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import cgt
from cgt import core
from cgt import nn
import numpy as np
import cPickle as pickle
from scipy.stats import norm
import matplotlib.pyplot as plt
from example_utils import fetch_dataset
'''
MNIST manifold demo (with 2-dimensional latent z) using variational autoencoder
'''
rng = np.random.RandomState(1234)
... | nebw/cgt | examples/demo_variational_autoencoder.py | Python | mit | 10,799 | [
"Gaussian"
] | 04c16d6edbaa7eb6a51d75c38133d904ebed0100ca273287cbf25d275e06b758 |
"""
========================
Random Number Generation
========================
Use ``default_rng()`` to create a `Generator` and call its methods.
=============== =========================================================
Generator
--------------- ---------------------------------------------------------
Generator ... | MSeifert04/numpy | numpy/random/__init__.py | Python | bsd-3-clause | 7,521 | [
"Gaussian"
] | fdd737334300f902c2afac52a4b6b57c40355fe7d9c968aa3285f4eb734a525b |
""" Basic setuptools script for DIRAC.
Does not contain any dependency
"""
import sys
import os
import glob
# Actual setuptools
from setuptools import setup, find_packages
# Find the base dir where the setup.py lies
base_dir = os.path.abspath(os.path.dirname(__file__))
# Take all the packages but the scripts and... | petricm/DIRAC | setup.py | Python | gpl-3.0 | 1,234 | [
"DIRAC"
] | e5043fc312d19cec5b4c31a704f8d760f265c5b9fb58aeea4b7acae168d46d1e |
"""
Component-level tests for builder.
"""
__author__ = "Dan Gunter <dkgunter@lbl.gov>"
__date__ = "4/24/14"
# Stdlib
import logging
import time
import unittest
# Package
from pymatgen.db.tests.common import ComponentTest, get_component_logger
_log = get_component_logger("comp_incr")
class BuilderComponentTest(Com... | materialsproject/pymatgen-db | pymatgen/db/builders/tests/comp_incr.py | Python | mit | 4,507 | [
"pymatgen"
] | 8a3d6afd3dfdf9d98c20ede9f18a9b61ba3a643b173eb9c5e52b31b6fd11ec47 |
# -*- coding: utf-8 -*-
#
# Markov Logic Networks
#
# (C) 2012-2015 by Daniel Nyga
# 2006-2011 by Dominik Jain
#
# 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, inclu... | danielnyga/pracmln | python2/pracmln/mln/learning/common.py | Python | bsd-2-clause | 9,913 | [
"Gaussian"
] | d7777abab3c7a4eff877ed129a9c6cda217ddd9c81d4b6c9eee6c0f746aa35a6 |
''' Significant lifting from https://jmetzen.github.io/2015-11-27/vae.html '''
import time
import numpy as np
import tensorflow as tf
import random
import matplotlib.pyplot as plt
import re, string
from sklearn.feature_extraction.text import CountVectorizer
from collections import defaultdict
import pickle as pkl
... | dricciardelli/vae2vec | VAE_def.py | Python | mit | 21,946 | [
"Gaussian"
] | 694ddac1c15db5e314d8a88a33df0e7dd07f43d16463e6ead449c3f58ea737af |
"""
==================================================
Plot different SVM classifiers in the iris dataset
==================================================
Comparison of different linear SVM classifiers on a 2D projection of the iris
dataset. We only consider the first 2 features of this dataset:
- Sepal length
- Se... | scikit-learn/scikit-learn | examples/svm/plot_iris_svc.py | Python | bsd-3-clause | 3,693 | [
"Gaussian"
] | 38ad949308e1622fa0ae31de1afe1d43c5e35d484055cfaf107f875dd42e27fd |
# Copyright (c) 2012 - N.P. de Klein
#
# This file is part of Python Mass Spec Analyzer (PyMSA).
#
# Python Mass Spec Analyzer (PyMSA) 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 ver... | davidmam/pyMSA | pyMSA/fileHandling.py | Python | gpl-3.0 | 10,017 | [
"OpenMS"
] | a12a149d489fee23577ba32bed8035eabe2c04dbf0d1b2a499715339f385ce89 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016 Haggi Krey, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of... | haggi/appleseed-maya | module/scripts/appleseed_maya/aetemplate/aemtap_standinlocatortemplate.py | Python | mit | 2,397 | [
"VisIt"
] | cf5662a20ee5c935636f80255c1d12d865a8314d8a05fd445eafa4c789dbf4bd |
##############################################################################
# Copyright (c) 2013-2017, 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... | TheTimmy/spack | var/spack/repos/builtin/packages/nwchem/package.py | Python | lgpl-2.1 | 7,627 | [
"Amber",
"NWChem"
] | 35446600beca41ba4fe7909a6aa770bd7cc1b44395b5f7c79ed46b940b398899 |
#
# Copyright (C) 2001-2005 Ichiro Fujinaga, Michael Droettboom, Karl MacMillan
# 2014 Fabian Schmitt
# 2009-2014 Christoph Dalitz
#
# 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 S... | hsnr-gamera/gamera | gamera/plugins/listutilities.py | Python | gpl-2.0 | 6,385 | [
"Gaussian"
] | 9f780ef5a32b84f17a53617f17f21f7477c7fadfed90e57237efb17e2758c597 |
# requires scikit bio [http://scikit-bio.org]
from skbio.parse.sequences import parse_fasta
import sys
if __name__ == '__main__':
with open(sys.argv[1], 'U') as in_file:
with open(sys.argv[2], 'w') as out_file:
for label, seq in parse_fasta(in_file):
seq = seq.replace("U", "T")... | ekopylova/sortmerna | rRNA_databases/scripts/edit_U_to_T_rna.py | Python | gpl-3.0 | 380 | [
"scikit-bio"
] | bf2cf5e985ec4551858d3f3aa53f693216e5d757ccaf95cdd96c66fb1db8cc74 |
"""
:mod:`svbjt` -- State-Variable-Based Bipolar Transistor
-------------------------------------------------------
.. module:: svbjt
.. moduleauthor:: Carlos Christoffersen
"""
from bjt import extrinsic_bjt
import numpy as np
import cardoon.circuit as cir
from cardoon.globalVars import const, glVar
import cppaddev... | cechrist/cardoon | cardoon/devices/svbjt.py | Python | gpl-3.0 | 19,632 | [
"xTB"
] | f9ce89c06b97cfaae8fe194718f94fac01f83d998bdbe53a0ca475d143dc22d6 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012-2013 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/exporters/xlsexporter.py | Python | gpl-2.0 | 4,485 | [
"VisIt"
] | de580503c26f43988d308b6bce2993139b5f6868ccb40032a0cc0e2661dddac9 |
#*************************************************************************
# Copyright (C) 2015 by Arash Bakhtiari
# You may not use this file except in compliance with the License.
# You obtain a copy of the License in the LICENSE file.
#
# Unless required by applicable law or agreed to in writing, software
# distribu... | arashb/tbslas | scripts/vis_plot_utils.py | Python | bsd-3-clause | 2,818 | [
"VTK",
"VisIt"
] | 405398af7facd62f1baa04e54df2eb09a89c77ee1878ddd617baf8f6109983c6 |
#!/usr/bin/env python
from ecmwfapi import ECMWFDataServer
server = ECMWFDataServer()
import os, os.path
fields_36912 = ""
fields_0 = "129.128/130.128/131.128/132.128/133.128/135.128/155.128"
for year in range(1979, 2015):
for f in fields_0.split('/'):
fn = "{0}.{1}.an.nc".format(year,f)
print(fn... | r-shekhar/ReanalysisUnifier | eraI_monthly/fetch_MSE.py | Python | mit | 1,147 | [
"NetCDF"
] | 704b2bdb3c8d6430ec2386cb06adc53b5289b191f6e438c7d57917e808bf2e28 |
#!/usr/bin/env python
# encoding: utf-8
#
# bpt.py
#
# Created by José Sánchez-Gallego on 19 Jan 2017.
from __future__ import division
from __future__ import print_function
from __future__ import absolute_import
import warnings
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
from mpl_toolkits.... | bretthandrews/marvin | python/marvin/utils/dap/bpt.py | Python | bsd-3-clause | 18,520 | [
"Galaxy"
] | ac82b9384eaac70be2d6cb4864c3bbaadcf3bff0c4d9da89ccdc1a38f9631d41 |
# -*- coding: utf-8 -*-
from wsgiref.simple_server import make_server
import threading
from selenium import webdriver
from lastuser_core.models import db
from lastuserapp import app
server_name = app.config.get('SERVER_NAME') or 'localhost:7001'
base_url = 'http://%s' % server_name
host, port = server_name.split(':'... | hasgeek/lastuser | features/environment.py | Python | bsd-2-clause | 1,055 | [
"VisIt"
] | de8c20d7d15c70791b0316fe0d41e3b913fc89081312d7c51284dc307c56bae9 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
These plugins modify the behavior of py.test and are meant to be imported
into conftest.py in the root directory.
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import __future__
from ... | AustereCuriosity/astropy | astropy/tests/pytest_plugins.py | Python | bsd-3-clause | 13,431 | [
"VisIt"
] | cd1dea25a4e4826038bc021d8b589f6322a33dfa8896a067eaec9c68daba3a55 |
# Nucleotide analysis from VCF files
# (c) 2017 Ali Rassolie
# Lumina sequencing
class annuc:
def __init__(self, **kwargs):
# Kwarg handling
self.spec_input = kwargs["dictinput"]
self.hass_input = kwargs["hass"]
self.output = kwargs["output"]
self.searchtype = kwargs["searchtype"]
self.pos_i... | HypoChloremic/annuc | annuc.py | Python | mit | 3,706 | [
"BWA"
] | 28a0a669fb06c034c4bef93f93551c73cdf35c70a8228885c64f2923f87e1382 |
#
# Copyright 2014-2015, 2017, 2021 Lars Pastewka (U. Freiburg)
# 2014-2015, 2020 James Kermode (Warwick U.)
# 2020 Petr Grigorev (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribu... | libAtoms/matscipy | matscipy/fracture_mechanics/clusters.py | Python | lgpl-2.1 | 4,414 | [
"ASE",
"Matscipy"
] | 9c3c2482404df30d61d83532cd9b94058ca0c4172104fa50baf4a4c202e7ad58 |
#!/usr/bin/env python
'''
File name: main_make_Thetainfo.py
Author: Guillaume Viejo
Date created: 16/08/2017
Python Version: 3.5.2
Theta modulation, returns angle
'''
import numpy as np
import pandas as pd
import scipy.io
from functions import *
# from pylab import *
import ipyparallel
import os... | gviejo/ThalamusPhysio | python/main_test_PHASE_THETA_HD.py | Python | gpl-3.0 | 7,839 | [
"Gaussian"
] | 2dea91e8bd68cd7febf79fa5f285c3c7902f9656654536c3bf41badf21219743 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2017 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | mdtraj/mdtraj | tests/test_reporter.py | Python | lgpl-2.1 | 10,137 | [
"MDTraj",
"OpenMM"
] | 62f2dcf4474315cf3121616ffb677642aebb28e4130cef8019b54e44d3f41feb |
__author__ = "{ ministry of promise }"
__copyright__ = "Copyright 2015, { ministry of promise }"
__license__ = "MIT"
__version__ = "0.1.0"
__maintainer__ = "Adam Nichols"
__email__ = "adam.j.nichols@gmail.com"
__status__ = "Development"
keyword_filterlist = [
u'account',
u'activity',
u'actor',
u'addres... | ministryofpromise/tlp | tlp/lib/filter_list.py | Python | mit | 43,519 | [
"ADF"
] | cb57e3dcb2236a4757557d18adcaf32f0ab49ccf05dee0ee7ebd5a6586767de5 |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | rdkit/rdkit-orig | rdkit/Chem/EState/UnitTestFingerprints.py | Python | bsd-3-clause | 1,588 | [
"RDKit"
] | e10bec8db44b609b9c66bc54f5b2741e43908860d7cd4ae749c2cb726642f2e6 |
import struct, binascii,hashlib
from Crypto.PublicKey import RSA
from Crypto.Cipher import PKCS1_OAEP
## serpent.py - pure Python implementation of the Serpent algorithm.
## Bjorn Edstrom <be@bjrn.se> 13 december 2007.
##
## Copyrights
## ==========
##
## This code is a derived from an implementation by Dr B... | gray-panda/grayrepo | 2020_flareon/11_rabbithole/__notworking/dsunsign.py | Python | gpl-2.0 | 74,080 | [
"Brian"
] | e565fd9d931d2a5fef3d3b0446e97c531f4f9dfa43f2fb766e1203e0b9f5c47d |
"""Particle filter implementation."""
import numpy as np
class ParticleFilter(object):
def __init__(self, num_points, init_coords, init_sigma, have_map,
have_imu):
"""Initialise num_points particles using an isotropic Gaussian with
variance init_sigma and mean init_coords. If tra... | qxcv/comp2550 | project/filter.py | Python | apache-2.0 | 7,753 | [
"Gaussian"
] | 6389a24f18fb2c0387186a6f16ff857a39d99d355a11349ac8f19ec636576c8d |
'''
.. module:: skrf.network
========================================
network (:mod:`skrf.network`)
========================================
Provides a n-port network class and associated functions.
Most of the functionality in this module is provided as methods and
properties of the :class:`Network` Class.
Networ... | hohe/scikit-rf | skrf/network.py | Python | bsd-3-clause | 141,218 | [
"Gaussian"
] | 6834317bc384623c2e9e41755a566b856ceea90a905d87fe64dee70b4e46a5db |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | fweik/espresso | testsuite/python/dawaanr-and-dds-gpu.py | Python | gpl-3.0 | 4,792 | [
"ESPResSo"
] | 0d4b24eae211a3783fcb93633ad064a32117ce98070fd323f631b4b6b6971585 |
'''
synbiochem (c) University of Manchester 2015
synbiochem is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=invalid-name
# pylint: disable=wrong-import-order
import unittest
from synbiochem.utils import neo... | synbiochem/synbiochem-py | synbiochem/utils/test/test_neo4j_utils.py | Python | mit | 2,255 | [
"VisIt"
] | e18fb7a13a134a3ffcfe16277ea671d29c7ff876a6701f70f799a7a4e407e6a3 |
#!/usr/bin/env python
"""Copyright 2010 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.8'
__date__ = 'May 17 2010'
#Basi... | danielsuo/mobot | src/move/Python/Encoder-simple.py | Python | mit | 3,692 | [
"VisIt"
] | 496dcf1560db122b2c1681adadb71a430f9da57f2ff10bc6eb5f246f4b17c89b |
#
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | doc/tutorials/06-active_matter/EXERCISES/rectification_geometry.py | Python | gpl-3.0 | 3,483 | [
"ESPResSo",
"ParaView",
"VTK"
] | d4d7c1b9e6e085b621add023d2916cd31a5e3ac34e5c81ab64af8ca9570ad818 |
import os
from confypy import Config
from confypy import Location
yamlConf = '.octobot/config.yaml'
ud = os.path.expanduser('~')
cwd = os.getcwd()
user_config = os.path.join(ud, yamlConf)
local_config = os.path.join(cwd, yamlConf)
env_keys = [
'OCTOBOT_INCOMING_WEBHOOK_URL',
'OCTOBOT_U... | aubricus/octobot | octobot/config.py | Python | mit | 914 | [
"Octopus"
] | 493b1bc4c498185c0d4094a8e0c34c38e69281803cd7a423ebb0cdd7065f19f4 |
TRIPLE_SCORES = {}
for index, triple in enumerate("""
ing$ ed$ es$ er$ ^co ^re ate ers$ ion$ ^de ^di ess$ atio ies$ tion ^ca ine ati
ica te$ ted ^su ive ting ions$ ^ma tes ^pa ier$ ^mi ere ^ba al$ red iest$ ove
era ^pe rat ic$ lly$ ^pro ble$ ring eri ty$ ^po est$ ent$ ^ha tions cat ity
^se ly$ lat able ^mo ina ene ^sa ... | jcrocholl/nxdom | languages/english.py | Python | mit | 111,819 | [
"ASE",
"BLAST",
"GULP",
"ORCA"
] | 95435f8316647006ae39708e08b668e9e31308a28440a883d2e20c2c468a04d7 |
#
# Loxodo -- Password Safe V3 compatible Password Vault
# Copyright (C) 2008 Christoph Sommer <mail@christoph-sommer.de>
#
# 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 ... | sommer/loxodo | src/frontends/wx/vaultframe.py | Python | gpl-2.0 | 24,282 | [
"Brian"
] | 3d0ced28a677d428a5dc97f768109bc692cf92c0664ccc133593f90a7210fc15 |
# Copyright 2018 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
#... | google/deepvariant | third_party/nucleus/util/vcf_constants_test.py | Python | bsd-3-clause | 8,955 | [
"ADF"
] | d51cdcaeb2ec44c75af6be3cbf473872c92df9c2d8808143e223d60d70954356 |
import sys
import subprocess
import os
import os.path
import shutil
import argparse
import tempfile
import re
import perform_stats
import time
import pickle
from parse_pra_output import parse_pra_output
from checkpoint_jobs import *
try:
fp = open("locations.txt")
except:
sys.stderr.println("locations.txt fil... | karroje/RAIDER_eval | RAIDER_eval.py | Python | gpl-3.0 | 87,080 | [
"BLAST"
] | 2a278f09256bff47838edfbd9b47840e0e922b6bcd679943a8d3307e79f28ec7 |
#!/usr/bin/env python3
# -*- encoding: <utf-8> -*-
# Sprax Lines 2017.04.01 Written with Python 3.5
# To re-import a library in Python 3.4+ (re-import), do:
# import importlib
# importlib.reload(nameOfModule)
'''text filter functions'''
import argparse
import heapq
import os.path
import re
import math
impor... | sprax/python | txt/text_filters.py | Python | lgpl-3.0 | 11,763 | [
"Octopus"
] | 2e29c2a4dbd3bd731ef954b01df0e48c473f86e59a6df18e94f8c9e1a87405cc |
'''
Created on Jan 24, 2014
@author: julian Garrido
'''
import os
import astropy.io.fits as fits
import sys
class whispCubes(object):
'''
This class read the fits files of whisp cubes and creates sql
commands to populate a postgres database
'''
def __init__(self, db):
'''
... | julian-garrido/feedCubesDB | src/readHeaders.py | Python | gpl-2.0 | 13,453 | [
"Gaussian"
] | 020c2b7c65248deb3afdf267ae2e8b12983127c2a745eabf57c09d0237ad9e9d |
from __future__ import print_function, absolute_import, division
import glob
import os
import numpy as np
from .utils import expand_path, num_samples
class BaseDatasetLoader(object):
short_name = None
def load(self):
raise NotImplementedError('should be implemented in subclass')
class MSMBuilderD... | cxhernandez/osprey | osprey/dataset_loaders.py | Python | apache-2.0 | 4,570 | [
"MDTraj"
] | 0e4e50a0d105fa34a15601cddf1fec54c1991b6a315bd37e2b6a5041206510da |
""" The TaskManagerAgentBase is the base class to submit tasks to external systems,
monitor and update the tasks and file status in the transformation DB.
"""
import datetime
from DIRAC import S_OK, S_ERROR, gMonitor, gLogger
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.TransformationSystem.Clien... | avedaee/DIRAC | TransformationSystem/Agent/TaskManagerAgentBase.py | Python | gpl-3.0 | 16,230 | [
"DIRAC"
] | 54a9e259455b737ad7f3bff9cb9c9df63db3876e32a74ff25993a694f6f9862f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# rss - RSS feed generator functions
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | heromod/migrid | mig/shared/rss.py | Python | gpl-2.0 | 5,207 | [
"Brian"
] | b6f570b7a19a83fa725ac2c60ff874ef509bb26c8fbc40a6bec367b48a5f8402 |
import random, math
from pymongo import MongoClient
from random import shuffle
#firsts = ['rushing', 'swift', 'majestic', 'glorious', 'royal', 'ancient', 'raging', 'royal', 'graceful', 'grand', 'regal', 'elegant']
#seconds = ['mountain', 'stream', 'forest', 'plains', 'ocean', 'vista', 'mesa', 'canyon', 'fjord', 'delta... | thepropterhoc/Cha_The_Pivot | names.py | Python | mit | 2,156 | [
"COLUMBUS",
"Octopus"
] | 01ff437a2ba8f83cb1879021294587bbded900f798071a016f6739476ded4199 |
import psi4
def test_psi4_basic():
"""tu1-h2o-energy"""
#! Sample HF/cc-pVDZ H2O computation
h2o = psi4.geometry("""
O
H 1 0.96
H 1 0.96 2 104.5
""")
psi4.set_options({'basis': "cc-pVDZ"})
psi4.energy('scf')
assert psi4.compare_values(-76.0266327341067125, psi4.get_var... | kratman/psi4public | tests/pytest/test_psi4.py | Python | gpl-2.0 | 8,661 | [
"Psi4"
] | 9933f0841c86cfdbbdf63b091ea0363d429a818be4f0d3c9d61f236655595997 |
import subprocess
import sys
import os
import linecache
import re
import numpy as np
if len(sys.argv)<3:
print 'An input file and setup file are needed as arguments'
print 'Input and setup files must be stored in folder RR_fitter/input/'
print 'Input file path name must be entered before setup file name'
print 'Ex... | elizabethswann/RR_fitter | run_fullshape_fitter.py | Python | mit | 2,183 | [
"Galaxy"
] | 9a1d17e41756272e2eed649913a8fc4551e882b05cdd13f6ca22b81be797a52a |
# Orca
#
# Copyright 2004-2009 Sun Microsystems Inc.
# Copyright 2010-2013 The Orca Team
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your... | chrys87/orca-beep | src/orca/messages.py | Python | lgpl-2.1 | 119,157 | [
"ORCA"
] | 64df7fc368524c44b1be889bd0414a43c647d9a3e551b36dec2dd028b4e9826b |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy, ... | alexholcombe/dot-jump | dataRaw/Fixed Cue/autoTest_dot-jump21Nov2016_14-32.py | Python | gpl-3.0 | 26,455 | [
"Gaussian"
] | 3521ba0c76a0583ebef92b910d2bf5903ca0000b63b60ddbc78b2432b615c371 |
# Copyright (c) 2014 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""
This script is intended for use as a GYP_GENERATOR. It takes as input (by way of
the generator flag config_path) the path of a json file that dictates the file... | wiltonlazary/arangodb | 3rdParty/V8/gyp/generator/analyzer.py | Python | apache-2.0 | 30,587 | [
"VisIt"
] | bb8aa790aa978f7d93159480d96d5b8bdacb6a92b55d4cfee1530ee4f556113b |
import ase.db
from ase.units import kcal, mol
from ase.data.g2_1_ref import ex_atomization, atomization
c = ase.db.connect('results.db')
# Energy of atoms:
atoms = {}
for d in c.select(natoms=1):
atoms[d.numbers[0]] = [d.energy, d.exx]
maepbe = 0.0
maeexx = 0.0
print(' PBE ... | robwarm/gpaw-symm | gpaw/test/big/kpb/check.py | Python | gpl-3.0 | 955 | [
"ASE"
] | 43d5dcf45a521f7e07eee041f4fec7638321a0e267547f71eee6d2a17832a365 |
"""Collection of DIRAC useful list related modules.
By default on Error they return None.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import six
import random
import sys
def uniqueElements(aList):
"""Utility to retrieve lis... | yujikato/DIRAC | src/DIRAC/Core/Utilities/List.py | Python | gpl-3.0 | 4,015 | [
"DIRAC"
] | 26ee456b02878fa6e5e5c24177a3f3c416e712a2b68471ec587c4280c9789845 |
# pykarta/maps/layers/vector.py
# An editable vector layer
# Copyright 2013--2017, Trinity College
# Last modified: 2 February 2017
import gtk
import cairo
import math
import weakref
from pykarta.maps.layers import MapLayer
from pykarta.geometry import Point, BoundingBox, LineString, Polygon
import pykarta.draw
#===... | david672orford/pykarta | pykarta/maps/layers/vector.py | Python | gpl-2.0 | 22,875 | [
"FLEUR"
] | 0642665be98147b081dadeeb705ed748257d5ffd3629d0d66e70e723075185fa |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-bigtable | scripts/fixup_bigtable_v2_keywords.py | Python | apache-2.0 | 6,488 | [
"VisIt"
] | 9acee9b98667757be89213d6dfa159755838a254c3708780394af120e138c849 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# 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)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/analysis/test_psa.py | Python | gpl-2.0 | 19,652 | [
"MDAnalysis"
] | 5a40ea42ea574cf4983486ca487e6e94fe35df41a220a717963029c8a09d62c8 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/signals.py | Python | gpl-3.0 | 804 | [
"Brian"
] | e4b196ad0ab04c5e506c901bb7524de9750baaeaf11bad37401ae71b809d209b |
#!/usr/bin/env python
# Media Dragon - the modular media manager
# Copyright (C) 2012 Brian Hrebec
#
# 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 y... | bhrebec/mediadragon | src/lib/ui/qt.py | Python | gpl-3.0 | 767 | [
"Brian"
] | e3b307a409569fd3fed541fa793ab995c89881b5740f4c539bda0215509e1a19 |
#! /usr/bin/python
#
# Copyrighted David Cournapeau
# Last Change: Sat Jun 09 10:00 PM 2007 J
"""This module implements some function of densities module in C for efficiency
reasons. gaussian, such as pdf estimation, confidence interval/ellipsoids,
etc..."""
__docformat__ = 'restructuredtext'
# This module uses a C... | jhmadhav/pynopticon | src/em/_c_densities.py | Python | gpl-3.0 | 7,087 | [
"Gaussian"
] | 67c06253e7ddd9fb961219dc54d245f53206add26fff26dbfa9ef347303c9376 |
#! /usr/bin/env python
"""
Module with fake companion injection functions.
"""
__author__ = 'Carlos Alberto Gomez Gonzalez, Valentin Christiaens'
__all__ = ['collapse_psf_cube',
'normalize_psf',
'cube_inject_companions',
'generate_cube_copies_with_injections',
'frame_inject... | vortex-exoplanet/VIP | vip_hci/fm/fakecomp.py | Python | mit | 28,708 | [
"Gaussian"
] | d3c21d279dd8a4f38151a9263a62c05a58aedeaa20e46e1bc57152d03d36d2de |
#!/usr/bin/env python3
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, Qiyun Zhu and Katharina Dittmar.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# --------------------... | DittmarLab/HGTector | hgtector/tests/test_analyze.py | Python | bsd-3-clause | 33,093 | [
"Gaussian"
] | 7abef91a94ccdaf327a5285a8bb2ff8d888dfddd610bcaf39d8e7c228ccdaa7b |
#!/usr/bin/env python
#
# fetchfa - Fetch fasta files from Entrez
#
# Copyright (C) 2013, Jian-Long Huang
# Licensed under The MIT License
# http://opensource.org/licenses/MIT
#
# Author: Jian-Long Huang (jianlong@ntu.edu.tw)
# Version: 0.4
# Created: 2013.1.24
#
# Required:
# * Biopython: http://biopython.org
#
# Usag... | jlhg/bdorpy | bdorpy/fetchfa.py | Python | mit | 4,623 | [
"Biopython"
] | d1478fdc93211edcde3103e6f76a294b7713bde8b13033bf26fdae4ea233e95e |
from django.db.models import Q
from django.http import HttpResponse, HttpResponseRedirect, JsonResponse
from django.shortcuts import get_object_or_404, redirect
from django.template import loader
import json
from cocomapapp.models import Tag, Topic, Post, Relation, Vote, Visit
from django.contrib.auth.models import Us... | bounswe/bounswe2016group11 | cocomapapp/views.py | Python | apache-2.0 | 34,067 | [
"VisIt"
] | f5ea5b71e800f4a03bc3b005d43de4a9e43b3406027a4dc31c4353990f52b239 |
# -*- coding: utf-8 -*-
# Begin CVS Header
# $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/bindings/python/unittests/Test_CReportDefinition.py,v $
# $Revision: 1.10 $
# $Name: $
# $Author: gauges $
# $Date: 2008/04/21 10:27:07 $
# End CVS Header
# Copyright (C) 2008 by Pedro Mendes, Virgin... | jonasfoe/COPASI | copasi/bindings/python/unittests/Test_CReportDefinition.py | Python | artistic-2.0 | 3,580 | [
"COPASI"
] | 9869216fa80c5c5b8467f8c2d0954f3baa205afbcd65b3691f046552e3b7f821 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simu... | liuwenf/moose | python/MooseDocs/tests/common/nodes/test_nodes.py | Python | lgpl-2.1 | 7,672 | [
"MOOSE"
] | 9481dd80cd8fa0d6ef4fe8707acb51304de64b340a52b446b94a94d73533a268 |
#***********************************************************************
# This code is part of pyCMPL
#
# Copyright (C) 2013
# Mike Steglich - Technical University of Applied Sciences
# Wildau, Germany
#
# pyCMPL is a project of the Technical University of
# Applied Sciences Wildau and the Institute f... | Mangara/ArboralExplorer | lib/Cmpl/pyCmpl/lib/pyCmpl/CmplSet.py | Python | apache-2.0 | 6,901 | [
"VisIt"
] | 205c1161ebb1699eb92a3fff05f7f3a2afcfa2d02e7e3b7986fc3a705fd0aa2a |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 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 General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_cfopeditor.py | Python | gpl-2.0 | 1,154 | [
"VisIt"
] | bb8c43abf652d78dd96bd5639ca5fdcbff129ebee43a377821b8bf4662862810 |
# YASARA PLUGIN
# TOPIC: pKaTool/EM_effect titration interface
# TITLE: Start pKaTool or EM_effect
# AUTHOR: Jens Nielsen
# LICENSE: GPL
# DESCRIPTION: This plugin starts EM_effect or pKaTool
#
# This is a YASARA plugin to be placed in the /plg subdirectory
# Go to www.yasara.com/plugins for docume... | dmnfarrell/peat | pKaTool/EM_effect_yasara.py | Python | mit | 1,142 | [
"YASARA"
] | 4a6cfd298870ce11f211f6633ec5fb4e1d280728df6daa6f1b611456c92766c4 |
"""
Enterprise Registration tests
"""
from regression.pages.enterprise.enterprise_const import (
ENT_COURSE_TITLE,
ENT_PORTAL_PASSWORD,
ENT_PORTAL_USERNAME
)
from regression.tests.enterprise.ent_test_base import EnterpriseTestBase
class TestEnterpriseRegistration(EnterpriseTestBase):
"""
Test Ent... | edx/edx-e2e-tests | regression/tests/enterprise/test_ent_registration.py | Python | agpl-3.0 | 1,700 | [
"VisIt"
] | fb005aa330e2993de0f1b2906f167b120fafa66cb2859eb8b00dc812bc69d522 |
# Functions for finding random points and orientations.
#
# Written by: Konrad Hinsen
# Last revision: 2000-8-9
#
"""This module defines various random quantities that are useful in
molecular simulations. For obtaining random numbers, it tries to use
the RNG module, which is part of the LLNL package distribution, whi... | fxia22/ASM_xf | PythonD/site_python/MMTK/Random.py | Python | gpl-2.0 | 5,293 | [
"Gaussian"
] | 955d2752054ef218d230d0113d65a213b9aff1f3d2b991580aefda99b838855c |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def drawPoints(myscreen, clpoints, ccpoints):
c=camvtk.PointCloud( pointlist=clpoints, collist=ccpoints)
c.SetPoints()
myscreen.addActor(c )
def drawFiber(myscreen, f, fibercolor=camvtk.red):
inter = f.getInts()
print "fi... | davidwusea/opencamlib | scripts/fiber_03_onetri_many-z-levels.py | Python | gpl-3.0 | 5,099 | [
"VTK"
] | bf5f1324c2c4e26955e373239abe4ffae8a1b98165abeb633c8028ec0b975362 |
# -*- coding: utf-8 -*-
"""
This is an example of VAE, whose p(z) is a mixture of Gaussian:
.. math::
p(z) = \\sum_{k=1}^K \\pi(k) p_{k}(z)
"""
import functools
import sys
from argparse import ArgumentParser
import tensorflow as tf
from pprint import pformat
from tensorflow.contrib.framework import arg_scope, ... | korepwx/tfsnippet | tfsnippet/examples/auto_encoders/mixture_vae.py | Python | mit | 9,150 | [
"Gaussian"
] | 5b064d6e0087e6cff45e5defa3e22d5969dff1e746ee149fb071f41e2417e8c0 |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
import warnings
from scipy.special import comb
from scipy.misc.doccer import inherit_docstring_from
from scipy import special
from scipy import optim... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/scipy/stats/_continuous_distns.py | Python | agpl-3.0 | 105,558 | [
"Gaussian"
] | e0bb556c7a48c614c1c009113e95f128ea2fcf4c17875359496466e47eb8f852 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/crystal/test_hart-forcade.py | Python | gpl-3.0 | 5,939 | [
"CRYSTAL",
"VASP"
] | 2565f53dde56348181e9cc8764503caab7409915644f6c1c1a99753a83877933 |
# A simple test for a vtkTkRenderWidget. Run it like so:
# python TestTkRenderWindowInteractor.py -B $VTK_DATA_ROOT/Baseline/Rendering
import os
import vtk
from vtk.test import Testing
import Tkinter
from vtk.tk.vtkTkRenderWindowInteractor import vtkTkRenderWindowInteractor
class TestTkRenderWindowInteractor(Testin... | aashish24/VTK-old | Rendering/Tk/Testing/Python/TestTkRenderWindowInteractor.py | Python | bsd-3-clause | 2,047 | [
"VTK"
] | baab87c42a17d5698e4a31ec0a06199207094745759669d0e0560bf056f33a08 |
#!/usr/bin/env python
#
# Copyright (c) 2010 Brian Knox (taotetek@gmail.com)
# License: GNU LGPLv3
#
# This file is part of Multi-Mechanize
#
"""a collection of functions and classes for multi-mechanize results files"""
import re
import fileinput
from datetime import datetime
try:
from sqlalchemy.ext.declara... | seznam/mcache-client | powertest/lib/resultsloader.py | Python | lgpl-3.0 | 7,162 | [
"Brian"
] | 7fe2ec02f1958611e030a931664532a188e806f29ddb9cbaa21d5e39161321ce |
import sys
import matplotlib as mpl
import torch.nn.functional as F
import torch.optim as optim
import torchvision
import torchvision.transforms as transforms
from tensorboardX import SummaryWriter
from torch import nn
from torch.autograd import Variable
from tqdm import trange
import gaussian
import util
from util i... | MaestroGraph/sparse-hyper | experiments/gconv-simple.py | Python | mit | 17,048 | [
"Gaussian"
] | 0643494d65badd9cf080d059f6fe41552dea1b4c4e49f597ed7dcba4904071c2 |
# ---
# jupyter:
# jupytext:
# formats: ipynb,.pct.py:percent
# text_representation:
# extension: .py
# format_name: percent
# format_version: '1.3'
# jupytext_version: 1.3.3
# kernelspec:
# display_name: Python 3
# language: python
# name: python3
# ---
# %% [markdown]
... | GPflow/GPflow | doc/source/notebooks/tailor/mixture_density_network.pct.py | Python | apache-2.0 | 11,118 | [
"Gaussian"
] | d36ab438c613d86fdc72d14891826e5af7021d1a422986f979dc0ebf9c10ab36 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# (c) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
#... | garyjyao1/ansible | lib/ansible/modules/core/files/find.py | Python | gpl-3.0 | 11,313 | [
"Brian"
] | a0c10ea7c3552cd12cfec5af66d5531ede91b61111759ae83f5150091c9e83f8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import warnings
from pymatgen.core.bonds import (
CovalentBond,
get_bond_length,
get_bond_order,
obtain_all_bond_lengths,
)
from pymatgen.core.periodic_table import Element
fro... | gmatteo/pymatgen | pymatgen/core/tests/test_bonds.py | Python | mit | 3,958 | [
"pymatgen"
] | ca6558fdfc63f59b27253b426f125961a53725e4568b26c28a2f31b4b4373d3b |
# Copyright (c) 2012, Cloudscaling
# 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 applicable... | xuweiliang/Codelibrary | nova/hacking/checks.py | Python | apache-2.0 | 28,873 | [
"VisIt"
] | 82cfc4c57b17605b61dad79cde0641d3d1a34dfcb80f179637caaa31d1e43b38 |
from __future__ import print_function
import os
import sys
import pickle
from math import pi
import numpy as np
from ase.units import Hartree, Bohr
import gpaw.mpi as mpi
from gpaw.response.chi0 import Chi0
from gpaw.response.kernel2 import calculate_Kxc
from gpaw.response.wstc import WignerSeitzTruncatedCoulomb
c... | robwarm/gpaw-symm | gpaw/response/df.py | Python | gpl-3.0 | 21,827 | [
"ASE",
"GPAW"
] | 2184a5e5472ca6bff507a4ffe9636eabe073ab20d628673455340a8f12f4cfd7 |
"""A convenience which constructs expression trees from an easy-to-read syntax
Use this unless you have a compelling reason not to; it performs some
optimizations that would be tedious to do when constructing an expression tree
by hand.
"""
from collections import Mapping
from inspect import isfunction, ismethod
fro... | smurfix/parsimonious | parsimonious/grammar.py | Python | mit | 19,455 | [
"VisIt"
] | 78501c810a5a9d5c5df3286f87d7f86ccde56ace74c595500a1fbe9c2f42d8d1 |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Chops alignments in a MAF file to piece of a specified length. A random set of
non overlapping chunks of exactly the specified chop length will be produced
usage: %prog [options] < maf > maf
-l, --length: Chop to exactly this length in columns (default 100)
"""
import s... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/maf_chop.py | Python | bsd-3-clause | 1,524 | [
"Galaxy"
] | 71cb5f67198e2ccd3750b4b47bcda494981e53880248cada9e57ac4164b7dd49 |
# 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)
import os
class Petsc(Package, CudaPackage, ROCmPackage):
"""PETSc is a suite of data structures and routines for the... | LLNL/spack | var/spack/repos/builtin/packages/petsc/package.py | Python | lgpl-2.1 | 33,000 | [
"NetCDF"
] | e96e77d65af8a7d87cc7c70656a2c9267199b3d8091dd5960f2d522ed3564e0c |
#!/usr/bin/env python
from math import sqrt
import gtk
from ase.gui.languages import translate as _
from ase.gui.widgets import pack, Help
class DFT(gtk.Window):
def __init__(self, gui):
gtk.Window.__init__(self)
self.set_title(_('DFT'))
vbox = gtk.VBox()
combo = gtk.combo_box_ne... | freephys/python_ase | ase/gui/dft.py | Python | gpl-3.0 | 1,485 | [
"ASE"
] | f1fd52205d00a9b588d285bb3f7d48338fc3a50621959c37095d5138ec3546e3 |
# -*- coding: utf-8 -*-
#
# test_3d_exp.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or... | tillschumann/nest-simulator | topology/examples/test_3d_exp.py | Python | gpl-2.0 | 2,956 | [
"Gaussian"
] | 5d2f7504bdbd43d8721f6bdd3d90ddd11ebb5b885801453831819e244c6f27a8 |
import argparse
import sys
import datetime
import os
from collections import OrderedDict
import json
import base64
import logging
from functools import partial
from itertools import chain
import pybedtools
import pysam
import vcf
import fasta_utils
mydir = os.path.dirname(os.path.realpath(__file__))
VCF_TEMPLATE = os... | msahraeian/metasv | metasv/generate_final_vcf.py | Python | bsd-2-clause | 29,341 | [
"pysam"
] | abbcba9787381c5ed3c9fd3fc1a9a321a061d8d522d3fe68f8be85650bb72675 |
"""
Hidden Markov Models
====================
.. autosummary::
:toctree: generated/
:nosignatures:
HMM
DiscreteHMM
GaussianHMM
StudentHMM
GMMHMM
"""
from __future__ import division, print_function, absolute_import
# noinspection PyUnresolvedReferences
from six.moves import range
from abc import... | evenmarbles/mlpy | mlpy/stats/dbn/hmm.py | Python | mit | 43,454 | [
"Gaussian"
] | 013ae2b6c897ce0b73cfd737b6857d01cb99305991608b96ede69e2a06eabbea |
# -*- coding: utf-8 -*
"""
pymeasure.liveplotting
----------------------
The liveplotting module is part of the pymeasure package. It allows
parallel 1D and 2D live plotting of multiple incoming data streams. The
focus of the module is on rapid and uncomplicated displaying of data
streams. Liv... | t--wagner/pymeasure | liveplot.py | Python | gpl-3.0 | 27,901 | [
"Gaussian"
] | 1c862f470a8b151d2bb2ab5e2502fc7069c23a0586ccd8392342e9945e63087c |
import copy
import pytest
from .utils import *
import numpy as np
import psi4
pytestmark = pytest.mark.quick
_vars_entered = {
'VAR A': 4.0,
'VaR B': -4.0,
'MATVAR A': psi4.core.Matrix.from_array(np.arange(6).reshape(2, 3)),
'MatvaR B': psi4.core.Matrix.from_array(np.arange(3).reshape(1, 3)),
'... | jgonthier/psi4 | tests/pytests/test_qcvars.py | Python | lgpl-3.0 | 8,520 | [
"Psi4"
] | 14841f4add67f0d1d2e96f790e1502c7403916d4ddff93f93e019abf7ce37e39 |
# Copyright 2017 the GPflow authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writi... | GPflow/GPflow | tests/gpflow/test_mean_functions.py | Python | apache-2.0 | 11,259 | [
"Gaussian"
] | 48e32b89525ec8402af1946758c6cc8efb45794cd71b8ebfc36dabe5ef30eb4f |
import os
import numpy as np
from ase.calculators.vasp import Vasp
def write_kpoints(self, fname='KPOINTS'):
"""Writes the KPOINTS file.
The KPOINTS file format is as follows:
line 1: a comment
line 2: number of kpoints
n <= 0 Automatic kpoint generation
n > 0 explicit n... | prtkm/jasp | jasp/jasp_kpts.py | Python | gpl-2.0 | 8,111 | [
"ASE",
"VASP"
] | e25a4f46cd09bd89e4e6f0e823b01357f4b19912a4edd52a0f3aa423dbf69482 |
##########
# LD 22
# The theme is alone
# it's a dumb theme
# fiona wrote this
##########
# System and Python lib imports
import sys
sys.path += ['.']
# Game engine imports
from myrmidon.myrmidon import MyrmidonGame, MyrmidonProcess
from myrmidon.consts import *
from pygame.locals import *
# Game imp... | Fiona/AreWeAlone | __main__.py | Python | mit | 4,157 | [
"Galaxy"
] | 2d7a5699c438dc910c74ee53f4c31cf0ba42c92196a8ecaffee813b1a3209bdc |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | amenonsen/ansible | lib/ansible/modules/network/avi/avi_pool.py | Python | gpl-3.0 | 23,241 | [
"VisIt"
] | 20b39938be275ab0437d780fe2189c17b34f6995465f9c5e66bfd8aa4f9cd6ca |
# hu.po
val = {" days." : " napok.",
"(all)" : "(összes)",
"(any)" : "(bármely)",
"(anyone)" : "(bárki)",
"(available)" : "(elérhető)",
"(blank)" : "(üres)",
"(both)" : "(mindkettő)",
"(everyone)" : "(mindenki)",
"(master user, not editable)" : "(kiemelt felhasználó, nem szerkeszthető)",
"(no change)" : "(nincs változ... | bobintetley/asm3 | src/asm3/locales/locale_hu.py | Python | gpl-3.0 | 197,966 | [
"Amber",
"VisIt"
] | 47306a87ff22b64a1ec644611a52ec3cdc3580616c0392b980ff8a9ff8951f28 |
from uaperrors import StepError
import sys
import os
from logging import getLogger
from abstract_step import AbstractStep
logger = getLogger('uap_logger')
class Macs2(AbstractStep):
'''
Model-based Analysis of ChIP-Seq (MACS) is a algorithm, for the identifcation
of transcript factor binding sites. MACS ... | kmpf/uap | include/steps/macs2.py | Python | gpl-3.0 | 22,914 | [
"Bowtie"
] | d6c52a6b99b90ae4da20ad1f250fa1cd1b9ecadf6074269c348e4d3641b502d6 |
# 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... | jiajiechen/mxnet | python/mxnet/contrib/text/embedding.py | Python | apache-2.0 | 34,598 | [
"VisIt"
] | c6b3e0dfd9cce8ed621863f7fc3d1e7cd6fe6f72fd9902c3cdee44f8c8c17ec3 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/procrouting/response/__init__.py | Python | lgpl-3.0 | 941 | [
"Psi4"
] | c6edc5ff89dbec5f7d80b85d285bb7f5af5bb5cb5c79969711c39b8d5eeca1db |
# Copyright 2000 by Jeffrey Chang. 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.
# Gavin E. Crooks 2001-11-03
# Minor extensions, some bug fixes, and major changes to the inte... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/SCOP/Residues.py | Python | apache-2.0 | 2,928 | [
"Biopython"
] | d8b91334615b5c8fe227c3f7eac7783f8984dbed0724fd23c88d80e8bf40589c |
#!/usr/bin/env python
#
# Copyright 2014 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""
Utilities for the modular DevTools build.
"""
from os import path
import os
try:
import simplejson as json
except ImportErr... | temasek/android_external_chromium_org_third_party_WebKit | Source/devtools/scripts/modular_build.py | Python | bsd-3-clause | 5,698 | [
"VisIt"
] | 752c7313cd0f6ab458c5e407150963a4c51a1e75b98a7926c3dc50ab20d9a3c0 |
import numpy as np
from ase.units import Hartree
from gpaw.occupations import FermiDirac, MethfesselPaxton
class KPoint:
eps_n = np.empty(1)
f_n = np.empty(1)
weight = 1.0
s = 0
k = KPoint()
def f(occ, x):
k.eps_n[0] = x
n, dnde, x, S = occ.distribution(k, 0.0)
return n, dnde, S
def ... | qsnake/gpaw | gpaw/test/occupations.py | Python | gpl-3.0 | 820 | [
"ASE",
"GPAW"
] | 7dbb00ef2c0a9226d8a5654a2c3b6273f7bad141567ac47f967b06be7c7b7b23 |
"""
fs.contrib.dropboxfs
========
A FS object that integrates with Dropbox.
"""
import time
import shutil
import optparse
import datetime
import tempfile
import calendar
from UserDict import UserDict
from fs.base import *
from fs.path import *
from fs.errors import *
from fs.filelike import StringIO
from dropbox i... | freak3dot/cdnjs | dropboxfs.py | Python | mit | 22,330 | [
"VisIt"
] | 3db034ae0d38e1c44c9d7d1270be453399da184cb07c48ffad7d9d6079769af1 |
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