debian/changelog

-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 <merlettaia@gmail.com>  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 <tille@debian.org>  Fri, 13 Jul 2018 23:21:02 +0200
 
 pdb2pqr (2.1.1+dfsg-2) unstable; urgency=medium
 

debian/compat

-9
+11

debian/control

@@ -5,7 +5,7 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
            Andreas Tille <tille@debian.org>
 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

-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 <moeller@debian.org>
            © 2010-2012 Manuel Prinz <manuel@debian.org>
-           © 2013-2015 Andreas Tille <tille@debian.org>
+           © 2013-2018 Andreas Tille <tille@debian.org>
 License: GPL-2+
 
 License: GPL-2+

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

@@ -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

@@ -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

+Description: Fix spelling
+Author: Andreas Tille <tille@debian.org>
+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

@@ -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

@@ -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

@@ -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