debian/0000775000000000000000000000000012312553040007163 5ustar debian/changelog0000664000000000000000000000067112312553037011047 0ustar ask (1.0.1-1ubuntu1) trusty; urgency=medium * Add fix-test-control-on-32bit-architectures.diff to fix tests on 32-bit arches. LP: #1256523 * debian/rules: Use --with python2 to fix python depend in control file -- Jackson Doak Tue, 18 Mar 2014 06:49:13 +1100 ask (1.0.1-1) unstable; urgency=low * Initial release (Closes: #713986) -- Pablo Oliveira Fri, 21 Jun 2013 10:44:16 +0200 debian/ask.10000664000000000000000000000422112312553037010030 0ustar .TH ASK "1" "June 2013" "ask 1.0.1" "User Commands" .SH NAME ask \- Adaptive Sampling Kit, a toolkit for sampling big experimental spaces .SH DESCRIPTION ASK stands for Adaptive Sampling Kit. Its main goal is accelerating long experiments. Two kinds of variables define an experiment: a response and a set of factors. The response is characterized on the factors' Cartesian product. When the space is small, the response can be measured for every point in the space. When the space is large, doing an exhaustive measurement is either not possible in terms of execution time or simply not practical. ASK tries to find good approximations of the response by sampling only a small fraction of the space. ASK features multiple active learning algorithms to prioritize the exploration of the interesting parts of the experimental space. .SH SYNOPSIS ask [\-h] [\-\-force_overwrite] [\-\-replay_only] [\-\-skip_model] [\-\-skip_reporter] [\-\-version] configuration .SH COMMAND LINE OPTIONS .TP configuration the experiment configuration file .TP \fB\-h\fR, \fB\-\-help\fR show this help message and exit .TP \fB\-\-force_overwrite\fR If a previous output directory is found its contents will be overwritten .TP \fB\-\-replay_only\fR (Must be run over a full previous ask run). Skip bootstrap and sampler modules, but runs previous labels through the model and reporter. This option is useful if one wants to run sampling and analyze results separately. .TP \fB\-\-skip_model\fR Skip model module. (WARNING: if the chosen control module relies on the output of the model module, this option fails.) .TP \fB\-\-skip_reporter\fR Skip reporter module. (WARNING: if the chosen control module relies on the output of the reporter module, this option fails.) .TP \fB\-\-version\fR show program's version number and exit .SH COPYRIGHT Copyright (C) 2011-2012 Universite de Versailles St-Quentin-en-Yvelines The Adaptive Sampling Kit (ASK) is released under the GNU General Public License, version 2. Please refer to the file LICENSE that accompanies your copy of ASK. .SH SEE ALSO For complete documentation, please refer to the ASK manual which should have been installed in /usr/share/doc/ask. debian/ask.manpages0000664000000000000000000000005612312553037011465 0ustar debian/ask.1 debian/ask-compare-time-series.1 debian/control0000664000000000000000000000340712312553037010600 0ustar Source: ask Section: science Priority: extra Build-Depends: debhelper (>= 8.0.0), texlive-latex-base, texlive-latex-extra, latex-xcolor, python (>=2.6), python-pygments, python-nose, python-argparse, python-numpy, python-scipy, r-base-core (>=2.5), r-cran-gbm, r-cran-rpart, r-cran-lattice, r-cran-rjson, r-cran-lhs, r-cran-tgp, r-cran-inline, r-cran-foptions X-Python-Version: >= 2.6 Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debian Science Maintainers Uploaders: Pablo Oliveira Standards-Version: 3.9.4 Homepage: https://code.google.com/p/adaptive-sampling-kit/ Vcs-Git: git://git.debian.org/git/debian-science/packages/ask.git Vcs-Browser: http://git.debian.org/?p=debian-science/packages/ask.git Package: ask Section: science Architecture: all Depends: ${python:Depends}, ${misc:Depends}, python (>=2.6), python-argparse, python-numpy, python-scipy, r-base-core (>=2.5), r-cran-gbm, r-cran-rpart, r-cran-lattice, r-cran-rjson, r-cran-lhs, r-cran-tgp, r-cran-inline, r-cran-foptions Description: Adaptive Sampling Kit for big experimental spaces Adaptive Sampling Kit (ASK) is a toolkit for sampling big experimental spaces. When the space is small, the response can be measured for every point in the space. When the space is large, doing an exhaustive measurement is either not possible in terms of execution time or simply not practical. ASK tries to find good approximations of the response by sampling only a small fraction of the space. ASK features multiple active learning algorithms to prioritize the exploration of the interesting parts of the experimental space. debian/links0000664000000000000000000000015212312553037010232 0ustar /usr/share/ask/ask /usr/bin/ask /usr/share/ask/utils/compare-time-series /usr/bin/ask-compare-time-series debian/rules0000775000000000000000000000032512312553037010251 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 # This has to be exported to make some magic below work. export DH_OPTIONS override_dh_auto_configure: %: dh $@ --with python2 debian/ask.lintian-overrides0000664000000000000000000000172512312553037013334 0ustar #Workaround for bug #692232 ask: unusual-interpreter usr/share/ask/bootstrap/latinsquare #!Rscript ask: unusual-interpreter usr/share/ask/bootstrap/lowdiscrepancy #!Rscript ask: unusual-interpreter usr/share/ask/common/coef-variation.R #!Rscript ask: unusual-interpreter usr/share/ask/model/gbm_build #!Rscript ask: unusual-interpreter usr/share/ask/model/gbm_predict #!Rscript ask: unusual-interpreter usr/share/ask/model/tgp_build #!Rscript ask: unusual-interpreter usr/share/ask/model/tgp_predict #!Rscript ask: unusual-interpreter usr/share/ask/reporter/generic/1D.R #!Rscript ask: unusual-interpreter usr/share/ask/reporter/generic/2D.R #!Rscript ask: unusual-interpreter usr/share/ask/sampler/amart #!Rscript ask: unusual-interpreter usr/share/ask/sampler/latinsquare #!Rscript ask: unusual-interpreter usr/share/ask/sampler/tgp #!Rscript ask: unusual-interpreter usr/share/ask/source/file #!Rscript ask: unusual-interpreter usr/share/ask/utils/compare-time-series #!Rscript debian/watch0000664000000000000000000000030012312553037010213 0ustar # watch control file for uscan version=3 http://code.google.com/p/adaptive-sampling-kit/downloads/list?can=1 .*/adaptive-sampling-kit-(\d[\d.]*)\.(?:zip|tgz|tbz2|txz|tar\.gz|tar\.bz2|tar\.xz) debian/ask-compare-time-series.10000664000000000000000000000206012312553037013677 0ustar .TH ASK-COMPARE-TIME-SERIES "1" "June 2013" "ask 1.0.1" "User Commands" .SH NAME ask-compare-time-series\- Compares times series generated by ask .SH DESCRIPTION This command plot one or more error timeseries files generated by the Adaptive Sampling Kit. It is useful to compare the accuracy of different sampling methods and configurations. .SH SYNOPSIS ask-compare-time-series output.png timeseries1.out [timeseries2.out...] .SH COMMAND LINE OPTIONS .TP output.png output file for producing the time-series plot comparison .TP timeseries1.out, ... one or more timeseries files produced by ask reporter modules .SH COPYRIGHT Copyright (C) 2011-2012 Universite de Versailles St-Quentin-en-Yvelines This script is part of the Adaptive Sampling Kit (ASK). The Adaptive Sampling Kit (ASK) is released under the GNU General Public License, version 2. Please refer to the file LICENSE that accompanies your copy of ASK. .SH SEE ALSO For complete documentation, please refer to the ASK manual which should have been installed in /usr/share/doc/ask. .PP .BR ask (1) debian/gbp.conf0000664000000000000000000000012112312553037010602 0ustar [DEFAULT] debian-branch=debian upstream-branch=master upstream-tag=v%(version)s debian/compat0000664000000000000000000000000212312553037010367 0ustar 8 debian/patches/0000775000000000000000000000000012312553040010612 5ustar debian/patches/fallback-to-rjson.diff0000664000000000000000000000121012312553037014754 0ustar --- a/common/configuration.R +++ b/common/configuration.R @@ -16,9 +16,14 @@ # Defines the conf function to help reading ASK configuration files from R # modules. -require(RJSONIO, quietly=T) -configuration = fromJSON(paste(readLines(args[1]), collapse=""), +if ("RJSONIO" %in% rownames(installed.packages())) { + require(RJSONIO, quietly=T) + configuration = fromJSON(paste(readLines(args[1]), collapse=""), simplify=F) +} else { + require(rjson, quietly=T) + configuration = fromJSON(paste(readLines(args[1]), collapse="")) +} conf <- function(key, default=NULL) { dollarkey = gsub("\\.","$", key) debian/patches/fix-test-control-on-32bit-architectures.diff0000664000000000000000000000073712312553037021100 0ustar --- tests/test-0003-control.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) --- a/tests/test-0003-control.py +++ b/tests/test-0003-control.py @@ -39,7 +39,7 @@ class ControlTests(CommandLineT): "modules": { "control": { "executable": "control/points", - "params": {"n": 2 ** 32}}}}) + "params": {"n": 2 ** 16}}}}) data = self.tfile("test1.data") r = self.run_module("control/points", debian/patches/series0000664000000000000000000000010412312553037012030 0ustar fallback-to-rjson.diff fix-test-control-on-32bit-architectures.diff debian/copyright0000664000000000000000000000524312312553037011130 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Adaptive Sampling Kit Source: https://code.google.com/p/adaptive-sampling-kit/ Files: * Copyright: 2011-2013 Universite de Versailles St-Quentin-en-Yvelines License: GPL-2 Files: debian/* Copyright: 2013 Pablo Oliveira License: GPL-2 Files: tests/scripttest/* Copyright: 2005-2007 Ian Bicking and contributors License: Expat Files: doc/*.tex doc/figures/* Copyright: 2011-2012 Universite de Versailles St-Quentin-en-Yvelines License: GFDL-NIV License: GPL-2 This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, version 2. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". License: Expat 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, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. License: GFDL-NIV Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the section entitled "GNU Free Documentation License". debian/source/0000775000000000000000000000000012312553040010463 5ustar debian/source/format0000664000000000000000000000001412312553037011677 0ustar 3.0 (quilt) debian/ask.install0000664000000000000000000000100512312553037011333 0ustar ask /usr/share/ask/ default.conf /usr/share/ask/ bootstrap/* /usr/share/ask/bootstrap/ common/* /usr/share/ask/common/ control/* /usr/share/ask/control/ model/* /usr/share/ask/model/ reporter/* /usr/share/ask/reporter/ sampler/* /usr/share/ask/sampler/ source/* /usr/share/ask/source/ utils/* /usr/share/ask/utils/ README /usr/share/doc/ask/ doc/ask-manual-*.pdf /usr/share/doc/ask/ examples/aiaik/ /usr/share/doc/ask/examples/ examples/custom-module/ /usr/share/doc/ask/examples/