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# Copyright 2012 by Tiago Antao. 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.
"""Phasing of genotype data
The Bio.PopGen.Phasing module provides utiity functionality to help... | tiagoantao/igrat | igrat/genetics/popgen/phasing/__init__.py | Python | agpl-3.0 | 1,421 | [
"Biopython"
] | 9b95d5d03e6921039b68285a9c73b9a509df6c2008578c15448551ecf39e1dc2 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
from setuptools import setup
setup(name='pynxc',
version='0.1.7',
description='A Python to NXC Converter for programming '
'LEGO MINDSTORMS Robots',
author='Brian Blais',
author_email='bblais@bryant.edu',
maintainer='Marek Šuppa',
... | xlcteam/pynxc | setup.py | Python | bsd-3-clause | 606 | [
"Brian"
] | b9180708d8bd9975d113071fb32d96dc1e803449e76a9e180c8f4feead71db93 |
import sys
sys.path.append("..")
from models import (Paper, Paragraph)
from time import sleep
from pymongo import MongoClient
from pymatgen.matproj.rest import (MPRester)
from articledownloader.articledownloader import (ArticleDownloader)
from os import (environ, path, remove, listdir, strerror)
from autologging impor... | olivettigroup/synthesis-database-public | synthesisdatabase/managers/download_manager.py | Python | mit | 13,774 | [
"pymatgen"
] | 328631f6a97d349b793906608a92673609b493e6594f6268da14fe9343a222cd |
#!/usr/bin/env python
"""
CsPython Tutorial Example 2
By Mark Gossage (mark@gossage.cjb.net)
A pure-Python script to show the use of Crystal Space.
To use this, ensure that your PYTHONPATH, CRYSTAL, and LD_LIBRARY_PATH
(or DYLD_LIBRARY_PATH for MacOS/X; or PATH for Windows) variables are set
approrpriately, and then ... | baoboa/Crystal-Space | scripts/python/tutorial2.py | Python | lgpl-2.1 | 8,916 | [
"CRYSTAL"
] | 2ad33f02a75cb580e16f40065b5ccb584bf21dae043bee23f3f41783d90bccd4 |
GEOIP_STANDARD = 0
GEOIP_MEMORY_CACHE = 1
DMA_MAP = {
500: 'Portland-Auburn, ME',
501: 'New York, NY',
502: 'Binghamton, NY',
503: 'Macon, GA',
504: 'Philadelphia, PA',
505: 'Detroit, MI',
506: 'Boston, MA',
507: 'Savannah, GA',
508: 'Pittsburgh, PA',
509: 'Ft Wayne, IN',
51... | mygu/django-googlemap | googlemap/ip2geo/const.py | Python | mit | 14,064 | [
"BWA",
"COLUMBUS"
] | 270531eaa93362b303306a257e50cf242bd03acf63940c350b2ac2382827c3a6 |
import os
import tempfile
from numpy.testing import assert_array_equal, assert_almost_equal
import pytest
try:
import rdkit
from rdkit import Chem
except ImportError:
rdkit = None
if rdkit is not None:
from oddt.toolkits.extras.rdkit.fixer import (AtomListToSubMol,
... | oddt/oddt | tests/test_rdkitfixer.py | Python | bsd-3-clause | 22,042 | [
"RDKit"
] | 041f0bf848f704f10ec262acbbf62a142ff53bd5372e1d38067e8b01b2c3a736 |
# FILE COPIED FROM conf.orig.py; DO NOT CHANGE
# -*- coding: utf-8 -*-
# Copyright 2014-2015 VPAC
#
# Karaage documentation build configuration file, created by
# sphinx-quickstart on Thu Jan 16 14:28:57 2014.
#
# This file is execfile()d with the current directory set to its containing
# dir.
#
# Note that not all pos... | Karaage-Cluster/karaage-debian | docs/programmer/conf.py | Python | gpl-3.0 | 9,010 | [
"Brian"
] | 20cf9a9797307a00aa52ef6443e78cae400a945606711040e2079adee868643d |
import pytest
from qcelemental.util import parse_version, which, which_import
from qcengine.testing import using
__all__ = [
'hardware_nvidia_gpu',
'using_cppe',
'using_dftd3',
'using_dftd3_321',
'using_gcp',
'using_mp2d',
'using_memory_profiler',
'using_networkx',
'using_psi4',
... | CDSherrill/psi4 | tests/pytests/addons.py | Python | lgpl-3.0 | 2,363 | [
"Psi4"
] | 973115488342fe99a2762623d5a07b7857ec3732e7b106bc82a115663a1535fd |
#!/usr/bin/env python
# -- coding: utf-8 --
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit http://feedparser.org/ for the latest version
Visit http://feedparser.org/docs/ for the latest documentation
Required: Python 2.1 or later
Recommended: Python 2.3 or later
... | tquilian/exeNext | exe/engine/feedparser.py | Python | gpl-2.0 | 122,955 | [
"NetCDF",
"VisIt"
] | 677e02f3e8d5d89da4903ebcbafef4b7a7079d7ab1a8719c5aafa7a425e33fa7 |
#!/eecs/research/asr/mingbin/python-workspace/hopeless/bin/python
import numpy, logging, argparse, time, copy, os, cPickle, sys
from subprocess import Popen, PIPE, call
from Queue import Queue
from threading import Thread
logger = logging.getLogger( __name__ )
if __name__ == '__main__':
parser = argparse.Argu... | nanalelfe/fofe-ner | conll2003-ner-trainer.py | Python | mit | 21,627 | [
"Gaussian"
] | 1665059b441134aaedc5126defba7001b3ac00c69be0d4830dd3f2b8b9b30e72 |
#!/usr/bin/python
# LICENSE: GPL2
# (c) 2014 Kamil Wartanowicz
import logging
from util import hextools
from util import types_g
from util import types
import sim_codes
import sim_router
from sim import file_parser
from sim import sim_files
SIM_ID_0 = 0
SIM_ID_ALL = 0xFF
logicalChannel = 0
INIT_CONTROL_CHANNEL = Tru... | kamwar/simLAB | sim/sim_ctrl_3g.py | Python | gpl-2.0 | 56,497 | [
"ADF"
] | d1cfa7b3dfa2b751ce0996683b0059aa5b4d4189585865f40e6a7453f521b633 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jH0ward/psi4 | psi4/driver/frac.py | Python | lgpl-3.0 | 27,116 | [
"Psi4"
] | 35df10d5bb611b2c47514fa9f6cb88f103cbbf0e10f0fd3137bf85e80204daa3 |
"""
This module adapted ANUGA
https://anuga.anu.edu.au/
------------
Implementation of Redfearn's formula to compute UTM projections from latitude and longitude
Based in part on spreadsheet
www.icsm.gov.au/gda/gdatm/redfearn.xls
downloaded from INTERGOVERNMENTAL COMMITTEE ON SURVEYING & MAPPING (ICSM)
http://www.ics... | squilter/MAVProxy | MAVProxy/modules/lib/ANUGA/redfearn.py | Python | gpl-3.0 | 6,398 | [
"Psi4"
] | 8d1f97e483dc465571779a8d0cfc2469513b0b32893fee94778f580388ec7263 |
import mdtraj as md
import mixtape.featurizer, mixtape.tica, mixtape.cluster, mixtape.markovstatemodel, mixtape.datasets, mixtape.subset_featurizer, mixtape.feature_selection
import numpy as np
import sklearn.pipeline, sklearn.externals.joblib
import mixtape.utils
n_iter = 2500
n_choose = 10
lag_time = 1
n_components... | kyleabeauchamp/PMTStuff | code/optimize_ala.py | Python | gpl-2.0 | 1,255 | [
"MDTraj"
] | c9a76d7ba66a38b7b24487fbe2b4d0266c30c9f002c015953077ccd6ffe0e22a |
""" DIRAC FileCatalog Security Manager mix-in class
"""
__RCSID__ = "$Id$"
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Security.Properties import FC_MANAGEMENT
_readMethods = ['exists', 'isFile', 'getFileSize', 'getFileMetadata',
'getReplicas','getReplicaStatus','getFileAncestors',
... | andresailer/DIRAC | DataManagementSystem/DB/FileCatalogComponents/SecurityManager.py | Python | gpl-3.0 | 12,580 | [
"DIRAC"
] | 7264f9dcee2b6f1d08746819dc8b998cc6cde2ded6be8f07f9b073a1d9775bfa |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | ankurankan/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 25,560 | [
"Gaussian"
] | 3987730f7f3c5894691a7ae032e4ea6bbb5868047815bf2edf2c97d37fdf6225 |
#!/usr/bin/env python
import numpy as np
from pyproj import Proj
from optparse import OptionParser
## @package nc2cdo
# \author Andy Aschwanden, University of Alaska Fairbanks, USA
# \brief Script makes netCDF file ready for Climate Data Operators (CDO).
# \details Script adds attributes and variables to a netCDF whic... | JohannesFeldmann/pism | util/nc2cdo.py | Python | gpl-2.0 | 8,952 | [
"NetCDF"
] | 993b7c61316555682fa9126f6d8987e59e027904826d9a13a3e7763b0e364247 |
""" test for RFIO plugin
"""
# FIXME: doesn't work ATM
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import unittest
import time
import os
import shutil
import mock
from DIRAC import S_OK
from DIRAC.Resources.Storage.test.Test_FilePlugin import (
m... | ic-hep/DIRAC | src/DIRAC/Resources/Storage/test/FIXME_Test_RFIOPlugIn.py | Python | gpl-3.0 | 32,994 | [
"DIRAC"
] | 8bf8699d018bb28e244ac2ec1114bd986c88ad69c309ce7bfbe245e28138f70f |
#!/usr/bin/env python
import os
from psp import atomconf_to_ionconf, gen_ion_conf_dict
from data.ONCV_PBEsol_conf import ONCV_PBEsol_conf
"""
This module controls the main calculating process.
"""
class task(object):
def __init__(self, atoms=None, calculator=None):
"""
Organize the tasks for analy... | mailhexu/pyDFTutils | resource/phonon_ana/pyFA/calculate.py | Python | lgpl-3.0 | 3,663 | [
"ABINIT",
"ASE"
] | 9bb3640eb65aee54f69b5a2ff030f26bdfa3e604cc39e3233f564e4b29aa163b |
"""
:mod: ReqClient
.. module: ReqClient
:synopsis: implementation of client for RequestDB using DISET framework
"""
import os
import time
import random
# # from DIRAC
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.Core.Utilities.List import randomize, fromC... | marcelovilaca/DIRAC | RequestManagementSystem/Client/ReqClient.py | Python | gpl-3.0 | 23,687 | [
"DIRAC"
] | 10d892f1d6b852a359b537449176ea8b7a89bfb70db3e92ab00d254323599f3d |
#!/usr/bin/env python
import matplotlib.pyplot as plt
import scipy.interpolate as scinterp
import scipy.signal
from scipy.ndimage import filters
import numpy as np
import peak_original
import sys
import random
import os
def moving_average(series, sigma=0.7):
b = scipy.signal.gaussian(39, sigma)
average = filte... | tayebzaidi/snova_analysis | Miscellaneous/SNANAanalysis_single.py | Python | gpl-3.0 | 3,617 | [
"Gaussian"
] | 57cb58f816aab737e1a07ba6693185b08b3e4746579b506a5034a9769cb6fa20 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | tersmitten/ansible | lib/ansible/modules/cloud/kubevirt/kubevirt_vm.py | Python | gpl-3.0 | 14,596 | [
"Galaxy"
] | 77e7c2e73cb6fdc028fdef1e24e7d0349bb407bc121a2a50d77b31828c023910 |
import os
from six.moves.urllib import request
import tarfile
import argparse
EXAMPLES = ['galaxy/survey-poles', 'galaxy/periodic-poles', 'galaxy/periodic-pkmu']
def download_data(dirname, example):
"""
Download the pyRSD-data github tarball to the specified directory
Parameters
----------
dirnam... | nickhand/pyRSD | pyRSD/quickstart/core.py | Python | gpl-3.0 | 2,405 | [
"Galaxy"
] | 162f0a2c301c2e39329d52a4543f3f8db3b549a1b825d933753e1bb29425e385 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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
# ... | bjolivot/ansible | lib/ansible/modules/network/lenovo/cnos_factory.py | Python | gpl-3.0 | 5,084 | [
"VisIt"
] | adc5b361111f5fde384db4f59747e0ea2da51c12a0d983cf1ad5154fd096e310 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
'''
Miscellaneous algorithms
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname(os.path.realpath(__file__))
>>> datadir = os.path.realpath(... | FCP-INDI/nipype | nipype/algorithms/misc.py | Python | bsd-3-clause | 51,576 | [
"Gaussian"
] | 70b8e139a255f78347bb07b275b05a580592472711f6f82d8ea9a7ef66febacf |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are ... | mikehulluk/morphforge | src/morphforgecontrib/simulation/synapse_templates/exponential_form/expsyn/neuron.py | Python | bsd-2-clause | 4,913 | [
"NEURON"
] | a364270a76b38eb059f5806ccc4ce078a55abf51a28a1ff51b57a5cc971242ed |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Implement DCD."""
from hoomd import _hoomd
from hoomd.filter import ParticleFilter, All
from hoomd.data.parameterdicts import ParameterDict
from hoomd.operat... | joaander/hoomd-blue | hoomd/write/dcd.py | Python | bsd-3-clause | 4,666 | [
"HOOMD-blue"
] | 7ed61417c0319c89ed97e76f0fa9b5ca32ac3f82ed043f484a897a7d77637e5d |
#!/usr/bin/env python
"""
desispec.io.emlinefit
====================
Routines for desi_emlinefit_afterburner.
"""
import numpy as np
from scipy.optimize import curve_fit
from desiutil.log import get_logger
allowed_emnames = ["OII", "HDELTA", "HGAMMA", "HBETA", "OIII", "HALPHA"]
def get_rf_em_waves(emname):
"""... | desihub/desispec | py/desispec/emlinefit.py | Python | bsd-3-clause | 15,666 | [
"Gaussian"
] | 77a7adbdf4a05222aa5111402f6783c16def8b49a242c94fb5b93e3cbf47b1bc |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# MD-Molecules-Hoomd documentation build configuration file, created by
# sphinx-quickstart on Thu Jun 23 11:30:44 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present i... | malramsay64/MD-Molecules-Hoomd | sphinx/source/conf.py | Python | mit | 10,328 | [
"HOOMD-blue"
] | 57efe2a1fba923e10a1f0314a37ab97cded370bac36a9a51869de7ebf3fb2f95 |
# coding: utf-8
from __future__ import unicode_literals
"""
This module implements equivalents of the basic ComputedEntry objects, which
is the basic entity that can be used to perform many analyses. ComputedEntries
contain calculated information, typically from VASP or other electronic
structure codes. For example, ... | rousseab/pymatgen | pymatgen/entries/computed_entries.py | Python | mit | 7,250 | [
"VASP",
"pymatgen"
] | 30794ac6cb717a467d5026846eb343a6d00dab73042a67be23dd0e7a6ca12d7f |
#!/usr/bin/python3
# The MIT License (MIT)
#
# Copyright (c) 2015 Brian Wray (brian@wrocket.org)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limi... | wrocket/Tulip-Chess | utils/digest_pgn.py | Python | mit | 3,505 | [
"Brian"
] | d66201fce2fb37af64baf7b6eda27b7fe6b8c482f0f7c81e1ee41c38d77249b5 |
#!/usr/bin/env python
# encoding: utf-8
"""
bigeval.py
Created by Brian Whitman on 2010-07-02.
Copyright (c) 2010 The Echo Nest Corporation. All rights reserved.
"""
import getopt
import sys
import os
import time
import socket
import subprocess
try:
import json
except ImportError:
import simplejson as json
im... | alexonea/3rdyrp | server/solr/util/bigeval.py | Python | mit | 20,372 | [
"Brian"
] | 75a45f4198a20285a44e00c5fb6dc2371ea59134d83ef6433ab361f2c038f136 |
#!/usr/bin/env python3
from sympy import *
from code_gen import *
# q: quaternion describing rotation from frame 1 to frame 2
# returns a rotation matrix derived form q which describes the same
# rotation
def quat2Rot(q):
q0 = q[0]
q1 = q[1]
q2 = q[2]
q3 = q[3]
# Rot = Matrix([[q0**2 + q1**2 - q2... | PX4/ecl | EKF/python/ekf_derivation/main.py | Python | bsd-3-clause | 26,693 | [
"DIRAC"
] | 29966de78327a68d05b5d784da2c580219111978f3dc325da360e302d808abd3 |
"""
@name: PyHouse/src/Modules/families/X10/_test/test_X10_xml.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com>
@copyright: (c) 2014-2017 by briank
@license: MIT License
@note: Created on Aug 6, 2014
@Summary:
"""
__updated__ = '2017-01-20'
import unittest
class Test(unittest.TestCa... | DBrianKimmel/PyHouse | Project/src/Modules/House/Family/X10/test/test_X10_xml.py | Python | mit | 450 | [
"Brian"
] | 7d8ad421a60a87ccda85e772ee50073c7c41ba0a73deb6bc5e37b693ecb51d15 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016 Haggi Krey, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of... | haggi/appleseed-maya | module/scripts/appleseed_maya/initialize.py | Python | mit | 43,173 | [
"VisIt"
] | bd769cc7553ca3e6aeb15ee792d67f5100777e5b1762fe85ab7ab707ec1686e7 |
"""
tests that obiwan runs end to end and get reasonalbe outputs for varietry of
cases. Travis CI runs this script
"""
from __future__ import print_function
if __name__ == "__main__":
import matplotlib
matplotlib.use('Agg')
import unittest
import run_200x200_pixel_regions as tools
#from run_200x200_pixel_regio... | legacysurvey/obiwan | tests/test_200x200_pixel_regions.py | Python | bsd-3-clause | 4,321 | [
"Galaxy"
] | 2d95ea277d0cc19ae3472b1c4c3afdbc10242138f62b39977ed18d95b8f69fdf |
# Copyright 2014 NeuroData (http://neurodata.io)
#
# 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 ag... | neurodata/ndstore | django/ndgraph/ndgraph.py | Python | apache-2.0 | 4,335 | [
"NEURON"
] | 5f0493e0cc8ecb3b881b54f8b4170a12806f4ab369bd879e6c1d9291d0805ca3 |
"""
Module provides utility functions to manipulate netCDF dataset.
- classify variable types of coordinate, coordinate bounds, grid mapping, scientific data,
auxiliary coordinate
- show original metadata of a variable
Reference code
http://netcdf4-python.googlecode.com/svn/trunk/docs/netCDF4-module.html
"""
imp... | hydroshare/hydroshare | hs_file_types/nc_functions/nc_utils.py | Python | bsd-3-clause | 19,029 | [
"NetCDF"
] | db1999393506e5c5aca5cdba0258e403adc6bc90ad68d8a7ffd4a68588beca80 |
"""
Copyright (C) 2011 N.D. Price Lab
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in th... | JohnCEarls/AUREA | src/AUREA/packager/DataCleaner.py | Python | agpl-3.0 | 15,106 | [
"DIRAC"
] | ebfa3a63a22d81c99bce9af7719e777b40f47baecc8887e2408f732d1a24067d |
# Django settings for JMS project.
import os
DEBUG = True
TEMPLATE_DEBUG = DEBUG
ADMINS = (
# ('Your Name', 'your_email@example.com'),
)
MANAGERS = ADMINS
DATABASES = {
'default': {
'ENGINE': 'django.db.backends.mysql', # Add 'postgresql_psycopg2', 'mysql', 'sqlite3' or 'oracle'.
... | RUBi-ZA/JMS | src/JMS/settings_example.py | Python | gpl-2.0 | 6,920 | [
"Galaxy"
] | 7e6563692eaae907c5f3e55ad83aa184aa467688bb927c24d0db63adeee9d71d |
#!/usr/bin/python2
# -*- coding: utf-8 -*-
#
# This file is part of occmodel - See LICENSE.txt
#
VERSION = 1,2,0
import sys
import os
import glob
import shutil
import subprocess
from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
def version_str():
re... | heartvalve/occmodel | setup.py | Python | gpl-2.0 | 3,903 | [
"VTK"
] | 6e40599e4b72f9fdfccabc84ad288ba2c21fb35a1b28e190a73a0e37d5e1c3f6 |
# -*- coding: utf-8 -*-
## Copyright 2015 Rasmus Scholer Sorensen, rasmusscholer@gmail.com
##
## This file is part of Nascent.
##
## Nascent is free software: you can redistribute it and/or modify
## it under the terms of the GNU Affero General Public License as
## published by the Free Software Foundati... | scholer/nascent | nascent/graph_sim_nx/simulator_dm.py | Python | agpl-3.0 | 30,634 | [
"Biopython"
] | 2ac403cf7fa1d91679dde264f6c7119a812b091c10c10d2dade3bb08ff256109 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/__init__.py | Python | lgpl-3.0 | 3,549 | [
"Psi4"
] | 498d7718c9d7b5318d4088bfe21009b64dfb77df3219f13c7ee7aeae90d46fb6 |
"""
This file is part of RAPD
Copyright (C) 2016-2018 Cornell University
All rights reserved.
RAPD is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, version 3.
RAPD is distributed in the hope that it will ... | RAPD/RAPD | src/sites/sercat_test.py | Python | agpl-3.0 | 87,524 | [
"CRYSTAL",
"Gaussian"
] | faeec610e06dbd9d1b387cd3be004473703b0884f8a38e161de9b30bccc00d3c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import json
import requests
from collections import defaultdict
from cookielib import LWPCookieJar
import numbers
import os
from os.path import dirname, join
from requests.packages import urllib3
import sys
from sys import platform
import time
if __debug__:
from traceback... | aoighost/EDMarketConnector | companion.py | Python | gpl-2.0 | 9,878 | [
"ORCA"
] | 0a30d2c1870cdf3b15a5e1f0a74bce88e362261b573a17e94826629e9af15bee |
""" Python test discovery, setup and run of test functions. """
import fnmatch
import functools
import inspect
import re
import types
import sys
import py
import pytest
from _pytest._code.code import TerminalRepr
from _pytest.mark import MarkDecorator, MarkerError
try:
import enum
except ImportError: # pragma: n... | Yukarumya/Yukarum-Redfoxes | python/pytest/_pytest/python.py | Python | mpl-2.0 | 89,413 | [
"VisIt"
] | 7c3ccfbf7e24aad607c6be933a3878e769575af6828c0037c7d154271a4ba35e |
import subprocess
import sys
import py
import _pytest
import pytest
MODSET = [
x
for x in py.path.local(_pytest.__file__).dirpath().visit("*.py")
if x.purebasename != "__init__"
]
@pytest.mark.parametrize("modfile", MODSET, ids=lambda x: x.purebasename)
def test_fileimport(modfile):
# this test ens... | pfctdayelise/pytest | testing/test_modimport.py | Python | mit | 723 | [
"VisIt"
] | b8517a49065c28d32166297485de5f10eb4fe7c5b44a5605ee3349e55254cc0f |
# Orca
#
# Copyright 2005-2008 Google Inc.
# Portions Copyright 2007-2008, Sun Microsystems, Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/acss.py | Python | gpl-3.0 | 3,182 | [
"ORCA"
] | a8cc75ba45af3093315e76cbbc9f10b51197da2ecf3ce7223bb7092b5fec0728 |
#!/usr/bin/env python
""" load Proteome into OSDF using info from data file """
import os
import re
from cutlass.ProteomeNonPride import ProteomeNonPride
import settings
from cutlass_utils import \
load_data, get_parent_node_id, list_tags, format_query, \
write_csv_headers, values_to_node_dict, write... | JAX-GM/osdf_submit | nodes/proteomeNonPride.py | Python | gpl-3.0 | 6,178 | [
"VisIt"
] | f54331ec84fb200506f3ea539917e9dc466638bffe13e6a73a1a9a8acaf6e259 |
#!/usr/bin/env python3
"""When all 18 chapters of a Ulysses Redux set have been written, run this script
to postprocess the index.html file that's been created.
Currently, this script performs the following actions:
* Updates the Git repo with currently existing code, then commits the code
to the current bra... | patrick-brian-mooney/UlyssesRedux | utility_scripts/postprocess-set.py | Python | gpl-3.0 | 17,067 | [
"Brian"
] | 7fac46940f4b7bde603c6e1d3cde0abf1099b6ae8631b75c6f1723b08c428715 |
# Copyright 2021 DeepMind Technologies Limited
#
# 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 agr... | deepmind/alphafold | alphafold/relax/amber_minimize.py | Python | apache-2.0 | 20,977 | [
"Amber",
"OpenMM"
] | 38aae1881a4cdd3694b2946e5e862257d741b5c9e214e0d1a70e3077b0d7ab20 |
#
#@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/BASIC.py | Python | gpl-2.0 | 4,076 | [
"Psi4"
] | de60c79242fa09322ff0025ec1a9609820e811d12fefab9b33adaf785dd7661c |
# this program corresponds to special.py
### Means test is not done yet
# E Means test is giving error (E)
# F Means test is failing (F)
# EF Means test is giving error and Failing
#! Means test is segfaulting
# 8 Means test runs forever
### test_besselpoly
### test_mathieu_a
### test_mathieu_even_coef
##... | FRidh/scipy | scipy/special/tests/test_basic.py | Python | bsd-3-clause | 121,781 | [
"Elk"
] | 95e6aa92637ff93bfbfd798aac5524a04164ccbcd8b8d0515e0fa04cba6f100d |
# Copyright 2017 Raytheon BBN Technologies
#
# 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
__all__ = ['SingleShotMeasurement']
import numpy... | BBN-Q/Auspex | src/auspex/filters/singleshot.py | Python | apache-2.0 | 14,503 | [
"Gaussian"
] | a261de3058ec548f246abc6fc5f856361c192a35de06b0c706d036f762421524 |
# -*- coding: utf-8 -*-
from django.conf import settings
GATEWAY_HOST = "www.moneybookers.com"
GATEWAY_URI = "/app/payment.pl"
TEST_GATEWAY_URI = "/app/test_payment.pl"
GATEWAY = "https://%s%s" % (GATEWAY_HOST, GATEWAY_URI)
TEST_GATEWAY = "https://%s%s" % (GATEWAY_HOST, TEST_GATEWAY_URI)
MERCHANT_ID = settings.MONEYB... | gotlium/django-moneybookers | moneybookers/conf.py | Python | bsd-2-clause | 14,400 | [
"BWA"
] | 74687ec7198b0c703ec9915ff27bf5a7a87ae6f8b97dc83725c3bb3f5d174005 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# License: BSD style
"""
The :mod:`sklearn.gaussian_process` module implements scalar Gaussian Process
based predictions.
"""
from .gaussian_process import Gaussi... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/sklearn/gaussian_process/__init__.py | Python | agpl-3.0 | 469 | [
"Gaussian"
] | 8462df0cee62ded4f3ee540c4af35ce62603823d0ec5509f633c6b77065aa3f3 |
# #############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Matthew Harrigan
# Contributors: Carlos Xavier Hernandez
#
# MDTraj i... | leeping/mdtraj | tests/test_selection.py | Python | lgpl-2.1 | 10,413 | [
"MDTraj"
] | f483d19e72aa0741a5a0b7c2eab285aef5b3ef5d373ac60b612d8d4903e3a15f |
"""
Matched Filter Burst Search
---------------------------
Figure 10.25
A matched filter search for a burst signal in time series data. A simulated
data set generated from a model of the form y(t) = b0 for t < T and
y = b0 + A exp[-a(t - T)] for t > T , with homoscedastic Gaussian errors with
sigma = 2, is shown in t... | eramirem/astroML | book_figures/chapter10/fig_matchedfilt_burst.py | Python | bsd-2-clause | 4,056 | [
"Gaussian"
] | 925b3f9da7c5f0c6cbfeb368bc49a86d198414e086adec6fb1248e143ad7e635 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Abinit Post Process Application
authors: Martin Alexandre, Vincent Stutzmann
last edited: May 2014
"""
#GUI
import gui.graph as Graph
import gui.conv as Conv
#Utility
import utility.write as Write
import utility.positions as Atom
import utility.analysis as Analysis... | jmbeuken/abinit | scripts/post_processing/appa/gui/atom_pos.py | Python | gpl-3.0 | 6,833 | [
"ABINIT"
] | 25011baeceb05310bae0a1566e4fe1eeb3ffc212b65ef4b1b248aa454d8f0d58 |
import numpy as np
import tempfile
from pygmin.angleaxis import RBTopology
from copy import deepcopy
from pygmin.utils import rotations
from pygmin.takestep import RotationalDisplacement
from pygmin.systems import BaseSystem, dict_copy_update, BaseParameters
from pygmin.transition_states import NEB, InterpolatedPathDe... | js850/PyGMIN | pygmin/angleaxis/aasystem.py | Python | gpl-3.0 | 7,828 | [
"PyMOL"
] | 7a443b5a19a239720b7025dd1b5faacf3fbb0c4dee04629110c0a0eb4b30d369 |
# $HeadURL$
__RCSID__ = "$Id$"
import time
import copy
import os.path
import GSI
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
from DIRAC.Core.Utilities.Network import checkHostsMatch
from DIRAC.Core.Utilities.LockRing import LockRing
from DIRAC.Core.Security import Locations
from DIRAC.Core.Security.X50... | coberger/DIRAC | Core/DISET/private/Transports/SSL/SocketInfo.py | Python | gpl-3.0 | 13,457 | [
"DIRAC"
] | 920483dd3e674c40de925b2a98c1cb7e594d658b429a1341100fb9c8f03f78a6 |
"""
../wps.py?request=execute
&service=wps
&version=1.0.0
&identifier=esmvaltool-perfmetrics
&status=true
&storeExecuteResponse=true
"""
import datetime
import shutil
import netCDF4
import urlparse
from pywps.Process import WPSProcess
import os
import logging
from jinja2 import FileSystemLoader, Environment,select... | c3s-magic/adaguc-services-esmvaltool-wps | processes/esmvaltool-clouds-interannual.py | Python | apache-2.0 | 9,149 | [
"NetCDF"
] | bddc1bf7dc212ed33194ea6e665c3071940d80f5dc70f8d8fb7ef560ad4fd383 |
# Copyright (C) 2017
# Jakub Krajniak (jkrajniak at gmail.com)
# 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:... | cgchemlab/chemlab | examples/pccg_lj/generator_box/polymer_melt.py | Python | gpl-3.0 | 5,452 | [
"ESPResSo"
] | cf07840e5e177f6509df03f3e7a528f42fd2a3904705689f0b2dc2ba632d82ae |
import string, re, sys, cStringIO
from array import array
__printdebug__ = 0
legal_dna = "ACGTNX-"
legal_protein = "ABCDEFGHIKLMNPQRSTUVWXYZ-"
complementTranslation = string.maketrans('ACTG', 'TGAC')
#
# load
#
def load(f, strict=0):
"""
Loads sequences in FASTA format from the given file object.
Retur... | tracykteal/replicate-filter | scripts/fasta.py | Python | gpl-3.0 | 4,596 | [
"BLAST"
] | 93678db17261f61f712cc732962e4a729172f2a90b63b0736042d53cb7e52e4e |
#!/usr/bin/env python
# add paths
import os, sys
for p in os.environ['PATH'].split(':'): sys.path.append(p)
# import modules
from co2 import CO2
from fillgaps import fill
from dewpoint import dewpoint
import os, re, stat, datetime
from netCDF4 import Dataset as nc
from optparse import OptionParser
from collections im... | schmidtfederico/psims | tapps/papsim/psims2met.py | Python | agpl-3.0 | 9,896 | [
"NetCDF"
] | 11d3e068da34c8840a0cffdb679cf2d2e08b07f9a87d428ed90a58a84534c860 |
"""
Galaxy root package -- this is a namespace package.
"""
__import__( "pkg_resources" ).declare_namespace( __name__ )
import re
import os
import sys
import platform
import pkg_resources
# patch get_platform() for better ABI recognition
def _get_build_platform():
plat = pkg_resources._get_build_platform()
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/__init__.py | Python | gpl-3.0 | 3,172 | [
"Galaxy"
] | c8269a999f3976648f388ca925d107bfea019966d8d46b17a78e3c47f528cf3e |
# -*- coding: utf-8 -*-
# python-holidays
# ---------------
# A fast, efficient Python library for generating country, province and state
# specific sets of holidays on the fly. It aims to make determining whether a
# specific date is a holiday as fast and flexible as possible.
#
# Authors: dr-prodigy <maurizio.... | ryanss/holidays.py | holidays/holiday_base.py | Python | mit | 18,835 | [
"COLUMBUS"
] | 24868b0c2955605de71f794a81b3834747a07f14e24844bb59185b5b9082d370 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | pmghalvorsen/gramps_branch | gramps/gui/plug/_dialogs.py | Python | gpl-2.0 | 11,705 | [
"Brian"
] | 5f98694836a826b3e50d4d800a78d736511d0eadbf1194f637aff4668132cd9a |
import version
VERSION = version.VERSION
__version__ = VERSION
import sys
this_module = sys.modules[__name__]
from stats import Statistics
stats = Statistics()
def init(secret, **kwargs):
"""Create a default instance of a analytics-python client
:param str secret: The Segment.io API Secret
Kwargs:
... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/analytics/__init__.py | Python | agpl-3.0 | 6,150 | [
"VisIt"
] | 572697d6e07796746c647d7e1591e07fadc58e2c61d6c37ab8a54808478d6387 |
#!/usr/bin/env python
#-----------------------------------------------------------------------------
# Copyright (c) 2013--, biocore development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
#-------------------------... | ekopylova/burrito-fillings | setup.py | Python | bsd-3-clause | 1,623 | [
"scikit-bio"
] | 563479f8fe891de56c5b7d1129bbc068f5bd0d6e37a4a32287fc1f0cd10ae2de |
########################################################################
# $HeadURL$
########################################################################
""" WMSHistory corrector for the group and ingroup shares
"""
__RCSID__ = "$Id$"
import datetime
import time as nativetime
from DIRAC.WorkloadManagementSystem.p... | avedaee/DIRAC | WorkloadManagementSystem/private/correctors/WMSHistoryCorrector.py | Python | gpl-3.0 | 8,899 | [
"DIRAC"
] | 5632099bb90d55d3113fdf94c2a7a4c5d8f6dea3b6ba0d12aced03ef0d4023d7 |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from scipy._lib._util import getfullargspec_no_self as _getfullargspec
import sys
import keyword
import re
import types
import warnings
import inspect
from itertools import zip_longest
from scipy._lib import doccer... | grlee77/scipy | scipy/stats/_distn_infrastructure.py | Python | bsd-3-clause | 137,015 | [
"Gaussian"
] | c6bbc430ef45f894c961e8a9d71f03ee8f05dfc0805c5aee87f04d640bbd0a09 |
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#-----------------------------------------------
# Set these parameters for adjoint flagging....
# location... | clawpack/adjoint | paper2_examples/acoustics_2d_ex3/setrun.py | Python | bsd-2-clause | 14,133 | [
"NetCDF"
] | e3a15d9061d07a4cb7a1e25f79ef1e5f375de90f58f544ab0fa211654fadab96 |
import numpy
from rdkit.ML.Cluster import Murtagh
print('1')
d = numpy.array([[10.0, 5.0], [20.0, 20.0], [30.0, 10.0], [30.0, 15.0], [5.0, 10.0]], numpy.float)
print('2')
# clusters = Murtagh.ClusterData(d,len(d),Murtagh.WARDS)
# for i in range(len(clusters)):
# clusters[i].Print()
# print('3')
dists = []
for i ... | rdkit/rdkit | rdkit/ML/Cluster/murtagh_test.py | Python | bsd-3-clause | 890 | [
"RDKit"
] | 3f91b875eb90f1ca52440d4337b03a5f17fcc290d4daec03e26270ea8d6b532c |
#!/usr/bin/env python
#
# $File: HeteroMatingSP.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistri... | BoPeng/simuPOP | docs/HeteroMatingSP.py | Python | gpl-2.0 | 1,679 | [
"VisIt"
] | a7ba78003f0cae27d63f69821ec7190bb03925baecf24873b7a9f0093abc4013 |
"""
Simulated annealing with restart applied to the traveling salesman problem.
The data needs to be in cvs format and the coordinates of the cities are
longitude and latitude. Thus, any gps data taken on the internet can
serve as input.
Once the annealing is done, the cities are plotted according to their
coordinate... | jaspreetj/Simulated-Annealing-Travelling-Salesman-Problem | sAnnealing.py | Python | mit | 13,867 | [
"VisIt"
] | 2ad70bf23f51311402023a97ea5973fe0aebbc0d77023d0d01d14398adf74faa |
#******************************************************************************
# *
# * ** * * * * *
# * * * * * * * * * *
... | sanguinariojoe/aquagpusph | tools/setup.py | Python | gpl-3.0 | 3,248 | [
"VisIt"
] | 532f58f567cf138793327f1b27d9e4485bd9edb49f872ed2b368d4954958cdfc |
# -*- coding: utf-8 -*-
"""
Definition of a hierarchy of classes for kernel functions to be used
in convolution, e.g., for data smoothing (low pass filtering) or
firing rate estimation.
Base kernel classes
~~~~~~~~~~~~~~~~~~~
.. autosummary::
:toctree: toctree/kernels/
Kernel
SymmetricKernel
Symmetric ... | apdavison/elephant | elephant/kernels.py | Python | bsd-3-clause | 18,784 | [
"Gaussian"
] | 15050f9f3f24544a43d85bc3285f53b37fa0d00cca22be4b6e83e9a4c5a0c723 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Functional tests using WebTest."""
import datetime as dt
import httplib as http
import logging
import unittest
import httpretty
import markupsafe
import mock
from nose.tools import * # flake8: noqa (PEP8 asserts)
import re
from framework.mongo.utils import to_mongo_ke... | acshi/osf.io | tests/test_webtests.py | Python | apache-2.0 | 42,791 | [
"VisIt"
] | 7995dda82a901477df2536f9a0e2d19897145ce6eb91fbbd181571c6271fa64a |
r"""
Sequences (:mod:`skbio.sequence`)
=================================
.. currentmodule:: skbio.sequence
This module provides classes for storing and working with biological sequences,
including generic sequences which have no restrictions on which characters can
be included, and sequences based on IUPAC-defined se... | johnchase/scikit-bio | skbio/sequence/__init__.py | Python | bsd-3-clause | 6,967 | [
"scikit-bio"
] | 39a81ca1428d81eb5c3fd9c9cbeba6c8d046ecdfdce4755d155d03b78e5c5f42 |
from sys import exit
from random import randint
class Scene(object):
def enter(self):
print "This scene is not yet configured. Subclass it and implement enter()"
exit(1)
class Engine(object):
def __init__(self, scene_map):
self.scene_map = scene_map
def play(self):
current_scene = self.scene_map.o... | michsien/Learning_python | exercises _1-44/ex43.py | Python | mit | 7,491 | [
"BLAST"
] | e1db668ffa2bcde01be339570fc724eee53b25d7fe6ecb5a79269fa892eef4b0 |
"""Read genome build configurations from Galaxy *.loc and bcbio-nextgen resource files.
"""
import ConfigParser
import glob
import os
import sys
from xml.etree import ElementTree
import toolz as tz
import yaml
from bcbio import utils
from bcbio.distributed import objectstore
from bcbio.log import logger
from bcbio.ng... | mjafin/bcbio-nextgen | bcbio/pipeline/genome.py | Python | mit | 14,472 | [
"Galaxy"
] | 4f8e85f3fb873dece895add920c8be45f5fbd63fb4843c6e9baa8c177b76689a |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | python/pyhit/tests/test_parser.py | Python | lgpl-2.1 | 7,103 | [
"MOOSE"
] | 2494a7e260b14687542ecee3dd5d149f11985daea0fee2438bde12da859e9de0 |
from __future__ import absolute_import
import os
import sys
import llvmbuild.componentinfo as componentinfo
import llvmbuild.configutil as configutil
from llvmbuild.util import fatal, note
###
def cmake_quote_string(value):
"""
cmake_quote_string(value) -> str
Return a quoted form of the given value th... | chubbymaggie/asap | utils/llvm-build/llvmbuild/main.py | Python | bsd-2-clause | 38,161 | [
"VisIt"
] | 1587ed46c9f8617e8ae6d12c44bc28fe63aa0df43874d59240f7e6a911912d21 |
"""
Computational Neurodynamics
Exercise 2
Simulates the movement of a robot with differential wheels under the
control of a spiking neural network. The simulation runs for a very
long time --- if you get bored, press Ctrl+C a couple of times.
(C) Murray Shanahan et al, 2015
"""
import numpy as np
import numpy.rando... | pmediano/ComputationalNeurodynamics | Fall2015/Exercise_2/RobotRun4L.py | Python | gpl-3.0 | 4,506 | [
"DIRAC"
] | 0952267c9917fe6d44d27402b7cd9281abac2824ec6ed702c53d06a1b427a9b8 |
import math
import models
import tensorflow as tf
import numpy as np
import utils
from tensorflow import flags
import tensorflow.contrib.slim as slim
FLAGS = flags.FLAGS
class LstmPositionalAttentionMaxPoolingModel(models.BaseModel):
"""Max pooling over temporal weighted sums (attention) of lstm outputs."""
def c... | wangheda/youtube-8m | youtube-8m-wangheda/all_frame_models/lstm_positional_attention_max_pooling_model.py | Python | apache-2.0 | 5,290 | [
"MOE"
] | 762fd2722a2cdd05b6d9a7390b7a1a35aad99827ba563d6dbfbe7bfc864dc3f2 |
from main import *
class StartPage(CachedPage):
cacheName = "StartPage"
def generatePage(self):
output = []
output.append( '''<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
<html xmlns="http://www.w3.org/1999/xhtml"><head>
<meta http-equiv=... | fbreuer/mathblogging | startpage.py | Python | agpl-3.0 | 5,028 | [
"VisIt"
] | 13020c648ebaa36ae8955d52fdbfb3ea41f9e3fe6912ed0d02efffed1f2bf923 |
# Copyright 2009 by Peter Cock & Cymon J. Cox. 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.
"""Alignment command line tool wrappers."""
__docformat__ = "restructuredtext en" ... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Align/Applications/__init__.py | Python | gpl-2.0 | 1,116 | [
"Biopython"
] | 8cafed44e5ee2e416e953b8e74f1664243717d37ed9f6d1eb6be757107ace3b1 |
import numpy
import pylab
import moose
import time
'''
This example implements a reaction-diffusion like system which is
bistable and propagates losslessly. It is based on the NEURON example
rxdrun.py, but incorporates more compartments and runs for a longer time.
The system is implemented in a function rather than a... | dilawar/moose-full | moose-examples/snippets/rxdFuncDiffusion.py | Python | gpl-2.0 | 1,949 | [
"MOOSE",
"NEURON"
] | d0dc36faf1cbd6a6bc9e208a76b7b85a1110032b700f43fcb9ae76a43ceb2da2 |
# 12-2016
VERSION_INFO = "Firefly 4.35"
PROTOCOL = 150101
| opennx/nx.client | version_info.py | Python | gpl-3.0 | 58 | [
"Firefly"
] | 8e3a8c577c84cf9019a545e026ec3ee2e97a75ac3feab69e46e23baf1f71d439 |
"""Routines of phonon and post-phonon calculations."""
# Copyright (C) 2021 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 o... | atztogo/phonopy | phonopy/phonon/__init__.py | Python | bsd-3-clause | 1,636 | [
"phonopy"
] | 10b6b9d0d062bc9df39dac3a0086e876c68573e6e16356bd5e8d503334c46024 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/auxiliary/base.py | Python | gpl-2.0 | 17,248 | [
"MDAnalysis"
] | 5547de40a0476a6c0156fd09eca5b5786f4a69f26d1fcca41f02268e67742883 |
# -*- coding: utf-8 -*-
r"""
.. _disc-filtering:
===================================
Background information on filtering
===================================
Here we give some background information on filtering in general, and
how it is done in MNE-Python in particular.
Recommended reading for practical applications ... | bloyl/mne-python | tutorials/preprocessing/25_background_filtering.py | Python | bsd-3-clause | 46,186 | [
"Gaussian"
] | de0f2be4b17b8aa63d322f6419c39ba9ec92456111f9f11c08f705fd238cb171 |
#
# Copyright (C) 2013,2014,2015,2016 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)... | KonradBreitsprecher/espresso | testsuite/correlation.py | Python | gpl-3.0 | 2,178 | [
"ESPResSo"
] | 55280e7c009de19b07b1a5bc0e4a8594eb91978f5dc1b8546bf1a0ffc1e5c2d2 |
import numpy
import matplotlib
import shutil
# matplotlib.use('agg')
from matplotlib import pylab, mlab, pyplot
import os
np = numpy
plt = pyplot
# plt.ion()
from argparse import Namespace
from glob import glob
import scipy.io
from scipy.signal import butter,lfilter,freqz
from scipy.interpolate import interp1d
#from s... | sao-eht/lmtscripts | 2017/pointing_lmt2017.py | Python | mit | 35,333 | [
"NetCDF"
] | 909d640314ce98f97c117af4c308b056c8c7352bd36162284079b25367b1c7ff |
#!/usr/bin/env python3
import os
import argparse
import sys
from time import sleep
import subprocess
import glob
mypath = os.environ["PATH"]
os.environ["PATH"] = "/home/wl45/python/bin:/home/wl45/opt:" + mypath
my_env = os.environ.copy()
parser = argparse.ArgumentParser(
description="This is a python3 script ... | luwei0917/awsemmd_script | repeat.py | Python | mit | 1,968 | [
"PyMOL"
] | 36d18b4a32880b9c4d8b66e8a9befd72782417bcea244525d393495d1baa938d |
import pysam
import sys
import collections
import operator
import sequence
from . samfile import Samfile
class Consensus(object):
def __init__(self, read_coverage_threshold=10):
self.read_coverage_threshold = read_coverage_threshold
def process_pileup_column(self, pileup_column):
base_count = ... | vishnubob/bones | bones/consensus.py | Python | mit | 3,686 | [
"pysam"
] | 40c7aa212241718ea71566db783a7beac505d78255d39079a252845b283cac4b |
# -*- coding: utf-8 -*-
"""Functional tests using WebTest.
See: http://webtest.readthedocs.org/
"""
import pytest
from flask import url_for
from octopus.models import User
from .factories import UserFactory
class TestLoggingIn:
def test_can_log_in_returns_200(self, user, testapp):
# Goes to homepage
res =... | quaintm/octopus | tests/test_functional.py | Python | bsd-3-clause | 3,313 | [
"Octopus"
] | 5b5824bcfee9a6edb22f7747038f4b0c88907b2a1702b67e8ba378d290cece42 |
import moose
import sys
from moosehandler import MooseHandler
class mooseElectrodes():
def currentClamp(self,paramDict,compartment):
self.updateTimeStepInfo()
self._pulseGen = moose.PulseGen("PulseGen",compartment)
self._setupPulseGen(paramDict)
self._iClamp = moose.DiffAmp("IClam... | BhallaLab/moose-thalamocortical | pymoose/gui/qt/mooseelectrodes.py | Python | lgpl-2.1 | 7,313 | [
"MOOSE"
] | 4933ca9d277b1bf7cec38c0506124e89aad195ea76cc43916d43b007933997e9 |
#!/usr/bin/env python
# polarizer.py - add Drude oscillators to LAMMPS data file.
# Agilio Padua <agilio.padua@univ-bpclermont.fr>
# Alain Dequidt <alain.dequidt@univ-bpclermont.fr>
# version 2017/02/03
import sys
import argparse
import random
from copy import deepcopy
usage = """Add Drude oscillators to LAMMPS data ... | jag1g13/lammps | tools/drude/polarizer.py | Python | gpl-2.0 | 28,213 | [
"LAMMPS"
] | 9f7e4acc67953856558636f60e4c1474e104639a7d8710bc565ce08fbd83b6a8 |
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