Changeset 2853

Timestamp:

Sep 24, 2012, 1:56:38 AM (11 years ago)

Author:

Peter

Message:

merge patch release 0.9.1 into trunk

Location:

trunk

Files:

• . (modified) (1 prop)
• Makefile.am (modified) (3 diffs)
• NEWS (modified) (1 diff)
• build_support/gen_yat_pc.sh.in (modified) (2 diffs)
• build_support/yat.pc.in (modified) (2 diffs)
• doc/Makefile.am (modified) (3 diffs)
• m4/my_version.m4 (modified) (1 diff)
• m4/version.m4 (modified) (1 diff)
• test/Makefile.am (modified) (4 diffs)
• test/alignment.cc (modified) (1 diff)
• test/alignment2.cc (copied) (copied from branches/0.9-stable/test/alignment2.cc)
• test/cmd_test.sh (copied) (copied from branches/0.9-stable/test/cmd_test.sh)
• yat/utility/Aligner.cc (modified) (2 diffs)
• yat/utility/CommandLine.cc (modified) (2 diffs)

trunk/Makefile.am

@@ -32 +32 @@
 EXTRA_DIST =
 MOSTLYCLEANFILES =
+## append targets to this variable for tests included in 'make installcheck'
+INSTALL_CHECK_TARGETS =
 
 FORCE:
@@ -65 +67 @@
   rm -rf doc/$(DX_HTML_OUTPUT) test/yathello test/testSubDir
 
+installcheck-local: $(INSTALL_CHECK_TARGETS)
+
 .PHONY: doc maintainer-check news-check svn-check svn-clean release
 
@@ -97 +101 @@
   && $(MAKE) $(AM_MAKEFLAGS) clean \
   && $(MAKE) $(AM_MAKEFLAGS) prefix=$$mcl_install \
+  && $(MAKE) $(AM_MAKEFLAGS) prefix=$$mcl_install doc \
   && $(MAKE) $(AM_MAKEFLAGS) prefix=$$mcl_install install \
   && $(MAKE) $(AM_MAKEFLAGS) prefix=$$mcl_install installcheck

trunk/NEWS

@@ -9 +9 @@
 
 yat 0.9.x series from http://dev.thep.lu.se/yat/svn/branches/0.9-stable
+
+version 0.9.1 (released 23 September 2012)
+  - bug in Aligner fixed (see bug #724)
+  - Commandline::parse now throws when finding '--no-foo' (bug #723)
+  - yat.pc now mentions Boost::System and Boost::Thread in Libs.private (#722)
+  - documentations is now installed again (bug #721)
+
+  A complete list of closed tickets can be found here [[br]]
+  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.9.1
 
 version 0.9 (released 16 September 2012)

trunk/build_support/gen_yat_pc.sh.in

@@ -2 +2 @@
 # @configure_input@
 
-# Copyright (C) 2011 Peter Johansson
+# Copyright (C) 2011, 2012 Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -84 +84 @@
 -e 's|@LDFLAGS[@]|@LDFLAGS@|g' \
 -e 's|@YAT_LDFLAGS[@]|@YAT_LDFLAGS@|g' \
+-e 's|@BOOST_THREAD_LIB[@]|@BOOST_THREAD_LIB@|g' \
+-e 's|@BOOST_SYSTEM_LIB[@]|@BOOST_SYSTEM_LIB@|g' \
 < $input

trunk/build_support/yat.pc.in

@@ -2 +2 @@
 
 # Copyright (C) 2008 Jari Häkkinen, Peter Johansson
-# Copyright (C) 2009, 2010 Peter Johansson
+# Copyright (C) 2009, 2010, 2012 Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -30 +30 @@
 Requires: gsl >= @gsl_version@
 Libs: -L${libdir} -lyat @YAT_LDFLAGS@ @LDFLAGS@
+Libs.private: @BOOST_THREAD_LIB@ @BOOST_SYSTEM_LIB@
 Cflags: @YAT_CPPFLAGS@ @YAT_CXXFLAGS@ @CPPFLAGS@ @CXXFLAGS@ -I${includedir}

trunk/doc/Makefile.am

@@ -44 +44 @@
 if DX_ENABLE_HTML
 html-local: doc/$(DX_HTML_OUTPUT)/index.html
+INSTALL_CHECK_TARGETS += installcheck-html
 endif
 
@@ -65 +66 @@
 install-html-local:
   @$(NORMAL_INSTALL)
-  @if test -d $(DX_HTML_OUTPUT); then \
+  @if test -d doc/$(DX_HTML_OUTPUT); then \
     test -z "$(DESTDIR)$(htmldir)" || \
     { $(MKDIR_P) "$(DESTDIR)$(htmldir)"; \
@@ -76 +77 @@
   rm -rf $(DESTDIR)$(htmldir)
 
+# check that html has been installed (only activated when DX_ENABLE_HTML)
+## see ticket #721
+installcheck-html:
+  $(AM_V_at) test -r "$(DESTDIR)/$(htmldir)/index.html" \
+  || { echo "no documentation installed" 1>&2; exit 1; }
+  $(AM_V_at)grep "yat.*$(VERSION)" "$(DESTDIR)/$(htmldir)/index.html" \
+  || { echo $(DESTDIR)/$(htmldir)/index.html not updated 1>&2; exit 1; }
+
 MOSTLYCLEANFILES += doc/doxygen.error

trunk/m4/my_version.m4

@@ -40 +40 @@
 m4_define([my_PATCH_VERSION], [$3])
 m4_define([my_DEV_BUILD], [$4])
-m4_define([my_VERSION],[$1.$2m4_if([$3],[0],,[$3])m4_if([$4],[true],[pre])])
+m4_define([my_VERSION],[$1.$2m4_if([$3],[0],,[.$3])m4_if([$4],[true],[pre])])
 ]) # my_version
 

trunk/m4/version.m4

@@ -67 +67 @@
 # yat-0.8.2  5:2:0
 # yat-0.9    6:0:0
+# yat-0.9.1  6:1:0
 #
 # *Accidently, the libtool number was not updated for yat 0.5

trunk/test/Makefile.am

@@ -33 +33 @@
 check_SCRIPTS = test/common_defs.sh
 
-EXTRA_PROGRAMS = test/alignment.test test/averager.test \
+EXTRA_PROGRAMS = test/alignment.test \
+  test/alignment2.test \
+  test/averager.test \
   test/averager1.test \
   test/averager3.test \
@@ -71 +73 @@
 
 DISTRIBUTED_TESTS = \
+test/cmd_test.sh \
 test/doxygen_test.sh \
 test/help_test.sh \
@@ -104 +107 @@
 
 # dependencies for lazycheck
+test/cmd_test.log: test/help.test test/common_defs.sh
 test/help_test.log: test/help.test test/common_defs.sh
 test/static_test.log: $(srcdir)/m4/yat.m4 test/common_defs.sh
@@ -196 +200 @@
   && rm -rf $(yat_hello_tmp_files)
 
-installcheck-local: yat-hello-check
+INSTALL_CHECK_TARGETS += yat-hello-check
 
 yat-hello-check: $(srcdir)/test/yat-hello-1.0.tar.gz

trunk/test/alignment.cc

@@ -101 +101 @@
   s >> peaksets;
 
+  utility::Matrix nm_score(peaksets.size(), peaksets.size(), 0);
+  utility::Matrix correct(nm_score);
   for (size_t i=0; i<peaksets.size()-1; i++) 
     for (size_t j=i+1; j<peaksets.size(); j++) {
       utility::Matrix dot_m;
       std::vector<std::pair<size_t,size_t> > path;
-      score(peaksets[i], peaksets[j], 1.0, dot_m, path);
+      nm_score(i,j) = score(peaksets[i], peaksets[j], 1.0, dot_m, path);
+      if (i==2 && j==3) {
+        for (size_t r=0; r<dot_m.rows(); ++r)
+          for (size_t c=0; c<dot_m.columns(); ++c)
+            if (dot_m(r,c) > 1e-5)
+              std::cerr << r << " " << c << " " << dot_m(r,c) << "\n";
+      }
     }
+  correct(0,1) = 4.947983;
+  correct(0,2) = 3.496081;
+  correct(0,3) = 4.960331;
+  correct(1,2) = 2.486868;
+  correct(1,3) = 11.407001;
+  correct(2,3) = 2.503420;
+
+  suite.add(suite.equal_range_fix(nm_score.begin(), nm_score.end(),
+                                  correct.begin(), 1e-6));
 
   std::string a("AGGUUGUCCGUGGUGAGUUCGCA");

trunk/yat/utility/Aligner.cc

@@ -48 +48 @@
   double Aligner::needleman_wunsch(const Matrix& s)
   {
-    Matrix m(s.rows()+1,s.columns()+1, std::numeric_limits<double>::min());
+    Matrix m(s.rows()+1,s.columns()+1, -std::numeric_limits<double>::max());
+    m(0, 0) = 0.0;
     // Init upper and left border of matrix
     for (size_t i=1; i<m.rows(); i++)
@@ -85 +86 @@
 
         if (cigar(i, j-1) == right) {
-          if (x(i-1, j)-horizon_gap_ > x(i,j)) {
+          if (x(i, j-1)-horizon_gap_ > x(i,j)) {
             x(i,j) = x(i,j-1) - horizon_gap_;
             cigar(i,j) = right;

trunk/yat/utility/CommandLine.cc

@@ -4 +4 @@
   Copyright (C) 2007 Jari Häkkinen, Peter Johansson, Markus Ringnér
   Copyright (C) 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2009, 2010, 2011 Peter Johansson
+  Copyright (C) 2009, 2010, 2011, 2012 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -176 +176 @@
         iter->second->parse(arg, last);
     }           
-    else if (iter==long_options_.end()) {
+    if (iter==long_options_.end()) {
       std::stringstream ss3;
       ss3 << "unrecognized option `" << key << "'\n" << try_help();