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"""Given a BAM file extract
1. Template len and std model
2. BQ model
3. GC bias model"""
import time
from multiprocessing import Pool
import pickle
import numpy as np
import pysam
import logging
logger = logging.getLogger(__name__)
def process_bam_section(bam_fname, reference, every=1, min_mq=0, max_bq=94, max_bp... | sbg/Mitty | mitty/empirical/bam2illumina.py | Python | apache-2.0 | 4,103 | [
"pysam"
] | 73dfd10c9ebec12209cfc0edacd1e837adf52213adc60ceedd016cf00ea72403 |
"""
==========================================
Statistical functions (:mod:`scipy.stats`)
==========================================
.. module:: scipy.stats
This module contains a large number of probability distributions as
well as a growing library of statistical functions.
Each included distribution is an instanc... | chaluemwut/fbserver | venv/lib/python2.7/site-packages/scipy/stats/__init__.py | Python | apache-2.0 | 9,109 | [
"Gaussian"
] | d95ffc01a75ea22066272b37a2c05f8323977fb8ba988133e5c7c73a011e2893 |
"""Implementation of the WebSocket protocol.
`WebSockets <http://dev.w3.org/html5/websockets/>`_ allow for bidirectional
communication between the browser and server.
WebSockets are supported in the current versions of all major browsers,
although older versions that do not support WebSockets are still in use
(refer ... | SickGear/SickGear | lib/tornado_py2/websocket.py | Python | gpl-3.0 | 51,461 | [
"VisIt"
] | 6b6fa87dcb939b34333ccce43946b66f32c4bd847aa1314076e9689067e58f30 |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
import pytest
import torch
from torch.nn.functional import pad
import pyro.distributions as dist
from pyro.distributions.util import broadcast_shape
from pyro.ops.gaussian import (
AffineNormal,
Gaussian,
... | uber/pyro | tests/ops/test_gaussian.py | Python | apache-2.0 | 15,446 | [
"Gaussian"
] | e759a671b41b11ab6fc66ef2f461ca1b7073663d04d49bf2d7fe4e13cb751b27 |
# 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... | taknevski/tensorflow-xsmm | tensorflow/contrib/learn/python/learn/learn_io/graph_io.py | Python | apache-2.0 | 34,510 | [
"VisIt"
] | 7c3e1d19f1893ff978c7c0ef945b9f37c123f2e740f4b4c6df1cb4c66d964ad6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2011, 2013 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as... | Freeseer/freeseer | src/freeseer/frontend/record/RecordingWidget.py | Python | gpl-3.0 | 10,562 | [
"VisIt"
] | c6ee097ec6c42fea48fddd074d7fa243312257e377514c2557741534a6acac62 |
from __future__ import absolute_import
import re
import json
import time
import logging
import random
import six
from django.conf import settings
from django.core.cache import cache
from six.moves.urllib.parse import parse_qsl
from sentry import http
from sentry.utils.safe import get_path
from sentry.utils.strings i... | mvaled/sentry | src/sentry/lang/javascript/errormapping.py | Python | bsd-3-clause | 3,769 | [
"VisIt"
] | f287283897546b294b7132e4056bbad005b0b48aebdb9528730c458e972d01d9 |
import sys
from DIRAC.Core.Base import Script
from DIRAC import gLogger
from DIRAC.ConfigurationSystem.Client.LocalConfiguration import LocalConfiguration
if __name__ == "__main__":
localCfg = LocalConfiguration()
localCfg.setConfigurationForWeb( "REST" )
localCfg.addMandatoryEntry( "/DIRAC/Setup" )
localC... | DIRACGrid/RESTDIRAC | RESTSystem/scripts/dirac-rest-server.py | Python | gpl-3.0 | 1,099 | [
"DIRAC"
] | a72de27364d2db3634c63b40f46a3c78c2d72fd5c3e0c840c9238d70dbd5ea56 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-deploy-scripts
# Author : Adria Casajus
########################################################################
"""
Deploy all scripts and extensions
"""
__RCSID__ = "$Id$"
import os
import shut... | Andrew-McNab-UK/DIRAC | Core/scripts/dirac-deploy-scripts.py | Python | gpl-3.0 | 6,487 | [
"DIRAC"
] | af4f7f0b594b85edc19492dfe3396e15033b0c9a5198006a815d225215674f1d |
import random
class commandHandler(object):
# Dictionary of lists for channel guns and trigger pull count
rouletteGun = 0
rouletteCount = 0
# Dictionary of lists for channel inventories
inventory = []
def __init__(self):
# initialize a loaded 6-chambered gun with one ... | DickieTheProgrammer/DickieBot | commands.py | Python | bsd-2-clause | 2,580 | [
"BLAST"
] | 577d5c70769c59473e1faea53da31c320dd0824eb2356786b01540bcd0ab5c0d |
from __future__ import division
import os, sys, subprocess
from glob import glob
import cPickle as pickle
import cv2
import numpy as np
import scipy.io as sio
import matplotlib
import matplotlib.pyplot as plt
import xlrd
import wx
import wx.lib.agw.floatspin as FS
import wx.lib.agw.multidirdialog as MDD
from plottin... | i-namekawa/TopSideMonitor | multitrack.py | Python | bsd-3-clause | 88,668 | [
"Gaussian"
] | 9af2a4beeebb7d48613930329c762aaf6edfc882446e88720b7938e32bc88c7f |
# Copyright 2007-2011 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 ... | sillvan/hyperspy | hyperspy/tests/signal/test_eds_tem.py | Python | gpl-3.0 | 6,842 | [
"Gaussian"
] | 601d65caa8df059358d59797a16c010e96f8ab8ca86799fc7cbbfdf165fdedd7 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2009 Douglas S. Blank
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as p... | arunkgupta/gramps | gramps/plugins/quickview/ageondate.py | Python | gpl-2.0 | 2,780 | [
"Brian"
] | 46e7eaf1dbc983118654e69ee90dad16de33c5e8818dd3d9999bb13e1b7fc527 |
#!/usr/bin/env python
# framework to start a simulated vehicle and connect it to MAVProxy
# Peter Barker, April 2016
# based on sim_vehicle.sh by Andrew Tridgell, October 2011
import optparse
import sys
import psutil
import atexit
import os
import subprocess
import tempfile
import getpass
import time
class CompatErr... | koustubh-dwivedy/ardupilot | Tools/autotest/sim_vehicle.py | Python | gpl-3.0 | 18,093 | [
"Firefly"
] | 0ea973d0207a51f7940e47a974635b02bffb0f0442feffb86304777197f6ffe5 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | wizmer/NeuroM | neurom/io/tests/test_utils.py | Python | bsd-3-clause | 12,734 | [
"NEURON"
] | 807da08d4e394b2bd4f89de3d5054f0a170c83dee9d34d556129d78980ee82bf |
"""
This is the play
"""
import numpy as np
import matplotlib.pyplot as plt
import math
from sklearn.datasets import make_blobs
from functions import selection_algorithm, scl
plot = True
verbose = False
tracking = False
selection = True
# Generate the data
n_samples = 1500
random_state = 20 # Does not converge
ran... | h-mayorquin/competitive_and_selective_learning | test_scl.py | Python | mit | 3,092 | [
"NEURON"
] | 7138549d901845ac6276fa6985b7f0dc83c39f1636aead5c58fc436c6dadeca0 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""Unit tests for the `iris.fileformats.netcdf.save` function."""
# Import iris.tests first so that some things can be initial... | pp-mo/iris | lib/iris/tests/unit/fileformats/netcdf/test_save.py | Python | lgpl-3.0 | 8,186 | [
"NetCDF"
] | c0e5966ceae35beddee94f2371c5e45d83cba623b6a5d50e3b3bacbf0b79d4e4 |
#!/usr/bin/env python
"""
castep.py
Various bits of python to read/write castep files
Copyright (c) 2010 Andrew Walker (a.walker@ucl.ac.uk)
All rights reserved.
"""
import re
import scipy as S
version = 0.1
# regular expression to match the whole of the final cell from a .castep file
dotcastep_latt_RE = re.compile... | duyuan11/elastic-constants | castep.py | Python | bsd-3-clause | 5,997 | [
"CASTEP",
"CRYSTAL"
] | 3d93c762eae9f4aaa3f9c0e2f626df7f4853c08f3a8f81045f0ecde6aa8d5afa |
import numpy as np
from ase.atoms import Atoms
def write_plt(filename, atoms, data):
if isinstance(atoms, Atoms):
cell = atoms.get_cell()
else:
cell = np.asarray(atoms, float)
if cell.ndim == 2:
c = cell.copy()
cell = c.diagonal().copy()
c.flat[::4] = 0.0
i... | askhl/ase | ase/io/plt.py | Python | gpl-2.0 | 1,605 | [
"ASE"
] | 4ddaad2e98885bec5530a6817d63be692b6f9d5ed46ceea0f1d8594267361221 |
#! /usr/bin/env python
""" An ASE interface to pwscf.
Users should set the environmental flag $PWSCF_COMMAND
to the command for pw.x e.g. 'pw.x' or 'mpirun -np 12 pw.x'
The default is 'mpirun -np 12 pw.x -npool 2 -ntg 2 -ndiag 3'
"""
import os
import re
from ase.calculators.general import Calculator
from os.path import... | mailhexu/pyDFTutils | pyDFTutils/espresso/Pwscf.py | Python | lgpl-3.0 | 41,702 | [
"ASE",
"CRYSTAL",
"ESPResSo"
] | 3679dbbba56626f6908631c681d08728ccaca784357285b5d2bb82b934b21d33 |
#
# Copyright 2017 Lars Pastewka (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# 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 Found... | libAtoms/matscipy | matscipy/drift.py | Python | lgpl-2.1 | 2,109 | [
"Matscipy"
] | 6a71d8565ac063edc19a0c5dbf1025e7cee5410ce71390b8646a4c043cc305e6 |
# #############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Matthew Harrigan
# Contributors: Robert T. McGibbon
#
# MDTraj is fre... | swails/mdtraj | mdtraj/core/selection.py | Python | lgpl-2.1 | 14,120 | [
"MDTraj",
"VisIt"
] | 5916f4b0467a1e51193f4de5da11c76661bce4bada67c1a5a2cda27574a31bfc |
# This file is part of Invenio.
# Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2014, 2015 CERN.
#
# Invenio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, o... | jmacmahon/invenio | modules/websession/lib/websession_templates.py | Python | gpl-2.0 | 120,946 | [
"VisIt"
] | 3607515e4ccaaf1082047a6b1d29c3ffabc6720a204ca1ebca79f4f279d236a0 |
"""
This module contains the CharmmWriter class and associated methods,
which outputs a psf/pdb file with CHARMM names and parameters.
It does this by converting atom names to CHARMM names, writing
intermediate files as necessary to invoke the vmd psfgen plugin.
Author: Robin Betz
Copyright (C) 2015 Robin Betz
"""
#... | drorlab/dabble | Dabble/param/charmm.py | Python | gpl-2.0 | 43,577 | [
"CHARMM",
"CRYSTAL",
"NAMD",
"VMD"
] | 797068b6c5cb7958d8ca7429def9ffc76f2df26b0e156095372b4d8c9fa3875d |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | SamStudio8/scikit-bio | skbio/stats/distance/tests/test_base.py | Python | bsd-3-clause | 24,805 | [
"scikit-bio"
] | 580c0bee22c9aceb8706f203527e350bce0a5defe9c34322fddd0f5d2534fac3 |
#!/usr/bin/env python
from __future__ import print_function
import roslib
roslib.load_manifest('lane_detection')
import rospy
import sys
from std_msgs.msg import Int32
import cv2
from sensor_msgs.msg import Image
from cv_bridge import CvBridge, CvBridgeError
from picamera import PiCamera
from picamera.array import PiRG... | isarlab-department-engineering/ros_dt_lane_follower | deprecated_nodes/old-lane-detection.py | Python | bsd-3-clause | 9,077 | [
"Gaussian"
] | e8ae718f85541133153fc183dc886a6d135909cd8f0f2ef5f09a0fb49bd57092 |
"""Utilities to assist with commerce tasks."""
import json
import logging
from urllib import urlencode
from urlparse import urljoin
import requests
import waffle
from django.conf import settings
from django.contrib.auth import get_user_model
from django.urls import reverse
from django.utils.translation import ugettext... | jolyonb/edx-platform | lms/djangoapps/commerce/utils.py | Python | agpl-3.0 | 15,617 | [
"VisIt"
] | dc26d43a0ebc727a0511dfb3a27b96867590764d789d8220b48c75de38eb08ee |
#!/usr/bin/env python2.6
import ssl
import xmlrpc.client
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-s", "--server", dest="server",
help="XMLRPC server URL", metavar="URL", default='https://geni.renci.org:11443/orca/xmlrpc')
parser.add_option("-c", "--cert", dest="c... | RENCI-NRIG/ahab | ahab_py/bin/listResources.py | Python | epl-1.0 | 1,509 | [
"ORCA"
] | 967b5f316b48e07315f70a633a0e5c2626d5e9a987491fdb3315af67916283d4 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/driver/qcdb/qcformat.py | Python | lgpl-3.0 | 4,080 | [
"Psi4"
] | 50b8bc4146b8fd7adefbc677c120b5c14f028c5b01f746d2d50b02265c5ecba8 |
# 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 http://mozilla.org/MPL/2.0/.
import datetime
import json
import os
import gzip
import shutil
import stat
from contextlib import contextmanager, clos... | Tayamarn/socorro | socorro/external/fs/crashstorage.py | Python | mpl-2.0 | 31,293 | [
"VisIt"
] | ec2244a891283c4221f2cf383d0125afcf8f4c0b2323bb7827c10aa479ac3fb5 |
# This file is part of MSMBuilder.
#
# Copyright 2011 Stanford University
#
# MSMBuilder 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... | msmbuilder/msmbuilder-legacy | MSMBuilder/project/project.py | Python | gpl-2.0 | 18,240 | [
"MDTraj"
] | 0670ab8102a2763e06b8dc6f884745f1301899161260aa0545fa962a39745cc6 |
""" This is the guy that you should use when you develop a script that interacts with DIRAC
And don't forget to call parseCommandLine()
"""
__RCSID__ = "$Id$"
import sys
import os.path
import inspect
from DIRAC.ConfigurationSystem.Client.LocalConfiguration import LocalConfiguration
from DIRAC.FrameworkSystem.Cl... | fstagni/DIRAC | Core/Base/Script.py | Python | gpl-3.0 | 3,829 | [
"DIRAC"
] | 826dd344370e044f09d46ef9aeee2e0760fb0f54125faa4eb239f636b542d480 |
"""
Analysis of log files.
"""
from __future__ import absolute_import
import collections
import warnings
from .amberlogfile import AmberLogFile
from .namdlogfile import NamdLogFile
__all__ = ['LogAnalyzer']
class LogAnalyzer(object):
"""Analyzing AMBER (including CHAMBER) mdout and NAMD log files."""
def ... | HuiLiuCode/pymdlog | pymdlog/analysis.py | Python | gpl-3.0 | 2,289 | [
"Amber",
"NAMD"
] | 4fdaf85d2bafc95d373cae8e400cb26ed0fe8af609836ee8fb4585da2ff77c67 |
#!/usr/bin/env python
from setuptools import setup, find_packages
from vaspy import __version__ as version
maintainer = 'Shao-Zheng-Jiang'
maintainer_email = 'shaozhengjiang@gmail.com'
author = maintainer
author_email = maintainer_email
description = "A pure Python library designed to make it easy and quick to manip... | PytLab/VASPy | setup.py | Python | mit | 3,589 | [
"Mayavi",
"VASP"
] | f2c902d095511c535ae466eb9f32f478d6ce7c1e5edddcfc8ce89d123cf44a20 |
from sdssgaussfitter import gaussfit
import numpy as np
from scipy import interpolate
import os,sys
from util import utils
from util.readDict import readDict
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
def aperture(startpx,startpy,radius=7):
r = radius
length = 2*r
height = le... | bmazin/ARCONS-pipeline | examples/Pal2012_landoltPhot/landoltFitRPsf.py | Python | gpl-2.0 | 7,657 | [
"Gaussian"
] | d7df86f3ac1bfb5af8a3f2f90ed85525ab067c531041b64a96969df30a7d3fda |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import numpy as np
from scipy.spatial.distance import cdist
import matplotlib.pyplot as plt
from math import sqrt
import matplotlib.animation as animation
from dana import *
''' Spikes model in computational neuroscience with Brian library. '''
# -------------... | Aurelien1609/Computational-model | frequency_model.py | Python | bsd-3-clause | 13,265 | [
"Brian",
"NEURON"
] | ff9d5054263d379e72d9318bce7d0ab90b06c1bb64c39adbeb28bd394d87d713 |
#-------------------------------------------------------------------------------
"""
ARCED IPOL demo app
A Review of Classic Edge Detectors
by Haldo Sponton and Juan Cardelino.
June 27, 2013
"""
#-------------------------------------------------------------------------------
from lib import base_app, build, http, imag... | juan-cardelino/ARCED-demo | sc_edges/app.py | Python | apache-2.0 | 12,294 | [
"Gaussian"
] | 159ba021e72dca57d1fb8c1e51f82eab1afb43843cf956afbf28f3950c6d086c |
"""Perception (Chapter 24)"""
import cv2
import keras
import matplotlib.pyplot as plt
import numpy as np
import scipy.signal
from keras.datasets import mnist
from keras.layers import Dense, Activation, Flatten, InputLayer, Conv2D, MaxPooling2D
from keras.models import Sequential
from utils4e import gaussian_kernel_2D... | Chipe1/aima-python | perception4e.py | Python | mit | 16,421 | [
"Gaussian"
] | c732ed27d7245704ce9f03df69c699cf47c989f859c82a22fc4437f7a4396034 |
from pycqed.measurement import measurement_control as mc
import adaptive
from pycqed.instrument_drivers.meta_instrument.LutMans import flux_lutman as flm
from pycqed.instrument_drivers.virtual_instruments import noise_parameters_CZ_new as npCZ
from pycqed.simulations import cz_superoperator_simulation_new_functions a... | DiCarloLab-Delft/PycQED_py3 | pycqed/simulations/spectral_tomography.py | Python | mit | 36,820 | [
"Gaussian"
] | 47ecc311487e5ad09f9b86cedb1a012aee0326b4f7f727b6bfc10aba8825e667 |
#!/usr/bin/env python
import os
import moose
import moose.utils as mu
import sys
import pylab
from collections import defaultdict
import moose_to_neuron as m2n
nrn_segs_ = {}
moose_compts_ = {}
soma_ = None
nrn_text_ = {} #defaultdict(list)
model_name_ = None
records_ = {}
dt_ = 50e-6
chanProto_ = [
['./cell... | BhallaLab/benchmarks | moose_nrn_equivalence_testing/comparision_with_simple_HH_model_additional_mechanism/check_equivalence.py | Python | gpl-2.0 | 1,726 | [
"MOOSE"
] | 6c06a64111382b200b3b049bd59ee7ed5b4b587a1f104a1b468741dd1fa7fe94 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2013, Jeroen Hoekx <jeroen.hoekx@dsquare.be>, Alexander Bulimov <lazywolf0@gmail.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANS... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/system/lvol.py | Python | bsd-3-clause | 16,671 | [
"Firefly"
] | d57fb89826875eb28942ea3d00b8be089fb40494c9bf7ef65c0819795d451cbc |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-configure
# Author : Ricardo Graciani
########################################################################
"""
Main script to write dirac.cfg for a new DIRAC installation and initial downl... | sposs/DIRAC | Core/scripts/dirac-configure.py | Python | gpl-3.0 | 18,495 | [
"DIRAC"
] | 3151bc94a96a3fe48c17aa998987cf0059b95f2b7733fbcb9ca4cff4103c1e03 |
# -*- coding: utf-8 -*-
# system
import sys
# libs
import json
import jsonschema
# local
import model
from p2w.parser import parser
from yacpdb.storage import dao
import yacpdb.entry
LIST_COMMON_STIPULATIONS = ["=", "+", "= black to move", "+ black to move", "see text"]
def load_schema(type="entry"):
with open... | dturevski/olive-gui | validate.py | Python | gpl-3.0 | 3,977 | [
"VisIt"
] | ae24b79aa7f3b992ff3eb3abe0d21d7f1575e0b1db55679ba6aa1ad3985cee33 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Demonstrate usage of LFPy.Network with network of ball-and-stick type
morphologies with active HH channels inserted in the somas and passive-leak
channels distributed throughout the apical dendrite. The corresponding
morphology and template specifications are in the file... | LFPy/LFPy | examples/example_network/example_network.py | Python | gpl-3.0 | 20,130 | [
"NEURON"
] | 5675905f747a30e84fc7ffaab49f13a01fff44c60fc1bb9d3a48e4f6fc68fe76 |
"""
Define common steps for instructor dashboard acceptance tests.
"""
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from __future__ import absolute_import
from lettuce import world, step
from mock import patch
from nose.tools import assert_in # pylint: disable=no-name-in-module
from c... | iivic/BoiseStateX | lms/djangoapps/instructor/features/common.py | Python | agpl-3.0 | 4,609 | [
"VisIt"
] | 813affa455a1e3877438943a83433efa3482562a3a929fc547b25500b471b4a2 |
"""
Python implementation of the fast ICA algorithms.
Reference: Tables 8.3 and 8.4 page 196 in the book:
Independent Component Analysis, by Hyvarinen et al.
"""
# Author: Pierre Lafaye de Micheaux, Stefan van der Walt, Gael Varoquaux,
# Bertrand Thirion, Alexandre Gramfort
# License: BSD 3 clause
import wa... | joshbohde/scikit-learn | sklearn/decomposition/fastica_.py | Python | bsd-3-clause | 11,978 | [
"Gaussian"
] | a26f129cc959cee08ed1e085f6387eebce2095d9b9beb707b20b83d14262ab4d |
'''Demonstrate the usage of hierarchical clustering and variational
Bayes (VBMerge) to reduce a given Gaussian mixture to a Gaussian
mixture with a reduced number of components.
'''
import numpy as np
from scipy.stats import chi2
import pypmc
# dimension
D = 2
# number of components
K = 400
# Wishart parameters: m... | fredRos/pypmc | examples/mixture_reduction.py | Python | gpl-2.0 | 2,810 | [
"Gaussian"
] | 3823d773bedd7ca627523ab843b023a14a674bb18a64688fb180c67fecdbb02f |
#!/usr/bin/env python2.6
import unittest
from test import test_support
from MY_jinja2 import nodes, compiler, Template
import MY_jinja2
import cStringIO
class NodeTests(unittest.TestCase):
def setUp(self):
self.generator = compiler.CodeGenerator()
self.data = '<html><body>hello, world<body></html>'
def test... | nnabeyang/MY_jinja2 | nodes.py | Python | bsd-3-clause | 8,926 | [
"VisIt"
] | 6f5a5adc325fb7f9a0672d314b68fdcd87f1bd00740528be29191da10a022ebd |
"""
Django module container for classes and operations related to the "Course Module" content type
"""
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime... | beni55/edx-platform | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 55,862 | [
"VisIt"
] | 53fb1fbe96554edce4b9edc4fc2504526638717374fd1ec7f40df0c80d470101 |
# hchannel.py ---
#
# Filename: hchannel.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Thu Jun 5 15:20:30 2014 (+0530)
# Version:
# Last-Updated:
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#
#
#
#
# This progr... | dilawar/moose-full | moose-core/tests/python/mus/hchannel.py | Python | gpl-2.0 | 2,223 | [
"MOOSE"
] | c10e9122b86738dab948db6d7651743c040cb44e07534ccc3fd62f38bba21e05 |
from owslib import fes, csw
from netCDF4 import Dataset as ncDataset
from netCDF4 import num2date, date2num
import pyugrid
import numpy as np
endpoint = "http://www.ngdc.noaa.gov/geoportal/csw"
uuid = '8BF00750-66C7-49FF-8894-4D4F96FD86C0'
uuid_filter = fes.PropertyIsEqualTo(propertyname='sys.siteuuid', literal="{{... | brandonmayer/comt_catalogue | parse_testbed.py | Python | gpl-2.0 | 7,572 | [
"NetCDF"
] | bd019c6fe1ffc1ae86bdb43e6928c0ca5f15f6c15593b6240b7627a79ba23aa1 |
import sys
import os
import glob
import yt
import numpy as np
from numpy import *
import astropy
from astropy.cosmology import Planck13 as cosmo
import findGalaxyProps as fGP
if __name__=="__main__":
snaps = np.sort(np.asarray(glob.glob("RD????/RD????"))) #ENZO format a list of snapshots in separate directori... | gsnyder206/vela-yt-sunrise | enzoGalaxyProps_rcs.py | Python | gpl-3.0 | 4,594 | [
"Galaxy"
] | beac9e6be6eb9c76fbf46536838fc843cb60f6d26b726d01fb4c04b5179f05c0 |
import numpy
import os
import pdb
import constants
import plot
import preprocess_GCAM, preprocess_IMAGE
import pygeoutil.util as util
def plot_GCAM_annual_diffs(nc_file, tme='', var='', legend='', ylabel=''):
"""
:return:
"""
arr_diff = util.max_diff_netcdf(nc_file, var = var)
arr_diff.insert(0,... | ritviksahajpal/LUH2 | LUH2/GLM/run_all.py | Python | mit | 2,331 | [
"NetCDF"
] | 59a9585f42c2260980957a3a6abd5a40f4663e8ee392ffd66467a52f60fc6af0 |
#coding:utf-8
## Spark Application - execute with spark-submit
## Imports
import os
import time
import pandas as pd
import commands
## Module Constants
APP_NAME = "ADF Spark Application"
TABLE_STOCKS_BASIC = 'stock_basic_list'
TABLE_STOCKS_PAIRS = 'stock_pairing_list45'
TABLE_WEIGHT = 'stock_linrreg.csv'
DownloadDir ... | lionelliang/PairTradingSpark | load-data-mongo.py | Python | gpl-2.0 | 2,457 | [
"ADF"
] | c4d04085b65843937a490dd99ea105910637f247de9dddaecf0001037228e1bd |
#from setuptools import setup
from distutils.core import setup
import sys
try:
import numpy
except ImportError:
print "*** package 'numpy' not found ***"
print "Please get it from http://numpy.scipy.org/ or install it through your package manager."
sys.exit(-1)
#try:
# import MDAnalysis
#except ... | zhuhong/MD-package | setup.py | Python | apache-2.0 | 1,061 | [
"MDAnalysis"
] | 9e49f835fb498c1ea201f5f6db034e746f1c56e4fd1ac78bc3368c8a865e0327 |
# coding=utf-8
# --------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for
# license information.
#
# Code generated by Microsoft (R) AutoRest Code Generator.
# Changes ... | lmazuel/azure-sdk-for-python | azure-mgmt-web/azure/mgmt/web/models/app_service_environment.py | Python | mit | 12,271 | [
"ASE"
] | 1caa39f45a5ddcdda70581593fcdccbc233d29c02a58d1f7f6bfced39d4862ba |
# --------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU... | paulojamorim/invesalius3 | invesalius/data/slice_.py | Python | gpl-2.0 | 70,939 | [
"VTK"
] | 767cfd90a694b9d20c4e88fe858f1c0b2c382d06db902b918d40a35224da7b62 |
# -*- coding: utf-8 -*-
'''
Phoenix Add-on
Copyright (C) 2015 Blazetamer
Copyright (C) 2015 lambda
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 Lic... | krisawatson/plugin.video.genesis | modules/indexers/nhlcom.py | Python | gpl-3.0 | 9,617 | [
"VisIt"
] | 8ec0221e0e2ba390b8c0e18a06ddf9836866501cc4d0a153c6234b1dd7bf50f3 |
# -*- coding: utf-8 -*-
# android_adb
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public L... | thica/ORCA-Remote | src/interfaces/android_adb/interface.py | Python | gpl-3.0 | 10,012 | [
"ORCA"
] | 80e5c93ad6af74acf21c05e451f704ccec4b9f92e5ac59dcfda815574663645c |
from django import forms
from django.contrib.admin.widgets import AdminRadioSelect, AdminRadioFieldRenderer
from edc_base.form.old_forms import BaseModelForm
from edc_constants.constants import ON_STUDY, MISSED_VISIT
from edc_visit_tracking.forms import VisitFormMixin
from tshilo_dikotla.choices import VISIT_REASON, ... | TshepangRas/tshilo-dikotla | td_maternal/forms/maternal_visit_form.py | Python | gpl-2.0 | 1,638 | [
"VisIt"
] | 7317a77a54ebc45de8a734f07b3b68a63c6bc1b2d09e6a89ca3f6d9a13ea75f8 |
#
# Copyright (C) 2013,2014,2015,2016 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)... | Smiljanic/espresso | testsuite/python/electrostaticInteractions.py | Python | gpl-3.0 | 4,743 | [
"ESPResSo"
] | ae7fcef771cab0b054b848b2167aaaf9cd113ecb5811592e0ed130e6fb6336f7 |
import sys
sys.path.append(sys.path[0] + "/..")
import MB
import subprocess
import time
import beatclient
import sys
class BeatObserver:
def __init__(self,drum_player):
self.player=drum_player
def notify(self):
pass
import wx
class PlayerP... | pauljohnleonard/MusicBox | src/gui/mainV2.py | Python | gpl-2.0 | 5,496 | [
"VisIt"
] | 495025eb85aac726445a08cd3a9f254aa8c4674ee7ad5e513fff7fc047540086 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2014 Liang Wang <liang.wang@cs.helsinki.fi>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
#
# Liang Wang @ CS Dept, Helsinki Univ, Finland
# 2014.05.01
#
import logging
import numpy
import tempfile
from scipy import linalg
fr... | pombredanne/panns | panns/utils.py | Python | gpl-2.0 | 5,104 | [
"Gaussian"
] | 050c5b0252be5f003ea9c21a1eb7655f3f441eee97f1b016dafffb841feb49c4 |
"""
Featurizes proposed binding pockets.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2017, Stanford University"
__license__ = "MIT"
import numpy as np
from deepchem.utils.dependencies impo... | rbharath/deepchem | deepchem/feat/binding_pocket_features.py | Python | mit | 1,839 | [
"MDTraj"
] | 4e33abcd499057a69fddf76e6d32a970758bfa978b9527d8fc24aeaab2010064 |
import pytest
from pysisyphus.calculators import EnergyMin, XTB
from pysisyphus.calculators.PySCF import PySCF
from pysisyphus.cos.NEB import NEB
from pysisyphus.helpers import geom_loader
from pysisyphus.init_logging import init_logging
from pysisyphus.testing import using
from pysisyphus.interpolate import interpola... | eljost/pysisyphus | tests/test_energymin/test_energymin.py | Python | gpl-3.0 | 2,211 | [
"PySCF",
"xTB"
] | 6d09a4d3a270167eae9195eda741ab95125caf5e4d3008b9757ce8e147cf21ff |
""" The JobDB class is a front-end to the main WMS database containing
job definitions and status information. It is used in most of the WMS
components
**Configuration Parameters**:
The following options can be set in ``Systems/WorkloadManagement/<Setup>/Databases/JobDB``
* *MaxRescheduling*: Set the ma... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/DB/JobDB.py | Python | gpl-3.0 | 78,385 | [
"DIRAC"
] | 008531a0ef668f27b95247a4e76c49f2a75514b7b4807145767a38dc70d6255d |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2008 James Friedmann <jfriedmannj@gmail.com>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2015-2016 Paul Franklin
#
# This program is free sof... | sam-m888/gramps | gramps/gen/plug/report/utils.py | Python | gpl-2.0 | 13,872 | [
"Brian"
] | d619c37144a1f0cccf2d4e30f1b2ae198a87c7e13060627b6fff051ed5b36e1a |
########################################################################
# File : LocalComputingElement.py
# Author : Ricardo Graciani, A.T.
########################################################################
""" LocalComputingElement is a class to handle non-grid computing clusters
"""
import os
import stat
i... | fstagni/DIRAC | Resources/Computing/LocalComputingElement.py | Python | gpl-3.0 | 10,674 | [
"DIRAC"
] | 693dd89fe2c680852041740fb934548a48e981b6e8abee422e86d70e57e26668 |
# -*- coding: utf-8 -*-
# Author: Óscar Nájera
# License: 3-clause BSD
"""
==================
RST file generator
==================
Generate the rst files for the examples by iterating over the python
example files.
Files that generate images should start with 'plot'
"""
from __future__ import division, print_functi... | sequana/sequana | doc/sphinxext/sphinx_gallery/gen_rst.py | Python | bsd-3-clause | 20,235 | [
"Mayavi"
] | f3b4f11371482e1e619ffddb848fd8874e3cf4b17c84325ef20e89986ee58796 |
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/main/models.py | Python | apache-2.0 | 23,302 | [
"Galaxy"
] | b0d0ff80a3388770c2ca8a963f89784c87389dca918fbef2941315d84e16794f |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Calculate properties of nuclei based on data parsed by cclib."""
import logging
import numpy as np
from cclib.method... | cclib/cclib | cclib/method/nuclear.py | Python | bsd-3-clause | 7,024 | [
"cclib"
] | c8bd8ad3ae7ad80c2d1c3c99fff1c1f0120aab4db77dc083cb6dce6327f54107 |
"""Functionality to query and extract information from aligned BAM files.
"""
import collections
import contextlib
import os
import itertools
import subprocess
import numpy
import pysam
import toolz as tz
from bcbio import utils
from bcbio.bam import ref
from bcbio.distributed import objectstore
from bcbio.distribute... | verdurin/bcbio-nextgen | bcbio/bam/__init__.py | Python | mit | 16,689 | [
"pysam"
] | ecdd8d9ba9cbb375291d734e85521bbfcec236b5f8c823a1e85a9859491ad297 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# Copyright: (c) 2015, Brian Coca <bcoca@ansible.com>
# Copyright: (c) 2016-2017, Konstantin Shalygin <k0ste@k0ste.ru>
# Copyright: (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING... | s-hertel/ansible | lib/ansible/modules/find.py | Python | gpl-3.0 | 17,400 | [
"Brian"
] | 4effbbf02c957b3cc58b1230b2876e996378431dd102f5f0bb6553e0a8e38de9 |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
import logging
from odoo import api, fields, models, tools, SUPERUSER_ID, _
from odoo.http import request
from odoo.addons.website.models import ir_http
from odoo.addons.http_routing.models.ir_http import url_for
_log... | ddico/odoo | addons/website_sale/models/website.py | Python | agpl-3.0 | 19,792 | [
"VisIt"
] | c1cf8aa447c92cd54a81419b98cec525cab70f2e3ada9ed06cb3ecec5d97056d |
# Copyright 2009-2014 Eucalyptus Systems, Inc.
#
# 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; version 3 of the License.
#
# This program is distributed in the hope that it will be useful,
# ... | eucalyptus/eucalyptus-database-server | eucadb/euca_db_postgresql.py | Python | bsd-2-clause | 11,929 | [
"VisIt"
] | d3a5da48b8e03eb13f8d706130d59c4753bae02f035ea868af0bff07991caff9 |
# -*- coding: utf-8 -*-
#
# evaluate_aeif_cond_alpha_RK5.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 o... | kristoforcarlson/nest-simulator-fork | pynest/examples/evaluate_aeif_cond_alpha_RK5.py | Python | gpl-2.0 | 6,745 | [
"NEURON"
] | 709a44403fdb6b24a3af3598c5e30fdb5d75717f52faa89685451a5fb8ec2289 |
#!/usr/bin/python
#
# @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 ... | andysim/psi4 | doc/sphinxman/document_psifiles.py | Python | gpl-2.0 | 3,241 | [
"Psi4"
] | ebf3e2eca2c8fe504c8426fbeed5c5893d0bddc67fa1f401be0dcf244567967e |
#!/usr/bin/env python
from __future__ import print_function
import optparse
import os
import os.path
import re
import shutil
import sys
parser = optparse.OptionParser()
parser.add_option('-d', '--export_dir', help='Directory where to export the datasets')
parser.add_option('-p', '--dir_prefix', help='How the export d... | PerlaTroncosoRey/tgac-galaxytools | tools/export_to_cluster/export_to_cluster.py | Python | mit | 1,903 | [
"Galaxy"
] | aed5344dbd7f7f0bc3a348decc467562cfacf6c515c347463fe143c6eb44ca5c |
#!/usr/bin/env python3
# ******************************************************************************
# $Id: gdal_sieve.py 124baa7f71f15396a661014a81b6c5b0c82c8004 2020-10-14 17:29:39 +0300 Idan Miara $
#
# Project: GDAL Python Interface
# Purpose: Application for applying sieve filter to raster data.
# Author:... | grueni75/GeoDiscoverer | Source/Platform/Target/Android/core/src/main/jni/gdal-3.2.1/swig/python/osgeo/utils/gdal_sieve.py | Python | gpl-3.0 | 7,486 | [
"NetCDF"
] | c7e6033e80a3ae20e6646c1bb79f1d5d79fab2114a4ca8443b4923e1c7afa058 |
#
# Copyright 2014-2015, 2021 Lars Pastewka (U. Freiburg)
# 2015 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General P... | libAtoms/matscipy | scripts/fracture_mechanics/quasistatic_crack.py | Python | lgpl-2.1 | 7,575 | [
"ASE",
"Matscipy"
] | 06a71c21cf5c5ceddb4ef956c68de88c161009c4b870a4d2a8b54132635cf0c5 |
"""
Set of utilities to retrieve Information from proxy
"""
import base64
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Security.X509Chain import X509Chain, g_X509ChainType
from DIRAC.Core.Security.VOMS ... | andresailer/DIRAC | Core/Security/ProxyInfo.py | Python | gpl-3.0 | 6,112 | [
"DIRAC"
] | 9766e042c7ba864fdba4c7d610483b2c45ce0827840fcfff075251b68248d3f9 |
########################################################################
# File : ARCComputingElement.py
# Author : A.T.
# Update to use ARC API : Raja Nandakumar
########################################################################
""" ARC Computing Element
Using the ARC API now
"""
from __future__ import ab... | yujikato/DIRAC | src/DIRAC/Resources/Computing/ARCComputingElement.py | Python | gpl-3.0 | 23,252 | [
"DIRAC"
] | 2ae7d9551a91974a16208cce1be8c3189fed681400e3ca019571eba2169db36e |
# Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: Apache-2.0
from typing import List, Tuple
import numpy as np
from emukit.core.loop.user_function import UserFunctionWrapper
def circular_gaussian(
mean: np.float = 0.0, variance: np.float = 1.0
) -> Tuple[User... | EmuKit/emukit | emukit/test_functions/quadrature/circular_gaussian.py | Python | apache-2.0 | 1,464 | [
"Gaussian"
] | 23fcdfdf651d13ed09d3ea6aa49f1acbdf29435b9b2e0022b0d5825f4e07256f |
"""Collection of :class:`~chainer.Function` implementations."""
from chainer.functions.activation.clipped_relu import clipped_relu # NOQA
from chainer.functions.activation.clipped_relu import ClippedReLU # NOQA
from chainer.functions.activation.crelu import crelu # NOQA
from chainer.functions.activation.crelu impor... | kashif/chainer | chainer/functions/__init__.py | Python | mit | 18,849 | [
"Gaussian"
] | 4b1001a51409370d98fdc73095f4a274e5b89774cb1cfc1df64e44f9d946a3fc |
""" Accounting Type for Pilot Submission
Filled by the "WorkloadManagement/SiteDirector" agent(s)
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseAccountingType
__RCSID__ = "$... | yujikato/DIRAC | src/DIRAC/AccountingSystem/Client/Types/PilotSubmission.py | Python | gpl-3.0 | 1,423 | [
"DIRAC"
] | cb16d7d885a5a5ff5c72a3eb0e5d28c13e5d02cde42390557d87b951be0e54b3 |
# -*- coding: utf-8 -*-
#
# Copyright 2019-2021 Ramil Nugmanov <nougmanoff@protonmail.com>
# This file is part of CGRtools.
#
# CGRtools 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 versi... | stsouko/CGRtools | CGRtools/utils/__init__.py | Python | lgpl-3.0 | 1,070 | [
"RDKit"
] | 77427f2c473831479f539f7e40b4853e13a8a5549c90d7f37a52643a9af8754b |
# Copyright 2018 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 | tldap/query.py | Python | gpl-3.0 | 5,378 | [
"Brian"
] | cf16a1da0087f98afc057731aa06e74a9c2adfb1332392ce1d8b5b9ea28988b6 |
from __future__ import print_function, absolute_import
import os
import argparse
import time
import matplotlib.pyplot as plt
import torch
import torch.nn.parallel
import torch.backends.cudnn as cudnn
import torch.optim
import torchvision.datasets as datasets
import _init_paths
from pose import Bar
from pose.utils.lo... | bearpaw/pytorch-pose | example/main.py | Python | gpl-3.0 | 17,704 | [
"Gaussian"
] | ad3aa79b0e94de28640145ccf756947983f8be56150310d36cc6a910b114cd43 |
# Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: Apache-2.0
import logging
from typing import List, Optional, Sequence, Tuple
import numpy as np
from .. import (
CategoricalParameter,
ContinuousParameter,
DiscreteParameter,
OneHotEncoding,
Ordin... | EmuKit/emukit | emukit/core/optimization/local_search_acquisition_optimizer.py | Python | apache-2.0 | 9,635 | [
"Gaussian"
] | 47f2564b2132c52dce42622bef2f7ea81675eb8186c4fa5b3b6d99024a8801f8 |
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #
# (c) 2010... | Chuban/moose | python/chigger/base/ChiggerFilterSourceBase.py | Python | lgpl-2.1 | 5,979 | [
"MOOSE",
"VTK"
] | 015bfbf229d22d4ba85556ec9100cd9078de2d08f2fa1893ac558f4fa52bfa8c |
##
# Copyright 2009-2016 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://vscentrum.be/nl/en),
# Flemish Research Foundation ... | wpoely86/easybuild-easyblocks | easybuild/easyblocks/c/cp2k.py | Python | gpl-2.0 | 32,451 | [
"CP2K"
] | 0959c36a8953d7963c23030a762e78001444e31f14892ad18a29b97e74c4704c |
# -*- 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 Gen... | jchodera/cclib | src/cclib/method/cspa.py | Python | lgpl-2.1 | 4,002 | [
"cclib"
] | 1256f15df7c38d3824e1d00d3ba7740cd0f9cf8cab9c7647d2429db0619c7d29 |
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
TensorGlyph()
| jeromevelut/Peavip | Testing/TensorGlyph.py | Python | gpl-3.0 | 124 | [
"ParaView"
] | ab67117f7645132d01f953633425764337a13c82c70dbc2dacc81f68409eb3ab |
#testsignal.py - generate some multi-dimensional test signals
#
#Author: Michael A. Casey
#Copyright (C) 2010 Bregman Music and Audio Research Studio
#Dartmouth College, All Rights Reserved
#
# A collection of test signal generators
#
# Bregman - python toolkit for music information retrieval
__version__ = '1.0'
__au... | folkengine/bregman | testsignal.py | Python | gpl-2.0 | 13,996 | [
"Gaussian"
] | 06d91f3293c38c7d398fcfb1e2f662fa08b80d368f2d8d79c1d403b87af9625d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
#
# 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 Licens... | caphrim007/ansible | lib/ansible/modules/network/cnos/cnos_image.py | Python | gpl-3.0 | 9,681 | [
"VisIt"
] | 9bbbbff32f79a5a68559fc0db04438481d5d47975962ddc08206a13a84846502 |
"""
Class for outlier detection.
This class provides a framework for outlier detection. It consists in
several methods that can be added to a covariance estimator in order to
assess the outlying-ness of the observations of a data set.
Such a "outlier detector" object is proposed constructed from a robust
covariance es... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/sklearn/covariance/outlier_detection.py | Python | mit | 6,611 | [
"Gaussian"
] | 57902aba710dab6a2a5611f25d918a597b811bbc9548968bc13d7d35eda0ff20 |
# 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... | michellemorales/OpenMM | models/lfads/lfads.py | Python | gpl-2.0 | 85,893 | [
"Gaussian"
] | d070694c9918cea141720f87244ed48d3137819802482e254bd383850caf45dc |
# -*- coding: utf-8 -*-
"""
The tools.py module contains generic functions that
are not specific to the Damon class, but used by it.
It is a module in the damon1 package.
"""
# Import system modules
import os
import sys
# Import numpy and other python modules
#import cPickle
import numpy as np
import numpy.random as... | Sohojoe/damon | damon1/tools.py | Python | apache-2.0 | 544,963 | [
"Gaussian"
] | fb360a59dc38b46a78ef46c184fe71b7a8619361fdad7287b8b86d6252e06c82 |
from __future__ import absolute_import, print_function
import sqlite3
import numpy as np
from ase.db import IdCollisionError
from ase.db.core import NoDatabase, ops
from ase.db.json import encode, decode
init_statements = """\
create table systems (
id text primary key,
unique_id text unique,
timestamp ... | grhawk/ASE | tools/ase/db/sqlite.py | Python | gpl-2.0 | 12,185 | [
"ASE"
] | 10e667b0bae02aea8c2a85ec213bd016793cb44e2f867fa151223de8bca52629 |
#!/usr/bin/python3
#
# Copyright (c) 2016 Mikkel Schubert <MikkelSch@gmail.com>
#
# 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
... | MikkelSchubert/paleomix | paleomix/pipelines/zonkey/pipeline.py | Python | mit | 22,698 | [
"pysam"
] | 1eb5ec3bf150440b8340c1c30a1c7f46bf430225906f6d676dbb2f211d365edc |
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