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"""
This file contains utilities to work with autodock vina.
"""
from typing import List, Optional, Tuple
import numpy as np
from deepchem.utils.typing import RDKitMol
from deepchem.utils.pdbqt_utils import pdbqt_to_pdb
def write_vina_conf(protein_filename: str,
ligand_filename: str,
... | lilleswing/deepchem | deepchem/utils/vina_utils.py | Python | mit | 7,504 | [
"OpenMM",
"RDKit"
] | 8b8ebfd604b3918c71639f907521a241b9b58829e4059064233bff9e5b0e8a2b |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
... | nuclear-wizard/moose | python/chigger/tests/displacement/displacement_mag.py | Python | lgpl-2.1 | 825 | [
"MOOSE"
] | 0461fa3b5608e005157886805e8f66f9a6bd637c78c6c0035cf664f70529d526 |
#### import the simple module from the paraview
f_name="f_234"
from paraview.simple import *
# create a new 'PVD Reader'
import os
def make_a_screenshot(path_to_insert):
# create a new 'PVD Reader'
home_dir=os.path.expanduser("~")
field_r_10pvd = PVDReader(FileName=[home_dir+path_to_insert+'/CSF_ref/Field_r_1.0... | andreashorn/lead_dbs | ext_libs/OSS-DBS/OSS_platform/Visualization_files/Paraview_field_CSF_ref.py | Python | gpl-3.0 | 3,448 | [
"ParaView"
] | d79ed1ecfb51f64673cf5ec1eb51899e6a13c766d6e5bc4038db191afe523122 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#from __future__ import division
import sys
import os
import subprocess
import numpy as np
import csv
import copy
import locale
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.lines as line
from matplotlib.figure import Figure
from... | Ralf3/samt2 | gui/samt2.py | Python | gpl-3.0 | 127,366 | [
"Gaussian"
] | 40ce82b4651464a406ff02e75193576455ec26b8f8442f24d9cf1b1d58c751ec |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
The TDDFT calculations by default use the same XC functional, grids, _numint
schemes as the ground state DFT calculations. Different XC, grids, _numint
can be set in TDDFT.
'''
import copy
from pyscf import gto, dft, tddft
mol = gto.M(atom='... | sunqm/pyscf | examples/tddft/30-change_xc_grids.py | Python | apache-2.0 | 1,470 | [
"PySCF"
] | c7839b0a0f75563151a54b5d7eb189b3216a45ac293d40e1dee2b1c7905da2a1 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains the error classes for the chemenv package.
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The Materials Project"
__credits__ = "Geoffroy Hautier"
__version__ = "2.0"
__maintainer... | materialsproject/pymatgen | pymatgen/analysis/chemenv/utils/chemenv_errors.py | Python | mit | 2,156 | [
"pymatgen"
] | 7daed08b727582f2ba733b3de524fc8c0227064933f5128242a3ff604efe84fc |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2010-2013 Francois Beaune, Jupiter Jazz Limited
# Copyright (c) 2014-2016 Francois Beaune, The appleseedhq Organi... | docwhite/appleseed | scripts/updatemany.py | Python | mit | 4,829 | [
"VisIt"
] | 32a5b6a8d598c3e7f015f2aa3cfd03cb762bcfcdc5dfc96fd8a500a8646d1f58 |
# VAE MLP for Fashion MNIST
# Code based on
# https://github.com/ageron/handson-ml2/blob/master/17_autoencoders_and_gans.ipynb
import superimport
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import os
figdir = "../figures"
def save_fig(fname):
plt.tight_layout()
plt.savefig(o... | probml/pyprobml | scripts/vae_mlp_fashion_tf.py | Python | mit | 4,538 | [
"Gaussian"
] | f4cb48c9f3d99ea1498c3c542a362701b763579b94545f59378dbbcff14b0106 |
"""Gaussian normalization to normalize standalone modality."""
import numpy as np
from scipy.stats import norm
from scipy.optimize import curve_fit
from .standalone_normalization import StandaloneNormalization
class GaussianNormalization(StandaloneNormalization):
"""Gaussian normalization to normalize standalo... | glemaitre/protoclass | protoclass/preprocessing/gaussian_normalisation.py | Python | gpl-2.0 | 8,129 | [
"Gaussian"
] | f8f33ac07ea6ce8fcadc8c27005c1b64a3ba345d8717cc9fe4ce01a481310d24 |
"""
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@diku.dk>, Rune M. Friborg <runef@diku.dk>
"""
import sys
from pycsp_import import *
from random import randint
# Running this multiple times, eventually causes a deadlock with output looking like this:
# python parallel_leaking... | runefriborg/pycsp | examples/problems/parallel_leaking_mobile_channelend_garbage_collection_pre_0.9.2.py | Python | mit | 1,741 | [
"Brian"
] | 05f8c9e6ca2d217baafab4728bb5b30506bcd258393ff149f33f63cd0e3a29ee |
"""
Certificate HTML webview.
"""
import logging
import urllib
from datetime import datetime
from uuid import uuid4
import pytz
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.http import Http404, HttpResponse
from django.template import RequestContext
from djan... | edx/edx-platform | lms/djangoapps/certificates/views/webview.py | Python | agpl-3.0 | 35,039 | [
"VisIt"
] | 7ba9eaf31bab52e2258c8f20590ea2a9b9076398faab535f7973b4ed8852451f |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import math
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_etree_fromstring,
compat_getpass,
compat_http_client,
... | jcoady9/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 90,109 | [
"VisIt"
] | ee748d4b3c1c72f805d886cd14164ecc1c8e91ea8a7f42ebe12916ba3dad37cc |
"""
Copyright 2009 Robert Steed
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, either version 3 of the License, or
(at your option) any later version.
This program is distributed i... | ElderDelp/elisp-collection | marks/bookmark_pyparser.py | Python | apache-2.0 | 16,429 | [
"VisIt"
] | e2ffe3b4459220dea3ac8e5c3b0c202e3a8b845073ad0f76e0967d32348cccc9 |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
##########################... | xyproto/turbine | djl/libs/SOAPpy/Server.py | Python | gpl-3.0 | 26,486 | [
"Brian"
] | ce6d68d923e0dd6fb34e3e09599bc2aa470f6c5c7e0f4a702dc1b2250447b531 |
import random
import unittest
from hearthbreaker.constants import MINION_TYPE
from tests.agents.testing_agents import PlayAndAttackAgent, OneCardPlayingAgent, CardTestingAgent, \
HeroPowerAndCardPlayingAgent
from tests.testing_utils import generate_game_for
from hearthbreaker.cards import *
from hearthbreaker.agen... | jomyhuang/sdwle | testsHB/card_tests/rogue_tests.py | Python | mit | 32,810 | [
"TINKER"
] | c7e907530cfe79fa2b559cc8fff6f834707453762221ac1cd9c62c04526f21ec |
# -*- coding: utf-8 -*-
# Copyright (c) 2010-2012 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... | takeshineshiro/swift | test/unit/proxy/test_server.py | Python | apache-2.0 | 407,033 | [
"MOOSE"
] | 1ab9ee40ce9d82a154fffb36abb065caa2fc3595ffc174e4b4ff468de23fd782 |
import os
from os import path
from pathlib import Path
from ...exechelper import func_exec_run
from ...fileop import PosixFileSystem
from ....util import Utility
bwa = path.join(path.abspath(path.dirname(__file__)), path.join('bin', 'bwa'))
def build_bwa_index(ref):
cmdargs = ['index', ref]
return func_exec_... | mainulhossain/phenoproc | app/biowl/libraries/bwa/adapter.py | Python | mit | 2,473 | [
"BWA"
] | a132df149aa8009db0f8f963a24aa5023b6bc8a47bf365593ce2c25c6b84da23 |
"""
Simple smoothing functions (f:trajectory->trajectory)
"""
import numpy as np
from scipy.signal import get_window, medfilt
from statsmodels.nonparametric.smoothers_lowess import lowess
def copy_trajectory(traj):
"""
Just a test.
"""
return traj.copy()
class FilterByCol(object):
"""
Filt... | Hezi-Resheff/trajectory-aa-move-ecol | metraj/smoothing/simple.py | Python | mit | 6,158 | [
"Gaussian"
] | fbb1f26fdadfe0ad0d41e1d585407d8c0d3aa69bd2333b894300b1f4b6634642 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkExtractUnstructuredGrid(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkExtractUnstructuredGrid.py | Python | bsd-3-clause | 523 | [
"VTK"
] | ed7d0130bed1812fa3a0890d68649d7b1411f090ca976344e97886574d423b84 |
"""
The subpackage ``preproc`` contains some useful cosmetics and pre-processing
functionalities:
- resizing frames and cubes : upscaling/pixel binning,
- shifting frames,
- rotating frames and cubes,
- cropping frames and cubes,
- removing bad pixels from frames and cubes,
- correcting nan values from frames and cube... | vortex-exoplanet/VIP | vip_hci/preproc/__init__.py | Python | mit | 1,529 | [
"Gaussian"
] | 005f4665087f7053dcc1230180a282b0eef9c82c4350d4f0c8301fce8ceea21c |
"""
This module contains all the code necessary for the VAE.
The general use is to instantiate a VAE with the appropriate
hyper parameters, then to train it with a dataset. You can
then load the resulting weights into a VAE later.
Much of this code was taken from here: https://blog.keras.io/building-autoencoders-in-k... | MaxStrange/ArtieInfant | Artie/internals/vae/vae.py | Python | mit | 18,464 | [
"Gaussian"
] | 96792c10e64bb7d885df29567cecaa1a47cbaf6a6d3fb3bd20c0cc1a19339e21 |
import math
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
from PyQt5.QtWidgets import QApplication, QMainWindow, QMenu, QVBoxLayout, QSizePolicy, QMessageBox, QWidget, QPushButton, QLabel
from P... | JarnoRFB/qtpyvis | gui.py | Python | mit | 10,473 | [
"NEURON"
] | e13164041481b2d40343f6bb29d53933a2f2dbf7f3a53fead6ab449ceb70a0f5 |
import ansiblelint.utils
from ansiblelint import AnsibleLintRule
class ForceShell(AnsibleLintRule):
id = 'AERISCLOUD0004'
shortdesc = 'Use shell or raw for any command execution'
description = 'Use shell or raw for any command execution'
tags = ['productivity']
def matchtask(self, file, task):
... | AerisCloud/AerisCloud | ansible/rules/ForceShell.py | Python | mit | 797 | [
"Galaxy"
] | be40eb3c7b27f19c43f93a006c93e7f2cf7e330f04ce4acf2fe162b6301be2e9 |
import json
import re
from ctypes import c_void_p, c_wchar_p
from decimal import Decimal
from logging import DEBUG, NullHandler, getLogger
from subprocess import CalledProcessError, check_output
from pymediainfo import MediaInfo
from pymediainfo import __version__ as pymediainfo_version
from knowit import VIDEO_EXTE... | ratoaq2/knowit | knowit/providers/mediainfo.py | Python | mit | 15,155 | [
"VisIt"
] | 0d46992255d72e2b4f85417b343ccf359bd0319ed7d81bb324c9ed4b9defd358 |
import numpy as np
from numpy.testing import assert_array_equal
import skimage
from skimage import data
from skimage.filter.thresholding import threshold_otsu, threshold_adaptive
class TestSimpleImage():
def setup(self):
self.image = np.array([[0, 0, 1, 3, 5],
[0, 1, 4, 3, ... | emmanuelle/scikits.image | skimage/filter/tests/test_thresholding.py | Python | bsd-3-clause | 3,165 | [
"Gaussian"
] | 017d3c49380ca238c40b3e036a8147156ebb1910a5aa49a3e2ea1fa79d1dab76 |
# If you are going to use the account module, you need to add the DAO to the ES
# mappings with
#
#ELASTIC_SEARCH_MAPPINGS = [
# octopus.modules.account.dao.BasicAccountDAO
#]
#
# To use the command line scripts, ensure that the following is configured in the CLI_SCRIPTS config:
#
# CLI_SCRIPTS = {
# "usermod" : "o... | JiscPER/magnificent-octopus | octopus/modules/account/settings.py | Python | apache-2.0 | 3,240 | [
"Octopus"
] | 277d80d181ade7beb21789cdeb3f5290aec328f5c187d5d4a81db34b756771c8 |
#!/usr/bin/env python2
# vim:fileencoding=UTF-8:ts=4:sw=4:sta:et:sts=4:fdm=marker:ai
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2013, Kovid Goyal <kovid at kovidgoyal.net>'
__docformat__ = 'restructuredtext en'
... | hazrpg/calibre | src/calibre/db/tests/writing.py | Python | gpl-3.0 | 35,903 | [
"MOOSE"
] | 9265e6b2980c4adaf49edfa7ff210a8493f03f6124d1ad26fabebe61c9d6af15 |
#
# Copyright (C) 2001-2017 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.
#
import unittest
from rdkit import Chem
from rdkit.Ch... | rdkit/rdkit | rdkit/Chem/UnitTestSATIS.py | Python | bsd-3-clause | 1,321 | [
"RDKit"
] | 23631d36401a4c0fad54e397d46fdf7e96485db4e8280afbbd76a588793b8fd0 |
#!/usr/bin/env python
# Copyright 2017 Calico 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/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | calico/basenji | bin/bam_cov.py | Python | apache-2.0 | 53,448 | [
"BWA",
"Gaussian",
"pysam"
] | 1705797e31d11c657ee4a10cecbd223d51bf338d42209935ee2b906f90a4c658 |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Pub... | ghutchis/cclib | src/cclib/parser/gaussianparser.py | Python | lgpl-2.1 | 66,688 | [
"Gaussian",
"cclib"
] | c9283444b2f64f377bdb040b17fbee1d65e9a9ae5069a7822ca528d9bbf7290a |
"""
Tests for discussion pages
"""
import datetime
import time
from unittest import skip
from uuid import uuid4
import pytest
from pytz import UTC
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.fixtures.discussion import (
Comment,
Response,
... | a-parhom/edx-platform | common/test/acceptance/tests/discussion/test_discussion.py | Python | agpl-3.0 | 64,162 | [
"VisIt"
] | 39d38cdb0326cdd1da3c1442c79d50e89b4a0402e42ceb4eb717d5982e5e12f3 |
# ============================================================================
#
# Copyright (C) 2007-2012 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... | jeroendierckx/Camelot | camelot/model/party.py | Python | gpl-2.0 | 41,237 | [
"VisIt"
] | 43695b90a0bad82c912771d7fb4f04a78daa69f05240e2af593b21e9e62b5edb |
# -*- coding: utf-8 -*-
##############################################################################
#
# Copyright (C) 2012-2013 Daniel Reis
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Sof... | pedrobaeza/project | service_desk/__openerp__.py | Python | agpl-3.0 | 2,102 | [
"CRYSTAL"
] | 7044e552742d5144c4fdb03f2652404cc914183c792a0e8aaa4f75f6aa80bd6d |
########################################################################
# File: IRODSStorageElementHandler.py
########################################################################
"""
:mod: IRODSStorageElementHandler
.. module: IRODSStorageElementHandler
:synopsis: IRODSStorageElementHandler is the implementati... | vmendez/DIRAC | DataManagementSystem/Service/IRODSStorageElementHandler.py | Python | gpl-3.0 | 22,751 | [
"DIRAC"
] | a265f6dfc55cea7ede330729f777af7dffb3bb05e13081bcdd2aef460aa181ea |
# -*- coding: utf-8 -*-
#
# 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
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General... | pmghalvorsen/gramps_branch | gramps/plugins/tool/extractcity.py | Python | gpl-2.0 | 26,027 | [
"Brian"
] | 45b858a0be2edbd58c9c69119ec1ec31a99f1074eeea2be335899c259a35e769 |
#!/usr/bin/env python
#default using python2.7.3
#-*- coding:utf-8 -*-
"""
A python program to serve UpStage ActionScript Client compilation and server deployment methods.
"""
import os, sys
appCanonicalPath = os.getcwd()
appServerDir = appCanonicalPath + '/server/src'
appClientDir = appCanonicalPath + '/client/src'
b... | upstage-org/UpStage | install.py | Python | gpl-2.0 | 3,328 | [
"VisIt"
] | c0e282a063d3a7b94d3907652cf8e3d407ce576cbaf9defa1946ed0033a3ae8b |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/alerts/alertsplugin.py | Python | gpl-2.0 | 8,843 | [
"Brian"
] | b94656df2b3580f317ad9da54de09908c58e3083b62f0819653387f7f647cacc |
# Copyright (c) 2021, TU Wien, Department of Geodesy and Geoinformation
# 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,... | TUW-GEO/ascat | src/ascat/h_saf.py | Python | mit | 15,899 | [
"Gaussian"
] | b47fb20ce463dbd6fe285531e407e1c4043c7319bbedc1818a58a0e0b934653f |
# Copyright (c) 2015 MaxPoint Interactive, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
# following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this list of conditi... | MaxPoint/bayes_logistic | bayes_logistic/bayes_logistic.py | Python | bsd-3-clause | 19,650 | [
"Gaussian"
] | 3dd799c04a90226ce15f566a6e7f051b96c97ddf27f1a8948a4ac3fd5124fdbe |
# Copyright (C) 2017 Philipp Schlegel
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program... | schlegelp/pymaid | pymaid/core.py | Python | gpl-3.0 | 42,360 | [
"NEURON"
] | c0a55136bb9f1023d5a1660ebea9d6b1a4784a64fc8745c5ffbdbe57b2159c3b |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2010-2011, Monash e-Research Centre
# (Monash University, Australia)
# Copyright (c) 2010-2011, VeRSI Consortium
# (Victorian eResearch Strategic Initiative, Australia)
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modificati... | UWA-FoS/docker-mytardis | src/forms.py | Python | gpl-3.0 | 37,243 | [
"Brian",
"CRYSTAL"
] | cd9ed7e3dc59e05c47d5b95e2864315502621bdbf0abde413d1d133e6f89a753 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | testsuite/python/constraint_shape_based.py | Python | gpl-3.0 | 34,389 | [
"ESPResSo"
] | b0b6e250cddd6d5db226934b5512dfaf17d00e4a5f7b25ec68996f0a4b62a06f |
#!/usr/bin/env python
# vim: tabstop=8 expandtab shiftwidth=4 softtabstop=4
class Mission:
def __init__(self, controller):
self.title = ""
self.intro = ""
self.description = ""
self.little_hint = ""
self.big_hint = ""
self.completion_message = "You did it!"
... | bruab/Bashy_Prototype | src/missions.py | Python | mit | 3,500 | [
"Brian"
] | 33f1fd02dcd064b95e3cb39113de8f41c290e718f3387f4bdf0103bafb7c7b86 |
#
# SHOUTcast E2
#
# $Id$
#
# Coded by Dr.Best (c) 2010
# Support: www.dreambox-tools.info
#
# This plugin is licensed under the Creative Commons
# Attribution-NonCommercial-ShareAlike 3.0 Unported
# License. To view a copy of this license, visit
# http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a let... | popazerty/e2-gui | lib/python/Plugins/Extensions/IniSHOUTcast/plugin.py | Python | gpl-2.0 | 46,031 | [
"VisIt"
] | 5d88e241c8332dee8e56fb05cd1b85214431b05a10474ee83702d48b95b9f90d |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/backends/pyside/widgets/color_chooser.py | Python | gpl-3.0 | 1,853 | [
"Brian"
] | 9928d89472d25f4ddfdfa7c1c54e080545227a3a71e3e972e85f630cf4b59c94 |
"""Tests for module gramcore.data.arrays"""
import os
import numpy
from PIL import Image
from nose.tools import assert_equal, assert_almost_equal, raises
from gramcore.data import arrays
def setup():
"""Create array fixtures for test_load_*"""
arr = numpy.zeros((20, 10), dtype='float')
arr[10, 5] = 249.... | cpsaltis/pythogram-core | src/gramcore/data/tests/test_arrays.py | Python | mit | 5,818 | [
"Gaussian"
] | e662482c1a1375c8cedae9c9d76ac4a872693c0cb84945f0a86e9b756f71e0ae |
# Copyright 2012 Patrick Varilly
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is di... | patvarilly/uwham | test_uwham2.py | Python | gpl-3.0 | 3,974 | [
"Gaussian"
] | d69b8f9452e7c164ce63f7747b93ddd59c4a76907082302aceb03ba343980783 |
from espei.optimizers.opt_base import OptimizerBase
from espei.optimizers.graph import OptNode
from pycalphad import Database
from scipy.optimize import minimize
import numpy as np
class TestOptimizer(OptimizerBase):
def _fit(self, symbol_names, datasets, target_values=None, initial_guess=None):
symbol_na... | PhasesResearchLab/ESPEI | tests/test_optimizer.py | Python | mit | 2,448 | [
"pycalphad"
] | ada0e9537606c2e2b63960d5e86ed3fee1c98c66c93cfa99d8fd084fa50f4a8b |
from . import forms
from collections import OrderedDict
from functools import reduce
import re
import json
#takes a product definition (dict) and transforms it to forms for display.
#returns a dict w/ form:
#'metadata_form': forms.DatasetTypeMetadataForm(),
#'measurements_form': forms.DatasetTypeMeasurementsForm(),
#... | ceos-seo/data_cube_ui | apps/data_cube_manager/utils.py | Python | apache-2.0 | 12,529 | [
"NetCDF"
] | dce3ce01f41c180d2b516d1c61166ef573a5379e0c8752647edec22e0267f8ef |
# coding: utf-8
import json
import re
from django.http import HttpResponse, HttpResponseBadRequest
from django.views.decorators.csrf import csrf_exempt
from django.core.mail import mail_admins
from django.core.validators import validate_email
from django.core.exceptions import ValidationError
from .models import Blac... | StreetVoice/django-celery-ses | djcelery_ses/views.py | Python | mit | 1,713 | [
"VisIt"
] | a038fb8ec8065072e10653563727c298660eb17052012224a9916505244d4df9 |
# Tell PyMOL we don't want any GUI features.
import __main__
__main__.pymol_argv = [ 'pymol', '-qxi' ]
# Importing the PyMOL module will create the window.
import pymol
# Call the function below before using any PyMOL modules.
pymol.finish_launching()
| gratefulfrog/lib | python/pymol/pymol_path/examples/launching/launch_viewer1.py | Python | gpl-2.0 | 258 | [
"PyMOL"
] | ccd9a9473de9f2b15b53437bfac1e19dafcb3b8146177693b6387b50e0861cf8 |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | flightgong/scikit-learn | sklearn/cluster/k_means_.py | Python | bsd-3-clause | 50,107 | [
"Gaussian"
] | 3e09593400471a56497819d81cc669d8bbc5a454023e2af13396c97ea67d71cf |
# coding: utf-8
from __future__ import unicode_literals, division, print_function
"""
Helper methods for generating gw input / and work flows.
"""
__author__ = "Michiel van Setten"
__copyright__ = " "
__version__ = "0.9"
__maintainer__ = "Michiel van Setten"
__email__ = "mjvansetten@gmail.com"
__date__ = "May 2014"
... | yanikou19/pymatgen | pymatgen/io/gwwrapper/helpers.py | Python | mit | 7,011 | [
"pymatgen"
] | 4a4eff41085f1764dfb70f7898ba69e8023ce4e086f491fa355355bdd3ef958d |
import sys
# usage: python TerrainDATtoVTK.py <tire number> <timestep> <ancf_flag> <list of files for this frame...>
def Parse(tire_num,timestep,use_ancf,file_name):
timestep.zfill(4)
pos = []
vel = []
connectivity = []
strain = []
# For each input file
# print('file: ' + file_name)
file = open(file_name, '... | rserban/chrono | src/projects/cosimulation/cosimulation_vehicle/CosimRender/TireDATtoVTK.py | Python | bsd-3-clause | 3,460 | [
"VTK"
] | 35608495ad4ff517bda8f229213e7e47b43e2f72a1ed710b26c481a45a2747a2 |
"""
Toolkit module
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
from pycsp.common.six import string_types
import pycsp.current as pycsp
if pycsp.trace:
from py... | runefriborg/pycsp | pycsp/common/toolkit.py | Python | mit | 3,573 | [
"Brian"
] | b70234ba05f4b38ec9913f151b1943a0b808ae19b6b6387711e65b69a8ffda34 |
from wxPython._controls import wxLIST_MASK_STATE
from wxPython._controls import wxLIST_STATE_SELECTED
import os.path
# Modified by Francois Malan, LUMC / TU Delft
# December 2009
#
# based on the SkeletonAUIViewer:
# skeleton of an AUI-based viewer module
# Copyright (c) Charl P. Botha, TU Delft.
# set to False for 3D... | nagyistoce/devide | modules/viewers/MaskComBinar.py | Python | bsd-3-clause | 62,014 | [
"VTK"
] | 8441a7fb987ebd62592bf1adb56a918e1b31ebf7e94e5c5a14f0458b85190204 |
# Copyright (c) 2003, 2004 Brian Sabbey
# contributions by Milosz Krajewski
# contributions by John Plevyak
import sys
import types
import os
import hashlib
import dparser_swigc
class user_pyobjectsPtr:
def __init__(self, this):
self.this = this
def __setattr__(self, name, value):
if name ==... | jplevyak/dparser | python/dparser.py | Python | bsd-3-clause | 11,694 | [
"Brian"
] | 3d004d49048dbd9774775307f4e771457d14aa071a879c01439380f8c67801a3 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import numpy as np
from pymatgen.analysis.defects.core import DefectEntry, Vacancy
from pymatgen.analysis.defects.corrections import (
BandEdgeShiftingCorrection,
BandFillin... | richardtran415/pymatgen | pymatgen/analysis/defects/tests/test_corrections.py | Python | mit | 12,260 | [
"VASP",
"pymatgen"
] | 641163cf813e7411c83383b47f352de9f6539993808db2c84292e929badea6e2 |
'''
Individual stages of the pipeline implemented as functions from
input files to output files.
The run_stage function knows everything about submitting jobs and, given
the state parameter, has full access to the state of the pipeline, such
as config, options, DRMAA and the logger.
'''
from utils import safe_make_d... | bjpop/complexo_pipeline | src/stages.py | Python | bsd-3-clause | 15,014 | [
"BWA"
] | 8f9acd5d4d7c8cab2b9d7178c96d7415f4d2711bf77b16d951c1e78fc53b4c70 |
"""
Custom stuff that is specific to the galaxy contest
"""
import theano
import theano.tensor as T
import numpy as np
from consider_constant import consider_constant
def clip_01(x):
# custom nonlinearity that is linear between [0,1] and clips to the boundaries outside of this interval.
return T.clip(x, 0, 1... | JasonTam/ndsb2015 | theano/custom.py | Python | mit | 39,141 | [
"Galaxy"
] | 40d9c4c35e1095148f78ed309304c9f95d20e949d9df1ee9f08f87f171d41222 |
from __future__ import unicode_literals
from .. import Provider as PersonProvider
class Provider(PersonProvider):
formats_female = (
'{{first_name_female}} {{last_name}}',
'{{first_name_female}} {{last_name}}',
'{{first_name_female}} {{last_name}}',
'{{first_name_female}} {{last_na... | deanishe/alfred-fakeum | src/libs/faker/providers/person/en/__init__.py | Python | mit | 86,769 | [
"Amber",
"Brian",
"COLUMBUS",
"CRYSTAL",
"Dalton",
"Desmond",
"MOE"
] | a5f6136ef555bf472849edbfe4d2f55062d77c01f9d949d93f128186c7b9b7d9 |
#
# commands.py - the GraalVM specific commands
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2016, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free ... | entlicher/truffle | mx.truffle/mx_truffle.py | Python | gpl-2.0 | 6,707 | [
"VisIt"
] | 5d54ed289a22ff806a2b55bb974d21dc7055c81a4fe58c28c8ab13b2bf5ec664 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import threading
from DIRAC import S_OK
from DIRAC.Core.Utilities import DEncode
from DIRAC.Core.Base.ExecutorModule import ExecutorModule
class PingPongExecutor(ExecutorModule):
@classmethod
def initiali... | yujikato/DIRAC | docs/source/DeveloperGuide/AddingNewComponents/DevelopingExecutors/PingPongExecutor.py | Python | gpl-3.0 | 1,101 | [
"DIRAC"
] | 761380ab2ce3b3f4ff140409a8e5fdc7f3df32eeb1825b0bff64b809392bf3e4 |
# ============================================================================
#
# Copyright (C) 2007-2012 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... | jeroendierckx/Camelot | camelot/admin/validator/object_validator.py | Python | gpl-2.0 | 8,127 | [
"VisIt"
] | 9f74970be00574e32a57528e240fd7af9b24645c254e2cf552b01d159d989062 |
#!/usr/bin/env python
#
# $File: sampleNuclearFamily.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can red... | BoPeng/simuPOP | docs/sampleNuclearFamily.py | Python | gpl-2.0 | 1,741 | [
"VisIt"
] | 9d3abab4c6f856b30c98b7857e4a4c7061fd2b4ad8a7f1d5c1061afdc38a9df8 |
"""Sample a trajectory from microstate MSM
{{header}}
Meta
----
depends:
- top.pdb
- trajs
"""
import mdtraj as md
from msmbuilder.io import load_trajs, save_generic, preload_top, backup, load_generic
from msmbuilder.io.sampling import sample_msm
## Load
meta, ttrajs = load_trajs('ttrajs')
msm = load_generic('... | mpharrigan/mixtape | msmbuilder/project_templates/msm/microstate-traj.py | Python | lgpl-2.1 | 820 | [
"MDTraj"
] | cd274cfd4c3a5b605990834ad64ec120bc2cb5dd2bbe16bbfcb8ab397ddb5dee |
"""
A first test for the ELBO on the diffusion problem.
The target is consisted of an and a Gaussian likelihood.
The approximating mixture has two components.
Author:
Panagiotis Tsilifis
Date:
6/16/2014
"""
import numpy as np
import matplotlib.pyplot as plt
import os
import cPickle as pickle
from scipy.st... | ebilionis/variational-reformulation-of-inverse-problems | unittests/test_optimize_diffusion_leftboundarydata.py | Python | gpl-2.0 | 5,954 | [
"Gaussian"
] | fe6ff7933bb2bfc12d76f9d88b3d00a0a0389a38706ab572ef652ed458167b87 |
"""A generic client for creating and managing transformations.
See the information about transformation parameters below.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import six
import json
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
from DIR... | ic-hep/DIRAC | src/DIRAC/TransformationSystem/Client/Transformation.py | Python | gpl-3.0 | 29,120 | [
"DIRAC"
] | dae21b07607ba4d7c839b3f8dce4ee51d1e60d50ec782b4a36cce91ed49218b5 |
#===============================================================================
# This file is part of TEMPy.
#
# TEMPy is a software designed to help the user in the manipulation
# and analyses of macromolecular assemblies using 3D electron microscopy maps.
#
# Copyright 2015 Birkbeck Colleg... | OniDaito/ChimeraXTempy | TEMPy/Cluster.py | Python | mit | 22,226 | [
"Gaussian"
] | e51efa97e4357e5fd9308ef49847dca16ac500aca64bf683e8f3462d65639185 |
# Author: Travis Oliphant
# 1999 -- 2002
from __future__ import division, print_function, absolute_import
import warnings
import threading
import sys
import timeit
from . import sigtools, dlti
from ._upfirdn import upfirdn, _UpFIRDn, _output_len
from scipy._lib.six import callable
from scipy._lib._version import Num... | sriki18/scipy | scipy/signal/signaltools.py | Python | bsd-3-clause | 116,009 | [
"Gaussian"
] | 199d26425624a11706e726ed4774c961f1e60a5719450f916967ca6ccb0b5ea9 |
# -*- coding: utf-8 -*-
#
# Copyright © 2013 Michael Rabbitt.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, mo... | agustinhenze/nikola.debian | nikola/plugins/compile/markdown/mdx_gist.py | Python | mit | 9,894 | [
"Brian"
] | f61a7c76c9a6aa72a02bdf53367849335171171278eeab827127f5e49a1a430d |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | renesugar/arrow | python/pyarrow/parquet.py | Python | apache-2.0 | 55,252 | [
"VisIt"
] | 0426bc51e85e233bfe802a4dc3a0cf74efc9760c0ac9e4242b52563d352d5452 |
# demo: generate the noninteracting DOS from the tight binding parameters
import sys
# directory for the main code
sys.path.append('..')
from int_2dhopping import *
from numpy import *
from share_fun import grule
from functions import rotate_all
nflavors = 3
nbin = 500
emin = -6.
emax = 6.
broadening = 0.05
mu = 0... | hungdt/scf_dmft | examples/calculate_dos_tight_binding.py | Python | mit | 1,020 | [
"Gaussian"
] | a92f6f16f8a62b309ab37a7b7a0b0fac5173d2efc6077dc4c1625abf51981712 |
"""
## Analysis of Experimental Data
This page is about the non-parametric a12 test. It is also a chance for us to discuss a little
statistical theory.
### Standard Header
"""
from __future__ import division
import sys
sys.dont_write_bytecode = True
from base import *
"""
## Background
For the most part, we ... | shanil-puri/mase | src/a12.py | Python | unlicense | 11,660 | [
"Gaussian"
] | 5dba9e6f46acac6a14225c07ed013ac95c39e0d0a4aab47dea25c3c7e576e103 |
#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# viz_atomeye.py
# Purpose: viz running LAMMPS simulation via AtomEye
# Syntax: viz_atomeye.py in.lammps Nfreq Nsteps
# in.lammps = LAMMPS input script
# Nfreq = dump and viz shapshot every this many steps
# ... | anshumang/lammps-analytics | python/examples/viz_atomeye.py | Python | gpl-2.0 | 1,913 | [
"LAMMPS"
] | 903895bd57c4df349c26667c41345427db9a8956727c73dc43f78d3bf8377c93 |
r"""OS routines for NT or Posix depending on what system we're on.
This exports:
- all functions from posix or nt, e.g. unlink, stat, etc.
- os.path is either posixpath or ntpath
- os.name is either 'posix' or 'nt'
- os.curdir is a string representing the current directory (always '.')
- os.pardir is a strin... | momm3/WelcomeBot | welcomebot/Lib/os.py | Python | mit | 37,442 | [
"VisIt"
] | f4959fe4996fd7506052a89a9fadd413c5a19495b94238a9e4a59856ad80128e |
# Copyright (C) 2012,2013,2016,2018
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the term... | niktre/espressopp | src/interaction/__init__.py | Python | gpl-3.0 | 4,459 | [
"ESPResSo"
] | 9c86cab359fd3584fc7d80fdd6333ad4411d4ffd219d3b4ba7cafeabf61aa43b |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Output of PDB files."""
from Bio._py3k import basestring
from Bio.PDB.StructureBuilde... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/PDB/PDBIO.py | Python | apache-2.0 | 8,382 | [
"Biopython"
] | 397486cbfde9d00522283f816756db362f220a13367b8faace267eca4ebbe8d9 |
# Copyright 2014-2019 The ODL contributors
#
# This file is part of ODL.
#
# This Source Code Form is subject to the terms of the Mozilla Public License,
# v. 2.0. If a copy of the MPL was not distributed with this file, You can
# obtain one at https://mozilla.org/MPL/2.0/.
"""Non Local Means functionals."""
from __f... | kohr-h/odl | odl/contrib/solvers/functional/nonlocalmeans_functionals.py | Python | mpl-2.0 | 3,997 | [
"Gaussian"
] | 65ce8c49e96b1ba3fa0e8e88a0315df0723dcec4496abe55f69655cea5cfc95d |
import numpy as np
import os
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import matplotlib.pyplot as plt
import time
from datetime import datetime
from matplotlib.dates import date2num, num2date
import pyroms
import pyroms_toolbox
import _remapping
class nctime(object):
pass
def remap(src_... | kshedstrom/pyroms | examples/Arctic_HYCOM/remap.py | Python | bsd-3-clause | 4,824 | [
"NetCDF"
] | 2949f13d5e45f1aab8a4be93994020c391d030abb41ac05783c71cfc04b15190 |
from pype import lexer
from pype import parser
from pype import ast
from pype.translate import SymbolTableVisitor
from pype.symtab import *
from pype.semantic_analysis import ASTVisitor
class PrettyString(ASTVisitor):
def __init__(self):
self.text = ''
def visit(self, node):
self.text += (node.__class__.__... | 207leftovers/cs207project | tests/pype/test_ast.py | Python | mit | 973 | [
"VisIt"
] | 9fbf3c7a5d3b21c0a7e05df2389592eaa9f55a8724b4eef88dba9050cda0485b |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005, 2007 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Soft... | tiagocardosos/stoq | stoqlib/reporting/till.py | Python | gpl-2.0 | 3,484 | [
"VisIt"
] | 09d7da891592174a2b059615e7b663706b62dce5703cd067fee7f8fa51c864c1 |
#!/usr/bin/env python
from __future__ import print_function, division, unicode_literals
import argparse
from os import path
from sys import version_info
from pymods.fldiff import Differ
from pymods.yaml_tools import is_available as has_yaml
if __name__ != '__main__':
raise ImportError('testcli.py is not an import... | abinit/abinit | tests/testtools.py | Python | gpl-3.0 | 5,635 | [
"ABINIT"
] | 379cbdf6a35e77f07dacd05d2abc62b99842c2fa94cc6fe636edc51cfdf9b080 |
import pyvw
# the dataset is triples of E, A, F where A[i] = list of words E_i
# aligned to, or [] for null-aligned
my_dataset = [
( "the blue house".split(),
([0], [2], [1]),
"la maison bleue".split() ),
( "the house".split(),
([0], [1]),
"la maison".split() ),
( "the flower".split... | martinpopel/vowpal_wabbit | python/word_alignment.py | Python | bsd-3-clause | 3,667 | [
"FLEUR"
] | 48aaf7416c98713c4d79dc434af437c406bd8986bb03952ec856dce68b497030 |
#!/usr/bin/env python2
import os, errno
import netCDF4 as nc
import numpy as np
import pandas as pd
import matplotlib.lines as mlines
import matplotlib.dates as dates
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from matplotlib import style
from scipy import integrate
def create_phen_file(la... | rhyswhitley/savanna_iav | src/setup_model/spa_input_creator.py | Python | cc0-1.0 | 21,324 | [
"NetCDF"
] | 8a9fddc2e66d1dbb7f83b51064adc13cacf06f6c4c54d76e6b6dfd32a037dbe0 |
# -*- coding: utf-8 -*-
# Copyright (C) 2019 - 2020 by Pedro Mendes, Rector and Visitors of the
# University of Virginia, University of Heidelberg, and University
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2017 - 2018 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc.,... | copasi/COPASI | copasi/bindings/python/unittests/Test_CModel.py | Python | artistic-2.0 | 13,019 | [
"COPASI"
] | 15dd769ce9c35b6f8e28bb4b27bf1b7a035dd54632270d70befca35d63b3b146 |
"""Collection of subsampling method on the neurons."""
import numpy as np
from McNeuron import Neuron
from McNeuron import Node
# finding main points
def get_main_points(neuron):
"""
Returning the index of branching points and end points.
Parameters
----------
neuron: Neuron
input neuron
... | RoozbehFarhoodi/McNeuron | subsample.py | Python | mit | 13,482 | [
"NEURON"
] | f4a89159f6a140cb00a876f7eba16be191e04a77a81e29130b1e552a43711f08 |
# Copyright 2009 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.
"""Tests for our Python 2/3 compatibility layer, Bio._py3k"""
import unittest
class ODTest(uni... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_py3k.py | Python | gpl-2.0 | 750 | [
"Biopython"
] | 5d2adf5c60cc296627c978ed118c70aa09ddc10fd1e9b7b6b0cbd87141f56fef |
import random
from .exceptions import ClientError
def catch_client_error(func):
"""
Decorator to catch the ClientError exception and translate it into a reply.
"""
def inner(message):
try:
return func(message)
except ClientError as e:
# If we catch a client er... | amureki/lunch-with-channels | core/utils.py | Python | mit | 2,997 | [
"Octopus"
] | 5ac955c59384f76f376d0b34c72a5dd84f78c4ae8827f6ea09c699cacff1c3a9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
from deepy.core.env import env
def get_fans(shape):
fan_in = shape[0] if len(shape) == 2 else np.prod(shape[1:])
fan_out = shape[1] if len(shape) == 2 else shape[0]
return fan_in, fan_out
class WeightInitializer(object):
"""
Initia... | zomux/deepy | deepy/utils/initializers.py | Python | mit | 4,085 | [
"Gaussian"
] | 67fdac991c3447af031435a568c677bbce29f177b76c9a6f6bcb92d87ad6108c |
#
# Propagator of the density matrix with MUBs
#
import numpy as np
import scipy.fftpack as fftpack
from scipy.special import hyp1f1
from scipy.special import laguerre
from scipy.special import hermite
from scipy.special import legendre
import sympy as sympy
from string import Template
import math
import h5py
impo... | cabrer7/PyWignerCUDA | GPU_Rho2D_MUBasis.py | Python | mit | 48,321 | [
"Gaussian"
] | df7b8aaa91f28e0f84440742e4f43293a354b0ed8155e4007e63330d72e75d29 |
# Copyright 2012-2014 Brian May
#
# This file is part of python-tldap.
#
# python-tldap 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 version.... | brianmay/python-tldap-debian | tldap/middleware.py | Python | gpl-3.0 | 1,797 | [
"Brian"
] | 72b1c057990d417fd51fd95e4f996adf4cc1ebd1d9fa432a113dc85a25ccc077 |
Pokedex = {
"Bulbasaur": {
"num": 1,
"species": "Bulbasaur",
"types": ["Grass", "Poison"],
"genderRatio": {"M": 0.875, "F": 0.125},
"baseStats": {"hp": 45, "atk": 49, "def": 49, "spa": 65, "spd": 65, "spe": 45},
"abilities": {"0": "Overgrow", "H": "Chlorophyll"},
"heightm": 0.7,
"weightkg": 6.9,
"col... | QuiteQuiet/PokemonShowdownBot | data/pokedex.py | Python | mit | 450,217 | [
"GULP"
] | 3f9c554030355844fdee5f86d5efa97d9e2a3aa4858a266741f725de9cd46ac1 |
# emacs: at the end of the file
# ex: set sts=4 ts=4 sw=4 et:
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### #
"""Stub file for a guaranteed safe import of duecredit constructs: if duecredit
is not available.
To use it, place it into your project codebase to be imported, e.g. copy as
... | MDAnalysis/mdanalysis | package/MDAnalysis/due.py | Python | gpl-2.0 | 2,589 | [
"MDAnalysis"
] | 9c4cd6d74b62236d541eb32b0802b1fdfd6271bf455bf6bb5bf1adc8e73c0b95 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
#
# This program is free software; you can redistribute it and/o... | sam-m888/gprime | gprime/plug/docgen/paperstyle.py | Python | gpl-2.0 | 6,290 | [
"Brian"
] | 7e5a6dc267cd4b35a963a9d0a174d41c707bfa7f0f690f01b1bef25b9da249be |
from __future__ import absolute_import
from builtins import range
import logging
import keras.backend as ker
from numpy import pi as pi_const
from numpy import sqrt
from keras.layers import Lambda, Multiply, Add, Dense, Concatenate
from keras.models import Input
from keras.models import Model
from .sampling import s... | gdikov/vae-playground | playground/models/networks/encoder.py | Python | mit | 23,104 | [
"Gaussian"
] | b79c60b6ab7a2284b2af0d6606fa393dc41fda1b0555c570e21e9d7394ff42d5 |
from neural_net_api import *
# Recitation example
nn_basic = NeuralNet(['in1', 2, 'in3', -1], ['neuron']) \
.join('in1', 'neuron', 1).join(2, 'neuron', 2).join('in3', 'neuron', -1) \
.join(-1, 'neuron', 2) \
.join('neuron', NeuralNet.OUT)
nn_basic_inputs = {'in1':5, 'in3':-1}
# boolean AND function
nn_AND... | jasonleaster/MIT_6.034_2015 | lab6/nn_problems.py | Python | gpl-2.0 | 3,023 | [
"NEURON"
] | 6ecfadaffb03a06c14cfb85d44254b5e202ad1fcbbfba059208248d5b5f3656d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# License AGPLv3 (https://www.gnu.org/licenses/agpl-3.0-standalone.html)
"""
This script helps to create a new branch for a new Odoo version from the
another existing branch, making the needed changes on contents.
Installation
============
For using this utility, you nee... | Yajo/maintainer-tools | tools/migrate_branch.py | Python | agpl-3.0 | 15,796 | [
"VisIt"
] | 5b47ffa5272328e29ab65165200df3a181c9f7c0c087795bf7368b93d84a569d |
# coding: utf-8
#### MEMORY BASED SHALLOW PARSER ######################################################################
# Copyright (c) 2003-2010 University of Antwerp, Belgium and Tilburg University, The Netherlands
# Vincent Van Asch <vincent.vanasch@ua.ac.be>, Tom De Smedt <tom@organisms.be>
# License: GNU General ... | clips/MBSP | tokenizer.py | Python | gpl-3.0 | 38,272 | [
"ASE"
] | 46699fd8c8c24c42c1ce7e25d6d05a2c48f0045563105c3addd5673640eead5e |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Overlap of two CISD wave functions (they can be obtained from different
geometries).
'''
from functools import reduce
import numpy
from pyscf import gto, scf, ci
#
# RCISD wavefunction overlap
#
myhf1 = gto.M(atom='H 0 0 0; F 0 0 1.1', basis='... | gkc1000/pyscf | examples/ci/32-wfn_overlap.py | Python | apache-2.0 | 1,591 | [
"PySCF"
] | a7ff2fdca00dcb5d98950880027c38c842a843fb00c8b1d106ecb4b4529fa757 |
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