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# vim: fileencoding=utf-8 et ts=4 sts=4 sw=4 tw=0 fdm=marker fmr=#{,#}
"""
An RPC service class using ZeroMQ as a transport and
the standard Python threading API for concurrency.
Authors
-------
* Alexander Glyzov
"""
#-----------------------------------------------------------------------------
# Copyright (C) 201... | Alidron/demo-nao | alidron-env/lib/python2.7/site-packages/netcall/threading/service.py | Python | mpl-2.0 | 8,621 | [
"Brian"
] | 1e8e252f8ff8c72598596ce3fa9a9dfae67a9c98db3b44be4b357b06524faeb1 |
"""
Defines the plugin to perform evaluation on the lfn name
"""
from DIRAC.Resources.Catalog.ConditionPlugins.FCConditionBasePlugin import FCConditionBasePlugin
class FilenamePlugin(FCConditionBasePlugin):
"""
This plugin is to be used when filtering based on the LFN name
"""
def __init__(self, co... | DIRACGrid/DIRAC | src/DIRAC/Resources/Catalog/ConditionPlugins/FilenamePlugin.py | Python | gpl-3.0 | 1,461 | [
"DIRAC"
] | e435de805ee02bdcad20f48edcdea44ff05f88c6bd5f882bbc509ad4ba2944eb |
"""Data model module"""
import pickle
import bpy
import bpy_extras
import mathutils
import numpy
import json
import zipfile
import tempfile
from . import layer
from . import kernel
from . import mesh
"""Contains all the connection results. The structure for this list is:
list of mapping sets ->
dict: 'c' for c... | MartinPyka/Parametric-Anatomical-Modeling | pam/model.py | Python | gpl-2.0 | 23,111 | [
"NEURON"
] | 9a1fcda94ed938c867061805137791e833d6b75fa398f3917df6c7bf309d0518 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import gzip
import json
import os
import random
import unittest
from collections import OrderedDict
import numpy as np
import pandas as pd
from monty.json import MontyEncoder, MontyDecoder
from pymatgen.core import yaml
from ... | vorwerkc/pymatgen | pymatgen/io/lammps/tests/test_data.py | Python | mit | 56,361 | [
"CHARMM",
"LAMMPS",
"pymatgen"
] | 65bc9c0210688bb9a9a074af2fe7310730f8f83163788966332c3b8149b8d573 |
import sys
import time
import traceback
from common.constants import privileges
from common.log import logUtils as log
from common.ripple import userUtils
from constants import exceptions
from constants import serverPackets
from helpers import chatHelper as chat
from helpers import countryHelper
from helpers import lo... | osuripple/pep.py | events/loginEvent.py | Python | agpl-3.0 | 10,684 | [
"MOE"
] | 48b7deffa510de1679d939ad17f8a96f743b459a432b50f0211d75214c408e26 |
#!/usr/bin/env python
"""
postprocess.py
Given an original BAM file produced by Qtip, and given a WASP "remap"
FASTQ file, construct a table with one record per remapped read and
with fields giving (a) the original MAPQ, (b) the Qtip-predicted MAPQs
(c) the number of remapped reads that aligned correctly, (d) same, b... | BenLangmead/qtip-experiments | experiments/wasp/postprocess.py | Python | mit | 13,664 | [
"BWA"
] | a997f824fd95c41e33c5a651b4dbeeb3a3db33714ea41bff5c0b8a35a01d3b41 |
"""
Copied from despotic/examples/gmcChem and modified
"""
from __future__ import print_function
import matplotlib
import pylab as pl
pl.switch_backend('Qt4Agg')
from astropy import units as u
from astropy import constants
import paths
from paths import fpath
from astropy.utils.console import ProgressBar
import pprint
... | adamginsburg/APEX_CMZ_H2CO | analysis/despotic_heating.py | Python | bsd-3-clause | 27,823 | [
"Gaussian"
] | e95e6a98899418acebd20d498980c5de9da16617dcb3e57338b112f406ac9d11 |
#!/usr/bin/env python
"""
refguide_check.py [OPTIONS] [-- ARGS]
Check for a Scipy submodule whether the objects in its __all__ dict
correspond to the objects included in the reference guide.
Example of usage::
$ python refguide_check.py optimize
Note that this is a helper script to be able to check if things ar... | matthew-brett/scipy | tools/refguide_check.py | Python | bsd-3-clause | 33,002 | [
"Gaussian"
] | 49a88f7712cd87fa5fb257b9ecac64373c664b5b668f77545cbab30ed444b8a8 |
"""
.. 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_bowtie_indexer.py | Python | apache-2.0 | 3,163 | [
"Bowtie"
] | b88a20c16b1af3f280222be7cd06a6a764d3d8167cf8dc15270e290685b44c31 |
# created by Chirath R, chirath.02@gmail.com
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import datetime
from smtplib import SMTPException
from django.contrib.auth.models import User
from django import forms
from django.contrib.sites.shortcuts import get_current_site
from django.forms.utils import... | csriharsha/fosswebsite | promotion/views.py | Python | mit | 12,307 | [
"VisIt"
] | 005e61b0979f0d3fd52845091eae6a97e3d81774e21151ec21f5100ffdd68823 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.StereoCapableWindowOn()
renWin.SetWindowN... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Rendering/Core/Testing/Python/stereoDresdenMace.py | Python | gpl-3.0 | 1,959 | [
"VTK"
] | 0b27147420720105601898efdbed593519fdee45ab3c0604dd3ae62e1458f27f |
#!/usr/bin/env python
import os
from horton import * # pylint: disable=wildcard-import,unused-wildcard-import
for z in range(1, 18):
for charge in range(-1, 3):
nel = z-charge
if nel <= 0:
continue
if nel%2 == 0:
mults = [1, 3, 5, 7, 9]
else:
... | theochem/horton | data/examples/hf_compare/mkinputs.py | Python | gpl-3.0 | 1,072 | [
"Gaussian"
] | 1c1b50bf73a3ad92bd5ff8a7d7a758dacae73a19d391ec9f3991e7cdba26dc12 |
#!/usr/bin/python
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Ansible is distributed... | Jmainguy/ansible-modules-core | files/xattr.py | Python | gpl-3.0 | 6,379 | [
"Brian"
] | ebf398c55d3f4d1965428c6599b38bb687b49b5710a7b623e33f09cd6333dc37 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2017 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A Beauchamp, Matthew Harr... | mattwthompson/mdtraj | tests/test_trajectory.py | Python | lgpl-2.1 | 25,917 | [
"MDTraj"
] | 2891a28b54272ff7da12e8c3e8375a4f54c087bfd0d91f4467feb96ed16af8fd |
# Maintained in full by:
# Catalyst Team <catalyst@gentoo.org>
# Release Engineering Team <releng@gentoo.org>
# Copyright: 2011 Brian Harring <ferringb@gmail.com>
# License: BSD/GPL2
# Copied & edited by: Brian Dolbec <dolsen@gentoo.org>
'''Version information and/or git version information
'''
import os
from snakeo... | benkohler/catalyst | catalyst/version.py | Python | gpl-2.0 | 1,863 | [
"Brian"
] | 6b0fc284511f609d39bfbd6bc58c823eb88da3d8617eaa456a7c6a2afd3a6cbb |
import django_databrowse
from dajaxice.core import dajaxice_autodiscover, dajaxice_config
from django.conf import settings
from django.conf.urls import patterns, include, url
from django.contrib import admin
from django.contrib.auth.decorators import login_required
from django.contrib.staticfiles.urls import staticfil... | botswana-harvard/edc-bhp074 | bhp074/config/urls.py | Python | gpl-2.0 | 3,426 | [
"VisIt"
] | b163f598192088c62d0ac97ded079214bb064b359192ab15643803325b647314 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import copy
import numpy as np
import operator
import astropy.units as u
from astropy.time import Time
from collections import Sequence
import warn... | StuartLittlefair/astroplan | astroplan/plots/time_dependent.py | Python | bsd-3-clause | 23,685 | [
"VisIt"
] | f97930430c865046247639da8812549310fc7dc3ceaa3c4bdb619a560303d6ae |
# This file is part of Sequana software
#
# Copyright (c) 2016-2020 - Sequana Development Team
#
# Distributed under the terms of the 3-clause BSD license.
# The full license is in the LICENSE file, distributed with this software.
#
# website: https://github.com/sequana/sequana
# documentation: http://sequana.rea... | sequana/sequana | sequana/ribodesigner.py | Python | bsd-3-clause | 3,810 | [
"pysam"
] | a49cdf2eb0477ff918291ca21c2d1c553f3ae9de2c86c79f43b1e68b81b18c9d |
# -*- coding: utf-8 -*-
from .util import unify_types
class Point(object):
"""Provides a basic Point in the 3D space"""
@classmethod
def origin(cls):
"""Returns the origin (0 | 0 | 0)"""
return cls(0, 0, 0)
o = origin
def __init__(self, *args):
"""Point(a, b, c)
Poin... | Kingdread/sgl | sgl/point.py | Python | gpl-3.0 | 2,636 | [
"VTK"
] | f9c3d0cb5e8734e1886a990e0b2026ac2d3a65d4fc3f8e0215af26a7897e87bf |
"""
Contains the variations() function for expanding an English word into multiple variations
by programmatically adding and removing suffixes.
Translated to Python from the ``com.sun.labs.minion.lexmorph.LiteMorph_en`` class of
Sun's `Minion search engine <https://minion.dev.java.net/>`_.
"""
import re
# Rule excep... | archatas/whoosh | whoosh/lang/morph_en.py | Python | apache-2.0 | 48,904 | [
"Octopus",
"VisIt",
"exciting"
] | bdef512963cf3fe848bdeb47db2f9799b1c8a97d0dc93eadfc700f0d85df11c5 |
# TODO: to be removed
###########################################################
# $HeadURL: $
###########################################################
"""
:mod: InheritedTask
===================
.. module:: InheritedTask
Helper class for testing RequestTask.
OBSOLETE
K.C.
"""
## imports
import time
## ... | avedaee/DIRAC | DataManagementSystem/test/InheritedTask.py | Python | gpl-3.0 | 829 | [
"DIRAC"
] | d9b1210ac086ea0d0d48f1e6d0f89ff684bafb28d2fe77430c13bc612a2bad1b |
import sys
import os
from setuptools import setup
from hived import __version__
BASE_PATH = os.path.dirname(__file__)
setup(
name='hived',
version=__version__,
description='Hived is a library for writing distributed daemons.',
long_description=open(os.path.join(BASE_PATH, 'README.md')).read(),
aut... | sievetech/hived | setup.py | Python | bsd-3-clause | 1,298 | [
"Dalton"
] | fc34a9d4dd7d92aced46ac5dbf106cb13131b775454b7afe1659e7278d20c51e |
#!/usr/bin/env python
import sys
import os.path
from optparse import OptionParser
from scipy.optimize import curve_fit
from numpy import (exp, cos, pi, tri, argsort, asarray, arange, mean, isnan,
zeros, square)
from qiime.parse import parse_distmat
__author__ = "Antonio Gonzalez Pena"
__copyright_... | wasade/qiime | qiime/plot_semivariogram.py | Python | gpl-2.0 | 5,408 | [
"Gaussian"
] | 710840ea7407565e8608f78691c7cd77fd319e8c41a8cdaf22d9ab8229315f57 |
"""
StompMQConnector tests
"""
import unittest
from mock import MagicMock
import DIRAC.Resources.MessageQueue.StompMQConnector as module
__RCSID__ = "$Id$"
HOST = 'mq.dirac.net'
PORT = 61631
VHOST = 'vhost'
USER = 'guest'
PASSWORD = 'guest'
QUEUE = 'TestQueue'
TOPIC = 'TestTopic'
ACKNOWLEDGEMENT = 'True'
MESSENGE... | arrabito/DIRAC | Resources/MessageQueue/test/Test_StompMQConnection.py | Python | gpl-3.0 | 5,401 | [
"DIRAC"
] | 12ea7283de6cb9205b0026a6c382cc015c860fa1be0f656f5bc0fe8aca30cdd1 |
'''
Generates the user input spikes to the liquid
'''
import brian_no_units # Speeds up Brian by ignoring the units
from brian import *
from brian_multiprocess_udp import BrianConnectUDP
import numpy
import time
outputclock_dt = 100 #in milliseconds
Number_of_Neurons_Output = 30*3
current_position = (0.445,0.... | ricardodeazambuja/BrianConnectUDP | examples/InputNeuronGroup_Baxter.py | Python | cc0-1.0 | 4,447 | [
"Brian",
"NEURON"
] | 6f1ccb6824ccfd296292b3143babba1edb59ef9f16b2591d1c09a557b94c111e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | dgasmith/psi4 | psi4/driver/p4util/inpsight.py | Python | lgpl-3.0 | 23,303 | [
"Jmol",
"Psi4"
] | db774b21ca491998ff56feca219c0048416876dc4b52bbf0a411de08a42a59fe |
#!/home/rsimons/miniconda2/bin/python
import matplotlib
import time
import os
import numpy as np
import matplotlib.pyplot as plt
from astropy.io import fits
import drizzlepac
import grizli
import glob
from grizli import utils
import importlib
from grizli.prep import process_direct_grism_visit
#from hsaquery import quer... | ivastar/clear | grizli_reduction.py | Python | mit | 33,227 | [
"VisIt"
] | 9cd2abd57d9463d17c70f687653b55d4ffc0a524a748af4ad4eecf7cf5f5ba25 |
# coding=utf-8
# Copyright 2017 The DLT2T Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | renqianluo/DLT2T | DLT2T/layers/modalities.py | Python | apache-2.0 | 18,113 | [
"Gaussian"
] | a8754604d618c47b6f2d0deec42bc718379c51fe2d92458c457b2d917c4f151e |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import errno
import filecmp
import os.path
import re
import tempfile
import sys
import subprocess
try:
from collections.abc import MutableSet
except ImportErr... | onecoolx/picasso | tools/gyp/pylib/gyp/common.py | Python | bsd-3-clause | 22,691 | [
"VisIt"
] | 1892a2c045a8271b8a17d9b94c990b71b4f20173b7649629482c2ab96d83ecc0 |
#!/usr/bin/env python
"""
Delete a given production
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Utilities.DIRACScript import DIRACScript as Script
@Script()
def main():
# Registering arguments w... | ic-hep/DIRAC | src/DIRAC/ProductionSystem/scripts/dirac_prod_delete.py | Python | gpl-3.0 | 906 | [
"DIRAC"
] | 3b5afd1648efc433673b26ae7b01e65ccef2af7f8f73752be46a488c1e65256e |
import ambgmin_ as GMIN
import pygmin.potentials.gminpotential as gminpot
import numpy as np
import pygmin.basinhopping as bh
from pygmin.optimize import _quench as quench
from pygmin.takestep import displace
# export PYTHONPATH=/home/ss2029/svn/GMIN/bin:$PWD/../..
GMIN.initialize()
pot = gminpot.GMINPotental(GMIN... | js850/PyGMIN | examples/amber/metenk/amber.py | Python | gpl-3.0 | 820 | [
"PyMOL"
] | ad89eb4128abcd72a4af3bb8641ec7d67fb181a2fa1b216ce100044f2db990dd |
from numpy import *
from rdkit.sping import pid
import math
def DrawSpiral(canvas,startColor,endColor,startRadius,endRadius,nLoops,degsPerSlice=70,degsPerStep=1,
startAngle=0,centerPos=None,dir=1):
if centerPos is None:
centerPos = (canvas.size[0]/2,canvas.size[1]/2)
nSlices = int(math.ceil(360*... | rdkit/rdkit-orig | rdkit/utils/spiral.py | Python | bsd-3-clause | 1,772 | [
"RDKit"
] | 4ada18cdcdea4db48c83093d675651adff435f073b63a9c562f78296a7078e64 |
#usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met... | mikehulluk/morphforge | src/morphforgecontrib/simulation/channels/exisitingmodfile/neuron.py | Python | bsd-2-clause | 3,577 | [
"NEURON"
] | 65a477c2a8faf9cf909a846db4a69bca8aec4ff1039eb680c88191b2de5f92f4 |
# Copyright 2014-2018 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/sgx/test/test_sgx_jk.py | Python | apache-2.0 | 3,748 | [
"PySCF"
] | 5ba167a5cc6150a736694b86c58b1e006360d2efe7b22ef8fe8003736cbc8890 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | dilawar/moose-full | moose-examples/snippets/crossComptSimpleReacGSSA.py | Python | gpl-2.0 | 5,435 | [
"MOOSE"
] | e056c8be792e0f303b666ac84d465ae30fb1b80f3aa2313f2233bedb76278009 |
# -*- 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/app.py | Python | gpl-2.0 | 6,385 | [
"VisIt"
] | 7fb78f53d5a4b5c9596e77d5989cae151d71bc4a4fa6915040a76ce9c54e8088 |
import itertools
import os
import random
from datetime import datetime
from typing import Any, Callable, Dict, List, Mapping, Sequence, Tuple
import pylibmc
import ujson
from django.conf import settings
from django.contrib.sessions.models import Session
from django.core.management import call_command
from django.core.... | shubhamdhama/zulip | zilencer/management/commands/populate_db.py | Python | apache-2.0 | 37,872 | [
"Amber"
] | 0fd46482cacbc4a178f9e9a5ccbc414d60d143e076fed1da39439b2e3a91d631 |
# -*- coding: utf-8 -*-
"""upload_docs
Implements a Distutils 'upload_docs' subcommand (upload documentation to
PyPI's packages.python.org).
"""
import os
import socket
import zipfile
import http.client
import base64
import urllib.parse
import tempfile
import sys, io
from base64 import standard_b64encode
from distut... | sebastian-software/jasy | util/patches/upload_docs.py | Python | mit | 5,928 | [
"VisIt"
] | 0a49499842d2203e9dd515f52013b06e95edff4fae3c57a1128e4e1849565a92 |
############################################
# Copyright (c) 2012 Microsoft Corporation
#
# Auxiliary scripts for generating Makefiles
# and Visual Studio project files.
#
# Author: Leonardo de Moura (leonardo)
############################################
import sys
import os
import glob
import re
import getopt
import ... | melted/z3 | scripts/mk_util.py | Python | mit | 123,962 | [
"cclib"
] | 1ee9cb8cce2c6c5df2502368d1f6e0a93592d1c004c1d8b819fc0e7110e61ffa |
import asyncio
import contextlib
import inspect
import logging.config
import os
from collections import OrderedDict
from functools import wraps
from typing import (
Awaitable,
Callable,
FrozenSet,
Iterable,
List,
Mapping,
MutableMapping,
Optional,
Sequence,
Set,
Tuple,
Ty... | aamalev/aioworkers | aioworkers/core/context.py | Python | apache-2.0 | 18,122 | [
"Octopus"
] | 94b7aeb02d28770d5d8b1987fc4fca229aafcdd62f1146754498bc3e57f1eb83 |
"""
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
>>> os.chdir(datadir)
"""
import os
import glob
from nipype.interfaces.base import (... | wanderine/nipype | nipype/interfaces/camino/convert.py | Python | bsd-3-clause | 31,720 | [
"VTK"
] | baa3aca096100aea7f1056216d0c12a893026359fd374b15edcd13ff499bbe59 |
#!/usr/bin/env python3
# -*-coding:Utf-8 -*
"""Use MCMC to find the stellar mass halo mass relation.
Based on the Behroozi et al 2010 paper.
Use a parametrization of the SHMR, plus a given HMF to find the expected SMF and compare it
to the observed SMF with its uncertainties using a likelihod maximisation.
Started o... | Gorbagzog/StageIAP | MCMC_SHMR_init.py | Python | gpl-3.0 | 41,076 | [
"TINKER"
] | 3aa12c664395ee3339fdd13abb7f9b86f982bba512ca7a8698de934ffb6b8580 |
import sys
import os
import shutil
import subprocess
if len( sys.argv ) == 2:
PG_DATA_DIR_DEFAULT = sys.argv[1]
else:
PG_DATA_DIR_DEFAULT = "/var/lib/postgresql/9.3/main"
PG_DATA_DIR_HOST = os.environ.get("PG_DATA_DIR_HOST", "/export/postgresql/9.3/main/")
PG_CONF = '/etc/postgresql/9.3/main/postgresql.conf'
... | kellrott/docker-galaxy-stable | galaxy/export_user_files.py | Python | mit | 5,116 | [
"Galaxy"
] | db15fcbd64130cdfb46096187518071435f30c5db49be42b20fafcc1fcbc6c8a |
# -*- coding: utf-8 -*-
import pytest
import sys
from test_base_class import TestBaseClass
try:
from collections import Counter
except ImportError:
from counter26 import Counter
aerospike = pytest.importorskip("aerospike")
try:
from aerospike.exception import *
except:
print "Please install aerospike ... | trupty/aerospike-client-python | test/test_get_many.py | Python | apache-2.0 | 6,346 | [
"ASE"
] | 2d727bbef72ceae20d4216bf4e44a80681c80936d5002ae660171dded15481cc |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides classes for predicting new structures from existing ones.
"""
from six.moves import zip
__author__ = "Will Richards, Geoffroy Hautie... | xhqu1981/pymatgen | pymatgen/structure_prediction/substitutor.py | Python | mit | 10,618 | [
"pymatgen"
] | 5a37310a576d029ae7f90007f7aa4633150aa466a0c17f784c2cb3031e8b8227 |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2012 Nebula, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# ... | tylertian/Openstack | openstack F/horizon/horizon/base.py | Python | apache-2.0 | 29,677 | [
"VisIt"
] | 843cb775a8b61630ee38db112d7d71db0c088f3c5594d2a7e776c1f1ab5255a8 |
# synapse.py ---
#
# Filename: synapse.py
# Description:
# Author:Upi Bhalla
# Maintainer:
# Created: Sat Jun 29 11:32:29 2013 (+0530)
# Version:
# Last-Updated: Thu Oct 2 2014 (+0530)
# By: Upi
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#
#
#
#
# This program is free softw... | BhallaLab/moose-examples | snippets/synapse.py | Python | gpl-2.0 | 2,454 | [
"MOOSE"
] | bdbfb820b8993ca38147a6673ac38dff1a53de6a9fbd8421815d7aa6d3d7709e |
"""Copyright 2012 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.8'
__date__ = 'May 17 2010'
import threading
from ctypes ... | danielsuo/mobot | src/move/PhidgetsPython/Phidgets/Devices/Encoder.py | Python | mit | 13,495 | [
"VisIt"
] | e45bac101fe5edd34468449feb69a95427034a7b3c8a3069c398d7cfc6cdcf24 |
from pytest import mark
from joblib import Memory
from lap import lapjv, lapmod
from lap.lapmod import get_cost
try:
from lap_old import lapjv as lapjv_old
except ImportError:
print(
'''If you get here, you do not have the old lapjv to compare to.
git clone git@github.com:gatagat/lapjv.... | gatagat/lapjv | bench/overview_dense.py | Python | bsd-2-clause | 2,387 | [
"pymatgen"
] | 7bb022190667beacd16b092bfbaab44b6d78410fabb51431038fb49c74b93488 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'openWECv2.ui'
#
# Created: Wed May 06 10:39:04 2015
# by: PyQt4 UI code generator 4.9.6
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
from matplotlib.backends import qt_compat
from matplotlib... | tverbrug/openWEC | Run/openWEC_WS.py | Python | gpl-3.0 | 76,610 | [
"exciting"
] | 192a6ffa637e783425e8cf1ea31d793a21c575ec1bdd8eef6c9cea27cc3c2408 |
import unittest
from mantid.simpleapi import *
from vesuvio.profiles import (create_from_str, GaussianMassProfile,
MultivariateGaussianMassProfile,
GramCharlierMassProfile)
# --------------------------------------------------------------------------------
# ... | ScreamingUdder/mantid | scripts/test/VesuvioProfileTest.py | Python | gpl-3.0 | 12,091 | [
"Gaussian"
] | ec8aa760a9d0c12523ce36369b9bb54c68d433df8b7ea6079c9138bfb94d8702 |
import tensorflow as tf
from tensorflow.python.platform import tf_logging as logging
from tensorflow.contrib.framework.python.ops.variables import get_or_create_global_step
import inception_preprocessing
from inception_resnet_v2 import inception_resnet_v2, inception_resnet_v2_arg_scope
import time
import os
from train_... | protossw512/bio-project | transfer_learning/eval.py | Python | mit | 6,381 | [
"VisIt"
] | 8ccef28ed845df0c6ece60edad4025767027c2ce41f903c1e6991cdb763a2048 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright Neil Brown ©2019-2021 <neil@brown.name>
# May be distributed under terms of GPLv2 - see file:COPYING
#
import socket, os, sys, fcntl, signal
if 'EDLIB_SOCK' in os.environ:
sockpath = os.environ['EDLIB_SOCK']
else:
sockpath = "/tmp/edlib-neilb"
try:
... | neilbrown/edlib | python/lib-server.py | Python | gpl-2.0 | 13,922 | [
"VisIt"
] | 8bb531ee2df724192ae268a885691ebb6b4ef5e4a5c485c25e43d4f79637c163 |
#
# Copyright 2015 Olli Tapaninen, VTT Technical Research Center of Finland
#
# 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... | ollitapa/MMP-TracerApi | Tests/MeshTests/meshLocalizationSpeedTest.py | Python | apache-2.0 | 2,473 | [
"VTK"
] | 13bffa6d3423e48515b58a2566ca2b959176fe9bc7eb0547bca61081f4bea4ec |
"""
======================================================================
A demo of structured Ward hierarchical clustering on an image of coins
======================================================================
Compute the segmentation of a 2D image with Ward hierarchical
clustering. The clustering is spatially ... | vortex-ape/scikit-learn | examples/cluster/plot_coin_ward_segmentation.py | Python | bsd-3-clause | 2,351 | [
"Gaussian"
] | 30ce3c1f4b51f7148438c7a7e9d680fc9a3433a8045e98f5f0aa1d9b39f20648 |
# Copyright (C) 2010-2018 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... | mkuron/espresso | testsuite/python/test_checkpoint.py | Python | gpl-3.0 | 12,820 | [
"ESPResSo"
] | 5a50297f39c95b1bcd4cb1c1f1374030271285b8728d96d4abf72b1bb8493d78 |
# Django Imports
from django.core.urlresolvers import reverse
# Python Imports
import decimal, random
# WaW Imports
from wawmembers.models import World, NewsItem
import wawmembers.variables as v
'''
Misc utility functions for turnchange.
'''
D = decimal.Decimal
################
### CALCULATIONS
################
de... | heidi666/WorldsAtWar | wawmembers/turnupdates.py | Python | mit | 13,722 | [
"Galaxy"
] | 0d41c8895df8a72ab8d06abd65662d23d973f31b1ca8df38f0908a1f2723535e |
# $Id$
#
# Copyright (C) 2000-2008 greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
""" code for dealing with composite models
For a model to be useable here, it should support the following API:
- _ClassifyExample(example)_, returns a classification
Other compatibility notes:
1) To use _Compo... | soerendip42/rdkit | rdkit/ML/Composite/Composite.py | Python | bsd-3-clause | 20,919 | [
"RDKit"
] | 021357e3024d99afc3b53c535c0f2cb55f84f110f48d408659a0ac1b53b1953f |
# cmdutil.py - help for command processing in mercurial
#
# Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from node import hex, nullid, nullrev, short
from i18n import _
import ... | jordigh/mercurial-crew | mercurial/cmdutil.py | Python | gpl-2.0 | 80,083 | [
"VisIt"
] | 38db18b0c21d0544fe9016f745d63cbfbce19e4de07ef5e541f02d7e8c8e029a |
# -*- coding: utf-8 -*-:
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
"""
This module contains the basic API for splinter drivers and elements.
"""
from splinter.meta import InheritedDocs
class DriverAP... | bmcculley/splinter | splinter/driver/__init__.py | Python | bsd-3-clause | 23,446 | [
"VisIt"
] | c4d0216a36eda69195ebdc615dce45239974134136f8311d91207fe4029c0b79 |
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #
# (c) 2010... | backmari/moose | python/chigger/base/ChiggerSource.py | Python | lgpl-2.1 | 3,624 | [
"MOOSE",
"VTK"
] | 806e93eab6c371f211a657f37e80b838e9e126f322256856eb543ae381145886 |
import pylab as pl
import numpy as np
import math
from math import pi, log
from scipy import optimize
from scipy.signal import argrelextrema
from scipy.integrate import simps
from scipy import fft, ifft
from scipy.optimize import curve_fit, leastsq
def gaussian(x, height, center, width):
return height*np.exp(-(... | DiamondLightSource/auto_tomo_calibration-experimental | old_code_scripts/old_get_radii.py | Python | apache-2.0 | 38,322 | [
"Gaussian",
"TINKER"
] | ded0a13a34a2eef233703bb395b890ede1c821ece4515654cabf8f4bf65b578d |
'''
Utility functions for NetCDF files
Copyright 2014, Jared Oyler.
This file is part of TopoWx.
TopoWx 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 l... | jaredwo/topowx | twx/utils/util_ncdf.py | Python | gpl-3.0 | 30,362 | [
"NetCDF"
] | 6b1eac75ba1c0a5cd4fb1c85b9d882c6f766a40f2f34bc2dd21fd275fcf439fd |
from django.contrib.staticfiles.urls import staticfiles_urlpatterns
from django.conf.urls import patterns, include, url
from django.contrib.auth.decorators import login_required
from django.conf import settings
from django.views.generic import RedirectView
from django.db.models import get_models
import django_databrows... | botswana-harvard/eit | eit/config/urls.py | Python | gpl-3.0 | 3,578 | [
"VisIt"
] | d77a7d732762013170bb199cac6662a77b812712b4a34acd6bb5ff457c664bfe |
"""Builds the ocr network.
Summary of available functions:
# Compute input images and labels for training. If you would like to run
# evaluations, use inputs() instead.
inputs, labels = distorted_inputs()
# Compute inference on the model inputs to make a prediction.
predictions = inference(inputs)
# Compute t... | Luonic/tf-cnn-lstm-ocr-captcha | ocr.py | Python | mit | 22,365 | [
"Gaussian"
] | 76a6e7d309948ae13ff8bce059c95797ad31343b33730f74237894e915c89768 |
"""Functionality to query and extract information from aligned BAM files.
"""
from __future__ import print_function
import collections
import os
import signal
import subprocess
import numpy
import pybedtools
import pysam
import toolz as tz
from six.moves import zip_longest
from bcbio import broad, utils
from bcbio.ba... | a113n/bcbio-nextgen | bcbio/bam/__init__.py | Python | mit | 25,448 | [
"BWA",
"pysam"
] | b82abbf462053088af7bf7267e0ce920f05bc6f2b678ce1ec54eed33307c75de |
from json import dumps
from pyusesthis import pyusesthis
from unittest.mock import patch
def _fake_response(response_type):
if response_type == 'hardware_all':
out_string = ('{"gear": [{"slug":"thinkpad-x220", "name":'
'"ThinkPad X220"}, {"slug":"xeon-e5-2680", '
... | ivuk/pyusesthis | tests/test_unit_pyusesthis.py | Python | mit | 8,619 | [
"Brian"
] | e269f64ee5ff0776c1061194f2c4965d7252c1b32d17aca086284c7e9188016f |
"""
KeepNote
Functions for iterating and inserting into textbuffers
"""
#
# KeepNote
# Copyright (c) 2008-2009 Matt Rasmussen
# Author: Matt Rasmussen <rasmus@mit.edu>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publish... | vatslav/perfectnote | keepnote/gui/richtext/textbuffer_tools.py | Python | gpl-2.0 | 18,481 | [
"VisIt"
] | 24ef4b14600f55f3ea877e0165ab492319dd15ad4bcc9640bb8180a93df810be |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Aug 26, 2012"
import unit... | dongsenfo/pymatgen | pymatgen/util/tests/test_string_utils.py | Python | mit | 3,361 | [
"pymatgen"
] | 66fc2d01472174ed92c4564b58081fc93e56fea27f4e2d6d87a25a60a9f7e736 |
"""Tests `dms_tools2.pacbio.CCS` class and related functions.
"""
import os
import unittest
import copy
import numpy
import pysam
import dms_tools2.pacbio
class test_pacbio_CCS(unittest.TestCase):
"""Tests `dms_tools2.pacbio.CCS` and related functions."""
def setUp(self):
"""Initialize a `CCS` ob... | jbloomlab/dms_tools2 | tests/test_pacbio_ccs.py | Python | gpl-3.0 | 3,123 | [
"pysam"
] | f5f0b127109ddf545fd648daf5bdfa20c98adbc9407e5eb2b41c4b11921a020c |
# Copyright (C) 2018
# Max Planck Institute for Polymer Research
#
# 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 Licens... | niktre/espressopp | testsuite/cap_force/test_cap_force.py | Python | gpl-3.0 | 9,172 | [
"ESPResSo"
] | 29fb83372638fb3924d090ee2fa9d04a7bd04c3fc87774043c4891ca0e16bc00 |
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 4.1.4.
... | mick-d/nipype | nipype/interfaces/fsl/model.py | Python | bsd-3-clause | 95,064 | [
"Gaussian"
] | b56fa54a54231ff3da662a86e2ced26545091070b2b01927908fb0e207e3f005 |
r"""
This module provides a server side mechanism to support uploading files
to the server.
$ python file_upload_handler.py --upload-directory .../path-to-upload-directory --upload-port port
--upload-directory
Path to directory where uploaded files should go. If this argument is not
... | hlzz/dotfiles | graphics/VTK-7.0.0/Web/Python/vtk/web/upload.py | Python | bsd-3-clause | 2,561 | [
"VTK"
] | 73f881f15b75d3baf5f16e0f0e974d2032cfa6eba9498cf290032af06c7de3e2 |
# Workflow with PLAMS
# A couple of useful function for extracting results:
@add_to_class(AMSResults)
def get_excitations(results):
"""Returns excitation energies (in eV) and oscillator strenghts (in Debye)."""
if results.job.ok():
exci_energies_au = results.readrkf('Excitations SS A','excenergies',fi... | miroi/open-collection | theoretical_chemistry/software_runs/ams/runs/plams_tests/excitations_workflow/ExcitationsWorkflow.py | Python | mit | 3,928 | [
"ADF"
] | 7f84b3a17cb17c667d13c8fb6322692be6dac3e84e4c049e14278b7f644226d1 |
import numpy as np
from time import clock, time
import datetime
import nest.topology as tp
import nest.pynestkernel as nk
from output import *
from parts import *
from synapses import *
import globals as g
connections = dict()
parts = dict()
def get_all_parts():
return g.all_parts
def generate_positions(nn)... | research-team/NEUCOGAR | NEST/cube/dopamine/3d/scripts/func.py | Python | gpl-2.0 | 10,849 | [
"Gaussian",
"NEURON"
] | 6e83382ed5a78a4c0033b0a90651ff6295a75daaec2ca7db3d609e7f5d30f214 |
# 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... | karllessard/tensorflow | tensorflow/python/ops/distributions/distribution.py | Python | apache-2.0 | 46,675 | [
"Gaussian"
] | 17e441ee082bc06f52a38438db49968e39701c2feba29cff3b4345990f490315 |
# Prepares a directory of ligand mol2 (sybyl atom types) and a
# a directory of receptor pqr (amber atom types) files
# for AMBER and AlGDock
# Run from the [TARGET]/ directory
# TODO: Identify rigid bodies for CDHMC
# Constants
job_block = 10
import argparse
parser = argparse.ArgumentParser()
parser.add_ar... | CCBatIIT/AlGDock | Pipeline/run_prep_ligand_and_complex_for_AlGDock.py | Python | mit | 6,869 | [
"Amber"
] | cad3d6bbd58a57bb6d457998c573a28637b85cd757ca1f3c81c0efcabc4b80a1 |
__author__ = 'James DeVincentis <james.d@hexhost.net>'
import ipaddress
import os
import re
import email.utils
import cif
hash_types = {
'uuid': re.compile(r'^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$'),
'md5': re.compile(r'^[a-fA-F0-9]{32}$'),
'sha1': re.compile(r'^[a-f... | Danko90/cifpy3 | lib/cif/types/basics.py | Python | gpl-3.0 | 7,203 | [
"Amber"
] | 58b789c9c532313bff77648e6ed11133c961b03519348afbdf953e008bdee242 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
""" Start Pymol and Bokeh server """
from __future__ import print_function
import time
import shlex
import subprocess
__author__ = "Jérôme Eberhardt"
__copyright__ = "Copyright 2016, Jérôme Eberhardt"
__lience__ = "MIT"
__maintainer__ = "Jérôme Eberhardt"
__email__ = "... | jeeberhardt/visualize | scripts/run_servers.py | Python | mit | 1,340 | [
"PyMOL"
] | b623bf5db3976c718f6a6eb923af7ba1ec89bc7c448bf92216cd8ef60e2ea652 |
import os
import re
import subprocess
from PyQt4 import QtGui
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from qgis.core import *
from animoveAlgorithm import AnimoveAlgorithm
try:
# QGIS 2.2
from processing.tools.vector import features, getUniqueValues, extractPoints
from processing.tools.dataobj... | gioman/radio_telemetry_tools | kernelDensity.py | Python | gpl-2.0 | 15,654 | [
"Gaussian"
] | 5046ebd4153cf8e9821ae0798ba9792a8afaf8e936d0437f4c058c50dc148f61 |
"""
kde
~~~
A variety of "other" KDE methods, not drawn directly from the literature.
"""
from . import predictor
import open_cp.predictors
import tkinter as tk
import tkinter.ttk as ttk
import open_cp.kde
import open_cp.gui.tk.util as util
import open_cp.gui.tk.richtext as richtext
import open_cp.gui.tk.tooltips as ... | QuantCrimAtLeeds/PredictCode | open_cp/gui/predictors/kde.py | Python | artistic-2.0 | 25,159 | [
"Gaussian"
] | bd1d02e7a8790a91ebf8cd8b0d0979ce400f195eed8415e28ef16bf2a4dc3258 |
#!/usr/bin/env python
import os
import numpy as np
from xmap_netcdf_reader import DetectorData
import readMDA
from memoize_core import Memoizer
store = {}
expiring_memoize = Memoizer(store)
from utils import memoize
#
# set up a CLASS for detector pixels
#
"""
This module provides an interface to a DetectorData ne... | Peter--K/Sakura | get_netcdf.py | Python | bsd-3-clause | 11,656 | [
"NetCDF"
] | 52761895e65453ddefbd7df6285d68c3f78f29ffc1dc3691e00f041eb9880a0d |
# 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 or agreed to in writing... | google-research/federated | reconstruction/shared/federated_trainer.py | Python | apache-2.0 | 24,635 | [
"Gaussian"
] | 2515f4a2900333ddb2468b8968d41494f0f2235f5ec5d618a779903adcf6e8aa |
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2015-2016 lamarpavel
#
# This file is part of qutebrowser.
#
# qutebrowser 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 th... | halfwit/qutebrowser | tests/unit/browser/webkit/test_cache.py | Python | gpl-3.0 | 12,991 | [
"VisIt"
] | ee4740a574b7756bd8a296af14a737cc00e6c3f942233e1eaf1cbd5d06c852c6 |
"""
@name: Modules/Core/Drivers/Http/Http_driver.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2020-2020 by D. Brian Kimmel
@license: MIT License
@note: Created on Jan 26, 2020
@summary:
"""
from Modules.Core.Utilities.debug_tools import PrettyFormatAny
__updated__ = '... | DBrianKimmel/PyHouse | Project/src/Modules/Core/Drivers/Http/Http_driver.py | Python | mit | 1,705 | [
"Brian"
] | ec649779e077d8b802a3ba1c43404d5f9ff71000ef5dc60af3168de80ac3d962 |
'''
GIS conversion/interpolation tools for use in VisIt
(http://wci.llnl.gov/codes/visit/).
Relies on ogr/gdal.
'''
__author__ = 'fluidmotion'
import os,sys
from osgeo import ogr, gdal
import numpy as np
import matplotlib.pyplot as plt
class shpTools():
'''
accepts line shapefile of contours ... | fluidmotion/visTools | visGIS.py | Python | mit | 8,415 | [
"VisIt"
] | cda122b510c7b3a0b5cd98fadd0df41ad7c670996e7e966d99168e072243665c |
#!/usr/bin/python
"""Channel impulse response in an EM reverberation chamber
Visit http://imagetheorymodel.manuamador.fr/ for the
latest version and more information
"""
__author__ = "Emmanuel Amador (emmanuel.amador@insa-rennes.fr)"
__version__ = "$Revision: 0.1 $"
__date__ = "$Date: 2011/06/12$"
__copyright__ = "Co... | manuamador/Misc | PostDoc_python/RC/ExampleCIRvect.py | Python | agpl-3.0 | 8,825 | [
"VisIt"
] | 0c089faeb65d3587e1f3385370270ad0b9b37c20ce52b295d102f9570a602045 |
__author__ = 'gph82'
#Minimal setup script
from setuptools import setup
import versioneer
meta_data = dict(name='molPX',
author='Guillermo Perez-Hernandez',
author_email='guille.perez@fu-berlin.de',
maintainer='Martin K. Scherer',
maintainer_email='m.scherer@fu-berlin.de',
version=versio... | markovmodel/molPX | setup.py | Python | lgpl-3.0 | 860 | [
"MDTraj"
] | 4e5e44a2841e2d917eb555a0e6160b84c8df835862003825d285d2544c9f1954 |
"""
This program contains various functions for fetching the html for a given page
and returning it.
Copyright (C) 2015 Team S
Team S comprises of :
* Charles Bos
* Daniel Bedingfield
* Joshua Coyle
* Oyinpreye Onita
* Sebastian Jakobsen
* Thomas Harris
This program is free software: you can redistribu... | charlesbos/s-compare | fetcher.py | Python | gpl-3.0 | 2,245 | [
"VisIt"
] | 58e636e3e03265ef503092f7dd6201a27ba1356b356076abc5f393bf4ada7d69 |
#!/usr/bin/env python
######################################################################
# Alchemical Analysis: An open tool implementing some recommended practices for analyzing alchemical free energy calculations
# Copyright 2011-2015 UC Irvine and the Authors
#
# Authors: Pavel Klimovich, Michael Shirts and Dav... | MobleyLab/alchemical-analysis | alchemical_analysis/alchemical_analysis.py | Python | mit | 62,295 | [
"Amber",
"Desmond",
"Gaussian",
"Gromacs"
] | cd096596f622483a1da3b068d2210f705210fb288e0fa4cf590fc64b6fed77f3 |
# -*- coding: utf-8 -*-
"""Tests for the reified assembler."""
import unittest
import networkx as nx
from pybel import BELGraph
from pybel.dsl import abundance, activity, degradation, fragment, pmod, protein, rna
from pybel.testing.utils import n
from pybel_tools.assembler.reified_graph.assembler import (
ACTIV... | pybel/pybel-tools | tests/test_reified_graph_assembler.py | Python | mit | 10,423 | [
"Pybel"
] | b3c95f5120359dee53d87d9ed575b369eeb3eca0c12877ee22e57fb2fe695dea |
"""
=================================================
Linear fascicle evaluation (LiFE)
=================================================
Evaluating the results of tractography algorithms is one of the biggest
challenges for diffusion MRI. One proposal for evaluation of tractography
results is to use a forward model t... | villalonreina/dipy | doc/examples/linear_fascicle_evaluation.py | Python | bsd-3-clause | 11,614 | [
"Gaussian"
] | 812db15fbd77a32ba214ec33151220d54cd8015f1c75261455007413312500bd |
# sql/expression.py
# Copyright (C) 2005-2011 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Defines the base components of SQL expression trees.
All components are derived ... | jokajak/itweb | data/env/lib/python2.6/site-packages/SQLAlchemy-0.6.7-py2.6.egg/sqlalchemy/sql/expression.py | Python | gpl-3.0 | 156,909 | [
"VisIt"
] | 628ebda069a2b7e2ba5e363b1b3a82eae21ea221df703d77ed0f4cf69a97cbfe |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-compute | tests/unit/gapic/compute_v1/test_image_family_views.py | Python | apache-2.0 | 43,138 | [
"Octopus"
] | 25e06b1867cdf36ad88cefddf2a6a6092bfd92a360b05e02bc21ee37a8b70381 |
"""
Delta printer linear least squares autocalibration.
Most of the code in this package is a pretty straightforward
translation of David Crocker's linear least squares calibration
algorithm: http://escher3d.com/pages/wizards/wizarddelta.php .
For additional information on the algorithm, visit the following
Wikipedia... | intelligent-agent/redeem | redeem/DeltaAutoCalibration.py | Python | gpl-3.0 | 17,351 | [
"VisIt"
] | c0467f94fdc7a3644c24b379769d73b141bc8da2bdba131715cd5b2db93d6776 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/stats/distance/_anosim.py | Python | bsd-3-clause | 8,588 | [
"scikit-bio"
] | 3fcf26b1d8c3021d58faa9f7395045774ca63edab7ace72c60d796f4351cdbd0 |
#
# 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... | jlopezmalla/spark | python/pyspark/ml/tests.py | Python | apache-2.0 | 75,135 | [
"Gaussian"
] | 5a7dfdb57dd22a3bfc2da57ac3d61a348590206aa78664230c40843b8ee65a12 |
"""
====================================================
How to convert 3D electrode positions to a 2D image.
====================================================
Sometimes we want to convert a 3D representation of electrodes into a 2D
image. For example, if we are using electrocorticography it is common to
create sca... | teonlamont/mne-python | examples/visualization/plot_3d_to_2d.py | Python | bsd-3-clause | 4,574 | [
"Mayavi"
] | df3a1af5a8f9ff82e5c9438478b46a47fc345ed4f732853e8843da5440aa0ab5 |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 3: Deep Learning and Neural Networks
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2015 by Jeff Heaton
Licensed under the Apache License, V... | trenton3983/Artificial_Intelligence_for_Humans | vol3/vol3-python-examples/examples/example_sunspots.py | Python | apache-2.0 | 4,339 | [
"VisIt"
] | 5c2e92b7a121962a8ba42b650bf357c79f967300dc2b6b94837cd48bd3929833 |
# -*- coding:utf-8 -*-
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 vers... | rsouza/pypln.web | pypln/web/core/tests/test_models.py | Python | gpl-3.0 | 2,752 | [
"NAMD"
] | 55c244ce14a304dffefe03a563a176e0152a55e71381dec52f864f7ab64d92b8 |
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