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#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2005-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012 Gary Burton
# Copyright (C) 2... | sam-m888/gramps | gramps/gui/viewmanager.py | Python | gpl-2.0 | 69,729 | [
"Brian"
] | cde72f2af4c3fd7aa71276e335ccd453c8b01bc823436987a6ff513c5babf1b5 |
import re
import ast
import sys
try:
from distutils.util import get_platform
is_windows = get_platform().startswith("win")
except ImportError:
# Don't break install if distuils is incompatible in some way
# probably overly defensive.
is_windows = False
try:
from setuptools import setup
except I... | jmchilton/pulsar | setup.py | Python | apache-2.0 | 3,694 | [
"Galaxy"
] | ebde0c90b3620fba8b80eb019b0e4650d77195dc6f4a84a2997aa5ec745f3a12 |
""" pycontact setup
by Maximilian Scheurer, Peter Rodenkirch
"""
from setuptools import setup, find_packages
from setuptools.extension import Extension
from Cython.Distutils import build_ext
from Cython.Build import cythonize
extensions = [Extension("PyContact.cy_modules.cy_gridsearch",
["PyCo... | maxscheurer/pycontact | setup.py | Python | gpl-3.0 | 2,253 | [
"MDAnalysis"
] | 5fb529c06e183957d7c7afc88370e3406609332789cb3eed7b79bf3c04676172 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import os
from pymatgen.io.feff.sets import FeffInputSet
from pymatgen.io.feff import FeffPot
from pymatgen.io.cif import CifParser
test_dir = os.path.... | migueldiascosta/pymatgen | pymatgen/io/feff/tests/test_sets.py | Python | mit | 2,669 | [
"FEFF",
"pymatgen"
] | 3ad1ce482cc10e599aa2a99ea1e96dbe9fde8e199028db05256d53924aa3d89b |
import unittest
from ase.io import read
from ase.calculators.emt import EMT
from geometricmd.curve_shorten import convert_vector_to_atoms, length, get_rotation
import math
import numpy as np
from scipy.optimize import check_grad
# Check length can be computed
def check_length(total_number_of_points):
try:
... | suttond/GeometricMD | tests/test_length.py | Python | lgpl-3.0 | 3,310 | [
"ASE"
] | 72d0e30d9019cc29c48b6c3efe3ef0d6016b87f80a310e1e528da462a6dda147 |
class ExampleCtrl(object):
"""Mealy transducer.
Internal states are integers, the current state
is stored in the attribute "state".
To take a transition, call method "move".
The names of input variables are stored in the
attribute "input_vars".
Automatically generated by tulip.dumpsmach o... | GaloisInc/planning-synthesis | examples/sitl_client/democontroller1.py | Python | bsd-2-clause | 36,424 | [
"VisIt"
] | f449f3a4ad9ccdecc0272298599a40b36353300a48d8b70e66bb6415b417c531 |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2008 Jan Decaluwe
#
# The myhdl 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 t... | cordoval/myhdl-python | myhdl/_extractHierarchy.py | Python | lgpl-2.1 | 12,586 | [
"VisIt"
] | dd820d639d48be45b1176499ac6e8ee7a9f4673bf4c0719a5bcd7007ebe4dde6 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/driver/qcdb/dbwrap.py | Python | lgpl-3.0 | 174,502 | [
"Gaussian",
"Psi4",
"PyMOL"
] | 78ee65e48b03ae4950f9e283584827ffe9cc468d6fb1b1256324bfd74f8dedc9 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Unit tests for moldenwriter module."""
import os
import unittest
import cclib
from cclib.io.filewriter import Missing... | gaursagar/cclib | test/io/testmoldenwriter.py | Python | bsd-3-clause | 5,052 | [
"GAMESS",
"cclib"
] | 739d71037b62b972b60efcdea151c0a73d76d3275ae06fc4ba0b4f594b10730f |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/core/test_residue.py | Python | gpl-2.0 | 2,055 | [
"MDAnalysis"
] | f5f267090a93988ab14125a773a51d77f96e5de24d9d9ebad6f0a5816e17c242 |
# -*- coding: utf-8 -*-
# Copyright 2020 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 o... | googleapis/python-vision | scripts/fixup_vision_v1_keywords.py | Python | apache-2.0 | 7,242 | [
"VisIt"
] | ea5b7b3200e3857331195514466f8626e3ab42a37d8b5136a6b1c9a4431803ac |
import numpy.random as random
import numpy as np
from ase import Atoms
from ase.calculators.neighborlist import NeighborList
from ase.lattice import bulk
atoms = Atoms(numbers=range(10),
cell=[(0.2, 1.2, 1.4),
(1.4, 0.1, 1.6),
(1.3, 2.0, -0.1)])
atoms.set_scaled_po... | suttond/MODOI | ase/test/neighbor.py | Python | lgpl-3.0 | 2,402 | [
"ASE"
] | fa3dde27298f06f5027ac97d763d390854412f7e6092dd7f47a113c2fda20848 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2008 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/slaves/paymentslave.py | Python | gpl-2.0 | 60,870 | [
"VisIt"
] | a02c0450bf0f0531b45475e1001e6033bc8439376ead0bcbc6efb396a256c406 |
from .._transcripts.transcript_base import TranscriptBase, Metric
from ..configuration.configuration import MikadoConfiguration
from ..configuration.daijin_configuration import DaijinConfiguration
from .transcript_methods import splitting, retrieval
from typing import List
from ..serializers.blast_serializer import Hit... | lucventurini/mikado | Mikado/transcripts/transcript.py | Python | lgpl-3.0 | 6,271 | [
"pysam"
] | e6f3b86dbaf0ee0156ba53cf18894f6945efb31e511dbbc500cc371dc64bd9f0 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import subpr... | nuclear-wizard/moose | python/TestHarness/tests/test_UnknownParam.py | Python | lgpl-2.1 | 726 | [
"MOOSE"
] | ff31f60f201495a04181f1ca69620771fe7090e3e6455c17558419eb306c0a75 |
# Generated by Django 2.1.5 on 2019-02-01 12:51
from django.conf import settings
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
dependencies = [
('activity_statistic', '0002_auto_20190201_1249'),
]
operations = [
migratio... | linea-it/dri | api/activity_statistic/migrations/0003_auto_20190201_1251.py | Python | gpl-3.0 | 827 | [
"VisIt"
] | d81f66df1f3c0ea03b9549d1cb2eacfbcce85fa722a6a91ab9d837054113b4b3 |
from pyPEG import *
import re
import types
_ = re.compile
class ParserError(Exception):pass
class WorkflowGrammar(dict):
def __init__(self):
peg, self.root = self._get_rules()
self.update(peg)
def _get_rules(self):
# 0 ?
# -1 *
# -2 +
#basic
de... | uliwebext/uliweb-redbreast | redbreast/core/spec/parser.py | Python | bsd-2-clause | 10,265 | [
"VisIt"
] | 2f854b2306317de10f406640d277fafdf38de5838ae594e20ec2567adb8297be |
#!/usr/bin/env python
#author: wowdd1
#mail: developergf@gmail.com
#data: 2014.12.07
from spider import *
sys.path.append("..")
from utils import Utils
from record import Record
class GithubSpider(Spider):
lang_list = [
"C",
"C++",
"C#",
"Clojure",
"CoffeeScript",
... | roscopecoltran/scraper | .staging/meta-engines/xlinkBook/update/update_github.py | Python | mit | 26,016 | [
"CRYSTAL"
] | 542065253fad5e3fdc55e6421ee4bd4b71d53ee10f3262e89369ca5e941ea4e7 |
# ******************************************************************************
# Copyright 2017-2018 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.apa... | NervanaSystems/neon | tests/test_gradient_conv.py | Python | apache-2.0 | 4,573 | [
"Gaussian"
] | 0a0613fc5ff05d692f0c6df1dbc8565861b2f9f801eaee4618a5f8f4777ea24e |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
#
# Copyright (C) 2020 Stoq Tecnologia <http://www.stoq.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 Software Foundation;... | stoq/stoq-server | stoqserver/utils.py | Python | gpl-2.0 | 1,629 | [
"VisIt"
] | 26248a5d2845cafefabcee7ad1ecb0c82857b7b3f0da491abc2a66045f2aa083 |
'''
This module contains the one-parameter exponential families used
for fitting GLMs and GAMs.
These families are described in
P. McCullagh and J. A. Nelder. "Generalized linear models."
Monographs on Statistics and Applied Probability.
Chapman & Hall, London, 1983.
'''
from nipy.fixes.scipy.stats.models... | yarikoptic/NiPy-OLD | nipy/fixes/scipy/stats/models/family/__init__.py | Python | bsd-3-clause | 409 | [
"Gaussian"
] | 7e96c07952af403a8009d23b0cf39481b067e0a843be53db40b87fae492c278a |
from __future__ import print_function
import sys
from copy import deepcopy
# kills the program when you hit Cntl+C from the command line
import signal
signal.signal(signal.SIGINT, signal.SIG_DFL)
from six import string_types
from pyNastran.gui.qt_version import qt_version
if qt_version == 4:
from PyQt4 import Qt... | saullocastro/pyNastran | pyNastran/gui/menus/results_sidebar.py | Python | lgpl-3.0 | 12,414 | [
"ADF"
] | f82508a9a4184182b866681a16333060ed3e02da8aa1686c64d0017709d3476e |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ---------------------... | anderspitman/scikit-bio | setup.py | Python | bsd-3-clause | 4,877 | [
"scikit-bio"
] | bd244aea61eb4acb7635f7a4f15ef44fce9502a290206ae003d4d5a4d7a3d353 |
#!/usr/bin/python
import os
import json
import urllib
import subprocess
import sys
url_base = "http://admin.ci.centos.org:8080"
api_key = os.environ['API_KEY']
count = os.environ['MACHINE_COUNT'] if os.environ.get('MACHINE_COUNT') != None else "1"
ver = "7"
arch = "x86_64"
req_url = "%s/Node/get?key=%s&ver=%s&arch=%s... | budhrg/vagrant-service-manager | .ci/jenkins-execute-script.py | Python | gpl-2.0 | 3,174 | [
"CDK"
] | b2e9d0e5f53b16792b2efae65640a37311b41b0f8deabbdac1aaf0cf47fb49a3 |
##############################################################################
# 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/elk/package.py | Python | lgpl-2.1 | 5,721 | [
"Elk"
] | a95b3e0f40e920d8ec1dcddc16ba83fdf4432d62218f598239b8cde446439655 |
# These tests don't work at the moment, due to the security_groups multi select not working
# in selenium (the group is selected then immediately reset)
from textwrap import dedent
import pytest
from riggerlib import recursive_update
from widgetastic_patternfly import CheckableBootstrapTreeview as Check_tree
from cfm... | izapolsk/integration_tests | cfme/tests/cloud_infra_common/test_provisioning.py | Python | gpl-2.0 | 26,237 | [
"VisIt"
] | e4853e74316187cc537f3b1d454db1e5e17b7bb5f84fc04a7c8967d915f2f162 |
"""
aRMSD log functions
(c) 2017 by Arne Wagner
"""
# Authors: Arne Wagner
# License: MIT
from __future__ import absolute_import, division, print_function
from builtins import range, input
try:
import numpy as np
except ImportError:
pass
class Logger(object):
""" An object used ... | armsd/aRMSD | armsd/alog.py | Python | mit | 77,989 | [
"Pybel",
"VTK"
] | 7a219d80e64458b499f6f6d88fd85c38a390b9936366bbc672ef97084056b3ad |
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# Licence: BSD 3 clause
from __future__ import print_function
import numpy as np
from scipy import linalg, optimize
from sklearn.base import BaseEstimator, RegressorMixin
from skl... | dwettstein/pattern-recognition-2016 | mlp/gaussian_process/gaussian_process.py | Python | mit | 35,002 | [
"Gaussian"
] | 887d9e75b6555a0ed41ab2c892ea8d5e19e4bb8b5b5eb025e9c95fb45ce05e51 |
from django.test import TestCase
from django.utils import timezone
from django.contrib.auth.models import User
from txtalert.apps.therapyedge.importer import Importer, SEX_MAP
from txtalert.apps.therapyedge.xmlrpc import client
from txtalert.core.models import Patient, MSISDN, Visit, Clinic
from txtalert.apps.therapyed... | praekelt/txtalert | txtalert/apps/therapyedge/tests/importer.py | Python | gpl-3.0 | 28,383 | [
"VisIt"
] | 86ba841b701e16a6d38ce1e95a1d5b259f5e6fbbcece2eeda398f891670ab86b |
#!/usr/bin/env python
"""
MHC Epitope analysis
Created September 2013
Copyright (C) Damien Farrell
"""
import sys, os, shutil, string, types
import csv, glob, pickle, itertools
import re
import time, random
from collections import OrderedDict
from operator import itemgetter
#import matplotlib
#matplotlib.... | dmnfarrell/epitopemap | modules/mhcpredict/analysis.py | Python | apache-2.0 | 12,607 | [
"BLAST"
] | 62080254679aadb7f394d02578c1bb5ff1341feea01e0e9220be8b75bed57361 |
from __future__ import absolute_import
import cython
cython.declare(PyrexTypes=object, Naming=object, ExprNodes=object, Nodes=object,
Options=object, UtilNodes=object, LetNode=object,
LetRefNode=object, TreeFragment=object, EncodedString=object,
error=object, warning=object... | hhsprings/cython | Cython/Compiler/ParseTreeTransforms.py | Python | apache-2.0 | 117,668 | [
"VisIt"
] | dab751da703a425f9c2127dcfe92e0f1389cebb41f4bc822262729526a25f2c1 |
'''
Created on Oct 12, 2015
@author: Aaron Klein
'''
import logging
import george
import numpy as np
from scipy import optimize
from copy import deepcopy
from robo.models.base_model import BaseModel
logger = logging.getLogger(__name__)
class GaussianProcess(BaseModel):
def __init__(self, kernel, prior=None,... | aaronkl/RoBO | robo/models/gaussian_process.py | Python | bsd-3-clause | 8,620 | [
"Gaussian"
] | 6483c580b2a15b373cafd06a7468866d972542d716628fa802ae080aefd4f81a |
#!/usr/bin/python3
#-*- coding:utf-8 -*-
'''
main part
'''
import asyncio
import sys
from itertools import zip_longest
from collections import namedtuple
import traceback
import aiohttp
from .taskqueue import TaskQueue, makeTask
from .log import logging
DEFAULT_HEADER = {'user-agent': 'Mozilla/5.0 (X11; Linux x86_6... | HeartUnchange/aiospider | aiospider/spider.py | Python | mit | 11,168 | [
"VisIt"
] | cf42b0f0ca544ac2fee28bf5f9394ca3b929bec18fec70f38850917d6a0b39d2 |
# RoboControl.py
# Contains class for connecting to a scenery robot network and send data as a thread-based class
# Version - 0.1
# Author - Brian Nguyen
# Requires Python 2.7
# Requires XInputJoystick library
import sys
import time
import threading
from collections import deque
from xinput import XInputJoystick
from ... | b-nguyen/scenery-robot | RoboControl.py | Python | mit | 5,566 | [
"Brian"
] | 2de7d58528f4699839a8b806964dcae6968846c03fcf16a6a56d269b0cf84f87 |
# -*- coding: utf-8 -*-
'''
Pupil Player Third Party Plugins by cpicanco
Copyright (C) 2016 Rafael Picanço.
The present file is distributed under the terms of the GNU General Public License (GPL v3.0).
You should have received a copy of the GNU General Public License
along with this program. If not, see <ht... | cpicanco/player_plugins | filter_opencv_adaptative_threshold.py | Python | gpl-3.0 | 3,542 | [
"Gaussian"
] | d083063ef78fff283a775d25d075a9ad4bd5794a6b74cbc930fc673dc89d0ce6 |
# Copyright (C) 2013 Ben Morris (ben@bendmorris.com)
# based on code by Eric Talevich (eric.talevich@gmail.com)
# 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.
"""Classes corresponding to NeXML trees.... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Phylo/NeXML.py | Python | gpl-2.0 | 1,219 | [
"Biopython"
] | 7d5bd08dabd23685fc4ac941eca3bf4ee675d248cc764384acb7f52d39d86fbf |
#!/usr/bin/env python
"""
Rotate shape
"""
from __future__ import print_function
import argparse
import time
import sys
import re
from icqsol.shapes.icqShapeManager import ShapeManager
from icqsol import util
# time stamp
tid = re.sub(r'\.', '', str(time.time()))
parser = argparse.ArgumentParser(description='Trans... | gregvonkuster/icqsol | examples/rotateShape.py | Python | mit | 1,899 | [
"VTK"
] | c06e4b9a1103cacd3fcef800a2d13511227ca985e4daa5a460064103ff089703 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import collections
import numpy as np
from pymatgen.core.lattice import Lattice
from pymatgen.core.periodic_table import Element, Specie, DummySpecie,\
ge... | xhqu1981/pymatgen | pymatgen/core/sites.py | Python | mit | 18,993 | [
"pymatgen"
] | 6fef8486ebe0a7c18b62ff7ce0b847cfe35b8632be24d039022923037798661b |
# This program reads a file representing web server logs in common log format and streams them into a PubSub topic
# with lag characteristics as determined by command-line arguments
import argparse
from google.cloud import pubsub_v1
import time
from datetime import datetime, timezone
import random
from anytree.importe... | GoogleCloudPlatform/training-data-analyst | quests/dataflow_python/streaming_event_generator.py | Python | apache-2.0 | 7,257 | [
"VisIt"
] | baa3fb964f6a1fdec70b83c147731f2860a2fc32fea4149381de762a1c3f7940 |
from selenium import webdriver
from torProfile import TorProfile
import selenium
import subprocess
import os
import signal
import time
import sys
import random
sleep_time = 5.0
browse_time = 120.0 # TODO: Find good value. 2 minutes?
load_timeout = 120.0
iface = "eth1"
dump_path = "PatternDumps"
urls = ["http://cbsne... | chhans/tor-automation | patterncapture.py | Python | mit | 3,938 | [
"VisIt"
] | 63dc1946202554c5359ed0fac15217846482687b5fd046142309eb78ab32c4f4 |
# encoding: utf-8
"calculator.py - module for choosing a calculator."
import gtk
from gettext import gettext as _
import os
import numpy as np
from copy import copy
from ase.gui.setupwindow import SetupWindow
from ase.gui.progress import DefaultProgressIndicator, GpawProgressIndicator
from ase.gui.widgets import pack,... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/gui/calculator.py | Python | gpl-2.0 | 80,415 | [
"ASE",
"CRYSTAL",
"FHI-aims",
"GPAW",
"VASP"
] | 8199c57ac222a28dc4625727830124cb2412d5903f2b13db198227a3f5c3fe79 |
#
# This file is part of the statismo library.
#
# Author: Marcel Luethi (marcel.luethi@unibas.ch)
#
# Copyright (c) 2011 University of Basel
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# ... | zarquon42b/statismo | modules/VTK/wrapping/tests/statismoTests/TestDataManager.py | Python | bsd-3-clause | 5,716 | [
"VTK"
] | ef1f2a6dd7e632ea92275210dc17d5c1185285592772ca81c4879261b8a36ae7 |
#
# Copyright (C) 2009, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# 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 requi... | litlpoet/rl-library | projects/packages/examples/mines-sarsa-python/sample_mines_environment.py | Python | apache-2.0 | 7,218 | [
"Brian"
] | 8931f85be10c0e72ca8707602cd3fd65348b978ef2fd6818761977b7cf3da47a |
"""IPyMOL: View and control your PyMOL sessions from the IPython Notebook"""
import sys
from setuptools import setup, find_packages
from ipymol import __name__, __version__
NAME = __name__
VERSION = __version__
def read(filename):
import os
BASE_DIR = os.path.dirname(__file__)
filename = os.path.join(BAS... | cxhernandez/ipymol | setup.py | Python | mit | 2,190 | [
"PyMOL"
] | 5c62de7cd99203403ecddc806667d14df42ca26ef4aceaa4757bff9b0c71edf2 |
'''
This class processes the neural activity output from a Nengo model,
where the information has been saved to file using the numpy.savez or
numpy.savez_compressed method. It is assumed that the simulation was
run with 1ms timestep.
The data is read in and binned into bin_size ms windows to get firing
rates, then is ... | studywolf/REACH-paper | analysis/utils/process_spikes.py | Python | gpl-3.0 | 4,016 | [
"Gaussian"
] | 57acc17f29e09167b7eccf0d45ca41b7a51aa7ddc40d85cfd047f7c62a8bc1d2 |
"""
.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
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.... | Multiscale-Genomics/mg-process-fastq | tests/test_pipeline_idamidseq.py | Python | apache-2.0 | 10,827 | [
"BWA"
] | e541c965e782a6633b7dccf3b377ad24f4c4c66ff4771be99b7fb601c2033e48 |
# -*- coding: utf-8 -*-
#
# brunel_delta_nest.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 Licen... | lekshmideepu/nest-simulator | pynest/examples/brunel_delta_nest.py | Python | gpl-2.0 | 11,657 | [
"NEURON"
] | c4fe4e0f3ca7a89996c815fa35e45aa207ab16948119dcaf39f8d6e3f255e226 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/media/lib/mediaitem.py | Python | gpl-2.0 | 15,388 | [
"Brian"
] | 217ebc2d78ebb69270970d717645c6f7e183eff14f921a6cd9a3dbde1ab14fe7 |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | devel/external/calculate_moffat_radii.py | Python | gpl-3.0 | 2,440 | [
"Galaxy"
] | d8d40f7cb62d36a23e5a0b92ad1dc79afc4d37ccd4af0bb22ab7675297eb9cf9 |
import COPASI
import sys
dm = COPASI.CRootContainer.addDatamodel()
assert (isinstance(dm, COPASI.CDataModel))
def print_group(label, group):
# type: (str, COPASI.CModelParameterGroup) -> None
""" This function takes a parameter group and prints it"""
print (label)
for i in range(group.size()):
... | jonasfoe/COPASI | copasi/bindings/python/examples/print_model_parameterset.py | Python | artistic-2.0 | 3,153 | [
"COPASI"
] | 1bf5a396c797be0b873f3ed8d0d9a54e5f498f41b47289fa5bab856e31587640 |
""" Class defining a production step """
__RCSID__ = "$Id$"
import json
from DIRAC import S_OK, S_ERROR
class ProductionStep(object):
""" Define the Production Step object
"""
def __init__(self, **kwargs):
""" Simple constructor
"""
# Default values for transformation step parameters
self.N... | fstagni/DIRAC | ProductionSystem/Client/ProductionStep.py | Python | gpl-3.0 | 2,042 | [
"DIRAC"
] | 7d3b100b0ec057081bb147dada5632269be39480252c0d03a6c892fc29b4ff3f |
"""
This module handles initial database propagation, which is only run the first
time the game starts. It will create some default channels, objects, and
other things.
Everything starts at handle_setup()
"""
import time
from django.conf import settings
from django.utils.translation import gettext as _
from evennia.... | jamesbeebop/evennia | evennia/server/initial_setup.py | Python | bsd-3-clause | 7,807 | [
"VisIt"
] | 65505c9c44f4adf00c9071529952150c03544603ee85e6b8ea73ea51baad8f4b |
# -*-python-*-
#
# Copyright (C) 1999-2006 The ViewCVS Group. All Rights Reserved.
#
# By using this file, you agree to the terms and conditions set forth in
# the LICENSE.html file which can be found at the top level of the ViewVC
# distribution or at http://viewvc.org/license-1.html.
#
# For more information, visit h... | foresthz/fusion5.1 | www/scm/viewvc/lib/popen.py | Python | gpl-2.0 | 10,509 | [
"VisIt"
] | 3016bbc6f6deb931ef5fffc4d7f618155e1cb8973e602a70098d75cf5230217a |
'''
'''
from __future__ import print_function
import shutil
from os.path import dirname, exists, join, realpath, relpath
import os, re, subprocess, sys, time
import versioneer
# provide fallbacks for highlights in case colorama is not installed
try:
import colorama
from colorama import Fore, Style
def ... | percyfal/bokeh | _setup_support.py | Python | bsd-3-clause | 15,547 | [
"GULP"
] | 106e01b11f649f0f0e0b231dd65eef0d83e33b26e5908871aab946cfc459ea35 |
""" DIRAC JobDB class is a front-end to the main WMS database containing
job definitions and status information. It is used in most of the WMS
components
The following methods are provided for public usage:
getJobAttribute()
getJobAttributes()
getAllJobAttributes()
getDistinctJobAttributes... | chaen/DIRAC | WorkloadManagementSystem/DB/JobDB.py | Python | gpl-3.0 | 70,102 | [
"DIRAC"
] | 867aa07137d16a5d5b1a9608b1c227a9e1681effce870b61697f62a6339b9a11 |
import logging
import re
from . import utils
#######################################################################################################################
# PUBLIC FUNCTIONS
#######################################################################################################################
def nifti2db... | LREN-CHUV/mri-meta-extract | data_tracking/nifti_import.py | Python | apache-2.0 | 5,700 | [
"VisIt"
] | c210210abe4ebe51ff824cb14ed7011be5401b8d57aac1e0766c88d0c072af31 |
../../../../share/pyshared/orca/outline.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/outline.py | Python | gpl-3.0 | 42 | [
"ORCA"
] | 4d562f0659105e59fcf111ca891246be8f38b3a7597c3d05d913a5b52a8d5614 |
#! /usr/bin/env python
# Formatting note: this file's maximum line length is 128 characters.
# TODO: Python 2.x/3.x compatibility
from multiprocessing import Process, Queue as mpQueue
from itertools import count, takewhile
from functools import reduce
from random import randrange
from math import log
def isqrt(n):
... | goulu/Goulib | Goulib/primefac.py | Python | lgpl-3.0 | 34,617 | [
"Gaussian"
] | ed020f1dd8315324aa776b6e0980f24a966ab4448c293324ba218c508e9b27eb |
""" BHMM: A toolkit for Bayesian hidden Markov model analysis of single-molecule trajectories.
This project provides tools for estimating the number of metastable states, rate
constants between the states, equilibrium populations, distributions
characterizing the states, and distributions of these quantities from
sing... | jchodera/bhmm | setup.py | Python | lgpl-3.0 | 5,373 | [
"Gaussian"
] | 156e14baa433f7c55e28445633647347c6f34c5275006c655f2f5b13f6afabaf |
# -*- coding: utf-8 -*-
#
# rate_neuron_dm.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 License,... | terhorstd/nest-simulator | pynest/examples/rate_neuron_dm.py | Python | gpl-2.0 | 5,547 | [
"NEURON"
] | ac5af906fc0ad06dfd8fd71035c3dbc6b95aeec48e1d158155e67f2bbef37e27 |
import sys
import os
import pytest
sys.path.insert(0, os.path.abspath('../../'))
from SeqFindr import blast
from SeqFindr import config
from SeqFindr import imaging
from SeqFindr import seqfindr
from SeqFindr import util
from SeqFindr import vfdb_to_seqfindr
| nbenzakour/SeqFindR | tests/unittests/context.py | Python | apache-2.0 | 261 | [
"BLAST"
] | f8446e2955dce477f813553dc6f3c9f82e41695565ecfcde3a6f9847034bb94e |
#!/usr/bin/env python
'''
Quantile regression model
Model parameters are estimated using iterated reweighted least squares. The
asymptotic covariance matrix estimated using kernel density estimation.
Author: Vincent Arel-Bundock
License: BSD-3
Created: 2013-03-19
The original IRLS function was written for Matlab by... | detrout/debian-statsmodels | statsmodels/regression/quantile_regression.py | Python | bsd-3-clause | 15,300 | [
"Gaussian"
] | a9f5a6ee62852ece7dfd414a1d280fc90d53fdf87a72133f7204581d28d4e60c |
import logging
import re
from importlib import import_module
import pycountry
from django.apps import apps
from django.conf import settings
from django.contrib.sessions.models import Session
from django.core.exceptions import ObjectDoesNotExist
from django.db import models
from django.template.defaultfilters import sl... | LabD/wagtail-personalisation | src/wagtail_personalisation/rules.py | Python | mit | 14,554 | [
"VisIt"
] | 5d3f85b4b719fdb92ad82542c60007e133adb25dc9cadcb3524b7bbfc4ec2f1b |
"""
Adapted from:
http://blog.macuyiko.com/post/2016/how-to-send-html-mails-with-oauth2-and-gmail-in-python.html
1. Generate and authorize an OAuth2 (generate_oauth2_token)
2. Generate a new access tokens using a refresh token(refresh_token)
3. Generate an OAuth2 string to use for login (access_token)
"""
import os
im... | kootenpv/yagmail | yagmail/oauth2.py | Python | mit | 5,292 | [
"VisIt"
] | e7856dc140646d29ab0134a75659c21bec4ab92b30eab8ff15040b04274662ef |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Module contains classes presenting Element and Specie (Element + oxidation
state) and PeriodicTable.
"""
__author__ = "Shyue Ping Ong, Michael Kocher"
__... | sonium0/pymatgen | pymatgen/core/periodic_table.py | Python | mit | 35,839 | [
"CRYSTAL",
"pymatgen"
] | e1eead9ecbb50562a83c7a82f665dbad8e7b8cd0068a5ca5050e6e56afa5e986 |
"""Example implementation of using a marshmallow Schema for both request input
and output with a `use_schema` decorator.
Run the app:
$ python examples/schema_example.py
Try the following with httpie (a cURL-like utility, http://httpie.org):
$ pip install httpie
$ http GET :5001/users/
$ http GET :50... | sloria/webargs | examples/schema_example.py | Python | mit | 3,870 | [
"Brian"
] | 5e2aa74127648fa7a7991e532fe04a68336141d035c4620a5b20805d73a5491b |
"""
DIRAC.WorkloadManagementSystem package
"""
__RCSID__ = "$Id$"
| fstagni/DIRAC | WorkloadManagementSystem/__init__.py | Python | gpl-3.0 | 70 | [
"DIRAC"
] | 5856cc31fbd43fc0421cd9c8492d48803f562116c0dd730666e257ea44a9a7ef |
from __future__ import print_function, division
from os.path import join
import tempfile
import shutil
from io import BytesIO
try:
from subprocess import STDOUT, CalledProcessError
from sympy.core.compatibility import check_output
except ImportError:
pass
from sympy.utilities.exceptions import SymPyDepre... | pbrady/sympy | sympy/printing/preview.py | Python | bsd-3-clause | 12,098 | [
"VisIt"
] | c6824f137499e3b72ba3f70aacae5bb88378a87e7a88a03ef5c9410c15ad4e80 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import warnings
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.transition_state import NEBAnalysis
import json
from pymatgen.analysis.transition_state import co... | gVallverdu/pymatgen | pymatgen/analysis/tests/test_transition_state.py | Python | mit | 3,242 | [
"pymatgen"
] | 8c9cf59325a33bd20e2452ba2be50936f9dd46b00b6276ef829b14512921715f |
#
# 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 us... | DataReplyUK/datareplyuk | GenesAssociation/spark-2.0.0-bin-hadoop2.7/python/pyspark/ml/clustering.py | Python | apache-2.0 | 37,032 | [
"Gaussian"
] | 05eceb69700e47667e1b618615440996c18a1eeb7b1618235614f78340655126 |
#!/usr/bin/env python
# coding=utf-8
# aeneas is a Python/C library and a set of tools
# to automagically synchronize audio and text (aka forced alignment)
#
# Copyright (C) 2012-2013, Alberto Pettarin (www.albertopettarin.it)
# Copyright (C) 2013-2015, ReadBeyond Srl (www.readbeyond.it)
# Copyright (C) 2015-2017, A... | danielbair/aeneas | aeneas/syncmap/__init__.py | Python | agpl-3.0 | 20,754 | [
"VisIt"
] | 6ef9c4607b15beee0cd6d6e76ae85677df5f58ead8e726b9e13d4a967065be75 |
"""Axis binary sensor platform tests."""
from homeassistant.components.axis.const import DOMAIN as AXIS_DOMAIN
from homeassistant.components.binary_sensor import (
DOMAIN as BINARY_SENSOR_DOMAIN,
BinarySensorDeviceClass,
)
from homeassistant.const import STATE_OFF, STATE_ON
from homeassistant.setup import asyn... | home-assistant/home-assistant | tests/components/axis/test_binary_sensor.py | Python | apache-2.0 | 2,246 | [
"VMD"
] | 3fe8122cb1c0a93a3705183539573520d653db2d037105c610b5ecd623378b74 |
# -*- coding: utf-8 -*-
#-----------------------------------------------------------------------------
# OpenModes - An eigenmode solver for open electromagnetic resonantors
# Copyright (C) 2013 David Powell
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gen... | DavidPowell/OpenModes | test/test_horseshoe.py | Python | gpl-3.0 | 10,192 | [
"Mayavi"
] | cf03be417721084cdb9f8cd55c96afbfd38c7ccf2bd64ad397f811a68967d6b6 |
#!/usr/bin/python
'''
Script to facilitate updating the sector map when at degree 33
'''
# Copyright 2008, 2015 Squiffle
# TODO: Would be nice to somehow check that the enemy list is up-to-date
# TODO: Command-line options to change filenames
# TODO: Command-line option to set jellyfish_sectors_for_empaths
from __f... | UEWBot/ssw-scripts | ssw_probes.py | Python | gpl-3.0 | 2,468 | [
"VisIt"
] | f7ddbcde18051dd8530b252f52ac78b9d889b441f849a574e381cf23ec786ac4 |
# Copyright 2004-2010 PyTom <pytom@bishoujo.us>
#
# 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 to use, copy, modify, mer... | MSEMJEJME/ReAlistair | renpy/display/motion.py | Python | gpl-2.0 | 44,134 | [
"VisIt"
] | bb6190a36897748fce41028617e6972233b4add2f8806595ea847f5b6942e302 |
"""Core API shared by cladecompare and cladeweb for running the algorithms."""
from __future__ import division
import contextlib
import logging
import os
import subprocess
import tempfile
# from cStringIO import StringIO
from copy import deepcopy
from math import fsum, log10
from os.path import basename
from Bio impo... | etal/cladecompare | cladecomparelib/core.py | Python | bsd-2-clause | 21,918 | [
"Biopython"
] | 9e4344642251aca0e52c249ff7778029e15bfcbed99e34a742ff2816f6f9116b |
from trbm_base import TRBMBase
from copy import deepcopy
import numpy as np
class TRBM(TRBMBase):
def __init__(self, number_visible_units=1, number_hidden_units=1, order=1, network=None):
self.visible_values = list()
self.hidden_values = list()
self.visible_to_visible_bias = list()
... | aleksandar-mitrevski/fault_and_anomaly_detection | generative_model_fd/brain/machines/trbm.py | Python | bsd-2-clause | 14,133 | [
"NEURON"
] | 5f5d0898837bc85d7fabfcf645a6fdae54cbf1f7d6700eb15520c150f86e17b8 |
from galaxy.util import rst_to_html
def lint_help(tool_xml, lint_ctx):
root = tool_xml.getroot()
helps = root.findall("help")
if len(helps) > 1:
lint_ctx.error("More than one help section found, behavior undefined.")
return
if len(helps) == 0:
lint_ctx.warn("No help section fo... | ssorgatem/pulsar | galaxy/tools/linters/help.py | Python | apache-2.0 | 939 | [
"Galaxy"
] | e4d93616068d5040eb78b10a70ce53d3b54035ade51565404f5f8d1520821dfa |
"""Provide the Reddit class."""
import asyncio
import configparser
import os
import re
import time
from itertools import islice
from logging import getLogger
from typing import (
IO,
TYPE_CHECKING,
Any,
Dict,
Generator,
Iterable,
Optional,
Type,
Union,
)
from warnings import warn
fr... | praw-dev/praw | praw/reddit.py | Python | bsd-2-clause | 33,704 | [
"VisIt"
] | c49fa6b7969fea06047007a19e64cf4da8bd0e681b7eb88c79b7f3fc2e4298fc |
accuracy = 1e-8
class Cell:
def __init__(self, vtkCell, bounds, q):
self.vtkCell = vtkCell
self.bounds = bounds
self.q = q
def __eq__(self, other):
global accuracy
if abs(self.q - other.q) > accuracy:
return false
if len(sel.bounds) != len(other.bounds):
return false
... | unterweg/peanoclaw | testscenarios/tools/compareResult.py | Python | bsd-3-clause | 5,050 | [
"VTK"
] | f0423a7b15664cbb71f3846a782615dae4319835a99e314577532781ef53c39e |
from django.core.management.base import BaseCommand
from schools.models import School, BoundaryType
from stories.models import Question, Questiongroup, QuestionType, QuestiongroupQuestions, Source
class Command(BaseCommand):
args = ""
help = """Populate DB with V3 GKA IVRS questions
./manage.py populatev... | klpdotorg/dubdubdub | apps/ivrs/management/commands/archived_commands/populatev3gkaivrsquestions.py | Python | mit | 4,419 | [
"VisIt"
] | 2e52caecb1e2cc08faf2611f5887b72f338d13c929bafc1a53caf694cbf4ffe7 |
# -*- coding: utf-8 -*-
# Copyright (c) 2012 EPFL (Ecole Polytechnique federale de Lausanne)
# Laboratory for Biomolecular Modeling, School of Life Sciences
#
# POW 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 Foundatio... | degiacom/POW | HeteroMultimer.py | Python | gpl-3.0 | 51,166 | [
"VMD"
] | e59b71d15132d96f3695102b1fb9e0c0474d254759ba36f3f88dad46e8b62c5b |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'knossos_cuber_widgets.ui'
#
# Created by: PyQt5 UI code generator 5.7
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_Dialog(object):
def setupUi(self, Dialog):
Dialo... | knossos-project/knossos_cuber | knossos_cuber/knossos_cuber_widgets.py | Python | gpl-2.0 | 32,759 | [
"Gaussian"
] | 4ca28870fd3c7f4ba9fea7956f76e604e1bc8887c20d6ec19645f5898010fc35 |
"""
Utility for converting Grow sites that use multiple locales in one repository
over to a format that uses separate files for each locale.
This is required for all versions of Grow after 0.1.0.
Usage:
grow convert --type=content_locale_split
"""
from boltons import iterutils
from collections import OrderedDic... | grow/grow | grow/conversion/content_locale_split.py | Python | mit | 15,529 | [
"VisIt"
] | 207d35dbf5724f53ce4d71c665da5cda0a968e2d6f338d0b0d88e25a1243ff38 |
import numpy as np
import multiprocessing as mp
import Starfish.constants as C
import csv
import h5py
from astropy.table import Table
from astropy.io import ascii
def multivariate_normal(cov):
np.random.seed()
N = cov.shape[0]
mu = np.zeros((N,))
result = np.random.multivariate_normal(mu, cov)
prin... | gully/Starfish | Starfish/utils.py | Python | bsd-3-clause | 11,039 | [
"Gaussian"
] | ac699431019c5bddd00a6246982bc9572546600543898be629462f0d51fd14ad |
#!/usr/bin/env python
"""This tool runs free energy calculations with Amber MMPBSA.py.
"""
__author__ = "Ole Weidner"
__email__ = "ole.weidner@rutgers.edu"
__copyright__ = "Copyright 2013-2014, The RADICAL Project at Rutgers"
__license__ = "MIT"
import imp
import os, sys, uuid
import optparse
#from radica... | radical-cybertools/HT-BAC | src/radical/ensemblemd/htbac/bin/simchain.py | Python | mit | 2,959 | [
"Amber"
] | a5affdd87e7bdde1c1128bc6efddaf5e6917f79d9f72149d2466ae511293f765 |
"""
Add-on to make the MonitoringClient works with an IOLoop from a Tornado Server
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import tornado.ioloop
from DIRAC import gLogger
class MonitoringFlusherTornado(object):
"""
... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/Client/MonitoringClientIOLoop.py | Python | gpl-3.0 | 1,027 | [
"DIRAC"
] | f6bfa93b9429fa29a46f4f3bf5ab9238b5d4c5d96ff9b86a1bee0833b667b8b3 |
# 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... | tqchen/tvm | python/tvm/relay/transform/memory_alloc.py | Python | apache-2.0 | 14,547 | [
"VisIt"
] | bfb30f09622194e4606049df269a6e125e12060302054ac6e1d15cc59975a242 |
class BaseVisitor(object):
def __init__(self, compiler):
self._compiler = compiler
def _visit_list(self, nodes, *args, **kwargs):
return [self.visit(node, *args, **kwargs) for node in nodes]
def visit(self, node, *args, **kwargs):
return node.accept(self, *args, **kwargs)
| helgefmi/Easy | src/easy/visitors/base.py | Python | mit | 311 | [
"VisIt"
] | 3fe0a9f2d21aaaeaaafa4de4f705205fa77f4ab84962f68f2a176ac77e947a1d |
# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
"""
Gaussian Processes classification examples
"""
import GPy
default_seed = 10000
def oil(num_inducing=50, max_iters=100, kernel=None, optimize=True, plot=True):
"""
Run a Gaussian process ... | TianpeiLuke/GPy | GPy/examples/classification.py | Python | bsd-3-clause | 6,767 | [
"Gaussian"
] | e0ef5b35df6253d2603fb68c1539e50ca85f4f7f86bd6a7f69f39099d35059c0 |
from __future__ import print_function, division, unicode_literals
import os
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.core.operations import SymmOp
from pymatgen.io.vasp.outputs import Vasprun, Locpot, Volum... | ashtonmv/twod_materials | twod_materials/electronic_structure/analysis.py | Python | gpl-3.0 | 25,907 | [
"DIRAC",
"VASP",
"pymatgen"
] | 98ebf052be3aeadaad1496bab8b0a687660bfdbaabec671db70214ea3714267a |
###############################################################################
# TwoPowerTriaxialPotential.py: General class for triaxial potentials
# derived from densities with two power-laws
#
# amp/[4pia^3]
# ... | jobovy/galpy | galpy/potential/TwoPowerTriaxialPotential.py | Python | bsd-3-clause | 18,183 | [
"Gaussian"
] | 710f9c6ae6b56fbf0886c460a26ae11d53e58bff4d5d119a0f27d565a894fb2a |
from numbers import Real, Integral
import numpy as np
from . import _batoid
from .constants import globalCoordSys, vacuum
from .coordSys import CoordSys
from .coordTransform import CoordTransform
from .trace import applyForwardTransform, applyForwardTransformArrays
from .utils import lazy_property, fieldToDirCos
from... | jmeyers314/batoid | batoid/rayVector.py | Python | bsd-2-clause | 52,447 | [
"Gaussian"
] | 2c7719df4d8633674b8cd201bdf16cbe87fe54b17427453ca9fc3b1ee4e98e2e |
import unittest
from noaaclass import noaaclass
from datetime import datetime
import time
class TestGvarimg(unittest.TestCase):
def remove_all_in_server(self):
sub_data = self.noaa.subscribe.gvar_img.get()
ids = [d['id'] for d in sub_data if '[auto]' in d['name']]
if len(ids):
... | gersolar/noaaclass | tests/gvarimg_test.py | Python | mit | 7,304 | [
"NetCDF"
] | 6c6eae5c74bce8e6da02507f85b417fa31ed786de8500607690e9012381ee033 |
#
# Get coordination count from LAMMPS custom dump command
# (ID,x,y,z,coordination) for each timestep
#
# Gonzalo Aguirre <graguirre@gmail.com>
#
import sys, getopt
def usage():
print >> sys.stderr, "Options:"
print >> sys.stderr, " -h Show help"
print >> sys.stderr, " -i <inputfile> Input file"
print >> sys... | graguirre/Coord-LAMMPS | parser.py | Python | gpl-2.0 | 1,504 | [
"LAMMPS"
] | e260d0f8e934f501f04df61b3eaafd0eb405b18cc65a9e4dc5df29d18f0b74bd |
'''Convert to and from Roman numerals
This program is part of 'Dive Into Python 3', a free Python book for
experienced programmers. Visit http://diveintopython3.org/ for the
latest version.
'''
class OutOfRangeError(ValueError): pass
class NotIntegerError(ValueError): pass
roman_numeral_map = (('M', 1000),
... | ctasims/Dive-Into-Python-3 | examples/roman5.py | Python | mit | 2,748 | [
"VisIt"
] | b016c90abf6dd5bf130210e47fa06cf3449dfcbc2f28a2ffd3897df891e72a4a |
import numpy as np
from ase.data import atomic_numbers as ref_atomic_numbers
from ase.lattice.spacegroup import Spacegroup
from ase.cluster.base import ClusterBase
from ase.cluster.cluster import Cluster
class ClusterFactory(ClusterBase):
directions = [[1, 0, 0],
[0, 1, 0],
[0,... | grhawk/ASE | tools/ase/cluster/factory.py | Python | gpl-2.0 | 8,613 | [
"ASE",
"CRYSTAL"
] | 8f3f8f94fb584ca304c9502d3cf9e577c84bfb71c39cd8d0a524290086615905 |
# -*- coding: utf8 -*-
"""
"""
__author__ = "Jérôme Samson"
__copyright__ = "Copyright 2014, Mikros Image"
import os
import sys
import csv
import time
import datetime
from optparse import OptionParser
import numpy as np
import pygal
from pygal.style import *
try:
import simplejson as json
except ImportEr... | mikrosimage/OpenRenderManagement | src/pulitools/stats/display_2dim_usage.py | Python | bsd-3-clause | 8,423 | [
"Octopus"
] | 783b84fb4263dc4c09a609ab74fb919875ad546a2d145c09c5f65352e7a223df |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# createvgrid - [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 ... | heromod/migrid | mig/cgi-bin/createvgrid.py | Python | gpl-2.0 | 1,110 | [
"Brian"
] | d7ea7f9c02abce765941bf061f1147a17d37120287bed825e991803346c59fa6 |
"""semi-views for the `group_messaging` application
These are not really views - rather context generator
functions, to be used separately, when needed.
For example, some other application can call these
in order to render messages within the page.
Notice that :mod:`urls` module decorates all these functions
and turn... | coffenbacher/askbot-devel | askbot/deps/group_messaging/views.py | Python | gpl-3.0 | 11,261 | [
"VisIt"
] | ef20c61453e3e244e617856ff3cfd88a4c49e9b544ec2809c8987c7c0bf57341 |
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