Changeset 3966

Timestamp:

Aug 11, 2020, 4:54:36 AM (3 years ago)

Author:

Peter

Message:

merge changes in 0.17-stable branch (since 0.17.1) into trunk.

Location:

trunk

Files:

• . (modified) (1 prop)
• NEWS (modified) (1 diff)
• build_support/Makefile.am (modified) (2 diffs)
• configure.ac (modified) (5 diffs)
• doc/Makefile.am (modified) (1 diff)
• doc/doxygen.config.in (modified) (4 diffs)
• m4/yat_common.m4 (modified) (2 diffs)
• test/Makefile.am (modified) (1 diff)
• test/fileutil.cc (modified) (1 diff)
• test/interpolation.cc (modified) (1 diff)
• test/yat_pc_test.sh (modified) (4 diffs)

trunk/NEWS

@@ -22 +22 @@
 
 yat 0.17.x series from http://dev.thep.lu.se/yat/svn/branches/0.17-stable
+
+version 0.17.2 (released NOT YET)
+  - Generating documentation now works with Doxygen 1.8.19 (bug #954)
+  - GSL, HTSLIB, Boost.Thread and Boost.System are not declated private
+    in pkg-config file yat.pc (bug #952).
+
+  A complete list of closed tickets can be found here [[br]]
+  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.17.2
 
 version 0.17.1 (released 8 July 2020)

trunk/build_support/Makefile.am

@@ -56 +56 @@
   -e 's|@YAT_CONFIG_LDFLAGS[@]|$(YAT_CONFIG_LDFLAGS)|g' \
   -e 's|@PACKAGE[@]|$(PACKAGE)|g' \
+  -e 's|@PACKAGE_VERSION[@]|$(PACKAGE_VERSION)|g' \
   -e 's|@PACKAGE_BUGREPORT[@]|$(PACKAGE_BUGREPORT)|g' \
   -e 's|@PACKAGE_URL[@]|$(PACKAGE_URL)|g' \
@@ -63 +64 @@
   -e 's|@YAT_PATCH_VERSION[@]|$(YAT_PATCH_VERSION)|g' \
   -e 's|@YAT_DEV_BUILD[@]|$(YAT_DEV_BUILD)|g' \
+  -e 's|@canonical_abs_top_srcdir[@]|$(canonical_abs_top_srcdir)|g' \
   -e 's|@abs_top_srcdir[@]|$(abs_top_srcdir)|g' \
   -e 's|@abs_top_builddir[@]|$(abs_top_builddir)|g'

trunk/configure.ac

@@ -10 +10 @@
 # Copyright (C) 2010, 2011 Peter Johansson
 # Copyright (C) 2012 Jari Häkkinen, Peter Johansson
-# Copyright (C) 2013, 2014, 2015, 2016, 2017, 2018, 2019 Peter Johansson
+# Copyright (C) 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -452 +452 @@
 ])
 
-#doxygen stuff
-DX_HTML_OUTPUT=html
-AC_SUBST(DX_HTML_OUTPUT)
-
 AC_CONFIG_FILES([build_support/gen_yat_pc.sh],
                 [chmod +x build_support/gen_yat_pc.sh])
 AC_CONFIG_FILES([Makefile
-     doc/doxygen.config
      doc/first_page.doxygen
                  test/defs.sh
@@ -504 +499 @@
 # Dependency to GSL is noted via 'Requires' field
 YAT_VAR_REMOVE([YAT_PC_LIBS_PRIVATE], [-lgsl $YAT_CBLAS_LIB $LIBM])
-YAT_SET_CONTAINS([$yat_libyat_la_LIBADD], [-lgsl], [
-  YAT_PC_REQUIRES_PRIVATE="gsl > YAT_REQUIRED_GSL_VERSION"
-], [
-  YAT_PC_REQUIRES="gsl > YAT_REQUIRED_GSL_VERSION"
-])
+YAT_PC_REQUIRES="gsl >= YAT_REQUIRED_GSL_VERSION"
 
 # ignore this whole htslib thing if --without-htslib
@@ -514 +505 @@
   # htslib comes with a pc file, so we can require htslib in yat.pc
   YAT_VAR_REMOVE([YAT_PC_LIBS_PRIVATE], [$HTS_LIBS -lz])
-  # if libyat is linking in -lhts, linking against libyat is
-  # sufficient and put htslib in 'requires private:', otherwise put
-  # them in 'require:'.
-  YAT_SET_CONTAINS([$yat_libyat_la_LIBADD], [-lhts], [
-    YAT_PC_REQUIRES_PRIVATE="$YAT_PC_REQUIRES_PRIVATE htslib"
-  ], [
-    YAT_PC_REQUIRES="$YAT_PC_REQUIRES htslib"
-  ])
+  YAT_PC_REQUIRES="$YAT_PC_REQUIRES htslib"
 ])
 
@@ -532 +516 @@
   ], [
     # move lib from $YAT_PC_LIBS_PRIVATE to $YAT_PC_LIBS
-    YAT_VAR_REMOVE([$YAT_PC_LIBS_PRIVATE], [$lib])
+    YAT_VAR_REMOVE([YAT_PC_LIBS_PRIVATE], [$lib])
     YAT_PC_LIBS="$YAT_PC_LIBS $lib"
   ])

trunk/doc/Makefile.am

@@ -41 +41 @@
 
 if DX_ENABLE_HTML
-html-local: doc/$(DX_HTML_OUTPUT)/index.html
+html-local: doc/html/index.html
 INSTALL_CHECK_TARGETS += installcheck-html
 endif
 
-doc/$(DX_HTML_OUTPUT)/index.html: $(DOXYGEN_DEPS)
-  $(AM_V_GEN)
-  $(AM_V_at){ cat doc/doxygen.config && \
-  echo "INPUT = $(DOXYGEN_INPUT)" && \
-  echo GENERATE_HTML = YES; } | $(DOXYGEN) - $(yat_dev_null);
+doc/doxygen.config: doc/doxygen.config.in
+  $(AM_V_GEN)echo "# $@ generated by make from doc/doxygen.config.in." \
+  > $@-t \
+  && $(edit) '$(srcdir)/doc/doxygen.config.in' >> $@-t \
+  && echo "INPUT = $(DOXYGEN_INPUT)" >> $@-t \
+  && mv $@-t $@
+
+doc/html/index.html: $(DOXYGEN_DEPS)
+  $(AM_V_GEN)$(DOXYGEN) doc/doxygen.config $(yat_dev_null)
+
 
 install-data-hook: install-html

trunk/doc/doxygen.config.in

@@ -1 @@
-# @configure_input@
 # $Id$
 
@@ -464 +463 @@
 # generate HTML output.
 
-GENERATE_HTML          = NO
+GENERATE_HTML          = YES
 
 # The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
@@ -470 +469 @@
 # put in front of it. If left blank `html' will be used as the default path.
 
-HTML_OUTPUT            = @DX_HTML_OUTPUT@
+HTML_OUTPUT            = html
 
 # The HTML_HEADER tag can be used to specify a personal HTML header for
@@ -482 +481 @@
 # standard footer.
 
-HTML_FOOTER            = @abs_srcdir@/footer.html
+HTML_FOOTER            = @abs_top_srcdir@/doc/footer.html
 
 # The HTML_STYLESHEET tag can be used to specify a user defined cascading

trunk/m4/yat_common.m4

@@ -1 +1 @@
 ## $Id$
 #
-# Copyright (C) 2009, 2010, 2012, 2013, 2014, 2018 Peter Johansson
+# Copyright (C) 2009, 2010, 2012, 2013, 2014, 2018, 2020 Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -61 +61 @@
 AC_DEFUN([YAT_SET_CONTAINS],
 [
-AS_IF([AS_ECHO([$1]) | tr ' ' '\n' | grep '^$2$' > /dev/null], [$3], [$4])
+AS_IF([AS_ECHO([$1]) | tr ' ' '\n' | grep "^$2$" > /dev/null], [$3], [$4])
 ]) #YAT_SET_CONTAINS
 

trunk/test/Makefile.am

@@ -253 +253 @@
 
 if DX_ENABLE_HTML
-test/doxygen_test.log: doc/$(DX_HTML_OUTPUT)/index.html
+test/doxygen_test.log: doc/html/index.html
 endif
 

trunk/test/fileutil.cc

@@ -4 +4 @@
   Copyright (C) 2006 Jari Häkkinen
   Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2009, 2010, 2012 Peter Johansson
+  Copyright (C) 2009, 2010, 2012, 2020 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat

trunk/test/interpolation.cc

@@ -4 +4 @@
   Copyright (C) 2008 Jari Häkkinen, Peter Johansson
   Copyright (C) 2009 Jari Häkkinen
-  Copyright (C) 2012 Peter Johansson
+  Copyright (C) 2012, 2020 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat

trunk/test/yat_pc_test.sh

@@ -2 +2 @@
 # $Id$
 #
-# Copyright (C) 2013, 2014, 2015, 2017 Peter Johansson
+# Copyright (C) 2013, 2014, 2015, 2017, 2020 Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -85 +85 @@
 CXXFLAGS = `$PKG_CONFIG yat --cflags-only-other`
 # add -L to link to local libyat
-LDFLAGS = -L$abs_top_builddir/yat/${lt_cv_objdir} `$PKG_CONFIG yat --libs --static`
+LDFLAGS = -L$abs_top_builddir/yat/${lt_cv_objdir} `$PKG_CONFIG yat --libs-only-L --libs-only-other`
+LDLIBS = `$PKG_CONFIG yat --libs-only-l`
+
 all: prog
 
-# Default make rule is problematic with static libs
+# Make the rules explicit to allow also non-GNU make.
 prog.o: prog.cc
   \$(CXX) -c -o \$@ \$< \$(CPPFLAGS) \$(CXXFLAGS)
 prog: prog.o
-  \$(CXX) -o \$@ \$< \$(CXXFLAGS) \$(LDFLAGS)
+  \$(CXX) -o \$@ \$< \$(CXXFLAGS) \$(LDFLAGS) \$(LDLIBS)
 EOF
 
@@ -101 +103 @@
 #include <yat/random/random.h>
 #include <yat/omic/BamFile.h>
+#include <yat/omic/VcfFile.h>
 int main()
 {
@@ -107 +110 @@
 x(0) = gauss();
 theplu::yat::omic::OutBamFile out;
+theplu::yat::omic::VcfFile vcf;
 return 0;
 }