[med-svn] r10914 - in trunk/packages/pdb2pqr/trunk/debian: . patches

Manuel Prinz manuel at alioth.debian.org
Sun May 20 17:35:42 UTC 2012 

Author: manuel
Date: 2012-05-20 17:35:42 +0000 (Sun, 20 May 2012)
New Revision: 10914

Added:
   trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch
Removed:
   trunk/packages/pdb2pqr/trunk/debian/propka.docs
Modified:
   trunk/packages/pdb2pqr/trunk/debian/changelog
   trunk/packages/pdb2pqr/trunk/debian/control
   trunk/packages/pdb2pqr/trunk/debian/patches/series
   trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs
   trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install
   trunk/packages/pdb2pqr/trunk/debian/propka.dirs
   trunk/packages/pdb2pqr/trunk/debian/propka.install
   trunk/packages/pdb2pqr/trunk/debian/rules
Log:
Updated package to new upstream version

Modified: trunk/packages/pdb2pqr/trunk/debian/changelog
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/changelog	2012-05-20 17:03:42 UTC (rev 10913)
+++ trunk/packages/pdb2pqr/trunk/debian/changelog	2012-05-20 17:35:42 UTC (rev 10914)
@@ -7,6 +7,10 @@
   * New upstream version
   * Updated Standards-Version to 3.9.3. No changes needed.
   * Changed Maintainer to Debian Med team.
+  * Pass -fPIC to CXXFLAGS. Thanks to Konstantinos Margaritis for the patch!
+    Closes: 654240. LP: 935357.
+  * Updated PROPKA packaging to new version. (It's written in Python now.)
+  * Added fix-hashbangs.patch.
 
  -- Andreas Tille <tille at debian.org>  Wed, 16 May 2012 09:32:56 +0200
 

Modified: trunk/packages/pdb2pqr/trunk/debian/control
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/control	2012-05-20 17:03:42 UTC (rev 10913)
+++ trunk/packages/pdb2pqr/trunk/debian/control	2012-05-20 17:35:42 UTC (rev 10914)
@@ -9,7 +9,7 @@
  python-support, python-dev, python-numpy,
  autoconf, automake, libtool, autotools-dev
 Standards-Version: 3.9.3
-XS-Python-Version: 2.6
+XS-Python-Version: 2.7
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/pdb2pqr/trunk/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/pdb2pqr/trunk/
 Homepage: http://pdb2pqr.poissonboltzmann.org/pdb2pqr/
@@ -42,8 +42,9 @@
  on larger clusters.
 
 Package: propka
+XB-Python-Version: ${python:Versions}
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
 Suggests: pdb2pqr
 Description: Modify the protonation state of protein structures
  PropKa is a tool to modify the protonation state of a protein structure

Added: trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch	                        (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch	2012-05-20 17:35:42 UTC (rev 10914)
@@ -0,0 +1,24 @@
+--- pdb2pqr-1.8.repack.orig/pdb2pka/inputgen_pKa.py
++++ pdb2pqr-1.8.repack/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 $
+ #
+--- pdb2pqr-1.8.repack.orig/propka30/Source/corresponding_atoms.py
++++ pdb2pqr-1.8.repack/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
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/python3.0
++#!/usr/bin/python
+ #
+ # * This library is free software; you can redistribute it and/or
+ # * modify it under the terms of the GNU Lesser General Public

Modified: trunk/packages/pdb2pqr/trunk/debian/patches/series
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/patches/series	2012-05-20 17:03:42 UTC (rev 10913)
+++ trunk/packages/pdb2pqr/trunk/debian/patches/series	2012-05-20 17:35:42 UTC (rev 10914)
@@ -1 +1,2 @@
 fix-includes.patch
+fix-hashbangs.patch

Modified: trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs	2012-05-20 17:03:42 UTC (rev 10913)
+++ trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs	2012-05-20 17:35:42 UTC (rev 10914)
@@ -1,6 +1,5 @@
 /usr/bin
 /usr/lib/pdb2pqr/pdb2pka/substruct
-/usr/lib/pdb2pqr/propka
 /usr/share/doc/pdb2pqr
 /usr/share/man/man1
 /usr/share/pdb2pqr/dat

Modified: trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install	2012-05-20 17:03:42 UTC (rev 10913)
+++ trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install	2012-05-20 17:35:42 UTC (rev 10914)
@@ -7,8 +7,6 @@
 pdb2pka/*.py			usr/share/pdb2pqr/pdb2pka
 pdb2pka/ligandclean/*.py	usr/share/pdb2pqr/pdb2pka/ligandclean
 pdb2pka/substruct/*.py		usr/share/pdb2pqr/pdb2pka/substruct
-propka/*.py			usr/share/pdb2pqr/propka
 # Binary parts
 pdb2pka/_pMC_mult.so		usr/lib/pdb2pqr/pdb2pka
 pdb2pka/substruct/Algorithms.so	usr/lib/pdb2pqr/pdb2pka/substruct
-propka/_propkalib.so		usr/lib/pdb2pqr/propka

Modified: trunk/packages/pdb2pqr/trunk/debian/propka.dirs
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/propka.dirs	2012-05-20 17:03:42 UTC (rev 10913)
+++ trunk/packages/pdb2pqr/trunk/debian/propka.dirs	2012-05-20 17:35:42 UTC (rev 10914)
@@ -1 +1,2 @@
 /usr/bin
+/usr/share/propka

Deleted: trunk/packages/pdb2pqr/trunk/debian/propka.docs
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/propka.docs	2012-05-20 17:03:42 UTC (rev 10913)
+++ trunk/packages/pdb2pqr/trunk/debian/propka.docs	2012-05-20 17:35:42 UTC (rev 10914)
@@ -1,4 +0,0 @@
-propka/AUTHORS
-propka/ChangeLog
-propka/NEWS
-propka/README

Modified: trunk/packages/pdb2pqr/trunk/debian/propka.install
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/propka.install	2012-05-20 17:03:42 UTC (rev 10913)
+++ trunk/packages/pdb2pqr/trunk/debian/propka.install	2012-05-20 17:35:42 UTC (rev 10914)
@@ -1 +1 @@
-propka/propka			usr/bin
+propka30/*			usr/share/propka

Modified: trunk/packages/pdb2pqr/trunk/debian/rules
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/rules	2012-05-20 17:03:42 UTC (rev 10913)
+++ trunk/packages/pdb2pqr/trunk/debian/rules	2012-05-20 17:35:42 UTC (rev 10914)
@@ -5,19 +5,33 @@
 VERSION  := $(shell dpkg-parsechangelog | awk '/^Version:/ { print $$2 }')
 UPSTREAM := $(shell echo "$(VERSION)"   | sed 's/-.\+$$//')
 
+# Compile with -fPIC on all platforms (fix for #636204, #654240)
+CFLAGS   = $(shell dpkg-buildflags --get CFLAGS)   -fPIC -I/usr/share/pyshared/numpy/core/include/numpy
+CXXFLAGS = $(shell dpkg-buildflags --get CXXFLAGS) -fPIC -I/usr/share/pyshared/numpy/core/include/numpy
+FFLAGS   = $(shell dpkg-buildflags --get FFLAGS)   -fPIC
+
 %:
 	dh $@
 
-# Compile with -fPIC on all platforms (fix for #636204)
+override_dh_auto_clean:
+	( 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 )
+	dh_auto_clean
+
 override_dh_auto_configure:
-	dh_auto_configure -- CFLAGS="$(dpkg-buildflags --get CFLAGS) -fPIC" FFLAGS="$(dpkg-buildflags --get FFLAGS) -fPIC"
+	dh_auto_configure -- CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" FFLAGS="$(FFLAGS)"
+	( 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_install:
-# Fix !#/bin/env shebang: substitute with #!/usr/bin/python
-	sed -i -e '1c#!/usr/bin/python' pdb2pka/inputgen_pKa.py
+### Fix !#/bin/env shebang: substitute with #!/usr/bin/python
+##	sed -i -e '1c#!/usr/bin/python' pdb2pka/inputgen_pKa.py
 # Install Debian-provided stuff
 #   Install wrappers
 	for app in /usr/share/pdb2pqr/pdb2pqr.py /usr/share/pdb2pqr/src/psize.py; do \
@@ -25,11 +39,16 @@
 			>debian/pdb2pqr/usr/bin/$$(basename $${app} .py) && \
 		chmod 0755 debian/pdb2pqr/usr/bin/$$(basename $${app} .py); \
 	done
+	for app in usr/share/propka/propka.py; do \
+		sed -e "s, at SCRIPT@,$${app}," debian/wrapper.sh \
+			>debian/propka/usr/bin/$$(basename $${app} .py) && \
+		chmod 0755 debian/propka/usr/bin/$$(basename $${app} .py); \
+	done
 #   Install man pages
 	xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml
 	xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/psize.1.xml
 	xmlto -o debian/propka/usr/share/man/man1/  man debian/propka.1.xml
-	dh_auto_install
+#	dh_auto_install
 
 override_dh_fixperms:
 	dh_fixperms

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