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# Package level logger
import random
import string
import itertools
import logging
logger = logging.getLogger("assetid")
logger.addHandler(logging.NullHandler())
class IoosUrn(object):
""" https://geo-ide.noaa.gov/wiki/index.php?title=IOOS_Conventions_for_Observing_Asset_Identifiers """
def __init__(self, *... | axiom-data-science/assetid | assetid/urn.py | Python | mit | 9,163 | [
"NetCDF"
] | a53da9202c8f840d3f9eab29d867b56eaadf841602f0b0371e460449a4d75126 |
"""
.. _tut-compute-covariance:
Computing a covariance matrix
=============================
Many methods in MNE, including source estimation and some classification
algorithms, require covariance estimations from the recordings.
In this tutorial we cover the basics of sensor covariance computations and
construct a no... | pravsripad/mne-python | tutorials/forward/90_compute_covariance.py | Python | bsd-3-clause | 7,983 | [
"Gaussian"
] | 1459f88b8fe88f6fecae6afbb024e16ec7916831ab8993e408247f4ec66b0915 |
import json
from DIRAC.Core.Base.Client import Client, createClient
from DIRAC import S_OK, S_ERROR
from DIRAC.DataManagementSystem.private.FTS3Utilities import FTS3JSONDecoder
@createClient('DataManagement/FTS3Manager')
class FTS3Client(Client):
""" Client code to the FTS3 service
"""
def __init__(self, url=... | fstagni/DIRAC | DataManagementSystem/Client/FTS3Client.py | Python | gpl-3.0 | 3,980 | [
"DIRAC"
] | 6482bf9c5979a5d5645e67f4ff420cb279f5ddb0e3df3658167c92f1905059bc |
# Author: Travis Oliphant
# 2003
#
# Feb. 2010: Updated by Warren Weckesser:
# Rewrote much of chirp()
# Added sweep_poly()
from __future__ import division, print_function, absolute_import
import numpy as np
from numpy import asarray, zeros, place, nan, mod, pi, extract, log, sqrt, \
exp, cos, sin, polyval, po... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/scipy/signal/waveforms.py | Python | mit | 21,039 | [
"Gaussian"
] | 728777047b024932af77547d85860ee70e58c4c9e4a63a1c799551c8abdaf006 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
""" Test macro caller functions """
import os
import sys
sys.path.insert(0, os.path.join(os.pardir, os.pardir))
from unittest import main, TestCase
from module_test import *
from sneakylang.macro_caller import *
from sneakylang.treebuilder import TreeBuilder
from sneaky... | andrejtokarcik/python-sneakylang | sneakylang/test/test_macro_caller.py | Python | bsd-3-clause | 3,825 | [
"ADF"
] | 966cd6a2f1a36471fc6b634b7b91d796676d266edcf381d43d7ec338e800ad4f |
#!/usr/bin/env python
"""
This file is a series of tasks to preprocess COBRE dataset
Installation
------------
It runs on Python > 3.3 or Python2.7 and uses invoke (or Fabric when a Python3 version is released) to execute
the tasks from the command line.
- requirements
pip install invoke
pip install git@github.com:N... | alexsavio/cobre | fabfile.py | Python | bsd-3-clause | 68,111 | [
"Gaussian"
] | 7a1649b37d01e99c61e30449aa57780dc217c296f0de17a5909d1bc2267de042 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import setup, find_packages
import os
here = os.path.abspath(os.path.dirname(__file__))
with open(os.path.join(here, 'README.rst')) as f:
readme = f.read()
# Extras requirements for optional dependencies
extras = {
'analysis': ['weblogo>=3.7'],... | HubLot/PBxplore | setup.py | Python | mit | 2,043 | [
"MDAnalysis"
] | d74232c9dab0d7726774d0d9c19c4c20f1fd9fee1609a425b1fc9b7977dfecae |
"""This file contains code for use with "Think Stats" and
"Think Bayes", both by Allen B. Downey, available from greenteapress.com
Copyright 2014 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
from __future__ import print_function, division
"""This file contains class definitions for:
H... | santosfamilyfoundation/SantosCloud | app/traffic_cloud_utils/plotting/thinkstats2.py | Python | mit | 73,337 | [
"Gaussian"
] | a3781161afc124b415da613e5984111f9e71b97deea37f56ee6b4b0755e5ac79 |
import ast
from nose.tools import raises
from jaspyx.ast_util import ast_store, ast_load, ast_call
from jaspyx.tests.visitor.v8_helper import V8Helper
class TestAssignSingleTarget(V8Helper):
def test_single_assign(self):
assert self.run(
[
ast.Assign(
[ast_s... | iksteen/jaspyx | jaspyx/tests/visitor/test_assign.py | Python | mit | 5,319 | [
"VisIt"
] | 140f687f08fdddeec77f9e11845039d1bb701b39ac55044681b64bdf9bccbdc5 |
# Copyright 2016 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... | petewarden/tensorflow_makefile | tensorflow/contrib/distributions/python/ops/gaussian.py | Python | apache-2.0 | 8,018 | [
"Gaussian"
] | 74285a655bd180ac26a36e653f43706717f68e75ffaef4e21ba952d92a574801 |
##############################################################################
# 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-acgh/package.py | Python | lgpl-2.1 | 2,036 | [
"Bioconductor"
] | 95bc130b8885f2510a0212d70099c59994a21ae91b71d6cf21bd561ed7412207 |
# 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 ... | Kami/libcloud | libcloud/common/digitalocean.py | Python | apache-2.0 | 7,037 | [
"VisIt"
] | 724810bf9017048f74a8d02528002e4938937ec5b8f743989876947bafda32c1 |
"""This module provides tools for finding the best fit object model by marginalising
over the space of possible PSFs.
For LkCa15 testing, see ./marginalise_image.py.
"""
from __future__ import print_function, division
import mdp
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import pdb... | mikeireland/pynrm | psf_marginalise.py | Python | mit | 37,909 | [
"Gaussian"
] | d09ea34b3a0a4deff98ff0b3d3cb9abd9f630a7e668a03e6a2368a3a03386f3c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2016 Loreto Parisi <loretoparisi@gmail.com>
# Copyright (C) 2016 Silvio Olivastri <silvio.olivastri@gmail.com>
# Copyright (C) 2016 Radim Rehurek <radim@rare-technologies.com>
"""
USAGE: $ python -m gensim.scripts.word2vec2tensor --input <Word2Vec model f... | duyet-website/api.duyet.net | lib/gensim/scripts/word2vec2tensor.py | Python | mit | 3,539 | [
"VisIt"
] | 7e43282163bfa8259a96c58c66a274a0cb3512aa5accb6ab85572df5fac633a4 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | espressomd/espresso | testsuite/python/drude.py | Python | gpl-3.0 | 11,112 | [
"Avogadro",
"ESPResSo",
"LAMMPS"
] | b2365a35738e07fbceb5ab1d6113d2c54d1ff642d0b4fc23af691320d5254705 |
"""
=======================================
Simulate raw data using subject anatomy
=======================================
This example illustrates how to generate source estimates and simulate raw data
using subject anatomy with the :class:`mne.simulation.SourceSimulator` class.
Once the raw data is simulated, gener... | mne-tools/mne-tools.github.io | 0.20/_downloads/348fd8e6a5e2100dbbbef2df40123b87/plot_simulated_raw_data_using_subject_anatomy.py | Python | bsd-3-clause | 9,580 | [
"Gaussian"
] | 2c013c030fec859f42b1c480c1d1d066f6b5adb9dbf3d664b2605141be36a721 |
"""Identify program versions used for analysis, reporting in structured table.
Catalogs the full list of programs used in analysis, enabling reproduction of
results and tracking of provenance in output files.
"""
import os
import contextlib
import subprocess
import sys
import yaml
import toolz as tz
from bcbio import... | fw1121/bcbio-nextgen | bcbio/provenance/programs.py | Python | mit | 12,080 | [
"BWA",
"Galaxy",
"HTSeq"
] | 796e276f44072da64cd1ae22fd1d617db4827f0fb2201ae972b7c24292f8bac3 |
# -*- coding: utf-8 -*-
from osv import fields
from datetime import date,datetime,time
import logging
_logger = logging.getLogger(__name__)
#时间段选择
def time_for_selection(self,cr,uid,context = None):
ret = [("%02i:00" % i,"%02i时30分" % i) for i in range(24)] + [("%02i:30" % i,"%02i时00分" % (i+1)) for i in range(24)]
... | chengdh/openerp-ktv | openerp/addons/ktv_sale/ktv_helper.py | Python | agpl-3.0 | 5,772 | [
"VisIt"
] | fa7392b32c257735cd583f1313bf9825f49d5647734173ea0ba506ec16ad39e9 |
"""
@name: C:/Users/briank/workspace/PyHouse/src/Modules.Core.Utilities._test/test_obj_defs.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2017 by D. Brian Kimmel
@license: MIT License
@note: Created on Aug 7, 2015
@Summary:
Passed all 3 tests - DBK - 2016-11-22
""... | DBrianKimmel/PyHouse | Project/src/Modules/Core/Utilities/_test/test_obj_defs.py | Python | mit | 1,513 | [
"Brian"
] | 2a0b3c78072276370967d136f751f3824234c8bf3e6e2aad0a36d26cfd0b0636 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
from scipy.ndimage import correlate1d, _ni_support, gaussian_filter, \
binary_erosion
from scipy import math
def square_gaussian_filter1d(input, sigma, axis = -1, output ... | nipy/nipy-labs | nipy/labs/group/displacement_field.py | Python | bsd-3-clause | 11,761 | [
"Gaussian"
] | cb9d68e1caf76efe1355585720d1c65d7e0882dd6ed984427bd6b41810dec12b |
# A bunch of CONVERTERS for the Fit part of Alphabet.
import os
import math
from array import array
import optparse
import ROOT
from ROOT import *
import scipy
#### LINEAR ####
class LinearFit:
def __init__(self, init_var, range_min, range_max, name, Opt):
self.Opt = Opt
self.rm = range_min
self.rp = range_max... | anovak10/plots | DDTmethod/Converters.py | Python | mit | 9,313 | [
"Gaussian"
] | 5b1e3072c241966c52f3e74beca93c5ab7be83318ef02bd288fe6700b73de835 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from time import strftime # use for clock simulation - shows time!
from time import sleep # use for delay in loops - wait for n sec.!
from threading import Thread # use to create a single threat for time
import sys # for unicode_to_kos0006u
import types ... | DeathPoison/roomControll | Socket/socketMaster.py | Python | mit | 6,222 | [
"TINKER"
] | fe29700c03a4285d91d738d995c40a87f38b8b0f46dfc00e4a8349a454558ec6 |
"""A module containing convenient methods for general machine learning"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
from __future__ import absolute_import
from builtins import zip
from builtins import int
from builtins import range
from future import ... | wittawatj/kernel-gof | kgof/util.py | Python | mit | 9,350 | [
"Gaussian"
] | 942f671017b6b810d5c209e098a3e8ac4ea3af898693ef00d13a187225393268 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | modules/geochemistry/test/tests/time_dependent_reactions/changing_pH_ferric_hydroxide.py | Python | lgpl-2.1 | 1,773 | [
"MOOSE"
] | c48bed83c1af273cfd88810e49d51045073a83b8b537db464da415d0bb4df8f6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import json
import numpy as np
from pymatgen import Lattice, Structure, Specie, Element
from pymatgen.transformations.standard_trans... | setten/pymatgen | pymatgen/transformations/tests/test_advanced_transformations.py | Python | mit | 25,380 | [
"VASP",
"pymatgen"
] | 90cb3212736f381eb4f6e525902901c0f33a8eb7650bb5b3fae1599aed010119 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# tests/server/server.py
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list... | 0x0mar/king-phisher | tests/server/server.py | Python | bsd-3-clause | 7,990 | [
"VisIt"
] | a2fa3a073165e0361d995638f426cf1feefea4b8a7766e09ca10d76f5ed31154 |
#!/usr/bin/env python
"""
FCKeditor - The text editor for internet
Copyright (C) 2003-2006 Frederico Caldeira Knabben
Licensed under the terms of the GNU Lesser General Public License:
http://www.opensource.org/licenses/lgpl-license.php
For further information visit:
http://www.fckeditor.net/
"Support Open Sour... | viollarr/henriquecursos | site/FCKeditor/_samples/py/sampleposteddata.py | Python | apache-2.0 | 1,828 | [
"VisIt"
] | 3b52b04cac651de15df37c71b81d44e31fb91cd46216e8740d18341b45e59265 |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'experiment'
tab.settings['Output file name'] = 'mgo.exp'
#
# Change the first scenario tab to single crystal
#
tab = self.notebook
tab.switchScenario(0,scenarioType='Single crystal')
#
tab = self.notebook.scenarios[0]
tab.settings['Unique direction - ... | JohnKendrick/PDielec | Examples/Experiment/drude-lorentz/script.py | Python | mit | 1,292 | [
"CRYSTAL"
] | 73750ca77b5e0e1eaa0ba8b80cfdf6c98440b9d24e508b3f7a49ab77cc568ad4 |
try:
any = any
except NameError:
def any(iterable):
for element in iterable:
if element:
return True
return False
import sys
from typehandlers.codesink import CodeSink
from typehandlers.base import TypeLookupError, TypeConfigurationError, CodeGenerationError, NotSup... | cawka/pybindgen-old | pybindgen/utils.py | Python | lgpl-2.1 | 7,846 | [
"VisIt"
] | edc29cd43795c08165f619d4dd903afd93f31386b48b7ab40e722f620333f110 |
# Copyright 2015 Planet Labs, Inc.
#
# 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 wr... | planetlabs/datalake-api | setup.py | Python | apache-2.0 | 2,140 | [
"Brian"
] | 843be31ceb1a51dbdbf96688f4c24fc89dca067eca228ed08a9fa1892218b54f |
# -*- coding: iso-8859-15 -*-
"""
routes
======
This module establishes and defines the Web Handlers and Websockets
that are associated with a specific URL routing name. New routing
associations must be defined here.
Notes
-----
For more information regarding routing URL and valid regular expressions
visit: http://w... | isis2304/python-server | routes.py | Python | mit | 796 | [
"VisIt"
] | 5de6f06578105c277cfb7ba92f490b64085314288664522973c1b3dffce9ed72 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
=========================================================================
Program: Visualization Toolkit
Module: TestNamedColorsIntegration.py
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or ... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Core/Testing/Python/financialField3.py | Python | bsd-3-clause | 10,952 | [
"VTK"
] | fd0120f0c6cf1d47c11b4a65a6b6edfefbb94808d9423db29568440ef503b192 |
import numpy as np
import moose
print( '[INFO] Using moose from %s' % moose.__file__ )
import time
# Does not guarantee thread determinism in multithreaded Gsolve/Ksolve.
moose.seed( 10 )
def printCompt(compt):
print( 'x0=%s, x1=%s, diffLength=%s, numDiffCompt=%d' % (compt.x0, compt.x1,
compt.diffLength, ... | dilawar/moose-core | tests/core/test_gsolve_parallel.py | Python | gpl-3.0 | 3,474 | [
"MOOSE",
"NEURON"
] | 595ec6badafaa4d3b362a26f57d1e6af6b80861a64b8ae4416b653ff3ce8a018 |
import numpy as np
import mbuild as mb
class Betacristobalite(mb.Compound):
"""The beta-cristobalite form of SiO2.
Area per port specifies the density of attachment sites in nm^2.
The crystal is expanded to yield an area per port of 0.25 nm^2, the
typical density of alkane monolayers on SiO2 althoug... | Jonestj1/mbuild | mbuild/lib/surfaces/betacristobalite.py | Python | mit | 1,592 | [
"CRYSTAL"
] | 376c7157e3ddf67719c92ee344d09982d6dcf2582886a408b368f1e5a2e68a9e |
###
### This script retrieves the coverage profiles of RNA-seq and Ribo-seq for all ribosomal protein genes. It stores it as text files.
###
import sys,numpy,HTSeq
import multiprocessing,multiprocessing.pool
def analysis(genomicFeature):
'''
This function computes the histograms of reads across transcript le... | adelomana/30sols | SI/extra/coverage/profiler.py | Python | gpl-3.0 | 7,122 | [
"HTSeq"
] | 5e501b2d4952989cb66379a2326f676cf3ec5bd5440f3b4309925bbfc2bd967b |
from dateutil import parser
from hs_core.hydroshare.utils import get_resource_file_name_and_extension
from hs_file_types.models import GeoRasterLogicalFile, GeoRasterFileMetaData, GenericLogicalFile, \
NetCDFLogicalFile, GeoFeatureLogicalFile, GeoFeatureFileMetaData, RefTimeseriesLogicalFile, \
TimeSeriesLogic... | ResearchSoftwareInstitute/MyHPOM | hs_file_types/tests/utils.py | Python | bsd-3-clause | 32,673 | [
"NetCDF"
] | 355d70163dd7e721567578df69ee65b2ab38d81015519711d3e5bce6753e3068 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import os, ... | nuclear-wizard/moose | python/TestHarness/schedulers/RunPBS.py | Python | lgpl-2.1 | 6,785 | [
"MOOSE"
] | 60c0e90a8d9ab6b6cbe0df691b143fad3fecfc97c28582699127aba39f4e28c2 |
# coastlib, a coastal engineering Python library
# Copyright (C), 2019 Georgii Bocharov
#
# 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) a... | georgebv/coastlib | coastlib/stats/extreme.py | Python | gpl-3.0 | 165,750 | [
"Gaussian"
] | 6bff41fdbc981d317beda312a6d7cab2d018d85709c29ffe7560f4cee2453711 |
"""testCount3.py.
Written by: Brian O'Dell, October 2017
A program to run each program a 500 times per thread count.
Then uses the data collected to make graphs and tables that
are useful to evaluate the programs running time.
"""
from subprocess import *
import subprocess
from numba import jit
import numpy as np
im... | brian-o/CS-CourseWork | CS491/count3Java/testCount3java.py | Python | gpl-3.0 | 2,658 | [
"Brian"
] | 1f95f2e071a7bf4e6af00478f00783753aaa19d83e500a050f73ee994d60b9e0 |
#!/usr/bin/env python2.7
import pysam, argparse, sys
parser = argparse.ArgumentParser(description='Helps with genome curation using linked paired-end read information from subsetted regions of a genome.', formatter_class=argparse.ArgumentDefaultsHelpFormatter, add_help=False)
#Required arguments
required = parser.add... | alexherns/biotite-scripts | pysam_mismatched.py | Python | mit | 5,255 | [
"pysam"
] | ad67106210322f2e08543e91a9dc7ea71fd5c5577327e546426287f3ef148a1c |
import os
import botocore
import ast
import pytest
ROOTDIR = os.path.dirname(botocore.__file__)
def _all_files():
for rootdir, dirnames, filenames in os.walk(ROOTDIR):
if 'vendored' in dirnames:
# We don't need to lint our vendored packages.
dirnames.remove('vendored')
f... | boto/botocore | tests/functional/test_six_imports.py | Python | apache-2.0 | 1,840 | [
"VisIt"
] | a49560abb5dae0877f089f1eb035712c11588b7aeac6662b8d1e68f9b43b4d9c |
# FIXME: to bring back to life
from __future__ import print_function
from DIRAC.Resources.Catalog.FileCatalogClient import FileCatalogClient
import cmd
import sys
from DIRAC.DataManagementSystem.Client.CmdDirCompletion.AbstractFileSystem import DFCFileSystem
from DIRAC.DataManagementSystem.Client.CmdDirCompletion.Di... | fstagni/DIRAC | tests/Integration/DataManagementSystem/FIXME_dfc_dir_completion.py | Python | gpl-3.0 | 1,254 | [
"DIRAC"
] | a58212fc0a3483ce6a61626b086ed228847a3e07ee4a22ec073088f1d8374af4 |
#TODO: Set dbkey to proper UCSC build, if known
import urllib
from galaxy import datatypes, config
import tempfile, shutil
def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
"""Sets the name of the data"""
data_name = param_dict.get( 'name', 'HbVar query' )
data_type = param_dict.get( '... | dbcls/dbcls-galaxy | tools/data_source/hbvar_filter.py | Python | mit | 2,585 | [
"Galaxy"
] | a62fb767d2f3d7dd14959ca714c985854a8144cb3de0172a8eaabfd7f388e216 |
"""
Contains Experiment and Injection classes.
"""
import os
import logging
import numpy
from pint import DimensionalityError
from bayesitc.units import ureg, Quantity
# Use logger with name of module
logger = logging.getLogger(__name__)
class Injection(object):
"""
Data from a single injection.
Se... | choderalab/bayesian-itc | bayesitc/experiments.py | Python | gpl-3.0 | 36,645 | [
"Gaussian"
] | bb4af474d42086652228b661ccc71a0f63a23e755d467e5a4929b0cdc179dc3f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from time import sleep
from statusthing import StatusThing, ColorRGBA
try:
import colorama
def colorize(text,fg=None,bg=None):
try:
cfg = colorama.ansi.Fore.__dict__[fg.upper()] if fg is not None else ''
rfg = colorama.ansi.Fore.__d... | JnyJny/StatusThing | Bindings/Python/Demo.py | Python | mit | 8,856 | [
"VisIt"
] | 6133bafc09823d7ee8ca33dc1c635afe43c915e2de32ccbb59d8c376d3b5f8fb |
"""
Statistical tools for time series analysis
"""
from statsmodels.compat.python import (iteritems, range, lrange, string_types,
lzip, zip, long)
from statsmodels.compat.scipy import _next_regular
import numpy as np
from numpy.linalg import LinAlgError
from scipy import stats
f... | bert9bert/statsmodels | statsmodels/tsa/stattools.py | Python | bsd-3-clause | 44,980 | [
"ADF"
] | 63a17d359f42fc0790767b88e97a40f3bc8fe6c2b8f20f16aa2449041ce1d24a |
"""Solar analemma."""
from ._skyBase import RadianceSky
from ..material.light import Light
from ..geometry.source import Source
from ladybug.epw import EPW
from ladybug.sunpath import Sunpath
import os
try:
from itertools import izip as zip
writemode = 'wb'
except ImportError:
# python 3
writemode = ... | ladybug-analysis-tools/honeybee | honeybee_plus/radiance/sky/analemma.py | Python | gpl-3.0 | 9,941 | [
"EPW"
] | b470ee2d75c10a22443b88aefe424b8a8dda1d5e9e9403313bf0df779f08a940 |
import subprocess
import traceback
from PyQt5 import QtCore, QtWidgets, QtGui
from config import VERSION, ICONS8_URL, LOADINGIO_URL, GITHUB_URL, GPL_URL, EXE
from update import Updater
from utils import get_download_window
license_txt = None
def show_msgbox(title, msg, icon=QtWidgets.QMessageBox.NoIcon, details=No... | FranzPio/yt-dl | src/dialogs.py | Python | gpl-3.0 | 11,382 | [
"VisIt"
] | 9a588985c4288315241bc40a43c9c38d6f1d212e75749ced5b2c8967677eeec2 |
#--------------------------------------------------------------------------
# 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 ... | fabio-otsuka/invesalius3 | invesalius/constants.py | Python | gpl-2.0 | 25,058 | [
"VTK"
] | 52005fe0d876b136f93374039fc519adc48970a07ed58deb35cc285f1523f543 |
# -*- coding: utf-8 -*-"""
"""
Created on Wed Aug 6 11:06:31 2014
@author: schmidan
"""
import ctypes
import numpy as np
def printCov():
print(r""" available covariance functions:
cov functions:
CovLinearard
CovLinearone
CovMatern3iso
CovMatern5iso
CovNoise
... | Luk0r/gaupro | python/gaupro2.py | Python | mit | 9,196 | [
"Gaussian"
] | 7c7d40647e4b1b35b11e1b9034a27020d966645ad9f0cbdb112a25d6725025d2 |
"""
Analysis of the origin of the diffraction pattern based on indexed and
measured intensities.
"""
from __future__ import annotations
def cctbx_crystal_from_dials(crystal):
space_group = crystal.get_space_group()
unit_cell = crystal.get_unit_cell()
from cctbx.crystal import symmetry as crystal_symmetr... | dials/dials | algorithms/symmetry/origin.py | Python | bsd-3-clause | 3,885 | [
"CRYSTAL"
] | 9f73b5d30b661fddfc1d55c793b624fd864615fdde93a0a40187a1fddd7173f7 |
#######################################################
# Copyright (c) 2015, ArrayFire
# All rights reserved.
#
# This file is distributed under 3-clause BSD license.
# The complete license agreement can be obtained at:
# http://arrayfire.com/licenses/BSD-3-Clause
######################################################... | arrayfire/arrayfire_python | arrayfire/vision.py | Python | bsd-3-clause | 15,473 | [
"Gaussian"
] | 671c59ab54f443c52a81f1723f90bca3ad903271e1c708fdd2b8b7b3bed6ea75 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2005-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012 Gary Burton
# Copyright (C) 2... | gramps-project/gramps | gramps/gui/viewmanager.py | Python | gpl-2.0 | 69,159 | [
"Brian"
] | 1c1cd0000e57b15e3abc351160f657c090c1f3f2d766d9c08a516ac4d9aa0c2d |
""" GOCDBClient module is a client for the GOC DB, looking for Downtimes.
"""
__RCSID__ = "$Id$"
import urllib2
import time
import socket
from datetime import datetime, timedelta
from xml.dom import minidom
from DIRAC import S_OK, S_ERROR, gLogger
def _parseSingleElement( element, attributes = None ):
"""
Given... | calancha/DIRAC | Core/LCG/GOCDBClient.py | Python | gpl-3.0 | 11,486 | [
"DIRAC"
] | 8661f52df2ee0c3c3b36b2d58ae2bf60343ff38e1edcbae55a01c3548a12a496 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Opencv(CMakePackage, CudaPackage):
"""OpenCV is released under a BSD license and hence it'... | rspavel/spack | var/spack/repos/builtin/packages/opencv/package.py | Python | lgpl-2.1 | 18,013 | [
"VTK"
] | 56c9a7f5efdcda46ff70eeb1be8de69766e5ee0cdcc5d48b0ad40869e15a43a5 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-ban-site
# Author : Stuart Paterson
########################################################################
"""
Remove Site from Active mask for current Setup
Example:
$ dirac-admin-ban-site LCG.I... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_ban_site.py | Python | gpl-3.0 | 3,372 | [
"DIRAC"
] | f39601e30358a9adb415e46163eace278fc7adff1da78cad255535c731f9247b |
# Copyright 2017 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... | jbedorf/tensorflow | tensorflow/python/autograph/pyct/compiler.py | Python | apache-2.0 | 4,980 | [
"VisIt"
] | 7a2c7ad38f177d1a04a2ee32b60a01bb0642de0745cfed1532b94350b49159c9 |
#!/usr/bin/env python
from SPAdesPipeline.OLCspades.accessoryFunctions import *
__author__ = 'adamkoziol'
class DegeneratePrimers(object):
def objectifier(self):
import primerobject
# Initialise the primer object
self.runmetadata = primerobject.PrimerObject(self)
if self.batch:
... | adamkoziol/vtyper | primerdegenerator.py | Python | mit | 6,765 | [
"Biopython"
] | aac1e94f5ead80b5d49313e89ad560736e1cae2e6aaf94cfd44fe304359398d9 |
##
# Copyright 2013-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | ULHPC/easybuild-easyconfigs | test/easyconfigs/easyconfigs.py | Python | gpl-2.0 | 71,491 | [
"ABINIT",
"ASE",
"Amber",
"BLAST",
"Bioconductor",
"CP2K",
"Elk",
"GPAW",
"NetCDF",
"PySCF",
"WIEN2k",
"pysam"
] | b5e0979ffa2cc93ee7e0c4933da74085f7c2b90287b2c2bd955f924d246577b2 |
# -*-coding:utf8-*-
from __future__ import print_function
"""
This file is part of SkyLab
Skylab 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 ve... | zdgriffith/skylab | skylab/ps_model.py | Python | gpl-3.0 | 30,216 | [
"Gaussian"
] | 9c3276ea2c78f27281927898942747d675f091eb610cc20c0697537b00c9b8dc |
# Script to try and validate focus detection algorithms
from __future__ import division
import numpy as np
import matplotlib.pyplot as plt
import cv2
from scipy import ndimage
import scipy.signal
from PIL import Image
import zstackLib
import time
plt.ion()
filename = '/home/brian/git/pyZstack/lena.tif'
image = Image... | gtg556h/pyZstack | sharpnessAlgorithm/callLaplacian.py | Python | mit | 1,389 | [
"Brian"
] | a2ea8b2835366e9aa3fa84619c32a87a989cdff3fad29d08e180178fff858893 |
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpatterns = [
url(r'^$', TemplateView.as_view(template_name='page... | ToferC/gcclassifier | config/urls.py | Python | mit | 1,607 | [
"VisIt"
] | 70b5697cc6c6b5df2899915d95ff516980be662cfbb6adaef6aeec922f925f96 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2004-2005 Eero Tamminen
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Peter Landgren
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012 Paul Franklin
#
# This program i... | arunkgupta/gramps | gramps/plugins/drawreport/statisticschart.py | Python | gpl-2.0 | 42,816 | [
"Brian"
] | 90431c192f2a25cf2f4a87ebc38a56f47a9a89add70829526d010c890e88896b |
import Avogadro
import unittest
from numpy import *
class TestAtom(unittest.TestCase):
def setUp(self):
self.molecule = Avogadro.molecules.addMolecule()
def test_type(self):
atom = self.molecule.addAtom()
self.assertEqual(atom.type, Avogadro.PrimitiveType.AtomType)
def test_pos(self):
atom = se... | rcplane/periodicdisplay | reference/avogadro/libavogadro/src/python/unittest/atom.py | Python | gpl-2.0 | 3,207 | [
"Avogadro"
] | 5f87be128b4d555e7ed63184f23cd4757d215d42515236f3b714f4e91921452f |
# Configuration file for jointcal
from lsst.meas.algorithms import LoadIndexedReferenceObjectsTask
# Select external catalogs for Astrometry
config.astrometryRefObjLoader.retarget(LoadIndexedReferenceObjectsTask)
config.astrometryRefObjLoader.ref_dataset_name='pan-starrs'
config.astrometryRefObjLoader.filterMap = {
... | LSSTDESC/ReprocessingTaskForce | config/w_2017_52/jointcalConfig.py | Python | gpl-2.0 | 1,496 | [
"VisIt"
] | 9d7231bbad628e6f13c34a0114ca73ee21f2959b5b9dc770cfb8c9839944a4a6 |
# Copyright (c) 2014 Evalf
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, s... | wijnandhoitinga/nutils | nutils/mesh.py | Python | mit | 29,584 | [
"VTK"
] | 7f2dfeec4c8726bcc8b28cc444d1fa412ec237f1b31294bf184cdb767736a2ec |
##
## This file is part of the libsigrokdecode project.
##
## Copyright (C) 2014 Sławek Piotrowski <sentinel@atteo.org>
##
## 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 ... | zeldin/libsigrokdecode | decoders/rfm12/pd.py | Python | gpl-3.0 | 18,323 | [
"CRYSTAL"
] | 88da09fb3369ae61a9eb38564c34e266cf1bf829ccd31105adc85bb586406f91 |
# Copyright 2001 by Katharine Lindner. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# standard library
import sys
import string
import copy
import array
import os
import re
i... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/ECell/__init__.py | Python | apache-2.0 | 14,130 | [
"Biopython"
] | ac4878ac8fcbb41c99aac55f4dffcdd43583e437db701b537d6628b930c369c2 |
from spectral_cube import SpectralCube
from astropy.io import fits
import matplotlib.pyplot as plt
import astropy.units as u
import numpy as np
from scipy.optimize import curve_fit
from scipy import *
import time
import pprocess
from astropy.convolution import convolve
import radio_beam
import sys
def gauss_fitter(reg... | jakeown/GAS | GAS/gauss_fit.py | Python | mit | 9,175 | [
"Gaussian"
] | aed55e94d82060de7051acfad40d57f87bee4d8ec2161ce45741cb06edb51a66 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/mooseutils/tests/test_PostprocessorReader.py | Python | lgpl-2.1 | 3,943 | [
"MOOSE"
] | d8e29714b5a1bb0751e7724eff5aa9a541b357e234ec9a21b26dc34ae5baeba9 |
# Copyright (C) 2012 Mathias Brodala
#
# 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, or (at your option)
# any later version.
#
# This program is distributed in the hope that... | virtuald/exaile | plugins/osd/__init__.py | Python | gpl-2.0 | 12,754 | [
"FLEUR"
] | dba35b2d073c211ac50e2cd63c5184d6acbf594f3017cafa76e4581d68a7aba0 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetR... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/General/Testing/Python/TestDiscreteMarchingCubes.py | Python | gpl-3.0 | 2,317 | [
"VTK"
] | 44276a71bb21ec1585f666124a6c47c037264211430ee14cca87c7e0d03e6a8b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2015 by Gaik Tamazian
# gaik (dot) tamazian (at) gmail (dot) com
import argparse
import bioformats.bed
import bioformats.gff3
import csv
import logging
import os
import vcf
from chromosomer.fragment import AlignmentToMap
from chromosomer.fragment import Se... | gtamazian/Chromosomer | chromosomer/cli.py | Python | mit | 15,881 | [
"BLAST"
] | 850a8373970cfcfe2ade8b1477155b693d8748cf32a78f28db427ce0dced49f4 |
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# https://www.lammps.org/ Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE-A... | jeremiahyan/lammps | python/lammps/core.py | Python | gpl-2.0 | 78,731 | [
"LAMMPS"
] | 114eaf91c0a83481fc7651dfac2cf4d08cf53b04ea41c4486ec5b67b60ec6ae7 |
import PythonQt
from PythonQt import QtGui, QtCore
from director import pointpicker
from director import vtkNumpy as vnp
from director import vtkAll as vtk
import numpy as np
class ImageView(object):
def __init__(self):
self.autoResetCamera = False
self.view = PythonQt.dd.ddQVTKWidgetView()
... | patmarion/director | src/python/director/imageview.py | Python | bsd-3-clause | 5,326 | [
"VTK"
] | 8b749d4a21fb5482e08ad70d7d8b66d23589eb98b669d9bc595fc4826fe67730 |
# This file is part of MOOSE simulator: http://moose.ncbs.res.in.
# MOOSE 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.
# MOOSE is ... | dilawar/moose-full | moose-core/python/libmumbl/nml_parser/NetworkML.py | Python | gpl-2.0 | 39,154 | [
"MOOSE",
"NEURON"
] | 53bb578cfb05c2be42c55c20af79e044b311dae7f61e1c7822fe7aa10ce8396f |
#!/usr/bin/env python
"""
Post-process the individual cell output files resulting from running the
OpenIFS single column model over a grid of cells.
The program takes a single input which is a configuration file in INI
format. This is the same configuration file used to run the model that
generated the column output f... | aopp-pred/openifs-scmtiles | openifs_pp_main.py | Python | apache-2.0 | 13,073 | [
"NetCDF"
] | 5c1a29abc0dc4db651b451e287800187bbe752e55cb07784a708d3769d5eb71f |
from abc import ABCMeta, abstractmethod
import os
import subprocess
import collections
import psutil
import shlex
from pychemia import pcm_log
class CodeRun:
__metaclass__ = ABCMeta
def __init__(self, executable, workdir='.', use_mpi=False):
"""
CodeRun is the superclass defining the operation... | MaterialsDiscovery/PyChemia | pychemia/code/codes.py | Python | mit | 10,796 | [
"ABINIT"
] | ef97b60c7cadffc96229577b0954f048180177fac14932283b9ba55ee0aae343 |
""" DISET request handler base class for the TransformationDB.
"""
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.TransformationSystem.DB.TransformationDB import Tr... | vmendez/DIRAC | TransformationSystem/Service/TransformationManagerHandler.py | Python | gpl-3.0 | 29,811 | [
"DIRAC"
] | 2c0240965e28df8b0061f07d30d84e013147a239fc997d474090832a0de5f3c8 |
from aiida import load_dbenv
load_dbenv()
from aiida.orm import Code, DataFactory, WorkflowFactory
StructureData = DataFactory('structure')
ParameterData = DataFactory('parameter')
import numpy as np
import os
import pymatgen
import pymatgen.symmetry.analyzer
##########################
structure_id = 'mp-2176' #MgO... | abelcarreras/aiida_extensions | workflows/launcher/launch_qha_vasp_mp.py | Python | mit | 7,549 | [
"CRYSTAL",
"pymatgen"
] | 620424b5207320316fac0d71186bbc3d3cc7a1ed06012cdc12e03fd3642d77e4 |
import os, sys, inspect
import sqlite3 as sql
import pickle as pkl
from datetime import datetime
import re
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.pyplot as plt
import numpy as np
from scipy.interpolate import griddata
import numpy.ma as ma
from numpy.random import uniform, seed
HOME = ... | foci/ArcOn-r2 | scripts/arcon_view2.py | Python | lgpl-3.0 | 7,013 | [
"ParaView"
] | 97d08d0c8be904aac8b7f8a0eb205fdec1d28206de0556585ff61a1444390824 |
'''
Created on Jun 2, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
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... | madhavsuresh/chimerascan | chimerascan/lib/sam.py | Python | gpl-3.0 | 8,356 | [
"pysam"
] | e5f3310aaef91c65fe31ed21b7dad44f8d411325b63e00ba3ad3363bfdf84e6b |
# Copyright 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
UA_TYPE_MAPPING = {
'chromeos':
'Mozilla/5.0 (X11; CrOS x86_64 9202.60.0) '
'AppleWebKit/537.36 (KHTML, like Gecko) '
'Chrome/57.... | endlessm/chromium-browser | third_party/catapult/telemetry/telemetry/internal/browser/user_agent.py | Python | bsd-3-clause | 1,542 | [
"Galaxy"
] | 4cebef3ffe67072bf6a26ad89617f9d3ff2d6586e598f4831f70c569f7f29079 |
from datetime import datetime as dt
import os
from enum import IntEnum
import logging
from typing import Optional
from netCDF4 import Dataset, num2date
from hyo2.soundspeed.base.geodesy import Geodesy
from hyo2.soundspeed.profile.dicts import Dicts
from hyo2.soundspeed.profile.profile import Profile
from hyo2.soundspe... | hydroffice/hyo_soundspeed | hyo2/soundspeed/atlas/regofsoffline.py | Python | lgpl-2.1 | 8,583 | [
"NetCDF"
] | 8b68bea013e2239fcc9cb1fd4a6bcef631b8971df8aeb46370f03a87b487ed04 |
import sys
sys.path.insert(1, "../../../")
import h2o
def offsets_and_distributions(ip,port):
# cars
cars = h2o.upload_file(h2o.locate("smalldata/junit/cars_20mpg.csv"))
cars = cars[cars["economy_20mpg"].isna() == 0]
cars["economy_20mpg"] = cars["economy_20mpg"].asfactor()
offset = h2o.H2OFrame(py... | mrgloom/h2o-3 | h2o-py/tests/testdir_algos/deeplearning/pyunit_offsets_and_distributionsDeeplearning.py | Python | apache-2.0 | 1,660 | [
"Gaussian"
] | a8a6e14492144d7eeec03e877bcbed894ebc069634d8221fb8439ba887eb07e3 |
import galaxy.model
from galaxy.model.orm import *
from galaxy.model.mapping import context as sa_session
from base.twilltestcase import *
not_logged_in_security_msg = 'You must be logged in as an administrator to access this feature.'
logged_in_security_msg = 'You must be an administrator to access this feature.'
im... | volpino/Yeps-EURAC | test/functional/test_security_and_libraries.py | Python | mit | 122,639 | [
"Galaxy",
"VisIt"
] | 4f35c64651a5989124d4e4aac545b925f0aa2f4139df3230db88b074f596e738 |
# -*- coding: latin-1 -*-
##############################################################################
# Copyright (C) 2012 by BSC-CNS #
# Author: Carlos Tripiana Montes <carlos.tripiana@bsc.es> #
# ... | fercook/SciViz | Geometries/STL_from_Paraview/stl_extractor.py | Python | gpl-2.0 | 17,575 | [
"ParaView",
"VisIt"
] | 7c025f042ef85d8a1b3af6b30ca179694306eb28cf442552a954d20ccabb16af |
#!/usr/bin/env python3
#
# Code related to ESET's Linux/Moose research
# For feedback or questions contact us at: github@eset.com
# https://github.com/eset/malware-research/
# Olivier Bilodeau <bilodeau@eset.com>
#
# This code is provided to the community under the two-clause BSD license as
# follows:
#
# Copyright (C)... | eset/malware-research | moose/lib/elan2.py | Python | bsd-2-clause | 8,851 | [
"MOOSE"
] | 7802691b41a6801b29f56bef8a2e6a8a816d10cf0bf5d75bce27e82145a2d62a |
# -*- coding: utf-8
# pylint: disable=line-too-long
"""Lots of under-the-rug, operational garbage in here. Run. Run away."""
import os
import sys
import json
import copy
import platform
from tabulate import tabulate
# yes, this library is imported but never used, but don't remove it
# unless you want to explode `bo... | merenlab/anvio | anvio/__init__.py | Python | gpl-3.0 | 204,703 | [
"BLAST",
"Bowtie"
] | b3ce44d996edb7f664f63dfbdb401a3e77d1da2c271281a88a2f642b41f0e3d5 |
# Author: Travis Oliphant, 2002
#
# Further updates and enhancements by many SciPy developers.
#
from __future__ import division, print_function, absolute_import
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, around, unique, asarray,
... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/scipy/stats/morestats.py | Python | apache-2.0 | 94,567 | [
"Gaussian"
] | 6a45eea4ded3b7435a56703ac27bc8022a745fbc6b6fb4ac6123f26498a44304 |
"""
SALTS XBMC Addon
Copyright (C) 2014 tknorris
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
T... | odicraig/kodi2odi | addons/plugin.video.salts/scrapers/2ddl_scraper.py | Python | gpl-3.0 | 8,193 | [
"ADF"
] | 375408c81889bd5285a156b21aa50fc5a60558fa642483a70c29da71c98a2fa9 |
import random
import math
#################################################
# Parameters
#################################################
dt = 0.001 # simulation time step
t_rc = 0.02 # membrane RC time constant
t_ref = 0.002 # refractory period
t_pstc = 0.1 # post-synaptic time constant
N_A = 50... | harshkothari410/snn-image-segmentation | nef.py | Python | mit | 7,869 | [
"NEURON"
] | c553b9b328d36854e0b1c52016cc80ab9cc14c06ad325ad3e22740e30d0d5b24 |
#
# 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/tfpark/test_tf_dataset.py | Python | apache-2.0 | 18,397 | [
"ORCA"
] | 56334d178a62f2630655ed98f2a1f3424ec3da60b6552a7d55e425855240cdb7 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | liuwenf/moose | python/chigger/tests/exodus/labels/cells.py | Python | lgpl-2.1 | 1,299 | [
"MOOSE"
] | 8201a84ce69ebea2216f80c9b2f9e92fbd5340b2d449efb8f4652ef1e5ec0b04 |
import json
import re
current_index = 0
def new_item_stack(input):
if type(input) == str:
return (input, 1, 0)
elif type(input) == list:
if len(input) == 1:
input.append(1)
if len(input) == 2:
input.append(0)
return input
def new_item_stacks(input, s... | 19Spleen/CrystalBlocks | generate_recipes.py | Python | gpl-3.0 | 3,803 | [
"CRYSTAL"
] | fbb07b99049cb568ffe91ef4c239c361662f4236fd2350fb4172d35ba7ee9a21 |
#!/usr/bin/env python
# Take the json in the file given as first argument and convert it to the JSON
# format needed for import. Should do all cleanup of data and removal of
# unneeded entries too.
import sys
import os
import json
import re
import urllib
script_dir = os.path.basename(__file__)
base_dir = os.path.joi... | mysociety/pombola | pombola/south_africa/data/members-interests/convert_to_import_json.py | Python | agpl-3.0 | 22,213 | [
"Brian"
] | a5c495c994d874af1c7d9c5d172b537e50ad045a3a7a93465583fc1899243132 |
"""
Module for Continuous-Time Recurrent Neural Networks.
This pure python version solves the differential equations
using a simple Forward-Euler method. For a higher precision
method, use the C++ extension with 4th order Runge-Kutta.
"""
from neat.nn import nn_pure as nn
try:
import psyco; psyco.full()
except... | davidmfinol/py3NEAT | neat/ctrnn/ctrnn_pure.py | Python | gpl-3.0 | 3,379 | [
"NEURON"
] | 9fff27414ec6390bd7e382d0e2a6084f141766bb0cd065d3b52b674848523dc6 |
#! /usr/bin/env python3
#
# Author: Martin Schreiber
# Email: schreiberx@gmail.com
# Date: 2017-06-17
#
import sys
import math
import cmath
import os
d = os.path.dirname(os.path.realpath(__file__))
sys.path.append(d+'/..')
import EFloat as ef
from trexi.TREXI_GaussianCoefficients import *
from trexi.TREXI_Gaussian... | schreiberx/sweet | mule_local/python/mule_local/rexi/trexi/TREXI_GaussianPhi0.py | Python | mit | 1,230 | [
"Gaussian"
] | e6104d4e78985eaadf87dd696669476604fe455daad5d8283b291e695d08447b |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_saleinvoiceprinterdialog.py | Python | gpl-2.0 | 1,298 | [
"VisIt"
] | bb69dd2df0d7bb2b41035150e8e18c7f52e9526ae99b04992eacb9d9e406f090 |
# -*- coding: utf-8 -*-
#
# test documentation build configuration file, created by
# sphinx-quickstart on Fri Feb 7 11:33:27 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All ... | MikeDMorgan/scRNAseq | pipeline_scRnaseq/conf.py | Python | mit | 13,218 | [
"pysam"
] | db2892bd69eb3d7f10d8ad37d8fb78f08969434938a2586361e33457f788b06e |
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