[med-svn] [Git][med-team/sap][master] SAP packaging revisited
Steffen Möller
gitlab at salsa.debian.org
Wed May 23 16:47:51 BST 2018
Steffen Möller pushed to branch master at Debian Med / sap
Commits:
b8d3974b by Steffen Moeller at 2018-05-23T17:46:59+02:00
SAP packaging revisited
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,4 +3,12 @@ sap (1.1.3-1) UNRELEASED; urgency=low
* Initial release
* Moved packaging from SVN to Git
+ [ Steffen Moeller with a status report ]
+ * Copyright information is not clearly stated in source code
+ * 2nd test fails, introducing "nan" where there should be
+ coordinates in PDF file
+ * There are not too many free tools for structure comparisons
+ and let alone for historical reasons SAP would be nice not
+ to be missed.
+
-- Andreas Tille <tille at debian.org> Mon, 28 May 2012 17:14:53 +0200
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -1,12 +1,12 @@
Source: sap
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>, Steffen Moeller <moeller at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10)
-Standards-Version: 4.1.2
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sap.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/sap.git
+Standards-Version: 4.1.3
+Vcs-Browser: https://salsa.debian.org/med-team/sap
+Vcs-Git: https://salsa.debian.org/med-team/sap.git
Homepage: https://web.archive.org/web/20160305092412/http://mathbio.nimr.mrc.ac.uk/wiki/Software#SAP
Package: sap
=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -2,9 +2,33 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: http://mathbio.nimr.mrc.ac.uk/download/SAP/sap-1.1.1.tar.gz
Files: *
-Copyright: © 2008-2010 Willie Taylor <wtaylor at nimr.mrc.ac.uk>
-License: GPL-v3
+Copyright: 1999-2010 Willie R. Taylor <wtaylor at nimr.mrc.ac.uk> (program author)
+ 2007 Alessandro Pandini : SAP web server
+ 2007 Jens Kleinjung : code release
+ 2008 Siv Hollup : code update to ANSI C standard
+License: GPL-3.0+
+
+Files: src/*
+Copyright: 5. Aug. 1994. Andris Aszodi
+License: GPL-3.0+
Files: debian/*
Copyright: © 2012 Andreas Tille <tille at debian.org>
-License: GPL-v3
+License: GPL-3.0+
+
+License: GPL-3.0+
+ 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 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 <https://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -8,3 +8,8 @@
get-orig-source:
mkdir -p ../tarballs
uscan --verbose --force-download --destdir=../tarballs
+
+override_dh_auto_clean:
+ if [ -r Makefile ]; then $(MAKE) clean; fi
+ dh_clean
+ rm -f tests/plot.rms tests/super.pdb
=====================================
debian/upstream/metadata
=====================================
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -7,6 +7,23 @@ Reference:
Pages: 19-32
DOI: 10.1385/1-59259-368-2:19
URL: http://www.springerprotocols.com/Abstract/doi/10.1385/1-59259-368-2:19
+ PMID: 11084900
+ - Author: >
+ Inge Jonassen and Ingvar Eidhammer and Svenn H.Grindhaug and
+ William R. Taylor
+ Title: >
+ Searching the protein structure databank with weak sequence patterns
+ and structural constraints.
+ Journal: J. Mol. Biol.
+ Year: 2000
+ Month: 12
+ Day: 8
+ Volume: 304
+ Number: 4
+ Pages: 599-619
+ DOI: 10.1006/jmbi.2000.4211
+ URL: https://www.sciencedirect.com/science/article/pii/S0022283600942116
+ PMID: 11099383
- Author: William R. Taylor
Title: Protein structure comparison using iterated double dynamic programming
Journal: Protein Science
@@ -17,11 +34,23 @@ Reference:
DOI: 10.1110/ps.8.3.654
PMID: 10091668
URL: http://onlinelibrary.wiley.com/doi/10.1110/ps.8.3.654/abstract
- eprint: http://onlinelibrary.wiley.com/doi/10.1110/ps.8.3.654/pdf
+ ePrint: http://onlinelibrary.wiley.com/doi/10.1110/ps.8.3.654/pdf
+ - Author: William R. Taylor
+ Title: Searching for the ideal forms of proteins.
+ Year: 2000
+ Month: 2
+ Day: 1
+ Volume: 28
+ Number: 2
+ Pages: 264-269
+ PMID: 10816140
+ URL: http://www.biochemsoctrans.org/content/28/2/264.long
+ ePrint: http://www.biochemsoctrans.org/content/28/2/264.full.pdf
+ DOI: 10.1042/bst0280264
Registry:
- Name: OMICtools
Entry: NA
- Name: bio.tools
Entry: NA
- Name: SciCrunch
- Entry: NA
\ No newline at end of file
+ Entry: NA
View it on GitLab: https://salsa.debian.org/med-team/sap/commit/b8d3974be7f4b9683a7f99039ab69a0e4ff773b6
--
View it on GitLab: https://salsa.debian.org/med-team/sap/commit/b8d3974be7f4b9683a7f99039ab69a0e4ff773b6
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