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# -*- coding: utf-8 -*-
""" Module gifted
Provides functionality for reading and writing animated GIF images.
Use write_gif to write a series of numpy arrays or PIL images as an
animated GIF. Use read_gif to read an animated gif as a series of numpy
arrays.
Note that since July 2004, all patents on the LZW compressi... | levi-rs/gifted | gifted/gifted.py | Python | bsd-3-clause | 35,791 | [
"NEURON"
] | d4cff7f9a898e05a253a5ee978ea665cb18629fd3b6178484bc7a01ed9dd3027 |
# Orca
#
# Copyright 2004-2009 Sun Microsystems Inc.
# Copyright 2010-2011 The Orca Team
# Copyright 2012 Igalia, S.L.
#
# 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... | GNOME/orca | src/orca/orca.py | Python | lgpl-2.1 | 28,530 | [
"ORCA"
] | be57ace019f253f6ab90683e8b93150aa12254b13ba006ccdf7c4cc334484296 |
# CLEANUP NOTES (for ISHAN):
# - add documentation for each method
# - add comments inline explaining each piece
# - add a unit test for each method (at least)
# future
from __future__ import annotations
# stdlib
from typing import Any
from typing import List as TypeList
from typing import Optional
# third party
fro... | OpenMined/PySyft | packages/syft/src/syft/core/adp/scalar/abstract/scalar.py | Python | apache-2.0 | 1,478 | [
"Gaussian"
] | 051f3bb25a3a1228174127d25559591a4c7e84a22877463c805b14b9f5283f4b |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/sklearn/ensemble/forest.py | Python | agpl-3.0 | 41,898 | [
"Brian"
] | 70332f50177c22d4fc5fbc0263d3b9fe04fe68ac988453836d627fac9f9cc463 |
# Copyright 2003-2009 by Bartek Wilczynski. 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.
"""Tools for sequence motif analysis (DEPRECATED, see Bio.motifs instead).
This modul... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/Motif/__init__.py | Python | apache-2.0 | 5,092 | [
"Biopython"
] | 50f49464dde1ec92bb843b0d8ab985b5bf3bb24937d76bd3da88f8c18c7a305e |
import sys
sys.path.insert(1, "../../../")
import h2o
def link_incompatible_error(ip,port):
print("Reading in original prostate data.")
prostate = h2o.import_file(path=h2o.locate("smalldata/prostate/prostate.csv.zip"))
print("Throw error when trying to create model with incompatible logit link... | weaver-viii/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_link_incompatible_errorGLM.py | Python | apache-2.0 | 985 | [
"Gaussian"
] | 3a9fc598563419cb040746c614494c41bccc4ecf70c4859e4b17b2a3bb6fe05d |
from setuptools import setup, find_packages
import imp
version = imp.load_source('crema.version', 'crema/version.py')
setup(
name='crema',
version=version.version,
description="Convolutional-recurrent estimators for music analysis",
author='Brian McFee',
url='http://github.com/bmcfee/crema',
... | bmcfee/crema | setup.py | Python | bsd-2-clause | 1,596 | [
"Brian"
] | a4f22d0c98b76281108b318ac7ce0442d560c9c0f21ae153547a89aaa9087b6c |
"""
Django settings for Exchange project.
For more information on this file, see
https://docs.djangoproject.com/en/1.7/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/1.7/ref/settings/
"""
# Build paths inside the project like this: os.path.join(BASE_DIR, ...)
i... | SINTEF-Infosec/Incident-Information-Sharing-Tool | Exchange/settings.py | Python | apache-2.0 | 3,811 | [
"Amber"
] | 95a55d281d2c94d3d57a8c79eaceeff3567a526787b4272e1d7c3a5c4c5eef4b |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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... | gph82/PyEMMA | pyemma/coordinates/data/featurization/featurizer.py | Python | lgpl-3.0 | 30,879 | [
"MDTraj"
] | 49dc7204a2fb3d28b1d66bed6ea44ace927f8d09f42d9f001d7bcfc79ad3a925 |
from galaxy.managers import base as manager_base
class LDDAManager( manager_base.ModelManager ):
""" A fairly sparse manager for LDDAs.
"""
def __init__( self ):
"""
Set up and initialize other managers needed by lddas.
"""
pass
def get( self, trans, id, check_accessi... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/managers/lddas.py | Python | gpl-3.0 | 518 | [
"Galaxy"
] | 4b54a33fb41741bb6224aa150894db633364138649df440007428d39e30e0dd4 |
# Orca
#
# Copyright 2006-2008 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 (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/httpserver.py | Python | gpl-3.0 | 5,107 | [
"ORCA"
] | 356d67d915e45a058b3e20f617101c38246fab42fb4dcc54af998eca3affba62 |
import re
from pygments.lexers.theorem import IsabelleLexer
from pygments.lexer import RegexLexer, inherit, bygroups, words
from pygments.token import *
from . import encoding
__all__ = ['IsarLexer']
class IsarLexer(IsabelleLexer):
name = 'Isabelle/Isar'
keyword_cartouche_text = ('text', 'txt', 'text_raw',
... | KITPraktomatTeam/Praktomat | src/utilities/isar_lexer.py | Python | gpl-2.0 | 24,376 | [
"Bowtie"
] | 61c5a9afbe1245838a7e7f294fb623705327ad256a0d1dac8550c029e047e0c9 |
import os
from os.path import join as pjoin
import numpy as np
import h5py
from gps_viewer import read_gps_fields
from WGS84toENU import WGS84toECEF, WGS84toENU
from pipeline_config import EXPORT_STEP, EXPORT_START, MAPPING_PATH, ICP_ITERS, ICP_MAX_DIST, NUM_CPUS
from graphslam_config import MATCH_JSON_DATA, CHUNK_SIZE... | sameeptandon/sail-car-log | mapping/sandbox/graphslam/chunk_and_align.py | Python | bsd-2-clause | 5,357 | [
"VTK"
] | 414b8c0d82019578c57f08a0083dc05df46e79e997a55ce50c75a211508ceb39 |
#!/usr/bin/env python3
# -*- coding=utf-8 -*-
"""
cry2cif\n\n
Read the last geometry corresponding to the CRYSTALLOGRAPHIC CELL on a
CRYSTAL09 output file and print it in a cif format. If geometry
optimization did not converge, input geometry is printed instead.
"""
# TODO:
# * returns coordinates instead of write ... | gVallverdu/myScripts | CRYSTAL/cry2cif.py | Python | gpl-2.0 | 7,246 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | 9f17d1ca622a9d8ac35c6fbed0c90143cc262316cfc129f48e071549c112913e |
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
import numpy as np
from rdkit import Chem
import itertools, operator
from deepchem.feat import Featurizer
from deepchem.feat.mol_graphs import ConvMol
def one_of_k_encoding(x, allowable_set):
if x not in a... | bowenliu16/deepchem | deepchem/feat/graph_features.py | Python | gpl-3.0 | 5,773 | [
"RDKit"
] | 3db79ed9e095690295e0992c0c4bdeb6ffc10f0a76c2912a83a6ed48e5f5623a |
from django.conf import settings
from django.db import models
from django.utils import timezone
from patients.models import Patient
class BaseActe(models.Model):
"""
Base Abstract class for for differnets actions
made by usej
"""
patient = models.ForeignKey(
Patient, related_... | jgirardet/unolog | unolog/actes/models.py | Python | gpl-3.0 | 1,489 | [
"VisIt"
] | 0b89dc5a4ddddea18047f66e5b2b2f662314ff240eac48725e7754089f9ed475 |
# Copyright 2013-2021 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 collections import defaultdict
from spack import *
from spack.util.environment import is_system_path
class Cdo(Aut... | LLNL/spack | var/spack/repos/builtin/packages/cdo/package.py | Python | lgpl-2.1 | 10,082 | [
"NetCDF"
] | 5daf458f2e315d74110c9cee940cb6998d5a53797afdff00c9506eb6954783b6 |
########################################################################
# $HeadURL $
# File: FileCatalogHandler.py
########################################################################
"""
:mod: FileCatalogHandler
.. module: FileCatalogHandler
:synopsis: FileCatalogHandler is a simple Replica and Metadata Cat... | Sbalbp/DIRAC | DataManagementSystem/Service/FileCatalogHandler.py | Python | gpl-3.0 | 27,381 | [
"DIRAC"
] | 3c8e5859724ef4e5a61a86e61ce03b65130071b9677124f53073409ceeeb5ab9 |
"""
This is a setup.py script generated by py2applet
Usage:
python setup.py py2app
"""
from setuptools import setup
APP = ['main.py']
DATA_FILES = [
'config.json',
'firefly-blacklist.txt',
'firefly-blacklist.meta.json',
'firefly-hosts.txt',
'firefly-hosts.meta.json',
'firefly-hosts-disabl... | Jonavin/firefly-proxy | setup_mac.py | Python | bsd-2-clause | 826 | [
"Firefly"
] | 71a96ba7e6006da35f4c2442ecc7f67e2eceffc652440d7d032d4d2b6cd8da8e |
# Copyright 2016 Mingbo Cai, Princeton Neuroscience Instititute,
# Princeton University
#
# 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... | lcnature/brainiak | brainiak/reprsimil/brsa.py | Python | apache-2.0 | 211,992 | [
"Gaussian"
] | cd84a148f8270fb7a16c3150d7e0990c60922e2e55f0e7b09b4275ecb5b0bf42 |
class Display:
def visit(self, state_machine):
states = state_machine.states
for state in states.values():
print "state: ", state.name
for transition in state.transitions_out.values():
print " transition: ", transition.name, " attributes: ",
for attribute_or_group in transition.a... | bwtaylor/statemach | visitors/display.py | Python | apache-2.0 | 392 | [
"VisIt"
] | 3890a196fc331e38d203619589ea33107eb5ae415f5eb88769a9189946aa9104 |
# $Id$
#
# Copyright (C) 2003 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import six
from rdkit.VLib.Node import VLibNode
class SupplyNode(VLibNode):
""" base class for nodes which supply things
Assumptions:
1) no parents
Usage Example:
>>> supplier = SupplyNode(contents=[1,2,3])
... | rvianello/rdkit | rdkit/VLib/Supply.py | Python | bsd-3-clause | 1,492 | [
"RDKit"
] | 23af8f1b73244f7ed97781cf1ba0d7f295dd09e7355e900042556e92d6cb4d16 |
import os
import sys
import time
import socket
import inspect
import traceback
import pickle
import uuid
from GangaCore.Runtime.GPIexport import exportToGPI
from GangaCore.GPIDev.Base.Proxy import addProxy, stripProxy
from GangaCore.Utility.Config import getConfig
from GangaCore.Utility.logging import getLogger
#from G... | ganga-devs/ganga | ganga/GangaDirac/BOOT.py | Python | gpl-3.0 | 7,982 | [
"DIRAC"
] | 1fdbc43fc2a4acec244fdc965c9779737728eb093d37a84b3d9ef6e741e02be0 |
"""
NetCDF reader/writer module.
This module is used to read and create NetCDF files. NetCDF files are
accessed through the `netcdf_file` object. Data written to and from NetCDF
files are contained in `netcdf_variable` objects. Attributes are given
as member variables of the `netcdf_file` and `netcdf_variable` objects... | scipy/scipy-svn | scipy/io/netcdf.py | Python | bsd-3-clause | 28,822 | [
"NetCDF"
] | 2d65540f9b4ca31001e60b018553ac4a6c0c5d60c41031733483ec0a5224e468 |
"""
Tools for the instructor dashboard
"""
import json
import operator
import dateutil
from django.contrib.auth.models import User # lint-amnesty, pylint: disable=imported-auth-user
from django.http import HttpResponseBadRequest
from django.utils.translation import ugettext as _
from edx_when import api
from opaque... | eduNEXT/edunext-platform | lms/djangoapps/instructor/views/tools.py | Python | agpl-3.0 | 8,924 | [
"VisIt"
] | e998c91b2b60b135d494acbe790f69025ea0ba0296f749f72d282abb904f5639 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module implements a Composition class to represent compositions,
and a ChemicalPotential class to represent potentials.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "0.1"
__maintainer... | yanikou19/pymatgen | pymatgen/core/composition.py | Python | mit | 29,842 | [
"pymatgen"
] | 5668a8b25df2cf6e5ea176586f78aa8b3dc09316e32b260cfec894062031781d |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import print_function
import gyp.common
import gyp.simple_copy
import multiprocessing
import optparse
import os.path
import re
import shlex
import ... | pyokagan/gyp | pylib/gyp/input.py | Python | bsd-3-clause | 114,987 | [
"VisIt"
] | 10683fcc40c5524ada6a3da4400baf4c735feb5badae30c2c641c399c846e2f7 |
import json
import glob
import time
import re
import os
from collections import Counter
from itertools import chain
import requests
import settings
from nltk.tokenize import word_tokenize
PROFILE_URL = u'https://www.okcupid.com/profile/{username}'
QUESTIONS_URL = u'https://www.okcupid.com/profile/{username}/ques... | ned2/okdata | okc.py | Python | mit | 16,915 | [
"VisIt"
] | 038678a7ca9dcc7b200a76ce66fcc0829e66b42de9fd17626ee151004ee20b32 |
"""
=======
Plotter
=======
.. moduleauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com>
"""
from __future__ import print_function
import matplotlib
import matplotlib.pyplot
import matplotlib.figure
import numpy as np
import astropy.units as u
import copy
import inspect
try:
from matplotlib.cbook import BoundMetho... | mikelum/pyspeckit | pyspeckit/spectrum/plotters.py | Python | mit | 31,130 | [
"Gaussian"
] | 9cc62897613a994bdd8d2f4170d1b87e32bd5b29b76e3db73821152e187871ed |
# Copyright 2000 by Andrew Dalke. 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.
# The Prosite patterns are defined at http://www.expasy.ch/txt/prosuser.txt
#
# The PA (PAtte... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Prosite/Pattern.py | Python | gpl-2.0 | 16,587 | [
"Biopython"
] | 61bc6d0fe983802639276b2f58443f70563a26a73b7b9eecbf2c3d6428db449a |
"""
Uniweb validator project
w3c.py : Checks URL against W3C validators in various ways
Copyright (c) 2009 Brian Shumate
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, incl... | brianshumate/uniweb | surfbot/utils/w3c.py | Python | bsd-2-clause | 3,219 | [
"Brian"
] | 13f910fd6b559f01446cac87f4b287fc2abd08956a2775895d7a9174147b2657 |
"""
Extremely simple utility class to send mails
"""
import os
import socket
from smtplib import SMTP, SMTP_SSL
from email.mime.application import MIMEApplication
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
from getpass import getuser
from DIRAC import gLogger, S_OK, S_ERRO... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/Mail.py | Python | gpl-3.0 | 4,124 | [
"DIRAC"
] | e1a7568481552cec7beb8ab3ae2fa1917ece72acc0281d8c538724fff3ff2fbb |
# Adapted from Bio.AlignIO.FastaIO copyright 2008-2011 by Peter Cock.
# Copyright 2012 by Wibowo Arindrarto.
# 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.
"""Bio.SearchIO sup... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/SearchIO/FastaIO.py | Python | apache-2.0 | 25,572 | [
"BLAST",
"Biopython"
] | bd8d3032fba626e4e600202a7d56298d0e352f1c5ed17de1be0f8edf7d535d2e |
import os
import glob
import sys
import shutil
import pysam
from bcbio.pipeline import config_utils
from bcbio.distributed.transaction import file_transaction, tx_tmpdir
from bcbio.utils import (safe_makedir, file_exists)
from bcbio.provenance import do
from bcbio import utils
from bcbio.log import logger
from bcbio.p... | chapmanb/bcbio-nextgen | bcbio/ngsalign/bismark.py | Python | mit | 6,398 | [
"pysam"
] | 69365195a18e0530b7d8eb86b36268b1487ca523a86e49cf415b70de43c73404 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* 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
... | nuclear-wizard/moose | python/chigger/tests/new_files/new_files.py | Python | lgpl-2.1 | 1,104 | [
"MOOSE"
] | 83a177d53678b899e842277ee96e78f45be0fc35a29ca6a2841cb530342c0ce4 |
#mono_gauss_coil model
#conversion of DebyeModel.py
#converted by Steve King, Mar 2016
r"""
This Debye Gaussian coil model strictly describes the scattering from
*monodisperse* polymer chains in theta solvents or polymer melts, conditions
under which the distances between segments follow a Gaussian distribution.
Provid... | SasView/sasmodels | sasmodels/models/mono_gauss_coil.py | Python | bsd-3-clause | 2,912 | [
"Avogadro",
"Gaussian"
] | 120bbf6625d47904d80564e342134261f9d192ab6f7416fee5971d5883c6a183 |
import subprocess
import sys
import time
from datetime import datetime
#print(sys.argv[0])
print("""
Wifi Packet Sniffer v0.1
-------------------------------
Options:
-c Channel to listen on
-m Target address
-i Interface to use
Credits:
Re-scripted by scriptedp0ison
Original program airodump-ng created by Tho... | scriptedp0ison/Kali-Linux-Wifi-Short-Cut-Scripts | get_client.py | Python | gpl-3.0 | 1,554 | [
"VisIt"
] | 022c12fff59a58346adccb3782c70b2e9f9c1f80c58ee7cda6f2914a468b57ab |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/client/client_rpc.py
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice... | securestate/king-phisher | king_phisher/client/client_rpc.py | Python | bsd-3-clause | 24,921 | [
"VisIt"
] | 41742e828a64655a879610b5d744472cd750075df2b071d30fb2da4808fb5189 |
# electronics.py ---
#
# Filename: electronics.py
# Description:
# Author: Subhasis Ray
# Maintainer: Dilawar Singh
import numpy as np
import moose
class ClampCircuit(object):
"""Container for a Voltage-Clamp/Current clamp circuit."""
defaults = {
'level1': 25.0,
'width1': 50.0,
'dela... | BhallaLab/moose-examples | squid/electronics.py | Python | gpl-2.0 | 3,586 | [
"MOOSE"
] | 585d9b83d5a7faee10ee1619bfc57d541d6baf9a6de101d11ce80c459a8c7858 |
'''-------------------------------------------------------------------------------
Tool Name: CreateInflowFileFromECMWFRunoff
Source Name: CreateInflowFileFromECMWFRunoff.py
Version: ArcGIS 10.3
Author: Environmental Systems Research Institute Inc.
Updated by: Environmental Systems Research Instit... | CI-WATER/erfp_data_process_ubuntu_aws | CreateInflowFileFromECMWFRunoff.py | Python | mit | 11,619 | [
"NetCDF"
] | 88fe13085be57276bc40cd97349ed41642501b727e3eccb1cc1106d818ae8130 |
# DEPTH-FIRST-SEARCH
# A graph is searched depth first by visiting an initial
# vertex and then visiting one of its neighbours. After
# visiting this neighbour you visit one of its neighbours
# and so on. If you come to a vertex with no neighbors you
# backtrack one stage and visit another neighbour of the
# previous... | melayev/algods | dfs.py | Python | mit | 1,714 | [
"VisIt"
] | c482ea83aa7c25cf86e5f87a0b563f2d08bc0814c00a9376a91478c27b33743f |
"""Module for reading, writing, compressing and converting files.
Please note, some of the functions in this module were created and tested using
VTK 5. VTK 6 introduced a number of backwards-incompatible changes, including
replacing 'SetInput()' with 'SetInputData()' and 'SetInputConnection'.
"""
import glob
... | ajgeers/utils | utils/iolib.py | Python | bsd-2-clause | 12,457 | [
"VTK"
] | f14f80c2c947198e53f32800d8fabbb92bea1cbc0693bc2450c45be41462f8ec |
try:
import hashlib as md5
except:
import md5
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.ConfigurationSystem.Client.PathFinder import getServiceSection
from DIRAC.AccountingSystem.private.Plotters import gPlottersList
from DIRAC.AccountingSystem.private.Policies import gPoliciesList
class MainReporter:
... | sposs/DIRAC | AccountingSystem/private/MainReporter.py | Python | gpl-3.0 | 2,070 | [
"DIRAC"
] | 505b6b1fa46df3aefa8eb7a19d7302124bf6ac32142463fdf5b24dc9f5ff5f19 |
##########################################################################
#
# Copyright 2008-2010 VMware, Inc.
# All Rights Reserved.
#
# 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 withou... | EoD/apitrace | wrappers/gltrace.py | Python | mit | 55,234 | [
"VisIt"
] | ceec5b69fc3bb5024a8f3e82ac6378b982d01f707413fb5c2df99f1717cf693a |
import numpy as np
import scipy.special
from scipy import constants
import computations
import data_processing
def test_mie():
"""Test the functions involved in the Mie coefficients computation.
Compare to values obtained with Wolfram Alpha.
"""
n = 1
a = 10e-9
omega = 2.48 / constants.hbar ... | rjurga/plasmon-fluorescence | tests.py | Python | mit | 16,104 | [
"CRYSTAL"
] | 74b5f81a13fe5e64c44ed9726bacbfa50303489ad0fad9674c5c4d530aa2e7ca |
# -*- coding: UTF-8 -*-
"""
``trinity_mapping``
-----------------------------------------------------------------
:Authors: Menachem Sklarz
:Affiliation: Bioinformatics core facility
:Organization: National Institute of Biotechnology in the Negev, Ben Gurion University.
A class that defines a module for running ``ali... | bioinfo-core-BGU/neatseq-flow_modules | neatseq_flow_modules/RNA_seq/trinity_mapping.py | Python | gpl-3.0 | 17,105 | [
"Bowtie"
] | 6f1a6baa94708be445935242dc409ac60d0ddac45614a084d6d906edf6e17aae |
##############################################################################
##
## Copyright (C) 2014-2016, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "... | VisTrails/VisTrails | vistrails/core/reportusage.py | Python | bsd-3-clause | 12,618 | [
"VTK"
] | 68d73abebf4c6c69c6bf8f048be1792fc6af5cdc6139deba2aaee297b8eca5fe |
from __future__ import print_function
import psi4
from psi4.driver import qcdb
#! A test of the basis specification. Various basis sets are specified outright and in blocks, both
#! orbital and auxiliary. Constructs libmints BasisSet objects through the constructor that calls
#! qcdb.BasisSet infrastructure. Checks th... | kratman/psi4public | tests/python/mints9/input.py | Python | gpl-2.0 | 8,970 | [
"Psi4"
] | 6e5ebbef360a1a6cf2bb4bf50d6d44da19cfe56f43bc5bf83451f1fc46a2bf4a |
#!/usr/bin/env python
"""
modules for large scale experiment runs includes:
- reading of genome sequence in fasta format
- manual cleaning of genome and annotation files
- feature annotation db for querying details
- creating star genome indicies
Requirement:
STAR aligner: https://github.com/alex... | vipints/genomeutils | fetch_remote_data/prepare_data.py | Python | bsd-3-clause | 15,195 | [
"BWA",
"Biopython"
] | 51ac0fb0ed692f6e7fc0ae882fe9ff6e7492eecc5430ad614efcb9e0429469fe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# shapes.py
#
# Copyright 2015 Carlos Eduardo Sequeiros Borja <casebor@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; eithe... | casebor/labioscripts | python/shapes_tapa.py | Python | gpl-3.0 | 10,847 | [
"Amber"
] | f3b28716bd3e807e6b0d3a1084800076584283a0c67b59e0db19a9887eebf09f |
# -*- coding: utf-8 -*-
"""Tests for :mod:`pybel.manager`."""
| pybel/pybel | tests/test_manager/__init__.py | Python | mit | 63 | [
"Pybel"
] | c559c00364647dcb3fce6dde582359d525e79dc9e80c70d172fb19aedbf0b35a |
########################################################################
# $Id$
########################################################################
""" FileManagerBase is a base class for all the specific File Managers
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gLog... | vmendez/DIRAC | DataManagementSystem/DB/FileCatalogComponents/FileManagerBase.py | Python | gpl-3.0 | 49,658 | [
"DIRAC"
] | e797ffd57e4f23510a8f12a6674886299038f0268225ec538bfaff0e0844d4b5 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Top-level presubmit script for Chromium.
See http://dev.chromium.org/developers/how-tos/depottools/presubmit-scripts
for more details about the presu... | mou4e/zirconium | PRESUBMIT.py | Python | bsd-3-clause | 64,946 | [
"VisIt"
] | 73c03dc325168a0a5d63c158ec65589a3800f14bea235698dcf21bc3646d5706 |
# coding=utf-8
"""Create contour from shakemap raster layer."""
import logging
import os
import shutil
from datetime import datetime
import numpy as np
from osgeo import gdal, ogr
from osgeo.gdalconst import GA_ReadOnly
from qgis.core import QgsFeatureRequest, QgsVectorLayer
from safe.common.exceptions import (
... | AIFDR/inasafe | safe/gis/raster/contour.py | Python | gpl-3.0 | 18,679 | [
"Gaussian"
] | 61ad390e4f573a37be00e1e748a00f5c41563a5635e07af7e996311935e6f936 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RSummarizedexperiment(RPackage):
"""SummarizedExperiment container.
The Summarized... | iulian787/spack | var/spack/repos/builtin/packages/r-summarizedexperiment/package.py | Python | lgpl-2.1 | 2,278 | [
"Bioconductor"
] | 822b0de0d413974025eb6111d683bbb51713ed1eebc3db6bf9b50b02c38ebe2a |
# -*- coding: utf-8 -*-
# SPDX-FileCopyrightText: 2016-2019 The Atlite Authors
#
# SPDX-License-Identifier: GPL-3.0-or-later
"""
Base class for Atlite.
"""
# There is a binary incompatibility between the pip wheels of netCDF4 and
# rasterio, which leads to the first one to work correctly while the second
# loaded on... | FRESNA/atlite | atlite/cutout.py | Python | gpl-3.0 | 18,723 | [
"NetCDF"
] | fa0ce0dd611a34f2b050fc135f65e2aed2ba29d12100772c6d8eef2f9a9df09c |
__RCSID__ = "$Id$"
import socket
import select
import time
import os
from DIRAC.Core.DISET.private.Transports.BaseTransport import BaseTransport
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
class PlainTransport(BaseTransport):
def initAsClient... | fstagni/DIRAC | Core/DISET/private/Transports/PlainTransport.py | Python | gpl-3.0 | 4,076 | [
"DIRAC"
] | cfd65e8191edeee8f91b2c7c23251d1293863b536f2ec1f8bda9fe03a9e808df |
"""
This is the boilerplate default configuration file.
Changes and additions to settings should be done in the config module
located in the application root rather than this config.
"""
config = {
# webapp2 sessions
'webapp2_extras.sessions' : {'secret_key': 'Force_be_with'},
# webapp2 authentication
'webapp2_extras... | LuckDragon82/demo | config/localhost.py | Python | lgpl-3.0 | 4,151 | [
"VisIt"
] | c70d2e63d2557596455290420b4700112f05bf3dca829fcd9fd18f60ba6d5347 |
# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/DBAP-algorithm | third_party/rlkit_library/examples/skewfit/sawyer_door.py | Python | apache-2.0 | 5,220 | [
"Gaussian"
] | 36815222cc8bc60bb7c582b9f511a6c9a9d150cf860b48da6cca4b61183b7845 |
import logging
import multiprocessing
import re
import os
import tempfile
import yaml
import sys
from collections import OrderedDict
import click
import urllib
# Adapted from: https://github.com/pnnl/atlas/blob/master/atlas/conf.py
logging.basicConfig(level=logging.INFO, datefmt="%Y-%m-%d %H:%M", format="[%(asctime)s... | nioo-knaw/hydra | conf.py | Python | mit | 7,810 | [
"BLAST"
] | 21439bdfe8c043ee7defdea4c8918ad8d50dcb1cad23c72f055715701c5a66ea |
"""
Cost layers.
TODO: write more documentation
"""
__docformat__ = 'restructedtext en'
__authors__ = ("Razvan Pascanu "
"KyungHyun Cho "
"Caglar Gulcehre ")
__contact__ = "Razvan Pascanu <r.pascanu@gmail>"
import numpy
import copy
import logging
import theano
import theano.tensor as TT... | neozhangthe1/coverage_model | build/lib/groundhog/layers/cost_layers.py | Python | bsd-3-clause | 59,101 | [
"Gaussian"
] | 97f8ad9d8431fd85098bdfcfca04910d0432d701d38b38fa2189e2dd2402f4fd |
#!/usr/bin/env python3
##ON APP MACHINE
import sys
from os import listdir, mkdir
from os.path import isdir, dirname, abspath
import os
import subprocess
import weakref
from scipy import fftpack
import numpy as np
## some global variables, this needs to be fixed at some point
default_raw_data_loc = None#"/exp_app... | Bhare8972/LOFAR-LIM | LIM_scripts/utilities.py | Python | mit | 11,568 | [
"Brian"
] | de9aee678156fe3e80ea9ddab17931f7cf83cd3694d606bc560ca66b24286ea8 |
#!/usr/bin/env python
# Script to convert Amber protein hydrogens (created by ambpdb) into Gromacs
# names. For some reason, eg. HB2 + HB3 are expected to be HB1 and HB2 in the
# Gromacs aminoacids.rtp parameter files.
# Requirements: Biopython
# Desired PDB file should be the first argument. Output is renamed PDB w... | rtb1c13/scripts | SAXS_MD/AmbPDB_2_GMX.py | Python | gpl-2.0 | 6,501 | [
"Amber",
"Biopython",
"Gromacs"
] | ef2ce9d4ecd396bf5562d88bec49c12ec76cbe6a0c9dd41ca5ef1a6ce5a4eb81 |
"""
Test Logger Wrapper
"""
__RCSID__ = "$Id$"
import logging
from io import StringIO
from DIRAC.FrameworkSystem.private.standardLogging.LoggingRoot import LoggingRoot
from DIRAC.FrameworkSystem.private.standardLogging.Logging import Logging
gLogger = LoggingRoot()
def cleaningLog(log):
"""
Remove date a... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/private/standardLogging/test/TestLogUtilities.py | Python | gpl-3.0 | 2,343 | [
"DIRAC"
] | 0c73c24856295f6a80de3e83612c8a746db0d7a3b3ad20b15810cb2f7985bfa5 |
import unittest
from .enum import Enum
class TestEnum(unittest.TestCase):
def test_string_conversion(self):
column = Enum('test_column', 'ENUM', enum_values=['asdf', 'qwerty'], default='qwerty')
self.assertEquals("`test_column` ENUM('asdf', 'qwerty') DEFAULT \'qwerty\'", str(column))
self.a... | cmancone/mygrations | mygrations/core/definitions/columns/enum_test.py | Python | mit | 808 | [
"ADF"
] | bc3fb2e51273b0caa965ff6bfee4401902a2ada14a27681259bade9939c00070 |
#!/usr/bin/env python
#
# Copyright (C) 2014 Brian Caswell <bmc@lungetech.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 Software without restriction, including without limitation
# the rights... | f0rki/cb-multios | tools/generate-polls/examples/bookworm/bookworm.py | Python | mit | 4,548 | [
"Brian"
] | 2195f59586e15efd01f33e7f70afe61bafd52618b64cdb1d9c8dafd3fefbe1f3 |
# This module is free software. You can redistribute it and/or modify it under
# the terms of the MIT License, see the file COPYING included with this
# distribution.
from __future__ import division
"""
General utils files for general purpose functions
"""
import re
import os
#Biopython
from Bio import SeqIO
import ... | RamiOran/SeqCov | utils/general_utils.py | Python | mit | 15,763 | [
"Biopython"
] | 388d15a4d3ae61d1a7589262922c3f9e662edcb16e5fc76211258538833db0bd |
# (c) 2014, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.... | pheanex/ansible | lib/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 4,023 | [
"Brian"
] | aa6a5ec4800e08af8d376ca09c52ff18e4728d95b885aba743cf79c1edd148c8 |
# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Scientific Package. This package holds all simulators, and
# analysers necessary to run brain-simulations. You can use it stand alone or
# in conjunction with TheVirtualBrain-Framework Package. See content of the
# documentation-folder for more details. See also http://ww... | rajul/tvb-library | tvb/datatypes/mode_decompositions_data.py | Python | gpl-2.0 | 4,446 | [
"Gaussian"
] | ccb5844d1e3a2c76a1fc63ab70b20c9914c2027022f29247faac97560e8f09a4 |
#!/usr/bin/env python
#
from distutils.core import setup,Extension
from distutils import sysconfig
import os, sys, re, glob, shutil
version='2009.Q1b2'
module_ext = sysconfig.get_config_var('SO')
if sys.platform=="win32":
install_base="Lib/site-packages"
else:
install_base = os.path.join(sysconfig.get_conf... | rdkit/rdkit-orig | setup.py | Python | bsd-3-clause | 3,461 | [
"RDKit"
] | 8ebfd24860d2f7a12d003e962f02b1ab2a9714329175073c423c7dbd49d517e6 |
'''Parameter sweep (2D): shared procedures.'''
from __future__ import absolute_import, print_function
import numpy as np
from grid_cell_model.submitting.factory import SubmitterFactory
from grid_cell_model.submitting.arguments import ArgumentCreator
from grid_cell_model.submitting.noise.slopes import (DefaultSelecto... | MattNolanLab/ei-attractor | grid_cell_model/simulations/007_noise/param_sweep.py | Python | gpl-3.0 | 4,305 | [
"Gaussian"
] | 4627cc6cbde8cb855d56bc2f334bbf45457401c9b88c9ae8074d576265cd0c2b |
from ase import *
print [a.get_potential_energy() for a in PickleTrajectory('H.traj')]
images = [PickleTrajectory('H.traj')[-1]]
for i in range(4):
images.append(images[0].copy())
images[-1].positions[6, 1] = 2 - images[0].positions[6, 1]
neb = NEB(images)
neb.interpolate()
for image in images:
image.set_calcu... | freephys/python_ase | ase/test/neb.py | Python | gpl-3.0 | 571 | [
"ASE"
] | a5485ed1457edd09bf32274909b48ba1b9e3dfe381c1c620cd4f14b014f8578e |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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... | markovmodel/PyEMMA | pyemma/coordinates/tests/test_fragmented_trajectory.py | Python | lgpl-3.0 | 10,158 | [
"MDTraj"
] | 30fe81e077be5276421e4b866bcad5eea5d7341a1a80220eab70e42df09a6612 |
"""
.. versionadded:: v6r20
FTS3Agent implementation.
It is in charge of submitting and monitoring all the transfers. It can be duplicated.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN FTS3Agent
:end-before: ##END FTS3Agent
:dedent: 2
:caption: FTS3Agent options
"""
from __future__ import... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/Agent/FTS3Agent.py | Python | gpl-3.0 | 20,683 | [
"DIRAC"
] | 71fa26820bd2db8ffe5b25e6d3df90c58dd7ac29bf9d4354921be905923ffd1a |
# Rebinding to a cluster
# Run by:
# $ python run.py [N] [runs] [outFilename] [Logmode, default=False]
#
# Arguments:
# - N: Number of particles in cluster
# - runs: Number of simulation runs
# - outFilename: Name of output file
# - Logmode: false by default, if True, only 1 VTK-logged run is
# performed.... | gfrd/egfrd | samples/memorytools/cluster.py | Python | gpl-2.0 | 10,318 | [
"VTK"
] | 1e5590b7745cf6758174b45f4093df4c6ea49e2ed2d5317b6521b7d139bef950 |
#! /usr/bin/env python
"""Calculate viral taxonomy abundance from BLAST and Bowtie inputs.
Use '-h' for parameter help.
"""
import os
import re
import argparse
import blast
parser = argparse.ArgumentParser(description =
('Calculate viral taxonomy abundance for each sample from PHAST'
'viral database... | chrisLanderson/rumen_virome | scripts/viral_taxa_blast2tsv.py | Python | mit | 3,865 | [
"BLAST",
"Bowtie"
] | 48ad6214500daaa4c9527c3fca2bf10b925a68d821e8ff3834d5b1aa5d889467 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements representations of slabs and surfaces, as well as
algorithms for generating them. If you use this module, please consider
citing the following work::
R. Tran, Z. Xu, B. Radhakris... | richardtran415/pymatgen | pymatgen/core/surface.py | Python | mit | 87,059 | [
"pymatgen"
] | fcd6904ea24f3d4fb398844871fb7b03f16e5f70221c17f3a63a111965856383 |
# -*- coding: utf-8 -*-
#
# tsodyks_facilitating.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 Li... | SepehrMN/nest-simulator | pynest/examples/tsodyks_facilitating.py | Python | gpl-2.0 | 5,620 | [
"NEURON"
] | bfa8dd5e82947eb4a03baee8f29d510fd0dd9295ed84e02ee11602a5720cd14f |
# Generate UV-Vis spectra from electronic structure TDHF/TDDFT output files.
# Copyright (C) 2014 Li Research Group (University of Washington)
#
# 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... | liresearchgroup/uvspecgen | uvspec/generate.py | Python | gpl-3.0 | 3,106 | [
"Gaussian"
] | c708c61675dc0c8ed7e330569fd2ffcbf42c133336e46c11495d163fa9f02a38 |
# This file is part of Buildbot. Buildbot 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, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without eve... | denny820909/builder | lib/python2.7/site-packages/buildbot-0.8.8-py2.7.egg/buildbot/changes/svnpoller.py | Python | mit | 17,125 | [
"Brian"
] | c6ee6cebb5316101c9122b06b364bf802cc40a90f4ed3ada65b71884900d110d |
# Databricks notebook source
# MAGIC %md
# MAGIC
# MAGIC # [SDS-2.2, Scalable Data Science](https://lamastex.github.io/scalable-data-science/sds/2/2/)
# MAGIC
# MAGIC This is used in a non-profit educational setting with kind permission of [Adam Breindel](https://www.linkedin.com/in/adbreind).
# MAGIC This is not lic... | raazesh-sainudiin/scalable-data-science | db/2/2/054_DLbyABr_03a-BatchTensorFlowWithMatrices.py | Python | unlicense | 6,018 | [
"Gaussian"
] | 92f383182ba078dd5dc208a7c21eb9590de9c853b924891811d41203a89d0556 |
#! CCSD dipole with user-specified basis set
import psi4
psi4.set_output_file("output.dat", False)
h2o = psi4.geometry("""
0 1
H
O 1 0.957
H 2 0.957 1 104.5
""")
psi4.set_options({'freeze_core': 'false'})
psi4.basis_helper("""
# Sadlej-pVTZ
spherical
****
H 0
S 4 1.00
33.8650140000 0.00606... | ashutoshvt/psi4 | tests/python/cc54/input.py | Python | lgpl-3.0 | 4,053 | [
"Psi4"
] | 185c8664d8dbe6d1925c118436247e52e717768f8114d504ada7143e2181dfe2 |
from __future__ import print_function
import numpy as np
from numpy import zeros, ones, einsum
from .constants import tol6, tol8, tol12, Ha2eV, kb_HaK
from .mathutil import delta_lorentzian
from . import EigFile, Eigr2dFile, FanFile, DdbFile, GkkFile
__author__ = "Gabriel Antonius"
__all__ = ['QptAnalyzer']
clas... | jmbeuken/abinit | scripts/post_processing/ElectronPhononCoupling/ElectronPhononCoupling/core/qptanalyzer.py | Python | gpl-3.0 | 34,212 | [
"DIRAC"
] | b0b8dbe6d1c83ea8b9b09f42206c7561554a5156367c4b677ffa30ccc2ff52aa |
#
# tsne.py
#
# Implementation of t-SNE in Python. The implementation was tested on Python 2.5.1, and it requires a working
# installation of NumPy. The implementation comes with an example on the MNIST dataset. In order to plot the
# results of this example, a working installation of matplotlib is required.
# The ... | afraser/CellProfiler-Analyst | cpa/tsne.py | Python | gpl-2.0 | 5,205 | [
"Gaussian"
] | 19443cc85cf3ba62aad79dc3d4331e460883e83ce4333dcc8455d6f9c891d732 |
# Copyright 2017 Amazon.com, Inc. or its affiliates. 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. A copy of the License
# is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file acc... | artemsok/sockeye | sockeye/layers.py | Python | apache-2.0 | 28,551 | [
"Gaussian"
] | 9a3f8675dfffca44bf2ab512c14ef444a2c07019fbbd675c1ad0352c1412c641 |
import copy
import hyperchamber as hc
import inspect
import math
import operator
import os
import re
from functools import reduce
import pyparsing
import hypergan
import torch
import torch.nn as nn
from .gan_component import GANComponent
from hypergan.gan_component import ValidationException
from hypergan.layer_shape... | 255BITS/HyperGAN | hypergan/configurable_component.py | Python | mit | 32,342 | [
"DIRAC"
] | 57f453c1a9b980ac591391d18e935227cc73f49512d324d5cb70ff70a6a0272e |
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2020, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it
# und... | graalvm/mx | mx_compdb.py | Python | gpl-2.0 | 5,256 | [
"VisIt"
] | 318b30996a0bfb1c7510967f8cdff0925a84f2be3ee143d009c6bec87092ec4a |
"""Rewrite assertion AST to produce nice error messages"""
import ast
import _ast
import errno
import itertools
import imp
import marshal
import os
import re
import struct
import sys
import types
from fnmatch import fnmatch
import py
from _pytest.assertion import util
# pytest caches rewritten pycs in __pycache__.
... | jaraco/pytest | _pytest/assertion/rewrite.py | Python | mit | 36,408 | [
"VisIt"
] | eb323067c6c1fa56007179e82feaebc742ee2ed5bfdff1b103a1e8c0c2e52b69 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'ui/ui_semiautomaticclassificationplugin.ui'
#
# Created by: PyQt5 UI code generator 5.11.3
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_SemiAutomaticClassificationPlugin(objec... | semiautomaticgit/SemiAutomaticClassificationPlugin | ui/ui_semiautomaticclassificationplugin.py | Python | gpl-3.0 | 841,489 | [
"VisIt"
] | 67be0e08edb3b7528cc32326b3247b48a02507661e0af18d4a74ce0f927cc464 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
man_page_text = """
nbody_by_type.py reads a LAMMPS data file ... | smsaladi/moltemplate | moltemplate/nbody_by_type.py | Python | bsd-3-clause | 30,585 | [
"LAMMPS"
] | fd6035b4c399d258841e8f670a900cfc9dfd4c7e1e9510eb84222f416d182e67 |
import os
from gpaw import GPAW, restart
from ase import Atoms
from gpaw.test import equal
from math import sqrt
import numpy as np
modes = ['gpw']
try:
import h5py
modes.append('hdf5')
except ImportError:
pass
d = 3.0
atoms = Atoms('Na3', positions=[( 0, 0, 0),
( 0, 0, d),
... | qsnake/gpaw | gpaw/test/restart.py | Python | gpl-3.0 | 1,993 | [
"ASE",
"GPAW"
] | 17ba3efe1c985142c070950707458a585896b4e2b80e1a0c46c6cea70e9d53a7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# (c) 2012 Michal Kalewski <mkalewski at cs.put.poznan.pl>
#
# This file is a part of the Simple Network Simulator (sim2net) project.
# USE, MODIFICATION, COPYING AND DISTRIBUTION OF THIS SOFTWARE IS SUBJECT TO
# THE TERMS AND CONDITIONS OF THE MIT LICENSE. YOU SHOULD H... | mkalewski/sim2net | sim2net/utility/__init__.py | Python | mit | 728 | [
"VisIt"
] | 49b99d9de0234e377c759063a39809ee521f369092b1270de7eb4906e7ba0a9b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# tail - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the ... | heromod/migrid | mig/cgi-bin/tail.py | Python | gpl-2.0 | 1,096 | [
"Brian"
] | 35c1a80cdf3cdf2f65ed0b700bce4192ff847f506b471b5e68068faf1a3ab094 |
# Python standard modules
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.mlab as mlab
from mpl_toolkits.mplot3d import Axes3D
import seaborn as sns
import statsmodels.api as sm
import matplotlib.colors as mcolors
import matplotlib as mpl
from matplotlib.pylab import *... | Thomsen22/MissingMoney | Plots/Peak Load Reserve Plots/plotsPLR.py | Python | gpl-3.0 | 13,539 | [
"Amber"
] | 8eeba3750c47fb27ad41bc92813e226e75697c0502a966e8b04a30a40259dc9b |
import HTSeq
import argparse
import os.path
from CommonFastaFunctions import Create_Blastdb
from CommonFastaFunctions import LoadAlelleFasta
from CommonFastaFunctions import LoadAlellicProfileGeneric
from CommonFastaFunctions import WriteFasta
from CommonFastaFunctions import runBlast
from CommonFastaFunctions import r... | mickaelsilva/pythonscripts | AlleleCalling/ParalogRemove.py | Python | gpl-2.0 | 2,157 | [
"BLAST",
"HTSeq"
] | f83585c846b49b185a113d693e3bb14157435f965a52d0696133988828962194 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'Indicator.source'
db.add_column('profiles_indicator', 'source', self.gf('django.db.models.... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0045_auto__add_field_indicator_source.py | Python | mit | 15,170 | [
"MOE"
] | 0501be25706d5ba972b8c72750649f4327d8fc1a03b25d4bad9751e6f62d4086 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
LAMDA Query Tool
----------------
:Author: Brian Svoboda (svobodb@email.arizona.edu)
This package is for querying the Leiden Atomic and Molecular Database (LAMDA)
hosted at: http://home.strw.leidenuniv.nl/~moldata/.
Note:
If you use the data files... | ceb8/astroquery | astroquery/lamda/__init__.py | Python | bsd-3-clause | 701 | [
"Brian"
] | 3a2623fb883c350d2543abca0bfee4951d9f0ce1a0980c9277e3bce4f3ae77de |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from django.conf import settings
from django.http import HttpResponse
from django.test import TestCase
from zilencer.models import Deployment
from zerver.views import get_invitee_emails_set, do_change_password
from zerver.models import (
get_realm, ge... | ahmadassaf/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 31,655 | [
"VisIt"
] | ea8c3e7a34939c0b000c13755754e3d1b118bf899c57479e78f62df46521e184 |
# -*- coding: utf-8 -*-
## begin license ##
#
# "Meresco Components" are components to build searchengines, repositories
# and archives, based on "Meresco Core".
#
# Copyright (C) 2007-2008 SURF Foundation. http://www.surf.nl
# Copyright (C) 2007-2011 Seek You Too (CQ2) http://www.cq2.nl
# Copyright (C) 2007-2009 Stich... | seecr/meresco-components | meresco/components/web/webquery.py | Python | gpl-2.0 | 9,266 | [
"VisIt"
] | 1cc83756ba59b8ce612424796ea1a397539c1b273ed29d9c8d5ed3a8605d799d |
from suggestive.util import retry_function, retry
from suggestive.error import RetryError
import logging
import webbrowser
import pylastfm
logger = logging.getLogger(__name__)
logger.addHandler(logging.NullHandler())
def get(data, keys, default=None):
if not keys:
return data
if not isinstance(dat... | thesquelched/suggestive | suggestive/lastfm.py | Python | bsd-2-clause | 4,198 | [
"VisIt"
] | be5fb648a8b05eaf2c9a8451e1de9c123d77d50f527c1c656624b31cbe60fba2 |
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