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from ase import *
from ase.dft import monkhorst_pack
from ase.structure import bulk
from gpaw import *
from gpaw.test import equal
import numpy as np
a0 = 5.43
cell = bulk('Si', 'fcc', a=a0).get_cell()
Si = Atoms('Si2', cell=cell, pbc=True,
scaled_positions=((0,0,0), (0.25,0.25,0.25)))
kpts = monkhorst_pac... | ajylee/gpaw-rtxs | gpaw/test/exx_q.py | Python | gpl-3.0 | 1,155 | [
"ASE",
"GPAW"
] | 26625acab1367fff93a66c99935dd404907e19c38cc30158e6a0a222a344daa7 |
import unittest, random, sys, time
sys.path.extend(['.','..','py'])
import h2o, h2o_cmd, h2o_hosts, h2o_glm, h2o_import as h2i, h2o_exec as h2e
def define_params():
paramDict = {
'standardize': [None, 0,1],
'beta_epsilon': [None, 0.0001],
'family': [None, 'gaussian', 'binomial', 'pois... | woobe/h2o | py/testdir_single_jvm/test_GLM2_params_rand2.py | Python | apache-2.0 | 2,725 | [
"Gaussian"
] | 27d47451f7f10e344dc183af816744c5e0e150d6fa813118cb4a26de2c7b53ae |
# shamelessly copied from pliExpertInfo (Vali, Mirakels, Littlesat)
from os import path
from enigma import iServiceInformation, iPlayableService
from Components.Converter.Converter import Converter
from Components.Element import cached
from Components.config import config
from Tools.Transponder import ConvertToHumanRe... | openatv/enigma2 | lib/python/Components/Converter/PliExtraInfo.py | Python | gpl-2.0 | 25,454 | [
"Galaxy"
] | 1f884a7134a99447383e583cf733e4a0df8d4131b008a86e9e22f85b92d25322 |
# -*- coding: utf-8 -*-
"""
Created on 25 Jun 2014
@author: Éric Piel
Copyright © 2014-2015 Éric Piel, Delmic
This file is part of Odemis.
Odemis is free software: you can redistribute it and/or modify it under the terms of the GNU
General Public License version 2 as published by the Free Software Foundation.
Odem... | gstiebler/odemis | src/odemis/acq/stream/_static.py | Python | gpl-2.0 | 39,904 | [
"Gaussian"
] | 2e8530add6ef30e8b41e0ffdf60a259e3e43e053a1e0d2c10593e9c362ba3581 |
# Copyright 2017 The 'Scalable Private Learning with PATE' 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
#
# ... | tensorflow/privacy | research/pate_2018/ICLR2018/rdp_bucketized.py | Python | apache-2.0 | 7,703 | [
"Gaussian"
] | 8d979d07a1e6f9a6666d0661abe78537364e7b09cdfee2b830c5fa5b616d2938 |
#!/usr/bin/env python
import os, pygtk, gtk, webbrowser
import playlist
EDIT_WIDTH, EDIT_HEIGHT = 300, 200
#
# Provides a standard menu for open, save, help, etc..
# Main widget: menubar
#
class Menu:
pymp, popup, path = None, None, None
#
# Creates the menu and adds it to the provided treeview.
#
def _... | jantman/TuxTruck-wxPython | pymp/menu.py | Python | gpl-3.0 | 7,477 | [
"VisIt"
] | 2fd5b896abd5d809c9fdc1594737c907742c8fa77c6fd728d8e18efb2235ee34 |
# Copyright 2016 Brian Innes
#
# 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, ... | brianinnes/vPiP | python/vPiP/__init__.py | Python | apache-2.0 | 623 | [
"Brian"
] | 7abfea5d3f8215d75d08927a2916f3ce1fa826854cecda8ff9e1a56d89d8a8ac |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2012, Hsiaoming Yang <http://lepture.com>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above c... | hiphopsmurf/bitcoin-secured | online/build/livereload/livereload/__init__.py | Python | mit | 4,165 | [
"VisIt"
] | a1525c7366fa78924aba48cdb32a34f81416c88932e36b147e51ccc3a1a98ef1 |
import sys
sys.path.append("..")
from identify_locus import *
import pytest
import pysam
def test_randomletters_len():
length = 5
letters = randomletters(length)
assert len(letters) == length
def test_randomletters_diff():
length = 10
letters1 = randomletters(length)
letters2 = randomletters(l... | Oshlack/STRetch | scripts/tests/test_identify_locus.py | Python | mit | 6,140 | [
"pysam"
] | 20a229c26f73d5d551ccc21b2abe0245f802514f1c38c7fd88ac7fad00dc383f |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License")
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... | okkhoy/rlglue-python3-codec | src/tests/test_rl_episode_experiment.py | Python | apache-2.0 | 1,851 | [
"Brian"
] | 533ee1bb831883282e69cfc7ec246d709e369536193ef027dbdb1c30658e0bc6 |
import sys
import unittest
sys.path.append('./code')
from transforms import Transform, UnivariateGaussianization
from models import MoGaussian
from numpy import abs, all
Transform.VERBOSITY = 0
class Test(unittest.TestCase):
def test_inverse(self):
"""
Make sure inverse Gaussianization is inverse to Gaussianiz... | lucastheis/isa | code/transforms/tests/univariategaussianization_test.py | Python | mit | 2,311 | [
"Gaussian"
] | 07980b6b1220d85e1c7ba3f083095cd1997646ff58a03aa9f5d52edf0af3a3cc |
# -*- coding: utf-8 -*-
import numpy as np
import scipy.integrate as sci
import scipy.optimize as opt
import time
import tarfile
import os
import csv
from montagn_utils_Lu import *
from montagn_classes import *
from montagn_polar import *
import matplotlib.pyplot as plt
from gui_random import *
######################... | lukaltair/MontAGN_V2 | montagn/montagn_launch.py | Python | gpl-3.0 | 37,476 | [
"Gaussian"
] | 8b631ad1e539221407977fbd5f20434b215da2ddfa4f20c7e13db486a8499799 |
# Copyright 2012 Jake Ross
#
# 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, soft... | UManPychron/pychron | pychron/mv/locator.py | Python | apache-2.0 | 28,476 | [
"Gaussian"
] | 0a6971c5c7bce2097925d7cf133b57610f80e0aa7c0fe51658e632f66dd4f3c9 |
"""
Maximum likelihood covariance estimator.
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Gael Varoquaux <gael.varoquaux@normalesup.org>
# Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
# avoid division truncation
from __future__ import division
import warnin... | depet/scikit-learn | sklearn/covariance/empirical_covariance_.py | Python | bsd-3-clause | 8,679 | [
"Gaussian"
] | 72102aa34412079d9f8992260bb262c61bd353f47705f9d47255857815db505b |
from dateutil import parser
import tempfile
from django.conf import settings
from django.contrib.sessions.middleware import SessionMiddleware
from django.contrib.messages.storage.fallback import FallbackStorage
from django.test import TestCase, RequestFactory
from hs_core.models import ResourceFile
from hs_core.hydro... | RENCI/xDCIShare | hs_core/testing.py | Python | bsd-3-clause | 36,160 | [
"NetCDF"
] | 1dd6e2455c8fb261d3bba9f3d01adf3ab2eae9e49feef8a29443d7b05dc24adc |
# ------------------------------------------------------------------------------
# Copyright (c) 2010-2013, EVEthing team
# 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... | madcowfred/evething | thing/tasks/wallettransactions.py | Python | bsd-2-clause | 8,753 | [
"VisIt"
] | aa243703b7f38378b3ce3c9f3a5eef3c50fc42882c75d02204530da37917c61e |
import StringIO, csv, yaml, uuid, time
from datetime import datetime
from bioblend.galaxy import GalaxyInstance
from items import SequencerOutputItem, SeqDataSampleItem
# dataset states corresponding to a 'pending' condition
_PENDING_DS_STATES = set(
["new", "upload", "queued", "running", "setting_metadata"]
... | crs4/omero.biobank | bl/vl/app/workflow_wrapper/galaxy_wrapper.py | Python | gpl-2.0 | 16,473 | [
"Galaxy"
] | 938a5158d4a9e6f8fc415c157aae6c82182db5ccc9a29cf197bb6992a74e7c66 |
tutorial_tests = """
Let's try a simple generator:
>>> def f():
... yield 1
... yield 2
>>> for i in f():
... print(i)
1
2
>>> g = f()
>>> next(g)
1
>>> next(g)
2
"Falling off the end" stops the generator:
>>> next(g)
Traceback (most recent call last... | mancoast/CPythonPyc_test | fail/323_test_generators.py | Python | gpl-3.0 | 50,625 | [
"VisIt"
] | 1c5317374d257c6aa15db1a8f8c5f60869ff3898fb1003fb46e49b4d86619111 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
import numpy as np
import tensorflow as tf
from zhusuan.diagnostics import *
class TestEffectiveSampleSize(tf.test.TestCase):
def test_effective_sample_size(self):
rng = np.random.Random... | thu-ml/zhusuan | tests/test_diagnostics.py | Python | mit | 1,091 | [
"Gaussian"
] | 32e599b04a9d3860b3f1dec3d7ee0f2b1ef9231a48b62236c7323d4ee4312e08 |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 2: Nature-Inspired Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2014 by Jeff Heaton
Licensed under the Apache License, Versi... | PeterLauris/aifh | vol2/vol2-python-examples/examples/capstone_alife/run_milestone2.py | Python | apache-2.0 | 1,032 | [
"VisIt"
] | 10e1c79c42df5dfd9a1ed1be4726e8d837fc3a5047cfbe8862589cce523d0e02 |
import Cython.Build
from setuptools import setup
from setuptools.extension import Extension
import numpy as np
# read the contents of your README file
from os import path
this_directory = path.abspath(path.dirname(__file__))
with open(path.join(this_directory, 'README.md'), encoding='utf-8') as f:
long_descriptio... | philippdre/omniCLIP | setup.py | Python | gpl-3.0 | 1,733 | [
"Biopython",
"pysam"
] | c835813c7bbe89eaa6d930e1611d8cf60cdaea3ff9da814672bc2b55ccf7d519 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RRandomfields(RPackage):
"""Simulation and Analysis of Random Fields
Methods for the ... | LLNL/spack | var/spack/repos/builtin/packages/r-randomfields/package.py | Python | lgpl-2.1 | 1,712 | [
"Gaussian"
] | cc59be1cf5b099a35b6234ce8a948a6960d5ea728ccaeb7abc234944a7976b7a |
#!/usr/bin/env python
#
# $File: simuOpt.py $
# $LastChangedDate$
# $Rev$
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free softw... | BoPeng/simuPOP | simuOpt.py | Python | gpl-2.0 | 12,392 | [
"VisIt"
] | 97bec8ae1d4bc74d2b4a62c6a6f757443607ab73e071a8d270195d5919bfd14f |
# 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/pbc/tools/pywannier90.py | Python | apache-2.0 | 35,627 | [
"CRYSTAL",
"PySCF",
"Wannier90"
] | 5cc0305fb381121147395e1e5eeb12d4abd8897cd400c346e8c7781b6031ad21 |
"""
Least squares anomaly detection demo on static data.
In this example, we generate some points from a 2-D Gaussian mixture,
and then plot the response of the anomaly detection model across the data
space given some different parameter settings.
The plots show training data as black crosses, contours in blue indica... | lsanomaly/lsanomaly | lsanomaly/notebooks/static_mix.py | Python | mit | 2,937 | [
"Gaussian"
] | 01ecbb30ee1684554a38ce32efe4b8f947132ddb1c27b6dd63fda316f30cc287 |
#
# Copyright (C) 2019, 2020, 2021 Smithsonian Astrophysical Observatory
#
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any late... | anetasie/sherpa | sherpa/utils/tests/test_psf_rebinning_unit.py | Python | gpl-3.0 | 15,233 | [
"Gaussian"
] | cd84e809bb46e12267b4cca2d533250d48cc83360827ec36f762975c75e882b9 |
from functools import wraps
import numpy as np
import networkx as nx
import vigra
import collections
from contextlib import contextmanager
from .box import Box
class BlockflowArray(np.ndarray):
def __new__(cls, shape, dtype=float, buffer=None, offset=0, strides=None, order=None, box=None):
obj = np.ndarr... | stuarteberg/blockflow | blockflow/blockflow.py | Python | mit | 15,659 | [
"Gaussian"
] | 92802fc4df3a874a0e71d98fefbb2ee61b61cbc89ca94e3ef40f461e5d41a208 |
"""
A set of ML-related functions that are used in a variety of models.
==============
Copyright Info
==============
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, o... | bdol/bdol-ml | utils/ml_functions.py | Python | lgpl-3.0 | 1,867 | [
"Brian"
] | 491b546f3e2964fbd91ab8fccbb40c8b62f49ce27c5b52eb854a57d19cef1d9b |
""" Utility Class for threaded agents (e.g. TransformationAgent)
Mostly for logging
"""
import time
from DIRAC import gLogger
__RCSID__ = "$Id$"
AGENT_NAME = ''
class TransformationAgentsUtilities(object):
""" logging utilities for threaded TS agents
"""
def __init__(self):
""" c'tor
"""
sel... | andresailer/DIRAC | TransformationSystem/Agent/TransformationAgentsUtilities.py | Python | gpl-3.0 | 2,767 | [
"DIRAC"
] | 39ab030bd63b574f1bc4e3206847f4ba6904b60734221aa5ce73fd7800c42fc2 |
# -*- coding: utf-8 -*-
# Copyright 2008-2013 Jaap Karssenberg <jaap.karssenberg@gmail.com>
'''Package with source formats for pages.
Each module in zim.formats should contains exactly one subclass of
DumperClass and exactly one subclass of ParserClass
(optional for export formats). These can be loaded by L{get_pars... | gdw2/zim | zim/formats/__init__.py | Python | gpl-2.0 | 43,556 | [
"VisIt"
] | b848642300753fc12dfd49e899602daf2a95237ce41d44759a85b318d99921dd |
"""Soundex algorithm
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.2 $"
__date__ = "$Date: 2004/05/06 21:36:36 $"
__copyright__ ... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/soundex/stage1/soundex1c.py | Python | mit | 2,335 | [
"VisIt"
] | 6bcdf60c6c164544b16acf95ff01008eaf86d95450780fbb4d0073dc2d849fda |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import pickle
import numpy as np
import warnings
from pymatgen import SETTINGS
import scipy.constants as const
from pymatgen.util.te... | matk86/pymatgen | pymatgen/io/vasp/tests/test_inputs.py | Python | mit | 32,454 | [
"VASP",
"pymatgen"
] | dd18795fba96bdab71de9acfc40cb45a92688c44fb0dc3d8f1cd285f3c9a5d04 |
#!/usr/bin/env python
#
# Copyright (c) 2014, Steven Caron <steven@steven-caron.com> All rights reserved.
#
# FabricArnold Extension
# test_0003
import os
import time
import math
from arnold import *
testNumber = "test_0003"
print("[FabricArnold::TestSuite] Generating reference image for {0}...".format... | wildparky/FabricArnold | tests/test_0003/reference.py | Python | bsd-3-clause | 2,639 | [
"Gaussian"
] | 199babc34f24b8a15b17ec50ed0409e92305fcf6d752e4c72032c543a311c78a |
# -*- coding: utf-8 -*-
# Copyright 2007-2022 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 y... | jat255/hyperspy | hyperspy/signal.py | Python | gpl-3.0 | 259,911 | [
"Gaussian"
] | 2a7d92f6f39231ad99e1f11a8ad5ab397ab29d7541805e3cd75a7cdf657c54b4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2014-2020 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/li... | sunqm/pyscf | pyscf/scf/addons.py | Python | apache-2.0 | 40,634 | [
"PySCF"
] | 5e0f0bdea57896e002e9ea0a2897a9d580de460c3421ddda0c1da8566c3fc8dd |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | MJJoyce/climate | examples/taylor_diagram_example.py | Python | apache-2.0 | 5,081 | [
"NetCDF"
] | f11e06f04dc32f411ebc7a1ba04d95781f7947b359bcbcfc861ada06d8c65a3e |
#!/usr/bin/env python
# ________ _______________ ____________
# ___ __/__ ____(_)_ /__ /______________ ___/_ /__________________ _______ ___
# __ / __ | /| / /_ /_ __/ __/ _ \_ ___/____ \_ __/_ ___/ _ \ __ `/_ __ `__ \
# _ / __ |/ |/ /_ / / /_... | ActianCorp/twitter-streaming | python/twitterStream.py | Python | apache-2.0 | 4,498 | [
"VisIt"
] | e984a7565168bada63a52dfbeebd5aa18a54113c22179c55672c26be79f50ccf |
# Load dependencies
import ovito.io
import ovito.io.particles
# Load the native code modules
import CrystalAnalysis
# Register export formats.
ovito.io.export_file._formatTable["ca"] = CrystalAnalysis.CAExporter
| srinath-chakravarthy/ovito | src/plugins/crystalanalysis/resources/python/ovito/io/crystalanalysis/__init__.py | Python | gpl-3.0 | 214 | [
"OVITO"
] | a1fa8ef2980b64e0d2faae7b44d917201b04c42f6fb0451f92f973ba1fa78c91 |
from common.hgraph.hgraph import NonterminalLabel
from common import log
import itertools
# Some general advice for reading this file:
#
# Every rule specifies some fragment of the object (graph, string or both) that
# is being parsed, as well as a visit order on the individual elements of that
# fragment (tokens or e... | isi-nlp/bolinas | parser/vo_item.py | Python | mit | 19,950 | [
"VisIt"
] | f9e09ac79068e3354326aa468ba30d9aba9605dac39952f9d220fff562613de9 |
#!/usr/bin/env python
# encoding: utf-8
# Thomas Nagy, 2010 (ita)
"""
Classes and functions required for waf commands
"""
import os, imp, sys
from waflib import Utils, Errors, Logs
import waflib.Node
# the following 3 constants are updated on each new release (do not touch)
HEXVERSION=0x1060700
"""Constant updated o... | Gnomescroll/Gnomescroll | server/waflib/Context.py | Python | gpl-3.0 | 16,338 | [
"VisIt"
] | c3201bc8c21c9041182a880764465ed266fdfb6d59f7091c3117c298b8d9b8ec |
#Dump each file to a flattened array-feature vector is all files interleaved
import glob
import os
import numpy as np
from scipy.io import netcdf as ncd
def extract_data(filename, var_name):
fp = ncd.netcdf_file(os.path.join('../data',filename))
d = fp.variables[var_name][:,:,:]
fp.close()
return d
if __name__ ... | story645/spfinal | dataexport.py | Python | bsd-3-clause | 1,139 | [
"NetCDF"
] | d5770c0ee781aeb2bd31a35c7e5a2e14d3a431018ea360ba83b36ec3ae2c1ce4 |
#!/usr/bin/env python
import sys
import os
import re
import tempfile
import subprocess
import fileinput
import shutil
import optparse
import urllib2
import gzip
from ftplib import FTP
import tarfile
from galaxy.util.json import from_json_string, to_json_string
def stop_err(msg):
sys.stderr.write(msg)
sys.exi... | mr-c/tools-iuc | data_managers/data_manager_snpeff/data_manager/data_manager_snpEff_download.py | Python | mit | 8,487 | [
"Galaxy"
] | 0a1677f80ace212c88f05b193bdc1ee47bca84fb2fc58e4c4a3728b7d2111200 |
import numpy
import sklearn.cluster
import time
import scipy
import os
import audioFeatureExtraction as aF
import audioTrainTest as aT
import audioBasicIO
import matplotlib.pyplot as plt
from scipy.spatial import distance
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import sklearn.discriminant_analysis
im... | muthu1993/InteliEQ | audioSegmentation.py | Python | apache-2.0 | 46,767 | [
"Gaussian"
] | e8600f9287df2f164a4999f3b9afe49444bab7e3773b89dd563bfdb63053bb9b |
#!/usr/bin/env python
"""Read the contents of a single file containing DFT output and create a csv style file of information"""
from __future__ import print_function
import numpy as np
import os, sys
import PDielec.Utilities as Utilities
import PDielec.__init__
version = PDielec.__init__.__version__
def print_help():
... | JohnKendrick/PDielec | PDielec/p1reader.py | Python | mit | 3,741 | [
"ABINIT",
"CASTEP",
"CRYSTAL",
"GULP",
"VASP",
"phonopy"
] | 9014523d6554bdf9e2bfcfc1ffb1e72d7a1fbab8bb770bcd57a36751bfc640e6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# lswww v2.3.1 - A web spider library
# Copyright (C) 2006 Nicolas Surribas
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of th... | teknolab/teknolab-wapiti | wapiti/net/lswww.py | Python | gpl-2.0 | 32,330 | [
"VisIt"
] | 6903c2381716ce6462d40ec835c9f3fdca3afdb1def828c3c6f7fd15af3ba07f |
import os
from setuptools import setup, find_packages
from setuptools.extension import Extension
import numpy as np
here = os.path.abspath(os.path.dirname(__file__))
try:
README = open(os.path.join(here, 'README.rst')).read()
except IOError:
README = ''
# Test if rdkit is present with INCHI support
try:
f... | NLeSC/MAGMa | job/setup.py | Python | apache-2.0 | 2,099 | [
"RDKit"
] | 520146f7970cbfc84e50d5b3a32356c3ce1a53519ee1df438ab1b5a603714b2b |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import mock
import time
import unittest
import logging
import functools
from nose.tools import * # noqa: F403
import pytest
from framework.auth.core import Auth
from website import settings
import website.sea... | CenterForOpenScience/osf.io | osf_tests/test_elastic_search.py | Python | apache-2.0 | 62,145 | [
"Brian"
] | 512d140b27e633fc8edd7b26021632803807bf48cf6fc99d0992a16a285a6313 |
"""
Visualization functions for displaying spikes, filters, and cells.
"""
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import animation, cm, gridspec
from matplotlib.patches import Ellipse
from . import filtertools as ft
from .utils import plotwrapper
__all__ = ['raster', 'psth', 'raster_and_p... | baccuslab/pyret | pyret/visualizations.py | Python | mit | 19,921 | [
"Gaussian"
] | 56e596dad980059edb13767a3901d3c72f8f17254c4a21b38e7cfc54c5f4dce9 |
#! /usr/bin/env python
# Copyright (C) 2016 Li Yao <yaoli95@outlook.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to us... | RNAEDITINGPLUS/main | node/missenseOntology.py | Python | apache-2.0 | 3,650 | [
"pysam"
] | 761f98db64da030307c1f5bc4be9345e5a6bcd5fc40e3323f3f230fcaf2758c2 |
# -*- coding: utf-8 -*-
"""Copyright 2015 Roger R Labbe Jr.
FilterPy library.
http://github.com/rlabbe/filterpy
Documentation at:
https://filterpy.readthedocs.org
Supporting book at:
https://github.com/rlabbe/Kalman-and-Bayesian-Filters-in-Python
This is licensed under an MIT license. See the readme.MD file
for mor... | BrianGasberg/filterpy | filterpy/kalman/sigma_points.py | Python | mit | 14,788 | [
"Gaussian"
] | 02a754926e028a3d23e694607d095b01fe7c170bcbdea8cdc798df83dd0b8bc7 |
from django.test import TestCase, tag
from django.core.exceptions import ObjectDoesNotExist
from edc_base import get_utcnow
from edc_base.tests import SiteTestCaseMixin
from ..models import SubjectScheduleHistory
from ..schedule import Schedule
from ..site_visit_schedules import site_visit_schedules
from ..subject_sch... | botswana-harvard/edc-visit-schedule | edc_visit_schedule/tests/test_subject_schedule.py | Python | gpl-2.0 | 6,789 | [
"VisIt"
] | 635c77bb593c37a8f442f672424e87e1975c3df38b9b174ebbcc431ea9cfb617 |
from mayavi.core.api import registry
from simphony_mayavi.adapt2cuds import adapt2cuds
def load(filename, name=None, kind=None, rename_arrays=None):
""" Load the file data into a CUDS container.
Parameters
----------
filename : str
The file name of the file to load.
name : str
T... | simphony/simphony-mayavi | simphony_mayavi/load.py | Python | bsd-2-clause | 1,869 | [
"Mayavi"
] | dd291560aa56f790cb79e0f6a1b1da1627e8da515e1a9df9428befcbc8675fda |
''' AlwaysProbingPolicy module
'''
from DIRAC import S_OK
from DIRAC.ResourceStatusSystem.PolicySystem.PolicyBase import PolicyBase
__RCSID__ = '$Id$'
class AlwaysProbingPolicy(PolicyBase):
'''
The AlwaysProbingPolicy is a dummy module that can be used as example, it
always returns Probing status.
'''
... | fstagni/DIRAC | ResourceStatusSystem/Policy/AlwaysProbingPolicy.py | Python | gpl-3.0 | 776 | [
"DIRAC"
] | fb6c78ec19d302c2c93d09d6fbe0082b62fb08f4b9800664350c00d85b670d1e |
# Copyright 2000-2004 Brad Chapman.
# Copyright 2001 Iddo Friedberg.
# Copyright 2007-2010 by Peter Cock.
# 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.
"""Classes for generic ... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/Align/Generic.py | Python | apache-2.0 | 17,526 | [
"BLAST",
"BioPerl",
"Biopython"
] | 23be7a96bdce1cb69fde40197eeae2fa5828f4db8b1730992635af9d37ab5816 |
# -*- coding: utf-8 -*-
#
# hl_api_connections.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Lice... | obreitwi/nest-simulator | pynest/nest/lib/hl_api_connections.py | Python | gpl-2.0 | 34,873 | [
"NEURON"
] | ea2dc6be38080df903d881e94b7829104da8aef290396ba9b37e3629de622ffd |
#!/usr/bin/env python
################################################################################
# Copyright (C) 2014, 2015 GenAP, McGill University and Genome Quebec Innovation Centre
#
# This file is part of MUGQIC Pipelines.
#
# MUGQIC Pipelines is free software: you can redistribute it and/or modify
# it und... | ccmbioinfo/mugqic_pipelines | bfx/bwa.py | Python | lgpl-3.0 | 2,157 | [
"BWA"
] | 5766f2a93c54d53a16608518cc0ac294957aa640b09964ccaacb25fddbd1f4da |
# Copyright 2016 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as an Intergovernmental Orga... | blond-admin/BLonD | blond/beam/distributions.py | Python | gpl-3.0 | 41,361 | [
"Gaussian"
] | 28b6308d1b7b52526530fc8a23d34d993a3ca45edade5e309e24e00e852ab540 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-affypdnn/package.py | Python | lgpl-2.1 | 1,740 | [
"Bioconductor"
] | 6d75cb9bc9c4dbd30bf6d3f789ea425cb76038620ecbb57bc8f2653b4badda8b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest2 as unittest
import os
import warnings
from pymatgen.analysis.ewald import EwaldSummation, EwaldMinimizer
from pymatgen.io.vasp.inputs import Poscar
imp... | aykol/pymatgen | pymatgen/analysis/tests/test_ewald.py | Python | mit | 3,985 | [
"VASP",
"pymatgen"
] | 765e89d14cc19c1f70668cf6b339d55c1d5581d5ad1f641628eac7446bc1ca3a |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
from El.core import *
from ctypes import CFUNCTYPE
# S... | mcopik/Elemental | python/matrices.py | Python | bsd-3-clause | 87,208 | [
"Gaussian"
] | fbd02bbca64dd7ba89ffa5aba1398d53d913ff10c07845940bd16fed5da0d26a |
#!/usr/bin/env python
"""
"""
import vtk
def main():
colors = vtk.vtkNamedColors()
fileName = get_program_parameters()
# Read the image.
readerFactory = vtk.vtkImageReader2Factory()
reader = readerFactory.CreateImageReader2(fileName)
reader.SetFileName(fileName)
reader.Update()
ca... | lorensen/VTKExamples | src/Python/ImageProcessing/Attenuation.py | Python | apache-2.0 | 3,263 | [
"VTK"
] | 38f18d53ba51764229fbe7742b88450b6b60e4bd18af5f68dd6046cdf0c20351 |
# -*- coding: utf-8 -*-
"""
Created on Fri Jun 13 10:08:00 2014
@author: Fujitsu
"""
def UserDefined(Rawfile,Indicator,Ligand_index,Protein_index, Model_index,SpiltCriteria,
CV_Method,FeatureSelectionMode, Iteration, NumPermute, SpiltMethod):
import os
user = {}
user['Root'] = os.g... | Rnewbie/PCM | Descriptors_Extraction.py | Python | gpl-2.0 | 21,105 | [
"MOE",
"RDKit"
] | 883c792b46bb0c98aae9bb98598ac52a721f1c60aa0b67ff5e56e1ff8553f965 |
from pymol.wizard import Wizard
from pymol import cmd
import pymol
import traceback
sele_prefix = "_mw"
sele_prefix_len = len(sele_prefix)
indi_sele = "_indicate_mw"
obj_prefix = "measure"
class Measurement(Wizard):
modes = [
'pairs',
'angle',
'dihed',
'polar',
'heavy',
... | gratefulfrog/lib | python/pymol/wizard/measurement.py | Python | gpl-2.0 | 17,133 | [
"PyMOL"
] | b05eec2dfb42efc8eaccbd9b64e53e90c1ced47d51e6408444bd0c950fa4ee32 |
"""
Portable Executable (PE) 32 bit, little endian
Used on MSWindows systems (including DOS) for EXEs and DLLs
1999 paper:
http://download.microsoft.com/download/1/6/1/161ba512-40e2-4cc9-843a-923143f3456c/pecoff.doc
2006 with updates relevant for .NET:
http://download.microsoft.com/download/9/c/5/9c5b2167-8017-4bae-9... | mekolat/manachat | external/construct/formats/executable/pe32.py | Python | gpl-2.0 | 11,720 | [
"MOE"
] | 9eac6bef21ffacb584386cd640b42d569af0b3955fda7ea00122673084f7d274 |
import glob
import pandas as pd
import numpy as np
pd.set_option('display.max_columns', 50) # print all rows
import os
os.chdir("/gpfs/commons/home/biederstedte-934/evan_projects/correct_phylo_files")
normalB = glob.glob("binary_position_RRBS_normal_B_cell*")
mcell = glob.glob("binary_position_RRBS_NormalBCD19pCD27... | evanbiederstedt/RRBSfun | trees/chrom_scripts/total_chr01.py | Python | mit | 32,997 | [
"MCell"
] | 3b25ea7953fa2c49ac8fef9316da71f753f26138fe53e48f971dd03976b3475b |
'''
Code for method recommendation experiments for HCD Connect cases
Written by Mark Fuge and Bud Peters
For more information on the project visit:
http://ideal.umd.edu/projects/design_method_recommendation.html
To reproduce the experimental results just run:
python paper_experiments.py
... | IDEALLab/design_method_recommendation_JMD_2014 | paper_experiments.py | Python | apache-2.0 | 22,845 | [
"VisIt"
] | 5672af6e77a578d0265daf4fea151f003fade1e3cf933474b0853b41fb89512e |
from __future__ import absolute_import
from __future__ import division
from builtins import zip
from builtins import object
from .. import xtals
from ..misc import *
def fake_properties_calc_json(poscar_file):
"""Create a fake properties.calc.json file from a poscar.
Fills all the fields with ideal coordinate... | goirijo/thermoplotting | thermoplotting/casmfiles/properties.py | Python | mit | 7,461 | [
"CRYSTAL",
"VASP"
] | cf5692c480442ab0105bb0c1e7cc1342611821dd03261990ba13d2039ab782ab |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
from copy import deepcopy
from functools import partial
from gzip import GzipFile
import os
import os.path as op
import numpy as np
from scipy import sparse, linalg... | teonlamont/mne-python | mne/source_space.py | Python | bsd-3-clause | 112,114 | [
"Mayavi"
] | 8ae24a65da703af8521caa06e780849d9494cd6482bb4dd4f9e1c9831134be6f |
#!/usr/bin/env python
import cgi
import sqlite3
import random
with open("../templates/header.html", "r") as header:
print header.read()
with open("../templates/navbar.html", "r") as navbar:
print navbar.read()
#
# return HTML string for ingredient
#
def getIngredientHTML(index):
onSelectionString = ""
offSelectio... | kbrohkahn/kevin.broh-kahn.com | view-recipes/index.py | Python | apache-2.0 | 41,516 | [
"MOOSE"
] | 5234c772a0854d8ada1711da0c50a860f71868dd846e63dce7de016ee6a9dff0 |
'''
Created on Aug 5, 2014
@author: gearsad
'''
import vtk
import numpy
from math import sin,cos
from SceneObject import SceneObject
class LIDAR(SceneObject):
'''
A template for drawing a LIDAR point cloud.
Ref: http://stackoverflow.com/questions/7591204/how-to-display-point-cloud-in-vtk-in-different-colo... | GearsAD/semisorted_arnerve | arnerve/scene/LIDAR.py | Python | mit | 4,034 | [
"VTK"
] | b8f68ed4b9540c98526d6461912ef90d60b2f9dadd999d40d0a27899f270814b |
"""methods_utils.py:
Some non-standard functions generic to moose.
This library may not be exposed to end-users. Intended for development by
the maintainer of this file.
Last modified: Sat Jan 18, 2014 05:01PM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NC... | subhacom/moose-core | python/moose/methods_utils.py | Python | gpl-3.0 | 1,287 | [
"MOOSE"
] | 2c9606324a42f5c677355edcc4734162885362db657d0808f3de62f8559cd5a2 |
"""
Create and put Requests to move files.
List of operations:
#. ReplicateAndRegister LFNs
#. Check for Migration
#. Remove all other replicas for these files
"""
import os
from DIRAC import gLogger
from DIRAC.Core.Base.Script import Script
from DIRAC.Core.Utilities.List import breakListIntoChunks
from DIRAC.Core.U... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_create_moving_request.py | Python | gpl-3.0 | 11,475 | [
"DIRAC"
] | 9417ef1e8b582ed5b1f4f962a54d7a2bba368b0d74cce8249c08a90d99036a97 |
import os
import pymatgen as pmg
import pymatgen.io.nwchem as nwchem
from cage.landscape import LandscapeAnalyzer
from cage import Cage
from json import JSONDecodeError
"""
Small utility scripts that support the use of the cage package.
"""
# Elements to ignore for the surface facet determination
IGNORE = (pmg.El... | mbercx/cage | cage/cli/commands/util.py | Python | mit | 8,566 | [
"NWChem",
"pymatgen"
] | 680ce095a8e502a62240e2f532897bd6832145424b8aca46cf620a86a7e11403 |
print("""
FEM simulation using getfem++ and siconos.
""")
import siconos.kernel as kernel
import numpy as np
import getfem as gf
from matplotlib.pyplot import *
class SiconosFem:
""" The set of matrices required by Siconos, from a Finite Element Model
"""
def __init__(self):
self.nbdof = 0
... | bremond/siconos | examples/Mechanics/FEM/python/block_friction.py | Python | apache-2.0 | 7,780 | [
"ParaView",
"VTK"
] | 8177345b0846c1d7e42d3ab5d498ac7da7447caec78561cee51117559f623a9f |
from setuptools import setup
setup(name='suspenders',
version='0.2.6',
description='Allows the merging of alignments that have been annotated using pylapels into a single alignment that picks the highest quality alignment.',
url='http://code.google.com/p/suspenders',
author='James Holt',
... | holtjma/suspenders | setup.py | Python | mit | 515 | [
"pysam"
] | 0c585afa8bf88bb79671c814eba69b24e78611c2a5e9022159f2d5dea84f9253 |
"""
Container page in Studio
"""
from bok_choy.page_object import PageObject
from bok_choy.promise import Promise, EmptyPromise
from common.test.acceptance.pages.studio import BASE_URL
from common.test.acceptance.pages.common.utils import click_css, confirm_prompt
from common.test.acceptance.pages.studio.utils impor... | louyihua/edx-platform | common/test/acceptance/pages/studio/container.py | Python | agpl-3.0 | 20,916 | [
"VisIt"
] | f4667eac5d24c71148e8754496f84434aaa5aae25a4e33987ce3f1bf37781e4d |
from gpaw.fd_operators import Gradient
import numpy as np
from gpaw.grid_descriptor import GridDescriptor
from gpaw.mpi import world
if world.size > 4:
# Grid is so small that domain decomposition cannot exceed 4 domains
assert world.size % 4 == 0
group, other = divmod(world.rank, 4)
ranks = np.arange(... | qsnake/gpaw | gpaw/test/gradient.py | Python | gpl-3.0 | 1,766 | [
"GPAW"
] | dd8de563bb0dc36d3c55808ba9ee83170078bcac7c5fe36ae0afe6a824d01bf8 |
# -*- 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 snippet show how to "test" a Facebook feature: the creation of an event.
It creates an event by going to http://www.facebook.c... | nikolas/splinter | samples/test_facebook_events.py | Python | bsd-3-clause | 2,705 | [
"VisIt"
] | 9ffc61b82b732b714a25e83905eba6b11807b342982a332c2514dfba2c8de15a |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains an algorithm to solve the Linear Assignment Problem.
It has the same functionality as linear_assignment.pyx, but is much slower
as it is vectorized in numpy rather than cython
"""
__author__ = "Will ... | vorwerkc/pymatgen | pymatgen/optimization/linear_assignment_numpy.py | Python | mit | 8,191 | [
"pymatgen"
] | fa96d4aeee952276f9821cc0814a5e51c3573aa34e9617c3fe756311af554828 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2003-2005 Edgewall Software
# Copyright (C) 2003-2005 Jonas Borgström <jonas@edgewall.com>
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution. The terms
# are also available at htt... | cyphactor/lifecyclemanager | testenv/trac-0.10.4/trac/env.py | Python | gpl-3.0 | 18,288 | [
"VisIt"
] | 008122754771332d3436a2780661adcdbe90419b58fc6e7e1efb95771fbc6a59 |
import os, time
from datetime import datetime
import pyinsane.abstract as pyinsane
from PIL import Image
def getScanners():
devices = pyinsane.get_devices()
# load pickle devices if no one connect (only for debugging)
if len(devices) == 0:
import pickle
f = open('devices.dump', 'rb')
... | RoboMod/Online-Scanner-Interface | app/helpers.py | Python | gpl-2.0 | 2,455 | [
"ADF"
] | 69b30f71a7953d373f970b7d7208f5f6ea3ab000ac92581c70bda30eb4365bd6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
from fractions import Fraction
import numpy as np
from monty.design_patterns import cached_class
import textwrap
from pymatgen.core import Lattice
from pymatgen.electronic_structure.core import Mag... | blondegeek/pymatgen | pymatgen/symmetry/maggroups.py | Python | mit | 22,653 | [
"CRYSTAL",
"pymatgen"
] | 7500f042bdcbcad2d8753eeb6341afb5d7b4d60deee961a5086b6acc19d753b2 |
#!/usr/bin/env python
"""Script to read a com file created by amboniom and make changes
required to oniom calculation."""
# python modules
import argparse
#our modules
import molecules
import gaussian
PARSER = argparse.ArgumentParser(
description = 'Reads the output of amboniom and makes changes for oniom',
form... | eduardoftoliveira/oniomMacGyver | omg/dock++/amboniom_to_oniom.py | Python | gpl-3.0 | 1,323 | [
"Amber",
"Gaussian"
] | c2ab464aa877040f93d6f0c997eb526dcd6fa9364a2562547bda5459c2b4876f |
from rdkit import Chem
from rdkit.Chem import Descriptors
from rdkit.Chem import PandasTools
from rdkit.Chem import FilterCatalog
import pandas as pd
try:
# Import extra, proprietary functions
from websdf.extra import extra
except:
extra = None
params = FilterCatalog.FilterCatalogParams()
params.AddCatalo... | samoturk/websdf | websdf/calculations.py | Python | bsd-3-clause | 4,228 | [
"Open Babel",
"RDKit"
] | 077685687ba7fb8a025c7d358c71027cc44d97aef832ed6475508342f0569fa1 |
from contextlib import contextmanager
import os
import sys
import unittest
from rdkit import RDConfig
from rdkit.Chem import FeatFinderCLI
from io import StringIO
class TestCase(unittest.TestCase):
def test_FeatFinderCLI(self):
smilesFile = os.path.join(RDConfig.RDDataDir, 'NCI', 'first_5K.smi')
... | bp-kelley/rdkit | rdkit/Chem/UnitTestFeatFinderCLI.py | Python | bsd-3-clause | 2,752 | [
"RDKit"
] | dc873acb93e5299b65eea9ea09e832100d27b65414c6cb639ee5bc5b8f6c0543 |
#!/usr/bin/env python
__author__ = "Mike McCann"
__copyright__ = "Copyright 2011, MBARI"
__license__ = "GPL"
__maintainer__ = "Mike McCann"
__email__ = "mccann at mbari.org"
__status__ = "Development"
__doc__ = '''
Load small sample of data from OPeNDAP and other data sources at MBARI
for testing purposes. The colle... | google-code-export/stoqs | loaders/loadTestData.py | Python | gpl-3.0 | 2,577 | [
"NetCDF"
] | fe892de82a0c91ca0f2ac8c096a30faf253374db374b7bd468f017c2dde26226 |
from Bio import SeqIO
from Bio.Seq import Seq, translate
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet.IUPAC import IUPACUnambiguousDNA, IUPACProtein
from Bio.Blast import NCBIXML
from Bio.Blast.Applications import NcbiblastpCommandline
import sys, glob, os... | pjtatlow/geneysis | python/functions.py | Python | mit | 28,887 | [
"BLAST"
] | 04c260e5a935fa18ee5180b67f9627adc3d060fdf25cb84d2c47b6a55f03af97 |
#!/usr/bin/env python3
# Copyright (C) 2016, 2017(H)
# 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, ei... | espressopp/espressopp | examples/adress/fadress_selfadjusting/peptide-adres-selfadjusting.py | Python | gpl-3.0 | 21,994 | [
"ESPResSo",
"Gromacs"
] | b495843f212a8623e689bb1f954f9d6809b7ffd1a5a9f022b2d4bb0f49813785 |
# Author: Felix Wiemann
# Contact: Felix_Wiemann@ososo.de
# Revision: $Revision: 4163 $
# Date: $Date: 2005-12-09 05:21:34 +0100 (Fri, 09 Dec 2005) $
# Copyright: This file has been placed in the public domain.
# This is a mapping of Unicode characters to LaTeX equivalents.
# The information has been extracted from
# ... | alon/polinax | libs/external_libs/docutils-0.4/docutils/writers/newlatex2e/unicode_map.py | Python | gpl-2.0 | 73,666 | [
"Bowtie"
] | f3c28e130bc5a45cd4801ec0544a85023ace4530f7f46560b15dc575914d216f |
# -*- coding: utf-8 -*-
"""
Output Plugin for generic external encoders with piping.
Copyright (c) 2006-2008 by Nyaochi
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of t... | rinrinne/cueproc-alternative | src/ce_extpipe.py | Python | gpl-2.0 | 1,707 | [
"VisIt"
] | 0ed4b00d84ec5d597741990a29265d9d3f360f69a2e965511a7520d09e54c835 |
import simtk.unit as u
from simtk.openmm import app
import simtk.openmm as mm
from openmoltools import gafftools, system_checker
ligand_name = "sustiva"
ligand_path = "./chemicals/%s/" % ligand_name
temperature = 300 * u.kelvin
friction = 0.3 / u.picosecond
timestep = 0.1 * u.femtosecond
prmtop = app.AmberPrmtopFile... | Clyde-fare/openmoltools | examples/test_example.py | Python | gpl-2.0 | 1,421 | [
"OpenMM"
] | 301fefc97d7fa156c72134b995f58459c919d9951af748fbdd6df3aefb3b0419 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import ast
import logging
from sys import version_info
from .errors import ScriptSyntaxError
supported_nodes = ('arg', 'assert', 'assign', 'attribute', 'augassign',
'binop', 'boolop', 'break... | nickchen-mitac/fork | src/ava/job/validator.py | Python | apache-2.0 | 7,468 | [
"VisIt"
] | 0c58c95d41f6cbab6e8827fee344f29b083699ba740c89d3a767f67b2cb03a3f |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2014, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | chetan51/nupic | nupic/algorithms/anomaly_likelihood.py | Python | gpl-3.0 | 22,129 | [
"Gaussian"
] | ab046cc02e76ecbcbb906a218a108274a13bc886c2916e7cfe46f6e0564302d5 |
'''Module with EMC_writer class to save dense frames in EMC format'''
from __future__ import print_function
import os
import numpy as np
try:
import h5py
HDF5_MODE = True
except ImportError:
HDF5_MODE = False
class EMCWriter(object):
"""EMC file writer class
Provides interface to write dense inte... | duaneloh/Dragonfly | utils/py_src/writeemc.py | Python | gpl-3.0 | 7,979 | [
"MOE"
] | 7fb222019ab3d165c6279ca3b01748560d450579a0abb7b0afe5629e6880e59f |
import numpy as np
from gpaw.utilities.blas import gemm
from gpaw.utilities import pack, unpack2
from gpaw.utilities.timing import nulltimer
class EmptyWaveFunctions:
def __nonzero__(self):
return False
def set_eigensolver(self, eigensolver):
pass
def set_orthonormalized(self, flag)... | ajylee/gpaw-rtxs | gpaw/wavefunctions/base.py | Python | gpl-3.0 | 15,526 | [
"GPAW"
] | e4d73aeb71c49ac7e9021dd53e59cace2bf5bd8f52ababa1d1de295c1ee3c389 |
# Version: 0.12
"""
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
[](... | hgenru/python-schemator | versioneer.py | Python | mit | 36,719 | [
"Brian"
] | 7b7acba4d79b2eef35de501d0a2024755499d96bd17940828daed1f0707ab351 |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse, sys, fnmatch, os, dma_resolver, shlex, pickle, re
import shutil
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help='Output directory')
parser.add_argument(
'--bootloade... | ethomas997/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 58,725 | [
"CRYSTAL"
] | 2ca0afa0fe4e32e73138b4b91cbf3a0517d07ab0422e7612f6868b0d3628b8d4 |
#!/usr/bin/python
import numpy as np
import pylab as pl
from auryntools import *
# This code snipped assumes that you have run the example simulation
# sim_coba_binmon with default paramters.
# This generates spk output files under /tmp/
filename = "/tmp/coba.0.e.spk"
seconds = 0.1
sf = AurynBinarySpikeFile(file... | idiot-z/auryn | tools/python/simple_spike_raster.py | Python | gpl-3.0 | 466 | [
"NEURON"
] | 9b3c2d6b0a3400fca3b25a3057192f70f97f06d36f96e04db688703da64cdb1a |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser Gen... | jchodera/cclib | src/cclib/method/volume.py | Python | lgpl-2.1 | 10,208 | [
"Gaussian",
"VTK",
"cclib"
] | 1f78da6f52e829d537bdd2c6f5c190e1c8049285bfe6a515ca869b107fc9505e |
# Copyright (C) 2004, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
"""Vector class, including rotation-related functions."""
import numpy
def m2rotaxis(m)... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/PDB/Vector.py | Python | gpl-2.0 | 9,097 | [
"Biopython"
] | 516c7b7be4e9b4a5337e8e2c41b1d8528c4fa736824502f094c1c28cabd31e94 |
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