Author: lkajan-guest Date: 2012-08-13 16:53:57 +0000 (Mon, 13 Aug 2012) New Revision: 12038
Added: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/setup.py.in trunk/packages/rcsb-core-wrapper/trunk/debian/patches/wrapper trunk/packages/rcsb-core-wrapper/trunk/debian/patches/wrapper-module Removed: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/pythonwrapper trunk/packages/rcsb-core-wrapper/trunk/debian/patches/wrapper Modified: trunk/packages/rcsb-core-wrapper/trunk/debian/control trunk/packages/rcsb-core-wrapper/trunk/debian/patches/objectfiles trunk/packages/rcsb-core-wrapper/trunk/debian/patches/series trunk/packages/rcsb-core-wrapper/trunk/debian/rules Log: python module for python versions is made Modified: trunk/packages/rcsb-core-wrapper/trunk/debian/control =================================================================== --- trunk/packages/rcsb-core-wrapper/trunk/debian/control 2012-08-13 15:39:13 UTC (rev 12037) +++ trunk/packages/rcsb-core-wrapper/trunk/debian/control 2012-08-13 16:53:57 UTC (rev 12038) @@ -1,16 +1,17 @@ Source: librcsb-core-wrapper Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Debian Python Modules Team <[email protected]>, +Uploaders: Laszlo Kajan <[email protected]> Build-Depends: debhelper (>= 7.0.50~), doxygen, graphviz, libboost-python-dev, libxerces-c-dev, - python-all-dev, python-all-dbg + python-all-dev Standards-Version: 3.9.3 Section: libs Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rcsb-core-wrapper/trunk Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rcsb-core-wrapper/trunk/ DM-Upload-Allowed: yes Homepage: http://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html +X-Python-Version: >= 2.5 Package: librcsb-core-wrapper0 Architecture: any @@ -73,18 +74,3 @@ classes for accessing data dictionaries and mmCIF format data files. . This library provides Python bindings for librcsb-core-wrapper. - -Package: python-librcsb-core-wrapper-dbg -Architecture: any -Section: debug -Priority: extra -Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, librcsb-core-wrapper0 (= ${binary:Version}), python-dbg -Provides: ${python:Provides} -Breaks: ${python:Breaks} -Description: debugging symbols for python-librcsb-core-wrapper - The RCSB Core Wrapper library was developed to provide an object-oriented - application interface to information in mmCIF format. It includes several - classes for accessing data dictionaries and mmCIF format data files. - . - This package contains the detached debug symbols for - python-librcsb-core-wrapper. Modified: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/objectfiles =================================================================== --- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/objectfiles 2012-08-13 15:39:13 UTC (rev 12037) +++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/objectfiles 2012-08-13 16:53:57 UTC (rev 12038) @@ -167,7 +167,7 @@ UTIL_LOC = https://svn-dev.wwpdb.org/svn-rcsb/build/util UTIL_MODULE = util CHECKOUT_SCRIPT = checkout.sh -@@ -66,7 +65,9 @@ +@@ -66,7 +65,24 @@ export WWPDB_XERCESC_LIB=xerces-c; \ ./$(COMPILE_SCRIPT)' @@ -175,17 +175,7 @@ +# lkajan: the reason for this is that I do not want to set prerequisites here just now, so I make it made always +.PHONY: lib/librcsb-core-wrapper.la +lib/librcsb-core-wrapper.la: - +@sh -c 'cd ./$(UTIL_MODULE); \ - export PIC=-fPIC; \ - export WWPDB_PYTHON_INC=/apps/python/include/python2.5; \ -@@ -79,12 +80,28 @@ - export WWPDB_XERCESC_LIB_DIR=/apps/xerces-3.0.1/lib; \ - export WWPDB_XERCESC_LIB=xerces-c; \ - ./$(COMPILE_SCRIPT)' -+ libtool --quiet --mode=link $(CXX) -version-info 0:0:0 -rpath /usr/lib $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o lib/librcsb-core-wrapper.la lib/*.lo -+ -+compile_lnx_41: lib/librcsb-core-wrapper.la -+ +@sh -c 'cd ./$(UTIL_MODULE); \ ++ +sh -c '\ + export PIC=-fPIC; \ + export WWPDB_PYTHON_INC=/apps/python/include/python2.5; \ + export WWPDB_PYTHON_LIB_DIR=/apps/python/lib; \ @@ -196,6 +186,18 @@ + export WWPDB_XERCESC_INC=/apps/xerces-3.0.1/include; \ + export WWPDB_XERCESC_LIB_DIR=/apps/xerces-3.0.1/lib; \ + export WWPDB_XERCESC_LIB=xerces-c; \ ++ ( cd ./$(UTIL_MODULE); ./$(COMPILE_SCRIPT) ); \ ++ libtool --mode=link $(CXX) -version-info 0:0:0 -rpath /usr/lib $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -l$${WWPDB_XERCESC_LIB} -o lib/librcsb-core-wrapper.la lib/*.lo' ++ ++compile_lnx_41: lib/librcsb-core-wrapper.la + +@sh -c 'cd ./$(UTIL_MODULE); \ + export PIC=-fPIC; \ + export WWPDB_PYTHON_INC=/apps/python/include/python2.5; \ +@@ -78,13 +94,14 @@ + export WWPDB_XERCESC_INC=/apps/xerces-3.0.1/include; \ + export WWPDB_XERCESC_LIB_DIR=/apps/xerces-3.0.1/lib; \ + export WWPDB_XERCESC_LIB=xerces-c; \ +- ./$(COMPILE_SCRIPT)' + exit 0;' debug: @@ -203,7 +205,7 @@ clean_build: @sh -c 'cd ./$(UTIL_MODULE); ./$(CLEAN_SCRIPT)' -+ @rm -rf lib/* ++ @rm -rf lib/* lib/.??* test: test-all Deleted: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/pythonwrapper =================================================================== --- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/pythonwrapper 2012-08-13 15:39:13 UTC (rev 12037) +++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/pythonwrapper 2012-08-13 16:53:57 UTC (rev 12038) @@ -1,36 +0,0 @@ ---- a/Makefile -+++ b/Makefile -@@ -96,6 +96,22 @@ - export WWPDB_XERCESC_LIB=xerces-c; \ - exit 0;' - -+# lkajan: for testing -+.PHONY: wrapper -+wrapper: -+ +@sh -c 'cd ./$(UTIL_MODULE); \ -+ export PIC=-fPIC; \ -+ export WWPDB_PYTHON_INC=/usr/include/python2.7; \ -+ export WWPDB_PYTHON_LIB_DIR=/apps/python/lib; \ -+ export WWPDB_PYTHON_LIB=python2.7; \ -+ export WWPDB_BOOST_INC=/apps/boost/include/boost-1_41; \ -+ export WWPDB_BOOST_PYTHON_LIB_DIR=/apps/boost/lib; \ -+ export WWPDB_BOOST_PYTHON_LIB=boost_python-mt-py27; \ -+ export WWPDB_XERCESC_INC=/apps/xerces-3.0.1/include; \ -+ export WWPDB_XERCESC_LIB_DIR=/apps/xerces-3.0.1/lib; \ -+ export WWPDB_XERCESC_LIB=xerces-c; \ -+ ( cd ../wrapper && make OPT=-O install );' -+ - debug: - @sh -c 'cd ./$(UTIL_MODULE); ./$(COMPILE_SCRIPT) debug' - ---- a/wrapper/Makefile -+++ b/wrapper/Makefile -@@ -140,7 +140,7 @@ - $(L_MOD_LIB): $(OBJ_FILES) $(ALL_DEP_LIBS) - # Create module library - -- @cd $(OBJ_DIR); $(CCC) $(LINK_METHOD) $(EXT_LIBS_DIRS) $(OBJ_FILES) $(ALL_DEP_LIBS) $(EXT_LIBS) $(SYS_LIBS) -o ../$@ -+ cd $(OBJ_DIR); $(CCC) $(LINK_METHOD) $(EXT_LIBS_DIRS) $(OBJ_FILES) -L../../lib/.libs -lrcsb-core-wrapper $(EXT_LIBS) $(SYS_LIBS) -o ../$@ - - - # Rule for making object files Modified: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/series =================================================================== --- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/series 2012-08-13 15:39:13 UTC (rev 12037) +++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/series 2012-08-13 16:53:57 UTC (rev 12038) @@ -1,4 +1,4 @@ -wrapper +wrapper-module rm-duplicate-module bash make_pair @@ -6,4 +6,5 @@ parallel-build Makefile objectfiles -pythonwrapper +wrapper +setup.py.in Added: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/setup.py.in =================================================================== --- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/setup.py.in (rev 0) +++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/setup.py.in 2012-08-13 16:53:57 UTC (rev 12038) @@ -0,0 +1,109 @@ +--- /dev/null ++++ b/wrapper/python/setup.py.in +@@ -0,0 +1,49 @@ ++#!/usr/bin/env python ++ ++from distutils import sysconfig ++from distutils.core import setup, Extension ++import os ++import platform ++import sys ++ ++# lkajan: we follow the example of libtorrent-rasterbar here - thank you very much for that! ++def parse_cmd(cmdline, prefix, keep_prefix = False): ++ ret = [] ++ for token in cmdline.split(): ++ if token[:len(prefix)] == prefix: ++ if keep_prefix: ++ ret.append(token) ++ else: ++ ret.append(token[len(prefix):]) ++ return ret ++ ++config_vars = sysconfig.get_config_vars() ++if "CFLAGS" in config_vars and "-Wstrict-prototypes" in config_vars["CFLAGS"]: ++ config_vars["CFLAGS"] = config_vars["CFLAGS"].replace("-Wstrict-prototypes", " ") ++if "OPT" in config_vars and "-Wstrict-prototypes" in config_vars["OPT"]: ++ config_vars["OPT"] = config_vars["OPT"].replace("-Wstrict-prototypes", " ") ++ ++source_list = os.listdir(os.path.join(os.path.dirname(__file__), "src")) ++source_list = [os.path.join("src", s) for s in source_list if s.endswith(".C")] ++ ++# g++ -O -fPIC -ansi -Werror -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -I./include -I../include -I/usr/include/python2.7 -I/apps/boost/include/boost-1_41 -ftemplate-depth-128 -fno-inline -Wall -c src/TypeCodePyWrap.C -o ./obj/TypeCodePyWrap.o ++# 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', ++ version='1.000', ++ author = 'RCSB PDB Software Team', ++ author_email='[email protected]', ++ description = 'Python bindings for librcsb-core-wrapper', ++ long_description = 'Python bindings for librcsb-core-wrapper', ++ url = 'http://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html', ++ platforms = 'any', ++ license = 'RCSB PDB SOFTWARE LICENSE AGREEMENT', ++ ext_modules = [Extension('CorePyWrap', ++ sources = source_list, ++ language='c++', ++ include_dirs = ['../../include'] + parse_cmd(extra_cmd, '-I'), ++ library_dirs = ['../../lib/.libs'] + parse_cmd(extra_cmd, '-L'), ++ extra_compile_args = parse_cmd(extra_cmd, '-D', True), ++ libraries = ['rcsb-core-wrapper', 'boost_python-py%1d%1d' % ( sys.version_info[0], sys.version_info[1] )] + parse_cmd(extra_cmd, '-l'))], ++) +--- a/wrapper/Makefile ++++ b/wrapper/Makefile +@@ -101,11 +101,16 @@ + .PHONY: ../etc/Makefile.platform all install export clean clean_build + + +-all: install ++all: build + ++.PHONY: build ++build: python/setup.py + + install: $(M_MOD_LIB) + ++python/setup.py: python/setup.py.in ++ sed -e 's!@C++FLAGS@!$(C++FLAGS)!g; s!@DEFINES@!$(DEFINES)!g; s!@EXT_COMP_OPT@!$(EXT_COMP_OPT)!; s!@EXT_LIBS_DIRS@!$(EXT_LIBS_DIRS)!g; s!@EXT_LIBS@!$(EXT_LIBS)!g;' < "$<" > "$@" ++ ln -sf ../src python/src + + export: + mkdir -p $(EXPORT_DIR) +@@ -135,6 +140,7 @@ + @rm -f $(M_MOD_LIB) + @rm -f $(M_AGR_LIB) + @rm -f *.pyc ++ @rm -f python/setup.py + + + $(L_MOD_LIB): $(OBJ_FILES) $(ALL_DEP_LIBS) +--- a/Makefile ++++ b/Makefile +@@ -11,7 +11,7 @@ + CLEAN_DOC_SCRIPT = clean_doc.sh + EXPORT_SCRIPT = export.sh + +-all: compile_lnx_41 ++all: wrapper + + compile: + @echo +@@ -98,7 +98,7 @@ + + # lkajan: for testing + .PHONY: wrapper +-wrapper: ++wrapper: lib/librcsb-core-wrapper.la + +@sh -c 'cd ./$(UTIL_MODULE); \ + export PIC=-fPIC; \ + export WWPDB_PYTHON_INC=/usr/include/python2.7; \ +@@ -110,7 +110,7 @@ + export WWPDB_XERCESC_INC=/apps/xerces-3.0.1/include; \ + export WWPDB_XERCESC_LIB_DIR=/apps/xerces-3.0.1/lib; \ + export WWPDB_XERCESC_LIB=xerces-c; \ +- ( cd ../wrapper && make OPT=-O install );' ++ ( cd ../wrapper && make OPT=-O );' + + debug: + @sh -c 'cd ./$(UTIL_MODULE); ./$(COMPILE_SCRIPT) debug' Deleted: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/wrapper =================================================================== --- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/wrapper 2012-08-13 15:39:13 UTC (rev 12037) +++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/wrapper 2012-08-13 16:53:57 UTC (rev 12038) @@ -1,7 +0,0 @@ ---- a/local/modules.txt -+++ b/local/modules.txt -@@ -9,4 +9,3 @@ - svn https://svn-dev.wwpdb.org/svn-rcsb/pdbml/modules/pdbml-parser pdbml-parser Latest - svn https://svn-dev.wwpdb.org/svn-rcsb/pdbml/modules/pdbml-parser pdbml-parser Latest - svn https://svn-dev.wwpdb.org/svn-wwpdb/third-party/cctbx cctbx Latest --svn https://svn-dev.wwpdb.org/svn-wwpdb/core/wrapper wrapper Latest Copied: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/wrapper (from rev 12036, trunk/packages/rcsb-core-wrapper/trunk/debian/patches/pythonwrapper) =================================================================== --- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/wrapper (rev 0) +++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/wrapper 2012-08-13 16:53:57 UTC (rev 12038) @@ -0,0 +1,36 @@ +--- a/Makefile ++++ b/Makefile +@@ -96,6 +96,22 @@ + export WWPDB_XERCESC_LIB=xerces-c; \ + exit 0;' + ++# lkajan: for testing ++.PHONY: wrapper ++wrapper: ++ +@sh -c 'cd ./$(UTIL_MODULE); \ ++ export PIC=-fPIC; \ ++ export WWPDB_PYTHON_INC=/usr/include/python2.7; \ ++ export WWPDB_PYTHON_LIB_DIR=/apps/python/lib; \ ++ export WWPDB_PYTHON_LIB=python2.7; \ ++ export WWPDB_BOOST_INC=/apps/boost/include/boost-1_41; \ ++ export WWPDB_BOOST_PYTHON_LIB_DIR=/apps/boost/lib; \ ++ export WWPDB_BOOST_PYTHON_LIB=boost_python-mt-py27; \ ++ export WWPDB_XERCESC_INC=/apps/xerces-3.0.1/include; \ ++ export WWPDB_XERCESC_LIB_DIR=/apps/xerces-3.0.1/lib; \ ++ export WWPDB_XERCESC_LIB=xerces-c; \ ++ ( cd ../wrapper && make OPT=-O install );' ++ + debug: + @sh -c 'cd ./$(UTIL_MODULE); ./$(COMPILE_SCRIPT) debug' + +--- a/wrapper/Makefile ++++ b/wrapper/Makefile +@@ -140,7 +140,7 @@ + $(L_MOD_LIB): $(OBJ_FILES) $(ALL_DEP_LIBS) + # Create module library + +- @cd $(OBJ_DIR); $(CCC) $(LINK_METHOD) $(EXT_LIBS_DIRS) $(OBJ_FILES) $(ALL_DEP_LIBS) $(EXT_LIBS) $(SYS_LIBS) -o ../$@ ++ cd $(OBJ_DIR); $(CCC) $(LINK_METHOD) $(EXT_LIBS_DIRS) $(OBJ_FILES) -L../../lib/.libs -lrcsb-core-wrapper $(EXT_LIBS) $(SYS_LIBS) -o ../$@ + + + # Rule for making object files Copied: trunk/packages/rcsb-core-wrapper/trunk/debian/patches/wrapper-module (from rev 12036, trunk/packages/rcsb-core-wrapper/trunk/debian/patches/wrapper) =================================================================== --- trunk/packages/rcsb-core-wrapper/trunk/debian/patches/wrapper-module (rev 0) +++ trunk/packages/rcsb-core-wrapper/trunk/debian/patches/wrapper-module 2012-08-13 16:53:57 UTC (rev 12038) @@ -0,0 +1,7 @@ +--- a/local/modules.txt ++++ b/local/modules.txt +@@ -9,4 +9,3 @@ + svn https://svn-dev.wwpdb.org/svn-rcsb/pdbml/modules/pdbml-parser pdbml-parser Latest + svn https://svn-dev.wwpdb.org/svn-rcsb/pdbml/modules/pdbml-parser pdbml-parser Latest + svn https://svn-dev.wwpdb.org/svn-wwpdb/third-party/cctbx cctbx Latest +-svn https://svn-dev.wwpdb.org/svn-wwpdb/core/wrapper wrapper Latest Modified: trunk/packages/rcsb-core-wrapper/trunk/debian/rules =================================================================== --- trunk/packages/rcsb-core-wrapper/trunk/debian/rules 2012-08-13 15:39:13 UTC (rev 12037) +++ trunk/packages/rcsb-core-wrapper/trunk/debian/rules 2012-08-13 16:53:57 UTC (rev 12038) @@ -6,16 +6,39 @@ export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed -# lkajan: we borrow from libtorrent-rasterbar here (thank you) +# lkajan: we borrow from libtorrent-rasterbar and pythonmagick here (thank you) PYVERSIONS=$(shell pyversions -vr) -ALLPY=$(PYVERSIONS) $(PYVERSIONS:%=%-dbg) +# lkajan: the below could include debug versions like in python-libtorrent +ALLPY=$(PYVERSIONS) # Uncomment this to turn on verbose mode. -#export DH_VERBOSE=1 +export DH_VERBOSE=1 %: - dh $@ --parallel --with python2 + dh $@ --parallel --with python-support +.PHONY: override_dh_auto_build +override_dh_auto_build: override_dh_auto_build-nopy override_dh_auto_build-py + +.PHONY: override_dh_auto_build-nopy +override_dh_auto_build-nopy: + dh_auto_build --parallel + +.PHONY: override_dh_auto_build-py +override_dh_auto_build-py: override_dh_auto_build-nopy + dh_auto_build --parallel --sourcedirectory=wrapper/python + +.PHONY: override_dh_auto_install +override_dh_auto_install: override_dh_auto_install-nopy override_dh_auto_install-py + +.PHONY: override_dh_auto_install-nopy +# lkajan: TODO, use dh_install +override_dh_auto_install-nopy: + +.PHONY: override_dh_auto_install-py +override_dh_auto_install-py: + dh_auto_install --sourcedirectory=wrapper/python + .PHONY: override_dh_strip override_dh_strip: dh_strip --dbg-package=librcsb-core-wrapper0-dbg @@ -30,6 +53,5 @@ .PHONY: override_dh_auto_clean override_dh_auto_clean: - rm -rf build build-py* dh_auto_clean - + rm -rf wrapper/python/build _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
