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# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import datetime
class Migration(migrations.Migration):
dependencies = [
('cenet', '0005_auto_20160801_1639'),
]
operations = [
migrations.AddField(
model_name='neuron',
... | Si-elegans/Web-based_GUI_Tools | cenet/migrations/0006_auto_20160801_1939.py | Python | apache-2.0 | 704 | [
"NEURON"
] | 09d3f73107db1707a9538e0a070686a5cec82c9223c920a55de8ff92d7806237 |
# vim: set et sw=4 sts=4 fileencoding=utf-8:
#
# Copyright 2014 Dave Jones <dave@waveform.org.uk>.
#
# This file is part of umansysprop.
#
# umansysprop 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 v... | loftytopping/UManSysProp_public | umansysprop/renderers.py | Python | gpl-3.0 | 12,936 | [
"Pybel"
] | 0e4287c7d84ec2216dac7c2eb9d11a36f51ef3669209cf08a60da2a77965b31d |
"""
Various bayesian regression
"""
from __future__ import print_function
# Authors: V. Michel, F. Pedregosa, A. Gramfort
# License: BSD 3 clause
from math import log
import numpy as np
from scipy import linalg
from scipy.linalg import pinvh
from .base import LinearModel
from ..base import RegressorMixin
from ..util... | raghavrv/scikit-learn | sklearn/linear_model/bayes.py | Python | bsd-3-clause | 19,730 | [
"Gaussian"
] | fa100e0c35d28062d58c3c752bb112c2571c8e38e235916146cb781f49efba67 |
"""
.. _tut_compute_covariance:
Computing a covariance matrix
=============================
Many methods in MNE, including source estimation and some classification
algorithms, require covariance estimations from the recordings.
In this tutorial we cover the basics of sensor covariance computations and
construct a no... | adykstra/mne-python | tutorials/source-modeling/plot_compute_covariance.py | Python | bsd-3-clause | 8,845 | [
"Gaussian"
] | 6e2458855e12ec03288f7a788087f4c70fd1ac5b7dc9516e7f1c900ca86d9c7c |
"""
Tests for django.utils.
"""
from unittest import TestCase
from django.utils import html, checksums, text
from django.utils.functional import SimpleLazyObject
import timesince
import datastructures
import datetime_safe
import itercompat
import tzinfo
from decorators import DecoratorFromMiddlewareTests
from funct... | t11e/django | tests/regressiontests/utils/tests.py | Python | bsd-3-clause | 9,845 | [
"ADF"
] | d4f01d1b7f624644b809a3f116e68e2e4d9f39c6b692b8bd92c04cc100201d60 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | anksp21/Community-Zenpacks | ZenPacks.AndreaConsadori.MRV/ZenPacks/AndreaConsadori/MRV/modeler/plugins/MrvL2DeviceMap.py | Python | gpl-2.0 | 1,374 | [
"VisIt"
] | 0fe00d2748c920cc7bd61d67b07040fcb5889c819bc4dce24c12ec95d2255384 |
from menpo.base import name_of_callable
from menpofit import checks
from menpofit.fitter import MultiScaleParametricFitter
from .algorithm import AlternatingRegularisedLandmarkMeanShift
from .result import UnifiedAAMCLMResult
class UnifiedAAMCLMFitter(MultiScaleParametricFitter):
r"""
Class defining a Unifie... | grigorisg9gr/menpofit | menpofit/unified_aam_clm/fitter.py | Python | bsd-3-clause | 9,448 | [
"Gaussian"
] | bb5dc1be310dcf25fcdc5378188dd043bfe2dbdf8556a456c6ba9f063767dac0 |
# flake8: noqa: F403, F405
from __future__ import absolute_import, division, print_function
from tests.core import mock
from trakt import Trakt
from trakt.interfaces.calendars import Base
from datetime import date, datetime
from dateutil.tz import tzutc
from hamcrest import *
from httmock import HTTMock
import pytest... | fuzeman/trakt.py | tests/test_calendars.py | Python | mit | 11,176 | [
"Galaxy"
] | 40ad516a77fca2eca78132aa5ae6ecf833fd5bd9c2f18f3822d721df0e0b4ed4 |
from func import *
# ATTTENTION! Maybe there are some mistakes in neuron parameters!
# Write to alexey.panzer@gmail.com.
logger = logging.getLogger('neuromodulation')
startbuild = datetime.datetime.now()
nest.ResetKernel()
nest.SetKernelStatus({'overwrite_files': True,
'local_num_threads': 1,
... | research-team/NEUCOGAR | NEST/cube/dopamine/integrated/scripts/neuromodulaton.py | Python | gpl-2.0 | 6,953 | [
"NEURON"
] | c421b65ba0012eb7e561ffdf1b24dfbdeeafcbec3a943813c765a145eebc17bc |
from django.conf.urls import url
from django.contrib.auth.decorators import login_required
from . import views
urlpatterns = [
url(r'^clinics/patient/$', views.VisitView.as_view(), name='visit'),
url(r'^reports/region/(?P<pk>\d+)/pdf/$',
login_required(views.LGAClinicsReport.as_view()),
name... | myvoice-nigeria/myvoice | myvoice/clinics/urls.py | Python | bsd-2-clause | 1,528 | [
"VisIt"
] | 47bbe6bd15b644e3eb2f0680763cdc979356d55c76be12814256c5ed0b7d943b |
"""Retrieve indexed genomes using Galaxy's rsync server resources.
http://wiki.galaxyproject.org/Admin/Data%20Integration
"""
from __future__ import print_function
import os
import shutil
import subprocess
from xml.etree import ElementTree
from cloudbio.custom import shared
# ## Compatibility definitions
server = ... | chapmanb/cloudbiolinux | cloudbio/biodata/galaxy.py | Python | mit | 9,239 | [
"BWA",
"Bowtie",
"Galaxy"
] | 58e29634ac6cfb1790b3d47a6bd2606fcb08b5b81240a94ccf785138beb9d0ef |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008-2012 Brian G. Matherly
# Copyright (C) 2009 Rob G. Healey <robhealey1@gmail.com>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012-2014 Paul Franklin
#
# This program is free software... | jralls/gramps | gramps/plugins/textreport/birthdayreport.py | Python | gpl-2.0 | 27,489 | [
"Brian"
] | dd400d61c883792d82152d5a524947688c2b356fc6ae420e417aa4458912ab5c |
#!/usr/bin/env python
import pyscf
mol = pyscf.gto.M(
atom=[['O', (0.000000000000, -0.143225816552, 0.000000000000)],
['H', (1.638036840407, 1.136548822547, -0.000000000000)],
['H', (-1.638036840407, 1.136548822547, -0.000000000000)]],
#basis='6-31G',
basis='sto-3g',
verbose=1,
... | shivupa/pyci | examples/h2o_dz.py | Python | gpl-3.0 | 455 | [
"PySCF"
] | e041b31a98f1efa5596a0fc5f3bc8c3b318667286a0fb854e95c8e9ed1cf5e69 |
import ddapp.vtkAll as vtk
import ddapp.thirdparty.numpyjsoncoder as nje
from collections import OrderedDict
from ddapp import fieldcontainer
from ddapp import transformUtils
from ddapp import lcmUtils
from ddapp.utime import getUtime
import drc as lcmdrc
import pprint
import json
class ConstraintEncoder(nje.NumpyEn... | gizatt/director | src/python/ddapp/ikconstraintencoder.py | Python | bsd-3-clause | 2,228 | [
"VTK"
] | d3ce4dcd1ef7b91ccc6ca4e0fa5f57c67c7193e757cfcf1600c5890876921587 |
# Copyright (c) 2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
from .posterior import Posterior
from ...util.linalg import jitchol, backsub_both_sides, tdot, dtrtrs, dtrtri,pdinv
from ...util import diag
from ...core.parameterization.variational import VariationalPoste... | ptonner/GPy | GPy/inference/latent_function_inference/var_dtc_parallel.py | Python | bsd-3-clause | 18,379 | [
"Gaussian"
] | ad1696a9726c6d66c0e8d3d4f07b97cb212754315c22defc37cc03bc5d7c7181 |
"""
CCD Spot Measurements
=====================
Analyse laboratory CCD PSF measurements by forward modelling.
:requires: PyFITS
:requires: NumPy
:requires: SciPy
:requires: astropy
:requires: matplotlib
:requires: VISsim-Python
:requires: emcee
:requires: sklearn
:version: 1.1
:author: Sami-Matias Niemi
:contact: s... | sniemi/EuclidVisibleInstrument | sandbox/spotForwardModelGaussianApprox.py | Python | bsd-2-clause | 72,584 | [
"Gaussian"
] | 8dde2d5e01519b7b784262efc59cadff8fceb86613553b9255bf00d6f873c657 |
#!/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
# ... | gptech/ansible | lib/ansible/modules/network/lenovo/cnos_factory.py | Python | gpl-3.0 | 5,013 | [
"VisIt"
] | 237d4c7ab065a8ffdfe1b07949a252e5e5c0d9df21444fd7fe2c6d0da3483b7e |
#!/usr/bin/env python
""" File Catalog Client Command Line Interface. """
__RCSID__ = "$Id$"
import cmd
import commands
import os.path
import time
import sys
from types import DictType, ListType
from DIRAC.Core.Security.ProxyInfo import getProxyInfo
from DIRAC.Core.Utilities.List import uniqueElements
from DIRAC.In... | marcelovilaca/DIRAC | DataManagementSystem/Client/FileCatalogClientCLI.py | Python | gpl-3.0 | 66,562 | [
"DIRAC"
] | 030066a2d8333a8ee408ff7153eec111374f47f05ba6630c2f698f7df44d63ae |
""" command line options, ini-file and conftest.py processing. """
import argparse
import copy
import inspect
import os
import shlex
import sys
import types
import warnings
from functools import lru_cache
from pathlib import Path
from types import TracebackType
from typing import Any
from typing import Callable
from ty... | randyzingle/tools | kub/services/archive/cdk/python/sample-app/.env/lib/python3.6/site-packages/_pytest/config/__init__.py | Python | apache-2.0 | 40,336 | [
"VisIt"
] | 33b6af05ad347ae22ba6bb1f700c96d5b99836ed4086766d5c98499d9c2d7713 |
#!/usr/bin/env python
import sys
import os.path
try:
from setuptools import setup, Extension
except ImportError:
sys.stderr.write( "Could not import 'setuptools', falling back to 'distutils'.\n" )
from distutils.core import setup, Extension
if sys.version_info[0] < 2 or sys.version_info < 5:
sys.stder... | detrout/htseq | setup.py | Python | gpl-3.0 | 2,590 | [
"HTSeq"
] | 2168ec04301c45defbe4987101ab8fcfbed4e4aff01243f0ec4d1444f356390b |
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
from sys import stdout
outfreq = 1e5
simlength = 1e9
pdb = PDBFile('folded.pdb')
forcefield = ForceField('amber99sb.xml', 'amber99_obc.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=NoCutoff)
integrator = LangevinIn... | LCLS/Protein-Folding-Sims | hp24stab/sims/300K/91gamma/simulateFoldedPdb.py | Python | mit | 751 | [
"OpenMM"
] | e69c3e3c3ed597d364f6ef080f145e6a3a9cbd6e6f35c5be91a6ab297eb5218b |
# coding=utf-8
from __future__ import absolute_import
from __future__ import print_function
from __future__ import unicode_literals
import ast
import io
GETTEXT_FUNCTIONS = ('gettext', 'gettext_lazy', 'gettext_noop', 'ugettext', 'ugettext_lazy', 'ugettext_noop')
PGETTEXT_FUNCTIONS = ('pgettext', 'pgettext_lazy')
NGE... | kmichel/po-localization | po_localization/python_extractor.py | Python | mit | 6,017 | [
"VisIt"
] | 3e91b705a82a61f1582bfb9aeb1675f5c442d4bb1ff36ff80d0dfef9ae10c636 |
"""Install packages via the Conda package manager: http://conda.pydata.org/
"""
from __future__ import print_function
import collections
import json
import os
import shutil
import subprocess
import yaml
from cloudbio.package.shared import _yaml_to_packages
ENV_PY_VERSIONS = collections.defaultdict(lambda: "python=3")... | chapmanb/cloudbiolinux | cloudbio/package/conda.py | Python | mit | 15,735 | [
"Bioconda",
"Bioconductor"
] | 0111a316971fe3da4b17fc52197a761e6785fa0293d0e5a004343ae4d04c6509 |
# Copyright (c) 2012 OpenStack Foundation
# 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 ... | jumpstarter-io/nova | nova/tests/compute/test_resource_tracker.py | Python | apache-2.0 | 50,801 | [
"exciting"
] | cb6fc971c27d23c4b90d1828037650f1472b845f3859f81265e182de51ef5926 |
# Copyright (c) 2018 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""Interpolate data valid at one set of points to another in multiple dimensions."""
from __future__ import division
import logging
import numpy as np
from scipy.interpolate impor... | jrleeman/MetPy | metpy/interpolate/points.py | Python | bsd-3-clause | 12,783 | [
"Gaussian"
] | 42bffb1864273538d2c33a727be933134496c045d30d01b48011f0711abb935c |
# Copyright (C) 2004-2008 Paul Cochrane
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distribut... | paultcochrane/pyvisi | pyvisi/renderers/vtk/renderer.py | Python | gpl-2.0 | 1,947 | [
"VTK"
] | d0cb968240b57a0c8c68d5e0fe6bca1bb979800193b25b778928e0de4e81749d |
import inspect
import warnings
import collections
import cython
from sklearn.neighbors import KNeighborsClassifier
from sklearn.neighbors import KernelDensity
import numpy.linalg as la
import numpy as np
from scipy.spatial.distance import cosine
from sklearn.metrics.pairwise import cosine_similarity
import os
import s... | alliemacleay/MachineLearning_CS6140 | Homeworks/HW7/__init__.py | Python | mit | 10,385 | [
"Gaussian"
] | f438efbba76d66e54d9a0a817e3338dc672c864e1a62f7bc408e441059af6ea4 |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 3: Deep Learning and Neural Networks
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2015 by Jeff Heaton
Licensed under the Apache License, V... | jeffheaton/aifh | vol3/vol3-python-examples/examples/example_mnist_drop.py | Python | apache-2.0 | 2,528 | [
"VisIt"
] | 06363308fc32c10106da04f4ecc0c1e83d9578cc3af1b3cd7c95845467bd7fdc |
from io import StringIO
import os.path as op
import pandas as pd
import numpy as np
import pytest
import bioframe
testdir = op.realpath(op.dirname(__file__))
def test_make_chromarms():
### test the case where columns have different names
df1 = pd.DataFrame(
[["chrX", 0, 8]],
columns=["chro... | open2c/bioframe | tests/test_extras.py | Python | mit | 7,994 | [
"pysam"
] | ff8774145757254f221fec405b2747d9e2fa1072f9ae2710dfdaed7cc11ff856 |
import subprocess
import time
import numpy as np
from config import *
def run_Struck(seq, rp, bSaveImage):
x = seq.init_rect[0] - 1
y = seq.init_rect[1] - 1
w = seq.init_rect[2]
h = seq.init_rect[3]
path = './results/'
if not os.path.exists(path):
os.makedirs(path)
command = map(... | stevenwudi/Kernelized_Correlation_Filter | scripts/bscripts/run_Struck.py | Python | gpl-3.0 | 818 | [
"Gaussian"
] | ed34624ebf5bcb785d16cc1aa93b5b54a0255d165988a2db8c54caea3f5b6c6d |
# Copyright (C) 2016
# Max Planck Institute for Polymer Research & JGU Mainz
#
# 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 th... | govarguz/espressopp | testsuite/FileIOTests/dump_xyz/test_dump_xyz.py | Python | gpl-3.0 | 7,295 | [
"ESPResSo"
] | a801d5d7d507a93edf5a85d0534a070ce001a8929a4803c3ae2149c801d0cbbe |
# #
# Copyright 2012-2019 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 (... | gppezzi/easybuild-framework | test/framework/filetools.py | Python | gpl-2.0 | 91,816 | [
"NetCDF"
] | 4d945d4b0e97a34dc9dbc489889e2c9e816bc298e3ce33f83653ac984a99151b |
#!/usr/bin/env python
from __future__ import division
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout", "Jose Antonio Navas Molina"]
__license__ = "GPL"
__version__ = "1.8.0-dev"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
f... | wasade/qiime | qiime/parallel/blast.py | Python | gpl-2.0 | 4,254 | [
"BLAST"
] | 936dfbed06084e404551d895378d3f34f691e176df2b808d61cc8b65de80602c |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/procrouting/__init__.py | Python | lgpl-3.0 | 1,133 | [
"Psi4"
] | 2abcc0d41fc6a1803f32f83c7375fa60b5278e7f0cd06ca9f971cd6d49b2a84a |
# coding: utf-8
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..utils import (
ExtractorError,
unsmuggle_url,
)
from ..compat import (
compat_parse_qs,
compat_urlparse,
)
class SenateISVPIE(InfoExtractor):
_COMM_MAP = [
['ag', '76440', 'http://ag-f.akamaihd.net'],
... | valmynd/MediaFetcher | src/plugins/youtube_dl/youtube_dl/extractor/senateisvp.py | Python | gpl-3.0 | 5,378 | [
"EPW"
] | 02357c6c47e15f5ade177cdde15131f7327a912ba34913c457cc8472485db1c3 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/driver/qcdb/periodictable.py | Python | lgpl-3.0 | 78,202 | [
"CFOUR",
"Psi4"
] | 4d82136f429bd21b950eff232de5fe9fdec6c2121322c12ce16eda48e3ec15fa |
# init.py ---
#
# Filename: init.py
# Description:
# Author:
# Maintainer:
# Created: Wed May 23 21:24:11 2012 (+0530)
# Version:
# Last-Updated: Fri May 25 11:42:08 2012 (+0530)
# By: subha
# Update #: 74
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# Initialize model prototypes
... | dilawar/moose-full | moose-examples/traub_2005/py/channelinit.py | Python | gpl-2.0 | 1,190 | [
"MOOSE"
] | b389fb69cf698ed22d77bdf430bd307f7c22ae085ff5a6a5966ead0f575a4e5b |
#! /usr/bin/env python
import six
from six.moves.configparser import ConfigParser
from ..framework import services
from ..printers.nc.database import Database as NcDatabase
# from ..printers.vtk.vtu import Database as VtkDatabase
from ..utils.prefix import names_with_prefix, strip_prefix
from .utils import (
con... | csdms/pymt | pymt/portprinter/port_printer.py | Python | mit | 3,297 | [
"NetCDF",
"VTK"
] | 10720e88f135a0b9dd906f07caf1f7a16ff63ddcef81ef5a83de342bb86788c8 |
# Copyright (c) 2003-2010 Sylvain Thenault (thenault@gmail.com).
# Copyright (c) 2003-2010 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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 t... | isohybrid/dotfile | vim/bundle/git:--github.com-klen-python-mode/pylibs/pylint/lint.py | Python | bsd-2-clause | 38,248 | [
"VisIt"
] | c786d908564da71ab1ca61e781f2ad540fd2291857fa983ea9bdc8375edbef1c |
"""Copyright 2012 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.8'
__date__ = 'May 17 2010'
import threading
from ctypes ... | danielsuo/mobot | src/move/PhidgetsPython/Phidgets/Devices/Servo.py | Python | mit | 14,514 | [
"VisIt"
] | 06fe64714f5c226ac831265f98b3ce7e16fece1bf4e769ebcf40581896b09fd4 |
"""Gaussian process experiments."""
| kastnerkyle/gp2 | gp2/__init__.py | Python | bsd-3-clause | 36 | [
"Gaussian"
] | b03c4a53cc7e44f7c99c2771d5f5594261243c159f3e9f12955256a6cb13c690 |
# Copyright (C) 2016 Henrique Pereira Coutada Miranda
# All rights reserved.
#
# This file is part of yamboparser
#
from .yambofile import *
import os
import numpy as np
class YamboFolder():
"""
Takes as input a folder name that is the folder where yambo saved r-* o-* l-* and netcdf files
"""
def __i... | henriquemiranda/yambopy | yamboparser/yambofolder.py | Python | bsd-3-clause | 1,353 | [
"NetCDF",
"Yambo"
] | 4b2164bc56308dbc9a1776fcd6a693b200f721591863db5a2382c646e48543b9 |
# This is a plain copy from librosa's display test system, because
# Brian is a titan.
# CREATED:2015-02-17 14:41:28 by Brian McFee <brian.mcfee@nyu.edu>
# this function is lifted wholesale from matploblib v1.4.2,
# and modified so that images are stored explicitly under the tests path
from __future__ import (absolut... | urinieto/msaf | tests/mpl_ic.py | Python | mit | 12,060 | [
"Brian"
] | 97d09bdfe61be79b21ed8f16e3c4b6ce2394239d646e57c85d10b284a3162277 |
from header_common import *
from header_operations import *
from module_constants import *
from header_parties import *
from header_skills import *
from header_mission_templates import *
from header_items import *
from header_triggers import *
from header_terrain_types import *
from header_music import *
from header_ma... | DRSkaggs/pw_ms_sys_src | module_scripts.py | Python | bsd-3-clause | 717,283 | [
"VisIt"
] | 157aae84803a1099d6579473d71ffd012db50f42e923d3ee208b065268e2f355 |
"""Hilbert spaces for quantum mechanics.
Authors:
* Brian Granger
* Matt Curry
"""
from sympy import Basic, Interval, oo, sympify
from sympy.printing.pretty.stringpict import prettyForm
from sympy.physics.quantum.qexpr import QuantumError
__all__ = [
'HilbertSpaceError',
'HilbertSpace',
'ComplexSpace',
... | pernici/sympy | sympy/physics/quantum/hilbert.py | Python | bsd-3-clause | 19,017 | [
"Brian"
] | 8aff278be63799cd14daab5533b69791266851abb8f5873ad8bbd0c36505b565 |
# 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... | chris-chris/tensorflow | tensorflow/contrib/distributions/python/ops/mvn_linear_operator.py | Python | apache-2.0 | 14,902 | [
"Gaussian"
] | 7c816dffff04655a7238d8d4fee9cb519aa7984f884410543f3ad14762a41447 |
# Author: Travis Oliphant
# 1999 -- 2002
from __future__ import division, print_function, absolute_import
import warnings
import threading
from . import sigtools
from scipy._lib.six import callable
from scipy._lib._version import NumpyVersion
from scipy import linalg
from scipy.fftpack import (fft, ifft, ifftshift, ... | dch312/scipy | scipy/signal/signaltools.py | Python | bsd-3-clause | 81,613 | [
"Gaussian"
] | 51739003c567126ddca9417cfa3fb9732c2665cbaf4ab5dabb8c373e5303da35 |
# -*- coding: utf-8 -*-
"""
.. note::
Functions for opening, editing, and saving Langmuir input files.
.. moduleauthor:: Adam Gagorik <adam.gagorik@gmail.com>
"""
import langmuir as lm
import collections
import StringIO
import re
try:
import numpy as np
except ImportError:
np = None
try:
import panda... | LangmuirSim/langmuir | LangmuirPython/langmuir/parameters.py | Python | gpl-2.0 | 8,759 | [
"Gaussian"
] | 7791c6f371cf542612a4c29470107b8432c447d44bf73a2ccd42811a2003c5eb |
from tools.load import LoadMatrix
from sg import sg
lm=LoadMatrix()
traindat=lm.load_numbers('../data/fm_train_real.dat')
testdat=lm.load_numbers('../data/fm_test_real.dat')
train_label=lm.load_labels('../data/label_train_multiclass.dat')
parameter_list=[[traindat,testdat, train_label,10,2.1,10.,1e-5,False],
[train... | AzamYahya/shogun | examples/undocumented/python_static/multiclass_multiclasslibsvm.py | Python | gpl-3.0 | 1,094 | [
"Gaussian"
] | 7cb4a16e84b3cca9a864a6e7f03950200f118b0de8b5a85b5cb990501357f3c0 |
import unittest
from test import support
import sys
import random
import math
import array
# Used for lazy formatting of failure messages
class Frm(object):
def __init__(self, format, *args):
self.format = format
self.args = args
def __str__(self):
return self.format % self.args
# S... | timm/timmnix | pypy3-v5.5.0-linux64/lib-python/3/test/test_long.py | Python | mit | 50,829 | [
"Brian"
] | f71de2bc7c8fc9427a09eebb8c1be32ccaa478a3d212873cae81e4290b5300c5 |
import shogun as sg
import data
import numpy as np
# load data
feature_matrix = data.swissroll()
# create features instance
features = sg.RealFeatures(feature_matrix)
# create Kernel Locally Linear Embedding converter instance
converter = sg.KernelLocallyLinearEmbedding()
# set target dimensionality
converter.set_ta... | besser82/shogun | applications/tapkee/samples/klle.py | Python | bsd-3-clause | 1,043 | [
"Gaussian"
] | deb1d1753cc75168ca7616eea5d8ede0bafca9575d2ff50a002c6383484838c9 |
from __future__ import absolute_import
from __future__ import division
import logging
import time
import functools
import random
import cgi
import warnings
import inspect
try:
import simplejson as json
except ImportError:
import json # pyflakes.ignore
from tornado.ioloop import PeriodicCallback
import torna... | virtuald/pynsq | nsq/reader.py | Python | mit | 31,307 | [
"BLAST"
] | bc52dab8686acb800e53d8278808647902cba2f7be41c9f5aeaacff9b7efa7b8 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... | brianmay/karaage | karaage/projects/views.py | Python | gpl-3.0 | 11,809 | [
"Brian"
] | 8fd79d950113b3ca9eb14f7039785d272bbbc485396207bbedaf0b1de5a0f4d7 |
import sys
import argparse
import hashlib
import time
prefix = ["cam", "video", "x", "a", "www", "ftp", "ssl", "tftp", "www1",
"www2", "noc", "smtp", "pop", "ssl", "secure", "images", "th",
"img", "download", "mail", "remote", "blog", "webmail", "server",
"ns1", "vpn", "m", "shop", ... | 360netlab/DGA | code/bigviktor/dga.py | Python | mit | 28,164 | [
"VisIt",
"exciting"
] | 5ba0b83b8d7e42a24350c0262513db44da7e24dac46cfab23eff0aeb16ae7258 |
# revset.py - revision set queries for mercurial
#
# Copyright 2010 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
import re
import parser, util, error, discovery, hbisect, phases
import node
import... | ya790206/temp_hg | mercurial/revset.py | Python | gpl-2.0 | 90,267 | [
"VisIt"
] | c104e05a0ac0616986d310cdfd06ff1ce4387f1b26e246795168cffee4a3925f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module defines filters for Transmuter object.
"""
__author__ = "Will Richards, Shyue Ping Ong, Stephen Dacek"
__copyright__ = "Copyright 2011, The M... | xhqu1981/pymatgen | pymatgen/alchemy/filters.py | Python | mit | 11,447 | [
"pymatgen"
] | dd7e855de6e04448658cfc8098d8fa24a2e61fb78f117e7ea6d4b6846522fe11 |
import os
import numpy as np
import unittest
from astropy.table import Table, Column
from astropy.io import fits
from desisim.quickcat import quickcat
from desitarget.targetmask import desi_mask, bgs_mask, mws_mask
import desimodel.io
class TestQuickCat(unittest.TestCase):
@classmethod
def setUpClass(cls)... | desihub/desisim | py/desisim/test/test_quickcat.py | Python | bsd-3-clause | 9,038 | [
"Galaxy"
] | 5953041bfd4216c18aa2887217988266c0d4ec91402eceb9e2943d646a1a5a40 |
# -*- coding: utf-8 -*-
"""Dependency graph implementation."""
from __future__ import absolute_import, print_function, unicode_literals
from collections import Counter
from textwrap import dedent
from kombu.utils.encoding import bytes_to_str, safe_str
from celery.five import items, python_2_unicode_compatible
__all... | cloudera/hue | desktop/core/ext-py/celery-4.2.1/celery/utils/graph.py | Python | apache-2.0 | 9,249 | [
"VisIt"
] | d8c7c7fcf7ca2495ce342118e4415f3f8cb0876807a2ad83c3567c81c1aa8474 |
#!/usr/bin/env python
# "H_combination_output_analysis.py target.fasta fliCdatabase.fasta fljBdatabase.fasta"
# must have ispcr and primers of fliC and fljB at the same directory
import os
from Bio import SeqIO
import sys
from Bio.Blast import NCBIXML
from Initial_Conditions import phase1
from Initial_Conditions impo... | denglab/SeqSero | libs/H_combination_output_analysis.py | Python | gpl-2.0 | 10,748 | [
"BLAST"
] | 44a8c33649bffb4308990964e5b72a3f95cb6a8bf09caf4080d1c1334529d77a |
"""
A Martel format to parse the NLM's XML format for Medline.
http://www.nlm.nih.gov/databases/dtd/nlmmedline_010319.dtd
http://www.nlm.nih.gov/databases/dtd/nlmmedlinecitation_010319.dtd
http://www.nlm.nih.gov/databases/dtd/nlmcommon_010319.dtd
Formats:
citation_format Format for one MedlineCitation.
format ... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Medline/nlmmedline_010319_format.py | Python | apache-2.0 | 11,749 | [
"Biopython"
] | 478b13fbfa5af51fd5edef0be82ed7df6e47e3bb519e2224ec2e57aa58dab9f6 |
# Copyright 2009 by Cymon J. Cox. 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.
"""Command line wrapper for the multiple alignment program PROBCONS.
http://probcons.stanford.e... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Align/Applications/_Probcons.py | Python | gpl-2.0 | 3,747 | [
"Biopython"
] | f4e8269c2ed316db9782d39ff1a87dc458a3d5a6c2b911a37db335ad862a0ee7 |
# -*- coding: utf-8 -*-
#
# test_regression_issue-1034.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 ... | hakonsbm/nest-simulator | pynest/nest/tests/test_regression_issue-1034.py | Python | gpl-2.0 | 13,621 | [
"NEURON"
] | 5661a9f308a47877aae4b5dd4711b5c47c3af48304efdf23db6a9a039dfebb69 |
"""
Test courseware search
"""
import json
import uuid
from common.test.acceptance.tests.helpers import remove_file
from common.test.acceptance.pages.common.logout import LogoutPage
from common.test.acceptance.pages.studio.overview import CourseOutlinePage as StudioCourseOutlinePage
from common.test.acceptance.pages.... | romain-li/edx-platform | common/test/acceptance/tests/lms/test_lms_cohorted_courseware_search.py | Python | agpl-3.0 | 14,461 | [
"VisIt"
] | 37d2022e962cdf9e52156394567519e913ada29d0b241fa88062c9854ece1359 |
"""
==============
Marching Cubes
==============
Marching cubes is an algorithm to extract a 2D surface mesh from a 3D volume.
This can be conceptualized as a 3D generalization of isolines on topographical
or weather maps. It works by iterating across the volume, looking for regions
which cross the level of interest. ... | davidam/python-examples | scikit/plot_marching_cubes.py | Python | gpl-3.0 | 2,128 | [
"Mayavi"
] | 1e905d0936dabea8f158210417b33ce40fcec5ee8d1bc51e47c6efb05a23126d |
# - coding: utf-8 -
# Copyright (C) 2008-2010 Toms Bauģis <toms.baugis at gmail.com>
# Dual licensed under the MIT or GPL Version 2 licenses.
# See http://github.com/tbaugis/hamster_experiments/blob/master/README.textile
import math
import datetime as dt
import gtk, gobject
import pango, cairo
import re
try:
im... | pacoqueen/Brunilda | lib/graphics.py | Python | gpl-3.0 | 68,301 | [
"FLEUR"
] | f3a1e82c2fcac467bef0d32ae3032a6f309fa1164b6f410c20001e616a3381e3 |
# cd pySU/pyMultidark/trunk/bin/fortranfile-0.2.1/
import sys
import numpy as n
import os
from os.path import join
from astropy.io import fits
import time
import cPickle
from scipy.interpolate import interp1d
from scipy.optimize import curve_fit
from scipy.stats import scoreatpercentile as sc
from scipy.stats import n... | JohanComparat/nbody-npt-functions | bin/bin_DF/test_scripts/densityField-function-tracers.py | Python | cc0-1.0 | 39,112 | [
"Galaxy",
"Gaussian"
] | eb26e05d6af6f06210a7f600081717e6e42024eafe7ab855cfe54d50f8a4391f |
# Copyright (C) 2014
# Jakub Krajniak
# Copyright (C) 2012,2013,2015
# 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 redistribut... | espressopp/espressopp | src/FixedQuadrupleListAdress.py | Python | gpl-3.0 | 3,404 | [
"ESPResSo"
] | 8e47efc97d2538542cfdf64a834784b7e8ae5eb21c572d163d0e43a3bfe9f23c |
"""
simple, elegant templating
(part of web.py)
Template design:
Template string is split into tokens and the tokens are combined into nodes.
Parse tree is a nodelist. TextNode and ExpressionNode are simple nodes and
for-loop, if-loop etc are block nodes, which contain multiple child nodes.
Each node can emit som... | aaronsw/watchdog | vendor/webpy/web/template.py | Python | agpl-3.0 | 45,234 | [
"VisIt"
] | 8708aa3a7995980a27461199ce3309da0f7b42de08806bd954a17dc984fbd30c |
from check_grad import check_grad
from utils import *
from logistic import *
import matplotlib.pyplot as plt
def run_logistic_regression(hyperparameters):
# TODO specify training data
train_inputs, train_targets = load_train()
valid_inputs, valid_targets = load_valid()
test_inputs, test_targets = lo... | ouyangyike/Machine-Learning-and-Data-Mining | Logistic Regression/logistic_regression_template4.py | Python | mit | 3,764 | [
"Gaussian"
] | d1e505e7acbb9a211340318e3d74618c32070acf3c2d64fff2db228102a607a1 |
# coding=utf-8
"""Text encoding UTF-8"""
class SystemVariables:
"""SystemVariables(String, String, String, String, Boolean, [String],
(String), [String], String)
Class for constructing required system variables for the bot.
SystemVariables.prefix_qualifier
String
Command qualifier.
... | SamuiNe/Sophia-py | bot_system.py | Python | mit | 19,066 | [
"VisIt"
] | d0b76d457517ae16460843eb41e932a1dde645eae27d2bb604f816fa8f095284 |
# -*- coding: utf-8 -*-
from __future__ import division
import sqlite3
import os
#from rdkit import Chem
#import textract
#import PyPDF2
class ProteinParser(object):
'''
A class to parse protein information
'''
def __init__(self, handle):
'''
Initialise the class with the handle
'''
self... | jmp1985/metrix-database | protein_parser.py | Python | bsd-2-clause | 3,400 | [
"RDKit"
] | 0b2a956a151954417e260e87b0007c474255cd547027034ab8c758293f126267 |
"""
respa.py: Implements the rRESPA multiple time step integration method.
This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. ... | choderalab/openmmtools | openmmtools/respa.py | Python | mit | 4,798 | [
"OpenMM"
] | 0412b98b1ad38cb4796c66b39830b6797bc4937f75351727db3e4bc88865a0fc |
# This was copied from CPython 3.6
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ThreadPoolExecutor."""
__author__ = "Brian Quinlan (brian@sweetapp.com)"
import atexit
from concurrent.futures import _base
import itertools
try:
import queue
e... | blaze/distributed | distributed/_concurrent_futures_thread.py | Python | bsd-3-clause | 5,445 | [
"Brian"
] | 7205f5cae2db13d5712d402626ddd1098867335316eb8f83de3bc99d68ece217 |
#!/usr/bin/env python
'''
figures for centralMS paper
'''
import os
import h5py
import pickle
import numpy as np
import corner as DFM
from scipy.interpolate import interp1d
from scipy.stats import multivariate_normal as MNorm
from letstalkaboutquench.fstarforms import fstarforms
# -- centralms --
from centralms i... | changhoonhahn/centralMS | doc/paper.py | Python | mit | 102,367 | [
"Galaxy",
"TINKER"
] | 415ed8e8e14a0ef85df1a4e071798e4a1741147d1bf03dc9262958a7dff02092 |
""" Principal Component Analysis
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Olivier Grisel <olivier.grisel@ensta.org>
# Mathieu Blondel <mathieu@mblondel.org>
# Denis A. Engemann <d.engemann@fz-juelich.de>
#
# License: BSD 3 clause
from math import log, sqrt
import warnin... | Tong-Chen/scikit-learn | sklearn/decomposition/pca.py | Python | bsd-3-clause | 25,784 | [
"Gaussian"
] | 3a789b25f812112fe156411e4fe5e88dd2c7ec072c00676b84d915c8bbcc2029 |
#!/usr/bin/env python
"""
..__main__.py
~~~~~~~~~~~~~~~~
Picasso command line interface
:authors: Joerg Schnitzbauer, Maximilian Thomas Strauss
:copyright: Copyright (c) 2016-2019 Jungmann Lab, MPI of Biochemistry
"""
import os.path
def picasso_logo():
print(" ____ _____________ _______... | jungmannlab/picasso | picasso/__main__.py | Python | mit | 51,014 | [
"Gaussian"
] | fc6e954e66223d2f88347318c2e7340443fe3470d90be45fd63d09ef1b3cb13d |
from itertools import product
import nose.tools as nt
import numpy as np
from scipy.stats import t as tdist
from scipy.stats import laplace, logistic, norm as ndist
from ..convenience import lasso, step, threshold
from ..query import optimization_sampler
from ...tests.instance import (gaussian_instance,
... | selective-inference/selective-inference | selectinf/randomized/tests/sandbox/test_sampling.py | Python | bsd-3-clause | 8,790 | [
"Gaussian"
] | ff5beb3d795ce706f0e4082ce3c5fb7e8fb97b8504931cbf0f396eaae77c0377 |
"""
===========================
Formaldehyde cm-line fitter
===========================
This is a formaldehyde 1_11-1_10 / 2_12-2_11 fitter. It includes hyperfine
components of the formaldehyde lines and has both LTE and RADEX LVG based
models
Module API
^^^^^^^^^^
"""
from __future__ import print_function
import nu... | low-sky/pyspeckit | pyspeckit/spectrum/models/formaldehyde.py | Python | mit | 38,797 | [
"Gaussian"
] | 22e32a15d42ad4cd2c836e9e0aa37f0981f34814647ce6cdd1b77a6f51e6e9ba |
# $Id$
#
# Copyright (C) 2007-2010 Greg Landrum
# All Rights Reserved
#
from rdkit import Chem
class PropertyMol(Chem.Mol):
""" allows rdkit molecules to be pickled with their properties saved.
>>> from rdkit.six.moves import cPickle
>>> m = Chem.MolFromMolFile('test_data/benzene.mol')
>>> m.GetProp('_Name... | adalke/rdkit | rdkit/Chem/PropertyMol.py | Python | bsd-3-clause | 2,804 | [
"RDKit"
] | 1d99135f89db87c35e113f224a36f126763256f4b89a1b8babc423f38280d500 |
from __future__ import print_function
from __future__ import absolute_import
import numpy as np
import six
try:
import enthought.mayavi as mayavi
except ImportError:
try:
import mayavi
except ImportError:
mayavi = None
if mayavi:
from mayavi import mlab
from mayavi.core.source im... | lokik/sfepy | sfepy/postprocess/utils.py | Python | bsd-3-clause | 2,564 | [
"Mayavi"
] | eaf844d61a5435a0af895075f9c73560ed1619f02dd337ee4bbd7d95bc6c09df |
#!/usr/bin/env python
# Author: Brian Binovsky
# Date: 4/14/2014
# Purpose: Very simple example
# License: BSD (3 term)
# Notes: Revised after initial commit as a test.
import pygtk
import gtk
import os
class DirectoryExample(object):
def delete_event(self, widget, event, data=None):
gtk... | bbinovsky/gtk_dir_example | gtk_dir_example.py | Python | bsd-3-clause | 2,400 | [
"Brian"
] | f097b3d83a0829c14a4ab0dfc9569dbf12d1f113c310b5ea69774321161570e9 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | ravibhure/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 42,549 | [
"VisIt"
] | c0bd5a8a4d2309655b1b087c3371d3ed278b7681667df357912aaefdcbe588e2 |
# 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... | ghchinoy/tensorflow | tensorflow/python/autograph/core/converter.py | Python | apache-2.0 | 12,834 | [
"VisIt"
] | 1195ab40aa0bca7524afc407618fde6a9792dc0467d5171b9ada1e4aaa2cbbc3 |
"""
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_import import *
import time
import random
@io
def sleep_long():
time.sleep(2)
@io
def sleep_random()... | runefriborg/pycsp | test/guardtest.py | Python | mit | 4,995 | [
"Brian"
] | 14badcadc47a6888c899dc6cd5116d0b6bb44241a4163ef3e8b1959ffea72d6e |
# Released under The MIT License (MIT)
# http://opensource.org/licenses/MIT
# Copyright (c) 2013-2015 SCoT Development Team
import unittest
from importlib import import_module
import numpy as np
import scot
from scot import plainica, datatools
from scot.var import VAR
class TestICA(unittest.TestCase):
def setU... | scot-dev/scot | scot/tests/test_plainica.py | Python | mit | 2,466 | [
"Gaussian"
] | c915385bacbbae67af5f74202ba45d72efc5b87dce020107b13c3e9e3bf418fe |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
fileName1, fileName2, useMarchingCubes, noSkin, noSkeleton = get_program_parameters()
if useMarchingCubes:
print('Using vtkMarchingCubes.')
else:
print('Using vtkFlyingEdges3D.')
colorLut = CreateFrogLut(... | lorensen/VTKExamples | src/Python/Visualization/FlyingFrogSkinAndTissue.py | Python | apache-2.0 | 8,604 | [
"Gaussian",
"VTK"
] | 206053d4ac2289738190c60490a10032582f3e6cde1bc4849594386a94799776 |
#!/usr/bin/env python
# Copyright 2004, Magnus Hagdorn
#
# This file is part of GLIMMER.
#
# GLIMMER 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
# (at your option) an... | glimmer-cism/PyCF | progs/ran_topo.py | Python | gpl-2.0 | 5,954 | [
"NetCDF"
] | 751e39f52047e05c67f6eca0898ae95cb296c5f15d63e8a525c39efc3b1c49d8 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | wscullin/spack | var/spack/repos/builtin/packages/lammps/package.py | Python | lgpl-2.1 | 3,722 | [
"LAMMPS",
"NetCDF"
] | b3ec7cfc48f28fcbdfd63018eef9e5799a39df943eb98d8635aca01575c90ad1 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
import os
import threading
import time
from subprocess import call, Popen, PIPE, STDOUT
import json
# - - - - - - - - - - - - - - - - - -
# - - SPEAK MESSAGE CONTROLLER - - -
# - - - - - - - - - - - - - - - - - -
class SpeakMessageController:
def __init__(self, audioP... | infiniteloop-inc/crystal-signal | bin/SpeakMessageController.py | Python | bsd-3-clause | 4,141 | [
"CRYSTAL"
] | 1569a35678ceb2a6067ff60a64cd03d811afe5d25f0164395302e4443161b042 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/util/tty/color.py | Python | gpl-2.0 | 7,184 | [
"Psi4"
] | 7760385d43d7dd802ea37a9ada048ab73719eb09dcf58083a1b5fa41c7009dcd |
from time import time # noqa
import scipy as sp # noqa
import schrpy as sch # noqa
testpot = sch.step_potential(10, 0)
xo = sch.gaussian(-15, 5., 2).func
solver = sch.schroedinger(testpot, xo, dx=0.05, dt=0.05, tmax=30)
t = time()
Z = solver.solve()
print('spent', time() - t, 'seconds.')
sp.save('step_potential3.np... | tmaeda11235/schroedinger_solver | tests/step.py | Python | mit | 359 | [
"Gaussian"
] | 18b325a3fc7004b80d2a7b70c59de35821d01ea66f6485d889bde1b20a50e0c5 |
import torch
import torch.nn as nn
import matplotlib.pyplot as plt
import torch.nn.functional as F
import torchvision.transforms as transforms
import torchvision.utils as vutils
from pytorch_lightning import LightningModule, Trainer
from data import CelebADataModule
from argparse import ArgumentParser
from einops impo... | probml/pyprobml | vae/standalone/vae_logcosh_celeb_lightning.py | Python | mit | 7,909 | [
"Gaussian"
] | c27a2850fb72ec07b52d899713695e7cfceb28c20627f4c5167b676b6eb66d19 |
from setuptools import setup, find_packages
setup(
name='cage',
version='0.1',
packages=find_packages(exclude=['docs']),
install_requires=[
'matplotlib',
'scipy',
'numpy',
'click',
'pymatgen'
],
entry_points='''
[console_scripts]
cage=cage... | mbercx/cage | setup.py | Python | mit | 344 | [
"pymatgen"
] | 292332aea83514900440bfa1c23542f4e204031121d0a2fa456311a34b385ff9 |
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
class wsMeshSmooth(ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
... | nagyistoce/devide | modules/filters/wsMeshSmooth.py | Python | bsd-3-clause | 3,861 | [
"VTK"
] | f7d366b6b78e6c07967592faba9c62a785fa27db5272a7a12902ea22ed34887f |
#import scipy as sp
from scipy.io import loadmat
import numpy as np
import git as git
import tables as tables
import datetime as dt
class Database():
"""
A class for working with an HDF5 database.
Basically a wrapper around pytables.
"""
def __init__(self):
"""
.. no... | bps10/emmetrop | emmetrop/database/Database.py | Python | mit | 11,465 | [
"Brian",
"NEURON"
] | 2b8827730290a9254a6bfd5c8c9eb27f222e7a783a71d6e79fd6a9aaee0113f2 |
"""
Module om DVS berichten uit InfoPlus te kunnen verwerken.
"""
import xml.etree.cElementTree as ET
import isodate
import datetime
import pytz
import logging
import re
# Vraag een logger object:
__logger__ = logging.getLogger(__name__)
def parse_trein(data):
"""
Vertaal een XML-bericht over een trein (uit ... | geertw/rdt-infoplus-dvs | infoplus_dvs.py | Python | gpl-3.0 | 44,760 | [
"Elk"
] | a54842613a0a821efa053b08074df78f20442d4090038339578c7e21e0ed18bc |
# 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... | jiaphuan/models | research/lfads/synth_data/generate_chaotic_rnn_data.py | Python | apache-2.0 | 8,412 | [
"Gaussian",
"NEURON"
] | f775b18893172c776196051a5ecc5a9cc6e6f00c1df4f8f211453eef07abf770 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from itertools import chain, combinations
from pymatgen.core.periodic_table import Element
from pymatgen.core.composition import Composition
'''
This module implements a MolecularOrbital class to represent ba... | dongsenfo/pymatgen | pymatgen/core/molecular_orbitals.py | Python | mit | 4,395 | [
"CRYSTAL",
"pymatgen"
] | 16a2371b64561ce10ef954920c4e665062ae1961e02eaf15a1178718df0dbd81 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/header.py | Python | lgpl-3.0 | 2,659 | [
"Psi4"
] | 3b40956cbed136af93a897a9d6290ceabde83a91fb1ffd22f22b7c3702d2a97b |
# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is... | sn-amber/mylpp | src/vmd.py | Python | gpl-2.0 | 8,592 | [
"VMD"
] | 1516ab268e481e7ae774ea914e9583dc3ff5b786e3af79636ede427ff2ac546d |
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