[med-svn] r16739 - in trunk/packages/pdb2pqr/trunk/debian: . patches

Sun Apr 20 08:44:58 UTC 2014

Author: tille
Date: 2014-04-20 08:44:58 +0000 (Sun, 20 Apr 2014)
New Revision: 16739

Removed:
   trunk/packages/pdb2pqr/trunk/debian/patches/fix-hardening.patch
   trunk/packages/pdb2pqr/trunk/debian/patches/fix-hurd.patch
   trunk/packages/pdb2pqr/trunk/debian/patches/fix-includes.patch
Modified:
   trunk/packages/pdb2pqr/trunk/debian/changelog
   trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch
   trunk/packages/pdb2pqr/trunk/debian/patches/series
   trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.docs
   trunk/packages/pdb2pqr/trunk/debian/rules
Log:
Several updates to new upstream version


Modified: trunk/packages/pdb2pqr/trunk/debian/changelog
===================================================================

--- trunk/packages/pdb2pqr/trunk/debian/changelog	2014-04-19 14:07:09 UTC (rev 16738)
+++ trunk/packages/pdb2pqr/trunk/debian/changelog	2014-04-20 08:44:58 UTC (rev 16739)
@@ -1,4 +1,4 @@
-pdb2pqr (1.9+dfsg-1) UNRELEASED; urgency=medium
+pdb2pqr (1.9.0+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream version
   * Adapted watch file

Deleted: trunk/packages/pdb2pqr/trunk/debian/patches/fix-hardening.patch
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/patches/fix-hardening.patch	2014-04-19 14:07:09 UTC (rev 16738)
+++ trunk/packages/pdb2pqr/trunk/debian/patches/fix-hardening.patch	2014-04-20 08:44:58 UTC (rev 16739)
@@ -1,14 +0,0 @@
-Subject: Pass LDFLAGS to the linker for hardening
-From: Manuel Prinz <manuel at debian.org>
-Last-Update: 2012-06-22
---- a/configure
-+++ b/configure
-@@ -3308,7 +3308,7 @@
- 
- PY_SHARED=$PY_SHARED
- 
--PY_LDFLAGS=$PY_LDFLAGS
-+PY_LDFLAGS="$PY_LDFLAGS $LDFLAGS"
- 
- PY_HEADER=$PY_HEADER
- 

Modified: trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch	2014-04-19 14:07:09 UTC (rev 16738)
+++ trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch	2014-04-20 08:44:58 UTC (rev 16739)
@@ -1,24 +1,24 @@
 Subject: Fixes "broken" hashbangs
 From: Manuel Prinz <manuel at debian.org>
 Last-Update: 2012-06-21
---- pdb2pqr-1.8.repack.orig/pdb2pka/inputgen_pKa.py
-+++ pdb2pqr-1.8.repack/pdb2pka/inputgen_pKa.py
+--- a/pdb2pka/inputgen_pKa.py
++++ b/pdb2pka/inputgen_pKa.py
 @@ -1,4 +1,4 @@
 -#!/bin/env python
 +#!/usr/bin/python
  #
- # $Id: inputgen_pKa.py 974 2011-06-30 14:58:03Z jens_nielsen $
+ # $Id$
  #
---- pdb2pqr-1.8.repack.orig/propka30/Source/corresponding_atoms.py
-+++ pdb2pqr-1.8.repack/propka30/Source/corresponding_atoms.py
+--- a/propka30/Source/corresponding_atoms.py
++++ b/propka30/Source/corresponding_atoms.py
 @@ -1,4 +1,4 @@
 -#!/usr/local/bin/python3.0
 +#!/usr/bin/python
  
  #
  # * This library is free software; you can redistribute it and/or
---- pdb2pqr-1.8.repack.orig/propka30/Source/rotate.py
-+++ pdb2pqr-1.8.repack/propka30/Source/rotate.py
+--- a/propka30/Source/rotate.py
++++ b/propka30/Source/rotate.py
 @@ -1,4 +1,4 @@
 -#!/usr/local/bin/python3.0
 +#!/usr/bin/python

Deleted: trunk/packages/pdb2pqr/trunk/debian/patches/fix-hurd.patch
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/patches/fix-hurd.patch	2014-04-19 14:07:09 UTC (rev 16738)
+++ trunk/packages/pdb2pqr/trunk/debian/patches/fix-hurd.patch	2014-04-20 08:44:58 UTC (rev 16739)
@@ -1,14 +0,0 @@
-Subject: Fix build issues on HURD
-From: Barry deFreese <bdefreese at debian.org>
-Last-Update: 2012-05-29
---- pdb2pqr-1.8.repack.orig/configure
-+++ pdb2pqr-1.8.repack/configure
-@@ -3297,6 +3297,8 @@
-       PY_LDFLAGS="-lF77 -lm -lM77 -lsunmath";;
-    darwin*)
-       PY_LDFLAGS="${LDFLAGS} -Wl,-framework -Wl,Python -bundle";;
-+   gnu*)
-+      PY_SHARED="-shared";;
- esac
- 
- case $host_cpu in

Deleted: trunk/packages/pdb2pqr/trunk/debian/patches/fix-includes.patch
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/patches/fix-includes.patch	2014-04-19 14:07:09 UTC (rev 16738)
+++ trunk/packages/pdb2pqr/trunk/debian/patches/fix-includes.patch	2014-04-20 08:44:58 UTC (rev 16739)
@@ -1,14 +0,0 @@
-Subject: Fixes a build issue due to a wrong #include directive
-From: Manuel Prinz <manuel at debian.org>
-Last-Update: 2011-01-30
---- a/pdb2pka/substruct/Algorithms.cpp
-+++ b/pdb2pka/substruct/Algorithms.cpp
-@@ -40,7 +40,7 @@
- #include "Python.h"
- #include "clique/bk.h"
- #include "clique/util.h"
--#include "arrayobject.h"
-+#include "numpy/arrayobject.h"
- //#include "smiles.h"
- /*----------------------------------------------------------------------------*/
- using namespace std;

Modified: trunk/packages/pdb2pqr/trunk/debian/patches/series
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/patches/series	2014-04-19 14:07:09 UTC (rev 16738)
+++ trunk/packages/pdb2pqr/trunk/debian/patches/series	2014-04-20 08:44:58 UTC (rev 16739)
@@ -1,4 +1 @@
-fix-includes.patch
 fix-hashbangs.patch
-fix-hurd.patch
-fix-hardening.patch

Modified: trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.docs
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.docs	2014-04-19 14:07:09 UTC (rev 16738)
+++ trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.docs	2014-04-20 08:44:58 UTC (rev 16739)
@@ -1,4 +1,3 @@
 AUTHORS
-ChangeLog
 NEWS
-README
+README*

Modified: trunk/packages/pdb2pqr/trunk/debian/rules
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/rules	2014-04-19 14:07:09 UTC (rev 16738)
+++ trunk/packages/pdb2pqr/trunk/debian/rules	2014-04-20 08:44:58 UTC (rev 16739)
@@ -18,17 +18,22 @@
 	( cd pdb2pka && \
 	  if [ -e pMC_mult_wrap.cpp.saved ]; then mv pMC_mult_wrap.cpp.saved pMC_mult_wrap.cpp; fi && \
 	  if [ -e pMC_mult.py.saved ]; then mv pMC_mult.py.saved pMC_mult.py; fi )
+	find . -name *.pyc -delete
+	find . -name *.so -delete
+	find . -name *.os -delete
+	rm -f *.cgi .sconsign.dblite .variables.cache pdb2pqr.py html/server.html src/aconf.py
 	dh_auto_clean
 
 override_dh_auto_configure:
 	dh_auto_configure
+	python scons/scons.py
 	( cd pdb2pka && \
 	  cp -a pMC_mult_wrap.cpp pMC_mult_wrap.cpp.saved && \
 	  cp -a pMC_mult.py pMC_mult.py.saved && \
 	  swig -c++ -python -o pMC_mult_wrap.cpp pMC_mult.i )
 
 # Disable tests, as they need an internet connection to download files
-override_dh_auto_test:
+# override_dh_auto_test:
 
 override_dh_auto_install:
 # Install Debian-provided stuff
@@ -59,6 +64,9 @@
 	chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py
 	chmod 0755 debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py
 
+override_dh_installchangelogs:
+	dh_installchangelogs ChangeLog.md
+
 # Remark: The following uscan command requires devscripts > 2.12.4 which is not
 #         yet released at the time of this package release.  The code can be obtained
 #         via


