diff -Nru solvate-1.0/debian/changelog solvate-1.0/debian/changelog --- solvate-1.0/debian/changelog 2008-03-22 02:32:31.000000000 +0000 +++ solvate-1.0/debian/changelog 2020-06-05 16:36:47.000000000 +0000 @@ -1,3 +1,25 @@ +solvate (1.0-3) unstable; urgency=medium + + * Team Upload. + + [ Steffen Möller ] + * Add new d/u/metadata file + * Update metadata with ref to conda + + [ Nilesh Patra ] + * Add autopkgtests + * Fix with cme + * Fix location of doc-base installed docs + + [ Andreas Tille ] + * Remove trailing whitespace in debian/copyright (routine-update) + * Add salsa-ci file (routine-update) + * DEP5 + * solvate-doc is Section: non-free/doc + * Deactivate watch file + + -- Nilesh Patra Fri, 05 Jun 2020 22:06:47 +0530 + solvate (1.0-2) unstable; urgency=low [ David Paleino ] @@ -19,4 +41,3 @@ * Initial release. -- Steffen Moeller Fri, 28 Dec 2007 01:45:03 +0100 - diff -Nru solvate-1.0/debian/compat solvate-1.0/debian/compat --- solvate-1.0/debian/compat 2008-03-22 02:32:31.000000000 +0000 +++ solvate-1.0/debian/compat 1970-01-01 00:00:00.000000000 +0000 @@ -1 +0,0 @@ -10 diff -Nru solvate-1.0/debian/control solvate-1.0/debian/control --- solvate-1.0/debian/control 2008-03-22 02:32:31.000000000 +0000 +++ solvate-1.0/debian/control 2020-06-05 16:36:47.000000000 +0000 @@ -1,14 +1,16 @@ Source: solvate Maintainer: Debian Med Packaging Team -Uploaders: Steffen Moeller , Charles Plessy +Uploaders: Steffen Moeller , + Charles Plessy Section: non-free/science XS-Autobuild: yes Priority: optional -Build-Depends: debhelper (>= 10) -Standards-Version: 4.1.4 +Build-Depends: debhelper-compat (= 13) +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/solvate Vcs-Git: https://salsa.debian.org/med-team/solvate.git -Homepage: http://www.mpibpc.mpg.de/grubmueller/solvate +Homepage: https://www3.mpibpc.mpg.de/groups/grubmueller/start/index.html +Rules-Requires-Root: no Package: solvate Architecture: any @@ -17,12 +19,13 @@ Description: arranges water molecules around protein structures For molecular dynamics simulations it is sometimes appropriate not to model in the vacuum but to have the proteins surrounded - by their solvent. This program computes the location of water + by their solvent. This program computes the location of water molecules such that the resulting PDB files become suitable for further analyses. Package: solvate-doc Architecture: all +Section: non-free/doc Depends: ${misc:Depends} Description: Documentation for solvate HTML documentation for solvate, the tool to prepare diff -Nru solvate-1.0/debian/copyright solvate-1.0/debian/copyright --- solvate-1.0/debian/copyright 2008-03-22 02:32:31.000000000 +0000 +++ solvate-1.0/debian/copyright 2020-06-05 16:36:47.000000000 +0000 @@ -1,50 +1,42 @@ -This package was debianized by Steffen Moeller on -Fri, 28 Dec 2007 01:45:03 +0100. - -It was downloaded from http://www.mpibpc.mpg.de/groups/grubmueller/start/index.html - -Upstream Author: - - Helmut Grubmueller - -Copyright: - - Helmut Grubmueller 1996 - -License: - +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: solvate +Source: https://www3.mpibpc.mpg.de/groups/grubmueller/start/index.html + +Files: * +Copyright: 1996 Helmut Grubmueller +License: no_fee General License Agreement and Lack of Warranty - + . This software is distributed in the hope that it will be useful but without any warranty. The author does not accept responsibility to anyone for the consequences of using it or for whether it serves any particular purpose or works at all. No warranty is made about the software or its performance. - + . Use and copying of this software and the preparation of derivative works based on this software are permitted, so long as the following conditions are met: - + . The copyright notice and this entire notice are included intact and prominently carried on all copies and supporting documentation. - + . No fees or compensation are charged for use, copies, or access to this software. You may charge a nominal distribution fee for the physical act of transferring a copy, but you may not charge for the program itself. - + . If you modify this software, you must cause the modified file(s) to carry prominent notices describing the changes, who made the changes, and the date of those changes. Please do inform the author about major modifications. - + . Any work distributed or published that in whole or in part contains or is a derivative of this software or any part thereof is subject to the terms of this agreement. The aggregation of another unrelated program with this software or its derivative on a volume of storage or distribution medium does not bring the other program under the scope of these terms. - + . This software is made available as is, and is distributed without warranty of any kind, either expressed or implied. In no event will the author or his institutions be liable to you for damages, @@ -56,13 +48,14 @@ even if you have been advised of the possibility of such damages, or for any claim by any other party, whether in an action of contract, negligence, or other tortuous action. - + . SOLVATE is written by Helmut Grubmüller, Theoretical Biophysics Group, Institut für Medizinische Optik, Ludwig-Maximilians-Universität München, München, Germany. Copyright © 1996. All rights reserved. - - -The Debian packaging is (C) 2007, Steffen Moeller and -is licensed under the GPL, see `/usr/share/common-licenses/GPL'. +Files: debian/* +Copyright: 2007-2008 Steffen Moeller +License: + The Debian packaging is licensed under the GPL, see + `/usr/share/common-licenses/GPL'. diff -Nru solvate-1.0/debian/rules solvate-1.0/debian/rules --- solvate-1.0/debian/rules 2008-03-22 02:32:31.000000000 +0000 +++ solvate-1.0/debian/rules 2020-06-05 16:36:47.000000000 +0000 @@ -22,4 +22,3 @@ # # in debian/solvate-doc.docs # #cp *.pdb *.psf $(CURDIR)/debian/solvate/usr/share/doc/solvate-doc/ - diff -Nru solvate-1.0/debian/salsa-ci.yml solvate-1.0/debian/salsa-ci.yml --- solvate-1.0/debian/salsa-ci.yml 1970-01-01 00:00:00.000000000 +0000 +++ solvate-1.0/debian/salsa-ci.yml 2020-06-05 16:36:47.000000000 +0000 @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml diff -Nru solvate-1.0/debian/solvate-doc.doc-base solvate-1.0/debian/solvate-doc.doc-base --- solvate-1.0/debian/solvate-doc.doc-base 2008-03-22 02:32:31.000000000 +0000 +++ solvate-1.0/debian/solvate-doc.doc-base 2020-06-05 16:36:47.000000000 +0000 @@ -5,5 +5,5 @@ Section: Science/Biology Format: HTML -Index: /usr/share/doc/solvate-doc/docu_html/docu.html -Files: /usr/share/doc/solvate-doc/docu_html/*.html /usr/share/doc/solvate-doc/docu_html/*.gif +Index: /usr/share/doc/solvate/docu_html/docu.html +Files: /usr/share/doc/solvate/docu_html/*.html /usr/share/doc/solvate/docu_html/*.gif diff -Nru solvate-1.0/debian/tests/control solvate-1.0/debian/tests/control --- solvate-1.0/debian/tests/control 1970-01-01 00:00:00.000000000 +0000 +++ solvate-1.0/debian/tests/control 2020-06-05 16:36:47.000000000 +0000 @@ -0,0 +1,4 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr + diff -Nru solvate-1.0/debian/tests/run-unit-test solvate-1.0/debian/tests/run-unit-test --- solvate-1.0/debian/tests/run-unit-test 1970-01-01 00:00:00.000000000 +0000 +++ solvate-1.0/debian/tests/run-unit-test 2020-06-05 16:36:47.000000000 +0000 @@ -0,0 +1,24 @@ +#!/bin/bash +set -e + +pkg=solvate + +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp /usr/share/doc/${pkg}/* -a "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" +gunzip -r * + +echo 'Test 1' +solvate -r 20.91 -s -v bpti test1 +echo 'PASS' +echo + +echo 'Test 2' +solvate -n 2 -r 40.33 -t 2 -bulk -psf -ion globh test2 +echo 'PASS' + diff -Nru solvate-1.0/debian/upstream/metadata solvate-1.0/debian/upstream/metadata --- solvate-1.0/debian/upstream/metadata 1970-01-01 00:00:00.000000000 +0000 +++ solvate-1.0/debian/upstream/metadata 2020-06-05 16:36:47.000000000 +0000 @@ -0,0 +1,9 @@ +Registry: + - Name: OMICtools + Entry: OMICS_31018 + - Name: bio.tools + Entry: NA + - Name: SciCrunch + Entry: NA + - Name: conda:bioconda + Entry: NA diff -Nru solvate-1.0/debian/watch solvate-1.0/debian/watch --- solvate-1.0/debian/watch 2008-03-22 02:32:31.000000000 +0000 +++ solvate-1.0/debian/watch 2020-06-05 16:36:47.000000000 +0000 @@ -1,2 +1,3 @@ -version=3 -http://www.mpibpc.mpg.de/groups/grubmueller/start/software/solvate/node2.html http://www.mpibpc.mpg.de/groups/grubmueller/start/software/solvate/solvate_(.*)\.tar\.Z +version=4 +opts=dversionmangle=s/.*/0.No-Site/ \ +https://people.debian.org/~eriberto/ FakeWatchNoUpstreamSiteForThisPackage-(\d\S+)\.gz