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# 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... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/tensorflow/contrib/learn/python/learn/datasets/synthetic.py | Python | bsd-2-clause | 6,827 | [
"Gaussian"
] | d6d2e2ee7bdc6b14d820986efec0035ccc8f2a844e0ea7811488d597cb722efe |
"""
local path implementation.
"""
from __future__ import with_statement
from contextlib import contextmanager
import sys, os, re, atexit, io
import py
from py._path import common
from py._path.common import iswin32
from stat import S_ISLNK, S_ISDIR, S_ISREG
from os.path import abspath, normpath, isabs, exists, isdir... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/py/_path/local.py | Python | bsd-3-clause | 32,093 | [
"VisIt"
] | b0bf5dda172d1a3899bb65e771c642003eb30614d3b54b61bfbd6a12284cd2bd |
#
# Copyright 2008, 2009 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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 t... | dursobr/Pythics | pythics/instruments/Zaber_Txxxx_5xx.py | Python | gpl-3.0 | 7,774 | [
"Brian"
] | 44fd10be8c61c33a5d59ba760c8e358da29723aea1dd1b2cc1f6ae0c3a9691c0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Unit tests for defect transformations
"""
__author__ = "Bharat Medasani"
__copyright__ = "Copyright 2014, The Materials Project"
__version__ = "0.1"
__maintainier__ = "Bharat Medasani"
__email__ = "mbkum... | dongsenfo/pymatgen | pymatgen/transformations/tests/test_defect_transformations.py | Python | mit | 1,573 | [
"pymatgen"
] | 83f9688f4ddfcb8210e82b4ba70a9cbca438bc49568e4345a156f3eb613bc24d |
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
ImageDotProduct()
| jeromevelut/Peavip | Testing/ImageDotProduct.py | Python | gpl-3.0 | 128 | [
"ParaView"
] | a51822f20ba774e2328a572fff1177a8c7fb7a739dd400851b2b4a643decb5f5 |
# numkit --- data fitting
# Copyright (c) 2010 Oliver Beckstein <orbeckst@gmail.com>
# Released under the "Modified BSD Licence" (see COPYING).
"""
:mod:`numkit.fitting` --- Fitting data
======================================
The module contains functions to do least square fits of functions of
one variable f(x) to da... | jandom/GromacsWrapper | numkit/fitting.py | Python | gpl-3.0 | 10,082 | [
"Gaussian"
] | f9185205ca3ddbd9a6eccff50f2ebca26c2d9119395104ed7972950f6d8d25c6 |
#!/usr/bin/env python
"""
Get summary informations of all productions
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base import Script
from DIRAC.Core.Utilities.PrettyPrint import printTable
Script.setUsageMessage('\n'.join([__doc__.split('\n')[1]]))
Script.parseCommandLine()
from DIRAC.ProductionSystem.C... | fstagni/DIRAC | ProductionSystem/scripts/dirac-prod-get-all.py | Python | gpl-3.0 | 1,169 | [
"DIRAC"
] | 1ae365b477e2ed6be3c1120e1fd806fdc5a32191559aa66b6b90d1ec6534dbd5 |
# Copyright (c) 2005 Gavin E. Crooks <gec@compbio.berkeley.edu>
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentat... | pbenner/tfbayes | tfbayes/corebio/seq.py | Python | gpl-2.0 | 23,992 | [
"Biopython"
] | bc7d2179e587a6d70cdef761a99f75e67b1f8df3a69bb5408f8ec5533817089e |
# -*- coding: utf-8 -*-
"""Functions to make 3D plots with M/EEG data."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Mainak Jas <maina... | drammock/mne-python | mne/viz/_3d.py | Python | bsd-3-clause | 135,094 | [
"VTK"
] | 8ee4112d85f52f098d5d08af940b165f20938042ec9b509f7f5c700eb7e88aa9 |
r"""
=======================================
Robust vs Empirical covariance estimate
=======================================
The usual covariance maximum likelihood estimate is very sensitive to the
presence of outliers in the data set. In such a case, it would be better to
use a robust estimator of covariance to guar... | chrsrds/scikit-learn | examples/covariance/plot_robust_vs_empirical_covariance.py | Python | bsd-3-clause | 6,484 | [
"Gaussian"
] | 06ea8c5398e2ea32f99a0dab8b08c9ae4bd62d2bf12762279db6fdb0ae5fad96 |
#!/usr/bin/ python
# -*- coding: utf-8 -*-
# *************************************** #
#
# Author: Semen Budenkov
# Date: 27/02/2017
#
# *************************************** #
import time
import logging
import numpy as np
from sklearn import linear_model
from sklearn.neural_network import MLPClassifier
from... | Semen52/nlp4u | models/src/classification.py | Python | mit | 8,424 | [
"Gaussian"
] | e2759f94dbbd522c1e191be88e0415791e06affeba9cf6924b7c92dcd9a59cfc |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/auxiliary/XVG.py | Python | gpl-2.0 | 11,522 | [
"Gromacs",
"MDAnalysis"
] | 12a3c1d1a68486b63a2478de520e7a8251279af57fb85b29dc7561dee00da0a7 |
"""
==============
Blob Detection
==============
Blobs are bright on dark or dark on bright regions in an image. In
this example, blobs are detected using 3 algorithms. The image used
in this case is the Hubble eXtreme Deep Field. Each bright dot in the
image is a star or a galaxy.
Laplacian of Gaussian (LoG)
-------... | michaelpacer/scikit-image | doc/examples/plot_blob.py | Python | bsd-3-clause | 2,796 | [
"Galaxy",
"Gaussian"
] | 1dedfb2284c15d0ef41595bab24e3e88d5457df049e6e629fb7456999a81ba54 |
from bok_choy.page_object import PageObject, PageLoadError, unguarded
from bok_choy.promise import BrokenPromise, EmptyPromise
from common.test.acceptance.pages.lms.course_page import CoursePage
from common.test.acceptance.pages.common.paging import PaginatedUIMixin
from common.test.acceptance.tests.helpers import disa... | louyihua/edx-platform | common/test/acceptance/pages/lms/edxnotes.py | Python | agpl-3.0 | 20,687 | [
"VisIt"
] | a8e57979b3e72a3f998782ec8a7a937a748682e27e5f932be49cfa7e169c5ab0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Implementation for `pmg analyze` CLI.
"""
import logging
import multiprocessing
import os
import re
from tabulate import tabulate
from pymatgen.apps.borg.hive import (
SimpleVaspToComputedEntryDrone... | gmatteo/pymatgen | pymatgen/cli/pmg_analyze.py | Python | mit | 5,282 | [
"VASP",
"pymatgen"
] | 7bfdae69dd3f2726a9c37d1ccf06f24cb48eec1bc17fc6d5acf0928bceddbdbf |
#
# @file TestModifierSpeciesReference.py
# @brief ModifierSpeciesReference unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by ... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestModifierSpeciesReference.py | Python | bsd-3-clause | 3,950 | [
"VisIt"
] | 0a46d33dffb6f66dfb33ca713577e26235906ce7b512af6a6a9c1f8b34370d85 |
# (C) British Crown Copyright 2014 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | ghislainp/iris | lib/iris/fileformats/grib/_load_convert.py | Python | gpl-3.0 | 77,975 | [
"Gaussian"
] | 79232bb2cd40d56da534861dcbd5ad298a3aaf26461770759c25d99eeedb58a3 |
#
# Brian C. Lane <bcl@redhat.com>
#
# Copyright 2014 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use, modify,
# copy, or redistribute it subject to the terms and conditions of the GNU
# General Public License v.2. This program is distributed in the hope that it
# will be useful,... | jikortus/pykickstart | pykickstart/commands/sshkey.py | Python | gpl-2.0 | 3,583 | [
"Brian"
] | 10ed4eccfb55540cd940bea014f7e02161b69424a5c0c43f88d8388c75c88d3d |
##
# @package RAMS.NXT
# @file NXTSensor.py
# @author Brian Kim
# @date 7/24/14
# @brief a python wrapper around the roams assembly to interface with NXT sensors
from NXTPort import NXTPort
class NXTSensor( NXTPort ):
def getData( self ):
return None
| briansan/rams | RAMS/nxt/NXTSensor.py | Python | bsd-3-clause | 268 | [
"Brian"
] | 747c23f0e1cd96f1e4ae6c4414d8ab707edcb190d9eaf7165247b896486b68ae |
#
# 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... | shakamunyi/beam | sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py | Python | apache-2.0 | 15,049 | [
"VisIt"
] | ebaf7945050c4b891b1682f1d09998c05084e65449252876241bc508c0ed47f2 |
"""
parser.http.movieParser module (imdb package).
This module provides the classes (and the instances), used to parse the
IMDb pages on the akas.imdb.com server about a movie.
E.g., for Brian De Palma's "The Untouchables", the referred
pages would be:
combined details: http://akas.imdb.com/title/tt0094226/combi... | nopjmp/SickRage | lib/imdb/parser/http/movieParser.py | Python | gpl-3.0 | 80,843 | [
"Brian"
] | 1a9ccc6ab6616866e8dc1dbeb1ea3437c1a59f718aec6065a07ae6a6ab8b8284 |
"""
BoltzTraP2 is a python software interpolating band structures and
computing materials properties from dft band structure using Boltzmann
semi-classical transport theory.
This module provides a pymatgen interface to BoltzTraP2.
Some of the code is written following the examples provided in BoltzTraP2
BoltzTraP2 has... | davidwaroquiers/pymatgen | pymatgen/electronic_structure/boltztrap2.py | Python | mit | 47,328 | [
"ASE",
"BoltzTrap",
"VASP",
"pymatgen"
] | 37083fdad55d0d09eed909c3073a6c69d1123ba193180de8cda48f92cead0343 |
"""
KeepNote
Notebook indexing
"""
#
# KeepNote
# Copyright (c) 2008-2011 Matt Rasmussen
# Author: Matt Rasmussen <rasmus@alum.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 published by
# the Free Software Founda... | brotchie/keepnote | keepnote/notebook/connection/fs/index.py | Python | gpl-2.0 | 16,245 | [
"VisIt"
] | 0dcb34625ca2333c576774e7fca6feb9e3be4aa9a7fafa873da08de003ac512a |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of t... | maheshp/novatest | nova/tests/network/test_manager.py | Python | apache-2.0 | 111,111 | [
"FEFF"
] | f293d85a0d9be25bb120780b9dffd79c205f83b4ff60b2c9e0d32ceadc86bdbe |
import os
import unittest
import numpy as np
from pymatgen.analysis.graphs import StructureGraph
from pymatgen.core.structure import Structure
from pymatgen.electronic_structure.cohp import Cohp
from pymatgen.electronic_structure.core import Spin
from pymatgen.io.lobster.lobsterenv import LobsterNeighbors
from pymatg... | materialsproject/pymatgen | pymatgen/io/lobster/tests/test_lobsterenv.py | Python | mit | 27,085 | [
"pymatgen"
] | 1450075233e5e4805f03f15b7b5e5b23823c2c39c1ebbff7b007437bb3f269d9 |
"""Photoreceptor neuron models."""
from math import exp
import random
import numpy as np
from ..neuron import Neuron, action_potential_trough, action_potential_peak, Normal
class Photoreceptor(Neuron):
"""A specialized neuron that is sensitive to light."""
_str_attrs = ['id', 'pixel', 'potential']
# Elec... | napratin/nap | nap/vision/photoreceptor.py | Python | mit | 11,161 | [
"NEURON"
] | 8f6e04fd23acca24be33da295b7f4809d66875d026c4e511127b3e5908b5eb6b |
# Manual stimulus used to find the receptive field position and size.
#
# Copyright (C) 2010-2012 Huang Xin
#
# See LICENSE.TXT that came with this file.
from Experiments.Experiment import ExperimentConfig,ManbarExp,MangratingExp
ExperimentConfig(data_base_dir='data',new_cell=True)
# When a neuron is isolated in Pl... | chrox/RealTimeElectrophy | Experimenter/man_stimulus_new_cell.py | Python | bsd-2-clause | 717 | [
"NEURON"
] | 415a5c620591ea3490f0afbedc12767d423764fe89b89996f9c65f1c1918c686 |
# Copyright 2019 DeepMind Technologies Limited. 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 ... | deepmind/dqn_zoo | dqn_zoo/networks.py | Python | apache-2.0 | 11,570 | [
"Gaussian"
] | 8861f457dc16bc7a85a7377de5293cfeaf9b56e64e19dc0ec49ab9a93302d385 |
import simtk.unit as u
import numpy as np
@property
def masses_per_mole(snapshot):
"""
Returns
-------
masses_per_mole : list of simtk.unit.Quantity with length n_atoms
atomic masses (with simtk.unit attached) in units of mass/mole
"""
try:
simulation = snapshot.engine.simulatio... | jhprinz/openpathsampling | openpathsampling/engines/openmm/features/masses.py | Python | lgpl-2.1 | 1,428 | [
"Dalton",
"MDTraj",
"OpenMM"
] | 0996c667764964f08518cca94eecc0f25cf2ff4cdc1b0a32a91ee441f0e8bc7d |
import numpy as np
try:
from openbabel import openbabel as ob
from openbabel import pybel
except ModuleNotFoundError:
pass
from pysisyphus.calculators.Calculator import Calculator
from pysisyphus.constants import BOHR2ANG, AU2KJPERMOL, AU2KCALPERMOL
def _getpluginnames(ptype):
plugins = ob.vectorStr... | eljost/pysisyphus | pysisyphus/calculators/OBabel.py | Python | gpl-3.0 | 2,619 | [
"Pybel"
] | eaab7d83d6031c5ebbf30495f47429b8f4c1a61c0868cc3291d138b4eafc5de6 |
"""
Performance test created using multi-mechnize to analyze time
for query processing with ElasticSearch.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import random
import time
from DIRAC.WorkloadManagementSystem.DB.ElasticJobParametersDB import Ela... | yujikato/DIRAC | tests/Performance/ESJobMonitoring/test_scripts/query.py | Python | gpl-3.0 | 868 | [
"DIRAC"
] | ff098b3f5b19a4abd8b8394315c7d54c431ec2c567403da091b0df78ef7aca08 |
# $HeadURL: $
""" diracmock
This module must be imported before running any unit tests. It provides all the
necessary mocks.
"""
#import mock
import unittest
__RCSID__ = '$Id: $'
# The following is the check to make sure it is in place
#if mock.__version__ < '1.0.1':
# raise ImportError( 'Too old version of m... | Sbalbp/DIRAC | ResourceStatusSystem/PolicySystem/test/diracmock.py | Python | gpl-3.0 | 1,191 | [
"DIRAC"
] | bf9ca9a5cff09db15d6746206d41669c745f3354795ab1b555caa2f0120c427a |
"""Service to predict the probability of a person to default a loan.
How to use:
firefly predict.predict
"""
import os
from sklearn.externals import joblib
from config import MODELS_DIR
def load_model(filename):
path = os.path.join(MODELS_DIR, filename)
print("reading", path)
return joblib.load(path... | amitkaps/full-stack-data-science | credit-risk-deploy/predict.py | Python | mit | 1,153 | [
"Firefly"
] | 2bad20ef0c2d0a7cc4571e612d6317f34c5d186b31e42e5c319a5c97f496f955 |
#!/usr/bin/env python
import os
import platform
import sys
try:
import yaml
except ImportError:
print('Please install pyyaml (try: pip install pyyaml)')
sys.exit(1)
import subprocess as sp
import shlex
import argparse
import tempfile
if sys.version_info.major == 3:
PY3 = True
from urllib.request i... | instituteofpathologyheidelberg/bioconda-recipes | simulate-travis.py | Python | mit | 13,993 | [
"Bioconda"
] | 360e7c0f2e2475f72c25c3dabdd3e678cf75e1646cc14f3eead19c4eddb69833 |
# file: energyShellDistribution.py
#
# This code computes the energy among spherical harmonic coefficients for
# successive shells. See for instance Fig. 2 (bottom) in our ArXiv preprint
# http://arxiv.org/abs/1602.01301
#
# Copyright (c) J. Flamant, April 2016.
#
# This program is free ... | jflamant/sphericalEMC | dataGeneration/energyShellDistribution.py | Python | gpl-3.0 | 2,130 | [
"VisIt"
] | 5a7f624f5dda43d91f45992b0fb7d3c6e2dc4bb6458d8f2daa094d3a713eddc5 |
#!/usr/bin/env python
#
# Copyright (c) 2012-2013
# Nexa Center for Internet & Society, Politecnico di Torino (DAUIN)
# Simone Basso <bassosimone@gmail.com>
#
# This file is part of Neubot <http://www.neubot.org/>.
#
# Neubot is free software: you can redistribute it and/or modify
# it under the terms of the G... | bassosimone/neubot-server | regress/neubot/utils_path.py | Python | gpl-3.0 | 13,003 | [
"VisIt"
] | 3cb80d9fa5c17daae1579fb99a61a484260548b050970be252bd7320ff5d8c8e |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2013-2014 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published b... | SNoiraud/gramps | gramps/plugins/textreport/endoflinereport.py | Python | gpl-2.0 | 13,427 | [
"Brian"
] | f280f82158fdf325d3226ef6c9101c589097e4c17adf3264040ce56eb969db55 |
'''
Created on 03.09.2014
@author: Jan-Hendrik Prinz, David W.H. Swenson
'''
from . import range_logic
import abc
from openpathsampling.netcdfplus import StorableNamedObject
import numpy as np
import warnings
# TODO: Make Full and Empty be Singletons to avoid storing them several times!
def join_volumes(volume_list... | choderalab/openpathsampling | openpathsampling/volume.py | Python | lgpl-2.1 | 21,931 | [
"OpenMM"
] | d1047fb3577e34b2f3971791e84f3befe025f7c2fdac462588541ab824677b7f |
#!/usr/bin/env python
from __future__ import print_function
import sys
from Bio import SeqIO
from Bio.Seq import Seq
from dark.sequence import findPrimerBidiLimits
def trimPrimers(primer, verbose):
"""
@param primer: A BioPython C{Bio.Seq} primer sequence.
@param verbose: A C{bool}, if C{True} output ad... | acorg/dark-matter | bin/trim-primers.py | Python | mit | 1,709 | [
"Biopython"
] | 4b5af0d5c8f57419485a02a0d98a9f7affd5931c75bd62050ecd7bc37afcf281 |
#! /usr/bin/env python3
from pandas import *
import sklearn
from sklearn.naive_bayes import GaussianNB
from sklearn.naive_bayes import MultinomialNB
from sklearn.grid_search import GridSearchCV
import numpy as np
import random
STYLE = "American_IPA"
""" Performs cross validation on data using a given method
Retur... | cycomachead/info290 | project/code/analysis/bayes.py | Python | bsd-2-clause | 2,931 | [
"Gaussian"
] | e761317e36f50760be2b63aa611f4e35dbce113ac3a57c24d6b0557d5484038b |
# detection anomalies from SDSS using global PCA method
from ex import *
import ex.pp.mr as mr
from ex.ml import *
import utils
import detector
import report
import sdss_info as sinfo
class ScoreReducer(mr.BaseReducer):
'''map each file to its anomaly score and embedding coordinates
'''
def __init__(sel... | excelly/xpy-ml | sdss/detection/detection_global_pca.py | Python | apache-2.0 | 4,588 | [
"Galaxy"
] | 619ca5a8042876e4a9689896c6a4d2961e5c6323a54f3972201c279f9722c953 |
#
# Copyright (C) 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 vers... | KonradBreitsprecher/espresso | testsuite/actor.py | Python | gpl-3.0 | 3,049 | [
"ESPResSo"
] | 29cdadb397a371068e5c8a9e2d52894dcd18ff167356ec6cf12cc33569b240bd |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/coordinates/memory.py | Python | gpl-2.0 | 24,241 | [
"MDAnalysis"
] | 5f3137629d4e3befa542dafdb908b7ea662f97681e4b64b405a147150e19c139 |
import os
import math
import numpy as np
import operator
import vtkAll as vtk
import vtkNumpy
import functools
import ihmc
from director import lcmUtils
from director import ioUtils
from director import segmentation
from director import objectmodel as om
from director import visualization as vis
from director.debugVis... | patmarion/director | src/python/director/continuouswalkingdemo.py | Python | bsd-3-clause | 51,714 | [
"VTK"
] | a68dbebd85fe948a1dd50b5d3e7772d7d16f678d69047b178765aae9b76ef553 |
"""Useful utility methods for GTK."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import gtk
from zeroinstall.support import tasks
class Template:
"""Wrapper for GtkBuilder widget tree that throws a sensible exception if the widget isn't found."""
def __ini... | dsqmoore/0install | zeroinstall/gtkui/gtkutils.py | Python | lgpl-2.1 | 4,033 | [
"VisIt"
] | 7b7c88a3569a94a22418c67f162772aff51609d86bb51be53b9994d45a27fa80 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2008-2013 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... | tiagocardosos/stoq | stoqlib/lib/payment.py | Python | gpl-2.0 | 3,324 | [
"VisIt"
] | a53eacdba2665bb47c2f1e8454a304d6cd2c720b53f0eb71baf5e279caf20abf |
# symcompartment.py ---
#
# Filename: symcompartment.py
# Description:
# Author:
# Maintainer:
# Created: Thu Jun 20 17:47:10 2013 (+0530)
# Version:
# Last-Updated: Wed Jun 26 11:43:47 2013 (+0530)
# By: subha
# Update #: 90
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
... | BhallaLab/moose-examples | symcomp/symcomp.py | Python | gpl-2.0 | 3,064 | [
"MOOSE"
] | 3110369b79078cec668843f3dd2f635ff19018be747d8ce2d7a5e252a3b63d7f |
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import
import ast
import numba
from numba import *
from numba import visitors, nodes, error, functions, function_util
logger = logging.getLogger(__name__)
from numba.external import pyapi
from numba.typesystem import is_obj, promote_cl... | shiquanwang/numba | numba/specialize/exceptions.py | Python | bsd-2-clause | 5,960 | [
"VisIt"
] | e330dcc9945de0888ef15eef599775fc934f420280d63ef29d06b7cbaf0be809 |
# -*- coding: utf-8 -*-
"""
ast
~~~
The `ast` module helps Python applications to process trees of the Python
abstract syntax grammar. The abstract syntax itself might change with
each Python release; this module helps to find out programmatically what
the current grammar looks like and allows... | huran2014/huran.github.io | wot_gateway/usr/lib/python2.7/ast.py | Python | gpl-2.0 | 11,805 | [
"VisIt"
] | 724b370737c840ea3618bddb22c40377fcc3aef1a1598c0c4c0e3a5ad18f0025 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | snerg/nerf/model_utils.py | Python | apache-2.0 | 10,969 | [
"Gaussian"
] | d715910587c35025ba3fb9d997af864d53b9b85297ebc90c1bd3d942c2b2bfbd |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Tests for RGB Images
"""
from __future__ import absolute_import, division, print_function, unicode_literals
import sys
import os
import tempfile
import numpy as np
from numpy.testing import assert_equal
from ...convolution import convolve, Gaussia... | joergdietrich/astropy | astropy/visualization/tests/test_lupton_rgb.py | Python | bsd-3-clause | 9,343 | [
"Gaussian"
] | 5915480b8819257c392238181faef7f7648df4feb8ac516b259e635abf051000 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyMetasv(PythonPackage):
"""An accurate and integrative structural-variant caller for next... | iulian787/spack | var/spack/repos/builtin/packages/py-metasv/package.py | Python | lgpl-2.1 | 785 | [
"pysam"
] | f0e974813c11862aef0fd93dda62c459c35659a20d416bd0369ba6e3bf72c826 |
# Copyright (c) 2006 John Gilman
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# ... | JohnReid/bioinf-utilities | python/corebio/ssearch_io/__init__.py | Python | mit | 7,320 | [
"BLAST",
"BioPerl"
] | 8414bb986fda622635134ada836fcd3ae733b1231d05d79233018018ba418ce6 |
##from pyNN.utility import get_script_args
#
##from pyNN.spiNNaker2_nest import *
##from pyNN.random import NumpyRNG, RandomDistribution
from pylab import *
#from NeuroTools.signals import *
from numpy import ones
#simulator_name = get_script_args(1)[0]
#exec("from pyNN.%s import *" % simulator_name)
#FUNCION THAT C... | dhgarcia/babelModules | pynnModules/Network/gaussiancreatejose.py | Python | gpl-3.0 | 22,081 | [
"Gaussian",
"NEURON"
] | 845a3acd81330afadf1f7b88044a61da83cca8963ebbd9f5617ee7ffa4d54af7 |
# -*- coding: utf-8 -*-
"""
Write EC and SMC Meshes in legacy VTK format as .vtk.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Relative import path for the DumpMeshToLegacyFormat script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__)... | BlueFern/DBiharMesher | meshes/c960/Dump960MeshLegacyFormat.py | Python | gpl-2.0 | 889 | [
"VTK"
] | 4f9e0375011c9bc3cce63427340f979b458340a1f1ea3b470d37044541c3e815 |
"""
A python library for performing reciprocal space reconstruction from single crystal x-ray measurements.
"""
from .meerkat import *
| aglie/meerkat | meerkat/__init__.py | Python | mit | 136 | [
"CRYSTAL"
] | 0e00744eaf617bde6d43e76ee3ce3f508839776d60f0a0a821f6a1811fae0bb5 |
from ase import Atoms, Atom
from ase.parallel import parprint, paropen
from ase.units import Hartree, Bohr
from gpaw import GPAW, debug, dry_run, PoissonSolver
from gpaw.mixer import Mixer, MixerSum, MixerDif, BroydenMixer, BroydenMixerSum
from gpaw.poisson import FixedBoundaryPoissonSolver
from gpaw import restart as... | robwarm/gpaw-symm | gpaw/transport/calculator.py | Python | gpl-3.0 | 130,816 | [
"ASE",
"GPAW"
] | 7bc3889b2bde3200cc05a40cde3ddcba6ae4ffa6d1a96cd9f30e60e765db61e9 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <markdowncell>
# This HTML version of is provided for convenience, but it is not the best
# format for the book. In particular, some of the symbols are not rendered
# correctly.
#
# You might prefer to read the [PDF
# version](http://thinkstats.com/thinkstats.pdf)... | chappers/Data-Science | Think-Stats/4 Continuous Distributions.py | Python | mit | 32,150 | [
"Gaussian"
] | b38bdae87ede1eeae31618c4672ca68fa07d75d89103d3045c4083c7e995f6c4 |
import sys, os
import numpy as np
from numpy.random import randn
import pandas as pd
from scipy import stats
import matplotlib as mpl
mpl.use('Agg') # helps on mac --> maybe not necessary on linux? check?
import matplotlib.pyplot as plt
import seaborn as sns
import re
import argparse
##################################... | bluegenes/MakeMyTranscriptome | scripts/util/pipePlot.py | Python | bsd-3-clause | 10,386 | [
"BLAST"
] | e14c11f9d28bda3d0e0cf70b38607d06269c4ec9eaf65a829b4ce611e8c5e757 |
import PythonQt
from PythonQt import QtCore, QtGui
import ddapp.objectmodel as om
import ddapp.visualization as vis
from ddapp import transformUtils
from ddapp import applogic as app
from ddapp import vtkAll as vtk
import numpy as np
class SplineEndEffectorPlanner(object):
def __init__(self, handFactory, robot... | edowson/director | src/python/ddapp/splinewidget.py | Python | bsd-3-clause | 9,972 | [
"VTK"
] | 958b1ad5fc9a8986ba42ba2c9ec7394786876894411a9e522bcd3ec769982d00 |
# Add your pmg_tk startup scripts to this directory...
# here are two examples: (copy to new ".py" files and remove comment marks)
# === BEGIN EXAMPLE: myplugin.py ===
#
#from Tkinter import *
#from pymol import cmd
#
#def __init__(self):
# self.menuBar.addcascademenu('Plugin', 'MyPlugin', 'Sample Plugin',
# ... | gratefulfrog/lib | python/pmg_tk/startup/__init__.py | Python | gpl-2.0 | 1,454 | [
"PyMOL"
] | b69bae9eaa591cc88c2102ec0e9a576b150393f9df6526b5ef0c1dd8ba0f13be |
import ez_setup
ez_setup.use_setuptools()
from setuptools import setup, find_packages
import sys
sys.path.insert(0, 'alan')
import version as proj_version
import alan.version as proj_version
setup(
name='alan',
author='Brian Mearns',
author_email='bmearns@ieee.org',
url='https://g... | mearns/alan | setup.py | Python | agpl-3.0 | 2,019 | [
"Brian"
] | ceb6d28e7e4734d13772ff062de898606178e192210a5b3f1648684c35efcc1a |
import numpy as np
from cs231n.layers import *
from cs231n.layer_utils import *
class TwoLayerNet(object):
"""
A two-layer fully-connected neural network with ReLU nonlinearity and
softmax loss that uses a modular layer design. We assume an input dimension
of D, a hidden dimension of H, and perform classific... | shengshuyang/StanfordCNNClass | assignment2/cs231n/classifiers/fc_net.py | Python | gpl-3.0 | 14,645 | [
"Gaussian"
] | ada7c56b98e8c71a3b74e0cb38ee9c913582a65018b2600c5d28c786d491b7c7 |
"""
A VTK RenderWindowInteractor widget for wxPython.
Find wxPython info at http://wxPython.org
Created by Prabhu Ramachandran, April 2002
Based on wxVTKRenderWindow.py
Fixes and updates by Charl P. Botha 2003-2008
Updated to new wx namespace and some cleaning up by Andrea Gavana,
December 2006
"""
"""
Please see... | jmerkow/VTK | Wrapping/Python/vtk/wx/wxVTKRenderWindowInteractor.py | Python | bsd-3-clause | 24,421 | [
"VTK"
] | 11b9c87b1a3e491fb81a78b9f5a5bbce8b001adaf47256acbe9753954e6e10e3 |
# Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Code to work with data from the KEGG database.
References:
Kanehisa, M. and Goto, S.; ... | zjuchenyuan/BioWeb | Lib/Bio/KEGG/__init__.py | Python | mit | 2,693 | [
"Biopython"
] | a09195cfaf1e76352bbb3d702b2d7e25bc948b9853f30039de98c0b5e9447387 |
"""High level summaries of samples and programs with MultiQC.
https://github.com/ewels/MultiQC
"""
import collections
import glob
import io
import json
import mimetypes
import os
import pandas as pd
import shutil
import numpy as np
from collections import OrderedDict
import pybedtools
import six
import toolz as tz
im... | vladsaveliev/bcbio-nextgen | bcbio/qc/multiqc.py | Python | mit | 26,574 | [
"HTSeq"
] | 01fa36766b561d803466bd520576119fa3c94d3a2512354c10b93994f6253cc6 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2011, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.zenoss.OpenStackSwift | ZenPacks/zenoss/OpenStackSwift/parsers/SwiftRecon.py | Python | gpl-2.0 | 5,592 | [
"VisIt"
] | 2665837294884c67673e959f0d13ac6a07dd24067c0be374cd8e4b722c76a2d5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import logging
import traceback
import re
from omero_version import omero_version
from webclient.webclient_gateway import OmeroWebGateway
logger = logging.getLogger(__name__)
def upgradeCheck():
# upgrade check:
# -------------
# On each startup OMERO.web che... | jballanc/openmicroscopy | components/tools/OmeroWeb/omeroweb/webadmin/webadmin_utils.py | Python | gpl-2.0 | 1,526 | [
"VisIt"
] | 5a4e6f5eec3d9799bb742a2d60ddcfd48a2021cffb459ccb4c6879a091ef1741 |
__author__ = 'befulton'
import unittest
import make_data_files
def generate(lines):
for line in lines:
yield line
class CollectlTests(unittest.TestCase):
def test_build_datasets_returns_last_line_time_as_end_time(self):
lines = ["20140919 13:10:49\n",
"20140919 ... | mr-c/trinityrnaseq | trinity-plugins/collectl/Tests.py | Python | bsd-3-clause | 7,668 | [
"Bowtie"
] | cec3dc846a953a1cfc8529ba49e7b573a6fd9fb4fff53b2d6e9fde406081518f |
########################################################################
# $Id$
########################################################################
""" SandboxHandler is the implementation of the Sandbox service
in the DISET framework
"""
__RCSID__ = "$Id$"
import os
import time
import random
import types
imp... | vmendez/DIRAC | WorkloadManagementSystem/Service/SandboxStoreHandler.py | Python | gpl-3.0 | 18,569 | [
"DIRAC"
] | 0c95638ba93a1adc828ee778baaf36750c08b0629c92ce09d41085c4462b935c |
#Alex Holcombe alex.holcombe@sydney.edu.au
#See the github repository for more information: https://github.com/alexholcombe/twoWords
from __future__ import print_function
from psychopy import monitors, visual, event, data, logging, core, sound, gui
import psychopy.info
import numpy as np
from math import atan, log, cei... | alexholcombe/twoWords | specialFieldsStudentCode/twoWordsExperimentInvertedbackMay2AlexContinue4.py | Python | mit | 53,260 | [
"Elk"
] | 7db1fb2b2969d178b68f796a0dfc2d45dc46ead1911e355eaa10d60dbcb85f84 |
# Originally Copyright (c) 2013 Daniel Bader (http://dbader.org)
# Taken directly from: https://dbader.org/blog/monochrome-font-rendering-with-freetype-and-python
# And modified slightly by John Donovan (http://geospark.co.uk).
#
# Released under the MIT License (MIT)
# See the LICENSE file, or visit http://opensource.... | GeoSpark/ILI9341-font-packer | src/font.py | Python | mit | 5,327 | [
"VisIt"
] | 16b2e232bb9005fd3db3c81c70c4b6c28071ad27b81b9c47995156a009c25153 |
"""
======================
Working with ECoG data
======================
MNE supports working with more than just MEG and EEG data. Here we show some
of the functions that can be used to facilitate working with
electrocorticography (ECoG) data.
"""
# Authors: Eric Larson <larson.eric.d@gmail.com>
# Chris Hold... | mne-tools/mne-tools.github.io | 0.15/_downloads/plot_ecog.py | Python | bsd-3-clause | 2,762 | [
"Mayavi"
] | eb86daef0afdf4795c424e009484e66aac7cd748591147ccbc14391500a2a2ea |
"""Structure optimization. """
import sys
import pickle
import time
from math import sqrt
from os.path import isfile
import numpy as np
from ase.parallel import rank, barrier
from ase.io.trajectory import PickleTrajectory
class Dynamics:
"""Base-class for all MD and structure optimization classes.
Dynamic... | grhawk/ASE | tools/ase/optimize/optimize.py | Python | gpl-2.0 | 5,891 | [
"ASE"
] | 35c7e1b3d70271db03d60fa7e8ac50e0e477fb6e5c8f495ec473f0c128a4b516 |
import numpy as np
import os
import mdtraj as md
from mdtraj.utils.delay_import import import_
import tempfile
from distutils.spawn import find_executable
import simtk.unit as units
import copy
from .utils import temporary_directory
PACKMOL_PATH = find_executable("packmol")
HEADER_TEMPLATE = """
# Mixture
toleranc... | choderalab/openmoltools | openmoltools/packmol.py | Python | mit | 13,377 | [
"MDTraj",
"OpenMM"
] | 6e82f8907a32804bd933ef819dbc9fc87ba6caa5fc59ce0b0611b51d2702705a |
"""
:mod:`Consts` -- constants module
============================================================================
evolve have defaults in all genetic operators, settings and etc, this is an issue to helps the user in the API use and minimize the source code needed to make simple things. In the module :mod:`Consts`, ... | UdeM-LBIT/GAPol | lib/ga/evolve/Consts.py | Python | gpl-3.0 | 5,048 | [
"Gaussian"
] | 6e67fedab3ae0ee46efa0cd36084af43cc2531c54bb8ff4142ec9a2d8bae31d2 |
# Made by Fulminus
# Quest 347: Go Get The Calculator.
import sys
from net.sf.l2j.gameserver.model.quest import State
from net.sf.l2j.gameserver.model.quest import QuestState
from net.sf.l2j.gameserver.model.quest.jython import QuestJython as JQuest
# NPCs to talk to
BRUNON = 7526
SILVERA = 7527
SPIRON = 7532
BALANKI... | Barrog/C4-Datapack | data/jscript/quests/347_GoGetTheCalculator/__init__.py | Python | gpl-2.0 | 4,454 | [
"CRYSTAL"
] | 43c2852ab0284f5bbf252255e3579fa0f7dda2554171808c5b34f71019d17e57 |
import math
import random
import logging
from .text import verbs
from .fight import Escape, FightAction
from . import util
class Event:
def __init__(self, time, person, worldview):
self.time = time
self.worldview = worldview
self.person = person
def clauses(self, diary):
"""A g... | flexo/nanogenmo2015 | novel/event.py | Python | mit | 11,376 | [
"VisIt"
] | 5953f3501b41247898c857099985d5461ce9b474eafb18b925f5eabbf92890b3 |
import os
import sys
from ase import Atom
from gpaw import GPAW
from gpaw.cluster import Cluster
from gpaw.test import equal
fname='H2_PBE.gpw'
fwfname='H2_wf_PBE.gpw'
txt = None
# write first if needed
try:
c = GPAW(fname, txt=txt)
c = GPAW(fwfname, txt=txt)
except:
s = Cluster([Atom('H'), Atom('H', [0,... | qsnake/gpaw | gpaw/test/mgga_restart.py | Python | gpl-3.0 | 1,315 | [
"ASE",
"GPAW"
] | e416a6e69d3fa84edec9e49f160bc4c437939c4fcb8bb5c25466c35aeb828c1c |
"""
========================================
Special functions (:mod:`scipy.special`)
========================================
.. currentmodule:: scipy.special
Nearly all of the functions below are universal functions and follow
broadcasting and automatic array-looping rules. Exceptions are
noted.
.. seealso::
`... | Eric89GXL/scipy | scipy/special/__init__.py | Python | bsd-3-clause | 29,815 | [
"Gaussian"
] | b4f2c1294a4392ab62eb772a091fcbd451718ba25c6eef427a5fbaa9101aad5e |
#!/usr/bin/env python3
# SOF-ELK® Supporting script
# (C)2020 Lewes Technology Consulting, LLC
#
# This script will read a file or directory tree of JSON VPC Flow logs and output in a format that SOF-ELK® can read with its NetFlow ingest feature
# See https://docs.microsoft.com/en-us/azure/network-watcher/network-watc... | philhagen/sof-elk | supporting-scripts/azure-vpcflow2sof-elk.py | Python | gpl-3.0 | 9,896 | [
"Elk"
] | 0d744e419c8b63b779f0a2849583b0f9e9dd56b20d03ba920c02918bbae32e10 |
# -*- coding: utf-8 -*-
"""
Optical elements
----------------
Module :mod:`~xrt.backends.raycing.oes` defines a generic optical element in
class :class:`OE`. Its methods serve mainly for propagating the beam downstream
the beamline. This is done in the following sequence: for each ray transform
the beam from global t... | kklmn/xrt | xrt/backends/raycing/oes.py | Python | mit | 93,431 | [
"CRYSTAL"
] | e509c099416ed280784cd37362076a9882923425f425e99640a95e8d676f1bb5 |
from check_grad import check_grad
from utils import *
from logistic import *
import matplotlib.pyplot as plt
def run_logistic_regression(hyperparameters):
# TODO specify training data
train_inputs, train_targets = load_train()
valid_inputs, valid_targets = load_valid()
# N is number of examples; M i... | ouyangyike/Machine-Learning-and-Data-Mining | Logistic Regression/logistic_regression_regularized_penalty2.py | Python | mit | 5,461 | [
"Gaussian"
] | fed46d1842928a1d255c6ed84afd77588f2a260c24e83609960b6a589762049d |
# Copyright Anne M. Archibald 2008
# Released under the scipy license
import numpy as np
import warnings
from .ckdtree import cKDTree, cKDTreeNode
__all__ = ['minkowski_distance_p', 'minkowski_distance',
'distance_matrix',
'Rectangle', 'KDTree']
def minkowski_distance_p(x, y, p=2):
"""Compu... | e-q/scipy | scipy/spatial/kdtree.py | Python | bsd-3-clause | 33,896 | [
"Galaxy"
] | b7a6a92058543a582605ade43f046a5e609479d1426bbf4bb249c7005441396f |
from sys import stdout
from scipy import zeros, exp, pi, sqrt, arange, array, log
from matplotlib import pyplot as plt
def perror(string):
stdout(string)
exit(0)
def calSigma2(width):
s = width / 2.0 / sqrt(2.0 * log(2.0))
return s * s
def mixGaussian(centers, heights, rmin, rmax, interval, width):
x = arang... | Bismarrck/SimpleSpectra | spectra.py | Python | gpl-3.0 | 3,219 | [
"Gaussian"
] | 5a92220e5abb124d6a67b82d1e332e16e3ab305e6ec090014485b7bfeca4381a |
"""
Defines the plugin to take storage space information given by WLCG Accounting Json
https://twiki.cern.ch/twiki/bin/view/LCG/AccountingTaskForce#Storage_Space_Accounting
https://twiki.cern.ch/twiki/pub/LCG/AccountingTaskForce/storage_service_v4.txt
https://docs.google.com/document/d/1yzCvKpxsbcQC5K9MyvXc-vBF... | ic-hep/DIRAC | src/DIRAC/Resources/Storage/OccupancyPlugins/WLCGAccountingJson.py | Python | gpl-3.0 | 4,575 | [
"DIRAC"
] | c6db8873cb9c5c1898a4af7bdd9140ca464090736c438fd8799542686608c4ca |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides input and output from the CSSR file format.
"""
import re
from monty.io import zopen
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
__autho... | gmatteo/pymatgen | pymatgen/io/cssr.py | Python | mit | 2,885 | [
"pymatgen"
] | 06a5e83cc0dade67f2985f634230c7361f28c75c14c68049d95638a40c29a3a0 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | kevin-coder/tensorflow-fork | tensorflow/contrib/layers/python/layers/feature_column_test.py | Python | apache-2.0 | 53,784 | [
"MOOSE",
"Octopus"
] | a5e82ea0156e14b301f209f2271049cad2070b2a1761b12285ca3e88b30abf4b |
from setuptools import setup, find_packages
import sys, os
version = '0.1.9alpha'
setup(name='gfirefly',
version=version,
description="Achieve firefly based on gtwisted",
long_description="""Achieve firefly based on gtwisted""",
classifiers=[], # Get strings from http://pypi.python.org/pypi?%3... | yangdw/PyRepo | src/annotation/gfirefly/gfirefly/setup.py | Python | mit | 1,038 | [
"Firefly"
] | 3318052029ae5a5de0116b9fa8bbbecb92bdc3a458a33c73fda9dec62385c2c2 |
from __future__ import absolute_import
from perses.utils.openeye import createOEMolFromSDF, extractPositionsFromOEMol
from perses.annihilation.relative import HybridTopologyFactory, RepartitionedHybridTopologyFactory
from perses.rjmc.topology_proposal import PointMutationEngine
from perses.rjmc.geometry import FFAllAn... | choderalab/perses | perses/app/relative_point_mutation_setup.py | Python | mit | 35,580 | [
"MDTraj",
"OpenMM"
] | 4c218031f7e38dc0d1845d60ceb2d1a052f2ddaf7fd507cb2146218d7bd6dcef |
"""Benchmarking module for AlignedSegment functionality"""
import timeit
iterations = 10000
repeats = 5
setup_binary_tag = """
import pysam
import array
read = pysam.AlignedSegment()
read.set_tag('FZ', array.array('H', range(1000)))
"""
setup_binary_tag_from_file = """
import pysam
with pysam.AlignmentFile("../test... | daler/pysam | benchmark/AlignedSegment_bench.py | Python | mit | 1,175 | [
"pysam"
] | a5154b8ed4882a0cdc1843680c0cdfd7b61a22c87a11eb45f1fa064bf17dd59a |
#
# Copyright (C) 2013,2014 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... | rbardak/espresso | samples/python/coulomb_debye_hueckel.py | Python | gpl-3.0 | 7,846 | [
"ESPResSo"
] | 1cb999368b46fda8a608c1c97dc91fc7d4c2b87104e50f9961756ea02ddb389f |
import atexit, logging, os, sys, tempfile
import pkg_resources
pkg_resources.require( "twill==0.9" )
pkg_resources.require( "Paste" )
pkg_resources.require( "PasteDeploy" )
pkg_resources.require( "Cheetah" )
import twill, unittest, time
import os, os.path, subprocess, sys, threading
import httplib
from paste import ... | dbcls/dbcls-galaxy | test/functional/__init__.py | Python | mit | 5,445 | [
"Galaxy"
] | e416224873d25ae591c1e81c66c6149a8062ff1fc5fbcd44cedff507cfa44bf7 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
import argparse
import json
import os
import os.path
from socorro.lib.datetimeutil import JsonDTEncoder
from socorro.li... | lonnen/socorro | socorro/scripts/fetch_crash_data.py | Python | mpl-2.0 | 7,578 | [
"VisIt"
] | 7cae90f366e9c9168c37a522abb50ef31b6eedfb7e53bd8622ee3c61ea51ae01 |
#!/usr/bin/env python
# This example demonstrates the use of multiline 2D text using
# vtkTextMappers. It shows several justifications as well as
# single-line and multiple-line text inputs.
import vtk
font_size = 14
# Create the text mappers and the associated Actor2Ds.
# The font and text properties (except jus... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/Annotation/Python/multiLineText.py | Python | gpl-3.0 | 6,590 | [
"VTK"
] | 8d506b95f579a7da38b37e78bc1f12c6ec5dc162fb38a81b55c01731a86b581f |
#!/usr/bin/env python
# Parallel Python Software: http://www.parallelpython.com
# Copyright (c) 2005-2012, Vitalii Vanovschi
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of... | idaholab/raven | framework/contrib/pp/ppserver.py | Python | apache-2.0 | 15,320 | [
"VisIt"
] | 108baf5dd16b29c16f967e3e12ba926a021b078ba3e1680f470c9b62bb153e06 |
"""
Arguments:
:-p: project
:--copy-config: <target directory path>: copy configuration files to target directory path;
:--sum: <log file directory> create a summary of the results logged in the specified directory.
:-f: <file>: check a single file;
:-d: <directory>: check all the NetCDF files in a directory... | martinjuckes/ceda_cc | ceda_cc/ccinit.py | Python | bsd-3-clause | 11,070 | [
"NetCDF"
] | 68f95fbaac0da2e2a41956d04d6ad1909f0b0ee9f4e96a83edcfc28c8737915e |
try:
from galaxy.jobs.runners.util.cli import (
CliInterface,
split_params
)
code_dir = 'lib'
except ImportError:
from lwr.managers.util.cli import (
CliInterface,
split_params
)
code_dir = '.'
def get_shell(params):
cli_interface = CliInterface(code_dir=cod... | jmchilton/lwr | lwr/managers/util/cli/factory.py | Python | apache-2.0 | 426 | [
"Galaxy"
] | 02c1dcac2d374c453b3460ea4568213b547e6ba1e244caab1b35835ee63af255 |
from __future__ import print_function
'''Constant pressure/stress and temperature dynamics.
Combined Nose-Hoover and Parrinello-Rahman dynamics, creating an NPT
(or N,stress,T) ensemble.
The method is the one proposed by Melchionna et al. [1] and later
modified by Melchionna [2]. The differential equations are integ... | suttond/MODOI | ase/md/npt.py | Python | lgpl-3.0 | 31,935 | [
"ASE",
"NetCDF"
] | af6a2c71a137b1d28f6f2229b61dff9c06915b94ffaa59b2273cfda63597cb5a |
from Sire.IO import *
from Sire.Mol import *
from Sire.MM import *
from Sire.FF import *
from nose.tools import assert_equal, assert_almost_equal
def _getEnergies(s):
intraclj = IntraFF("intraclj")
intraclj.add(s.molecules())
intraff = InternalFF("intraff")
intraff.setUse14Calculation(True)
intr... | michellab/SireUnitTests | unittests/SireIO/test_growrite.py | Python | gpl-3.0 | 3,592 | [
"Amber",
"Gromacs"
] | 944a8868da73c2899fad7ce605710b7f7dae8ac9841a23e7bdc681a5d119870b |
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