text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
"""Main PAC class."""
import numpy as np
import logging
from tensorpac.spectral import spectral, hilbertm
from tensorpac.methods import (get_pac_fcn, pacstr, compute_surrogates,
erpac, ergcpac, _ergcpac_perm, preferred_phase,
normalize)
from tensorpac.gcmi ... | EtienneCmb/tensorpac | tensorpac/pac.py | Python | bsd-3-clause | 36,901 | [
"Gaussian"
] | fd958ef21ca7854714f77c7cd4934202b2bb9f8cfd4cf765907f8b4e893ebd82 |
import os, sys
import vtktools
import numpy as np
import matplotlib as mpl
mpl.use('ps')
import matplotlib.pyplot as plt
import matplotlib.tri as tri
from paraview.simple import *
## READ archive (too many points... somehow)
label = sys.argv[1]
dayi = int(sys.argv[2])
dayf = int(sys.argv[3])
days = int(sys.argv[... | jungla/ICOM-fluidity-toolbox | 2D/U/plot_T_hw.py | Python | gpl-2.0 | 3,539 | [
"ParaView"
] | 747f3c15895677dac99ac26894055942b1184c623fc050c16ec4e04dd21abad0 |
"""
@file create_hdf5.py
"""
import h5py
import numpy as np
import scipy.stats as ss
from os.path import join
def generate_data(path):
distributions = {'Gaussian': {'options': dict(loc=0, scale=0.1),
'name': 'norm'},
'Exponential': {'options': dict(loc=-0.5, scal... | ernestyalumni/MLgrabbag | visualization/bokehplus/app/simple_hdf5/create_hdf5.py | Python | mit | 1,069 | [
"Gaussian"
] | bb7b806d69c29ced9e8a9aa7309db5a783878fcf6dd068b72c3b4804e3bc9cb7 |
##############################################################
# Date: 20/01/16
# Name: plot_spacing.py
# Author: Alek Petty
# Description: Script to plot spacing between ATM points
# Input requirements: ATM and DMS for a given section
# Output: 1 km ATM spacing
import matplotlib
matplotlib.use("AGG")
import IB_funct... | akpetty/ibtopo2016 | plot_spacing.py | Python | gpl-3.0 | 11,351 | [
"NetCDF"
] | 3e1f0eed131e8d09b9864005ddbe0f83f84b9df1c925971087cab4fdd174f585 |
# -*- coding: utf-8 -*-
"""Utilities for reformatting and analyzing spiking data"""
import numpy as np
from copy import deepcopy
from itertools import product
from scipy import signal
from scipy.stats.mstats import zscore
from scipy.signal import medfilt
from scipy.signal import resample
from scipy.signal import welch,... | voytekresearch/fakespikes | fakespikes/util.py | Python | mit | 20,574 | [
"Gaussian",
"NEURON"
] | 5de859abbaa36804d9f01480239d814c8d6373c92403ac7e04e9288a2a25cf1f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import vtk
import vtk.test.Testing
import math
month_labels = ["Jan", "Feb", "Mar", "Apr", "May", "Jun",
"Jul", "Aug", "Sep", "Oct", "Nov", "Dec"]
book = [5675, 5902, 6388, 5990, 5575, 7393, 9878, 8082, 6417, 5946, 5526, 5166]
new_popular =... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Charts/Core/Testing/Python/TestStackedPlot.py | Python | gpl-3.0 | 3,585 | [
"VTK"
] | f5bb9187577298409b118f370a050e5d039990bac09097b16b094aeb5b3487d3 |
"""
This example checks plotting functions for binary sources. It is
derived from example_11_binary_source.py
"""
import MulensModel as mm
import matplotlib.pyplot as plt
import numpy as np
# First, prepare the data. There is nothing very exciting in this part,
# so you may skip it.
t_0_1 = 6100.
u_0_1 = 0.2
t_0_2 = ... | rpoleski/MulensModel | examples/example_17_1L2S_plotting.py | Python | mit | 3,004 | [
"exciting"
] | ec343bb40fea92ea38e8c2bc5e67a0af415ecfdc3aece64827be3fb3544c9240 |
# -*- coding: utf-8 -*-
"""Fragments.
The addition of a fragment results in an entry called :data:`pybel.constants.VARIANTS`
in the data dictionary associated with a given node. This entry is a list with dictionaries
describing each of the variants. All variants have the entry :data:`pybel.constants.KIND` to identify... | pybel/pybel | src/pybel/parser/modifiers/fragment.py | Python | mit | 2,907 | [
"Pybel"
] | 6441bba651cc0c4a674f2f9e3aa8b65905287cb658714da928329319c52f77ad |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
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
urlpat... | Jurevic/BB-8_droid | config/urls.py | Python | mit | 1,618 | [
"VisIt"
] | 49cba0b2a92af4431271db1b4c3d26476b5bc457693e0735499c70069d5b64c2 |
# -*- Python -*-
#
# @file test_2D_2D_diag.py
# @brief MultivariateRandomMixture validation tests
#
# Copyright (C) 2013 EADS IW France
#
# Author(s) : Denis Barbier, IMACS
# Sofiane Haddad, IMACS
#
# This program is free software; you can redistribute ... | sofianehaddad/MVRM | test/test_2N_2N_diag.py | Python | lgpl-3.0 | 3,094 | [
"Gaussian"
] | cd3928da012620abff538dfcc9129f1ed55e1a71e8337c522966d231fba28216 |
# Copyright 2020 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
from dataclasses import dataclass
from pants.backend.python.util_rules.pex import PexInterpreterConstraints
from pants.backend.python.util_rules.pex_environment import PythonExecutable
fr... | jsirois/pants | src/python/pants/backend/python/dependency_inference/import_parser.py | Python | apache-2.0 | 6,496 | [
"VisIt"
] | b6ef8e84b62c5c142775ea0ca29903f2cf2dce9a40ef7518458f8014b93e3be1 |
"""
Linear Discriminant Analysis and Quadratic Discriminant Analysis
"""
# Authors: Clemens Brunner
# Martin Billinger
# Matthieu Perrot
# Mathieu Blondel
# License: BSD 3-Clause
from __future__ import print_function
import warnings
import numpy as np
from scipy import linalg
from .extern... | waterponey/scikit-learn | sklearn/discriminant_analysis.py | Python | bsd-3-clause | 28,643 | [
"Gaussian"
] | 53941702885df991c2269ebb70da356c078280fc1fad380e721b50f347979c0a |
import pytest, py
from _pytest.main import Session
class TestCollector:
def test_collect_versus_item(self):
from pytest import Collector, Item
assert not issubclass(Collector, Item)
assert not issubclass(Item, Collector)
def test_compat_attributes(self, testdir, recwarn):
modc... | Akasurde/pytest | testing/test_collection.py | Python | mit | 23,112 | [
"VisIt"
] | 85a6769febef1356da22595cdb4845170dc114c3c657b5cefca013288f7c7ea8 |
from py.config.options import Boolean, Integer, String, StringList
class ALLOW_IRQ_NESTING(Boolean):
value = True
tag = ["build"]
undef = True
descr = "If set to !0, allow nested irq processing"
class ARM_CLK(Boolean):
value = False
tag = ["general"]
undef = True
descr = "Arm clock in hz"
class BENCHM... | anandkp92/waf | py/waf/defaults/options.py | Python | gpl-2.0 | 57,446 | [
"CRYSTAL"
] | c26610bdb75285d87cfbd69c4aa5ab8cf78888d8205a2431daf1a0d45727dc7a |
# -*- coding: utf-8 -*-
"""
====================
Zen
====================
* Tools for reading and writing files for Zen and processing software
* Tools for copying data from SD cards
* Tools for copying schedules to SD cards
Created on Tue Jun 11 10:53:23 2013
@author: jpeacock-pr
"""
#==================... | MTgeophysics/mtpy | mtpy/usgs/zen.py | Python | gpl-3.0 | 107,020 | [
"Gaussian"
] | 257050105ca2534830c24bf03dca781dcb247aac5c4982440736c1fab0d75825 |
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import json
import logging
import os, shutil, zipfile
import subprocess
from urllib.parse import urlparse
#
# DatabaseInteractor
#
class DatabaseInteractor(slicer.ScriptedLoadableModule.ScriptedLoadableModule):
def __init__(self... | ClementMirabel/DatabaseInteractorExtension | DatabaseInteractor/DatabaseInteractor.py | Python | apache-2.0 | 79,849 | [
"VTK"
] | d2928ce17b3f1b2eaf944f47145a3ef28f02008d2a824782cdf4838dee044ee8 |
from __future__ import print_function
import h2o
import sys
sys.path.insert(1,"../../../") # allow us to run this standalone
from tests import pyunit_utils
from h2o.estimators.gbm import H2OGradientBoostingEstimator
from h2o.estimators.random_forest import H2ORandomForestEstimator
from h2o.estimators.deeplearning impo... | mathemage/h2o-3 | h2o-py/tests/testdir_algos/stackedensemble/pyunit_stackedensemble_regression.py | Python | apache-2.0 | 7,468 | [
"Gaussian"
] | 953e57e28434c2aa338979b8a0f09c3a34dcbdfd6ac120f3cef4f17e9317cf23 |
# Copyright (c) 2015,Vienna University of Technology,
# Department of Geodesy and Geoinformation
# All rights reserved.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND F... | TUW-GEO/SMDC-performance | smdc_perftests/performance_tests/test_scripts.py | Python | bsd-3-clause | 14,747 | [
"NetCDF"
] | cdc0b857c3378cd27ae6ba10da9fa3ab6bad113e6ca0a20fdc3383745a005f02 |
# Copyright (C) 2007 Alexandre Conrad, alexandre (dot) conrad (at) gmail (dot) com
# Copyright (C) 2009 Alexandre Bourget, alex@bourget.cc
#
# This module is part of FormAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
from formalchemy import config
from sqlalchemy.or... | abourget/formalchemy-abourget | formalchemy/utils.py | Python | mit | 4,067 | [
"VisIt"
] | acb596b98477daba4c6545db2e4ac532c7fe2d1f2f1a3ca847fbc63de0184c91 |
# -*- coding: utf-8 -*-
"""
Created on Thu Sep 8 09:21:38 2016
@author: Felipe Leno
This file implements our advisor-advisee proposal.
This agent act as SARSA, and the exploration strategy is changed according to our proposal
"""
from sarsatile import SARSATile
from threading import Thread
from advice_util import ... | cowhi/HFO | experiments/agents/adhoc.py | Python | mit | 8,788 | [
"VisIt"
] | 1b5a91512b641bfae42bdf6d6e524a46467454899b3984cea42c52367fba7682 |
# $HeadURL$
__RCSID__ = "$Id$"
import os, stat, tempfile, shutil
from DIRAC import S_OK, S_ERROR, gConfig, rootPath, gLogger
import DIRAC.Core.Security.Locations as Locations
import DIRAC.Core.Security.File as File
from DIRAC.Core.Security.BaseSecurity import BaseSecurity
from DIRAC.Core.Security.X509Chain import X509... | marcelovilaca/DIRAC | Core/Security/VOMS.py | Python | gpl-3.0 | 12,587 | [
"DIRAC"
] | 6161f79cee05ca8ec2c90cd91696a9297d4091adf58df48d7a4b7782499ba411 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio-Query-Parser.
# Copyright (C) 2014, 2016 CERN.
#
# Invenio-Query-Parser 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
# Licens... | tiborsimko/invenio-query-parser | invenio_query_parser/ast.py | Python | gpl-2.0 | 4,058 | [
"VisIt"
] | 7aa762e805e5c05eb3bbde0f77a1d211eec8c05c9229273b6efb5016520a9a47 |
#! /usr/bin/env python
from __future__ import print_function
from openturns import *
from otsvm import *
# instantiate a kernel=Gaussian with sigma = 2
kernel = ExponentialRBF(2)
x = Point(2, 2.0)
y = Point(2, 1.0)
print(' kernel ([2 2],[1 1]) = %.12g' % kernel(x, y))
print(' dkernel/dx_i([2 2],[1 1]) = ', repr(kern... | openturns/otsvm | python/test/t_ExponentialRBF_std.py | Python | lgpl-3.0 | 696 | [
"Gaussian"
] | 21ece5697b48ab21176570cf8fabc85746acfdc6aeb4c62caed223c2c41140c3 |
#!/usr/bin/env python
# this script writes out WB to Repbase blast matches and takes those with no hit to repbase and blasts them agianst one another
# USE:collapse_WB_REPB.py <blast_comparison_file>
# example:/lscr2/andersenlab/kml436/git_repos2/Transposons/files$ python ../scripts/collapse_WB_REPB.py WB_REPB_blast_f... | klaricch/Transposons2 | scripts/collapse_WB_REPB.py | Python | mit | 3,872 | [
"BLAST"
] | 4b59981e378b4d54ce31125e4c0481b219730d62f7c0be64b2fa6e2197cbd2c2 |
"""
@created_at 2014-07-17
@author Exequiel Fuentes <efulet@gmail.com>
@author Brian Keith <briankeithn@gmail.com>
Basado en el trabajo de Juan Bekios-Calfa <juan.bekios@ucn.cl>
"""
# Se recomienda seguir los siguientes estandares:
# 1. Para codificacion: PEP 8 - Style Guide for Python Code (http://legacy.python.or... | efulet/pca | pca/lib/graph.py | Python | mit | 4,256 | [
"Brian"
] | b5991a93cc46e26b66ac3da6ff7e207a08544ee89c6ad50858c9fb56f9c2a08e |
# Copyright (C) 2016 Lewis, Peloton
########################################################################
# Python script to compute CMB weak lensing biases (N0, N1)
# and derivatives. Internal computations are done in Fortran.
# Authors: (Fortran) Antony Lewis, (Python, and f2py) Julien Peloton
# Contact: j.peloton... | JulienPeloton/lensingbiases | LensingBiases.py | Python | gpl-3.0 | 14,283 | [
"Gaussian"
] | 6c69230c7552ddc01cec99a636704bf277e1791f219b680441bbe5f421eba8b9 |
# modified mexican hat wavelet test.py
# spectral analysis for RADAR and WRF patterns
# NO plotting - just saving the results: LOG-response spectra for each sigma and max-LOG response numerical spectra
# pre-convolved with a gaussian filter of sigma=10
import os, shutil
import time, datetime
import pickle
imp... | yaukwankiu/armor | tests/modifiedMexicanHatTest15_march2014wrf.py | Python | cc0-1.0 | 7,794 | [
"Gaussian"
] | d550095ca62f3252c1980b4bc6894b32cd143081b1845701f717fcfc728c383f |
###
### This script can be run with pvpython rather than pvbatch, as it does not
### need mpi.
###
### Purpose:
###
### Read all timesteps of the halos point files (vtu), each of which has a
### fiew halo points, and also read the resampled magnitude image data files
### (vti).
###
### For the few halo points... | Kitware/cinema | scripts/data_generation/cosmology/hacc_magnitude_halos_tent.py | Python | bsd-3-clause | 11,003 | [
"ParaView"
] | 5a6a425d5e244cc49655a04b9d30966aa6d81941605c509e61bfaadc6c3f355c |
#_PYTHON_INSERT_SAO_COPYRIGHT_HERE_(2007)_
#_PYTHON_INSERT_GPL_LICENSE_HERE_
from math import sqrt
from sherpa.utils import SherpaTestCase
from sherpa.optmethods import optfcts
## from sherpa.optmethods import myoptfcts
from sherpa.optmethods import _tstoptfct
class test_optmethods(SherpaTestCase):
def setUp(self... | brefsdal/sherpa | sherpa/optmethods/tests/test_optmethods.py | Python | gpl-2.0 | 11,391 | [
"Gaussian",
"VisIt"
] | b06023cee5a9df92c21b1c0b28b46e44d8d34419d4639a682044cb118a7ce781 |
# coding: utf-8
# Copyright (c) Materials Virtual Lab
# Distributed under the terms of the BSD License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
import random
import numpy as np
import pandas as pd
from copy import copy
from pymatgen import Structure
def doc_from(stru... | materialsvirtuallab/veidt | veidt/potential/processing.py | Python | bsd-3-clause | 8,390 | [
"pymatgen"
] | 159ac56acad87e4b6c3fb4e59407f62fc47e6bcace368d1cdc910486a19eeda1 |
#!/usr/bin/env python3
# Implementation of BEB model, see: [1]
# Electron-impact ionization cross sections for polyatomic molecules, radicals, and ions
# Yong-Ki Kim and Karl K. Irikura, 2000
# https://doi.org/10.1063/1.1336281
# The original paper:
# Binary-encounter-dipole model for electron-impact ionization
# K... | PHOTOX/photoxrepo | MISC/BEB/beb.py | Python | mit | 8,370 | [
"Gaussian"
] | 99044094f5b77da33d66d2f35d624a65e95e5fca2f250a351d2de6a43decf85c |
# -*- coding: UTF-8 -*-
# Copyright (C) 2016 Sylvain Taverne <taverne.sylvain@gmail.com>
#
# 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) ... | hforge/itools | itools/pkg/build_gulp.py | Python | gpl-3.0 | 4,312 | [
"GULP"
] | 997d40931f2b393e09bba9fea6b10455a91043e64a027e1b3119f940cd61bc1e |
# Copyright 2017 Canonical Ltd.
# Licensed under the LGPLv3, see LICENCE file for details.
from unittest import TestCase
import requests
from mock import (
patch,
)
from httmock import (
HTTMock,
urlmatch,
response
)
import macaroonbakery.httpbakery as httpbakery
ID_PATH = 'http://example.com/somep... | fabricematrat/py-macaroon-bakery | macaroonbakery/tests/test_bakery.py | Python | lgpl-3.0 | 9,500 | [
"VisIt"
] | 4c22d42663aad20cc084bbd35ae8b4cb333916468dedc144a14f304c5c103514 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | symbolic_functionals/syfes/scf/scf_test.py | Python | apache-2.0 | 6,472 | [
"PySCF"
] | 0346b45ba66594598027118c0a4f2851541d1a20918d98ce379df90bb06d6afa |
#!/usr/bin/env python
import os
from optparse import OptionParser
from ase.io.trajectory import print_trajectory_info
from ase.io.bundletrajectory import print_bundletrajectory_info
description = 'Print summary of information from trajectory files.'
def main():
p = OptionParser(usage='%prog file.traj [file2.traj ... | grhawk/ASE | tools/ase/cli/info.py | Python | gpl-2.0 | 667 | [
"ASE"
] | b4caad3e64f11525a89a36b7a110d64e9bf5618e2900a842a76410cc76c43e7f |
from django.http import HttpResponse, HttpResponseRedirect
from django.template import RequestContext, loader
from django import forms
from django.shortcuts import render
from scrape.models import Article
from scrape.models import Rating
import collections
import random
import results
def index(request):
retur... | ajerneck/rand-art | randart/scrape/views.py | Python | gpl-2.0 | 2,562 | [
"exciting"
] | 906d82dc08c8fb602e4bf27508c0211c657ab3273195bdfe9827cb34e91452ca |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import gobject
import gtk, os, pango, sys
from zeroinstall import _
from zeroinstall.injector import model, writer
from zeroinstall import support
from zeroinstall.gtkui import gtkutils
import utils
... | timdiels/0install | zeroinstall/0launch-gui/impl_list.py | Python | lgpl-2.1 | 6,820 | [
"VisIt"
] | 0bf5a9d80df3e9cdb0a91a6242ae9cfbef780969933ea3d67f74a1e20b4aba76 |
# -*- coding: utf-8 -*-
import os
import os.path as osp
import sys
import argparse
import pickle
import six
import glob
from itertools import chain
from collections import defaultdict
import yaml
import xarray as xr
import psyplot
from psyplot.docstring import docstrings
from psyplot.warning import warn
from psyplot.co... | Chilipp/psyplot | psyplot/__main__.py | Python | gpl-2.0 | 16,946 | [
"NetCDF"
] | dca280fc9e67d06502659636ec07ce1bfbf205881303654930026d9769a757eb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
spectro14: FAME-UHD (ESRF/BM16) X-ray emission spectrometer
===========================================================
"""
import math
import numpy as np
from sloth.utils.bragg import (
HC,
SI_ALAT,
GE_ALAT,
d_cubic,
get_dspacing,
kev2wlen,
... | maurov/xraysloth | sloth/inst/spectro14.py | Python | bsd-3-clause | 5,511 | [
"CRYSTAL"
] | 1abf29ca288334e465725f5cb37959ef7b08779cd453dfb7618dec5488b5fbe9 |
# Original code: Copyright 2014 The University of Melbourne
# Copyright 2015 VPAC
#
# This file is part of Karaage.
#
# Karaage is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, ... | monash-merc/karaage | karaage/tests/client.py | Python | gpl-3.0 | 3,908 | [
"VisIt"
] | 6c03a79b01c09e2036cd22c8d35f6c69f1b14a2fc328716de080d334851a1d88 |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# Redistribution and use in ... | licode/scikit-xray | skbeam/core/recip.py | Python | bsd-3-clause | 12,782 | [
"CRYSTAL"
] | ed317cf8d5729f23921dc35856f36f01e5a3c452eb70bccb5af9448f94cf7e58 |
from theory import *
from galaxy import *
from orbitreducer import *
from pyoglue import *
| adrn/GalaxySynth | synthetic/__init__.py | Python | mit | 91 | [
"Galaxy"
] | 8a32d6c3c078623e3d468294cf093bbb9c474288e03d458f106574f0d2b4e728 |
"""
Main module from which the application is started and the web interface mounted
To start the application directly using the python web server, you can just do
::
python web.py
Refer to server installation documentation for more details how to deploy in production.
"""
from octopus.core import app, initialis... | JiscPER/jper-oaipmh | service/web.py | Python | apache-2.0 | 1,408 | [
"Octopus"
] | fbbbf91d23c6805d1ba6b4477a2e060a632a7b14757aed201fd0dae97cf9348e |
## \file
## \ingroup tutorial_roofit
## \notebook -nodraw
## Data and categories: latex printing of lists and sets of RooArgSets
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
import ROOT
# Setup composite pdf
# --------------------------------------
# Declare o... | root-mirror/root | tutorials/roofit/rf407_latextables.py | Python | lgpl-2.1 | 3,044 | [
"Gaussian"
] | 7fccf783110968907c67d43c8e851b28961a6f18170817b4f15cfc1783aca3a0 |
#coding:utf-8
import os, sys
import timeit
import numpy, math
import scipy.spatial.distance as sp
import common_functions
################################################
# Parameters
################################################
# define the default parameters
train = "DR1"
test = "DR2"
lesions = ["exsudato-duro... | piresramon/retina.bovw.plosone | source/mid_level_script.py | Python | gpl-3.0 | 9,219 | [
"Gaussian"
] | cba8735572ccb21c42094c77e50395069bda2dcb5ea37bab361c608f886326d0 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ProcessPoolExecutor.
The follow diagram and text describe the data-flow through the system:
|======================= In-process =====================|== Out-of-process ==|
+----------+ +----------... | cstipkovic/spidermonkey-research | python/futures/concurrent/futures/process.py | Python | mpl-2.0 | 14,847 | [
"Brian"
] | 4811c31de39069b5f437a7bbc10ddb59e87f3fa6607d71b365f4988409adef1d |
# Copyright 2019 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... | petewarden/tensorflow | tensorflow/python/keras/layers/preprocessing/image_preprocessing.py | Python | apache-2.0 | 52,762 | [
"Gaussian"
] | a1e4a7ef06cac9c27f1fa6a161622774edf99a77385b3427dec351e343f61e56 |
# Copyright 2017 Google, Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | jiaphuan/models | research/learned_optimizer/problems/problem_generator.py | Python | apache-2.0 | 35,915 | [
"Gaussian"
] | 213f4f1b80e9216a3c325d788ff9d81edec7d0e390eac72edb106416171fcb13 |
"""User-friendly public interface to polynomial functions. """
from __future__ import print_function, division
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple
)
from sympy.core.mul import _keep_coeff
from sympy.core.symbol import Symbol
from sympy.core.basic import preorder_traversal
... | Arafatk/sympy | sympy/polys/polytools.py | Python | bsd-3-clause | 173,160 | [
"Gaussian"
] | 152bfa632eb4a920dc148a59682a28ebb0fdc8c2ef8a5998aead6630a21a8366 |
# coding: utf-8
"""
PyKrige
=======
Code by Benjamin S. Murphy and the PyKrige Developers
bscott.murphy@gmail.com
Summary
-------
Contains class OrdinaryKriging3D.
References
----------
.. [1] P.K. Kitanidis, Introduction to Geostatistcs: Applications in
Hydrogeology, (Cambridge University Press, 1997) 272 p.
..... | bsmurphy/PyKrige | pykrige/ok3d.py | Python | bsd-3-clause | 39,755 | [
"Gaussian"
] | cb5d0705963e250af188b718232deb1b8b662ff33ab269fd65965295196e7ae4 |
#!/usr/bin/python
#=============================================================================================
# Test MBAR by performing statistical tests on a set of of 1D harmonic oscillators, for which
# the true free energy differences can be computed analytically.
#
# A number of replications of an experiment i... | kyleabeauchamp/pymbar | examples/harmonic-oscillators/harmonic-oscillators-distributions.py | Python | lgpl-2.1 | 12,247 | [
"Gaussian"
] | 77d38c6afea68b095e21a11394d5cd043afc8ddc5d16892c0f19bd517d90de9e |
"""
SLSClient class is a client for the SLS DB, looking for Status of a given Service.
"""
import socket
import urllib2
from xml.dom import minidom
from DIRAC import S_OK, S_ERROR
def getAvailabilityStatus( sls_id, timeout = None ):
"""
Return actual SLS availability status of entity in sls_id.
Use SLS API: fa... | avedaee/DIRAC | Core/LCG/SLSClient.py | Python | gpl-3.0 | 1,532 | [
"DIRAC"
] | 9369029db2f37534be65d8096896fc2626e596aec952e7891b03594ae5232f1e |
"""
This pipeline is intended to extract spatial information --- euclidean
distance to the neareast neighbour contour point --- from standalone file.
"""
import os
import numpy as np
from protoclass.data_management import T2WModality
from protoclass.data_management import GTModality
from protoclass.preprocessing im... | I2Cvb/mp-mri-prostate | pipeline/feature-extraction/spatial/pipeline_extraction_distance_contour.py | Python | mit | 4,060 | [
"Gaussian"
] | 935cfc0273578b35a28891d0713971989b0fcf4faa7ace82ede4f5d91ff6d08e |
from __future__ import absolute_import
import ast
import re
import operator as op
import pyparsing
from ..exceptions import CloudflareSolveError
from . import JavaScriptInterpreter
# ------------------------------------------------------------------------------- #
_OP_MAP = {
ast.Add: op.add,
... | alfa-addon/addon | plugin.video.alfa/lib/cloudscraper/interpreters/native.py | Python | gpl-3.0 | 8,626 | [
"VisIt"
] | 953652c4338f30cd48a119c120afaf4beb73bdb64b7020d1edd058464fd461d2 |
"""
Acceptance tests for the certificate web view feature.
"""
from common.test.acceptance.tests.helpers import UniqueCourseTest, EventsTestMixin, load_data_str, get_element_padding
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc, CourseUpdateDesc... | TheMOOCAgency/edx-platform | common/test/acceptance/tests/lms/test_certificate_web_view.py | Python | agpl-3.0 | 9,797 | [
"VisIt"
] | 7b13851ede172650d85e70552582e0cbc761510596ad155589ab8051b91c611b |
# -*- coding: utf-8 -*-
#
# Maximum Temperature Renderer for Dreambox/Enigma-2
# Coded by Vali (c)2010
# Support: www.dreambox-tools.info
#
#
# This plugin is licensed under the Creative Commons
# Attribution-NonCommercial-ShareAlike 3.0 Unported License.
# To view a copy of this license, visit http://crea... | sklnet/opendroid-enigma2 | lib/python/Components/Renderer/DMCHDMaxTemp.py | Python | gpl-2.0 | 2,083 | [
"VisIt"
] | 02040f3be5e9012472d80eb2d22c0343a7ef7f02a1809d3663e8a957c4021194 |
#! test fragment decomposition + to/from_dict
import numpy as np
import psi4
from psi4.driver import qcdb
def test_chgmult(expected, cgmpdict, label):
rc, rfc, rm, rfm = expected
qcdb.compare_integers(rc, cgmpdict['molecular_charge'], label + ': c')
qcdb.compare_integers(rm, cgmpdict['molecular_multiplici... | amjames/psi4 | samples/python/mints13/test.py | Python | lgpl-3.0 | 4,091 | [
"Psi4"
] | cc3d9c5ce6177f17a35ec44a49471e2d65d7355cb4a04f24b6182f81fb0e8d12 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/core/ui/plugindialog.py | Python | gpl-2.0 | 5,363 | [
"Brian"
] | aae43906326840ec2192847760084482bf68854bf98c864b2c95fd2e8ed43582 |
'''
Code for generating the sham catalogs.
Author : ChangHoon Hahn
'''
import os
import h5py
import numpy as np
from numpy import log10, Inf
from scipy import integrate, interpolate, ndimage
def DownloadedCatalog(catalog='bolshoi'):
''' Take .list format downloaded catalog and load it into an .hdf5 file for... | mjvakili/gambly | code/sham.py | Python | mit | 40,863 | [
"Gaussian"
] | 8185ce4596e15dabb278ccb1b8ca5e1acc49d58848354485e17459bcad994cb3 |
# Copyright (C) 2010-2018 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... | mkuron/espresso | testsuite/python/elc_vs_mmm2d_neutral.py | Python | gpl-3.0 | 5,884 | [
"ESPResSo"
] | 4f0e659fb4e810c4fdd86b7460f807536f7175631ced5656f0c019f31faa1995 |
# -*- coding: utf-8 -*-
#
# @most/core documentation build configuration file, created by
# sphinx-quickstart on Mon Jun 12 07:51:42 2017.
#
# 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.
#
... | axefrog/core | docs/conf.py | Python | mit | 4,803 | [
"Brian"
] | b1e57354d9d11bfd4f961f69b0e6f38dd695659afa01f3bbe0675426a4286684 |
"""
This file is part of the DiffractionMicroscopy project.
Copyright 2016 David W. Hogg (NYU, SCDA).
This piece of code does nothing related to diffraction.
It only shows that you can reconstruct an image from small numbers of
photons taken in exoposures at unknown orientations.
# issues
- Should we apply the rotati... | davidwhogg/DiffractionMicroscopy | code/toyproblems/twodimage.py | Python | mit | 8,207 | [
"Gaussian"
] | 773cf1577ce5f6dd08bde95a3f24d2b621defab8f156aaeba3513136366e5fdd |
"""
Plots the 2D pressure field from a IBAMR simulation at saved time-steps using
the visualization software VisIt.
"""
from snake.ibamr.simulation import IBAMRSimulation
simulation = IBAMRSimulation()
body_name = 'flyingSnake2dAoA35ds004filledInside' # file name (no extension)
simulation.plot_field_contours_visit... | barbagroup/cuIBM | external/snake-0.3/examples/ibamr/plotPressure.py | Python | mit | 591 | [
"VisIt"
] | d7bf20f79c9df5a180124505d06182bafd92a8889538b70e2645ace7d2c171f1 |
from neo.core.baseneo import BaseNeo
class Unit(BaseNeo):
"""
A :class:`Unit` regroups all the :class:`SpikeTrain` objects that were emitted
by a neuron during a :class:`Block`. The spikes may come from different :class:`Segment` objects
within the :class:`Block`, so this object is not contained in... | tkf/neo | neo/core/unit.py | Python | bsd-3-clause | 1,869 | [
"NEURON"
] | 6b3c269c889c14c00f6439ed3cecfa1cd87121f03b54b1e34337198522bef0e9 |
# Copyright 2016 Brian Innes
#
# 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, ... | brianinnes/vPiP | python/test2.py | Python | apache-2.0 | 1,586 | [
"Brian"
] | 9e6b34f7ffb49eff9e16f077d08fe059f21cadeabe84ca61b2b287bf167f564b |
#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# viz_gl.py
# Purpose: viz running LAMMPS simulation via GL tool in Pizza.py
# Syntax: viz_gl.py in.lammps Nfreq Nsteps
# in.lammps = LAMMPS input script
# Nfreq = dump and viz shapshot every this many steps
# ... | Dixon3/lammps | python/examples/viz_gl.py | Python | gpl-2.0 | 1,952 | [
"LAMMPS"
] | 7ffbcb8e4ddf667899808f5b0b3fcecc38ee1e502281def7b1c898ee85038545 |
# 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... | ZhangXinNan/tensorflow | tensorflow/contrib/kfac/python/ops/estimator.py | Python | apache-2.0 | 20,349 | [
"Gaussian"
] | 4f95d4487dc2da9393085940310ed7f5294696ca1d8048852c59f353d25ea8b3 |
import os.path as osp
import pickle
import time
import numpy as np
from mastic.selection import CoordArray
from mastic.molecule import Atom, Bond
# must set this to pickle substantiated systems sometimes
#sys.setrecursionlimit(100000)
# load the system type pickle in
inputs_path = osp.realpath("../../examples/sEH-T... | salotz/mast | prototypes/profile_system/profile_bond_creation.py | Python | mit | 1,629 | [
"RDKit"
] | 9c287c5f2604f10984965936dcb87f8627c91cdb4090979026ba61608a4abb48 |
#
# Copyright 2014 Flytxt
#
# 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 ... | himanshu14/GMM | GMMclustering.py | Python | apache-2.0 | 8,344 | [
"Gaussian"
] | d111ed2073c6b752379ba879660f517d9819b1e1a04b5b7ed50fa0cac1b354b5 |
# Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![Latest Version]
... | jtwhite79/pyemu | versioneer.py | Python | bsd-3-clause | 68,612 | [
"Brian"
] | e5d1bd168335fa5e80818c932767e526d0e58b159146e288c1810ab7fd2fb359 |
from __main__ import vtk, qt, ctk, slicer
import numpy
import copy
from math import *
from slicer.ScriptedLoadableModule import *
import os
import pickle
import time
from slicer.util import VTKObservationMixin
class ModelAddedClass(VTKObservationMixin):
def __init__(self, anglePlanes):
VTKObservationM... | fbudin69500/AnglePlanes-Extension | AnglePlanes/AnglePlanes.py | Python | apache-2.0 | 69,029 | [
"VTK"
] | 2e5aee6ea155507ee7e9df53b1e32b7e42c258bdc12fa10a5bb1ee71a1c66f99 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | GNOME/orca | src/orca/scripts/apps/soffice/braille_generator.py | Python | lgpl-2.1 | 6,388 | [
"ORCA"
] | a2343789c745cadc3a3e0fb2631a9956d272173ae6b206e5226c58d4257509ad |
# 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... | fweik/espresso | testsuite/python/simple_pore.py | Python | gpl-3.0 | 3,020 | [
"ESPResSo"
] | 470aa1efb6d07874aea074df8c1cc5252a7b90f3612f5870b0fe96ac0990f3ea |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Calculation methods related to volume based on cclib data."""
from __future__ import print_function
import c... | Schamnad/cclib | src/cclib/method/volume.py | Python | bsd-3-clause | 9,899 | [
"Gaussian",
"VTK",
"cclib"
] | c1df094f373b02fd5f7f6842417993189684d8ee5561dda5d459fe650a724fc1 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | fedepad/espressopp | src/integrator/__init__.py | Python | gpl-3.0 | 2,833 | [
"ESPResSo"
] | 09929ecb6ef776e41581b8c84278d3b6f4b9ad944b0832d136ca9cd0bcd5142a |
# -*- coding:utf-8 -*-
"""PyHdust *spectools* module: spectroscopy tools
Algumas definicoes: para todas as rotinas funcionarem, todos os espectros devem
estar agrupados num mesmo caminho (`path`), em estrutura de
noite/estrelas/espec.
Currently the functions only read ``*.cal.fits`` files. The ``.cal`` suffix means ... | danmoser/pyhdust | pyhdust/spectools.py | Python | gpl-3.0 | 130,184 | [
"Gaussian"
] | ed75e46ab82f21701cb49538289d991236f0c8d2c6263638cefe2cebf51186fb |
import mdtraj as md
import tensorflow as tf
import tftraj.rmsd_op
import numpy as np
import math
def main():
rmsd_op = tftraj.rmsd_op.load()
traj = md.load(['../../fs_peptide/trajectory-{}.xtc'.format(i + 1) for i in range(28)],
top='../../fs_peptide/fs-peptide.pdb')
traj = traj[::10]
... | mdtraj/tftraj | examples/rmsd-consensus/rmsd-consensus.py | Python | mit | 1,368 | [
"MDTraj"
] | bad833d978384e6b4fa5e25edb3295f80e181b6278a5914ed84b1a9cc6c7028e |
#!/usr/bin/python
import sys
def read_in_fasta_sequences(input_file,input_file_format):
"""Function that reads in a file of sequences
Using biopython SeqIO and returns a list of SeqIO seq record objects"""
import Bio.SeqIO
sequence_record_list=[]
for seq_record in Bio.SeqIO.parse(input_file,inp... | fmaguire/scripts | rosalind/rosalind_solutions.py | Python | mit | 4,346 | [
"Biopython"
] | d74b79ed93d63fe2314781e3885b41b08035a8e8ff5355461ba7867a3e2fc038 |
# -*- 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_sellablecategoryeditor.py | Python | gpl-2.0 | 1,701 | [
"VisIt"
] | a6877382be6629745f802c59f7e240b3bc64a8415f27a972cb89f357b2b48d36 |
# -*- coding: utf-8 -*-
#
desc = 'Noise with a color bar'
# phash = 'f54b0ba50bb10bf4'
phash = 'fd5a0bb503f50354'
def plot():
from numpy.random import randn
from matplotlib import pyplot as plt
import numpy as np
# Make plot with vertical (default) colorbar
fig = plt.figure()
ax = fig.add_sub... | dougnd/matplotlib2tikz | test/testfunctions/noise.py | Python | mit | 748 | [
"Gaussian"
] | 421d107b81e9e67b3889efa96f88cfd5d652ceb0394b4c0140fe416dfc50de39 |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | Forage/Gramps | gramps/plugins/textreport/simplebooktitle.py | Python | gpl-2.0 | 7,542 | [
"Brian"
] | 3b94b7eddf27b1b7fb5cc720313989825d22c1c67a9f2833da7cf9a72a13fc6c |
# -*- 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... | tiagocardosos/stoq | stoqlib/gui/test/test_account_editor.py | Python | gpl-2.0 | 4,606 | [
"VisIt"
] | e3744b98ac0d63952acb871a586266e773209d239e09de5bb594f53fd9444d3c |
"""
deep Boltzmann machines (greedy unsupervised pretraining + supervised training)
"""
import logging
from itertools import repeat
from .abcs import OpTrain
from tsdl.data import OpDataset
from tsdl.tools import Classification
from lazyflow.operator import InputSlot
from pylearn2.models import mlp
from pylearn2.m... | burgerdev/hostload | tsdl/classifiers/deep.py | Python | mit | 7,930 | [
"CDK"
] | 28a64ed09bf9ff162aabb9f760974eea4f2dd71131eb7687ce93d6dc71cc5c39 |
class mutation_stability(object):
'''
check mutation and format it so that it's compatible with foldx structure 1HA0 and 2YP7
'''
def __init__(self, mut, structure):
self.mut = mut # list of mutations
self.mut_chain_info =[]
self.structure = structure # either 1HA0 or 2YP7
... | blab/stability | augur/stability-data/foldx_essentials/mutation_stability.py | Python | agpl-3.0 | 2,451 | [
"FoldX"
] | c5b8c30a6a1c3680c4b2eb5abdfc49cdad6b3f2f6ff6048be488585a6393f6a3 |
#!/usr/bin/env python
# Todo Copy V1.4 by Dan Rahmel
# (c) Copyright 2007-2017 by Dan Rahmel
# Created December 21, 2007
# Todo Copy can be controlled either by direct commands or through an XML-based batch file.
# If no parameters are given when it is executed, it will look for the batch file tc_autorun.xml
# and exe... | drahmel/todocopy | todocopy.py | Python | gpl-2.0 | 83,140 | [
"VisIt"
] | 1cc04ee9cc8c77b6444fe47472e671a6073093294c2db44f7e10757e6e0d5313 |
from sqlalchemy import create_engine
from sqlalchemy.orm import sessionmaker
from models import *
engine = create_engine('postgresql://catalog:catalog@localhost:5432/catalog')
base.Base.metadata.bind = engine
DBSession = sessionmaker(bind=engine)
session = DBSession()
# Create a first user for entering items
user = u... | caasted/aws-flask-catalog-app | database_fill.py | Python | mit | 21,493 | [
"Galaxy",
"VisIt"
] | a54097013d80a62b779ecbc78988cedabbf7e734ae01f2e2442c10ff274a6f7f |
from __future__ import annotations
from scitbx.array_family import flex
from dials.algorithms.clustering import plots
from dials.util.observer import Observer, singleton
def uc_params_from_experiments(experiments):
uc_params = [flex.double() for i in range(6)]
for expt in experiments:
uc = expt.crys... | dials/dials | algorithms/clustering/observers.py | Python | bsd-3-clause | 1,973 | [
"CRYSTAL"
] | 1d63a50337fc4887d2c03669acc4630239fa58fe6eb513623598ce2329ae255c |
# -*- coding: utf-8 -*-
# Copyright (C) 2012, Almar Klein, Ant1, Marius van Voorden
#
# This code is subject to the (new) BSD license:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of s... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/images2gif/images2gif.py | Python | gpl-3.0 | 38,106 | [
"NEURON"
] | cfb5b69881a5b65d7fa25bdc6a1a1f42fd6743dba03be2258253c5ab705b6782 |
# VAPiD is an extremely lightweight virus genome annotator that takes any number of viral genomes and annotates them
# producing files suitable for NCBI submission
# Vapid Version
VERSION = 'v1.6.6'
import subprocess
import re
import argparse
import timeit
import os
from Bio.Seq import Seq
from Bio.Blast import NCBIW... | rcs333/ClinVirusSeq | vapid.py | Python | mit | 47,219 | [
"BLAST"
] | 4588fd00bc15a2ebeea104fa4b3038bff901ded17b4af39a47885f9c96ad422e |
# -*- 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-datalabeling | tests/unit/gapic/datalabeling_v1beta1/test_data_labeling_service.py | Python | apache-2.0 | 417,398 | [
"Octopus"
] | 1c85054294524d682bd88ec694948ea33367ad2724cf6030ebae8e87ca4a224b |
############################################
# Copyright (c) 2012 Microsoft Corporation
#
# Auxiliary scripts for generating Makefiles
# and Visual Studio project files.
#
# Author: Leonardo de Moura (leonardo)
############################################
import sys
import os
import glob
import re
import getopt
import ... | traiansf/z3-java | scripts/mk_util.py | Python | mit | 123,782 | [
"cclib"
] | 698889b8287ace66e5a181923dd736993473bc8a54df4823afd19538e94a615e |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either vers... | marscher/PyEMMA | pyemma/coordinates/tests/test_featurereader_and_tica.py | Python | lgpl-3.0 | 4,496 | [
"MDTraj"
] | 0421315e8b1d0ae8c2975c090ce1b9b81a69718ff29aac52accad7c163dc797d |
import os
from os.path import dirname, join
from collections import OrderedDict
import pandas as pd
import numpy as np
import json
from bokeh.io import curdoc
from bokeh.layouts import row, widgetbox, column, gridplot, layout
from bokeh.models import Select, Div, Column, \
HoverTool, ColumnDataSource, Button, RadioB... | joshgabriel/dft-crossfilter | CompleteApp/crossfilter_prec_app/main.py | Python | mit | 28,527 | [
"DMol3",
"VASP"
] | 4e7fa96f435c4f59f352f40bae6e4bf8ca34d207943171fd7e418850f8ecdfe8 |
"""Convolutional/Variational autoencoder, including demonstration of
training such a network on MNIST, CelebNet and the film, "Sita Sings The Blues"
using an image pipeline.
Copyright Parag K. Mital, January 2016
"""
import tensorflow as tf
import numpy as np
import os
from libs.dataset_utils import create_input_pipel... | goddoe/super_resolution | src/libs/vae.py | Python | mit | 19,291 | [
"Gaussian"
] | 3c8de51e9a722135df3920c33d7e65e4b9f0c4b6ae30fbb514d18fe70ea4ca01 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/alignment/tests/test_tabular_msa.py | Python | bsd-3-clause | 148,436 | [
"scikit-bio"
] | da7d9936f0f7cb6ee705feac4ecc465a0a28d83a71780da4188fcf6ae05132eb |
import numpy as np
from scipy import linalg
from scipy import spatial
# Covariance functions
def approx_quantile(coverage_prob, d, n, exp=1):
'''
Compute approximate coverage_prob quantile of maximal distance between n
spherically-distributed points with identity covariance and the origin.
Arguments... | awblocker/quantitation | lib/quantitation/emulate.py | Python | bsd-3-clause | 14,952 | [
"Gaussian"
] | 9831a236225e4d900a09c7f1e0f4e649848fecf2b50b0b165c91f9a44b0043a6 |
#!/usr/bin/env python
# vim:fileencoding=utf-8
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2013, Kovid Goyal <kovid at kovidgoyal.net>'
import sys
from functools import partial
from PyQt5.Qt import (
QMainWin... | sharad/calibre | src/calibre/gui2/tweak_book/editor/image.py | Python | gpl-3.0 | 11,020 | [
"Gaussian"
] | 586fe7d38b29668f7ab0d163c0c3805f31a5645e50c8be0d11ae51c55afd5249 |
# -*- 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-orchestration-airflow | tests/unit/gapic/service_v1beta1/test_image_versions.py | Python | apache-2.0 | 61,434 | [
"Octopus"
] | 13f1efbb451de4b28d1d99272a032e44cd4cdbe8586923aa24517c1332de4d5f |
"""
Visitor to generate a Graphviz .dot file with an AST representation.
"""
from pydot import pydot
import minivisitor
class GraphvizGenerator(minivisitor.PrintTree):
"""
Render a minivect AST as a graphviz tree.
"""
def __init__(self, context, name, node_color=None, edge_color=None,
... | markflorisson/minivect | minivect/graphviz.py | Python | bsd-2-clause | 2,875 | [
"VisIt"
] | 12d5cd36d99c6c7da61c5c2b8273d07c930f948362c7f90caf2301f8b3d85dd8 |
""" StorageManagementDB is a front end to the Stager Database.
There are five tables in the StorageManagementDB: Tasks, CacheReplicas, TaskReplicas, StageRequests.
The Tasks table is the place holder for the tasks that have requested files to be staged.
These can be from different systems and have differe... | hgiemza/DIRAC | StorageManagementSystem/DB/StorageManagementDB.py | Python | gpl-3.0 | 56,306 | [
"DIRAC"
] | b2fa1d4304a99c06bff27a96f7e30a940b86a4a9e4fc8edb28f2cc0fa3048aaa |
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