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#!/usr/bin/env python
# encoding: utf-8
"""
Uniweb validator project
checksites.py
Copyright (c) 2009 Brian Shumate
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including... | brianshumate/uniweb | share/checksites.py | Python | bsd-2-clause | 1,913 | [
"Brian"
] | ea46d362aa0f0901fd9ac5e83849b29d2c79a281ae934cebd8c36c2ea39737e3 |
#!/usr/bin/env python
import numpy as np
import dendrogenous as dg
import ete3
from dendrogenous.settings import Settings as SettingsClass
import dendrogenous.utils
import os
import io
import re
import pymysql
import subprocess
import glob
import sqlite3
import logging
import numpy
from Bio import Phylo
from Bio i... | fmaguire/dendrogenous | dendrogenous/core.py | Python | bsd-3-clause | 21,903 | [
"BLAST",
"Biopython"
] | e6e17a1a455b9a693360eea7ffd1c3677a14f84b9900350620ba2b7a609d5161 |
from __future__ import absolute_import
import ast
import itertools
from types import FunctionType
from myhdl._util import _flatten
from myhdl._enum import EnumType
from myhdl._Signal import SignalType
class Data():
pass
def _getCellVars(symdict, arg):
gens = _flatten(arg)
data = Data()
data.symdict ... | gw0/myhdl | myhdl/_getcellvars.py | Python | lgpl-2.1 | 710 | [
"VisIt"
] | 2c95d86b537b4f331e362a08ebda2b6a8ffc772c1427c5cc4e7e580ce3df0078 |
"""
Implementation of RSA Public Key Encryption in Python
Kunal Gosar - Dec 2015 Visit me at: http://kunalgosar.me
"""
import random
class encrypter:
def __init__(self, lower=10**50, upper=10**100, e=65537):
self.pub_key, self.prv_key = self.__keygen(lower, upper, e)
def __keygen(self, lower, upper,... | kunalgosar/RSA-Encryption | RSA.py | Python | mit | 2,606 | [
"VisIt"
] | 72cecc85007c9c68534930d0bf4578b414caf45a9a0611727f97894610fe8e4b |
from abc import ABCMeta
from abc import abstractmethod
try:
from StringIO import StringIO as BytesIO
except ImportError:
from io import BytesIO
try:
from six import text_type
except ImportError:
from galaxy.util import unicodify as text_type
try:
from urllib import urlencode
except ImportError:
... | jmchilton/lwr | lwr/lwr_client/interface.py | Python | apache-2.0 | 3,817 | [
"Galaxy"
] | f8eb8abca3b67bfaa9556857601f2a1b2108c3feba8d11b0daea13e81022fcae |
#!/usr/bin/env python
# This example demonstrates how to use the vtkSphereWidget to control
# the position of a light.
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Start by loading some data.
dem = vtk.vtkDEMReader()
dem.SetFileName(VTK_DATA_ROOT + "/Data/SainteHe... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/GUI/Python/SphereWidget.py | Python | bsd-3-clause | 3,083 | [
"VTK"
] | 79da91b894acaba379f9334c35474e9b042d507b50cd0f5e4f41b1c24942204c |
# User creation spoke
#
# Copyright (C) 2013 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed in the... | mairin/anaconda | pyanaconda/ui/gui/spokes/user.py | Python | gpl-2.0 | 22,989 | [
"VisIt"
] | 12a7f689d15ab1157e486c2a1ba0fa0988491fc7408d78ab614eff3feb6e9def |
#!/usr/bin/env python
import argparse
import shutil
import icqsol_utils
# Parse Command Line.
parser = argparse.ArgumentParser()
parser.add_argument('--input', dest='input', help='Shape dataset selected from history')
parser.add_argument('--input_file_format_and_type', dest='input_file_format_and_type', help='Input f... | pletzer/galaxy-csg | tools/icqsol_add_texture/icqsol_add_texture.py | Python | mit | 2,295 | [
"VTK"
] | 3812a6a09caaf7754f72b0fea872d0d2fb163feb81d9a2846644111a981d54c2 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Custom Axes
###################
"""
#
#import seaborn as sns
#
#from exa.mpl import _plot_contour, _plot_surface
#from exatomic import Energy
#
#
#def _get_minimum(mindf):
# a... | exa-analytics/atomic | exatomic/mpl.py | Python | apache-2.0 | 23,126 | [
"Gaussian"
] | 0a9fd317200b7a5dbb7e6d4959c159980b3d6780c1b75200516f7922bb0b0e7e |
"""Test VTK_IGNORE_BTX setting to ensure that it is ON
"""
import sys
import vtk
from vtk.test import Testing
class TestIgnoreBTX(Testing.vtkTest):
def testIgnoreBTX(self):
"""Try to call a method that is BTX'd, to ensure VTK_IGNORE_BTX=ON
"""
stringArray = vtk.vtkStringArray()
in... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Common/Core/Testing/Python/TestIgnoreBTX.py | Python | gpl-3.0 | 477 | [
"VTK"
] | 4e96a8fb67e3fb3c29a72866dd8db2eacadc1e9c62d1065cb9f19a329c3edbfa |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | jralls/gramps | gramps/plugins/webreport/surname.py | Python | gpl-2.0 | 11,593 | [
"Brian"
] | c5c5debe19664a4ea3c0dfa13d602e780692745b949fb7008b30f282af211fc3 |
from apiclient.discovery import build
from oauth2client.client import OAuth2WebServerFlow
import httplib2
import gflags
import httplib2
from apiclient.discovery import build
from oauth2client.file import Storage
from oauth2client.client import OAuth2WebServerFlow
from oauth2client.tools import run_flow
from datetim... | neotea/google-calendar-display | server.py | Python | apache-2.0 | 8,164 | [
"VisIt"
] | af163b40e9cb5eb20f33b19730d73b56f5541aaab9eb256f5e639c0cf15e3dfb |
# -*- coding: utf-8
from yade import ymport, utils,pack,export
import gts,os
from yade import geom
#import matplotlib
from yade import plot
#from pylab import *
#import os.path, locale
#### set False when running in batch mode
#defaultTable = True
defaultTable = False
####-------------------------------------
####----... | anna-effeindzourou/trunk | examples/anna_scripts/triax/triaxial_E.py | Python | gpl-2.0 | 11,076 | [
"ParaView"
] | 6c5facc5b80f1117e9efeba8fcf0acf9fa48a5fb5a42612193526b05798c7198 |
# This file is part of fedmsg.
# Copyright (C) 2012 Red Hat, Inc.
#
# fedmsg 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 option) any later version.
#... | fedora-infra/fedmsg_meta_fedora_infrastructure | fedmsg_meta_fedora_infrastructure/tests/pkgdb.py | Python | lgpl-2.1 | 88,401 | [
"Bioconductor"
] | e930f4e61293bcfc3b25391a91238ea0388524863b8edcae33667ad551ef2391 |
# Copyright 2017 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 by applicable law or a... | skim1420/spinnaker | dev/validate_bom__test.py | Python | apache-2.0 | 38,012 | [
"ORCA"
] | 919c4fc8dd3c74043d1945bcef55c4d5a5cebcf11e0ea32fa1eb6efd540200d2 |
# -*- coding: utf-8 -*-
#
# one_neuron.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
... | lekshmideepu/nest-simulator | pynest/examples/one_neuron.py | Python | gpl-2.0 | 3,680 | [
"NEURON"
] | fe00445a78708a4afe0c5ef8131300a11fef9d1038b0318243a6642a5f41527d |
import os
import glob
import sys
import copy
import itertools
import logging
import numpy as np
from .utils import stack_files
from astropy.table import Column
from fermipy.utils import get_parameter_limits
def fit_region(gta,modelname,src_name,loge_bounds=None, **kwargs):
skip_opt = kwargs.get('skip_opt',[... | woodmd/haloanalysis | extpipe/fit_funcs.py | Python | bsd-3-clause | 16,120 | [
"Gaussian"
] | 2a6a32fd8b639e2e587cd456534526bf3f5b9fae3b8bb56e271ced20eb7ebc7e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import copy
from monty.serialization import loadfn # , dumpfn
from pymatgen.command_line.critic2_caller import Critic2Output
from pymatgen.core.structure import Molecule, Structure... | fraricci/pymatgen | pymatgen/analysis/tests/test_graphs.py | Python | mit | 38,226 | [
"pymatgen"
] | e254be444077bca9ee0cae2d2d7a75af0497f84a87a6b78c165d05b4bb7cef13 |
#### PATTERN | EN | INFLECT ########################################################################
# -*- coding: utf-8 -*-
# Copyright (c) 2010 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
######################################################... | clips/pattern | pattern/text/en/inflect.py | Python | bsd-3-clause | 36,230 | [
"Elk",
"Octopus"
] | 5c140129923617229220803d95a812db3734e99315fb9fc7d39136918ef2bb29 |
# -*- coding: utf-8 -*-
"""
"""
from __future__ import absolute_import
import re
from subprocess import call, check_call
import sys
import py
import pytest
@pytest.fixture(scope='session')
def session_tmpdir(request):
tmpdir_handler = getattr(request.config, '_tmpdirhandler', None)
if tmpdir_handler:
... | dairiki/humpty | tests/conftest.py | Python | bsd-3-clause | 5,206 | [
"VisIt"
] | d3dc1bd64bdaf324e2a3ece7399753c09cb39f6e166bf0ffef04c20e7c0b9241 |
# pysam versioning information
__version__ = "0.10.0"
__samtools_version__ = "1.3.1"
__bcftools_version__ = "1.3.1"
__htslib_version__ = "1.3.2"
| bioinformed/pysam | pysam/version.py | Python | mit | 149 | [
"pysam"
] | 1fc0a718fa836df664e1305d812a6b5b6e575de5615bc65ce35a62d4fb4a0601 |
class VehicleInfo(object):
def __init__(self):
"""
make_target: option passed to make to create binaries. Usually sitl, and "-debug" may be appended if -D is passed to sim_vehicle.py
default_params_filename: filename of default parameters file. Taken to be relative to autotest dir.
... | avrem/ardupilot | Tools/autotest/pysim/vehicleinfo.py | Python | gpl-3.0 | 13,904 | [
"Firefly"
] | 550884c5f49682eaae1c010d669a59615a224a12a13ce1cfde2de14b7777bdc3 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-asset | tests/unit/gapic/asset_v1/test_asset_service.py | Python | apache-2.0 | 162,124 | [
"Octopus"
] | e5d77f78a834d5b14b902c240b2c6bfdc83613bb948b24897b7ce0fd91fbecb0 |
# Copyright 2020 DeepMind Technologies Limited.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed... | deepmind/ferminet | ferminet/mcmc.py | Python | apache-2.0 | 9,058 | [
"Gaussian"
] | ff991c5625a806d84d3583e44af73b0646c6b231cbc788646d67d554a3783307 |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | galsim/position.py | Python | gpl-3.0 | 2,525 | [
"Galaxy"
] | 300c094094736480594b75712fd9a20ae0ad68842ecc54d5eede26b91fbe3d04 |
"""
See more here: http://www.pymolwiki.org/index.php/center_of_mass
DESCRIPTION
Places a pseudoatom at the center of mass
Author: Sean Law
Michigan State University
slaw (at) msu . edu
SEE ALSO
pseudoatom, get_com
"""
from __future__ import print_function
from pymol import cmd
def com(... | joy13975/elfin | pymol_scripts/extensions/deprecated/center_of_mass.py | Python | mit | 2,243 | [
"PyMOL"
] | e00f46e3ae34b3bbc73cd6699c5dacc2234deaa223d50d55e279c9081ed6a07b |
#
# basic run through the PDB with dynamically-sized labels
#
from glob import glob
import threading
import time
from pymol import cmd
import sys, os, os.path
import traceback
ent_dir = "pdb"
def load():
cmd.set("valence")
r = 0
list = glob("pdb/*/*")
# while list[0]!="pdb/f8/pdb1f8u":
# lis... | gratefulfrog/lib | python/pymol/pymol_path/test/inp/B09.py | Python | gpl-2.0 | 1,119 | [
"PyMOL"
] | 87789fdab649e2097a47df15be2ef5d6f583287b3bf5de0e4723011efa010abb |
"""Github setting 'Protect this branch' was disabled for a repo."""
from streamalert.shared.rule import rule
@rule(logs=['ghe:general'])
def github_disable_protect_this_branch(rec):
"""
author: @mimeframe
description: Github setting 'Protect this branch' was disabled for a repo.
W... | airbnb/streamalert | rules/community/github/github_disable_protect_this_branch.py | Python | apache-2.0 | 874 | [
"VisIt"
] | d17049a11a5be547953cf4ce3cb978bb311f24b207ee655e8d8f27e39d0c8d40 |
import numpy as np
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms, FixBondLength
from ase.db import connect
from ase.io import read
from ase.structure import molecule
from ase.test import must_raise
for name in ['y2.json', 'y2.db']:
c = connect(name)
print(name... | suttond/MODOI | ase/test/db2.py | Python | lgpl-3.0 | 1,480 | [
"ASE"
] | 3d5ffa7d0ab76fb5cf8f38ef6651e52b4560e441ffc4ea6fadaa413fb283f39c |
"""
An example showing the Julia set displayed as a z-warped surface.
The Julia set is a fractal (see http://en.wikipedia.org/wiki/Julia_set
). We display it here in a canyon-like view using mlab's surf function:
:func:`mayavi.mlab.surf`.
"""
# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Copyright (c) 20... | dmsurti/mayavi | examples/mayavi/mlab/julia_set.py | Python | bsd-3-clause | 832 | [
"Mayavi"
] | c186bf89cba8e172563ae33882c20ba15a0c684b4343d67f7fded8a4a5539e62 |
import itertools as it
import difflib
class Order:
def order_for(self, stage, elements):
self.elements = elements
return stage.visit(self)
#def case_present_past_future(self, stage):
# pass
#def case_seasons_of_year(self, stage):
# pass
def case_days_of_week(self, stag... | alepulver/my-thesis | results-tables/aggregators/order.py | Python | mit | 1,510 | [
"VisIt"
] | 0c175f0ae68e67601c986b940cc9b85dd69857f76f879541a4f37d3c0dc69d80 |
#! /usr/bin/env python3
#
# Affiche un fichier VRML 2 + capture
# RoBo - mai 2006
#
import vtk
import sys
#filename = "brain_bis_Rempli.wrl"
if len(sys.argv)!=2:
print('usage: ShowVRML.py file.wrl')
sys.exit()
filename = sys.argv[1]
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(re... | rboman/progs | metafor/biomec/vrml/ShowVRML.py | Python | apache-2.0 | 902 | [
"VTK"
] | faa41a8b9718e7ca07b6a3b2a1f8f92352cd7b3c02565acedbbf17848ebb38b5 |
#!/usr/bin/env python
import pysam
| yunlongliukm/chm1_scripts | MeasureeMapQV.py | Python | mit | 37 | [
"pysam"
] | 596be566692c78557c7b56bb56c7f1637c30e7b2d49af1b55492b342e53af522 |
# Copyright (C) 2013 by Ben Morris (ben@bendmorris.com)
# Based on Bio.Nexus, copyright 2005-2008 by Frank Kauff & Cymon J. Cox
# and Bio.Phylo.Newick, copyright 2009 by Eric Talevich.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file tha... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Phylo/CDAOIO.py | Python | gpl-2.0 | 15,371 | [
"Biopython"
] | 04da70a981b0b060c17936326fde1a97884ea03863628e6f20cfc23e9074e84f |
# Orca
#
# Copyright 2010 Joanmarie Diggs.
# Copyright 2014-2015 Igalia, S.L.
#
# 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 option) an... | pvagner/orca | src/orca/scripts/web/script_utilities.py | Python | lgpl-2.1 | 85,572 | [
"ORCA"
] | d10d2b798065bf26854fda048822996e17037edb858979fafc4788f8485962cb |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | algae_dice/algae.py | Python | apache-2.0 | 19,381 | [
"Gaussian"
] | bf6b77dc6e8c21e4d36669483e090f536a5ce9237a558f49ae1b121ebc30b1c9 |
# -*- coding: utf-8 -*-
"""
=====================
Cython related magics
=====================
Magic command interface for interactive work with Cython
.. note::
The ``Cython`` package needs to be installed separately. It
can be obtained using ``easy_install`` or ``pip``.
Usage
=====
To enable the magics below,... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/IPython/extensions/cythonmagic.py | Python | bsd-3-clause | 11,907 | [
"Brian"
] | 62198f8cda9cf04a067d0ddcbe639216f5aeade249ce829d7f1f46e7606ea351 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import gtk
import sys
from logging import info, warn
from zeroinstall import _, translation
from zeroinstall import SafeException
from zeroinstall.support import tasks, pretty_size
from zeroinstall.injector import do... | dsqmoore/0install | zeroinstall/0launch-gui/mainwindow.py | Python | lgpl-2.1 | 10,052 | [
"VisIt"
] | 595de48104383e4b9ea3900670eb05143e37eea8b84c310ba72ff10c685df9dd |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | MLnick/spark | python/pyspark/ml/regression.py | Python | apache-2.0 | 60,886 | [
"Gaussian"
] | 4e067acb0dcb5347082d5dc61541cfd22a32dcb00a9bb7106ac5fbf9de2f91ae |
# 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 +
from __future__ import (absolute_import, divi... | mganeva/mantid | Framework/PythonInterface/plugins/algorithms/DeltaPDF3D.py | Python | gpl-3.0 | 19,144 | [
"Gaussian"
] | 3271fb66084a38a4c8214b82b00a4fdbd095170bd97a2389144613bf2ccda855 |
# -*- coding: utf-8 -*-
# Copyright (c) 2006-2007, 2009-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2009 Mads Kiilerich <mads@kiilerich.com>
# Copyright (c) 2010 Daniel Harding <dharding@gmail.com>
# Copyright (c) 2012 FELD Boris <lothiraldan@gmail.com>
# Copyright (c) 2012-2014 Google, Inc.
... | axbaretto/beam | sdks/python/.tox/lint/lib/python2.7/site-packages/pylint/checkers/utils.py | Python | apache-2.0 | 27,930 | [
"Brian"
] | 1f29a4dd55294d1502d0f3e36a2f5f56253f47b85e3b35a5e7397ea9e4bd8f5d |
# -*- coding: utf-8 -*-
#
# hl_api_info.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... | zifeo/nest-simulator | pynest/nest/lib/hl_api_info.py | Python | gpl-2.0 | 5,653 | [
"VisIt"
] | 3a02a0ceb397fe1ccdbe09cad1fe57d5a03c540bf10970bd6d633d529686ebb4 |
import os
import sys
import json
import logging
import argparse
from typing import Iterable, TextIO
from collections import defaultdict
import dinopy
import networkx
from phasm.io import gfa
from phasm.io.sequences import FastaSource
from phasm.typing import ReadMapping, LocalAlignment, AlignmentsT
from phasm.overlap... | AbeelLab/phasm | phasm/cli/assembler.py | Python | mit | 26,901 | [
"Cytoscape"
] | 67b920ff4d950334f322b5e02a483958b09647785faad78c9d3be766c966d625 |
##############################################################################
# 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... | mfherbst/spack | var/spack/repos/builtin/packages/bwa/package.py | Python | lgpl-2.1 | 2,458 | [
"BWA"
] | 8b4789bd317e744c0e260e12ff2bf62580c52743450481196d3422bc19a86ee1 |
import numpy as np
from gym.spaces import Box
from metaworld.envs import reward_utils
from metaworld.envs.asset_path_utils import full_v2_path_for
from metaworld.envs.mujoco.sawyer_xyz.sawyer_xyz_env import SawyerXYZEnv, _assert_task_is_set
class SawyerFaucetOpenEnvV2(SawyerXYZEnv):
def __init__(self):
... | rlworkgroup/metaworld | metaworld/envs/mujoco/sawyer_xyz/v2/sawyer_faucet_open_v2.py | Python | mit | 4,112 | [
"Gaussian"
] | f741c1f8ec3f223de89512d342abd89ff1887564ba66c741b46953f3bd77b44f |
# Licensed under an MIT open source license - see LICENSE
"""
Utility functions for fil-finder package
"""
import itertools
import numpy as np
from scipy import optimize as op
import thread
import threading
import time
import os
def removearray(l, arr):
'''
Removes an array from a list. Code from
http... | dcolombo/FilFinder | fil_finder/utilities.py | Python | mit | 4,848 | [
"Gaussian"
] | 78bb0c14335f9bc32f678b6d28e716430fed8fb9d1afdc0f007e71db7ea2f2ed |
"""
This module calculates corrections for the species listed below, fitted to the experimental and computed
entries given to the CorrectionCalculator constructor.
"""
import os
import warnings
from collections import OrderedDict
from typing import Dict, List, Tuple, Union, Optional
import numpy as np
import plotly.g... | vorwerkc/pymatgen | pymatgen/entries/correction_calculator.py | Python | mit | 20,606 | [
"pymatgen"
] | a452c8f27d399e7c3536029f4d8f19dc1ff2ed1448a1649bfd24a2c98e458431 |
from datetime import datetime
from django.core.urlresolvers import reverse
from edc.audit.audit_trail import AuditTrail
from edc.subject.visit_tracking.models import BaseVisitTracking
from edc.subject.visit_tracking.settings import VISIT_REASON_NO_FOLLOW_UP_CHOICES
from ..choices import VISIT_REASON
class Maternal... | botswana-harvard/eit | eit/apps/eit_maternal/models/maternal_visit.py | Python | gpl-3.0 | 1,498 | [
"VisIt"
] | b336c12540edb3562c8047ede11edda41b9fcb8157419f2385968f8f4f2b6551 |
# coding=utf-8
# Copyright 2022 The Edward2 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 o... | google/edward2 | edward2/tensorflow/layers/made.py | Python | apache-2.0 | 9,581 | [
"Gaussian"
] | b7f7496e0f94d9e5074249eaa4f56ebd2eedbef47f11927e56eb17353c324ee2 |
from textwrap import dedent
import py, pytest
from _pytest.config import PytestPluginManager
from _pytest.main import EXIT_NOTESTSCOLLECTED, EXIT_USAGEERROR
@pytest.fixture(scope="module", params=["global", "inpackage"])
def basedir(request, tmpdir_factory):
from _pytest.tmpdir import tmpdir
tmpdir = tmpdir(r... | ionelmc/pytest | testing/test_conftest.py | Python | mit | 14,181 | [
"VisIt"
] | c878f95ac5c595b2f3779941f28d238e4283c66d82fe91529fc74c4d00a27cb5 |
"""
pygments.lexers.teal
~~~~~~~~~~~~~~~~~~~~
Lexer for TEAL.
:copyright: Copyright 2006-2022 by the Pygments team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
from pygments.lexer import RegexLexer, bygroups, include, words
from pygments.token import Comment, Name, Number, String, Te... | dscorbett/pygments | pygments/lexers/teal.py | Python | bsd-2-clause | 3,495 | [
"ASE"
] | 6e03db37ff54b5a8c7eb37e9ea58f895b46449e917fbf189684befc9017e7616 |
import numpy as np
import simtk.openmm as mm
import simtk.openmm.app as app
import simtk.unit as u
eu = u.kilocalories_per_mole
temperature = 288 * u.kelvin
pressure = 1.0 * u.atmosphere
friction = 1.0 / u.picosecond
pdb = app.PDBFile('resi-1-15.pdb')
forcefield = app.ForceField('amber99sb.xml',"tip3p.xml")
system ... | kyleabeauchamp/AlphaSynuclein | python/equilibrate.py | Python | apache-2.0 | 824 | [
"OpenMM"
] | 053fc8dc0b8690619bc40d6ceb73336175e983dda342db5c6fb119c964ad5202 |
# Copyright 2010-2013 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Testing Bio.TogoWS online code.
"""
from __future__ import print_function
import unitte... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_TogoWS.py | Python | gpl-2.0 | 23,363 | [
"Biopython"
] | 6941ae768599c5a5bbe92730da596d0597ad2ad895ec975b15df52cfe5283533 |
# Copyright 2017-2020 The GPflow Contributors. 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 appli... | GPflow/GPflow | gpflow/expectations/quadratures.py | Python | apache-2.0 | 6,486 | [
"Gaussian"
] | 5e96ff4d968c232885add520bc234ba4adf29f0fc08dc469533ae2f0a0107f2b |
"""
Acceptance tests for course in studio
"""
from nose.plugins.attrib import attr
from .base_studio_test import StudioCourseTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.users import CourseTeamPage
from ...pages.studio.index import DashboardPage
@attr('shard_2')
class CourseTeamPageT... | GbalsaC/bitnamiP | common/test/acceptance/tests/studio/test_studio_course_team.py | Python | agpl-3.0 | 14,133 | [
"VisIt"
] | a0fdef8105f121fdb8a6f2f2d5c64ae59217b6d62612c07b29283dd35b3b7845 |
# -*- coding: utf-8 -*-
'''
This module contains the necessary tools to crawl the sitemeter.com site and
extract the blog stats for the blogmeter project.
'''
# Imports
import bs4
import logging
import os.path
import random
import socket
import sys
import time
import traceback
import unicodedata
import urllib
from ... | heldergg/blogmeter | lib/webscraper/scrapstats.py | Python | gpl-3.0 | 8,225 | [
"VisIt"
] | 75cbfbc3f3262f0070cea94fdf82fc69bb30df5b773c711079a3c72e0dba8a1d |
#!/usr/bin/env python
from setuptools import setup
from CLAM.config import __version__
def main():
setup(name='CLAM',
version=__version__,
description='CLIP-seq Analysis of Multi-mapped reads',
author='Zijun Zhang',
author_email='zj.z@ucla.edu',
url='https://github.com/Xinglab/CLAM',
packages... | Xinglab/CLAM | setup.py | Python | gpl-3.0 | 549 | [
"pysam"
] | 85a84cd2d5f09b70dee41c94855f17c709a6844e5cf4b9193a292e6545dd8fc1 |
from views import *
from lookups import *
import rest as annotation
import requests
import primer3
import myvariant
import re
from utils import *
import itertools
import pysam
import csv
#hpo lookup
import phizz
import random
import orm
@app.route('/variant3/<variant_str>')
def variant_page3(variant_str):
db=get_... | pontikos/uclex_browser | views/variant.py | Python | mit | 7,029 | [
"pysam"
] | e0cca600c462942e3cb3a3b69874a435a88295c0611339b248a8bfce61e2e6e7 |
import predict as pd
import copy
import os
import numpy as np
import util
import shutil
import pickle
import pylab as plt
import pandas
import local_multiprocessing
import load_data
import features.featurization as feat
def check_feature_set_dims(feature_sets):
F2 = None
for set in feature_sets.keys():
... | mayavanand/RMMAFinalProject | azimuth/model_comparison.py | Python | bsd-3-clause | 31,399 | [
"Gaussian"
] | 461880d9a7452159f76a10f2e2cb3cb9cf0f5185dc096ef81be3e53f8bdf38c6 |
import os
import glob
import math
import zipfile
from shapely.geometry import MultiPoint, Point, mapping
from datetime import datetime
# NetCDF
import netCDF4
import pytz
from fiona import collection
from collections import OrderedDict
from paegan.logger import logger
import geojson
import tables
from tables impo... | axiom-data-science/paegan-transport | paegan/transport/export.py | Python | gpl-3.0 | 18,114 | [
"NetCDF"
] | fcc9da5cded49261d958d5ff31c410a6de582c1c7e533281a3927b3c29f02f3e |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | juanchopanza/NeuroM | neurom/fst/tests/test_core.py | Python | bsd-3-clause | 3,278 | [
"NEURON"
] | 7c3847ebb9051f7345290a6a2bf810f992d5585c3ad9f15cef9efbff8ff2bf6a |
from django.conf import settings
from django.db.models import F
from django.utils.module_loading import import_string
from wagtail_personalisation.models import Segment
from wagtail_personalisation.rules import AbstractBaseRule
from wagtail_personalisation.utils import create_segment_dictionary
class BaseSegmentsAda... | LabD/wagtail-personalisation | src/wagtail_personalisation/adapters.py | Python | mit | 8,495 | [
"VisIt"
] | 70f8a1fd91192913b73051cce17120fbfd3b351a711bbd09edc8397297cc4bad |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | likithkailas/StreamingSystems | python/pyspark/ml/regression.py | Python | apache-2.0 | 58,760 | [
"Gaussian"
] | 5178fd0b3f8ae3102682bf7bab8c1eb881672d1cf3bb0427cc64b6296ce1e9ae |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import numpy as np
from scipy.spatial import ConvexHull, Voronoi
from .volume import Volume
__author__ = 'Yuji Ikeda'
__version__ = '0.1.0'
class VolumeVoronoi(Vo... | yuzie007/ph_analysis | ph_analysis/structure/volume_voronoi.py | Python | mit | 2,740 | [
"VASP",
"phonopy"
] | c32db69598fa14774e5d4b55c1ada5a161ff1914b9993b150d0b617461f28c9f |
# -*- coding: utf-8 -*-
# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry
# and reaction kinetics.
# Copyright (C) 2008-2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, An Ghysels
# <An.Ghysels@UGent.be> and Matthias Vandichel <Matthias.Vandichel@UGent.be>
# Center for Molecular Modeling... | molmod/tamkin | tamkin/test/test_rotor.py | Python | gpl-3.0 | 18,551 | [
"Gaussian"
] | 483932d9570b5478ffbf70ed99175706d15b3c32ac464ce6d08fcea8f85cb952 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
# BEGIN PYTHON 2/3 COMPATIBILITY BOILERPLATE
from __future__ import absolute_import
from __future__ import with_statement
from __future__ import division
from __future__ import nested_scopes
from __future__ import generators
from __future__ import unicode_literals
from __future... | michaelerule/neurotools | functions.py | Python | gpl-3.0 | 4,609 | [
"Gaussian"
] | 548d0c5d9b8cc2d1e9974926368cd636191dfb2608d1376e756ffb34bcf530b8 |
import unittest
import requests_mock
from frontstage import app
from tests.integration.mocked_services import url_banner_api
class TestCookiesContact(unittest.TestCase):
def setUp(self):
self.app = app.test_client()
@requests_mock.mock()
def test_cookies_success(self, mock_request):
moc... | ONSdigital/ras-frontstage | tests/unit/views/test_cookies_and_contact.py | Python | mit | 1,570 | [
"VisIt"
] | aaf509532ac3672dc0430fb7decf98df5e43dfbc63588c4d9f08ca1c1e9437c7 |
#!/usr/bin/env python
"""
TurnkeyLaserExporter
-----------------------------------
Maintained by Turnkey Tyranny (https://github.com/TurnkeyTyranny/laser-gcode-exporter-inkscape-plugin)
Designed to run on Ramps 1.4 + Marlin firmware on a K40 CO2 Laser Cutter.
Based on think|haus gcode inkscape extension
Bas... | quillford/laser-gcode-exporter-inkscape-plugin | turnkeylaser.py | Python | gpl-2.0 | 66,956 | [
"VisIt"
] | 049f459186c8d9409d97976abe6d288f6d65c732bb329d821299517b41079297 |
'''Constant pressure/stress and temperature dynamics.
Combined Nose-Hoover and Parrinello-Rahman dynamics, creating an NPT
(or N,stress,T) ensemble.
The method is the one proposed by Melchionna et al. [1] and later
modified by Melchionna [2]. The differential equations are integrated
using a centered difference meth... | freephys/python_ase | ase/md/npt.py | Python | gpl-3.0 | 27,683 | [
"ASE",
"NetCDF"
] | d743dafe6c23e2b8a311a1b33ae0bc43d014ee5e5006fa63662b6e474d4a483d |
"""
Test helper functions and base classes.
"""
import inspect
import json
import unittest
import functools
import operator
import pprint
import requests
import os
import urlparse
from contextlib import contextmanager
from datetime import datetime
from path import Path as path
from bok_choy.javascript import js_defined... | jzoldak/edx-platform | common/test/acceptance/tests/helpers.py | Python | agpl-3.0 | 32,321 | [
"VisIt"
] | 37484072f146334a0031af8a3b341528418347b7ddb5c5f889e7816f6c66b598 |
#!/usr/bin/env python
# This is a test that:
# - gets the (DIRAC-free) PilotWrapper.py (that should be in input)
# - use its functions to generate a pilot wrapper
# - starts it
#
# It should be executed for different versions of python, e.g.:
# - 2.6.x
# - 2.7.x (x < 9)
# - 2.7.x (x >= 9)
# - 3.6.x
#
#
# Invoke this w... | yujikato/DIRAC | tests/Integration/WorkloadManagementSystem/Test_GenerateAndExecutePilotWrapper.py | Python | gpl-3.0 | 2,960 | [
"DIRAC"
] | 100ab93bba0cd3c4afb879ed2f0115449476cfdcdc41d2276fc6dde21f107563 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/lib/util.py | Python | gpl-2.0 | 45,707 | [
"LAMMPS",
"MDAnalysis"
] | 3015c7d882038185d3cec84b869aadea596776a87ec06d71d3025dd9d2ee59ca |
# -*- test-case-name: twisted.python.test.test_deprecate -*-
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
"""
Deprecation framework for Twisted.
To mark a method, function, or class as being deprecated do this::
from incremental import Version
from twisted.python.deprecate import d... | whitehorse-io/encarnia | pyenv/lib/python2.7/site-packages/twisted/python/deprecate.py | Python | mit | 26,775 | [
"Amber"
] | 9b712669f96e114da3f344554ad8f33607c620f8f63d8e1b5a761557705e083c |
"""
==========================
Gaussian HMM of stock data
==========================
This script shows how to use Gaussian HMM.
It uses stock price data, which can be obtained from yahoo finance.
For more information on how to get stock prices with matplotlib, please refer
to date_demo1.py of matplotlib.
"""
from __... | fivejjs/hmmlearn | examples/plot_hmm_stock_analysis.py | Python | bsd-3-clause | 2,793 | [
"Gaussian"
] | 1bcefdacfa8238e4e6d5a8fa8e6fc480ee093854f059c3a8a87e167611d3af50 |
"""module for producing astronomical plots
(c) 2007-2013 Matt Hilton
U{http://astlib.sourceforge.net}
This module provides the matplotlib powered ImagePlot class, which is designed to be flexible. ImagePlots can have RA, Dec. coordinate axes, contour overlays, and have objects marked in them, using WCS coordinates. ... | boada/astLib | astLib/astPlots.py | Python | lgpl-2.1 | 52,950 | [
"Gaussian"
] | 58addaea7a6d874a6fa414c3d20945288548621e62577476f46601ab08bf557a |
from numpy import (logical_and, asarray, pi, zeros_like,
piecewise, array, arctan2, tan, zeros, arange, floor)
from numpy.core.umath import (sqrt, exp, greater, less, cos, add, sin,
less_equal, greater_equal)
# From splinemodule.c
from .spline import cspline2d, sepfir2d... | pizzathief/scipy | scipy/signal/bsplines.py | Python | bsd-3-clause | 13,730 | [
"Gaussian"
] | 578d9b7e44818018cc0d045588a9f65e8a1891b99e1ca12b50ebde826a243ade |
import sys
import os
import numpy as np
from scipy.stats import norm
import math
import random
import cv2
import run
def make_sharp(k, sd):
'''Create a sharpen kernel.
Input:
k - the radius of the kernel.
sd - the standard deviation of the gaussian filter used to make the kernel.
Output:
output - a... | fieraloca/CODEPROJ | PYTHON/COMP_PHOTO/hw1/part2.py | Python | mit | 3,427 | [
"Gaussian"
] | 1e6ec04582f447d97af8c6a83a1d6e83cd4571dbe42634dc8bf40ccc4a7704f2 |
#########################################################################################
# LSF.py
# 10.11.2014
# Author: A.T.
#########################################################################################
""" LSF.py is a DIRAC independent class representing LSF batch system.
LSF objects are used as bac... | chaen/DIRAC | Resources/Computing/BatchSystems/LSF.py | Python | gpl-3.0 | 5,616 | [
"DIRAC"
] | 8d3e4ccedccb69d91643ebc452090582edd2e8c0d0ccb1c498202fa7a3211dd3 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyCheckmGenome(PythonPackage):
"""Assess the quality of microbial genomes recovered from i... | LLNL/spack | var/spack/repos/builtin/packages/py-checkm-genome/package.py | Python | lgpl-2.1 | 1,317 | [
"pysam"
] | 0c9dae239955b771939676973e9233ad8fe0433d8f6659b96502ff1459ed00fc |
##
# Copyright 2009-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | hpcuantwerpen/easybuild-easyblocks | easybuild/easyblocks/s/sas.py | Python | gpl-2.0 | 4,729 | [
"ASE"
] | 31210aa4d7910d8907dbf8b49484822444eb61d56588fc7411c933085a2305f0 |
# $Id$
#
# Copyright (C) 2008-2011 Greg Landrum
#
# @@ 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.
#
from rdkit import Chem
from rdkit import RDConfig... | AlexanderSavelyev/rdkit | rdkit/Chem/Draw/MolDrawing.py | Python | bsd-3-clause | 22,658 | [
"RDKit"
] | c4d01fbe4925bbce66f08dd21ecfa1100664309ef60911631f3b57514b2a0811 |
# sql/expression.py
# Copyright (C) 2005-2013 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Defines the base components of SQL expression trees.
All components are derived ... | VagrantApe/flaskMicroblog | venv/lib/python2.7/site-packages/sqlalchemy/sql/expression.py | Python | bsd-3-clause | 219,350 | [
"VisIt"
] | d49dbfd752acafc970883e2f6093b8b3e2c8f2e103322c8f2d2222e36703aaf3 |
# coding=utf-8
# Copyright 2016 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
from __future__ import (absolute_import, division, generators, nested_scopes, print_function,
unicode_literals, with_statement)
import ast
import in... | UnrememberMe/pants | src/python/pants/engine/rules.py | Python | apache-2.0 | 7,202 | [
"VisIt"
] | e5d38c84aa922115927ac91c15d083ace31c0146457793e5d7127eb4fa1feaa1 |
# -*- coding: utf-8 -*-
#
# hh_psc_alpha.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, o... | hakonsbm/nest-simulator | pynest/examples/hh_psc_alpha.py | Python | gpl-2.0 | 2,223 | [
"NEURON"
] | c4e0de05151fcea6b362f0d862319cecfaf3dee8fc547e77ee80a83f20d71622 |
from net_modules import keypoints_2d
import tensorflow as tf
import zutils.tf_math_funcs as tmf
import numpy as np
import zutils.pt_utils as ptu
import net_modules.auto_struct.utils as asu
import prettytensor as pt
import math
from zutils.py_utils import *
import zutils.tf_graph_utils as tgu
from net_modules.auto_str... | YutingZhang/lmdis-rep | net_modules/auto_struct/keypoint_encoder.py | Python | apache-2.0 | 23,819 | [
"Gaussian"
] | d565a97a3318b3261d929139b4bcc7840c037aec7879efeb2314f1d702bda3d9 |
# -*- coding: utf-8 -*-
#
# evaluate_quantal_stp_synapse.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 o... | HBPNeurorobotics/nest-simulator | pynest/examples/evaluate_quantal_stp_synapse.py | Python | gpl-2.0 | 6,275 | [
"NEURON"
] | d3d62bb934bfc908205a604aa68b0a4f49de5b29e531e16091e9dce6c528b536 |
###############################################################################
# begin : Sun Jan 8 21:24:38 BRST 2012
# copyright : (C) 2012 by Ricardo Niederberger Cabral,
# : (C) 2016 Dmitry Litvinenko
# email : ricardo dot cabral at imgseek dot net
# ... | anti1869/isk | src/isk/api/images.py | Python | gpl-3.0 | 23,743 | [
"VisIt"
] | 92522c247e395af5ca2668d05b32c2633a327f14867dab8bd66199b462672159 |
"""This module creates a Pygame surface from a source surface that
has "end caps" on its corners. The caps remain unscaled in the
destination surface and the rest is scaled/tiled.
This was inspired by Android's NinePatch and iOS'
resizableImageWithCapInsets
"""
import pygame
AUTHOR = 'Brian Hammond <brian@fictori... | fictorial/pygame-capresize | capresize.py | Python | mit | 6,358 | [
"Brian"
] | 70b2303f935685a276694cb946e192bb21d1b49b432d3a9b6958ef4025191a26 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | dyoung418/tensorflow | tensorflow/contrib/distributions/python/ops/mvn_diag_plus_low_rank.py | Python | apache-2.0 | 9,729 | [
"Gaussian"
] | b6711f901630a54d9d20741ceb0a53783a5c8c1dbea1e310fd8204565fd2e20a |
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE... | rbberger/lammps | python/lammps/mliap/pytorch.py | Python | gpl-2.0 | 2,356 | [
"LAMMPS"
] | b7ee4c982ecbfa0797a5477ef6aba9cd871795964aa0518098b34703a590bf2e |
"""SyGMa: Systematically Generating potential Metabolites"""
from builtins import str
import argparse
import sygma
import sys
from rdkit import Chem, RDLogger
RDLogger.logger().setLevel(RDLogger.ERROR)
import logging
logging.basicConfig()
logger = logging.getLogger('sygma')
def run_sygma(args, file=sys.stdout):
l... | 3D-e-Chem/sygma | sygma/script/__init__.py | Python | gpl-3.0 | 1,855 | [
"RDKit"
] | ba4d2a3ec04659c8a97a48a97684139b30a3d62ea84ea08225c6d2a0cf869257 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This package contains all battery-related application classes, including
representations of InsertionElectrodes and ConversionElectrodes.
"""
| vorwerkc/pymatgen | pymatgen/apps/battery/__init__.py | Python | mit | 240 | [
"pymatgen"
] | bd47d8926c67427fad03da70ebd9f9c8139413fb5738dce3071b925406ceb909 |
import logging
import numpy as np
import pytest
import nengo
from nengo.utils.functions import piecewise
from nengo.utils.numpy import filtfilt
from nengo.utils.testing import Plotter, allclose
logger = logging.getLogger(__name__)
def test_args(nl):
N = 10
d1, d2 = 3, 2
with nengo.Network(label='test_... | ZeitgeberH/nengo | nengo/tests/test_connection.py | Python | gpl-3.0 | 14,583 | [
"NEURON"
] | 22b2eb75c43cd931d467a5e0e7dafb94b93e5be5cca6c6439646b5244c012731 |
from modshogun import GMM, RealFeatures
from numpy import zeros
from numpy.ma.extras import unique
from numpy.random import randint
from kameleon_mcmc.distribution.Discrete import Discrete
from kameleon_mcmc.distribution.Gaussian import Gaussian
from kameleon_mcmc.distribution.MixtureDistribution import MixtureDistrib... | karlnapf/kameleon-mcmc | kameleon_mcmc/mcmc/samplers/GMMMetropolis.py | Python | bsd-2-clause | 3,990 | [
"Gaussian"
] | b1fe96b4394fa4a792547f98188a8f372a8988a6d2809c222a84d3189b485e57 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# ... | t0mk/ansible | lib/ansible/modules/network/lenovo/cnos_template.py | Python | gpl-3.0 | 7,136 | [
"VisIt"
] | f6ad882e69c53d73b5b9759faf71619e240e3683f2e88ad9d69d84071c8a6d1a |
from __future__ import division
import functools
import numpy as np
import scipy.sparse as sp
import pytest
from sklearn.metrics import euclidean_distances
from sklearn.random_projection import johnson_lindenstrauss_min_dim
from sklearn.random_projection import gaussian_random_matrix
from sklearn.random_projection ... | vortex-ape/scikit-learn | sklearn/tests/test_random_projection.py | Python | bsd-3-clause | 14,002 | [
"Gaussian"
] | d133c22d005ee551be2f8b3f814987354b52f7c9e4e4d6c6ab493733ca9dc9a0 |
from aces.materials.POSCAR import structure as Material
class structure(Material):
def getPOSCAR(self):
return self.directContcar()
#generated from minimized Bi4I4 tilt cell
return """POSCAR file written by OVITO
1.0
4.4448437691 0.0000000000 0.0000000000
2.2224218396 7.8117603831... | vanceeasleaf/aces | aces/materials/Bi4I4c.py | Python | gpl-2.0 | 1,891 | [
"ASE",
"OVITO"
] | 539a1800a26e2abea1702135c1e632524cd645ba71056c5abe5e0cb3dc0d92ec |
"""
This class includes all of the functions that used by MeshOperations.py for the creation of the mesh.
"""
from StandardModules import *
import sys
from PyQt4.QtGui import *
from export_geo import *
class PreMesh(DefineDomain):
"""
Once the user has selected something from the drop-downs and click... | janhui/test_engine | release/mesh_netcdf/PreMeshingFunctions.py | Python | lgpl-2.1 | 9,107 | [
"NetCDF"
] | d0615cfd993dd7d53728ada2b59d7cd1aacbcee2206fec58b7a0fc25a8e281ce |
"""
Very simple test case to verify bok-choy integration.
"""
from bok_choy.web_app_test import WebAppTest
from edxapp_pages.lms.info import InfoPage
class InfoPageTest(WebAppTest):
"""
Test that the top-level pages in the LMS load.
"""
@property
def page_object_classes(self):
return [In... | mjg2203/edx-platform-seas | common/test/bok_choy/tests/test_info_pages.py | Python | agpl-3.0 | 463 | [
"VisIt"
] | e837668f67331abe10d6a083945ead8aa508812e14366dcc16343921d24d3513 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines the VaspInputSet abstract base class and a concrete
implementation for the parameters developed and tested by the core team
of pymatgen, including the Materials Virtual Lab, Materials Pr... | mbkumar/pymatgen | pymatgen/io/vasp/sets.py | Python | mit | 110,153 | [
"BoltzTrap",
"VASP",
"pymatgen"
] | f1126956886ac1c38f7fa8c880d6b8664dd4f69067d84b80acbfb267e370226e |
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