Changeset 3966


Ignore:
Timestamp:
Aug 11, 2020, 4:54:36 AM (10 months ago)
Author:
Peter
Message:

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

Location:
trunk
Files:
11 edited

Legend:

Unmodified
Added
Removed
  • trunk

  • trunk/NEWS

    r3960 r3966  
    2222
    2323yat 0.17.x series from http://dev.thep.lu.se/yat/svn/branches/0.17-stable
     24
     25version 0.17.2 (released NOT YET)
     26  - Generating documentation now works with Doxygen 1.8.19 (bug #954)
     27  - GSL, HTSLIB, Boost.Thread and Boost.System are not declated private
     28    in pkg-config file yat.pc (bug #952).
     29
     30  A complete list of closed tickets can be found here [[br]]
     31  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.17.2
    2432
    2533version 0.17.1 (released 8 July 2020)
  • trunk/build_support/Makefile.am

    r3855 r3966  
    5656  -e 's|@YAT_CONFIG_LDFLAGS[@]|$(YAT_CONFIG_LDFLAGS)|g' \
    5757  -e 's|@PACKAGE[@]|$(PACKAGE)|g' \
     58  -e 's|@PACKAGE_VERSION[@]|$(PACKAGE_VERSION)|g' \
    5859  -e 's|@PACKAGE_BUGREPORT[@]|$(PACKAGE_BUGREPORT)|g' \
    5960  -e 's|@PACKAGE_URL[@]|$(PACKAGE_URL)|g' \
     
    6364  -e 's|@YAT_PATCH_VERSION[@]|$(YAT_PATCH_VERSION)|g' \
    6465  -e 's|@YAT_DEV_BUILD[@]|$(YAT_DEV_BUILD)|g' \
     66  -e 's|@canonical_abs_top_srcdir[@]|$(canonical_abs_top_srcdir)|g' \
    6567  -e 's|@abs_top_srcdir[@]|$(abs_top_srcdir)|g' \
    6668  -e 's|@abs_top_builddir[@]|$(abs_top_builddir)|g'
  • trunk/configure.ac

    r3960 r3966  
    1010# Copyright (C) 2010, 2011 Peter Johansson
    1111# Copyright (C) 2012 Jari Häkkinen, Peter Johansson
    12 # Copyright (C) 2013, 2014, 2015, 2016, 2017, 2018, 2019 Peter Johansson
     12# Copyright (C) 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Peter Johansson
    1313#
    1414# This file is part of the yat library, http://dev.thep.lu.se/yat
     
    452452])
    453453
    454 #doxygen stuff
    455 DX_HTML_OUTPUT=html
    456 AC_SUBST(DX_HTML_OUTPUT)
    457 
    458454AC_CONFIG_FILES([build_support/gen_yat_pc.sh],
    459455                [chmod +x build_support/gen_yat_pc.sh])
    460456AC_CONFIG_FILES([Makefile
    461      doc/doxygen.config
    462457     doc/first_page.doxygen
    463458                 test/defs.sh
     
    504499# Dependency to GSL is noted via 'Requires' field
    505500YAT_VAR_REMOVE([YAT_PC_LIBS_PRIVATE], [-lgsl $YAT_CBLAS_LIB $LIBM])
    506 YAT_SET_CONTAINS([$yat_libyat_la_LIBADD], [-lgsl], [
    507   YAT_PC_REQUIRES_PRIVATE="gsl > YAT_REQUIRED_GSL_VERSION"
    508 ], [
    509   YAT_PC_REQUIRES="gsl > YAT_REQUIRED_GSL_VERSION"
    510 ])
     501YAT_PC_REQUIRES="gsl >= YAT_REQUIRED_GSL_VERSION"
    511502
    512503# ignore this whole htslib thing if --without-htslib
     
    514505  # htslib comes with a pc file, so we can require htslib in yat.pc
    515506  YAT_VAR_REMOVE([YAT_PC_LIBS_PRIVATE], [$HTS_LIBS -lz])
    516   # if libyat is linking in -lhts, linking against libyat is
    517   # sufficient and put htslib in 'requires private:', otherwise put
    518   # them in 'require:'.
    519   YAT_SET_CONTAINS([$yat_libyat_la_LIBADD], [-lhts], [
    520     YAT_PC_REQUIRES_PRIVATE="$YAT_PC_REQUIRES_PRIVATE htslib"
    521   ], [
    522     YAT_PC_REQUIRES="$YAT_PC_REQUIRES htslib"
    523   ])
     507  YAT_PC_REQUIRES="$YAT_PC_REQUIRES htslib"
    524508])
    525509
     
    532516  ], [
    533517    # move lib from $YAT_PC_LIBS_PRIVATE to $YAT_PC_LIBS
    534     YAT_VAR_REMOVE([$YAT_PC_LIBS_PRIVATE], [$lib])
     518    YAT_VAR_REMOVE([YAT_PC_LIBS_PRIVATE], [$lib])
    535519    YAT_PC_LIBS="$YAT_PC_LIBS $lib"
    536520  ])
  • trunk/doc/Makefile.am

    r3018 r3966  
    4141
    4242if DX_ENABLE_HTML
    43 html-local: doc/$(DX_HTML_OUTPUT)/index.html
     43html-local: doc/html/index.html
    4444INSTALL_CHECK_TARGETS += installcheck-html
    4545endif
    4646
    47 doc/$(DX_HTML_OUTPUT)/index.html: $(DOXYGEN_DEPS)
    48   $(AM_V_GEN)
    49   $(AM_V_at){ cat doc/doxygen.config && \
    50   echo "INPUT = $(DOXYGEN_INPUT)" && \
    51   echo GENERATE_HTML = YES; } | $(DOXYGEN) - $(yat_dev_null);
     47doc/doxygen.config: doc/doxygen.config.in
     48  $(AM_V_GEN)echo "# $@ generated by make from doc/doxygen.config.in." \
     49  > $@-t \
     50  && $(edit) '$(srcdir)/doc/doxygen.config.in' >> $@-t \
     51  && echo "INPUT = $(DOXYGEN_INPUT)" >> $@-t \
     52  && mv $@-t $@
     53
     54doc/html/index.html: $(DOXYGEN_DEPS)
     55  $(AM_V_GEN)$(DOXYGEN) doc/doxygen.config $(yat_dev_null)
     56
    5257
    5358install-data-hook: install-html
  • trunk/doc/doxygen.config.in

    r3964 r3966  
    1 # @configure_input@
    21# $Id$
    32
     
    464463# generate HTML output.
    465464
    466 GENERATE_HTML          = NO
     465GENERATE_HTML          = YES
    467466
    468467# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
     
    470469# put in front of it. If left blank `html' will be used as the default path.
    471470
    472 HTML_OUTPUT            = @DX_HTML_OUTPUT@
     471HTML_OUTPUT            = html
    473472
    474473# The HTML_HEADER tag can be used to specify a personal HTML header for
     
    482481# standard footer.
    483482
    484 HTML_FOOTER            = @abs_srcdir@/footer.html
     483HTML_FOOTER            = @abs_top_srcdir@/doc/footer.html
    485484
    486485# The HTML_STYLESHEET tag can be used to specify a user defined cascading
  • trunk/m4/yat_common.m4

    r3728 r3966  
    11## $Id$
    22#
    3 # Copyright (C) 2009, 2010, 2012, 2013, 2014, 2018 Peter Johansson
     3# Copyright (C) 2009, 2010, 2012, 2013, 2014, 2018, 2020 Peter Johansson
    44#
    55# This file is part of the yat library, http://dev.thep.lu.se/yat
     
    6161AC_DEFUN([YAT_SET_CONTAINS],
    6262[
    63 AS_IF([AS_ECHO([$1]) | tr ' ' '\n' | grep '^$2$' > /dev/null], [$3], [$4])
     63AS_IF([AS_ECHO([$1]) | tr ' ' '\n' | grep "^$2$" > /dev/null], [$3], [$4])
    6464]) #YAT_SET_CONTAINS
    6565
  • trunk/test/Makefile.am

    r3963 r3966  
    253253
    254254if DX_ENABLE_HTML
    255 test/doxygen_test.log: doc/$(DX_HTML_OUTPUT)/index.html
     255test/doxygen_test.log: doc/html/index.html
    256256endif
    257257
  • trunk/test/fileutil.cc

    r3936 r3966  
    44  Copyright (C) 2006 Jari Häkkinen
    55  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
    6   Copyright (C) 2009, 2010, 2012 Peter Johansson
     6  Copyright (C) 2009, 2010, 2012, 2020 Peter Johansson
    77
    88  This file is part of the yat library, http://dev.thep.lu.se/yat
  • trunk/test/interpolation.cc

    r3936 r3966  
    44  Copyright (C) 2008 Jari Häkkinen, Peter Johansson
    55  Copyright (C) 2009 Jari Häkkinen
    6   Copyright (C) 2012 Peter Johansson
     6  Copyright (C) 2012, 2020 Peter Johansson
    77
    88  This file is part of the yat library, http://dev.thep.lu.se/yat
  • trunk/test/yat_pc_test.sh

    r3945 r3966  
    22# $Id$
    33#
    4 # Copyright (C) 2013, 2014, 2015, 2017 Peter Johansson
     4# Copyright (C) 2013, 2014, 2015, 2017, 2020 Peter Johansson
    55#
    66# This file is part of the yat library, http://dev.thep.lu.se/yat
     
    8585CXXFLAGS = `$PKG_CONFIG yat --cflags-only-other`
    8686# add -L to link to local libyat
    87 LDFLAGS = -L$abs_top_builddir/yat/${lt_cv_objdir} `$PKG_CONFIG yat --libs --static`
     87LDFLAGS = -L$abs_top_builddir/yat/${lt_cv_objdir} `$PKG_CONFIG yat --libs-only-L --libs-only-other`
     88LDLIBS = `$PKG_CONFIG yat --libs-only-l`
     89
    8890all: prog
    8991
    90 # Default make rule is problematic with static libs
     92# Make the rules explicit to allow also non-GNU make.
    9193prog.o: prog.cc
    9294  \$(CXX) -c -o \$@ \$< \$(CPPFLAGS) \$(CXXFLAGS)
    9395prog: prog.o
    94   \$(CXX) -o \$@ \$< \$(CXXFLAGS) \$(LDFLAGS)
     96  \$(CXX) -o \$@ \$< \$(CXXFLAGS) \$(LDFLAGS) \$(LDLIBS)
    9597EOF
    9698
     
    101103#include <yat/random/random.h>
    102104#include <yat/omic/BamFile.h>
     105#include <yat/omic/VcfFile.h>
    103106int main()
    104107{
     
    107110x(0) = gauss();
    108111theplu::yat::omic::OutBamFile out;
     112theplu::yat::omic::VcfFile vcf;
    109113return 0;
    110114}
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