text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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import os
from fontbakery.profiles.universal import UNIVERSAL_PROFILE_CHECKS
from fontbakery.status import INFO, WARN, ERROR, SKIP, PASS, FAIL
from fontbakery.section import Section
from fontbakery.callable import check, disable
from fontbakery.utils import filesize_formatting
from fontbakery.message import Message
fr... | googlefonts/fontbakery | Lib/fontbakery/profiles/googlefonts.py | Python | apache-2.0 | 256,747 | [
"VisIt"
] | 24e8be321d7f4cb0c474937d7bd82eeb6909b429abb1eb9acc58a1546922fb59 |
#########################################################################################
# Condor.py
# 10.11.2014
# Author: A.T.
#########################################################################################
""" Condor.py is a DIRAC independent class representing Condor batch system.
Condor objects are... | andresailer/DIRAC | Resources/Computing/BatchSystems/Condor.py | Python | gpl-3.0 | 8,224 | [
"DIRAC"
] | f7b12909450f2579efec222d40504dc4f25e1df9172f4216cfef3a3ce66b85bd |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
#
# 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; eith... | pmghalvorsen/gramps_branch | gramps/gen/plug/_plugin.py | Python | gpl-2.0 | 2,326 | [
"Brian"
] | 08ff728a252809891fbc10dd79ebdcd70f7c30b101b51bfc6de9ef482f0df18a |
"""
Classes to handle the .bed files
"""
import os
import os.path as op
import sys
import math
import logging
import numpy as np
from collections import defaultdict, OrderedDict
from itertools import groupby
from more_itertools import pairwise
from natsort import natsorted, natsort_key
from jcvi.formats.base import ... | tanghaibao/jcvi | jcvi/formats/bed.py | Python | bsd-2-clause | 71,192 | [
"BLAST"
] | ca06820e181ceb045ca587d204870fa016558ec2e2b128f6a5b68d84a60ebfc5 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
""" Module: LayerTriangulation
==========================
"""
from __future__ import print_function
from . import Observable
import numpy as np
from pytim import utilities
class LayerTr... | balazsfabian/pytim | pytim/observables/layer_triangulation.py | Python | gpl-3.0 | 3,242 | [
"MDAnalysis"
] | fd955db8aa481466d65e41f873ecd5ca3ff7c1951adf704783167a7707f9e524 |
# -*- coding: utf-8 -*-
"""Various Statistical Tests
Author: josef-pktd
License: BSD-3
Notes
-----
Almost fully verified against R or Gretl, not all options are the same.
In many cases of Lagrange multiplier tests both the LM test and the F test is
returned. In some but not all cases, R has the option to choose the ... | Averroes/statsmodels | statsmodels/sandbox/stats/diagnostic.py | Python | bsd-3-clause | 53,492 | [
"ADF"
] | a205bd11b7efb8a15021a857159c68b09bb43be7968dd6e24be6347b02c7b59a |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | tmerrick1/spack | var/spack/repos/builtin/packages/nco/package.py | Python | lgpl-2.1 | 3,016 | [
"NetCDF"
] | d002681dbe80269b83448e5a53dd2f22ef7ef325efbbe24ee3777ddef69bcc30 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import math
import itertools
import warnings
from functools import reduce
from math import gcd
from fractions import Fraction
from typing import List, Union, Dict, Tuple, Iterator, Optional
from pymatgen.uti... | dongsenfo/pymatgen | pymatgen/core/lattice.py | Python | mit | 47,498 | [
"ABINIT",
"CRYSTAL",
"pymatgen"
] | a09eb325a0560661dca6c182073dcf9686621d92a59570abd165563552cbf151 |
# -*- coding: utf-8 -*-
tlds = {
'casa',
'tc',
'cu',
'pro',
'xn--lgbbat1ad8j',
'rentals',
'meme',
'recipes',
'museum',
'xn--io0a7i',
'caravan',
'cn',
'is',
'sohu',
'dad',
'mm',
'bm',
'adult',
'lgbt',
'build',
'okinawa',
'sz',
'works',
'pub',
'rio',
'dz',
'technology... | jaredlunde/vital-tools | vital/debug/tlds.py | Python | mit | 9,174 | [
"MOE"
] | a0e04b6dc9e3ca71c0f4d98ed97d5d1139903fe0e4e1ff009905463aa4322c2e |
import urllib.request
import urllib.parse
import json
import time
import datetime
import sys
country = [['cn', "中国"], ["af", "阿富汗"], ["al", "阿尔巴尼亚"], ["dz", "阿尔及利亚"], ["us", "美国"], ["ad", "安道尔"], ["ao", "安哥拉"],
["ag", "安提瓜和巴布达"], ["ae", "阿联酋"], ["ar", "阿根廷"], ["am", "亚美尼亚"], ["au", "澳大利亚"], ["at", "奥地利... | jerry-sc/jerry-sc.github.io | home-map/baidu_tongji.py | Python | apache-2.0 | 6,552 | [
"VisIt"
] | 18db8df840e9dfd9c1b0bf01b4e8a931490569f15ddcf81673ae0d003fc507a8 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | marscher/mdtraj | MDTraj/formats/hdf5.py | Python | lgpl-2.1 | 39,801 | [
"MDTraj",
"OpenMM"
] | 5309ea060e4796c14d2d9056f1ac7c0da9dd9e654dd3b0662ed5a61cfca56702 |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008-2011 Daniel Moisset, Ricardo Quesada, Rayentray Tappa,
# Lucio Torre
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the... | eevee/cocos2d-mirror | cocos/director.py | Python | bsd-3-clause | 25,767 | [
"VisIt"
] | 5f542a74d5025658b1b2c530362cec32731b17529ee7d838d6245b7cf9959c18 |
"""
Autopsy Forensic Browser
Copyright 2019-2021 Basis Technology Corp.
Contact: carrier <at> sleuthkit <dot> org
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... | sleuthkit/autopsy | InternalPythonModules/android/fbmessenger.py | Python | apache-2.0 | 28,861 | [
"ORCA"
] | 4d8b6918bfd8824bc99d0622e0e630bffff05fce95af686118928ab7b6089cac |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License, Vers... | sparkslabs/kamaelia_ | Code/Python/Kamaelia/Kamaelia/Device/DVB/Core.py | Python | apache-2.0 | 17,299 | [
"CRYSTAL"
] | 5ab7c2345924e9381a2727cf643100ed5369dd7d12863414963fcf4138bec343 |
# -*- coding: utf-8 -*-
"""
@author: Oleg Ovchinnikov
"""
from __future__ import division, print_function, absolute_import
def apply_select_channel(file_in_h5,img_num,channel_num):
import numpy as np
import h5py as h5
main_h5_handle = h5.File(file_in_h5,'r+')
image_path="/Frame_%04i/Channel_%02i... | anugrah-saxena/pycroscopy | pycroscopy/processing/atom_finding.py | Python | mit | 39,056 | [
"Gaussian"
] | f0ba192e73f88d4ce24f8d7eac68824db9855eb31c8aafff49ef800aca496eed |
import cgi
from webob import Request, Response
from webob.exc import HTTPNotFound
import json
import functools
import logging
from .validator import validate_args, ValidationError
from .utils import json_encode, is_file, FileIter
from .version import __version__
import threading
from wsgiref.simple_server import make_s... | rorodata/firefly | firefly/app.py | Python | apache-2.0 | 8,353 | [
"Firefly"
] | bf9ba8d36d057356b68f599760d61e4c41690856539a4ef02811600a9ace2af6 |
#!/usr/bin/env python2
from sepath_core import *
from itertools import chain, islice
import re
import optparse
import sys
import numpy
import pysam
if __name__ == "__main__":
optParser = optparse.OptionParser(
usage = "%prog [options] alignment_file annotation_file",
description = \
... | mcieslik-mctp/sepath | sepath_isize.py | Python | gpl-2.0 | 4,948 | [
"HTSeq",
"pysam"
] | b22831a6de3022dc214e1202be317557eff7bc18bb00811786a63276c7a2c04b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2014-2015 Bitergia
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any la... | MetricsGrimoire/Octopus | setup.py | Python | gpl-3.0 | 1,147 | [
"Octopus"
] | 95a9670e8269f6bf0bc2b1225e6337ac421f3cf64192613c5b2dc9c9fde9f875 |
# Copyright 2013-2017, Brian May
#
# This file is part of python-alogger.
#
# python-alogger 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 ver... | Karaage-Cluster/python-alogger | alogger/__init__.py | Python | gpl-3.0 | 2,061 | [
"Brian"
] | 69d4c69cad3535f457bbac7ac6f7fd847f051b3c89ea9ecde6a2ec47619939a4 |
from numpy import *
import itertools
import time
import sys
# Import NN utils
from nn.base import NNBase
from nn.math import softmax, sigmoid
from nn.math import MultinomialSampler, multinomial_sample
from misc import random_weight_matrix
class RNNLM(NNBase):
"""
Implements an RNN language model of the form:... | kingtaurus/cs224d | old_assignments/assignment2/rnnlm.py | Python | mit | 6,981 | [
"Gaussian"
] | 94b3529cefb3902cce77278f09752ad07cadda030176bb7bded437cdd404420d |
# -*- coding: utf-8 -*-
# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry
# and reaction kinetics.
# Copyright (C) 2008-2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, An Ghysels
# <An.Ghysels@UGent.be> and Matthias Vandichel <Matthias.Vandichel@UGent.be>
# Center for Molecular Modeling... | molmod/tamkin | tamkin/rotor.py | Python | gpl-3.0 | 30,185 | [
"Gaussian"
] | 8d3d140548b48788b96d0186baa5ea8ef0487a98157ea9fe26c24f0106d21a61 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2015 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | eustislab/horton | horton/grid/test/test_uniform.py | Python | gpl-3.0 | 25,737 | [
"Gaussian"
] | b57aa23e0a38d48be2c0a2182bd13cce71f4aea4e3eff2169441f0f1bd492a3f |
# Copyright (C) 2008 Brailcom, o.p.s.
#
# 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 distributed ... | razr/opentts | src/api/python/opentts_config/config.py | Python | lgpl-2.1 | 36,227 | [
"ORCA"
] | 8f7d824f01ee9a12f26084f8e547fa4702de2afbae58999fbd6d3382ecd17ebc |
from collections import OrderedDict
from edc.constants import NOT_REQUIRED, ADDITIONAL
from edc.subject.visit_schedule.classes import (VisitScheduleConfiguration, site_visit_schedules,
MembershipFormTuple, ScheduleGroupTuple,
... | botswana-harvard/edc-bhp074 | bhp074/apps/eit_maternal/visit_schedule/eit_maternal_post_natal.py | Python | gpl-2.0 | 2,661 | [
"VisIt"
] | 09f868a74542921d3fddf7a2180d34af5615d5702a26f60302e6b482639a54a4 |
import math as m
import numpy as N
from scipy.constants import k, c
import lineshapes
def bimodal_voigt(transitions, fwhm_p):
def func(x, T, amp, drift):
# Pressure broadening/lorentzian part of profile
f = 0
V = lineshapes.voigt
# Assumes origin is located at the center of the firs... | l3enny/lasana | models.py | Python | mit | 2,258 | [
"Gaussian"
] | a410b3f328db5fb48a24fc860ee0efc2dcbe8358a97c36590d9c2ae0b6a80b97 |
# -*- coding: utf-8 -*-
# This is a list of words used by the word builder and word maze games and possibly other games built in the future
# these words are a naive translation of a part of most commonly used words in English in each sub-list in the list di
# first number is a number of words in the sub-list to avoid... | imiolek-ireneusz/eduActiv8 | i18n/custom/word_lists/fr_di.py | Python | gpl-3.0 | 5,017 | [
"FLEUR"
] | 7f7885c0db378ad1e407577547b86c5e39ad6dbd6c21e286688b1dbbe332739f |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse
import sys
import fnmatch
import os
import dma_resolver
import shlex
import pickle
import re
import shutil
import filecmp
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help=... | samuelctabor/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 95,211 | [
"CRYSTAL"
] | db6601a2f53d663409af8202239b3b95eb01e9dda99d2a9b2d4e6a2260e5c762 |
#!/usr/bin/python
"""Test of label guess functionality."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
sequence.append(KeyComboAction("<Control>Home"))
sequence.append(utils.StartRecordingAction())
sequence.append(KeyPressAction(0, None, "KP_Insert"))
sequence.append(KeyComboAction("Tab... | pvagner/orca | test/keystrokes/firefox/label_inference_mailman.py | Python | lgpl-2.1 | 6,393 | [
"VisIt"
] | aa3877e43b160b4bb7368f5b3f2cc16417798180ba41a1ed2c83e7d4a7aa7c37 |
import sys, string, base64
def alphabet_gen(key=""):
lowercase = list(string.ascii_lowercase)
uppercase = list(string.ascii_uppercase)
if key:
key = list(key)
key.reverse()
for char in key:
if char in lowercase or char in uppercase:
lowercase.insert(0, l... | yooow0t/message-encoder | message-encoder.py | Python | mit | 5,365 | [
"VisIt"
] | 49725e124eee20eee0128e7a1e1090689e8e147795dbf22db9dcf4c87a9d805e |
# -*- coding: utf-8 -*-
#
# two_neurons.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or... | flinz/nest-simulator | examples/nest/gap_junction/two_neurons.py | Python | gpl-2.0 | 2,714 | [
"NEURON"
] | 288c3f672da6aa9a4805075dc8b665f2b535f8e02c5d88bedc9b6c04e1f788a5 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/test/bigdl/orca/automl/xgboost/test_auto_xgb.py | Python | apache-2.0 | 7,653 | [
"ORCA"
] | 35d5c3de490a13a36342665a7117e9e70aab173b6135506d97ac1a7ca1eeda3d |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | rangadi/beam | sdks/python/apache_beam/runners/portability/fn_api_runner.py | Python | apache-2.0 | 68,611 | [
"VisIt"
] | 12c6a4e245cabf2ae2caf841db868c4faaa88fda9c24dce79ceb9e2f9751f580 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# create a scene with one of each ... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Rendering/Core/Testing/Python/pickCells.py | Python | gpl-3.0 | 16,540 | [
"VTK"
] | 7f6e93ea61c664ed219c3b3624f4794d017d10605b42b2248ae14db68b54969c |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import functools
import glob
import itertools
import jinja2
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import time
import urllib2
import zlib
from xml.etree import ElementTree
from cStringIO import Stri... | browseinfo/odoo_saas3_nicolas | addons/web/controllers/main.py | Python | agpl-3.0 | 76,064 | [
"VisIt"
] | b0ce15123d6ddf3808d272f13e9b71a39f4e2d651eae929894a2fa98432fa904 |
"""
This is only meant to add docs to objects defined in C-extension modules.
The purpose is to allow easier editing of the docstrings without
requiring a re-compile.
NOTE: Many of the methods of ndarray have corresponding functions.
If you update these docstrings, please keep also the ones in
core/fromnum... | ekalosak/numpy | numpy/add_newdocs.py | Python | bsd-3-clause | 222,615 | [
"Brian"
] | e7e798d973d99737581fcbf5e860d2cafeb3086d2271b07d4ebd167180f4a4b8 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import json
import frappe.utils
from frappe.utils import cstr, flt, getdate, comma_and, cint, nowdate, add_days
from frappe import _
from ... | ESS-LLP/erpnext-medical | erpnext/selling/doctype/sales_order/sales_order.py | Python | gpl-3.0 | 33,510 | [
"VisIt"
] | c523e2a48b4b030be001852d911158164df044e9e21d65c978672349cad747d0 |
#!/usr/bin/env python
import os
import sys
import csv
import time
import coards
import datetime
import numpy as np
from pupynere import netcdf_file
class ParserWriter(object):
'''
Handle all information needed to parse LR Waveglider CSV files and produce
NetCDF for each of them
'''
def __init__(... | stoqs/stoqs | stoqs/loaders/MarMenor/toNetCDF/plain2netcdf.py | Python | gpl-3.0 | 4,875 | [
"NetCDF"
] | fe14ad9f8ac5fa181a859c13916f6608587eafe912db37a3d20b7b81fec2f855 |
"""
import report
description = report.get_description()
print("Today's weather :", description)
"""
"""
import report as wr
description = wr.get_description()
print("Today's weather:", description)
"""
"""
from report import get_description
description = get_description()
print("Today's weather:", description)
"""
... | serggrom/python-projects | Part5.py | Python | gpl-3.0 | 3,884 | [
"MOE"
] | 5ea999b4cfbab6259c9f6e50f18fa88bb2e1c6840b31974ae0c7c0a2c935cc49 |
from neat import activations
from neat.nn import RecurrentNetwork
def assert_almost_equal(x, y, tol):
assert abs(x - y) < tol, "{!r} !~= {!r}".format(x, y)
def test_unconnected():
# Unconnected network with no inputs and one output neuron.
node_evals = [(0, activations.sigmoid_activation, sum, 0.0, 1.0,... | drallensmith/neat-python | tests/test_recurrent_network.py | Python | bsd-3-clause | 1,591 | [
"NEURON"
] | 293b2bf590bdbce2a396468d4fe026b93752fdd5cad8bb5e942cbdf78adabda8 |
# $Id: __init__.py 77 2008-03-18 16:32:47Z mp $
#
# Copyright (c) 2007-2008 ReThought Limited and Peloton Contributors
# All Rights Reserved
# See LICENSE for details
""" Plugins directory containing Peloton Core plugins that form
part of the distribution.
Peloton plugins hook into the main event loop so must be tho... | aquamatt/Peloton | src/peloton/plugins/__init__.py | Python | bsd-3-clause | 3,747 | [
"exciting"
] | 34569d1a9f5c5d19aa7231ba27a487bb12abb9853cf5519945e2225197940d05 |
# An example of embedding CEF browser in wxPython on Linux.
import ctypes, os, sys
libcef_so = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'libcef.so')
if os.path.exists(libcef_so):
# Import local module
ctypes.CDLL(libcef_so, ctypes.RTLD_GLOBAL)
if 0x02070000 <= sys.hexversion < 0x03000000:
... | drmelectronic/Despacho | wxpython.py | Python | bsd-3-clause | 20,420 | [
"VisIt"
] | dd860b4cbc53be3632d109d8979229fb33a725de04fc8274f84f70d624214303 |
import pytest
import psi4
import numpy as np
def test_pdms():
h2o = psi4.geometry("""
H
H 1 0.7
""")
psi4.set_options({"opdm": True, "num_roots": 3})
wfn = psi4.energy("fci/cc-pvdz", return_wfn=True)[1]
# Okay, I need three matrix comparisons...
ref_opdm = psi4.core.Matrix.fro... | jgonthier/psi4 | tests/pytests/test_detci_opdm.py | Python | lgpl-3.0 | 1,876 | [
"Psi4"
] | 922bf6e033071a524cd80d82e3c1cd823d9ac9627c558df334d9d922e85200ac |
# Generated from C:\Users\Akira\Documents\python_code\github\antlr4_tex2sym-master\TeX2Sym.g4 by ANTLR 4.7.2
from antlr4 import *
if __name__ is not None and "." in __name__:
from .TeX2SymParser import TeX2SymParser
else:
from TeX2SymParser import TeX2SymParser
# This class defines a complete generic vi... | AkiraHakuta/antlr4_tex2sym | gen/TeX2SymVisitor.py | Python | mit | 6,918 | [
"VisIt"
] | 0494a142726a0c946adb108f7e86d92da2a2d160208c1a261b5d077b08100941 |
# Copyright (c), Michael DeHaan <michael.dehaan@gmail.com>, 2012-2013
# Copyright (c), Toshio Kuratomi <tkuratomi@ansible.com> 2016
# Simplified BSD License (see licenses/simplified_bsd.txt or https://opensource.org/licenses/BSD-2-Clause)
SIZE_RANGES = {
'Y': 1 << 80,
'Z': 1 << 70,
'E': 1 << 60,
'P': 1... | drmrd/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 116,373 | [
"VisIt"
] | c61755c3f02efd62df0ff8f35c28194eb47ae1796a87a901b4971fad986a7ec0 |
#!/usr/bin/env python3
# coding: utf-8
from __future__ import unicode_literals
from collections import Counter
from molbiox.algor import interval
def find_next_contigs(samfile, contig, insertmax, orientation='fr'):
"""
:param samfile: pysam.calignmentfile.AlignmentFile object
:param contig: cont... | frozflame/molbiox | molbiox/algor/mapping2.py | Python | gpl-2.0 | 2,239 | [
"pysam"
] | 24fe5a33be5e449e5cf657390f077e10c406bae78a31c4aea7d077f14fe3d4be |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2010-2012 Gary Burton
# GraphvizSvgParser is based on the Gramps XML import
# DotSvgGenerator is based on the relationship graph
# report.
# ... | sam-m888/addons-source | GraphView/graphview.py | Python | gpl-2.0 | 154,196 | [
"FLEUR"
] | a3df45abe89d33c6a8a3ae103fd7cf9e3c3f923e437f1575cf38a79abe92a92b |
#!/usr/local/bin/python
'''
Post compromised credentials to ThreatExchange
'''
from __future__ import print_function
import argparse
import hashlib
import re
import time
from urllib import urlencode
from urllib2 import urlopen
FB_APP_ID = 'Your AppID Here'
FB_ACCESS_TOKEN = 'Your AccessToken Here'
SERVER = 'https:... | wxsBSD/ThreatExchange | threat_indicators/post_compromised_credentials.py | Python | bsd-3-clause | 3,918 | [
"Amber"
] | 56fd4a81791a086077a29bde48971944c288abe5a93cacf38d9e9ad58e9a11e9 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import unittest
from .estestcase import ESTestCase
from pyes.es import json
from pyes.query import *
from pyes.filters import TermFilter, ANDFilter, ORFilter, RangeFilter, RawFilter, IdsFilter, MatchAllFilter, NotFilter
from pyes.utils import ESRangeOp
cla... | rookdev/pyes | tests/test_queries.py | Python | bsd-3-clause | 23,663 | [
"MOE"
] | 1bd48473439f13fb78b5af300681199d1577c55c9a1683154ab6de7ad8ba5ca5 |
########################################################################
# File: FileCatalogHandler.py
########################################################################
"""
:mod: FileCatalogHandler
.. module: FileCatalogHandler
:synopsis: FileCatalogHandler is a simple Replica and Metadata Catalog service
"""... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/Service/TornadoFileCatalogHandler.py | Python | gpl-3.0 | 1,962 | [
"DIRAC"
] | a45dec7f615a0d371451bd28c5fefb68e8ed5d82565af3fceb5f0db1d030f972 |
# Natural Language Toolkit: Expectation Maximization Clusterer
#
# Copyright (C) 2001-2017 NLTK Project
# Author: Trevor Cohn <tacohn@cs.mu.oz.au>
# URL: <http://nltk.org/>
# For license information, see LICENSE.TXT
from __future__ import print_function, unicode_literals
try:
import numpy
except ImportError:
pa... | sdoran35/hate-to-hugs | venv/lib/python3.6/site-packages/nltk/cluster/em.py | Python | mit | 9,675 | [
"Gaussian"
] | 29cf23477488ff64d548a64ba686d58fc325b9f1976ddbe75cc5cce616789073 |
# ==================================================================================================
# Copyright 2012 Twitter, Inc.
# --------------------------------------------------------------------------------------------------
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... | foursquare/commons-old | src/python/twitter/pants/targets/python_requirement.py | Python | apache-2.0 | 1,645 | [
"Brian"
] | d7fd07239b175d8b992f96d06195331936b5199282eb153048dbc8d3bc48667c |
'''
Gaussian smoothing with Python.
'''
import cv2
import numpy as np
import math
import os
from scipy import signal
import matplotlib.pyplot as plt
def gaussian_filter(sigma, filter_length):
'''
Given a sigma, return a 1-D Gaussian filter.
@param sigma: float, defining the width of the filter
@para... | Vkomini/KU-Leuven | Computer Vision/Assignments/Assign1/smoothing1.py | Python | apache-2.0 | 2,402 | [
"Gaussian"
] | 0be300e168d8c536522cd40c53c55eaf760353bec3ef4e651961bbef072726be |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# icecream_survey.py
# EasyGUI example
# wolf@sourcefreedom.com
from random import randint
from easygui import *
import sys
while 1:
msgbox('''Hello, seeker!
There are many flavors of Ice Cream
This survey covers the most popular choices...''')
msgbox('''Ice cream... | wolf29/games | IceCream/Ice_Cream_Survey.py | Python | gpl-3.0 | 1,556 | [
"MOOSE"
] | 67e5128f168192d675aa042ad8bf019e483becd3651759d97c35dcd2bb145420 |
#
# @BEGIN LICENSE
#
# QCDB: quantum chemistry common driver and databases
#
# Copyright (c) 2011-2017 The QCDB Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of QCDB.
#
# QCDB is free software; you can redistribute it and/or modify
# it ... | cdsgroup/qcdb | qcdb/libmintsmolecule.py | Python | lgpl-3.0 | 126,691 | [
"Elk",
"Psi4"
] | e4a95e1278c841eee26506ff62fec4aed0c7f1544cc7c1adaa64cffab4a4b66a |
#!/usr/bin/env python
import matplotlib
from matplotlib.backends.backend_agg import FigureCanvasAgg
from matplotlib.figure import Figure,SubplotParams
from matplotlib.patches import Circle
from numpy import *
from models import genMWO
import StringIO
import Image
import urllib
import pickle
try:
import ephem3 as ep... | chrisrburns/obstool | navigator/plot_skyview_proj.py | Python | mit | 4,961 | [
"Galaxy"
] | ddcccbe4170f8968cb310d758c578c30a0a33fa7c60811c7896fab7ac6f1b101 |
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 11 23:37:05 2015
@author: Marcus Therkildsen
"""
from __future__ import division
import numpy as np
import matplotlib.pyplot as plt
from netCDF4 import Dataset
from mpl_toolkits.basemap import Basemap
import matplotlib.ticker
from matplotlib.dates import num2date
# from t... | MarcusTherkildsen/WeatherAnalysis | main.py | Python | mit | 3,069 | [
"NetCDF"
] | d803a0f5672602b677c4bc0d0ea1c6f5656c1c21b1ce2c39c4f9a16c824101cb |
#!/usr/bin/env python
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simu... | liuwenf/moose | python/MooseDocs/tests/common/builder/test_builder.py | Python | lgpl-2.1 | 2,441 | [
"MOOSE"
] | 179cff55227fb8be07c2d4d461eab658b758f19a1edce777172c25122c202833 |
#!/usr/bin/python
import numpy as np
import os
from glob import glob
import argparse
import subprocess
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.pyplot as plt
import matplotlib.tri as triang
import matplotlib.cm as cm
import readfiles
import parameterfile as pf
class cd:
def __init__(... | SijmeJan/Astrix | python/astrix/testsuite.py | Python | gpl-3.0 | 11,265 | [
"BLAST",
"VTK"
] | a4054b75ea2c620d618105b2a524f2893cd8e81cd58c5665d9b620d12f324b89 |
#!/usr/bin/env python
"""
Launch the File Catalog shell
Usage:
dirac-dms-filecatalog-cli [option]
Example:
$ dirac-dms-filecatalog-cli
Starting DIRAC FileCatalog client
File Catalog Client $Revision: 1.17 $Date:
FC:/>help
Documented commands (type help <topic>):
=======================================... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_filecatalog_cli.py | Python | gpl-3.0 | 2,138 | [
"DIRAC"
] | a92f602b1fa646b3b0a6b9849d271fca8759d7b8f09f2b5c8efeefe94123efed |
import numpy as np
from util import resolve, genson_dumps, get_global_seed, assert_kwargs_consumed
from internal_ops import GenSONOperand
from internal_ops import GenSONFunction
from internal_ops import registry
import logging
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)
def register_fun... | davidcox/genson | genson/functions.py | Python | mit | 8,655 | [
"Gaussian"
] | c885d22bfaa86eea0fce5ada6fe0a14a7752d9aa176e3268db795e4b63b12812 |
"""
Copyright (C) 2004-2015 Pivotal Software, Inc. All rights reserved.
This program and the accompanying materials are made available under
the terms of the 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
... | CraigHarris/gpdb | src/test/tinc/tincrepo/mpp/models/sql_tc.py | Python | apache-2.0 | 57,509 | [
"ORCA"
] | d110d2e34f48170052858d2b93504297d885a811cb49ea3cf74dfd1733a66997 |
#!/usr/bin/env python3
import os
import sys
import time
import logging
import argparse
import resource
import collections
import parallel_tools
import consensus
import swalign
import shims
# There can be problems with the submodules, but none are essential.
# Try to load these modules, but if there's a problem, load a ... | makrutenko/dunovo | make-consensi.py | Python | isc | 22,379 | [
"Galaxy"
] | 92e9ecd34e08f6a637852e3c3bae047be73341a3e68d4ba0792ce7d3a143809d |
'''
module of network Gaussian process constructors.
'''
import rbf.basis
import rbf.poly
from rbf import gauss
from pygeons.main.gptools import set_units,kernel_product
from pygeons.main import gpstation
# 2D GaussianProcess constructors
#####################################################################
def se(si... | treverhines/PyGeoNS | pygeons/main/gpnetwork.py | Python | mit | 6,313 | [
"Gaussian"
] | 1712a6c0a68e201cbc8074f718f070e21bccff9470fc8d3fdddb9e3d6085bb8d |
## \file
## \ingroup tutorial_roofit
## \notebook
##
## \brief Likelihood and minimization: visualization of errors from a covariance matrix
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
import ROOT
# Setup example fit
# ---------------------------------------
... | karies/root | tutorials/roofit/rf610_visualerror.py | Python | lgpl-2.1 | 6,823 | [
"Gaussian"
] | 403f959f9450d3972535601a6e6e736356923b08f6326d685696a623e65a2786 |
"""
Core visualization operations based on Mayavi.
Actual implementation of _Renderer and _Projection classes.
"""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric... | kambysese/mne-python | mne/viz/backends/_pysurfer_mayavi.py | Python | bsd-3-clause | 22,365 | [
"Mayavi",
"VTK"
] | 943203c5294f1a0b2bccd1d2f7c82e6ae2542cdbb131d042b8ec3f7dd9975a4c |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/map.py | Python | gpl-2.0 | 1,924 | [
"PyMOL"
] | 060b9ba98c604ea27718c29abaf7efd4bd952f96f169ee5f6c46013c039e9c13 |
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit http://feedparser.org/ for the latest version
Visit http://feedparser.org/docs/ for the latest documentation
Required: Python 2.1 or later
Recommended: Python 2.3 or later
Recommended: CJKCodecs and iconv_codec <http... | debugger06/MiroX | tv/lib/feedparser.py | Python | gpl-2.0 | 130,743 | [
"NetCDF",
"VisIt"
] | 37484ee57e33d6d0e68f68e98cb62c0a84223c7d2634984636d30bea1e56ed7c |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
# CREATED:2020-07-16 16:49:03 by Brian McFee <brian.mcfee@nyu.edu>
"""Unit tests for music notations"""
import os
import sys
try:
os.environ.pop("LIBROSA_CACHE_DIR")
except KeyError:
pass
import warnings
import numpy as np
import pytest
import librosa
@pytest.... | librosa/librosa | tests/test_notation.py | Python | isc | 6,664 | [
"Brian"
] | 300195c8649be4ba7c85cb2886f16b0b984af9e6217b83d2868e71d11a455264 |
#!/usr/bin/env python
"""
Creates a yaml file with all URL that needs to be downloaded, given a file with a list of all meta.yaml file.
Usage:
./get_urls.py meta_files.list
"""
import os
import sys
import yaml
# needs to be before the conda_build import
platform = sys.argv[2]
import conda.config as cc
cc.subdir... | gregvonkuster/cargo-port | .conda/get_urls.py | Python | mit | 1,707 | [
"Bioconda"
] | dbc6392b259a405df4be958632515f6d0039bae93c656b122c3e81037a544c56 |
# This module implements the basic class for pulses as well as some very
# generic pulse types.
#
# author: Wolfgang Pfaff
# Modified by: Sarwan Peiter
import numpy as np
from copy import deepcopy
def cp(pulse, *arg, **kw):
"""
create a copy of the pulse, configure it by given arguments (using the
ca... | yausern/stlab | devices/Tektronics_Sequencer/Pulse_lib.py | Python | gpl-3.0 | 17,847 | [
"Gaussian"
] | 6bd8f066c19a8fbe0a0319f5aeb6f6291d1f8d1cf0f061a5fb2ef52f0e583993 |
"""The FCOnly storage can only be used to register replicas in a FileCatalog.
It is used to preserve LFN metadata, no actual file content will be stored.
Example Configuration for Resources/StorageElement::
ARCHIVE-SE
{
BackendType = None
FCOnly
{
Access = remote
Protocol = dfc
}
}
... | andresailer/DIRAC | Resources/Storage/FCOnlyStorage.py | Python | gpl-3.0 | 1,686 | [
"DIRAC"
] | aea344d473c52944d31ef3e3a2a32147b98aa59802865b370e1422f9713ec626 |
import numpy as np
import itertools
from copy import deepcopy
import logging
log = logging.getLogger(__name__)
import pycqed.measurement.sweep_functions as swf
import pycqed.measurement.awg_sweep_functions as awg_swf
import pycqed.measurement.awg_sweep_functions_multi_qubit as awg_swf2
import pycqed.measurement.pulse_... | QudevETH/PycQED_py3 | pycqed/measurement/multi_qubit_module.py | Python | mit | 57,506 | [
"Gaussian"
] | faf33cff24c670142e8220d543b0b56f4a70ccbfd48424be9e64cc7ec7acb389 |
import sys, fileinput, os
from pythonparser import source, diagnostic, algorithm, parse_buffer
from .. import prelude, types
from ..transforms import ASTTypedRewriter, Inferencer, IntMonomorphizer, CastMonomorphizer
from ..transforms import IODelayEstimator
from ..validators import ConstnessValidator
class Printer(alg... | JQIamo/artiq | artiq/compiler/testbench/inferencer.py | Python | lgpl-3.0 | 3,622 | [
"VisIt"
] | 59a603357daabb6bdd793ccc9d4ea551fdc0965d50cb4468305e2967b625b5c7 |
##############################################################################
# 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... | skosukhin/spack | var/spack/repos/builtin/packages/r-graph/package.py | Python | lgpl-2.1 | 1,712 | [
"Bioconductor"
] | eebf372408abbf8f2e46a0721cf63a307933d3d16a5a00df279eb70391d25e0a |
"""
This module contain solvers for all kinds of equations:
- algebraic or transcendental, use solve()
- recurrence, use rsolve()
- differential, use dsolve()
- nonlinear (numerically), use nsolve()
(you will need a good starting point)
"""
from __future__ import print_function, division
f... | alephu5/Soundbyte | environment/lib/python3.3/site-packages/sympy/solvers/solvers.py | Python | gpl-3.0 | 104,914 | [
"Gaussian"
] | 93a9b0f4d6b9876e7fe99081840586481be4c935111a663ea2bce08f7e582dbe |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2002 Bruce J. DeGrasse
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2007 Robert Cawley <rjc@cawley.id.au>
# Copyright (C) 2008-2009 James Friedmann <jfriedm... | jralls/gramps | gramps/plugins/textreport/detdescendantreport.py | Python | gpl-2.0 | 51,153 | [
"Brian"
] | b50e77cf73a37b131fcff7e68f909f8092820a7ea8fba49eca01be9a4750d544 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import datetime
import glob
import operator
import optparse
import math
import os
import pyparsing
import re
import sys
import numbers
try: #Python 2.7
from collections import OrderedDict
except ImportError: # Python 2.6
from ordereddict import OrderedDict
try:
import s... | Public-Health-Bioinformatics/rcqc | rcqc.py | Python | cc0-1.0 | 44,146 | [
"Galaxy"
] | fae94aa3c50fb171023449545a50f9e8ce367a21ee94da5d24be21913fec5b12 |
# -*- coding: utf-8 -*-
# NOTE: the iso-8859-15 charset is not a mistake.
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an ... | yasharmaster/scancode-toolkit | src/commoncode/text.py | Python | apache-2.0 | 6,316 | [
"VisIt"
] | b00d1364924e91d4d66f1fe2b939d8fa2288743201d787718cac7afd9b8f387b |
# -*- coding: utf-8 -*-
"""
Shared functions for symbolic regression.
"""
#from SimpleMPI import MPI_map
## The grammar
#G.add_rule('CONSTANT', '', ['*gaussian*'], 10.0) ##TODO: HIGHLY EXPERIMENTAL
| ebigelow/LOTlib | LOTlib/Examples/SymbolicRegression/old/Shared.py | Python | gpl-3.0 | 204 | [
"Gaussian"
] | f663d3939023225c56fd8748265e8cd101dffe0ee1118baed1b8612e1980aa75 |
# 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 ... | liesbethvanherpe/NeuroM | neurom/viewer.py | Python | bsd-3-clause | 4,754 | [
"NEURON"
] | 79ba4f7b37f51214791bf652ef4010518d1234588e8ad9f455eddb4ce98ed18a |
import numpy as np
import scipy as sp
class Process:
"""Process description. It is implementing the
y(k+1) = u(k) + d(k)
where
- y(k) is the time that the process spent on the CPU
- u(k) is the time that the process is supposed to spend on the CPU
- d(k) is a disturbance related to critical sectio... | apapadopoulos/MultiCoreMigrationSimulator | libs/Process.py | Python | gpl-2.0 | 1,000 | [
"Gaussian"
] | 0c9398c57ece37c18a525afeee463518d2ac2beaa1a627be75e7bff3f4158e1a |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-appengine-admin | tests/unit/gapic/appengine_admin_v1/test_services.py | Python | apache-2.0 | 72,973 | [
"Octopus"
] | c5135ef5d8bd23d3790db3da19e02ea15d65922de668c574e87de37ec405b0c7 |
# Add the igl library to the modules search path
import sys, os
sys.path.insert(0, os.getcwd() + "/../")
import igl
# Load mesh
V = igl.eigen.MatrixXd()
F = igl.eigen.MatrixXi()
igl.readOFF("../../tutorial/shared/bumpy.off",V,F);
# Compute Gaussian curvature
K = igl.eigen.MatrixXd();
igl.gaussian_curvature(V,F,K);
... | sebastian-claici/AKVFParam | ext/libigl/python/tutorial/202_GaussianCurvature.py | Python | gpl-3.0 | 520 | [
"Gaussian"
] | 3e27ce1590c02373cd4a749e7af52b98d96712a2ba2dbc223758f0625274c6fc |
# -*- coding: utf-8 -*-
"""
@author: Jaap Verheggen, Guillaume Jacquenot
"""
from __future__ import division
import vtk
import numpy as np
import vtk.util.numpy_support as ns
import raytracer as ray
cosd = lambda angle: np.cos(angle / 180 * np.pi)
sind = lambda angle: np.sin(angle / 180 * np.pi)
tand = lambda angle:... | Gjacquenot/PyRayTracer | raytracer/raytrace-receiver2.py | Python | mit | 38,736 | [
"VTK"
] | af979893f60ec78a5503c21713eace0f3d17bd9ad15e6f21835e999d0b661da4 |
# -*- coding: utf-8 -*-
#
# test_parrot_neuron_ps.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the L... | lekshmideepu/nest-simulator | testsuite/pytests/test_parrot_neuron_ps.py | Python | gpl-2.0 | 10,622 | [
"NEURON"
] | 74c3cea213e068954775de0fe57149fc687e0aa7eeb49e6d0236bbfbe679b63b |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2016, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it
# u... | jtulach/mx | mx_javamodules.py | Python | gpl-2.0 | 17,050 | [
"VisIt"
] | ff773e44d97f6bd49b97eb729e64d7f69b95e5e8ca56f5bc44807ba7c97694b8 |
"""Crystal lattice specification"""
import itertools
import warnings
from copy import deepcopy
from math import pi, atan2, sqrt
import numpy as np
import matplotlib.pyplot as plt
from . import _cpp
from . import pltutils
from .utils import x_pi, with_defaults, rotate_axes
from .support.deprecated import LoudDeprecati... | MAndelkovic/pybinding | pybinding/lattice.py | Python | bsd-2-clause | 20,509 | [
"CRYSTAL"
] | 7dbd3183508cc782ac74586b166421a53931dd39f1cae284e82a2199ffdd47dc |
# moose.py ---
#
# Filename: moose.py
# Description: THIS IS OUTDATED CODE AND KEPT FOR HISTORICAL REFERENCE
# moose.py in this directory is the replacement for this
# script.
#
# Author: Subhasis Ray
# Maintainer:
# Copyright (C) 2010 Subhasis Ray, all rights reserved.
# Created: Sat Ma... | dilawar/moose-full | moose-core/python/moose/alternate.py | Python | gpl-2.0 | 40,055 | [
"MOOSE"
] | b9d98cff51d1e88b872a05c90774b764fe8576614a1bda2d2d29fc455b1e16dd |
import sys
from limix.core.mean import MeanKronSum
from limix.core.covar import Cov2KronSum
from limix.core.covar import Covariance
from limix.hcache import Cached, cached
import pdb
import numpy as NP
import scipy as sp
import scipy.linalg as LA
import time as TIME
from .gp_base import GP
from limix.core.covar.cov_re... | PMBio/limix | limix/core/gp/gp2kronSum.py | Python | apache-2.0 | 7,540 | [
"Gaussian"
] | 6b49bef4802413ca7771a0eeab425a06ef4902da7d0e48b9ed98e65a10163420 |
# Copyright 2018 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, s... | blowmage/gcloud-ruby | google-cloud-vision/synth.py | Python | apache-2.0 | 8,665 | [
"VisIt"
] | 4274995c8c17045c4381fc9c8bb5714a845e78ad94e19fd252b9c0f5fce272cb |
"""
Tests for QE DFT calculations.
"""
# pylint: disable=redefined-outer-name,unused-argument,protected-access
import os
import json
import shutil
import tempfile
import pytest
import numpy as np
import z2pack
@pytest.fixture(params=[z2pack.fp.kpoint.qe, z2pack.fp.kpoint.qe_explicit])
def qe_system(request, sample... | Z2PackDev/Z2Pack | tests/fp/test_espresso.py | Python | gpl-3.0 | 4,663 | [
"ESPResSo",
"Wannier90"
] | 9fc60be7eae48e2aee06a377a107f0387e4c087a6c2bb95f58d4e37250cb2bf8 |
"""Testing for kernels for Gaussian processes."""
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# License: BSD 3 clause
import numpy as np
from sklearn.utils.fixes import signature
from sklearn.gaussian_process.kernels import _approx_fprime
from sklearn.metrics.pairwise \
import PAIRWISE_KERNEL_FU... | BiaDarkia/scikit-learn | sklearn/gaussian_process/tests/test_kernels.py | Python | bsd-3-clause | 12,791 | [
"Gaussian"
] | 83d188972b0fc8abf2bf20a314787391920c536f68e72dc0ab6356b9becbc6c8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# @Author: Brian Cherinka, José Sánchez-Gallego, and Brett Andrews
# @Date: 2016-06-13
# @Filename: analysis_props.py
# @License: BSD 3-clause (http://www.opensource.org/licenses/BSD-3-Clause)
#
# @Last modified by: José Sánchez-Gallego (gallegoj@uw.edu)
# @Last modified ... | albireox/marvin | python/marvin/tools/quantities/analysis_props.py | Python | bsd-3-clause | 2,147 | [
"Brian"
] | 065407f8033f14335ef529cdd1355cfb7bb99a9010e86ebfad39773e6aa230ca |
# !usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-04-06 15:30:50
# @Last modified by: Brian Cherinka
# @Last Modified time: 2018-04-03 16:08:48
from __future__ import print_function, division, absolute_import
import os
import pytest
... | albireox/marvin | python/marvin/tests/web/frontend/conftest.py | Python | bsd-3-clause | 3,703 | [
"Brian"
] | 673afca8bd3e6027b50e34d4a6e62725292da7bcfffd14a7dd2df52924af5dea |
#!/usr/bin/env python
""" load Sample into OSDF using info from data file """
import os
import re
from cutlass.Sample import Sample
import settings
from cutlass_utils import \
load_data, get_parent_node_id, list_tags, format_query, \
write_csv_headers, values_to_node_dict, write_out_csv, \
load_node, get_field... | JAX-GM/osdf_submit | nodes/sample.py | Python | gpl-3.0 | 6,338 | [
"VisIt"
] | d2cf66c66b0dbd9ae9e080c065f007527a4d6fe3fefd0952711f0fe02bdaa7bc |
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 22 12:57:28 2016
@author: noel
"""
import os
import sys
import em.tools.CHARMM_Parser as CP
#import RTPParser as rp
class CenterOfMassCalculator(object):
def __init__(self,charmm_params):
self.mx_total = 0
self.my_total = 0
self.mz_total = 0
... | noelcjr/EntropyMaxima | em/describe/Molecular_Descriptors.py | Python | gpl-3.0 | 5,036 | [
"CHARMM"
] | 333d2596d6dab0fa57fbcd050e1a9dcff8ec87ea65dde9ddab29cb186f804a23 |
# -*- coding: UTF-8 -*-
""" Модуль для работы с нечеткими множествами.
Модуль реализует функциональность аппарата нечеткой логики в части работы с
нечеткими множествами. Он включает:
- абстрактный класс нечеткого множества,
- шаблоны для создания классификаторов различных видов.
В основном, модуль предназн... | sejros/PyInference | pyinference/fuzzy/set.py | Python | gpl-3.0 | 21,639 | [
"Gaussian"
] | cfc9a585b5c18dc474f7f0afd304f43a7c06a5af7863012baf3e2edbfc7837ec |
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use ... | Cloud-Elasticity-Services/as-libcloud | libcloud/compute/drivers/azure.py | Python | apache-2.0 | 107,838 | [
"VisIt"
] | a83db60b613477099d2fa3fa95dd6323ae66cdbf2060c75c1a4531b0b5cbaf50 |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy, ... | alexholcombe/dot-jump | dataRaw/test_dot-jump10Feb2017_09-31.py | Python | gpl-3.0 | 28,947 | [
"Gaussian"
] | fb7b16bc62abe003b1b9fb59e81d1a642964411703abc45bc6d711d4b801084f |
from math import sqrt
from ase import Atoms, Atom
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize import BFGS, QuasiNewton
from ase.neb import NEB
# Distance between Cu atoms on a (111) surface:
a = 3.6
d = a / sqrt(2)
fcc111 = Atoms(symbols='Cu',
cell=[(d, 0, ... | suttond/MODOI | ase/test/COCu111.py | Python | lgpl-3.0 | 1,834 | [
"ASE"
] | 070c5bc26e5523236c26fc42544230a819c1fedfb835ce3a1bc47cbf79eb5f5d |
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