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# -*- coding: utf-8 -*-
# crossComptSimpleReacGSSA.py
#
# Filename:crossComptSimpleReacGSSA.py
# Author: Upinder S. Bhalla
# Maintainer:
# Created: Oct 12 16:26:05 2014 (+0530)
# Version:
# Last-Updated: May 16 2017
# By: Upinder S. Bhalla
# Update #: Dec 14 2021
# By: HarshaRani .G.V
# URL... | BhallaLab/moose-examples | snippets/crossComptSimpleReacGSSA.py | Python | gpl-2.0 | 5,545 | [
"MOOSE"
] | 86abfbb39aa514009e0aec7e514b520140c3814665f2e19de64400e6833bc3c0 |
# vim: set encoding=utf-8
# Copyright (c) 2016 Intel Corporation
#
# 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 require... | karthikvadla16/spark-tk | python/sparktk/models/clustering/gmm.py | Python | apache-2.0 | 10,237 | [
"Gaussian"
] | 73346a2f6fb87e4da20f91082bef839d1b8324d0f7c293793576424abaa4936f |
from __future__ import (absolute_import, division, print_function, unicode_literals)
import datetime
import os
import re
import sys
#======================================================================================
def find_basedir(project, subproject):
""" Returns the base directory. If the subproject is kn... | dymkowsk/mantid | buildconfig/cmakelists_utils.py | Python | gpl-3.0 | 6,084 | [
"CRYSTAL"
] | 2312082d166ad6f37e819d9fb3b3e0f9f3e54eb6626f7a4af13bc2d94c30056e |
#
# Copyright (c) 2016 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/licensedcode/test_detection_validate.py | Python | apache-2.0 | 3,512 | [
"VisIt"
] | 14291c0eeb24d9d4dbc22d9eba5e059a468876bd67362029d24585d43a922053 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2006-2008 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Softw... | andrebellafronte/stoq | stoqlib/gui/dialogs/paymentmethod.py | Python | gpl-2.0 | 4,775 | [
"VisIt"
] | e6b990240dca4f9d8e8021ef967782fdbfc09b9e854ad0e7a707f07f458e85fe |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'GUI.ui'
#
# Created by: PyQt5 UI code generator 5.10.1
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_MainWindow(object):
def setupUi(self, MainWindow):
MainWindow.s... | andreashorn/lead_dbs | ext_libs/OSS-DBS/OSS_platform/GUI_tree_files/GUI.py | Python | gpl-3.0 | 176,194 | [
"NEURON"
] | aae9f9d68147f12118bced8406f877bf57dc56e863c80ba8def8593f5ca6f2f0 |
import numpy as np
__all__ = ["ARMA"]
def ARMA(length, phi=0.0, theta=0.0, std=1.0):
r"""
Generate time-series of a predefined ARMA-process based on this equation:
:math:`\sum_{j=1}^{\min(p,n-1)} \phi_j \epsilon[n-j] + \sum_{j=1}^{\min(q,n-1)} \theta_j w[n-j]`
where w is white gaussian noise. Equatio... | eichstaedtPTB/PyDynamic | PyDynamic/misc/noise.py | Python | lgpl-3.0 | 1,580 | [
"Gaussian"
] | d6f39eb3cc6815337db9b2a136a820f6841eb0f22fd3dbf4e957d783adcd4895 |
"""
Provide a library of processing functions.
The processing functions declare their item sources and input parameters along with a identifier, title, and
what UI sections they are likely to appear in.
The processing functions also declare how they are applied to sequences/collections and what form
their output take... | nion-software/nionswift | nion/swift/model/Processing.py | Python | gpl-3.0 | 12,839 | [
"Gaussian"
] | 889b409e246ac923f08b6252f95effee904a9d96f4d8e9603401afa2d0769929 |
import os
import sys
import json
from datamanagerpkg import ProtonCommunication_data_manager
from datamanagerpkg import GalaxyCommunication_data_manager
from sequencer.models import Experiments, GalaxyUsers
from sequencer.models import GalaxyJobs, ExperimentRawData
from sequencer.models import UserCommonJobs,Supported... | CARPEM/GalaxyDocker | data-manager-hegp/analysisManager/analysismanager/Add_Workflows.py | Python | mit | 8,118 | [
"Galaxy"
] | 0ea9ef275d483736841f365aff1ed528c1cf8178c9e44128acb2aace40abfa5c |
import mdtraj as md
import tempfile
import logging
from .utils import getoutput
logger = logging.getLogger(__name__)
logging.basicConfig(level=logging.DEBUG, format="LOG: %(message)s")
# http://ambermd.org/tutorials/advanced/tutorial15/Tutorial2.xhtml
# Run tLEaP with input file:
# $ tleap -f commands.in
TLEAP_TEMP... | kyleabeauchamp/openmoltools | openmoltools/amber.py | Python | gpl-2.0 | 3,518 | [
"MDTraj"
] | 1ca766adcabd3348e8e6eaa9c6d6aec271030a13417ae222f89c7d4556f7e2e3 |
#!/usr/bin/python3
#
# Polychromatic is licensed under the GPLv3.
# Copyright (C) 2017-2021 Luke Horwell <code@horwell.me>
#
"""
This module abstracts data from the OpenRazer Python library (and daemon)
and parses this for Polychromatic to use.
Project URL: https://github.com/openrazer/openrazer
"""
import os
# Impo... | lah7/polychromatic | pylib/backends/openrazer.py | Python | gpl-3.0 | 62,072 | [
"Firefly",
"VisIt"
] | f582f261a4575930a10f247285d0e48700ef81ac06b1f812abb0f4ea8792dc38 |
import os
from ase.io import read
from ase.neb import NEB
from ase.calculators.turbomole import Turbomole
from ase.optimize import BFGS
initial = read('initial.coord')
final = read('final.coord')
os.system('rm -f coord; cp initial.coord coord')
# Make a band consisting of 5 configs:
configs = [initial]
configs += [i... | grhawk/ASE | tools/doc/ase/calculators/turbomole_ex2_diffuse_usingNEB.py | Python | gpl-2.0 | 657 | [
"ASE",
"TURBOMOLE"
] | 54529637b29908608bc16bb69c43bd3fd107d1cb8c3c30c847070a4aa675bf33 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | espressomd/espresso | src/python/espressomd/io/writer/h5md.py | Python | gpl-3.0 | 3,488 | [
"ESPResSo"
] | a4e504da4ae02ab6d4150161885c0e33e9dfab8d1ec21842c056e28d8891c1c2 |
#!/usr/bin/env python
import unittest
import random
import nemo
class IzNetwork(nemo.Network):
def __init__(self):
nemo.Network.__init__(self)
self._type = self.add_neuron_type('Izhikevich')
def add_neuron(self, nidx, a, b, c, d, sigma, u, v):
nemo.Network.add_neuron(self, self._type... | brainstudio-team/NeMo | src/api/python/test.py | Python | gpl-2.0 | 14,056 | [
"NEURON"
] | 82e0b0af10ce90494dacfe1e69fe3550c3a4770ee6276e5864596a78e5f39e7e |
# -*- coding: utf-8 -*-
"""
Tests the "preview" selector in the LMS that allows changing between Staff, Learner, and Content Groups.
"""
from textwrap import dedent
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pa... | Stanford-Online/edx-platform | common/test/acceptance/tests/lms/test_lms_user_preview.py | Python | agpl-3.0 | 17,924 | [
"VisIt"
] | a7d9786ed45301236fef27a655fc0307e96214dfc0e8a3ecceb17492dce5e074 |
"""Testing for kernels for Gaussian processes."""
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# License: BSD 3 clause
import pytest
import numpy as np
from inspect import signature
from sklearn.gaussian_process.kernels import _approx_fprime
from sklearn.metrics.pairwise import (
PAIRWISE_KERNEL_... | manhhomienbienthuy/scikit-learn | sklearn/gaussian_process/tests/test_kernels.py | Python | bsd-3-clause | 13,726 | [
"Gaussian"
] | bed2ec0b8bd12943b1a80a2e34b141c52ea83b7bbcba515b344a949f89ab899e |
from __future__ import print_function
try:
from future_builtins import zip
except ImportError:
pass
from . import moose as _moose
_tick = 8
_base = '/_utils'
_path = _base + '/y{0}'
_counter = 0
_plots = []
_moose.Neutral( _base )
_defaultFields = {
_moose.Compartment : 'Vm',
_moose.ZombieCompartment : 'Vm... | subhacom/moose-core | python/moose/recording.py | Python | gpl-3.0 | 4,723 | [
"MOOSE"
] | 853de3e7cc58c0a441635b1c611f37aaae2bdf3e4ce073152b420d6784f14392 |
# Copyright (C) 2015-2021 Regents of the University of California
#
# 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 app... | BD2KGenomics/slugflow | src/toil/job.py | Python | apache-2.0 | 122,790 | [
"TINKER"
] | 62e15b34d181946e01732f0a34fe6e8eb8e4e467d7c168fb3b788f9713ceff44 |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy, ... | alexholcombe/dot-jump | dataRaw/Fixed Cue/test_dot-jump25Oct2016_17-11.py | Python | gpl-3.0 | 25,090 | [
"Gaussian"
] | c3f4c80d87e0b9fc79d4e60b2f7d6e2bc4dda2878546181358211d06384872a7 |
import numpy as np
from scipy.stats import norm
from mushroom_rl.core import Environment, MDPInfo
from mushroom_rl.utils.spaces import *
from mushroom_rl.utils.viewer import Viewer
class PuddleWorld(Environment):
"""
Puddle world as presented in:
"Off-Policy Actor-Critic". Degris T. et al.. 2012.
""... | carloderamo/mushroom | mushroom_rl/environments/puddle_world.py | Python | mit | 4,695 | [
"Gaussian"
] | 32e197e690e3acf30d856e354dccd382a393619b207c784b73de2664a21fb9f7 |
###############################################################################################
# Copyright 2016, Neil Slater.
#
# 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
#
# ... | neilslater/tabea_video_project | animation_stage_02.py | Python | apache-2.0 | 6,765 | [
"CRYSTAL"
] | 4f5194b9f4b6e21aa7d376a140adb4336f5ccce4267735ee0af65b06ff760258 |
# -*- coding: utf-8 -*-
#
# File: setuphandlers.py
#
# Copyright (c) 2008 by []
# Generator: ArchGenXML Version 2.0-beta10
# http://plone.org/products/archgenxml
#
# GNU General Public License (GPL)
#
__author__ = """unknown <unknown>"""
__docformat__ = 'plaintext'
import logging
logger = logging.getLogge... | uwosh/UWOshMusicRecruiting | setuphandlers.py | Python | gpl-2.0 | 9,848 | [
"VisIt"
] | 2f174017886e046dc6f755222a39942cb110bb94704980faad787b5e59d64c13 |
import numpy
import re
from .tools import *
from orbkit.qcinfo import QCinfo
from orbkit.display import display
from orbkit.orbitals import AOClass, MOClass
def read_gamess(fname, all_mo=False, spin=None, read_properties=False,
**kwargs):
'''Reads all information desired from a Gamess-US output file.... | orbkit/orbkit | orbkit/read/gamess.py | Python | lgpl-3.0 | 16,936 | [
"GAMESS"
] | b73f16824e5b45acbe3223764b7dc015fc1aa93995402f328085f11c7ffd2c96 |
import logging
from django.core.management.base import BaseCommand
from edc_content_type_map.models import ContentTypeMapHelper
logger = logging.getLogger(__name__)
class NullHandler(logging.Handler):
def emit(self, record):
pass
nullhandler = logger.addHandler(NullHandler())
class Command(BaseComma... | botswana-harvard/edc-content-type-map | edc_content_type_map/management/commands/sync_content_type.py | Python | gpl-2.0 | 851 | [
"VisIt"
] | 5f16be9298e0b79f4ebf53688ffc8bc50cc6263edfa3fde9d07d3d1f37f2f965 |
# -----BEGIN ORIGINAL LICENSE-----
# mn_wordlist.c
# Copyright (c) 2000 Oren Tirosh <oren@hishome.net>
#
# 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 withou... | Cashiuus/python-mnemonicode | mnemonicode/_wordlist.py | Python | bsd-3-clause | 21,475 | [
"Amber",
"BLAST",
"CASINO",
"CRYSTAL",
"Galaxy",
"Jaguar",
"NEURON",
"ORCA",
"Octopus"
] | 7e0c3bd44a3d3f9da6da6ee9904f1d85c2dda5cb7d2590ed67e68de04e160fe1 |
#!/usr/bin/env python
# coding: utf-8
# Project Source: https://github.com/renanvicente/zabbix-web-scenario
# Version: 0.0.1
# Author: Renan Vicente
# Mail: renanvice@gmail.com
# Website: http://www.renanvicente.com
# Github: https://www.github.com/renanvicente
# Linkedin: ... | renanvicente/zabbix-web-scenario | zabbix_web_scenario.py | Python | apache-2.0 | 4,945 | [
"VisIt"
] | f804802024f12329aab141cb85c041b5982394f3c3f9bbeb1b5640e5beb6cfa7 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/remotecontrol.py | Python | gpl-2.0 | 5,252 | [
"VisIt"
] | 81fcf5524958bc2bd25c9f781bd5dc3eb15cdc07b9dc1b9092d95a052ea5d6f1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
""" functions that creates image from a video file
Primarily intended for plotting, returns correlation images ( local or max )
See Also:
------------
@author andrea giovannucci
"""
from builtins import range
import cv2
import logging
import numpy as np
from scipy.ndim... | agiovann/Constrained_NMF | caiman/summary_images.py | Python | gpl-2.0 | 33,013 | [
"Gaussian"
] | ed0fcdd58264293ba0029da034a8041ffdc19fd001e33f8947c26837695c9f1d |
#!/usr/bin/python
#
# THIS FILE IS PART OF THE JOKOSHER PROJECT AND LICENSED UNDER THE GPL. SEE
# THE 'COPYING' FILE FOR DETAILS
#
# Jokosher's main class. It creates the majority of the main window GUI
# and gets everything up and running.
#
#----------------------------------------------------------------------------... | lxlxlo/jokosher-devel | Jokosher/JokosherApp.py | Python | gpl-2.0 | 68,617 | [
"VisIt"
] | b0e4199688da6efeb7e6f92685849b3139f550901ff0feef7437bdaa3837cfcf |
import ast
from .. import itypes
from . import functions, classes, expressions, assignment, modules
def parse_statements(statements, scope=None, class_type=None):
if isinstance(statements, str):
statements = [ast.parse(statements)]
parser = StatementBlockTypeParser(scope, class_type)
return parse... | furbrain/tested | tested/parsers/statements.py | Python | gpl-3.0 | 3,472 | [
"VisIt"
] | f6b9d077efbfb8e12242a4a19de02eebce7da782e3f99b8de20a034267c6171b |
"""
Message Queue Handler
"""
__RCSID__ = "$Id$"
import json
import logging
import socket
from DIRAC.Resources.MessageQueue.MQCommunication import createProducer
class MessageQueueHandler(logging.Handler):
"""
MessageQueueHandler is a custom handler from logging.
It has no equivalent in the standard logging ... | arrabito/DIRAC | FrameworkSystem/private/standardLogging/Handler/MessageQueueHandler.py | Python | gpl-3.0 | 1,385 | [
"DIRAC"
] | 783ae5f6ac2564e16f633cd758ea7a8633170eea32c5ccd9fae28c8dfeacbffa |
import regex
def parse(blast_fh, outfmt):
""" Function to provide similar use to biopython's SeqIO """
if str(outfmt) == "6":
return BlastParser.parse_outfmt_6(blast_fh=blast_fh)
class BlastParser(object):
"""
Just a shell of a BLAST parser so I don't have to rewrite this.
Wow, th... | hunter-cameron/Bioinformatics | python/mypyli/blastparser.py | Python | mit | 2,179 | [
"BLAST",
"Biopython"
] | 284b5aa788e747f814274c96b6493fe95943c7776942f921fe0c0a6f9ed9ce18 |
from compliance_checker.ioos import IOOS0_1Check, IOOS1_1Check
from compliance_checker.tests.resources import STATIC_FILES
from compliance_checker.tests import BaseTestCase
from netCDF4 import Dataset
import os
class TestIOOS0_1(BaseTestCase):
'''
Tests for the IOOS Inventory Metadata v0.1
'''
def se... | DanielJMaher/compliance-checker | compliance_checker/tests/test_ioos_profile.py | Python | apache-2.0 | 10,600 | [
"NetCDF"
] | 9bf809aee0d09b168f5e9765d3fc51e023ae6b6828214ee39184fe1fabb600c2 |
########################################################################
# File : ResourcesDefaults.py
# Author : Ricardo Graciani
########################################################################
"""
Some Helper class to access Default options for Different Resources (CEs, SEs, Catalags,...)
"""
from __futur... | petricm/DIRAC | ConfigurationSystem/Client/Helpers/ResourcesDefaults.py | Python | gpl-3.0 | 3,108 | [
"DIRAC"
] | 7bccabb64e82746e297789ea2b59580b5dc8b01348891800b4ee674522bf09d5 |
#! /usr/bin/python
#Guruprasad Ananda
"""
Filter based on nucleotide quality (PHRED score).
usage: %prog input out_file primary_species mask_species score mask_char mask_region mask_region_length
"""
from __future__ import division
from galaxy import eggs
import pkg_resources
pkg_resources.require( "bx-python" )
pk... | volpino/Yeps-EURAC | tools/regVariation/quality_filter.py | Python | mit | 9,250 | [
"Galaxy"
] | d6eaa0956c00b905e64151d2528fe6ca53cb5fd8a0e38a6fd71562d5f9c3f705 |
#!/usr/bin/env python
# Copyright 2014-2021 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/cc/ccsd_t_lambda_slow.py | Python | apache-2.0 | 4,357 | [
"PySCF"
] | 8d10c862c3547cfcc0a4e39a92a1ad5bde89d0ee527744d8b2986ed6df2349bc |
# -*- coding: utf-8 -*-
import logging
import txtorcon
from PyQt5.QtWidgets import QMessageBox
from twisted.internet.defer import inlineCallbacks
from gridsync import features
# From https://styleguide.torproject.org/visuals/
# "The main Tor Project color is Purple. Use Dark Purple as a secondary option"
TOR_PURPLE... | gridsync/gridsync | gridsync/tor.py | Python | gpl-3.0 | 2,094 | [
"VisIt"
] | ed3bc8656b78de2bf54595cc94c2ae418a6d202c6019582a590842a76be15310 |
"""Tests of routines in cells.py."""
import os
import numpy as np
import pytest
from phonopy import Phonopy
from phonopy.interface.phonopy_yaml import read_cell_yaml
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.structure.cells import (
ShortestPairs,
TrimmedCell,
compute_all_sg_permutatio... | atztogo/phonopy | test/structure/test_cells.py | Python | bsd-3-clause | 8,810 | [
"phonopy"
] | 50f32a833afafe6cbd1a788d5ec8780b9ce97f11167e40fa4765d3ea8e8b20d8 |
# coding=utf-8
import sys
import os
import shutil
import unittest
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', '..', 'resources', 'lib'))
sys.path.append(os.path.join(os.path.dirname(__file__), '..', '..', 'resources', 'lib', 'pyscraper'))
import xbmcaddon
from nfowriter import NfoWriter
from nfo_... | bruny/romcollectionbrowser | resources/tests/test_nfowriter.py | Python | gpl-2.0 | 14,038 | [
"ADF"
] | ab42cbf7eb0ac06409eaec61c5f5957f035feb6b6bb676239a99c679edeb6216 |
# coding=utf-8
"""
The XFSCollector collects XFS metrics using /proc/fs/xfs/stat.
#### Dependencies
* /proc/fs/xfs/stat
"""
import diamond.collector
import sys
class XFSCollector(diamond.collector.Collector):
PROC = '/proc/fs/xfs/stat'
def get_default_config_help(self):
config_help = super(XFS... | Ensighten/Diamond | src/collectors/xfs/xfs.py | Python | mit | 7,077 | [
"VisIt"
] | c3e3b957634cb26b24126e43c55213dcb687068d2e766bf56cb6cc4187c8b5cc |
""" Accounting Cache
"""
__RCSID__ = "$Id$"
import os.path
import time
import threading
from DIRAC import S_OK, S_ERROR, gLogger, rootPath, gConfig
from DIRAC.Core.Utilities.DictCache import DictCache
class DataCache( object ):
def __init__( self ):
self.graphsLocation = os.path.join( gConfig.getValue( '/Lo... | vmendez/DIRAC | AccountingSystem/private/DataCache.py | Python | gpl-3.0 | 3,185 | [
"DIRAC"
] | acb12bee916c08d9d0aaff5e18b7714e6b7e2f5b882f6b4b33681ee96510886e |
#!/usr/bin/python
import httplib
import httplib2
import os
import random
import sys
import time
import datetime
from apiclient.discovery import build
from apiclient.errors import HttpError
from apiclient.http import MediaFileUpload
from oauth2client.client import flow_from_clientsecrets
from oauth2client.file import ... | 98pm/youtube_upload_timelapse | googleapi.py | Python | apache-2.0 | 6,705 | [
"VisIt"
] | bfc9500dcb8457d15681ec8012219826cf38ebee63810457e7edbe0cc671873a |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/nwchem/package.py | Python | lgpl-2.1 | 9,805 | [
"Amber",
"NWChem"
] | 94865184be5b966a9cb1a2eaddf2934fff917fa88661bbd1f41428955f7fc423 |
#
# @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/share/psi4/databases/HBC6.py | Python | lgpl-3.0 | 161,641 | [
"Psi4"
] | 5948e23c9b32f5973d608d2090c582d97ce6293b69a8f68f84e5210e9be3db60 |
# c: 20.03.2008, r: 20.03.2008
input_name = 'input/sinbc.py'
output_name = 'test_sinbc.vtk'
from testsBasic import TestInput
class Test( TestInput ):
pass
| certik/sfepy | tests/test_input_sinbc.py | Python | bsd-3-clause | 160 | [
"VTK"
] | 5c9a16b7aaa8098c18e405dd245654e6e3c8e94d188d5810c60689415c78a6f8 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/qcdb/periodictable.py | Python | gpl-2.0 | 78,237 | [
"CFOUR",
"Psi4"
] | 5c7d62e20d8e09ed89321746419f9a4e8499ed47336638e32cd1c8fa4c0d835b |
'''
Created on 03.06.2011
@author: Sergey Khayrulin
'''
from __future__ import absolute_import
from Entity.Vertex import Vertex
from Entity.Face import Face
from Entity.Slice import Slice, AlternateSlice
from Entity.Helper import *
import pprint
import math
class Entity(object):
'''
Main Clas... | openworm/Blender2NeuroML | src/Entity/Entity.py | Python | mit | 21,651 | [
"NEURON"
] | 5f14e763a721e6e792ede3b3b43f1e909f86f9b73e2a913d751eca8b1b167f76 |
"""
Test helper functions.
"""
import os
import uuid
from regression.pages.studio import LOGIN_BASE_URL
from regression.pages.studio.utils import get_course_key
from regression.pages.whitelabel.activate_account import ActivateAccount
from regression.pages.whitelabel.const import ORG, UNUSED_REGISTRATION_FIELDS_MAPPIN... | edx/edx-e2e-tests | regression/tests/helpers/utils.py | Python | agpl-3.0 | 8,374 | [
"VisIt"
] | 87965d704da4c2ba020f3a7f999db45737301439c29bdda4ce615a1c342a342c |
#===============================================================================
#
# CSR_T_P.py
#
# This file is part of ANNarchy.
#
# Copyright (C) 2016-2020 Julien Vitay <julien.vitay@gmail.com>,
# Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
#
# This program is free software: you can redis... | ANNarchy/ANNarchy | ANNarchy/generator/Projection/OpenMP/CSR_T_P.py | Python | gpl-2.0 | 5,813 | [
"NEURON"
] | 606ae2e8b627f6d3c9e9efb9c9c65656785df16ac82b8a203c56977d4cdc2c11 |
"""
@package AlignerSpliter
@brief ...
@copyright [GNU General Public License v2](http://www.gnu.org/licenses/gpl-2.0.html)
@author Adrien Leger - 2014
* <adrien.leger@gmail.com>
* <adrien.leger@inserm.fr>
* <adrien.leger@univ-nantes.fr>
* [Github](https://github.com/a-slide)
* [Atlantic Gene Therapies - INSERM 1089] (... | a-slide/IsFinder | src/ShortReadAligner_test.py | Python | gpl-2.0 | 2,322 | [
"BLAST",
"BWA"
] | 64fdb78aba5fd9f6c91eef0b263819d8e4e946d29fea7eee954c8c5b344e6228 |
#!/bin/env python
""" Show request given its ID, a jobID or a transformation and a task """
__RCSID__ = "$Id: $"
import datetime
def convertDate( date ):
try:
value = datetime.datetime.strptime( date, '%Y-%m-%d' )
return value
except:
pass
try:
value = datetime.datetime.utcnow() - datetime.timede... | Andrew-McNab-UK/DIRAC | RequestManagementSystem/scripts/dirac-rms-request.py | Python | gpl-3.0 | 8,432 | [
"DIRAC"
] | 73bb2682b333ad9ea2a4f666df66aded28fe2af1a1c91496e376db4828d94e13 |
"""
This transform turns calls to delay() that use non-integer time
expressed in seconds into calls to delay_mu() that use int64 time
expressed in multiples of ref_period.
It does so by inserting multiplication/division/rounding operations around
those calls.
The seconds_to_mu and mu_to_seconds core language function... | kgilmo/penning_artiq | artiq/transforms/quantize_time.py | Python | gpl-3.0 | 3,862 | [
"VisIt"
] | c62ff22acc13f1de03f4e0fdd070bf632ea2951336bf93843b263cb82e88f083 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | Mega-DatA-Lab/mxnet | python/mxnet/gluon/model_zoo/vision/vgg.py | Python | apache-2.0 | 9,401 | [
"Gaussian"
] | c7097eccb5ef6fee87bdac6b332bab0dd094660eb578a7f3736c0800d8207b71 |
#/*
# *
# * SimilarTracks for Kodi.
# *
# * Copyright (C) 2015 Brian Hornsby
# *
# * This program is free software: you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation, either version 3 of the License, or
# * (at your option) a... | brianhornsby/script.similartracks | default.py | Python | gpl-3.0 | 8,605 | [
"Brian"
] | 086db4f311c0420b5fe4e7462ac89fb382a37c821140356bd60d721af40a2ab5 |
try:
from setuptools import setup
except:
from disutils.core import setup
dependencies = ['docopt', 'ed25519', 'scrypt', 'py-notify']
setup(
name='sqrl',
version='0.1.0',
description='Command line SQRL client',
url='http://gitbub.com/bushxnyc/sqrl',
author='Brian Pinkney',
author_email... | bushxnyc/sqrl | setup.py | Python | mit | 792 | [
"Brian"
] | 909208b9ad20095bf3a72ac5b98d9fb6c1b259c40ad7079bd219f21a08afbd70 |
#!/usr/bin/env python
#
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requir... | Aloomaio/googleads-python-lib | examples/adwords/v201802/error_handling/handle_policy_violation_error.py | Python | apache-2.0 | 6,157 | [
"VisIt"
] | 31d965613cea413b5d2a1a840ff7ba4cd68bb1ec1c281aed4426475b455d1b34 |
'''
Created on Nov 12, 2014
@author: alucard
'''
import vtk
from SceneObject import SceneObject
from scene import MenuItem
class MenuItemController(SceneObject):
def __init__(self, botManager, roleManager, renderManager, parent, iren, menuName):
'''
Initialize the MenuItemController.
... | GearsAD/semisorted_arnerve | arnerve/scene/MenuItemController.py | Python | mit | 19,922 | [
"VTK"
] | 3d956bcf97e8bc9ffd692b651448de466daf7d6968258ba88200ab6c8caa7d02 |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2020 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permission to us... | bgoli/pysces | pysces/PyscesSBML.py | Python | bsd-3-clause | 30,871 | [
"PySCeS"
] | 87dbe47d17fa3aecbb3644da921c943700d6bd45631c0678168c99d1342ca01b |
__RCSID__ = "$Id$"
# FIXME: if it requires a dirac.cfg it is not a unit test and should be moved to TestDIRAC
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
import unittest
from DIRAC.Resources.Storage.StorageFactory import StorageFactory
class StorageFactoryTestCase( unittest.TestCase ):
... | coberger/DIRAC | Resources/Storage/test/TestStorageFactory.py | Python | gpl-3.0 | 3,495 | [
"DIRAC"
] | 9d9567d36c058dfd502adf92de8b1e847a34dd89f49ee66fd4636041c52f9921 |
from threading import Thread
from uiautomator import device as d
from ctx.generators.util import Adb
class Actuator:
def execute_in_background(self, recipe):
thread = Thread(target=self.execute, args=(recipe,))
thread.start()
def execute(self, recipe):
for action in recipe['action']:... | fmca/ctxpy | samples/ifctt/action.py | Python | mit | 1,939 | [
"ORCA"
] | 8eae861efe73c048cd93456d276bf09311d186e701cde95946f3235fe63ecf2a |
"""
Creates postage stamp, sigma-map, and psf image for each selected galaxy.
Also creates catalog of guess parameters for each stamp, to be used in AIM.
Input:
-Sextractor catalog name
-Cluster FITS image name (argv)
-psf name
-sextractor output file names
-Pixel scale
-Pixel size cutoff
Output:
-Postage stamp for ... | Jmt354/Cluster-Analysis | run.py | Python | gpl-3.0 | 9,809 | [
"Galaxy"
] | 61c0bde2f010350b20ac8314c91472dec670e56897369963f2077c0e396073bd |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ProcessPoolExecutor.
The follow diagram and text describe the data-flow through the system:
|======================= In-process =====================|== Out-of-process ==|
+----------+ +----------... | mikhtonyuk/rxpython | concurrent/executors/process.py | Python | mit | 17,649 | [
"Brian"
] | 598ead73a13665e28dc520bbd2484de99c2fa96fbf8b4a97704b6581d0d740d3 |
from base import Parser1
class Foo(Parser1):
def visit(self, foo):
return 'bar'
| sourcesimian/pyPlugin | tests/plugins1.py | Python | mit | 94 | [
"VisIt"
] | ccb82b5867cf56c32dec91d791b58dccbbd2fb3fa9cc519e71df50a7889be55d |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | thaim/ansible | lib/ansible/modules/network/avi/avi_applicationprofile.py | Python | mit | 7,960 | [
"VisIt"
] | fb9fa7b0eeff3a766bc757a6deccbd64224b3cffca479f94af955a186c3cda7f |
'''
Created on Jul 31, 2015
@author: sergio
'''
import numpy as np
import ctypes
import numpy.ctypeslib as npct
import matplotlib.pyplot as plt
import psycopg2
import time
import neurodb.neodb.core
from math import e, pow
from scipy.optimize import leastsq
import neurodb
import random
from sklearn.cluster import KMea... | sergiohr/NeuroDB | test/test_multi.py | Python | gpl-3.0 | 7,558 | [
"Gaussian"
] | b14af262722efd3a4ef2720d2d62addb6917387c2d73ec7ee03ea3288479f34a |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# . documentation build configuration file, created by
# sphinx-quickstart on Thu Mar 19 17:41:28 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogene... | havok2063/SciScript-Python | docs/sphinx/conf.py | Python | apache-2.0 | 10,668 | [
"Brian"
] | f07f86d8669a1176536a4cd0dd8d68b4a4ead2f07eb061762bafd2e6f9d7e104 |
###############################################################################
# Copyright 2015-2020 University of Florida. All rights reserved.
# This file is part of UF CTS-IT's NACCulator project.
# Use of this source code is governed by the license found in the LICENSE file.
#######################################... | ctsit/nacculator | nacc/lbd/v3_1/ivp/builder.py | Python | bsd-2-clause | 19,110 | [
"VisIt"
] | 1fe787a1df224efeb41b2d7adf95fd19ce4fbec058c599ba317c315e314a835e |
###############################################################################
##
## 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 | scripts/dist/mac/setup.py | Python | bsd-3-clause | 4,175 | [
"VTK"
] | 1a1a9d605773ebaa7d6d5fecf6f79aa4ac75942d00c7eea5aec70db99f516b9d |
from typing import TypeVar, Tuple, List, Callable, Generic, Type, Union, Optional, Any, cast
from abc import ABC
from .utils import combine_alternatives
from .tree import Tree, Branch
from .exceptions import VisitError, GrammarError
from .lexer import Token
###{standalone
from functools import wraps, update_wrapper
f... | lark-parser/lark | lark/visitors.py | Python | mit | 20,653 | [
"VisIt"
] | 1de477ec66fbd20494f52cc5d767bc91a7a5e84a65de730c8bd83bf2fd3bc794 |
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
AUTHORS
The original version of this software, called LMFIT, was written in FORTRAN
as part of the MINPACK-1 package by XXX.
Craig Markwardt converted the FORTRAN code to IDL. The informati... | cebarbosa/fossilgroups | ppxf/cap_mpfit.py | Python | gpl-3.0 | 93,623 | [
"Gaussian"
] | 08c57236d8b49a6748b00eff8434232a2140ee18600eb379440b7b16da1f28b2 |
# Python 2's Lib/test/test_grammar.py (r66189)
# Python test set -- part 1, grammar.
# This just tests whether the parser accepts them all.
# NOTE: When you run this test as a script from the command line, you
# get warnings about certain hex/oct constants. Since those are
# issued by the parser, you can't suppress ... | leighpauls/k2cro4 | third_party/python_26/Lib/lib2to3/tests/data/py2_test_grammar.py | Python | bsd-3-clause | 30,527 | [
"GULP"
] | 02716a2fff54c1b66ea7c47de9659a29288859e0123e23557824f10f9b9ba89a |
# -*- coding: utf-8 -*-
#
# one_neuron_with_sine_wave.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 t... | HBPNeurorobotics/nest-simulator | doc/nest_by_example/scripts/one_neuron_with_sine_wave.py | Python | gpl-2.0 | 1,514 | [
"NEURON"
] | ab5e7acc59faead2f3e01308febc753902050be33658d5ad8321054858e6f903 |
# 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 *
from glob import glob
class Bowtie2(Package):
"""Bowtie 2 is an ultrafast and memory-efficient t... | rspavel/spack | var/spack/repos/builtin/packages/bowtie2/package.py | Python | lgpl-2.1 | 3,666 | [
"Bowtie"
] | 2a4758a4b59dcbbde6876ffdcaeaf00db9e372fe3d1e2f6e7e54c15bd9f54a23 |
import numpy as np
class AdaptiveSpike(object):
def __init__(self, n_inputs, n_outputs, n_neurons,
seed=None, learning_rate=1e-3,
has_neuron_state=True, smoothing=0):
self.rng = np.random.RandomState(seed=seed)
self.compute_encoders(n_inputs, n_neurons)
se... | tcstewar/minimal_adaptive_controller | adapt_spike.py | Python | gpl-3.0 | 3,603 | [
"NEURON"
] | 50844a8d1b409add356934720b93fcca4cf0d152d6fe2a576366237681860284 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | npuichigo/ttsflow | third_party/tensorflow/tensorflow/tools/common/public_api.py | Python | apache-2.0 | 4,753 | [
"VisIt"
] | 9022a9851e172cdd88c886924635b70ef79349dd87f95524100f47879c06aec6 |
#!/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_command.py | Python | gpl-3.0 | 5,736 | [
"VisIt"
] | 29b9b5cdd8df222ce2b9046e075a6aed8231f68858a75be71ebcd532708c86bc |
from check_grad import check_grad
from utils import *
from logistic import *
import matplotlib.pyplot as plt
def run_logistic_regression(hyperparameters):
# TODO specify training data
train_inputs, train_targets = load_train_small()
valid_inputs, valid_targets = load_valid()
# N is number of example... | ouyangyike/Machine-Learning-and-Data-Mining | Logistic Regression/logistic_regression_template3.py | Python | mit | 3,373 | [
"Gaussian"
] | c52e8a0de8eefa8a5286587a31880cf3ac4010ed15f388f306a35c1c390607c1 |
# Copyright (C) 2006 CAMP
# Please see the accompanying LICENSE file for further information.
from math import pi, log, sqrt
import numpy as np
from gpaw.utilities import _fact
"""Fourier filtering
This module is an implementation of this Fourier filtering scheme:
*A general and efficient pseudopotential Fourier... | qsnake/gpaw | gpaw/atom/filter.py | Python | gpl-3.0 | 6,297 | [
"GPAW",
"Gaussian"
] | 2544739e677b251ce27eb0f672c81a90db09bd67baf3193abed0e50955dd4980 |
""" TransformationAgent processes transformations found in the transformation database.
"""
import time, re, random, Queue, os, datetime, pickle
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.AgentModule import AgentModu... | sposs/DIRAC | TransformationSystem/Agent/TransformationAgent.py | Python | gpl-3.0 | 26,019 | [
"DIRAC"
] | b51567e5ea73b029f931e70a27e66f15b3e050398c892062739dd20116a0ff28 |
#-------------------------------------------------------------------------------
# Name: LIST
# Purpose: Create/hold a list for Human Generator
#
# Author: Rivan
#
# Created: 10/03/2014
# Copyright: (c) Rivan 2015
# Licence: GNU GENERAL PUBLIC LICENSE.
#----------------------------------------... | Liaku/CharGen_Fantasy | Human_Generator_LIST.py | Python | gpl-2.0 | 12,932 | [
"Amber"
] | 2ba5bbcc02a6544ec09d9d2d89e0b44b01d5553b1cf093925e78aafdb7b3e31e |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-get-pilot-output
# Author : Ricardo Graciani
########################################################################
"""
Retrieve available info about the given pilot
"""
__RCSID__ = "$Id$"
# pyli... | arrabito/DIRAC | Interfaces/scripts/dirac-admin-get-pilot-info.py | Python | gpl-3.0 | 2,543 | [
"DIRAC"
] | b9c8d0a00a243a2efa8c4cb8f220595c9ee83f0284d2db8d5a66d771c9d05d1e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 22 13:22:26 2015
@author: agiovann
"""
from builtins import map
from builtins import zip
from builtins import str
from builtins import range
import cv2
import json
import logging
import matplotlib.pyplot as pl
import matplotlib.patches as mpatches... | simonsfoundation/CaImAn | use_cases/custom/rois_Hendrik.py | Python | gpl-2.0 | 50,709 | [
"Gaussian",
"NEURON"
] | 87fdeb88c971f9858f0938e31a0d5aeae178b83ae5e43ff6ccdb8115a52154b0 |
# Copyright 2012 by Eric Talevich. 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.
"""Command-line wrapper for the tree inference program RAxML.
Derived from the help page for RA... | zjuchenyuan/BioWeb | Lib/Bio/Phylo/Applications/_Raxml.py | Python | mit | 20,423 | [
"Biopython"
] | f1b9ac7f301e0825f107e0e14ed39fb0684b4b6976108c4682c35883117fe1ae |
"""
Some portions adapted from https://github.com/warner/python-ecdsa/ Copyright (c) 2010 Brian Warner
who granted its use under this license:
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 with... | ionux/bitforge | bitforge/utils/ecdsa.py | Python | mit | 6,139 | [
"Brian"
] | b98842fbf52c2e02706ae86ff25431b806320cfc679025c13cc643418e2432db |
import copy
import gc
import pickle
import sys
import unittest
import weakref
from test import support
class FinalizationTest(unittest.TestCase):
def test_frame_resurrect(self):
# A generator frame can be resurrected by a generator's finalization.
def gen():
nonlocal frame
... | technologiescollege/Blockly-rduino-communication | scripts_XP/Lib/test/test_generators.py | Python | gpl-3.0 | 55,570 | [
"VisIt"
] | ead5c366cba839c8b6fd753663fb2c67bc5c0eca8a938873c9ae16ddf71b0e37 |
from ..biotools import load_record
from ..GraphicRecord import GraphicRecord
from ..CircularGraphicRecord import CircularGraphicRecord
from ..GraphicFeature import GraphicFeature
class BiopythonTranslatorBase:
"""Base class for all BiopythonTranslators.
This class needs to be complemented with methods comput... | TAMU-CPT/galaxy-tools | tools/genome_viz/dna_features_viewer/BiopythonTranslator/BiopythonTranslatorBase.py | Python | gpl-3.0 | 4,482 | [
"Biopython"
] | 3862b6989f22a0984338a2716a4a4faca0da7ea2e805be92f16557cd5bd5e1dc |
# -*- coding: utf-8 -*-
"""
Authors: Gonzalo E. Espinoza-Dávalos
IHE Delft 2017
Contact: g.espinoza@un-ihe.org
Repository: https://github.com/gespinoza/waterpix
Module: waterpix
"""
import os
import arcpy
import netCDF4
def output_nc_to_tiffs(output_nc, output_path):
"""
Create raster files from the... | wateraccounting/wa | Models/waterpix/wp_arcpy/output_nc_to_tiffs.py | Python | apache-2.0 | 3,744 | [
"NetCDF"
] | cba582d9ab5333495a1859b76aca284a2f43991180bef64b9b57026de011916c |
"""Identify program versions used for analysis, reporting in structured table.
Catalogs the full list of programs used in analysis, enabling reproduction of
results and tracking of provenance in output files.
"""
import os
import contextlib
import subprocess
import sys
import yaml
import toolz as tz
from bcbio import... | biocyberman/bcbio-nextgen | bcbio/provenance/programs.py | Python | mit | 11,886 | [
"BWA",
"Bioconductor",
"Galaxy",
"HTSeq"
] | 75c9ec50fb97d449ce1c3461db01e4edab1f255e926ab2200e5730d66bd9bd1d |
# -*- coding: utf-8 -*-
"""Connection configuration for PyBEL."""
import logging
import pystow
__all__ = [
"connection",
"PYBEL_MINIMUM_IMPORT_VERSION",
"PYBEL_HOME",
]
logger = logging.getLogger(__name__)
#: The last PyBEL version where the graph data definition changed
PYBEL_MINIMUM_IMPORT_VERSION =... | pybel/pybel | src/pybel/config.py | Python | mit | 745 | [
"Pybel"
] | 61e05d46d23ebe8fdeee7a4a0ed03affd23c3b8e6570a45fd832375b5baf9ead |
#!/usr/bin/env python
"""Phylotyper program main
Script for running various phylotyper functions
Examples:
To run subtyping routine on Stx1 genes:
$ python -m phylotyper subtype stx1 test/ecoli_stx1.ffn
"""
import argparse
import csv
import logging
import os
import pprint
import pkg_resources
import... | superphy/insilico-subtyping | phylotyper/run.py | Python | apache-2.0 | 35,621 | [
"BLAST"
] | ca2f2f0aa1a2f63f82b7855603bdfb4836eef799785933cb2979aa95a6c0513d |
#!/usr/bin/env python
#Processes uploads from the user.
# WARNING: Changes in this tool (particularly as related to parsing) may need
# to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools
import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile, codecs, binascii
from galaxy import eggs
# n... | volpino/Yeps-EURAC | tools/data_source/upload.py | Python | mit | 14,047 | [
"Galaxy"
] | 60b19cee33979a6e66797e0c3ceaba3ee106c30f3de23e2ef7131dc65bd51f8f |
# -*- coding: utf-8 -*-
"""
Created on Thu May 7 19:32:22 2015
@author: sternc1
"""
import pandas as pd
import numpy as np
import simtk.openmm as mm
import simtk.unit as u
import mdtraj as md
from copy import copy, deepcopy
import re
from cclib.parser import Gaussian
from cclib.parser.utils import convertor
from mdt... | hainm/Torsions | torsions/TorsionScanSet.py | Python | gpl-2.0 | 10,496 | [
"CHARMM",
"Gaussian",
"MDTraj",
"OpenMM",
"cclib"
] | 881ad348bca2655f21f1970b42bb2745df15cd52ce3b22d43ba35be9c14ed617 |
from __future__ import print_function
from __future__ import division
import os, sys
import csv
import unittest
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
from types import *
import math
import shutil
import pickle
import numpy as np
import zipfile
import json
import subproc... | pdedumast/ShapeVariationAnalyzer | ShapeVariationAnalyzer/ShapeVariationAnalyzer.py | Python | apache-2.0 | 106,269 | [
"VTK"
] | ef91f26cb93729162386a28b8527d3f98990fb6d416bfed481e75c3f6c6bb979 |
#!/usr/bin/env python
## Reads and manipulates Ed's galaxy property catalogs
## Requires pyfits, astLib
## sphe spehmakh@gmail.com
# import python essentials
import os
import sys
import time
import numpy as np
import math
import tempfile
import subprocess
# non-standard packages
import pyfits
from astLib.astWCS impor... | SpheMakh/HI-Inator | src/galProps.py | Python | gpl-2.0 | 6,783 | [
"Galaxy"
] | 2980ac5a51c183dabe1a4d4350b489a1ad909503797892f8b4dc878504be26d0 |
#!/usr/bin/env python3
#
# BIP39 English wordlist
# Source: https://github.com/bitcoin/bips/blob/master/bip-0039/english.txt
words = tuple("""
abandon
ability
able
about
above
absent
absorb
abstract
absurd
abuse
access
accident
account
accuse
achieve
acid
acoustic
acquire
across
act
action
actor
actress
actual
adapt
a... | mmgen/mmgen | mmgen/wordlist/bip39.py | Python | gpl-3.0 | 13,273 | [
"BLAST",
"CASINO",
"CRYSTAL",
"Galaxy",
"Jaguar",
"VisIt"
] | 783ca8977662ec094729549b91452577b4da6c5beb55cd4b0a9c6a7593bc8fee |
""" Test for StorageManagement clients
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=protected-access,missing-docstring,invalid-name
import unittest
from mock import MagicMock, patch
from DIRAC import S_OK, S_ERROR
from DIRAC.Storag... | ic-hep/DIRAC | src/DIRAC/StorageManagementSystem/Client/test/Test_Client_StorageManagementSystem.py | Python | gpl-3.0 | 8,286 | [
"DIRAC"
] | 3d7a4d472a055ac50c2dd4c40b5c60b5e893757a9f56181c14eddbd4d73a3f85 |
########################################################################
# File : ComputingElement.py
# Author : Stuart Paterson, A.T.
########################################################################
""" The Computing Element class is a base class for all the various
types CEs. It serves several purpos... | andresailer/DIRAC | Resources/Computing/ComputingElement.py | Python | gpl-3.0 | 19,133 | [
"DIRAC"
] | 004b16ef32b37f5edc914ec29527b91c928b743112043616036efd82eadd2a28 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | frreiss/tensorflow-fred | tensorflow/python/ops/linalg/linear_operator_test_util.py | Python | apache-2.0 | 44,656 | [
"Gaussian"
] | 7d1a35ebc83676927aa8fe809bf258ffd7e5649dccfc3657848e8e8cdcf76a03 |
# Copyright 2006 by Sean Davis. 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.
#
# $Id: __init__.py,v 1.12 2009-04-24 12:03:45 mdehoon Exp $
# Sean Davis <sdavis2 at mail dot ni... | zjuchenyuan/BioWeb | Lib/Bio/UniGene/__init__.py | Python | mit | 12,357 | [
"Biopython"
] | d902f277fcaa232168baa0684e1cd0216c665ac272d7e7f04cdfbbdda1903898 |
from unittest.mock import ANY, Mock, call
import pytest
from flask import url_for
from freezegun import freeze_time
from notifications_python_client.errors import HTTPError
import app
from tests import service_json
from tests.conftest import (
SERVICE_ONE_ID,
create_active_caseworking_user,
create_active_... | alphagov/notifications-admin | tests/app/main/views/test_accept_invite.py | Python | mit | 27,419 | [
"VisIt"
] | bc93e30f88e2f6bff0ee3b044af9345598097c77c2bb9cd99bf52e3aeaf2ebb5 |
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