[med-svn] [Git][med-team/mmseqs2][master] 2 commits: Modify test binary paths to /usr/lib/mmseqs2
Shayan Doust
gitlab at salsa.debian.org
Wed Jul 17 21:02:25 BST 2019
Shayan Doust pushed to branch master at Debian Med / mmseqs2
Commits:
86745997 by Shayan Doust at 2019-07-16T20:37:27Z
Modify test binary paths to /usr/lib/mmseqs2
In addition, move any required index files needed by the test binaries that CMake never moved itself.
- - - - -
59d0956b by Shayan Doust at 2019-07-16T22:32:50Z
Push copyright file.
Not sure what else could be missing, needs to be altered, or removed.
- - - - -
4 changed files:
- debian/copyright
- debian/mmseqs2.install
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/copyright
=====================================
@@ -1,16 +1,251 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: mmseqs2
-Source: <path_to_download>
-Comment: **** Before manually editing this file you should give ****
- scan-copyrights
- **** available in cme + lib-config-model-dpkg-perl ****
- **** package a try. For existing copyright files try ****
- cme update dpkg-copyright
+Source: https://github.com/soedinglab/MMseqs2
+Files-Excluded: lib/gzstream, lib/zstd
+Comment: The system-wide option of these libraries are much preferred than that in lib/
Files: *
-Copyright: 20xx-20yy <upstream>
-License: <license>
+Copyright: 2016 Söding Lab <https://mpibpc.mpg.de/soeding>
+License: GPLv3
+
+Files: lib/alp/*
+Copyright: 2008 John Spouge
+License: public_domain
+
+Files: lib/cadode/*
+Copyright: 2008 Michiaki Hamada
+License: public_domain
+
+Files: lib/kseq2/*
+Copyright: 2009 Milot Mirdita
+License: MIT
+
+Files: lib/ksw2/*
+Copyright: 2009 Attractive Chaos <attractor at live.co.uk>
+License: MIT
+
+Files: lib/omptl/*
+Copyright: 2006-2011 Fokko Beekhof <Fokko.Beekhof at unige.ch>
+License: LGPL
+
+Files: lib/tinyexpr/*
+Copyright: 2015-2018 Lewin van Winkle
+License: Zlib-Libpng License
Files: debian/*
Copyright: 2019 Shayan Doust <hello at shayandoust.me>
-License: <license>
+License: GPLv3
+
+License: GPLv3
+ 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.
+ .
+ This program 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 <http://www.gnu.org/licenses/>.
+
+License: LGPL
+ This version of the GNU Lesser General Public License incorporates
+ the terms and conditions of version 3 of the GNU General Public
+ License, supplemented by the additional permissions listed below.
+ .
+ 0. Additional Definitions.
+ .
+ As used herein, "this License" refers to version 3 of the GNU Lesser
+ General Public License, and the "GNU GPL" refers to version 3 of the GNU
+ General Public License.
+ .
+ "The Library" refers to a covered work governed by this License,
+ other than an Application or a Combined Work as defined below.
+ .
+ An "Application" is any work that makes use of an interface provided
+ by the Library, but which is not otherwise based on the Library.
+ Defining a subclass of a class defined by the Library is deemed a mode
+ of using an interface provided by the Library.
+ .
+ A "Combined Work" is a work produced by combining or linking an
+ Application with the Library. The particular version of the Library
+ with which the Combined Work was made is also called the "Linked
+ Version".
+ .
+ The "Minimal Corresponding Source" for a Combined Work means the
+ Corresponding Source for the Combined Work, excluding any source code
+ for portions of the Combined Work that, considered in isolation, are
+ based on the Application, and not on the Linked Version.
+ .
+ The "Corresponding Application Code" for a Combined Work means the
+ object code and/or source code for the Application, including any data
+ and utility programs needed for reproducing the Combined Work from the
+ Application, but excluding the System Libraries of the Combined Work.
+ .
+ 1. Exception to Section 3 of the GNU GPL.
+ .
+ You may convey a covered work under sections 3 and 4 of this License
+ without being bound by section 3 of the GNU GPL.
+ .
+ 2. Conveying Modified Versions.
+ .
+ If you modify a copy of the Library, and, in your modifications, a
+ facility refers to a function or data to be supplied by an Application
+ that uses the facility (other than as an argument passed when the
+ facility is invoked), then you may convey a copy of the modified
+ version:
+ .
+ a) under this License, provided that you make a good faith effort to
+ ensure that, in the event an Application does not supply the
+ function or data, the facility still operates, and performs
+ whatever part of its purpose remains meaningful, or
+ .
+ b) under the GNU GPL, with none of the additional permissions of
+ this License applicable to that copy.
+ .
+ 3. Object Code Incorporating Material from Library Header Files.
+ .
+ The object code form of an Application may incorporate material from
+ a header file that is part of the Library. You may convey such object
+ code under terms of your choice, provided that, if the incorporated
+ material is not limited to numerical parameters, data structure
+ layouts and accessors, or small macros, inline functions and templates
+ (ten or fewer lines in length), you do both of the following:
+ .
+ a) Give prominent notice with each copy of the object code that the
+ Library is used in it and that the Library and its use are
+ covered by this License.
+ .
+ b) Accompany the object code with a copy of the GNU GPL and this license
+ document.
+ .
+ 4. Combined Works.
+ .
+ You may convey a Combined Work under terms of your choice that,
+ taken together, effectively do not restrict modification of the
+ portions of the Library contained in the Combined Work and reverse
+ engineering for debugging such modifications, if you also do each of
+ the following:
+ .
+ a) Give prominent notice with each copy of the Combined Work that
+ the Library is used in it and that the Library and its use are
+ covered by this License.
+ .
+ b) Accompany the Combined Work with a copy of the GNU GPL and this license
+ document.
+ .
+ c) For a Combined Work that displays copyright notices during
+ execution, include the copyright notice for the Library among
+ these notices, as well as a reference directing the user to the
+ copies of the GNU GPL and this license document.
+ .
+ d) Do one of the following:
+ .
+ 0) Convey the Minimal Corresponding Source under the terms of this
+ License, and the Corresponding Application Code in a form
+ suitable for, and under terms that permit, the user to
+ recombine or relink the Application with a modified version of
+ the Linked Version to produce a modified Combined Work, in the
+ manner specified by section 6 of the GNU GPL for conveying
+ Corresponding Source.
+ .
+ 1) Use a suitable shared library mechanism for linking with the
+ Library. A suitable mechanism is one that (a) uses at run time
+ a copy of the Library already present on the user's computer
+ system, and (b) will operate properly with a modified version
+ of the Library that is interface-compatible with the Linked
+ Version.
+ .
+ e) Provide Installation Information, but only if you would otherwise
+ be required to provide such information under section 6 of the
+ GNU GPL, and only to the extent that such information is
+ necessary to install and execute a modified version of the
+ Combined Work produced by recombining or relinking the
+ Application with a modified version of the Linked Version. (If
+ you use option 4d0, the Installation Information must accompany
+ the Minimal Corresponding Source and Corresponding Application
+ Code. If you use option 4d1, you must provide the Installation
+ Information in the manner specified by section 6 of the GNU GPL
+ for conveying Corresponding Source.)
+ .
+ 5. Combined Libraries.
+ .
+ You may place library facilities that are a work based on the
+ Library side by side in a single library together with other library
+ facilities that are not Applications and are not covered by this
+ License, and convey such a combined library under terms of your
+ choice, if you do both of the following:
+ .
+ a) Accompany the combined library with a copy of the same work based
+ on the Library, uncombined with any other library facilities,
+ conveyed under the terms of this License.
+ .
+ b) Give prominent notice with the combined library that part of it
+ is a work based on the Library, and explaining where to find the
+ accompanying uncombined form of the same work.
+ .
+ 6. Revised Versions of the GNU Lesser General Public License.
+ .
+ The Free Software Foundation may publish revised and/or new versions
+ of the GNU Lesser General Public License from time to time. Such new
+ versions will be similar in spirit to the present version, but may
+ differ in detail to address new problems or concerns.
+ .
+ Each version is given a distinguishing version number. If the
+ Library as you received it specifies that a certain numbered version
+ of the GNU Lesser General Public License "or any later version"
+ applies to it, you have the option of following the terms and
+ conditions either of that published version or of any later version
+ published by the Free Software Foundation. If the Library as you
+ received it does not specify a version number of the GNU Lesser
+ General Public License, you may choose any version of the GNU Lesser
+ General Public License ever published by the Free Software Foundation.
+ .
+ If the Library as you received it specifies that a proxy can decide
+ whether future versions of the GNU Lesser General Public License shall
+ apply, that proxy's public statement of acceptance of any version is
+ permanent authorization for you to choose that version for the
+ Library.
+
+License: MIT
+ 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: public_domain
+ PUBLIC DOMAIN NOTICE
+ National Center for Biotechnology Information
+ .
+ With the exception of certain third-party files summarized below, this
+ software is a "United States Government Work" under the terms of the
+ United States Copyright Act. It was written as part of the authors'
+ official duties as United States Government employees and thus cannot
+ be copyrighted. This software is freely available to the public for
+ use. The National Library of Medicine and the U.S. Government have not
+ placed any restriction on its use or reproduction.
+ .
+ Although all reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the NLM and the U.S.
+ Government do not and cannot warrant the performance or results that
+ may be obtained by using this software or data. The NLM and the U.S.
+ Government disclaim all warranties, express or implied, including
+ warranties of performance, merchantability or fitness for any
+ particular purpose.
+ .
+ Please cite the author in any work or product based on this material.
=====================================
debian/mmseqs2.install
=====================================
@@ -1,4 +1,4 @@
-obj-x86_64-linux-gnu/src/test/* usr/share/doc/mmseqs2/test-binaries
+obj-x86_64-linux-gnu/src/test usr/lib/mmseqs2
util/bash-completion.sh usr/share/mmseqs2
README.md usr/share/doc/mmseqs2
examples usr/share/doc/mmseqs2
=====================================
debian/rules
=====================================
@@ -9,3 +9,14 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
dh $@
+
+override_dh_install:
+ dh_install
+ cp src/test/*.index debian/mmseqs2/usr/lib/mmseqs2/test
+ cp src/test/dataGap debian/mmseqs2/usr/lib/mmseqs2/test
+ cp src/test/dataLinear debian/mmseqs2/usr/lib/mmseqs2/test
+
+ # We also remove unneeded files & folders like CMake
+ rm -r debian/mmseqs2/usr/lib/mmseqs2/test/CMakeFiles \
+ debian/mmseqs2/usr/lib/mmseqs2/test/*.cmake \
+ debian/mmseqs2/usr/lib/mmseqs2/test/Makefile
=====================================
debian/tests/run-unit-test
=====================================
@@ -8,12 +8,9 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
-cp -r /usr/share/doc/${pkg}/test-binaries "${AUTOPKGTEST_TMP}"
+cp -r /usr/lib/${pkg}/test "${AUTOPKGTEST_TMP}"
-cd "${AUTOPKGTEST_TMP}"/test-binaries
-rm -r CMakeFiles cmake_install.cmake
-gunzip *
-chmod +x *
+cd "${AUTOPKGTEST_TMP}"/test
# Notice: Some tests have been excluded as they have user directories hard-coded.
# ... Maybe a patch soon to rectify this.
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/compare/e780b3a94987fb2cdd4d84b2668ea05c91e2099b...59d0956bf05f275a8e40eed6e65f67f7dfd4391f
--
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/compare/e780b3a94987fb2cdd4d84b2668ea05c91e2099b...59d0956bf05f275a8e40eed6e65f67f7dfd4391f
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190717/127d964f/attachment-0001.html>
More information about the debian-med-commit
mailing list