicit time integration in FEM
to solve... | chyalexcheng/multiscale | msFEM2DExplicit.py | Python | gpl-3.0 | 19,052 | [
"VTK"
] | 1db0589b1e668451d9954a891a50ed633a6d7a808f4ec133b71dea87e2263ed5 |
# -*- coding: utf-8 -*-
# Copyright (C) 2019 - 2020 by Pedro Mendes, Rector and Visitors of the
# University of Virginia, University of Heidelberg, and University
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2017 - 2018 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc.,... | copasi/COPASI | copasi/bindings/python/unittests/Test_CReport.py | Python | artistic-2.0 | 3,011 | [
"COPASI"
] | c7917929942000e341309b2e86bd5fec2fea27846214e3232c3829a38f2fd745 |
#!/usr/bin/env python
import SimpleHTTPServer, BaseHTTPServer, os
os.chdir('../games')
try:
print "Server starting. Visit http://localhost:8000/ in your browser."
BaseHTTPServer.test(
SimpleHTTPServer.SimpleHTTPRequestHandler,
BaseHTTPServer.HTTPServer
)
except KeyboardInterrupt:
... | Oreolek/undum | test_webservers/serve.py | Python | mit | 326 | [
"VisIt"
] | ec7738d7441de1edd8bf3f699befeef9212295e1b9597e5c4c8bf41fe163a0ab |
# ==================================================================================================
# Copyright 2011 Twitter, Inc.
# --------------------------------------------------------------------------------------------------
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... | foursquare/commons-old | src/python/twitter/common/dirutil/chroot.py | Python | apache-2.0 | 6,454 | [
"Brian"
] | 9bb53d35d1f40f4aac9ade1366f8fe81de77c397dc1f18976f65de8f4b13fa50 |
# 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/interaction/DihedralUniquePotential.py | Python | gpl-3.0 | 2,381 | [
"ESPResSo"
] | 0d2da0e0d2bf32f81cfca010f94602f92004cb67a836b2bb62f916225481e915 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# 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 Foundation, either version 3 of the License, or
# (at your option) any later version.
#
... | chrismeyersfsu/ansible | lib/ansible/modules/files/acl.py | Python | gpl-3.0 | 11,472 | [
"Brian"
] | 51b741a9917dd9dce14af16a00a0141cb4da268256edae6664092fe4249ac2c0 |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2020 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permission to us... | bgoli/pysces | pysces/contrib/__init__.py | Python | bsd-3-clause | 2,593 | [
"PySCeS"
] | 09a6d8380913f55d847cce09233186279507eb695c57782bb67bf4b086a59ca7 |
from ase.lattice.surface import fcc100, add_adsorbate
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
# 2x2-Al(001) surface with 3 layers and an
# Au atom adsorbed in a hollow site:
slab = fcc100('Al', size=(2, 2, 3))
add_adsorbate(slab, 'Au', 1.7, 'hollow'... | grhawk/ASE | tools/doc/tutorials/neb/diffusion1.py | Python | gpl-2.0 | 786 | [
"ASE"
] | 06fcd618ea03935ae4eb716455811c6f1fc90139bff7baccaa6dde2ff608c35e |
import unittest
import os
import random
import glob
import numpy as np
from pymatgen import SETTINGS
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.analysis.surface_analysis import SurfaceEnergyAnalyzer
from pymatgen.util.testing import PymatgenTest
__author__ = "Richard Tran"
__copyright__ = "Copyright ... | setten/pymatgen | pymatgen/analysis/tests/test_surface_analysis.py | Python | mit | 3,105 | [
"VASP",
"pymatgen"
] | 6a80397e3cdd8aeac673253c1bc945c51b702c763a7f877e5e8efdb5174bdfcc |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module define a WulffShape class to generate the Wulff shape from
a lattice, a list of indices and their corresponding surface energies,
and the total area and volume of the wulff shape,the weighted su... | czhengsci/pymatgen | pymatgen/analysis/wulff.py | Python | mit | 21,287 | [
"pymatgen"
] | c59b4314447d12c5fd6d7060ea62705367e1812930e0561b1e20f22ace65dcc2 |
#!/usr/bin/env python
from netCDF4 import Dataset
import sys
def ncdump(nc_fid, verb=True):
'''
ncdump outputs dimensions, variables and their attribute information.
The information is similar to that of NCAR's ncdump utility.
ncdump requires a valid instance of Dataset.
Parameters
----------... | ricardog/raster-project | projections/scripts/nc_dump.py | Python | apache-2.0 | 2,645 | [
"NetCDF"
] | 98d03a925b1ab72b937a4c7875913c6556cbd49dbf06406f347fab428181748b |
r"""
Clustal format (:mod:`skbio.io.clustal`)
========================================
.. currentmodule:: skbio.io.clustal
Clustal format (``clustal``) stores multiple sequence alignments. This format
was originally introduced in the Clustal package [1]_.
Format Support
--------------
**Has Sniffer: Yes**
+------+-... | jensreeder/scikit-bio | skbio/io/clustal.py | Python | bsd-3-clause | 11,464 | [
"scikit-bio"
] | 5d168c2fa927a7bc0678d8adeba5ee0c98e4b1297b44557fa2924e9914dd798a |
#Non-recursive way
def treeinorder(root):
stack = []
node = root
while len(stack) > 0 or node:
if node:
stack.append(node)
node = node.left
else:
node = stack.pop()
#visit node
node = node.right
| urashima9616/Leetcode_Python | BinaryInorderTraverse.py | Python | gpl-3.0 | 284 | [
"VisIt"
] | a80fb0041aaec5f387c64c52bf5e16bc1c8b3e6bbb23288db008e1f4018305b1 |
#!/usr/bin/python
import pysam
import string
import argparse
# The MIT License (MIT)
# Copyright (c) [2014] [Peter Hickey (peter.hickey@gmail.com)]
# 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 S... | PeteHaitch/Lister2BAM | Python/Lister_style_2_to_bam.py | Python | mit | 10,193 | [
"pysam"
] | 104067281e43b731d0cc10e641f4f507416cd33335cfed7722edefbc60bf3bf7 |
#!/usr/bin/env python
# Run this test like so:
# $ vtkpython TestImagePlaneWidget.py -D $VTK_DATA_ROOT \
# -B $VTK_DATA_ROOT/Baseline/Widgets/
#
# $ vtkpython TestImagePlaneWidget.py --help
# provides more details on other options.
import os
import os.path
import vtk
from vtk.test import Testing
class TestImagePl... | aashish24/VTK-old | Interaction/Widgets/Testing/Python/TestImagePlaneWidget.py | Python | bsd-3-clause | 5,604 | [
"VTK"
] | db75f526cdb20b27fd88c5b0096c8e19d42e56dc301d7bbd4038ca6f58018e0f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import math
import numpy as np
from pymatgen.core.periodic_table import Element
from itertools import combinations
"""
Utilities for generating nicer plots.
"""
__author__ = "Shyue Ping Ong"
__copyright__ =... | dongsenfo/pymatgen | pymatgen/util/plotting.py | Python | mit | 20,879 | [
"pymatgen"
] | 9e204c5babfda128fddb9a55cf48a35dbc265e0df4790286da372717dc17231b |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | Fanarim/test_case_monkey | config/urls.py | Python | mit | 1,513 | [
"VisIt"
] | 29fe9aa9c3679d727e0be3b3ebfb0337e242f27725efc21455cc541b616fd997 |
# -*- coding: utf-8 -*-
from __future__ import print_function
from owmeta_core.dataobject import ObjectProperty, Alias
from .connection import Connection
from .neuron import Neuron
from .biology import BiologyType
from .worm_common import WORM_RDF_TYPE
class Network(BiologyType):
""" A network of neurons """
... | openworm/PyOpenWorm | owmeta/network.py | Python | mit | 3,341 | [
"NEURON"
] | 8b1464209a53a39317ae42e6295496ea9188257c308d1547fd6b3779061b2bf8 |
'''@file wavenet.py
a wavenet classifier'''
import tensorflow as tf
from nabu.neuralnetworks.classifiers import classifier, layer
class Wavenet(classifier.Classifier):
''''a wavenet classifier'''
def _get_outputs(self, inputs, input_seq_length, targets=None,
target_seq_length=None, is_tr... | JeroenBosmans/nabu | nabu/neuralnetworks/classifiers/asr/wavenet.py | Python | mit | 2,744 | [
"Gaussian"
] | 33715c8a9223b3117b716310ff8a99f76e1ca450914d0c0de487dc44649992e7 |
import os
import yaml
def book_ids_from_frontmatter(frontmatter):
'''Return a list of book id hashes from frontmatter of list file.'''
sections = yaml.load(frontmatter)['sections']
books = []
for section in sections:
for source in section['listings']:
if source['type'] == 'book':... | Backlist/backlist-workflows | backlist.py | Python | mit | 1,832 | [
"VisIt"
] | b3c448dc6ed7997ce403cf8afd33f5763a53c123b797f51133488e7707cf1811 |
"""Mode Grueneisen parameter calculation."""
# Copyright (C) 2012 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source c... | atztogo/phonopy | phonopy/gruneisen/core.py | Python | bsd-3-clause | 5,688 | [
"phonopy"
] | ba436a877edd2004b821140e16689876b1d7c12cd37e6d1971cd6c1a57b47f38 |
# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Robert Layton <robertlayton@gmail.com>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Philippe Gervais <philippe.gervais@inria.fr>
# Lars Buitinck
... | huzq/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 69,087 | [
"Gaussian"
] | aa7b01ab66abf9ea268065070bb743659d81fcb360f4165e58b2c83e3a64372d |
#!/usr/bin/env python
"""
convert netCDF file to HDF5 using Scientific.IO.NetCDF and PyTables.
Jeff Whitaker <jeffrey.s.whitaker@noaa.gov>
This requires Scientific from
http://starship.python.net/~hinsen/ScientificPython
"""
import sys
from Scientific.IO import NetCDF
import tables as tb
# open netCDF file
ncfile =... | avalentino/PyTables | contrib/nctoh5.py | Python | bsd-3-clause | 1,869 | [
"NetCDF"
] | 4333367d54c3efc8eb4e463937da131182e3b565667167badba36ab147390a73 |
#!/usr/bin/env python
try:
from setuptools import setup
args = {}
except ImportError:
from distutils.core import setup
print("""\
*** WARNING: setuptools is not found. Using distutils...
""")
from setuptools import setup
try:
from pypandoc import convert
read_md = lambda f: convert(f, 'rst')
e... | rosenbrockc/aflow | setup.py | Python | mit | 1,713 | [
"ASE"
] | e3d146571aa76f472786dc08e0cedcd975fa8b6845228b001306e76390c2ccd8 |
#!/usr/local/bin/python
# ANI_blastn.py
# Script downloaded on 26 Jun 2017 from GitHub repostiory:
# https://github.com/juanu/ANI_analysis/blob/master/ANI_blastn.py
#
#Created on 4/2/2013
__author__ = 'Juan A. Ugalde'
def split_sequence_fragments(sequence, block_size):
"""
Function that takes a sequence of... | dacuevas/bioinformatics | misc/ANI_blastn.py | Python | mit | 11,922 | [
"BLAST"
] | 98333a6214d54ebe76d5f7b635f5eb78078f193be9aeffc61b0d8408a91ff0ac |
import os
import warnings
# cmr calls all available methods in ase.atoms detected by the module inspect.
# Therefore also deprecated methods are called - and we choose to silence those warnings.
warnings.filterwarnings('ignore', 'ase.atoms.*deprecated',)
from ase.test import NotAvailable
try:
import cmr
except Im... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/test/cmr/ase_rw.py | Python | gpl-2.0 | 1,018 | [
"ASE"
] | 6c62c59ac996ce6a8b85758aa6b29b7c06ae42790531d55970711d038568c4f1 |
#!/usr/bin/env python
"""
This tests the ability to send data back and forth between the CPU and GPU.
"""
import sys
import vtk
from vtk.test import Testing
from PistonTestCommon import *
class TestConversion(Testing.vtkTest):
def testConversion(self):
global args
writefiles = "SaveData" in... | hlzz/dotfiles | graphics/VTK-7.0.0/Accelerators/Piston/Testing/Python/TestConversion.py | Python | bsd-3-clause | 3,135 | [
"VTK"
] | 6a7f6a31c3d00a208f3bf2f6df4e34fcbb5eb2ebff180e74e73b7c14af22243b |
#
#-*- python -*-
#
# This file is part of the cellnopt package
#
# Copyright (c) 2014-2016 - EMBL-EBI
#
# File author(s): Thomas Cokelaer (cokelaer@ebi.ac.uk)
#
# Distributed under the GLPv3 License.
# See accompanying file LICENSE.txt or copy at
# http://www.gnu.org/licenses/gpl-3.0.html
#
# website: www.c... | cellnopt/cellnopt | cno/io/midas.py | Python | bsd-2-clause | 99,034 | [
"Gaussian"
] | 303ff478dd9ee9bd629064a71ae9011a7c4e101f7135599f8b54e1998c61490e |
"""
Qualityscore class
"""
import data
import logging
log = logging.getLogger(__name__)
class QualityScore ( data.Text ):
"""
until we know more about quality score formats
"""
file_ext = "qual"
class QualityScoreSOLiD ( QualityScore ):
"""
until we know more about quality score formats
... | icaoberg/cellorganizer-galaxy-tools | datatypes/qualityscore.py | Python | gpl-3.0 | 3,966 | [
"Galaxy"
] | 2e60c4aff57f3d003ae66073b12a871be9b63dcec40973021faae9399a013aa5 |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later ver... | spring01/libPSI | lib/databases/HTBH.py | Python | gpl-2.0 | 38,349 | [
"Psi4"
] | 83628a127ea09d5c288eb111c6db749cdb79428b1f80bd23e07d16664bb7b04e |
# Example code for how to load experiments and reflections in the DIALS
from __future__ import annotations
from libtbx.phil import parse
import dials.util.options
from dials.util import show_mail_handle_errors
help_message = """
pass experiment.expt indexed.refl
"""
phil_scope = parse(
"""
png = 'example... | dials/dials | doc/examples/read_experiment_and_data/experiment_data.py | Python | bsd-3-clause | 3,599 | [
"CRYSTAL"
] | cc43822fe928d38838aab4f069dd9f3914591ed15c0b78b09e65d2a299eacdc4 |
import argparse
import numpy as np
import matplotlib.pyplot as plt
import nest
# parse command line parameters
parser = argparse.ArgumentParser(description='Simulate a Brunel network.')
parser.add_argument('spikefile', type=str, help='output file (spikes)')
parser.add_argument('rasterfile', type=str, help='output fi... | INM-6/Python-Module-of-the-Week | session20_NEST/snakemake/scripts/simulateBrunel.py | Python | mit | 3,959 | [
"NEURON"
] | 65282c9fc95e274e85e96cd6a861d2c55c223de5df9a66e17a4d1cf75d42dd14 |
import pytest
import os
import numpy as np
from threeML.plugins.XYLike import XYLike
from threeML import Model, DataList, JointLikelihood, PointSource
from threeML import BayesianAnalysis, Uniform_prior, Log_uniform_prior
from threeML.analysis_results import MLEResults, load_analysis_results, AnalysisResultsSet
from a... | volodymyrss/3ML | threeML/test/test_analysis_results.py | Python | bsd-3-clause | 6,185 | [
"Gaussian"
] | fa98035c003e19bf7711aec766302f079d48ccd3eb5bb26fb9c5155475ec302d |
import fftoolbox as fftb
import numpy as np
from scipy.optimize import curve_fit
import time
import logging, sys
logger = logging.getLogger(__name__)
lf = '%(levelname)s: %(funcName)s at %(filename)s +%(lineno)s\n%(message)s\n'
logging.basicConfig(level=logging.DEBUG, format=lf)
molecule_name = 'water'
rank = 1
ra... | maxivanoff/fftoolbox | run-examples/run-water-dimers.py | Python | gpl-2.0 | 2,548 | [
"PyMOL"
] | 83999faf4cc15fdf28a6d781dba5f9d884b508d1e075deb2719f8ea8bb23860d |
"""
Graph visitors.
"""
class NoVisitor(Exception):
def __init__(self, *args):
self.args = args
def __str__(self):
return 'No transformer for Node: %s' % repr(self.args)
#------------------------------------------------------------------------
# Transformers
#----------------------------------... | davidcoallier/blaze | blaze/expr/visitor.py | Python | bsd-2-clause | 4,664 | [
"VisIt"
] | d4c8a253ee8e303ee69290be2b50db61f11b3933d1f779ea5c2885687d7b329e |
"""
Hidden Markov Models in Python.
This code is adapted in large part from code released by Roland Memisevic.
"""
from numpy import sum, zeros, ones, newaxis, pi, exp, log, dot, eye, diag, arccos, sqrt, array, vstack, prod, isfinite, inf, real, arange, sin, cos, hstack, where, mean, double, concatenate, shape
from ... | rbharath/switch | Switch/simple_ghmm.py | Python | bsd-2-clause | 7,934 | [
"Gaussian"
] | 93f7bb8b69e4873fef07eaad2a6de64c5d9776b86ee1f8fb3cb6372a816ded5e |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/BMED_8813_HAP/Features/multiple_features/results/cross_validate_categories_BMED_8813_HAP_scaled_method_II_force_shape.py | Python | mit | 4,065 | [
"Mayavi"
] | 70af41f7525acabac574409a5497951280d0788290525e9d225d74061064dbac |
########################################################################
# $HeadURL$
# File: RequestProxyHandler.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/07/20 13:18:41
########################################################################
""" :mod: RequestProxyHandler
=========================
... | avedaee/DIRAC | RequestManagementSystem/Service/RequestProxyHandler.py | Python | gpl-3.0 | 7,836 | [
"DIRAC"
] | c735c3b738d8ec72fc227e266ed3f6ba57f54d9a56a3c1ad047e7d6a6d2d164c |
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