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"""
FITC approximation for sparse pseudo-input GPs.
"""
from __future__ import division
from __future__ import absolute_import
from __future__ import print_function
import numpy as np
import scipy.linalg as sla
import itertools as it
from ._base import GP
from ..likelihoods import Gaussian
__all__ = ['FITC']
clas... | mwhoffman/pygp | pygp/inference/fitc.py | Python | bsd-2-clause | 7,826 | [
"Gaussian"
] | 5115a4d0bc522a69c78a70cadf93284b07415961fca66245c648781c2bcadc47 |
#!/usr/bin/env python
import vtk
def main():
fileName = get_program_parameters()
colors = vtk.vtkNamedColors()
colors.SetColor("A1Diff", [255, 204, 77, 255])
colors.SetColor("A2Amb", [51, 51, 255, 255])
colors.SetColor("A2Diff", [51, 255, 204, 255])
colors.SetColor("A3Amb", [230, 230, 230, ... | lorensen/VTKExamples | src/Python/Rendering/MotionBlur.py | Python | apache-2.0 | 3,359 | [
"VTK"
] | c6c457189473c4b6e708dd740a7fba0065fdd05a1ef2069c2b1b9ea2ec349298 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes used to define a non-periodic molecule and a
periodic structure.
"""
import math
import os
import json
import collections
import itertools
from abc import ABCMeta, abstractmeth... | tschaume/pymatgen | pymatgen/core/structure.py | Python | mit | 157,308 | [
"ABINIT",
"CRYSTAL",
"Gaussian",
"NetCDF",
"VASP",
"exciting",
"pymatgen"
] | be1eaf39ad0803ae95f50c43774303a2a1e31ea223b57097ca34ae9887239e6c |
##############################################################################
# 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-genomicalignments/package.py | Python | lgpl-2.1 | 2,941 | [
"Bioconductor"
] | 4db9d466bcd42b5367dd5e95bb79e9908b0a1a5ddc5f7621395d78ba585cce0e |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/core/ui/pluginform.py | Python | gpl-2.0 | 8,090 | [
"Brian"
] | fd6a6843260db75dface8be35464405ec866a91dfc794f857c3cc230fa6e55ec |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Brian Coca <brian.coca+dev@gmail.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_versi... | hryamzik/ansible | lib/ansible/modules/system/getent.py | Python | gpl-3.0 | 3,914 | [
"Brian"
] | e8c46217a041078f42c46917259b08fa8fdc130957983974b9392e2903857115 |
import os
import numpy as np
import math
import SimpleITK as sitk
from scipy import ndimage
import nibabel as nib
from PIL import Image
import scipy.misc
from scipy import signal
import yt
import matplotlib.pylab as pl
from yt.visualization.api import Streamlines
from mpl_toolkits.mplot3d import Axes3D
def doggen(sigm... | NeuroDataDesign/seelviz | Tony/scripts/tractography_latest.py | Python | apache-2.0 | 17,142 | [
"Gaussian"
] | 5be9b2fcddfd59a9bd4deb367e7a477bc4edeccd4368075f94010ad0418242ff |
from sqlalchemy import create_engine
from sqlalchemy.orm import sessionmaker
from setup import Base, User, Category, Item
engine = create_engine('postgresql://catalog:catalog@localhost/catalog')
# Bind the engine to the metadata of the Base class so that the
# declaratives can be accessed through a DBSession instance... | Morenito88/full_stack_p5 | full_stack_p3/db/populate.py | Python | mit | 15,115 | [
"Galaxy"
] | 7eebf61fbe5b27656dc50b9448e899caf76383ca5b2772bdfe944fafcfc4eb19 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/datafiles.py | Python | gpl-2.0 | 19,262 | [
"Amber",
"CHARMM",
"DL_POLY",
"GAMESS",
"Gromacs",
"LAMMPS",
"MDAnalysis",
"NAMD",
"NetCDF"
] | ee87cd5fe7d57983cadbcd07c5565031c4e4c7e11c4cc0389ef3eb53d4a1bb27 |
# -*- coding: utf-8 -*-
u"""
Using xrtQook for script generation
-----------------------------------
- Start xrtQook: type ``python xrtQook.pyw`` from xrt/xrtQook or, if you have
installed xrt by running setup.py, type ``xrtQook.pyw`` from any location.
- Rename beamLine to myTestBeamline by double clicking o... | yxrmz/xrtQook | __init__.py | Python | mit | 130,679 | [
"CRYSTAL"
] | fec755bcc92b090223c44ca54eae381b316f0bf636e64e0c0cfd1007157fefec |
###############################
# 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 | src/pylada/vasp/nlep/nlep_defaults.py | Python | gpl-3.0 | 5,708 | [
"CRYSTAL",
"VASP"
] | ae87fcab8644fb9a9e51d826999e2b3e75720a062e89cc2ded32b9f289134e0b |
#!/usr/bin/python
import httplib2
import os
import sys
from apiclient.discovery import build
from oauth2client.file import Storage
from oauth2client.client import flow_from_clientsecrets
from oauth2client.tools import run
# CLIENT_SECRETS_FILE, name of a file containing the OAuth 2.0 information for
# this applicat... | lhongskie/yt-samples-python | playlist_updates.py | Python | apache-2.0 | 2,473 | [
"VisIt"
] | bae06ca7320c45fce78797d620b2d5bec781bc137ec1caffa6f0732f3529cc4c |
#!/usr/bin/env python
from ase import Atoms
from gpaw import GPAW
from gpaw import ConvergenceError
from gpaw.mpi import rank
from gpaw.eigensolvers.rmm_diis_old import RMM_DIIS
from gpaw import setup_paths
# Use setups from the $PWD and $PWD/.. first
setup_paths.insert(0, '.')
setup_paths.insert(0, '../')
positi... | robwarm/gpaw-symm | doc/devel/256H2O/b256H2O.py | Python | gpl-3.0 | 3,642 | [
"ASE",
"GPAW"
] | 156099a7fb7ba7148a34085cd820f91a64915c6776634766dceaeb90b0411034 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | ennoborg/gramps | gramps/plugins/tool/verify.py | Python | gpl-2.0 | 66,904 | [
"Brian"
] | daa2d6e2d4baf173a2cb9c84e4f5a1100011b81de1902c89c0824534751ed8a9 |
# coding=utf-8
import gzip
import cPickle as pickle
import numpy as np
from whatami import whatable
from manysources.common.rdkit_utils import iterate_rdkit_mols_in_sdf_file
@whatable
class Molecules(object):
"""A collection of molecules, identified by unique ids and associated with some attributes."""
def... | sdvillal/manysources | manysources/common/molecules.py | Python | bsd-3-clause | 9,357 | [
"Pybel",
"RDKit"
] | 43b58bd39b015697aa5600c4dbbeeb78d236265655be3bcd16f32668420ae61e |
"""
=============================
Generic SpectralModel wrapper
=============================
.. moduleauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com>
"""
import numpy as np
from pyspeckit.mpfit import mpfit,mpfitException
from pyspeckit.spectrum.parinfo import ParinfoList,Parinfo
import copy
from astropy import lo... | bsipocz/pyspeckit | pyspeckit/spectrum/models/model.py | Python | mit | 41,139 | [
"Gaussian"
] | 9ed76017bd913bf060dad1190e6259e196dd4dc73692b10e54f6b7c34c73d7c1 |
# -*- coding: utf-8 -*-
"""
Author: Padarn Wilson
Performance of normal reference plug-in estimator vs silverman. Sample is drawn
from a mixture of gaussians. Distribution has been chosen to be reasoanbly close
to normal.
"""
from __future__ import print_function
import numpy as np
from scipy import stats
import matp... | hlin117/statsmodels | statsmodels/examples/ex_kde_normalreference.py | Python | bsd-3-clause | 1,704 | [
"Gaussian"
] | fa048f57a83d647a5c362d8ed41224cacdc09a5072454cda731c06df036b9e2b |
#!/usr/bin/env python
"""
Downloads files to temp locations. This script is invoked by the Transfer
Manager (galaxy.jobs.transfer_manager) and should not normally be invoked by
hand.
"""
import os, sys, optparse, ConfigParser, socket, SocketServer, threading, logging, random, urllib2, tempfile, time
galaxy_root = os.... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/scripts/transfer.py | Python | gpl-3.0 | 11,849 | [
"Galaxy"
] | 8d301d7f4fcf22123c27e3bb80c981000ace1e580323b0274a68e94aec35595a |
###########################################################################
#
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/l... | google/starthinker | dags/ga_timeline_dag.py | Python | apache-2.0 | 4,593 | [
"VisIt"
] | 30696fdc2a1fed07fc556d234dff866db27f30dcd10f54f98a6224a59c1409b2 |
# -*- coding: UTF-8 -*-
#
# Copyright (c) 2008, Yung-Yu Chen <yyc@solvcon.net>
#
# 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 source code must retain the above copyrigh... | yungyuc/solvcon | solvcon/io/vtkxml.py | Python | bsd-3-clause | 19,896 | [
"ParaView",
"VTK"
] | 90b9d0c9a07c00dcc009972f0ff68be9d5b99b7f978021dc17f03674e4284117 |
###########################################################################
#
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/l... | google/starthinker | dags/floodlight_monitor_dag.py | Python | apache-2.0 | 4,769 | [
"VisIt"
] | 15e15f231cb23880faf96396d67cd9544387dd08d6688f0636fc46f187eded67 |
from .visitor import TopVisitor, FuncVisitor, BlockVisitor
from .core import *
from .instructions import *
class DeclareVisitor(TopVisitor):
def __init__(self, reset):
self.reset = reset
def visit(self, top):
if self.reset:
top.reset_var_usage()
super().visit(top)
def... | simon816/Command-Block-Assembly | cmd_ir/optimizers.py | Python | mit | 25,248 | [
"VisIt"
] | 283a866f9fb13833c677fce0c0906cc3f8f595ad5e0a6de656a8a623381cbd8a |
# Copyright 2015, 2017 IBM Corp.
#
# 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 require... | phenoxim/nova | nova/tests/unit/virt/powervm/test_media.py | Python | apache-2.0 | 9,969 | [
"FEFF"
] | 984f315f02e452409ad105dc1c1277752c3a2b24e969a444a4b16531f35e4055 |
#
# Copyright (c) 2009, Georgia Tech Research Corporation
# 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 source code must retain the above copyright
# notice, thi... | ppp2006/runbot_number0 | qbo_stereo_anaglyph/hrl_lib/src/hrl_lib/mayavi2_util.py | Python | lgpl-2.1 | 4,736 | [
"Mayavi"
] | 464b56ba436944c945d0a3060f5814743d9745dba488e724817444857379eef0 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','... | ederelk/TiUIVisualEffectView | iphone/build.py | Python | mit | 7,637 | [
"VisIt"
] | a081ce2cf05544409b667184942b9a5a09559592bee7e113aa938da80a572d2f |
#!/usr/bin/env python
# Greg Von Kuster
"""
usage: %prog score_file interval_file chrom start stop [out_file] [options]
-b, --binned: 'score_file' is actually a directory of binned array files
-m, --mask=FILE: bed file containing regions not to consider valid
-c, --chrom_buffer=INT: number of chromosomes (... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/tools/stats/aggregate_scores_in_intervals.py | Python | gpl-3.0 | 8,731 | [
"Galaxy"
] | 133bdbda34692da310a6e1b72e582419507c76424612de51c2eba3b09d91a635 |
# -*- coding: utf-8 -*-
from yade import ymport, plot
from math import *
import numpy
#import getpass
#user=getpass.getuser()
#sys.path.append('/home/'+user+'/YADE-git/install/bin')
#from Functions import *
try:
os.mkdir('data')
except:
pass
try:
os.mkdir('paraview')
except:
pass
######################... | anna-effeindzourou/trunk | examples/anna_scripts/impact.py | Python | gpl-2.0 | 5,450 | [
"ParaView"
] | a3bc0e6a1839036e0308604ffd87ce877c5298c9769a7af4db135490fb6755a3 |
# -*- coding: utf-8 -*-
#
# balancedneuron.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,... | sanjayankur31/nest-simulator | pynest/examples/balancedneuron.py | Python | gpl-2.0 | 7,344 | [
"NEURON"
] | 2d224298783fee79905f0f1ca31c537bc33d468738e263abf4afec0f02d48389 |
# -*- coding: utf-8 -*-
# cldomain is a Common Lisp domain for the Sphinx documentation tool.
# Copyright (C) 2011-2014 Russell Sim <russell.sim@gmail.com>
# 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 F... | bscottm/sphinxcontrib-cldomain | sphinxcontrib/cldomain.py | Python | gpl-3.0 | 38,429 | [
"VisIt"
] | 7f471434ae1fc90207406e13e175d81a05266b29213c21cfd3021b22dddd9214 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Pedro Tabacof
# tabacof at gmail dot com
# April 2016
#
# Bayesian uncertainty in MNIST classification
#
# Dropout MLP model (based on Yarin Gal's approach)
# Variational MLP with Gaussian prior and posterior
#
# Based on the MNIST Lasagne example
# https://github.com/L... | tabacof/bayesian-nn-uncertainty | models.py | Python | mit | 10,001 | [
"Gaussian"
] | 72888e0289839667bfc31b55dd0e86818b5934a1d6afe99f951660b0769bedf1 |
import ast
import token
import tokenize
from os.path import islink
from StringIO import StringIO
from itertools import izip
from dxr.build import unignored
from dxr.filters import FILE, LINE
from dxr.indexers import (Extent, FileToIndex as FileToIndexBase,
iterable_per_line, Position, split_i... | pelmers/dxr | dxr/plugins/python/indexers.py | Python | mit | 15,109 | [
"VisIt"
] | f66068624a5ee835bfa5b4aea6365940b001813258348703b009b842802c9165 |
#!/usr/bin/env python2.7
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redis... | jtulach/mx | mx_sigtest.py | Python | gpl-2.0 | 5,599 | [
"VisIt"
] | 4c93e0b2e6f38e665460c294cba34a57c51edf90007c4cd187655f7bdeef96e0 |
#
# @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/p4util/text.py | Python | lgpl-3.0 | 6,992 | [
"Psi4"
] | d75de7944608c1674ad6948817287b5fb2caaf9a498a23be01f4e83904f2d26c |
import zipfile
import numpy as np
from mayavi.api import Engine
from mayavi import mlab
import math
class Mapper:
def __init__(self):
self.vmin = None
self.vmax = None
self.current_figure = -1
self.figure_offset_scale = 1.0
self.use_figure_offset_scale = True
try:
... | attilathedud/srtm_mapper | Mapper.py | Python | mit | 3,344 | [
"Mayavi"
] | dafb4c3e0b2c75a6613a484ef9bc8d9ffd69048ddcab28035a470763ac6f4712 |
""" Principal Component Analysis
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Olivier Grisel <olivier.grisel@ensta.org>
# Mathieu Blondel <mathieu@mblondel.org>
# Denis A. Engemann <d.engemann@fz-juelich.de>
# Michael Eickenberg <michael.eickenberg@inria.fr>
# ... | pratapvardhan/scikit-learn | sklearn/decomposition/pca.py | Python | bsd-3-clause | 25,995 | [
"Gaussian"
] | bd4757398130fed0aa3760f67bb36dd2d6d81a95c3faf45c3f54326a5b6d1ab4 |
# Copyright 2017 Max Planck Society
# Distributed under the BSD-3 Software license,
# (See accompanying file ./LICENSE.txt or copy at
# https://opensource.org/licenses/BSD-3-Clause)
"""The class implementing AdaGAN iterative training procedure.
"""
import logging
import numpy as np
import gan as GAN
import vae as VAE... | tolstikhin/adagan | adagan.py | Python | bsd-3-clause | 17,484 | [
"Gaussian"
] | 5e8f5b19451246b9f9905d76c282817685130b19853e28c46736d1c57cd02426 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | ashhher3/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 34,716 | [
"Brian"
] | f8b756cc6ab732afb1be5b0c81ccac81501441af5bedbdae7bbdc9f7320b0dc9 |
# -*- coding: utf-8 -*-
"""
Created on Wed Aug 16 16:38:35 2017
@author: racuna
"""
import matplotlib.pyplot as plt
import autograd.numpy as np
from mayavi import mlab
from numpy import random, cos, sin, sqrt, pi, linspace, deg2rad, meshgrid
from mpl_toolkits.mplot3d import Axes3D
from vision.camera import Camera
fr... | raultron/ivs_sim | python/vision/camera_distribution.py | Python | mit | 4,420 | [
"Mayavi"
] | b42f01a86c3d39b979174f8ef22cda93668e41b2cfa72e3efffe0765dea762a2 |
import os, glob, re, subprocess
class BigWigExtras():
def __init__(self,log):
self.log = log
self.MILLION = float(1000000)
self.mr_hash = {}
# not a ruffus task
def make_fastq_list(self, directorys):
fastqs = []
for directory in directorys:
... | mbiokyle29/pipelines | wig/big_wig_extras.py | Python | mit | 3,840 | [
"Bowtie"
] | 5c356f93798033a49fd35f383977db005fe16cf495cb743e44b1c173e1f7eb9b |
#
# @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/qcdb/exceptions.py | Python | lgpl-3.0 | 3,649 | [
"Psi4"
] | 18f362c8a06fa262add04dccf1fa9acb63704341622192b58920dc5fd76ccee2 |
#!/usr/bin/env python
"""
tidal_energy.py
State Estimation and Analysis for PYthon
Module to compute tidal energy from a column of data.
Written by Brian Powell on 03/30/16
Copyright (c)2010--2021 University of Hawaii under the MIT-License.
Notes
-----
Barotropic to Baroclinic conversion is given by:
.. math::
... | powellb/seapy | seapy/tidal_energy.py | Python | mit | 9,541 | [
"Brian"
] | 3e6985af128fdf26236b6989767f194e772f090f22b145ec70f5023a8a3906be |
##############################################################################
# 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... | krafczyk/spack | var/spack/repos/builtin/packages/shortstack/package.py | Python | lgpl-2.1 | 1,944 | [
"Bowtie"
] | 205455a87755640ab23d4e5dc71c5e554a1dfba230bba68c520686bfdc6dd283 |
# #!/usr/bin/env python
# -*- coding: utf-8 -*-
# <steadymark - markdown-based test runner for python>
# Copyright (C) <2012-2020> Gabriel Falcão <gabriel@nacaolivre.org>
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation
# files (the "Softw... | gabrielfalcao/steadymark | setup.py | Python | mit | 2,796 | [
"VisIt"
] | 5e7a37ddf070423ca69de29503b23577f7fe81b73352684198c4080433b33eff |
""" Unit tests for the Dirac interface module
"""
# pylint: disable=no-member, protected-access
import unittest
from DIRAC.Interfaces.API.Dirac import Dirac
class DiracTestCases(unittest.TestCase):
""" Dirac API test cases
"""
def setUp(self):
self.dirac = Dirac()
def tearDown(self):
pass
def te... | andresailer/DIRAC | Interfaces/API/test/Test_DIRAC.py | Python | gpl-3.0 | 998 | [
"DIRAC"
] | 009188974e73f25f8f173ed53ac13ed1de579b1a5198da7133ff23a8b8c81c93 |
"""
Use Mayavi to visualize the structure of a VolumeData
"""
from enthought.mayavi import mlab
import numpy as np
s = np.random.random((5, 5, 5))
# Put the side at 0
s[0, ...] = 0
s[-1, ...] = 0
s[:, 0, :] = 0
s[:, -1, :] = 0
s[..., 0] = 0
s[..., -1] = 0
mlab.figure(1, fgcolor=(0, 0, 0), bgcolor=(1, 1, 1))
mlab... | yarikoptic/NiPy-OLD | doc/neurospin/datasets/viz_volume_field.py | Python | bsd-3-clause | 541 | [
"Mayavi"
] | da45fe0ff2df92fe19e7c0ff64311d879424e50540ae8603ea9f58cddae01775 |
"""Leetcode 426. Convert Binary Search Tree to Sorted Doubly Linked List
Medium
URL: https://leetcode.com/problems/convert-binary-search-tree-to-sorted-doubly-linked-list/
Convert a Binary Search Tree to a sorted Circular Doubly-Linked List in place.
You can think of the left and right pointers as synonymous to the ... | bowen0701/algorithms_data_structures | lc0426_convert_binary_search_tree_to_sorted_doubly_linked_list.py | Python | bsd-2-clause | 3,432 | [
"VisIt"
] | a7b73033ade8f663e6267c52e9c0dbf1890d1bd39d5aeb10a5595740e59af696 |
import argparse
import textwrap
from Bio import SeqIO
import os
import shutil
from multiprocessing import cpu_count
class blastargument_parser():
# call on all our file type parsers in the sequence_anlysis_method
def __init__(self):
"""A customized argument parser that does a LOT of error checking"""
... | andrejbranch/pyigblast | arg_parse.py | Python | unlicense | 10,770 | [
"BLAST"
] | d751ef5cea87162fba947d7e9a9e4b65fa43247d0c6a23d690161cccd1151dfd |
###############################################################################
##
## Copyright 2011,2012 Tavendo GmbH
##
## 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
##
## ... | flyser/AutobahnPython | autobahn/autobahn/websocket.py | Python | apache-2.0 | 148,173 | [
"VisIt"
] | 1ff897139ae28641b270a2e2cacaac85da759bb0060a08ba8d0b6e6f39539866 |
# Checks all psi4 relevant files for proper boilerplate GNU license.
# This is sold as is with no warrenty-- probably should double check everything
# after running. I am not responsible if you break Psi4.
#
# Do not forget to do share/plugins by hand!
import os
# File type we know how to handle
ftypes = ['cc', 'h', ... | kannon92/psi4 | psi4/share/psi4/scripts/apply_license.py | Python | gpl-2.0 | 3,531 | [
"Psi4"
] | daf1801a832a0e666ef45bc7aa7f346ea3296f4f49c852cf2ef190e1c0f53ff7 |
# Import smorgasbord
import os
import sys
sys.path.insert(0, '../')
import gc
import pdb
import time
import csv
import shutil
import multiprocessing as mp
import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import astropy
astropy.log.setLevel('ERROR')
import astrop... | Stargrazer82301/CAAPR | CAAPR/CAAPR_IO/CAAPR_IO.py | Python | mit | 42,977 | [
"Galaxy"
] | 82b982958d21427ea1e61737f97aab30f402eff0c415aee50dee9678e95190ee |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import string
from importlib import import_module
import warnings
from django.conf import settings
from django.contrib.auth import get_user_model
from django.contrib.auth.models import AnonymousUser
from django.contrib.auth.signals import user_logged_in,... | jrief/django-shop | shop/models/customer.py | Python | bsd-3-clause | 15,460 | [
"VisIt"
] | de787002484ff8db772d36678dee7011c5aa3777103e3893cf8b24a19f67965d |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import time
import unittest
import logging
import functools
from nose.tools import * # flake8: noqa (PEP8 asserts)
import pytest
import mock
from framework.auth.core import Auth
from website import settings
i... | caseyrollins/osf.io | osf_tests/test_elastic_search.py | Python | apache-2.0 | 50,264 | [
"Brian"
] | 2620ea93521408d421595645edd91cfb6f49faf92e99b2a2c0f5587048f7ffa2 |
../../../../share/pyshared/orca/bookmarks.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/bookmarks.py | Python | gpl-3.0 | 44 | [
"ORCA"
] | 11f385cecb57751ba351a0e339dac926a23e5a014e6034e5d88c29b205eb5573 |
from __future__ import division, absolute_import, print_function
import os
import sys
import types
import re
from numpy.core.numerictypes import issubclass_, issubsctype, issubdtype
from numpy.core import product, ndarray, ufunc
__all__ = ['issubclass_', 'issubsctype', 'issubdtype',
'deprecate', 'deprecate_w... | ogrisel/numpy | numpy/lib/utils.py | Python | bsd-3-clause | 35,916 | [
"VisIt"
] | 7b26c20f239279447afd51ab95b51c4099c92f08eaf94aa03efbc7524a7d4e8b |
# The MIT License (MIT)
# Copyright (c) 2016, 2017, 2018 Massachusetts Institute of Technology
#
# Authors: Cody Rude
# This software has been created in projects supported by the US National
# Science Foundation and NASA (PI: Pankratius)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
... | skdaccess/skdaccess | skdaccess/utilities/grace_util.py | Python | mit | 10,538 | [
"NetCDF"
] | 94bb2e4b54941a49291bf31ef4ee9e79cf6e696e3f4a1fd8dc74917d19d264f4 |
# -*- coding: utf-8 -*-
# hhfit.py ---
# Description:
# Author:
# Maintainer:
# Created: Tue May 21 16:31:56 2013 (+0530)
# Commentary:
# Functions for fitting common equations for Hodgkin-Huxley type gate
# equations.
import traceback
import warnings
import numpy as np
import logging
logger_ = logging.getLogger('moo... | dilawar/moose-core | python/moose/neuroml2/hhfit.py | Python | gpl-3.0 | 8,486 | [
"MOOSE"
] | dbf122388ee9a5c105e86d6595858bf582d0621c5c4a3cc117f6c1728c5276ca |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1950-2020/regrid_HCHO_emissions_n96e_360d.py | Python | gpl-3.0 | 19,124 | [
"NetCDF"
] | 4f71d397a68863527df3a4a57bf41c06397f368adbc54deb5ca6d7771a8a4191 |
"""
================================
Gaussian Mixture Model Selection
================================
This example shows that model selection can be performed with
Gaussian Mixture Models using information-theoretic criteria (BIC).
Model selection concerns both the covariance type
and the number of components in the ... | bnaul/scikit-learn | examples/mixture/plot_gmm_selection.py | Python | bsd-3-clause | 3,337 | [
"Gaussian"
] | 2ea5b000fc24c80e38161731e090df357ada7aeb4cfe82ae8e71cd77334dce4d |
#!/usr/bin/env python
import argparse
import pysam
import sys
from subprocess import call
from re import sub
from os.path import basename
from os import remove, rename
from uuid import uuid4
def getRG(tags):
''' fetch RG, tags is from a pysam.AlignedRead.tags, returns RG name '''
for tag, val in tags:
... | chaelir/bamsurgeon | etc/postprocess.py | Python | mit | 9,181 | [
"pysam"
] | 791314d4b5059bd68305e27a7925e1fd92ee0279a24d67d9ba7602dd83c1216b |
#!/usr/bin/env python
"""
Deployment file to facilitate releases of monty.
"""
from __future__ import division
import glob
import requests
import json
import os
import re
from invoke import task
from monty.os import cd
from monty import __version__ as ver
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2... | gmatteo/monty | tasks.py | Python | mit | 3,701 | [
"pymatgen"
] | 3d4eb84c5c0c7e4314d1a480f796b3118eed15b51a6e8854ed11ed5478957ad4 |
# Copyright Bruno da Silva de Oliveira 2006. Distributed under the Boost
# Software License, Version 1.0. (See accompanying
# file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
import os
import sys
import shutil
import fnmatch
from zipfile import ZipFile, ZIP_DEFLATED
def findfiles(direct... | alexa-infra/negine | thirdparty/boost-python/libs/python/pyste/dist/create_build.py | Python | mit | 1,723 | [
"VisIt"
] | 4bebc0fb8fcba3ab87ef80a5a8b100143e8ba884921148d90ce2e5572f3c4865 |
'''Kernel Ridge Regression for local non-parametric regression'''
import numpy as np
from scipy import spatial as ssp
import matplotlib.pylab as plt
def kernel_rbf(x,y,scale=1, **kwds):
#scale = kwds.get('scale',1)
dist = ssp.minkowski_distance_p(x[:,np.newaxis,:],y[np.newaxis,:,:],2)
return np.exp(-0.5... | statsmodels/statsmodels | statsmodels/sandbox/regression/kernridgeregress_class.py | Python | bsd-3-clause | 7,727 | [
"Gaussian"
] | dc95f41a4163955f46ee70dd18d9c56ed43d69d65e50f8711d30cb7133338577 |
#!/usr/bin/env python
'''
Fly ArduPlane in SITL
AP_FLAKE8_CLEAN
'''
from __future__ import print_function
import math
import os
import time
from pymavlink import quaternion
from pymavlink import mavextra
from pymavlink import mavutil
from common import AutoTest
from common import AutoTestTimeoutException
from comm... | bugobliterator/ardupilot | Tools/autotest/arduplane.py | Python | gpl-3.0 | 125,964 | [
"Firefly"
] | 7da5e7e240041861c06d18446f6a0012c25e26e455af3cffb0679463495f3146 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
import logging
import threading
import time
from collections import namedtuple
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
FIRST_COMPLETED = 'FIRST_COMPLETED'
FIRST_EXCEPTION = 'FIRST_EXCEPTION'
ALL_COMPLETE... | piotroxp/scibibscan | scib/lib/python3.5/site-packages/astropy/utils/compat/futures/_base.py | Python | mit | 19,949 | [
"Brian"
] | c5d610e5dbadfdda3ab49ae6f8f0de4878c2944c77b157cb6a0332a81b5f2156 |
# -*- coding=utf-8 -*-
from __future__ import absolute_import, print_function
import logging
import os
import sys
import pip_shims.shims
import six
import six.moves
import tomlkit
import vistir
from six.moves.urllib.parse import urlparse, urlsplit, urlunparse
from vistir.compat import Path, fs_decode
from vistir.path... | kennethreitz/pipenv | pipenv/vendor/requirementslib/utils.py | Python | mit | 25,567 | [
"VisIt"
] | 22c79eb21a781c29502a0cdd126107f245592876e6aaee729e5aa23cb61f84e8 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyCrossmap(PythonPackage, SourceforgePackage):
"""CrossMap is a program for convenient con... | iulian787/spack | var/spack/repos/builtin/packages/py-crossmap/package.py | Python | lgpl-2.1 | 1,232 | [
"pysam"
] | 8af290f6b02b0a36fa20567a9300f505acd76817447cf2a04523974757fa637d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
""" Copyright 2005 - 2008 Gunnar Wrobel
2011 - Brian Dolbec
Distributed under the terms of the GNU General Public License v2
"""
__version__ = "0.1"
import sys
from layman.constants import codes, INFO_LEVEL, WARN_LEVEL, DEBUG_LEVEL, OFF
from layman.compatib... | jmesmon/layman | layman/output.py | Python | gpl-2.0 | 5,855 | [
"Brian"
] | b1e387e7c8bfd93408abde760b2ce94f320aef867be3d04080d83af8fff129f4 |
import contextlib
import collections
import pickle
import re
import sys
from unittest import TestCase, main, skipUnless, SkipTest
from typing import Any
from typing import TypeVar, AnyStr
from typing import T, KT, VT # Not in __all__.
from typing import Union, Optional
from typing import Tuple, List
from typing impor... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.6.0/Lib/test/test_typing.py | Python | mit | 55,042 | [
"VisIt"
] | b100805ab75473d391b1287b2dc0161a4019c5885d9103d1231f38d55b0cb898 |
########################################################################
# File : CPUNormalization.py
# Author : Ricardo Graciani
########################################################################
""" DIRAC Workload Management System Client module that encapsulates all the
methods necessary to handle CPU... | hgiemza/DIRAC | WorkloadManagementSystem/Client/CPUNormalization.py | Python | gpl-3.0 | 9,163 | [
"DIRAC"
] | 7eb4b47de4800e857bd40918415d581c6b43cce29d7a182fd70867e0e2095f30 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Tests for RGB Images
"""
import sys
import os
import tempfile
import pytest
import numpy as np
from numpy.testing import assert_equal
from astropy.convolution import convolve, Gaussian2DKernel
from astropy.visualization import lupton_rgb
try:
... | dhomeier/astropy | astropy/visualization/tests/test_lupton_rgb.py | Python | bsd-3-clause | 9,263 | [
"Gaussian"
] | c30eeed1ed53e0e4d9f4c28924f0fe441a63fd0d3553cf0f7e5cc17b507031c2 |
# Copyright (c) 2010 OpenStack Foundation
#
# 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 ... | psachin/swift | test/unit/common/middleware/test_staticweb.py | Python | apache-2.0 | 41,863 | [
"VisIt"
] | ad0672a2fd23499e06ccd7d57a321dde9ce95df973c9d735e68152a8cf56f89e |
# -*- coding: utf-8 -*-
# Spearmint
#
# Academic and Non-Commercial Research Use Software License and Terms
# of Use
#
# Spearmint is a software package to perform Bayesian optimization
# according to specific algorithms (the “Software”). The Software is
# designed to automatically run experiments (thus the code name
... | DavidMcDonald1993/ghsom | spearmint/spearmint/choosers/default_chooser.py | Python | gpl-2.0 | 28,796 | [
"Gaussian"
] | ffac7aee5bc88c2c95a7fa28c04b83241b6da24e8ae419a230ed6244c2996a24 |
"""
Support for control of Elk-M1 connected thermostats.
For more details about this platform, please refer to the documentation at
https://home-assistant.io/components/climate.elkm1/
"""
from homeassistant.components.climate import (
ATTR_TARGET_TEMP_HIGH, ATTR_TARGET_TEMP_LOW, PRECISION_WHOLE, STATE_AUTO,
ST... | PetePriority/home-assistant | homeassistant/components/elkm1/climate.py | Python | apache-2.0 | 7,006 | [
"Elk"
] | 25abbc6ca9658ac7cd1c3c758b838160b77ed2c81d80a8f286378be2fabd94bd |
#!/usr/bin/env ipython
from pylab import *
from numpy import *
from scipy.io.netcdf import netcdf_file
from datetime import datetime, time, timedelta
#------------ shared libraries:
"""
--- antes de modificar cosas, tener en cuenta los bugs en:
'../../shared_lib/COMENTARIOS.txt'
"""
import sys
sys.path.append('../../sh... | jimsrc/seatos | mcs/src/showme_group.py | Python | mit | 4,462 | [
"NetCDF"
] | aa2d6d146b2ff3a0b39b7cde91abafbebcec195ceb27315fd7c9cd3344b031f9 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2017 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | FarnazH/horton | horton/meanfield/test/test_libxc.py | Python | gpl-3.0 | 15,376 | [
"DIRAC"
] | 9dc81e6357340039ce0559d9492333f154151c6a3a095dc716fe63c851341ab1 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | aflaxman/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 34,862 | [
"Gaussian"
] | b361d358a68588581017067dde0b9645342b4b970c16a9a37405a09e780fd091 |
#!/usr/bin/python
#
# Copyright 2014 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required b... | dietrichc/streamline-ppc-reports | examples/adwords/v201409/error_handling/handle_policy_violation_error.py | Python | apache-2.0 | 4,201 | [
"VisIt"
] | 7511fdaaac933acd208037c50c83c0268fbbe42e87cd1f3faf4e601b5a16f341 |
"""
Instructor Dashboard Views
"""
import logging
import datetime
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation import ugettext as _
from django_future.csrf import ensure_csrf_cookie
from django.vie... | epam-mooc/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 19,067 | [
"VisIt"
] | 07c8b88e3f89b0cb898a6b8838a6121d615b352370782144ba3f5997928cb3dd |
import numpy as np
# TODO : derivatives, longer tails
def twodpeak( pars, x, y ):
"""
pars : (m0, m1x, m1y, m2xx, m2xy, m2yy)
x : x-coordinates, probably a 2D array (slow or tth)
y : y-coordinates, probably a 2D array (fast or eta)
Gaussian would be:
dx = x - m1x
dy = y - m1y
peak ... | jonwright/ImageD11 | sandbox/twodpeak.py | Python | gpl-2.0 | 3,004 | [
"Gaussian"
] | e9b5661051c7b9c666d9177a428e495989ddb23990eaba9851894b4112032a6c |
#!/usr/bin/env python
"""
DataSetAttr
"""
"""
Copyright 2001 Pearu Peterson all rights reserved,
Pearu Peterson <pearu@ioc.ee>
Permission to use, modify, and distribute this software is given under the
terms of the LGPL. See http://www.fsf.org
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OW... | ddempsey/PyFEHM | pyvtk/DataSetAttr.py | Python | lgpl-2.1 | 1,698 | [
"VTK"
] | cfbfa71ba012dec6ce0b09e4c3109578dcc2a7912a476a4c58ec4f3950f6c7b4 |
from experiments.utils import participant
try:
# for Django >= 1.10
from django.utils.deprecation import MiddlewareMixin
except ImportError:
# for Django < 1.10
MiddlewareMixin = object
class ExperimentsRetentionMiddleware(MiddlewareMixin):
def process_response(self, request, response):
#... | mixcloud/django-experiments | experiments/middleware.py | Python | mit | 742 | [
"VisIt"
] | eedd13ded073397fb70ec9a9335618b110a7a4bd51400477e890e767f242b843 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_rx_cui_identifier_search_response.py | Python | apache-2.0 | 10,147 | [
"VisIt"
] | 4776fa069b5388884b1d3ab4258377d56a9a81cdaf6ff3309ce2adeb18387082 |
#
# Copyright (C) 2013-2019 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... | fweik/espresso | testsuite/python/widom_insertion.py | Python | gpl-3.0 | 3,926 | [
"ESPResSo"
] | 59ad9a56fcc0165ad10c806ff766787204d6891359ae5debc277046988362b59 |
# -*- coding: utf-8 -*-
import json
import unittest
import networkx as nx
import py2cytoscape.util.util_dataframe as df_util
from py2cytoscape.data.cyrest_client import CyRestClient
def pp(dict_data):
print(json.dumps(dict_data, indent=4))
class CyRestClientTests(unittest.TestCase):
def setUp(self):
... | idekerlab/py2cytoscape | tests/test_network.py | Python | mit | 8,543 | [
"Cytoscape"
] | 64e6d359b93e28ec941573a8c0cc1df89cc3041672f03b6a7dbbde43af738416 |
# Copyright (C) 2010 CAMd
# Please see the accompanying LICENSE file for further information.
"""This module provides all the classes and functions associated with the
evaluation of exact exchange with k-point sampling."""
from math import pi, sqrt
from time import time
import numpy as np
from ase import Atoms
from... | ajylee/gpaw-rtxs | gpaw/xc/hybridk.py | Python | gpl-3.0 | 19,501 | [
"ASE",
"GPAW"
] | 3385e85d39fdbded2fda4ead9c015a1f83a360d49b7890bc079d6e7a752f2789 |
# encoding: utf-8
"""
Common implementation of the Projection class, to be sub-classed by
backend-specific Projection classes.
:copyright: Copyright 2006-2016 by the PyNN team, see AUTHORS.
:license: CeCILL, see LICENSE for details.
"""
try:
basestring
reduce
xrange
except NameError:
basestring = str
... | anupkdas-nus/global_synapses | pyNN-dispackgaes/common/projections.py | Python | gpl-3.0 | 21,618 | [
"NEURON"
] | 3cce18e8b9e284c6b65ece0c0e9ca50e04e009d6cedaf64690cf3bfbcfd0ec58 |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@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
# the Free Software ... | maartenq/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 11,063 | [
"Galaxy"
] | 85538dc18ad2b9d71c91b3e5a8353dd22ffc1b2e9e1477dd515a53427475f931 |
import Simple_atom
import numpy
import os
import sys
import MDAnalysis
import usage
import time as Time
'''
Should note that unit is A and A^2.
'''
def Get_Area_fromTOP(coor_file, base_list):
'''
Calculate the RMSD from coor_file.
'''
LIST_NUM=len(base_list)
atom_list=Simple_atom.Get_atom_list(co... | zhuhong/g4analysis | G4Analysis/G4_Area.py | Python | gpl-2.0 | 6,115 | [
"MDAnalysis"
] | 966477e6ee0a2c78f74a09ae448ca1170bf0e3ee5a138186fb857429c0d86a57 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/pmg_tk/PMGApp.py | Python | gpl-2.0 | 12,533 | [
"ChemPy",
"Gaussian",
"MOE",
"MacroModel",
"PyMOL"
] | d8f0d46b0a6348bfb604f6422ee7c3cdcf27eafddf20ef3c293192a600f3ec5f |
""" Information Theory functionality
"""
from rdkit.ML.InfoTheory.rdInfoTheory import *
| adalke/rdkit | rdkit/ML/InfoTheory/__init__.py | Python | bsd-3-clause | 89 | [
"RDKit"
] | 31b6a7a9b75c14eaad2d2f90f07e0fe2b253742059f5b65f85cfa2655b2b840e |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
#
# Copyright (C) 2020 Stoq Tecnologia <https://www.stoq.com.br>
# All rights reserved
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
# as published by the Free Software Foundation... | stoq/stoq-server | stoqserver/lib/eventstream.py | Python | gpl-2.0 | 8,627 | [
"VisIt"
] | 2dfe968caa85cc89a9b392026102271ee50f3baa43814a5aeaed0c509f20b38f |
from functools import partial
from kivy.properties import ObjectProperty, OptionProperty, StringProperty
from kivy.uix.accordion import AccordionItem
from kivy.uix.button import Button
from kivy.uix.gridlayout import GridLayout
from kivy.uix.modalview import ModalView
from kivy.uix.togglebutton import ToggleButton
c... | jmadajian/CinemaFlowWorks | kivy-designer-master/designer/components/playground_size_selector.py | Python | gpl-3.0 | 8,146 | [
"Galaxy"
] | ca3b742693f0782c9e7db843a5b6e1dc312b1d44784d53151c897bb17d840aa3 |
#!/usr/bin/env python
import os
import sys
import unittest
import pysam
import sam_utils
class TestMISO(unittest.TestCase):
"""
Test MISO functionality.
"""
def setUp(self):
# Find out the current directory
self.miso_path = \
os.path.dirname(os.path.abspath(os.path.expandus... | Xinglab/rmats2sashimiplot | src/MISO/misopy/test_miso.py | Python | gpl-2.0 | 7,024 | [
"pysam"
] | f4f80d05285b3bb3a1f0c05d1408ade05798ff9ee12e2c512dee1b6e2b6ebeee |
from __future__ import annotations
import collections
import copy
import logging
import math
import libtbx
from dxtbx.model import Crystal
from scitbx import matrix
from scitbx.array_family import flex
import dials.util
from dials.algorithms.indexing.compare_orientation_matrices import (
difference_rotation_matr... | dials/dials | algorithms/indexing/model_evaluation.py | Python | bsd-3-clause | 12,078 | [
"CRYSTAL"
] | 2f8af1f5796c969d4fe53b8b082f8944eb05e13b3be8a1411d34ccb2bc69249f |
#!/usr/bin/env python
#
# Transforms contact graph into secondary structure (currently dot-bracket format)
# http://projects.binf.ku.dk/pgardner/bralibase/RNAformats.html
#
import sys
import os
import re
import gzip
import networkx as nx
from StringIO import StringIO
from optparse import OptionParser
# biopython
from ... | mmagnus/rna-pdb-tools | rna_tools/tools/clarna_play/ClaRNAlib/graph-to-secondary-structure.py | Python | gpl-3.0 | 3,245 | [
"Biopython"
] | cb0f4d760013f1b8f1fe72cf416a6b124a39a721aa76971911e3fd713b3c0785 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'Visit.satisfied'
db.add_column(u'clinics_visit', 'satisfi... | myvoice-nigeria/myvoice | myvoice/clinics/migrations/0032_auto__add_field_visit_satisfied__add_field_visit_survey_started__add_f.py | Python | bsd-2-clause | 12,531 | [
"VisIt"
] | 0b8f5daf2a79b2036f97b95d4a3eb4cbd965b0d33251ce60da85f9c0cb491c75 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/calculator.py | Python | gpl-2.0 | 8,190 | [
"VisIt"
] | 28ce1fe8aaf0f9badb306808b759f0a967890f808261795061003930f7f10d91 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
# pylint: disable=no-init,too-few-public-meth... | mganeva/mantid | Testing/SystemTests/tests/analysis/WeightedLeastSquaresTest.py | Python | gpl-3.0 | 13,213 | [
"Gaussian"
] | 94f445cf9ca396e8dc9b74e9fa1e7c0b3f7a5ef1aae47a9be0f518dcaf8f3bc9 |
#!/usr/bin/env python3
# dl_poly_conv
# Converts DL_POLY REVCON file to pdb or xyz
import os, sys
REVCON = "REVCON"
DIR = os.getcwd().split("/")[-1] # by default, use directory name as file name
# TYPES
def get_atoms():
# returns atoms as a list of dicts with id, atom type, x, y z
atoms = []
with open(R... | keirwl/dl_poly_parse | dl_poly_conv.py | Python | mit | 1,851 | [
"DL_POLY"
] | 4f20ddefc821359e2012c80cf367bd8612d1246bce4aa87afe5b9f2c719bd226 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Part of the PsychoPy library
# Copyright (C) 2018 Jonathan Peirce
# Distributed under the terms of the GNU General Public License (GPL).
"""Converting code parameters and components from python (PsychoPy)
to JS (ES6/PsychoJS)
"""
import ast
import astunparse
import esp... | hoechenberger/psychopy | psychopy/experiment/py2js.py | Python | gpl-3.0 | 6,158 | [
"VisIt"
] | d426fdfad7f7266d2933bed570bd1d9cacbfd5163b59ff13413ea550d10c8cb7 |
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