[med-svn] r12083 - in trunk/packages/rcsb-core-wrapper/trunk/debian: . patches

Fri Aug 17 16:27:46 UTC 2012

Author: lkajan-guest
Date: 2012-08-17 16:27:46 +0000 (Fri, 17 Aug 2012)
New Revision: 12083

Added:
   trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap-dbg.install
   trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap.README.Debian
   trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap.examples
   trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap.install
Removed:
   trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.README.Debian
   trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.examples
   trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.install
Modified:
   trunk/packages/rcsb-core-wrapper/trunk/debian/control
   trunk/packages/rcsb-core-wrapper/trunk/debian/patches/hardening
   trunk/packages/rcsb-core-wrapper/trunk/debian/patches/setup.py.in
   trunk/packages/rcsb-core-wrapper/trunk/debian/rules
Log:
Python wrapper binary pack name changed to python-corepywrap; removed ${python:Provides}; adjusted hardening; fixed build deps versions; added python-*-dbg package

Modified: trunk/packages/rcsb-core-wrapper/trunk/debian/control
===================================================================

--- trunk/packages/rcsb-core-wrapper/trunk/debian/control	2012-08-17 16:19:27 UTC (rev 12082)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/control	2012-08-17 16:27:46 UTC (rev 12083)
@@ -3,8 +3,8 @@
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders:
  Laszlo Kajan <lkajan at rostlab.org>
-Build-Depends: debhelper (>= 7.0.50~), doxygen, graphviz, libboost-python-dev, libxerces-c-dev,
- python-all-dev,
+Build-Depends: debhelper (>= 7.3.5), doxygen, graphviz, libboost-python-dev, libxerces-c-dev,
+ python-all-dev (>= 2.6.6-3~), python-all-dbg,
  libtool, bison, flex
 Standards-Version: 3.9.3
 Section: libs
@@ -41,7 +41,7 @@
 Package: librcsb-core-wrapper-doc
 Section: doc
 Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${misc:Depends}
 Description: documentation for librcsb-core-wrapper0
  The RCSB Core Wrapper library was developed to provide an object-oriented
  application interface to information in mmCIF format. It includes several
@@ -54,7 +54,7 @@
 Section: debug
 Priority: extra
 Depends: librcsb-core-wrapper0 (= ${binary:Version}), ${misc:Depends}
-Enhances: librcsb-core-wrapper0-dev, python-librcsb-core-wrapper
+Enhances: librcsb-core-wrapper0-dev, python-corepywrap
 Description: debugging symbols for librcsb-core-wrapper0
  The RCSB Core Wrapper library was developed to provide an object-oriented
  application interface to information in mmCIF format. It includes several
@@ -63,16 +63,29 @@
  This package contains the detached debug symbols for the library and the
  Python bindings.
  
-Package: python-librcsb-core-wrapper
+Package: python-corepywrap
 Architecture: any
 Section: python
 Priority: extra
 Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, librcsb-core-wrapper0 (= ${binary:Version})
 Suggests: librcsb-core-wrapper0-dbg, librcsb-core-wrapper-doc
-Provides: ${python:Provides}
 Description: library that exports C++ mmCIF accessors to Python
  The RCSB Core Wrapper library was developed to provide an object-oriented
  application interface to information in mmCIF format. It includes several
  classes for accessing data dictionaries and mmCIF format data files.
  .
  This library provides Python bindings for librcsb-core-wrapper.
+ 
+Package: python-corepywrap-dbg
+Architecture: any
+Section: debug
+Priority: extra
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, librcsb-core-wrapper0 (= ${binary:Version}), python-dbg
+Suggests: librcsb-core-wrapper0-dbg, librcsb-core-wrapper-doc
+Description: library that exports C++ mmCIF accessors to Python
+ The RCSB Core Wrapper library was developed to provide an object-oriented
+ application interface to information in mmCIF format. It includes several
+ classes for accessing data dictionaries and mmCIF format data files.
+ .
+ This library provides Python bindings for librcsb-core-wrapper (debugging
+ interpreter).

Modified: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/hardening
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/hardening	2012-08-17 16:19:27 UTC (rev 12082)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/hardening	2012-08-17 16:27:46 UTC (rev 12083)
@@ -80,12 +80,12 @@
  # C compiler flags
 -CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
 -CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) 
++CFLAGS_NONANSI := $(CFLAGS) $(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES)
 +CFLAGS += $(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-+CFLAGS_NONANSI += $(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES)
  
  ## C++ compiler
  ## This part defines C++ compiler information
-@@ -128,9 +128,9 @@
+@@ -128,14 +128,14 @@
  EXT=C
  
  # C++ compiler flags
@@ -97,28 +97,25 @@
    $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES)
  
  # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+ # source code that is not maintained by PDB
+-C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
++C++FLAGS_RELAXED= $(CXXFLAGS) $(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
+   $(DEFINES) $(INCLUDES)
+ 
+ ## Fortran compiler
 @@ -158,8 +158,8 @@
  STATIC_LINKING=-static
  
  # Linker flags
 -LDFLAGS=$(ABI) -w $(STATIC_LINKING)
 -LDFLAGS_NO_STATIC=$(ABI) -w
++LDFLAGS_NO_STATIC := $(LDFLAGS) $(ABI) -w
 +LDFLAGS += $(ABI) -w $(STATIC_LINKING)
-+LDFLAGS_NO_STATIC += $(ABI) -w
  
  # Fortran linker
  F77_LINKER=f77
 --- a/pdbml-parser/Makefile
 +++ b/pdbml-parser/Makefile
-@@ -157,7 +157,7 @@
- 
- # General rule for making executables
- %: $(OBJ_DIR)/%.o $(M_MOD_LIB) $(ALL_DEP_LIBS)
--	$(CCC) $(LDFLAGS_NO_STATIC) $(EXT_LIBS_DIRS) $< $(M_MOD_LIB) $(ALL_DEP_LIBS) $(EXT_LIBS) $(MALLOCLIB) -lm -o $(L_BIN_DIR)/$@
-+	$(CCC) $(CPPFLAGS) $(LDFLAGS_NO_STATIC) $(EXT_LIBS_DIRS) $< $(M_MOD_LIB) $(ALL_DEP_LIBS) $(EXT_LIBS) $(MALLOCLIB) -lm -o $(L_BIN_DIR)/$@
- 	@cp -f $(L_BIN_DIR)/$@ $(M_BIN_DIR)/$@
- 
- 
 @@ -222,10 +222,10 @@
  
  # General rule for making object files

Modified: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/setup.py.in
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/setup.py.in	2012-08-17 16:19:27 UTC (rev 12082)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/setup.py.in	2012-08-17 16:27:46 UTC (rev 12083)
@@ -36,7 +36,7 @@
 +# g++ -shared -L/apps/boost/lib -L/apps/xerces-3.0.1/lib TypeCodePyWrap.o StlPyWrap.o CharPyWrap.o RcsbFilePyWrap.o ISTablePyWrap.o TableFilePyWrap.o CifFilePyWrap.o DicFilePyWrap.o DictObjFilePyWrap.o DataInfoPyWrap.o CifDataInfoPyWrap.o DictDataInfoPyWrap.o PdbMlFilePyWrap.o CorePyWrap.o -L../../lib/.libs -lrcsb-core-wrapper -lboost_python-mt-py27 -lxerces-c -lutil -lpthread -ldl -o ../lib/CorePyWrap.so
 +extra_cmd = '@DEFINES@'
 +
-+setup( name='python-librcsb-core-wrapper',
++setup( name='python-corepywrap',
 +	version='1.000',
 +	author = 'RCSB PDB Software Team',
 +	author_email='sw-help at rcsb.rutgers.edu',

Copied: trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap-dbg.install (from rev 12079, trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.install)
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap-dbg.install	                        (rev 0)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap-dbg.install	2012-08-17 16:27:46 UTC (rev 12083)
@@ -0,0 +1 @@
+usr/lib/python*/*-packages/CorePyWrap_d.so

Copied: trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap.README.Debian (from rev 12079, trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.README.Debian)
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap.README.Debian	                        (rev 0)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap.README.Debian	2012-08-17 16:27:46 UTC (rev 12083)
@@ -0,0 +1,12 @@
+RCSB Core Wrapper for Debian
+============================
+
+Testing the Python binding
+--------------------------
+After installation, you can test the Python binding like this:
+
+ 1: mkdir -p /tmp/test && pushd /tmp/test && mkdir -p ../data
+ 2: wget -O ../data/2j01.cif.gz http://www.rcsb.org/pdb/files/2J01.cif.gz
+ 3: gunzip ../data/2j01.cif.gz
+ 4: python /usr/share/doc/python-librcsb-core-wrapper/examples/CorePyWrapTests.py
+ 5: popd

Copied: trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap.examples (from rev 12079, trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.examples)
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap.examples	                        (rev 0)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap.examples	2012-08-17 16:27:46 UTC (rev 12083)
@@ -0,0 +1 @@
+test/*

Copied: trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap.install (from rev 12079, trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.install)
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap.install	                        (rev 0)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/python-corepywrap.install	2012-08-17 16:27:46 UTC (rev 12083)
@@ -0,0 +1,2 @@
+usr/lib/python*/*-packages/CorePyWrap.so
+usr/lib/python*/*-packages/*.egg-info

Deleted: trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.README.Debian
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.README.Debian	2012-08-17 16:19:27 UTC (rev 12082)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.README.Debian	2012-08-17 16:27:46 UTC (rev 12083)
@@ -1,12 +0,0 @@
-RCSB Core Wrapper for Debian
-============================
-
-Testing the Python binding
---------------------------
-After installation, you can test the Python binding like this:
-
- 1: mkdir -p /tmp/test && pushd /tmp/test && mkdir -p ../data
- 2: wget -O ../data/2j01.cif.gz http://www.rcsb.org/pdb/files/2J01.cif.gz
- 3: gunzip ../data/2j01.cif.gz
- 4: python /usr/share/doc/python-librcsb-core-wrapper/examples/CorePyWrapTests.py
- 5: popd

Deleted: trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.examples
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.examples	2012-08-17 16:19:27 UTC (rev 12082)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.examples	2012-08-17 16:27:46 UTC (rev 12083)
@@ -1 +0,0 @@
-test/*

Deleted: trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.install
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.install	2012-08-17 16:19:27 UTC (rev 12082)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/python-librcsb-core-wrapper.install	2012-08-17 16:27:46 UTC (rev 12083)
@@ -1,2 +0,0 @@
-usr/lib/python*/*-packages/*.so
-usr/lib/python*/*-packages/*.egg-info

Modified: trunk/packages/rcsb-core-wrapper/trunk/debian/rules
===================================================================
--- trunk/packages/rcsb-core-wrapper/trunk/debian/rules	2012-08-17 16:19:27 UTC (rev 12082)
+++ trunk/packages/rcsb-core-wrapper/trunk/debian/rules	2012-08-17 16:27:46 UTC (rev 12083)
@@ -10,7 +10,7 @@
 # lkajan: we borrow from libtorrent-rasterbar and pythonmagick here (thank you)
 PYVERSIONS=$(shell pyversions -vr)
 # lkajan: the below could include debug versions like in python-libtorrent
-ALLPY=$(PYVERSIONS)
+ALLPY=$(PYVERSIONS) $(PYVERSIONS:%=%-dbg)
 
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1


