Andreas Tille pushed to branch master at Debian Med / pdb2pqr
Commits: f0c71848 by Andreas Tille at 2018-07-13T22:14:41+02:00 Remove ancient X-Python-Version field - - - - - bbc96b47 by Andreas Tille at 2018-07-13T22:18:37+02:00 Fix homepage - - - - - 2d8c1617 by Andreas Tille at 2018-07-13T22:19:22+02:00 Update - - - - - 374fda03 by Andreas Tille at 2018-07-13T22:19:38+02:00 debhelper 11 - - - - - da3af1ad by Andreas Tille at 2018-07-13T22:20:29+02:00 Point Vcs fields to salsa.debian.org - - - - - d88684ad by Andreas Tille at 2018-07-13T22:20:29+02:00 Standards-Version: 4.1.5 - - - - - e99d1815 by Andreas Tille at 2018-07-13T22:24:58+02:00 Adapt docbase paths - - - - - 57f09ea8 by Andreas Tille at 2018-07-13T23:16:47+02:00 do not parse d/changelog - - - - - 4ccd5fd6 by Andreas Tille at 2018-07-13T23:20:52+02:00 Fix spelling - - - - - ca581224 by Andreas Tille at 2018-07-13T23:23:43+02:00 Upload to unstable - - - - - 11 changed files: - debian/changelog - debian/compat - debian/control - debian/copyright - debian/patches/fix_hardening_no_relro - debian/patches/fix_no_debug_symbols_warning - debian/patches/series - + debian/patches/spelling.patch - debian/pdb2pqr-doc.doc-base - debian/pdb2pqr.1.xml - debian/rules Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,4 +1,4 @@ -pdb2pqr (2.1.1+dfsg-3) UNRELEASED; urgency=medium +pdb2pqr (2.1.1+dfsg-3) unstable; urgency=medium [ Steffen Moeller ] * debian/upstream/metadata: @@ -8,7 +8,15 @@ pdb2pqr (2.1.1+dfsg-3) UNRELEASED; urgency=medium [ Tatiana Malygina ] * Enhance README.test and README.Debian - -- Tatiana Malygina <[email protected]> Tue, 05 Jul 2016 17:02:33 +0200 + [ Andreas Tille ] + * Remove ancient X-Python-Version field + * Fix Homepage + * debhelper 11 + * Point Vcs fields to salsa.debian.org + * Standards-Version: 4.1.5 + * d/rules: do not parse d/changelog + + -- Andreas Tille <[email protected]> Fri, 13 Jul 2018 23:21:02 +0200 pdb2pqr (2.1.1+dfsg-2) unstable; urgency=medium ===================================== debian/compat ===================================== --- a/debian/compat +++ b/debian/compat @@ -1 +1 @@ -9 +11 ===================================== debian/control ===================================== --- a/debian/control +++ b/debian/control @@ -5,7 +5,7 @@ Uploaders: Steffen Moeller <[email protected]>, Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 9), +Build-Depends: debhelper (>= 11~), gfortran, swig, xmlto, @@ -14,11 +14,10 @@ Build-Depends: debhelper (>= 9), python-numpy, scons, dos2unix -Standards-Version: 3.9.8 -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pdb2pqr.git -Vcs-Git: https://anonscm.debian.org/git/debian-med/pdb2pqr.git -Homepage: http://pdb2pqr.poissonboltzmann.org/pdb2pqr/ -X-Python-Version: 2.7 +Standards-Version: 4.1.5 +Vcs-Browser: https://salsa.debian.org/med-team/pdb2pqr +Vcs-Git: https://salsa.debian.org/med-team/pdb2pqr.git +Homepage: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html Package: pdb2pqr Architecture: any ===================================== debian/copyright ===================================== --- a/debian/copyright +++ b/debian/copyright @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: pdb2pqr Source: http://sourceforge.net/projects/pdb2pqr/ Files-Excluded: @@ -95,7 +95,7 @@ License: GPL-2+ Files: debian/* Copyright: © 2007-2010 Steffen Moeller <[email protected]> © 2010-2012 Manuel Prinz <[email protected]> - © 2013-2015 Andreas Tille <[email protected]> + © 2013-2018 Andreas Tille <[email protected]> License: GPL-2+ License: GPL-2+ ===================================== debian/patches/fix_hardening_no_relro ===================================== --- a/debian/patches/fix_hardening_no_relro +++ b/debian/patches/fix_hardening_no_relro @@ -5,7 +5,7 @@ Description: this fix prevents hardening-no-relro warning from appearing during --- a/SConscript-main.py +++ b/SConscript-main.py -@@ -100,6 +100,9 @@ +@@ -100,6 +100,9 @@ if env['EXTRA_CXXFLAGS']: if env['EXTRA_LINKFLAGS']: env.Append(LINKFLAGS = [env['EXTRA_LINKFLAGS']]) ===================================== debian/patches/fix_no_debug_symbols_warning ===================================== --- a/debian/patches/fix_no_debug_symbols_warning +++ b/debian/patches/fix_no_debug_symbols_warning @@ -3,8 +3,8 @@ Last-Update: 2016-06-15 Description: this fix prevents debug-file-with-no-debug-symbols warning from appearing during lintian run ---- pdb2pqr.orig/build_config.py -+++ pdb2pqr/build_config.py +--- a/build_config.py ++++ b/build_config.py @@ -58,7 +58,7 @@ #Set to True to build compiled extentions with debug headers. #Defaults to False ===================================== debian/patches/series ===================================== --- a/debian/patches/series +++ b/debian/patches/series @@ -3,3 +3,4 @@ no_privacy_breach_logo.patch do_not_try_to_build_removed_js_target.patch fix_hardening_no_relro fix_no_debug_symbols_warning +spelling.patch ===================================== debian/patches/spelling.patch ===================================== --- /dev/null +++ b/debian/patches/spelling.patch @@ -0,0 +1,24 @@ +Description: Fix spelling +Author: Andreas Tille <[email protected]> +Last-Update: Fri, 13 Jul 2018 22:26:48 +0200 + +--- a/pdb2pka/substruct/Algorithms.cpp ++++ b/pdb2pka/substruct/Algorithms.cpp +@@ -74,7 +74,7 @@ public: + /*----------------------------------------------------------------------------*/ + static char find_max_clique__doc__[] = + "This function takes a two-dimensional Numeric-array and \ +-interpretes it as the adjacency matrix of a graph. It then \ ++interprets it as the adjacency matrix of a graph. It then \ + uses the algorithm of Bron and Kerbosch to detect maximal \ + cliques in that graph and returns the nodes of a maximal clique. \ + It is assumed that the nodes 0..n-1 are given in the order as they \ +@@ -173,7 +173,7 @@ int collect_cliques(const _set *st, void + /*----------------------------------------------------------------------------*/ + static char find_cliques__doc__[] = + "This function takes a two-dimensional Numeric-array and \ +-interpretes it as the adjacency matrix of a graph. It then \ ++interprets it as the adjacency matrix of a graph. It then \ + uses the algorithm of Bron and Kerbosch to detect maximal \ + cliques in that graph and returns a list of lists containing \ + the nodes of all maximal cliques (up to 10000). It is assumed \ ===================================== debian/pdb2pqr-doc.doc-base ===================================== --- a/debian/pdb2pqr-doc.doc-base +++ b/debian/pdb2pqr-doc.doc-base @@ -5,5 +5,5 @@ Abstract: This guide explains the use of PDB2PQR Section: Science/Chemistry Format: HTML -Index: /usr/share/doc/pdb2pqr-doc/userguide.html -Files: /usr/share/doc/pdb2pqr-doc/userguide.html +Index: /usr/share/doc/pdb2pqr/userguide.html +Files: /usr/share/doc/pdb2pqr/userguide.html ===================================== debian/pdb2pqr.1.xml ===================================== --- a/debian/pdb2pqr.1.xml +++ b/debian/pdb2pqr.1.xml @@ -110,7 +110,7 @@ <term><option>--clean</option></term> <listitem> <para>Do no optimization, atom addition, or parameter assignment, just return - the original <acronym>PDB</acronym> file in alligned format.</para> + the original <acronym>PDB</acronym> file in aligned format.</para> </listitem> </varlistentry> <varlistentry> ===================================== debian/rules ===================================== --- a/debian/rules +++ b/debian/rules @@ -3,10 +3,6 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all -PACKAGE := $(firstword $(shell dh_listpackages)) -VERSION := $(shell dpkg-parsechangelog | awk '/^Version:/ { print $$2 }') -UPSTREAM := $(shell echo "$(VERSION)" | sed 's/-.\+$$//') - # Compile with -fPIC on all platforms (fix for #636204, #654240) export DEB_CFLAGS_MAINT_APPEND = -fPIC -I/usr/share/pyshared/numpy/core/include/numpy export DEB_CPPFLAGS_MAINT_APPEND = -fPIC -I/usr/share/pyshared/numpy/core/include/numpy View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/compare/a3711e859a99bcb76fcbd53a8826110c513d3248...ca581224593d4a73582be899adec415615e98471 -- View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/compare/a3711e859a99bcb76fcbd53a8826110c513d3248...ca581224593d4a73582be899adec415615e98471 You're receiving this email because of your account on salsa.debian.org.
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