[med-svn] [Git][med-team/librcsb-core-wrapper][master] 7 commits: Really really fix clean target. Closes: #1046372.

Santiago Vila (@sanvila) gitlab at salsa.debian.org
Sun Sep 13 01:08:05 BST 2026



Santiago Vila pushed to branch master at Debian Med / librcsb-core-wrapper


Commits:
db936ef9 by Santiago Vila at 2026-09-13T01:15:00+02:00
Really really fix clean target. Closes: #1046372.

(Also simplify debian/rules by moving things to debian/clean)

For reference, this is what happened in 1.005-14 while trying to build source after a binary build:

Package: librcsb-core-wrapper
Version: 1.005-14
[...]
dpkg-source: error: cannot represent changes to wrapper/CorePyWrap.so: binary file contents changed
dpkg-source: error: add wrapper/CorePyWrap.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
dpkg-source: error: cannot represent changes to wrapper/lib/CorePyWrap.so: binary file contents changed
dpkg-source: error: add wrapper/lib/CorePyWrap.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
dpkg-source: warning: executable mode 0755 of 'wrapper/lib/CorePyWrap.so' will not be represented in diff
dpkg-source: error: unrepresentable changes to source
dpkg-buildpackage: error: dpkg-source -b . subprocess failed with exit status 1

- - - - -
6c8c82ff by Santiago Vila at 2026-09-13T01:20:00+02:00
Drop unused lintian override.

- - - - -
a27d8d51 by Santiago Vila at 2026-09-13T01:25:00+02:00
Fix wrong patch metadata.

- - - - -
6767c602 by Santiago Vila at 2026-09-13T01:30:00+02:00
Drop commented reference to no longer existing patch.

- - - - -
7dfeb688 by Santiago Vila at 2026-09-13T01:35:00+02:00
Refresh patches.

- - - - -
c0f8bbb2 by Santiago Vila at 2026-09-13T01:40:00+02:00
d/salsa-ci.yml: Use the simplified version.

- - - - -
60c80fc8 by Santiago Vila at 2026-09-13T01:45:00+02:00
Upload for unstable as 1.005-15

- - - - -


27 changed files:

- debian/changelog
- debian/clean
- debian/librcsb-core-wrapper0t64.lintian-overrides
- debian/patches/INSTALL-is-cifinstall.patch
- debian/patches/bash
- debian/patches/devnull-log
- debian/patches/docs
- debian/patches/exit-in-shlib
- debian/patches/fix-makefile.patch
- debian/patches/gcc-8.patch
- debian/patches/generated-includes
- debian/patches/hardening
- debian/patches/make-4.4.1.patch
- debian/patches/make-shuffle-reverse.patch
- debian/patches/make_test_target
- debian/patches/objectfiles
- debian/patches/parallel-build
- debian/patches/python3.patch
- debian/patches/regcomp_cert_fix.patch
- debian/patches/rm-duplicate-module
- debian/patches/series
- debian/patches/spelling
- debian/patches/unistd
- debian/patches/wrapper-module
- debian/patches/xerces32.patch
- debian/rules
- debian/salsa-ci.yml


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+librcsb-core-wrapper (1.005-15) unstable; urgency=medium
+
+  * Team upload.
+  * Really really fix clean target. Closes: #1046372.
+  * Drop unused lintian override.
+  * Tidy up of debian/patches.
+  * Simplify salsa-ci.yml.
+
+ -- Santiago Vila <sanvila at debian.org>  Sun, 13 Sep 2026 01:45:00 +0200
+
 librcsb-core-wrapper (1.005-14) unstable; urgency=medium
 
   * d/watch: version=5


=====================================
debian/clean
=====================================
@@ -1,4 +1,9 @@
+*/obj/
+.pybuild/
 etc/Makefile.platform
+wrapper/CorePyWrap.so
+wrapper/lib/CorePyWrap.so
+wrapper/python/build/
 wrapper/python/python_corepywrap.egg-info/
 wrapper/python/setup.py
 wrapper/python/src


=====================================
debian/librcsb-core-wrapper0t64.lintian-overrides
=====================================
@@ -1,3 +1,2 @@
 # C++ shared library. See more in d/README.source.
 librcsb-core-wrapper0t64: no-symbols-control-file usr/lib/librcsb-core-wrapper.so.0.0.1
-librcsb-core-wrapper0t64: package-name-doesnt-match-sonames librcsb-core-wrapper0


=====================================
debian/patches/INSTALL-is-cifinstall.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Juhani Numminen <juhaninumminen0 at gmail.com>
-Last-Updated: Sun, 17 Jan 2021 13:38:46 +0200
+Last-Updated: 2021-01-17
 Description: build system will not work with any other INSTALL command
  Debhelper in compat 11 tries to set the INSTALL variable.
 


=====================================
debian/patches/bash
=====================================
@@ -1,6 +1,7 @@
 Author: Laszlo Kajan <lkajan at rostlab.org>
 Description: fixing shell - bash is meant instead of sh
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-August/016975.html
+
 --- a/util/compile.sh
 +++ b/util/compile.sh
 @@ -1,4 +1,4 @@


=====================================
debian/patches/devnull-log
=====================================
@@ -4,9 +4,10 @@ Description: do not attempt to remove log file when it is "/dev/null"
  but there is an error when it tries to remove this file, and it can not.
  This patch checks the log file name, and "/dev/null" is not removed.
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-September/017173.html
+
 --- a/cif-parser/include/CifParserBase.h
 +++ b/cif-parser/include/CifParserBase.h
-@@ -73,7 +73,9 @@ class CifParser : public CifScanner
+@@ -73,7 +73,9 @@
          **  \param[in] fileName - relative or absolute name of the CIF file
          **    that is to be parsed.
          **  \param[in] parseLogFileName - relative or absolute name of the file
@@ -19,7 +20,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Se
          **    parsing warnings and/or parsing errors.
 --- a/cif-parser/src/CifParserBase.C
 +++ b/cif-parser/src/CifParserBase.C
-@@ -148,7 +148,7 @@ void CifParser::Parse(const string& file
+@@ -148,7 +148,7 @@
      if (RcsbFile::IsEmpty(log))
      {
          log.close();


=====================================
debian/patches/docs
=====================================
@@ -1,9 +1,10 @@
 Author: Laszlo Kajan <lkajan at rostlab.org>
 Description: generate documentation
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-August/016975.html
+
 --- a/etc/Doxyfile-template
 +++ b/etc/Doxyfile-template
-@@ -123,7 +123,7 @@ INLINE_INHERITED_MEMB  = NO
+@@ -123,7 +123,7 @@
  # path before files name in the file list and in the header files. If set 
  # to NO the shortest path that makes the file name unique will be used.
  
@@ -12,7 +13,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
  # If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
  # can be used to strip a user-defined part of the path. Stripping is 
-@@ -250,7 +250,7 @@ EXTRACT_ALL            = YES
+@@ -250,7 +250,7 @@
  # If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
  # will be included in the documentation.
  
@@ -21,7 +22,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
  # If the EXTRACT_STATIC tag is set to YES all static members of a file 
  # will be included in the documentation.
-@@ -423,26 +423,26 @@ FILE_VERSION_FILTER    =
+@@ -423,26 +423,26 @@
  # The QUIET tag can be used to turn on/off the messages that are generated 
  # by doxygen. Possible values are YES and NO. If left blank NO is used.
  
@@ -52,7 +53,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
  # This WARN_NO_PARAMDOC option can be abled to get warnings for 
  # functions that are documented, but have no documentation for their parameters 
-@@ -798,7 +798,7 @@ TREEVIEW_WIDTH         = 250
+@@ -798,7 +798,7 @@
  # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
  # generate Latex output.
  
@@ -63,7 +64,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  # If a relative path is entered the value of OUTPUT_DIRECTORY will be 
 --- a/Makefile
 +++ b/Makefile
-@@ -115,10 +115,19 @@ clean_test:
+@@ -115,10 +115,19 @@
  
  ###
  doc:


=====================================
debian/patches/exit-in-shlib
=====================================
@@ -3,9 +3,10 @@ Description: library calls exit
  Not a fix, just making the error message go to standard error instead of
  standard output.
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-August/016975.html
+
 --- a/cif-file/src/ParentChild.C
 +++ b/cif-file/src/ParentChild.C
-@@ -287,7 +287,7 @@ void ParentChild::CreateAllRelations(
+@@ -287,7 +287,7 @@
  #ifdef VLAD_FIX
      if (parKeys.empty())
      {


=====================================
debian/patches/fix-makefile.patch
=====================================
@@ -4,7 +4,7 @@ Description: Salsa CI fails due to missing dir - just create it
 
 --- a/common/Makefile
 +++ b/common/Makefile
-@@ -104,6 +104,7 @@ clean: clean_build
+@@ -104,6 +104,7 @@
  
  $(M_MOD_LIB): $(L_MOD_LIB)
  #       Install header files
@@ -12,7 +12,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	@cd $(L_INCL_DIR); \
            ../$(INSTALL) $(INSTALLOPTS) $(HEADER_FILES) ../$(M_INCL_DIR)
  
-@@ -144,7 +145,9 @@ clean_build:
+@@ -144,7 +145,9 @@
  
  $(L_MOD_LIB): $(OBJ_FILES)
  #       Create module library
@@ -24,7 +24,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	$(RANLIB) $@
 --- a/wrapper/Makefile
 +++ b/wrapper/Makefile
-@@ -18,11 +18,11 @@ VPATH = $(OBJ_DIR)
+@@ -18,11 +18,11 @@
  
  EXT_COMP_OPT = -ftemplate-depth-128 -fno-inline -Wall
  
@@ -41,7 +41,7 @@ Description: Salsa CI fails due to missing dir - just create it
  
  SYS_LIBS = -lutil -lpthread -ldl
  
-@@ -141,11 +141,12 @@ clean_build:
+@@ -141,11 +141,12 @@
  
  $(L_MOD_LIB): $(OBJ_FILES) $(ALL_DEP_LIBS)
  #       Create module library
@@ -57,7 +57,7 @@ Description: Salsa CI fails due to missing dir - just create it
  
 --- a/Makefile
 +++ b/Makefile
-@@ -105,7 +105,7 @@ lib/librcsb-core-wrapper.la:
+@@ -105,7 +105,7 @@
  	 export WWPDB_XERCESC_INC=/usr/include; \
  	 export WWPDB_XERCESC_LIB_DIR=/usr/lib; \
  	 export WWPDB_XERCESC_LIB=xerces-c; \
@@ -68,7 +68,7 @@ Description: Salsa CI fails due to missing dir - just create it
  debug:
 --- a/cif-file-util/Makefile
 +++ b/cif-file-util/Makefile
-@@ -96,6 +96,7 @@ clean: clean_build
+@@ -96,6 +96,7 @@
  
  $(M_MOD_LIB): $(L_MOD_LIB)
  #       Install header files
@@ -76,7 +76,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	@cd $(L_INCL_DIR); \
            ../$(INSTALL) $(INSTALLOPTS) $(HEADER_FILES) ../$(M_INCL_DIR)
  
-@@ -132,7 +133,9 @@ clean_build:
+@@ -132,7 +133,9 @@
  
  $(L_MOD_LIB): $(OBJ_FILES)
  #       Create module library
@@ -88,7 +88,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	$(RANLIB) $@
 --- a/cif-file/Makefile
 +++ b/cif-file/Makefile
-@@ -96,6 +96,7 @@ clean: clean_build
+@@ -96,6 +96,7 @@
  
  $(M_MOD_LIB): $(L_MOD_LIB)
  #       Install header files
@@ -96,7 +96,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	@cd $(L_INCL_DIR); \
            ../$(INSTALL) $(INSTALLOPTS) $(HEADER_FILES) ../$(M_INCL_DIR)
  
-@@ -132,7 +133,9 @@ clean_build:
+@@ -132,7 +133,9 @@
  
  $(L_MOD_LIB): $(OBJ_FILES)
  #       Create module library
@@ -108,7 +108,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	$(RANLIB) $@
 --- a/cif-parser/Makefile
 +++ b/cif-parser/Makefile
-@@ -121,6 +121,7 @@ clean: clean_build
+@@ -121,6 +121,7 @@
  
  $(M_MOD_LIB): $(L_MOD_LIB)
  #       Install header files
@@ -116,7 +116,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	@cd $(L_INCL_DIR); \
            ../$(INSTALL) $(INSTALLOPTS) $(HEADER_FILES) ../$(M_INCL_DIR)
  
-@@ -169,7 +170,9 @@ clean_build:
+@@ -169,7 +170,9 @@
  
  $(L_MOD_LIB): $(addprefix obj/,$(OBJ_FILES))
  #       Create module library
@@ -128,7 +128,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	$(RANLIB) $@
 --- a/dict-obj-file/Makefile
 +++ b/dict-obj-file/Makefile
-@@ -114,6 +114,7 @@ all: install
+@@ -114,6 +114,7 @@
  install: $(TARGETS) $(M_BIN_DIR)/$(TARGET_SCRIPTS)
  
  $(M_BIN_DIR)/$(TARGET_SCRIPTS): $(L_BIN_DIR)/$(TARGET_SCRIPTS)
@@ -136,7 +136,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	cp -f $(L_BIN_DIR)/$(TARGET_SCRIPTS) $(M_BIN_DIR)/$(TARGET_SCRIPTS)
  
  
-@@ -143,6 +144,7 @@ clean: clean_build clean_test
+@@ -143,6 +144,7 @@
  # Rule for making executables
  %: $(OBJ_DIR)/%.o $(M_MOD_LIB) $(ALL_DEP_LIBS)
  	$(CCC) $(CPPFLAGS) $(LDFLAGS) $< $(M_MOD_LIB) $(ALL_DEP_LIBS) $(MALLOCLIB) -lm -o $(L_BIN_DIR)/$@
@@ -144,7 +144,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	@cp -f $(L_BIN_DIR)/$@ $(M_BIN_DIR)/$@
  
  
-@@ -167,6 +169,7 @@ clean_test:
+@@ -167,6 +169,7 @@
  
  $(M_MOD_LIB): $(L_MOD_LIB)
  #       Install header files
@@ -152,7 +152,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	@cd $(L_INCL_DIR); \
            ../$(INSTALL) $(INSTALLOPTS) $(HEADER_FILES) ../$(M_INCL_DIR)
  
-@@ -194,7 +197,9 @@ $(M_MOD_LIB): $(L_MOD_LIB)
+@@ -194,7 +197,9 @@
  
  $(L_MOD_LIB): $(OBJ_OTHER_FILES)
  #       Create module library
@@ -164,7 +164,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	$(RANLIB) $@
 --- a/pdbml-parser/Makefile
 +++ b/pdbml-parser/Makefile
-@@ -157,7 +157,9 @@ clean: clean_build clean_test
+@@ -157,7 +157,9 @@
  
  # General rule for making executables
  %: $(OBJ_DIR)/%.o $(M_MOD_LIB) $(ALL_DEP_LIBS)
@@ -174,7 +174,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	@cp -f $(L_BIN_DIR)/$@ $(M_BIN_DIR)/$@
  
  
-@@ -182,6 +184,7 @@ clean_test:
+@@ -182,6 +184,7 @@
  # Rule for making module library in master library directory
  $(M_MOD_LIB): $(L_MOD_LIB)
  #       Install header files
@@ -182,7 +182,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	@cd $(L_INCL_DIR); \
            ../$(INSTALL) $(INSTALLOPTS) $(HEADER_FILES) ../$(M_INCL_DIR)
  
-@@ -210,7 +213,9 @@ $(M_MOD_LIB): $(L_MOD_LIB)
+@@ -210,7 +213,9 @@
  # Rule for making module library in local library directory
  $(L_MOD_LIB): $(OBJ_OTHER_FILES)
  #       Create module library
@@ -194,7 +194,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	$(RANLIB) $@
 --- a/regex/Makefile
 +++ b/regex/Makefile
-@@ -105,6 +105,7 @@ clean: clean_build clean_test
+@@ -105,6 +105,7 @@
  
  $(M_MOD_LIB): $(L_MOD_LIB)
  #       Install header files
@@ -202,7 +202,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	@cd $(L_INCL_DIR); \
            ../$(INSTALL) $(INSTALLOPTS) $(HEADER_FILES) ../$(M_INCL_DIR)
  
-@@ -143,7 +144,9 @@ clean_test:
+@@ -143,7 +144,9 @@
  
  $(L_MOD_LIB): $(OBJ_FILES)
  #       Create module library
@@ -214,7 +214,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	$(RANLIB) $@
 --- a/tables/Makefile
 +++ b/tables/Makefile
-@@ -93,6 +93,7 @@ clean: clean_build
+@@ -93,6 +93,7 @@
  
  $(M_MOD_LIB): $(L_MOD_LIB)
  #       Install header files
@@ -222,7 +222,7 @@ Description: Salsa CI fails due to missing dir - just create it
  	@cd $(L_INCL_DIR); \
            ../$(INSTALL) $(INSTALLOPTS) $(HEADER_FILES) ../$(M_INCL_DIR)
  
-@@ -129,7 +130,9 @@ clean_build:
+@@ -129,7 +130,9 @@
  
  $(L_MOD_LIB): $(OBJ_FILES)
  #       Create module library


=====================================
debian/patches/gcc-8.patch
=====================================
@@ -5,7 +5,7 @@ Bug-Debian: https://bugs.debian.org/897795
 
 --- a/etc/make.platform.gnu4
 +++ b/etc/make.platform.gnu4
-@@ -34,7 +34,7 @@ ABI=
+@@ -34,7 +34,7 @@
  
  # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all
  # warnings as errors.


=====================================
debian/patches/generated-includes
=====================================
@@ -5,10 +5,8 @@ Description: fix up include path for generated header file that's moved
  I'm surprised this ever worked, but it doesn't work now.
 Last-Update: 2020-10-27
 
-Index: librcsb-core-wrapper-1.005/cif-parser/Makefile
-===================================================================
---- librcsb-core-wrapper-1.005.orig/cif-parser/Makefile
-+++ librcsb-core-wrapper-1.005/cif-parser/Makefile
+--- a/cif-parser/Makefile
++++ b/cif-parser/Makefile
 @@ -181,6 +181,7 @@
  	sh -c 'cd $(SRC_DIR); $(YACC) $(${^F:.y=_YACC_FLAGS}) ../$<'
  	mv $(^:.y=.tab.c) $(^:.y=.c)


=====================================
debian/patches/hardening
=====================================
@@ -1,9 +1,10 @@
 Author: Laszlo Kajan <lkajan at rostlab.org>
 Description: use hardening flags from environment
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-August/016975.html
+
 --- a/cif-file/Makefile
 +++ b/cif-file/Makefile
-@@ -141,5 +141,5 @@ $(L_MOD_LIB): $(OBJ_FILES)
+@@ -141,5 +141,5 @@
  
  # Rule for making object files
  %.o: $(SRC_DIR)/%.C
@@ -12,7 +13,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/cif-file-util/Makefile
 +++ b/cif-file-util/Makefile
-@@ -141,5 +141,5 @@ $(L_MOD_LIB): $(OBJ_FILES)
+@@ -141,5 +141,5 @@
  
  # Rule for making object files
  %.o: $(SRC_DIR)/%.C
@@ -21,7 +22,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/cif-parser/Makefile
 +++ b/cif-parser/Makefile
-@@ -181,17 +181,17 @@ obj/%Parser.o $(SRC_DIR)/%Parser.h: $(SR
+@@ -181,17 +181,17 @@
  	sh -c 'cd $(SRC_DIR); $(YACC) $(${^F:.y=_YACC_FLAGS}) ../$<'
  	mv $(^:.y=.tab.c) $(^:.y=.c)
  	mv $(^:.y=.tab.h) $(^:.y=.h)
@@ -45,7 +46,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/common/Makefile
 +++ b/common/Makefile
-@@ -153,5 +153,5 @@ $(L_MOD_LIB): $(OBJ_FILES)
+@@ -153,5 +153,5 @@
  
  # Rule for making object files
  %.o: $(SRC_DIR)/%.C
@@ -54,7 +55,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/dict-obj-file/Makefile
 +++ b/dict-obj-file/Makefile
-@@ -142,7 +142,7 @@ clean: clean_build clean_test
+@@ -142,7 +142,7 @@
  
  # Rule for making executables
  %: $(OBJ_DIR)/%.o $(M_MOD_LIB) $(ALL_DEP_LIBS)
@@ -63,7 +64,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  	@cp -f $(L_BIN_DIR)/$@ $(M_BIN_DIR)/$@
  
  
-@@ -203,10 +203,10 @@ $(L_MOD_LIB): $(OBJ_OTHER_FILES)
+@@ -203,10 +203,10 @@
  
  # Rule for making object files
  $(OBJ_DIR)/%.o: $(SRC_DIR)/%.C
@@ -78,7 +79,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/etc/make.platform.gnu4
 +++ b/etc/make.platform.gnu4
-@@ -108,8 +108,8 @@ NON_ANSI_C_FLAG=
+@@ -108,8 +108,8 @@
  C_WARNINGS=$(WARNINGS)
  
  # C compiler flags
@@ -89,7 +90,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
  ## C++ compiler
  ## This part defines C++ compiler information
-@@ -128,14 +128,14 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECA
+@@ -128,14 +128,14 @@
  EXT=C
  
  # C++ compiler flags
@@ -107,7 +108,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
    $(DEFINES) $(INCLUDES)
  
  ## Fortran compiler
-@@ -158,8 +158,8 @@ F77LIBS=
+@@ -158,8 +158,8 @@
  STATIC_LINKING=-static
  
  # Linker flags
@@ -120,7 +121,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  F77_LINKER=f77
 --- a/pdbml-parser/Makefile
 +++ b/pdbml-parser/Makefile
-@@ -222,10 +222,10 @@ $(L_MOD_LIB): $(OBJ_OTHER_FILES)
+@@ -222,10 +222,10 @@
  
  # General rule for making object files
  $(OBJ_DIR)/%.o: $(SRC_DIR)/%.C
@@ -135,7 +136,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/tables/Makefile
 +++ b/tables/Makefile
-@@ -138,5 +138,5 @@ $(L_MOD_LIB): $(OBJ_FILES)
+@@ -138,5 +138,5 @@
  
  # Rule for making object files
  %.o: $(SRC_DIR)/%.C
@@ -144,7 +145,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/wrapper/Makefile
 +++ b/wrapper/Makefile
-@@ -148,10 +148,10 @@ clean_build:
+@@ -142,10 +142,10 @@
  $(L_MOD_LIB): $(OBJ_FILES) $(ALL_DEP_LIBS)
  #       Create module library
  
@@ -159,7 +160,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/regex/Makefile
 +++ b/regex/Makefile
-@@ -152,7 +152,7 @@ $(L_MOD_LIB): $(OBJ_FILES)
+@@ -152,7 +152,7 @@
  
  # Rule for making object files
  %.o: $(SRC_DIR)/%.c
@@ -168,7 +169,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
  
  # Extra, non-used in PDB build
-@@ -180,18 +180,18 @@ TARGET   = $(L_BIN_DIR)/re
+@@ -180,18 +180,18 @@
  
  
  $(OBJ_DIR)/main.o: $(H) $(HEADER_FILES) $(SRC_DIR)/main.c $(L_INCL_DIR)/main.ih


=====================================
debian/patches/make-4.4.1.patch
=====================================
@@ -5,7 +5,7 @@ Description: Make sure make 4.4.1 will not stumble upon missing includes
 
 --- a/common/Makefile
 +++ b/common/Makefile
-@@ -25,7 +25,7 @@ LINCLUDES = -I$(L_INCL_DIR) -I$(M_INCL_D
+@@ -25,7 +25,7 @@
  #----------------------------------------------------------------------------
  # Include the appropriate compiler/platform definitions ...
  #----------------------------------------------------------------------------
@@ -16,7 +16,7 @@ Description: Make sure make 4.4.1 will not stumble upon missing includes
  ALL_DEP_LIBS =
 --- a/cif-file-util/Makefile
 +++ b/cif-file-util/Makefile
-@@ -25,7 +25,7 @@ LINCLUDES = -I$(L_INCL_DIR) -I$(M_INCL_D
+@@ -25,7 +25,7 @@
  #----------------------------------------------------------------------------
  # Include the appropriate compiler/platform definitions ...
  #----------------------------------------------------------------------------
@@ -27,7 +27,7 @@ Description: Make sure make 4.4.1 will not stumble upon missing includes
  ALL_DEP_LIBS =
 --- a/cif-file/Makefile
 +++ b/cif-file/Makefile
-@@ -25,7 +25,7 @@ LINCLUDES = -I$(L_INCL_DIR) -I$(M_INCL_D
+@@ -25,7 +25,7 @@
  #----------------------------------------------------------------------------
  # Include the appropriate compiler/platform definitions ...
  #----------------------------------------------------------------------------
@@ -38,7 +38,7 @@ Description: Make sure make 4.4.1 will not stumble upon missing includes
  TABLES_LIB    = $(M_LIB_DIR)/tables.a
 --- a/cif-parser/Makefile
 +++ b/cif-parser/Makefile
-@@ -25,7 +25,7 @@ LINCLUDES = -I$(L_INCL_DIR) -I$(M_INCL_D
+@@ -25,7 +25,7 @@
  #----------------------------------------------------------------------------
  # Include the appropriate compiler/platform definitions ...
  #----------------------------------------------------------------------------
@@ -49,7 +49,7 @@ Description: Make sure make 4.4.1 will not stumble upon missing includes
  CifParser_YACC_FLAGS = $(YACCFLAGS) -p cifparser_
 --- a/dict-obj-file/Makefile
 +++ b/dict-obj-file/Makefile
-@@ -28,7 +28,7 @@ LINCLUDES = -I$(L_INCL_DIR) -I$(M_INCL_D
+@@ -28,7 +28,7 @@
  #----------------------------------------------------------------------------
  # Include the appropriate compiler/platform definitions ...
  #----------------------------------------------------------------------------
@@ -60,7 +60,7 @@ Description: Make sure make 4.4.1 will not stumble upon missing includes
  CIF_FILE_UTIL_LIB = $(M_LIB_DIR)/cif-file-util.a
 --- a/pdbml-parser/Makefile
 +++ b/pdbml-parser/Makefile
-@@ -32,7 +32,7 @@ LINCLUDES = -I$(L_INCL_DIR) -I$(M_INCL_D
+@@ -32,7 +32,7 @@
  #----------------------------------------------------------------------------
  # Include the appropriate compiler/platform definitions ...
  #----------------------------------------------------------------------------
@@ -71,7 +71,7 @@ Description: Make sure make 4.4.1 will not stumble upon missing includes
  DICT_OBJ_FILE_LIB = $(M_LIB_DIR)/dict-obj-file.a
 --- a/regex/Makefile
 +++ b/regex/Makefile
-@@ -27,7 +27,7 @@ LINCLUDES = -I$(L_INCL_DIR) -I$(M_INCL_D
+@@ -27,7 +27,7 @@
  #----------------------------------------------------------------------------
  # Include the appropriate compiler/platform definitions ...
  #----------------------------------------------------------------------------
@@ -82,7 +82,7 @@ Description: Make sure make 4.4.1 will not stumble upon missing includes
  ALL_DEP_LIBS =
 --- a/tables/Makefile
 +++ b/tables/Makefile
-@@ -25,7 +25,7 @@ LINCLUDES = -I$(L_INCL_DIR) -I$(M_INCL_D
+@@ -25,7 +25,7 @@
  #----------------------------------------------------------------------------
  # Include the appropriate compiler/platform definitions ...
  #----------------------------------------------------------------------------
@@ -93,7 +93,7 @@ Description: Make sure make 4.4.1 will not stumble upon missing includes
  COMMON_LIB = $(M_LIB_DIR)/common.a
 --- a/wrapper/Makefile
 +++ b/wrapper/Makefile
-@@ -37,7 +37,7 @@ LINCLUDES = -I$(L_INCL_DIR) -I$(M_INCL_D
+@@ -37,7 +37,7 @@
  #----------------------------------------------------------------------------
  # Include the appropriate compiler/platform definitions ...
  #----------------------------------------------------------------------------


=====================================
debian/patches/make-shuffle-reverse.patch
=====================================
@@ -5,7 +5,7 @@ Description: Make sure necessary files are build even with make --shuffle=revers
 
 --- a/cif-parser/Makefile
 +++ b/cif-parser/Makefile
-@@ -196,3 +196,10 @@ obj/%ScannerBase.o: $(SRC_DIR)/%ScannerB
+@@ -196,3 +196,10 @@
  obj/%.o: $(SRC_DIR)/%.C
  	libtool --mode=compile $(CCC) $(CPPFLAGS) $(C++FLAGS) -c $< -o $(OBJ_DIR)/$(@F)
  


=====================================
debian/patches/make_test_target
=====================================
@@ -2,9 +2,10 @@ Author: Laszlo Kajan <lkajan at debian.org>
 Description: fixing #724151: No rule to make target `test-all', needed by `test'.
 Bug-Debian: http://bugs.debian.org/724151
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2013-September/022553.html
+
 --- a/Makefile
 +++ b/Makefile
-@@ -121,7 +121,7 @@ clean_build:
+@@ -117,7 +117,7 @@
  
  test: test-all
  


=====================================
debian/patches/objectfiles
=====================================
@@ -1,9 +1,10 @@
 Author: Laszlo Kajan <lkajan at rostlab.org>
 Description: use libtool for object files and shared library
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-August/016975.html
+
 --- a/cif-file/Makefile
 +++ b/cif-file/Makefile
-@@ -133,11 +133,13 @@ clean_build:
+@@ -133,11 +133,13 @@
  $(L_MOD_LIB): $(OBJ_FILES)
  #       Create module library
  	@cd $(OBJ_DIR); $(AR) $(AR_PUTFLAGS) ../$@ $(OBJ_FILES)
@@ -20,7 +21,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/cif-file-util/Makefile
 +++ b/cif-file-util/Makefile
-@@ -133,11 +133,13 @@ clean_build:
+@@ -133,11 +133,13 @@
  $(L_MOD_LIB): $(OBJ_FILES)
  #       Create module library
  	@cd $(OBJ_DIR); $(AR) $(AR_PUTFLAGS) ../$@ $(OBJ_FILES)
@@ -37,7 +38,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/cif-parser/Makefile
 +++ b/cif-parser/Makefile
-@@ -170,6 +170,8 @@ clean_build:
+@@ -170,6 +170,8 @@
  $(L_MOD_LIB): $(OBJ_FILES)
  #       Create module library
  	@cd $(OBJ_DIR); $(AR) $(AR_PUTFLAGS) ../$@ $(OBJ_FILES)
@@ -46,7 +47,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  	$(RANLIB) $@
  	@echo $@ " is up to date."
  
-@@ -179,14 +181,14 @@ $(OBJ_DIR)/%Parser.o: $(SRC_DIR)/%Parser
+@@ -179,14 +181,14 @@
  	@sh -c 'cd $(SRC_DIR); $(YACC) $(${^F:.y=_YACC_FLAGS}) ../$<'
  	mv $(^:.y=.tab.c) $(^:.y=.c)
  	mv $(^:.y=.tab.h) $(^:.y=.h)
@@ -66,7 +67,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/common/Makefile
 +++ b/common/Makefile
-@@ -145,11 +145,13 @@ clean_build:
+@@ -145,11 +145,13 @@
  $(L_MOD_LIB): $(OBJ_FILES)
  #       Create module library
  	@cd $(OBJ_DIR); $(AR) $(AR_PUTFLAGS) ../$@ $(OBJ_FILES)
@@ -83,7 +84,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/dict-obj-file/Makefile
 +++ b/dict-obj-file/Makefile
-@@ -193,6 +193,8 @@ $(M_MOD_LIB): $(L_MOD_LIB)
+@@ -193,6 +193,8 @@
  $(L_MOD_LIB): $(OBJ_OTHER_FILES)
  #       Create module library
  	@cd $(OBJ_DIR); $(AR) $(AR_PUTFLAGS) ../$@ $(OBJ_OTHER_FILES)
@@ -92,7 +93,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  	$(RANLIB) $@
  	@echo $@ " is up to date."
  
-@@ -204,5 +206,5 @@ $(OBJ_DIR)/%.o: $(SRC_DIR)/%.C
+@@ -204,5 +206,5 @@
  
  # Phony rule for making object files
  %.o: $(SRC_DIR)/%.C
@@ -101,7 +102,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/pdbml-parser/Makefile
 +++ b/pdbml-parser/Makefile
-@@ -211,6 +211,8 @@ $(M_MOD_LIB): $(L_MOD_LIB)
+@@ -211,6 +211,8 @@
  $(L_MOD_LIB): $(OBJ_OTHER_FILES)
  #       Create module library
  	@cd $(OBJ_DIR); $(AR) $(AR_PUTFLAGS) ../$@ $(OBJ_OTHER_FILES)
@@ -110,7 +111,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  	$(RANLIB) $@
  	@echo $@ " is up to date."
  
-@@ -225,5 +227,5 @@ $(OBJ_DIR)/%.o: $(SRC_DIR)/%.C
+@@ -225,5 +227,5 @@
  
  # Phony rule for making object files
  %.o: $(SRC_DIR)/%.C
@@ -119,7 +120,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/regex/Makefile
 +++ b/regex/Makefile
-@@ -144,13 +144,15 @@ clean_test:
+@@ -144,13 +144,15 @@
  $(L_MOD_LIB): $(OBJ_FILES)
  #       Create module library
  	@cd $(OBJ_DIR); $(AR) $(AR_PUTFLAGS) ../$@ $(OBJ_FILES)
@@ -136,7 +137,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
  
  # Extra, non-used in PDB build
-@@ -181,7 +183,7 @@ $(OBJ_DIR)/main.o: $(H) $(HEADER_FILES)
+@@ -181,7 +183,7 @@
  	$(CC) $(CFLAGS_NONANSI) -DPOSIX_MISTAKE -c $(SRC_DIR)/main.c -o $@
  
  $(OBJ_DIR)/split.o: $(H) $(HEADER_FILES) $(SRC_DIR)/split.c 
@@ -147,7 +148,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  	$(CC) $(CFLAGS_NONANSI) -DPOSIX_MISTAKE -c $(SRC_DIR)/debug.c -o $(OBJ_DIR)/$@
 --- a/tables/Makefile
 +++ b/tables/Makefile
-@@ -130,11 +130,13 @@ clean_build:
+@@ -130,11 +130,13 @@
  $(L_MOD_LIB): $(OBJ_FILES)
  #       Create module library
  	@cd $(OBJ_DIR); $(AR) $(AR_PUTFLAGS) ../$@ $(OBJ_FILES)
@@ -164,7 +165,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/Makefile
 +++ b/Makefile
-@@ -12,9 +12,7 @@ DOC_SCRIPT = doc.sh
+@@ -12,9 +12,7 @@
  CLEAN_DOC_SCRIPT = clean_doc.sh
  EXPORT_SCRIPT = export.sh
  
@@ -175,7 +176,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
  compile:  
  	@echo
-@@ -99,11 +97,23 @@ compile_wwpdb_py27:
+@@ -99,11 +97,23 @@
  
  
  


=====================================
debian/patches/parallel-build
=====================================
@@ -1,9 +1,10 @@
 Author: Laszlo Kajan <lkajan at rostlab.org>
 Description: allow parallel make
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-August/016975.html
+
 --- a/cif-parser/Makefile
 +++ b/cif-parser/Makefile
-@@ -167,7 +167,7 @@ clean_build:
+@@ -167,7 +167,7 @@
  	@rm -f $(M_AGR_LIB)
  
  
@@ -12,7 +13,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  #       Create module library
  	@cd $(OBJ_DIR); $(AR) $(AR_PUTFLAGS) ../$@ $(OBJ_FILES)
  	cp -f -t $(M_LIB_DIR) $(addprefix $(OBJ_DIR)/,$(OBJ_FILES) $(OBJ_FILES:.o=.lo))
-@@ -177,18 +177,21 @@ $(L_MOD_LIB): $(OBJ_FILES)
+@@ -177,18 +177,21 @@
  
  
  # Specific rules for making object files
@@ -44,7 +45,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
 --- a/dict-obj-file/Makefile
 +++ b/dict-obj-file/Makefile
-@@ -111,7 +111,10 @@ all: install
+@@ -111,7 +111,10 @@
  
  
  # Installation
@@ -56,7 +57,7 @@ Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-Au
  
  
  # Test
-@@ -141,7 +144,6 @@ clean: clean_build clean_test
+@@ -141,7 +144,6 @@
  %: $(OBJ_DIR)/%.o $(M_MOD_LIB) $(ALL_DEP_LIBS)
  	$(CCC) $(LDFLAGS) $< $(M_MOD_LIB) $(ALL_DEP_LIBS) $(MALLOCLIB) -lm -o $(L_BIN_DIR)/$@
  	@cp -f $(L_BIN_DIR)/$@ $(M_BIN_DIR)/$@


=====================================
debian/patches/python3.patch
=====================================
@@ -3,9 +3,9 @@ Last-Update: 2019-12-14
 Bug-Debian: https://bugs.debian.org/936910
 Description: Switch from Python2 to Python3
 
---- librcsb-core-wrapper.orig/Makefile
-+++ librcsb-core-wrapper/Makefile
-@@ -59,9 +59,9 @@
+--- a/Makefile
++++ b/Makefile
+@@ -55,9 +55,9 @@
  compile_lnx_38:
  	@sh -c 'cd ./$(UTIL_MODULE); \
           export PIC=-fPIC;  \
@@ -17,7 +17,7 @@ Description: Switch from Python2 to Python3
           export WWPDB_BOOST_INC=/apps/boost_1_38_0/include/boost-1_38; \
           export WWPDB_BOOST_PYTHON_LIB_DIR=/apps/boost_1_38_0/lib; \
           export WWPDB_BOOST_PYTHON_LIB=boost_python-gcc41-mt-1_38; \
-@@ -73,9 +73,9 @@
+@@ -69,9 +69,9 @@
  compile_lnx_41:
  	@sh -c 'cd ./$(UTIL_MODULE); \
          export PIC=-fPIC; \
@@ -29,7 +29,7 @@ Description: Switch from Python2 to Python3
          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-gcc41-mt-1_41; \
-@@ -88,9 +88,9 @@
+@@ -84,9 +84,9 @@
  compile_wwpdb_py27:
  	@sh -c 'cd ./$(UTIL_MODULE); \
          export PIC=-fPIC; \
@@ -41,8 +41,8 @@ Description: Switch from Python2 to Python3
          export WWPDB_BOOST_INC=$(TOP_INSTALL_DIR)/include; \
          export WWPDB_BOOST_PYTHON_LIB_DIR=$(TOP_INSTALL_DIR)/lib; \
          export WWPDB_BOOST_PYTHON_LIB=boost_python-mt; \
---- librcsb-core-wrapper.orig/cctbx/scitbx/boost_python/container_conversions.h
-+++ librcsb-core-wrapper/cctbx/scitbx/boost_python/container_conversions.h
+--- a/cctbx/scitbx/boost_python/container_conversions.h
++++ b/cctbx/scitbx/boost_python/container_conversions.h
 @@ -150,13 +150,12 @@
              || PyTuple_Check(obj_ptr)
              || PyIter_Check(obj_ptr)


=====================================
debian/patches/regcomp_cert_fix.patch
=====================================
@@ -7,9 +7,9 @@ Description: Henry Spencer regular expressions (regex) library contains a heap o
  This patch adapts the patch found at Origin (see above) to the
  regex code found in librcsb-core-wrapper.
 
---- librcsb-core-wrapper-1.005.orig/regex/src/regcomp.c
-+++ librcsb-core-wrapper-1.005/regex/src/regcomp.c
-@@ -93,6 +93,7 @@ int cflags;
+--- a/regex/src/regcomp.c
++++ b/regex/src/regcomp.c
+@@ -93,6 +93,7 @@
  	register struct parse *p = &pa;
  	register int i;
  	register size_t len;
@@ -17,7 +17,7 @@ Description: Henry Spencer regular expressions (regex) library contains a heap o
  #ifdef REDEBUG
  #	define	GOODFLAGS(f)	(f)
  #else
-@@ -115,7 +116,23 @@ int cflags;
+@@ -115,7 +116,23 @@
  							(NC-1)*sizeof(cat_t));
  	if (g == NULL)
  		return(REG_ESPACE);


=====================================
debian/patches/rm-duplicate-module
=====================================
@@ -1,9 +1,10 @@
 Author: Laszlo Kajan <lkajan at rostlab.org>
 Description: removal of duplicate module
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-August/016975.html
+
 --- a/local/modules.txt
 +++ b/local/modules.txt
-@@ -7,5 +7,4 @@ svn https://svn-dev.wwpdb.org/svn-rcsb/c
+@@ -7,5 +7,4 @@
  svn https://svn-dev.wwpdb.org/svn-rcsb/core/modules/cif-file-util cif-file-util Latest
  svn https://svn-dev.wwpdb.org/svn-rcsb/core/modules/dict-obj-file dict-obj-file Latest
  svn https://svn-dev.wwpdb.org/svn-rcsb/pdbml/modules/pdbml-parser pdbml-parser Latest


=====================================
debian/patches/series
=====================================
@@ -6,7 +6,6 @@ devnull-log
 docs
 objectfiles
 parallel-build
-# setup.py.in
 hardening
 spelling
 exit-in-shlib


=====================================
debian/patches/spelling
=====================================
@@ -1,9 +1,10 @@
 Author: Laszlo Kajan <lkajan at rostlab.org>
 Description: fix for spelling errors
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-August/016975.html
+
 --- a/wrapper/src/DataInfoPyWrap.C
 +++ b/wrapper/src/DataInfoPyWrap.C
-@@ -31,23 +31,23 @@ struct DataInfo_wrapper : DataInfo, bp::
+@@ -31,23 +31,23 @@
      }
  
      virtual ::std::vector< std::string > const & GetCatAttribute( ::std::string const & catName, ::std::string const & refCatName, ::std::string const & refAttribName ){


=====================================
debian/patches/unistd
=====================================
@@ -1,6 +1,7 @@
 Author: Laszlo Kajan <lkajan at rostlab.org>
 Description: fix for missing #include <unistd.h>
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-August/016975.html
+
 --- a/pdbml-parser/src/misc_util.C
 +++ b/pdbml-parser/src/misc_util.C
 @@ -1,5 +1,6 @@


=====================================
debian/patches/wrapper-module
=====================================
@@ -1,9 +1,10 @@
 Author: Laszlo Kajan <lkajan at rostlab.org>
 Description: preventing wrapper from being built along other modules
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-August/016975.html
+
 --- a/local/modules.txt
 +++ b/local/modules.txt
-@@ -9,4 +9,3 @@ svn https://svn-dev.wwpdb.org/svn-rcsb/c
+@@ -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


=====================================
debian/patches/xerces32.patch
=====================================
@@ -5,7 +5,7 @@ Description: Enable build against libxerces-c3.2
 
 --- a/etc/make.platform.gnu4
 +++ b/etc/make.platform.gnu4
-@@ -118,7 +118,7 @@ CFLAGS += $(OPT) $(ABI) $(PIC) $(ANSI_C_
+@@ -118,7 +118,7 @@
  CCC=g++
  
  # C++ compiler ANSI/NON-ANSI flags


=====================================
debian/rules
=====================================
@@ -49,9 +49,3 @@ override_dh_installdocs:
 
 override_dh_makeshlibs:
 	dh_makeshlibs -V
-
-override_dh_auto_clean:
-	dh_auto_clean
-	rm -rf wrapper/python/build
-	find . -name obj -type d | xargs rm -rf
-	rm -rf .pybuild


=====================================
debian/salsa-ci.yml
=====================================
@@ -1,4 +1,3 @@
 ---
 include:
-  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
-  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml



View it on GitLab: https://salsa.debian.org/med-team/librcsb-core-wrapper/-/compare/d8ead88dd07adbb1ebebfb338df90187705ef0ca...60c80fc831f27a2053fbf0680992a5fffb781a0b

-- 
View it on GitLab: https://salsa.debian.org/med-team/librcsb-core-wrapper/-/compare/d8ead88dd07adbb1ebebfb338df90187705ef0ca...60c80fc831f27a2053fbf0680992a5fffb781a0b
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