Changeset 4019

Timestamp:

Nov 6, 2020, 2:55:37 AM (3 years ago)

Author:

Peter

Message:

merge 0.18 into trunk

Location:

trunk

Files:

• . (modified) (1 prop)
• NEWS (modified) (1 diff)
• build_support/Makefile.am (modified) (1 diff)
• doc/Makefile.am (modified) (1 diff)
• m4/version.m4 (modified) (1 diff)
• m4/yat_check_libs.m4 (modified) (2 diffs)
• test/Makefile.am (modified) (1 diff)
• test/random_distribution.cc (deleted)
• test/yat_pc_test.sh (modified) (1 diff)
• yat/classifier/KernelLookup.h (modified) (3 diffs)
• yat/classifier/MatrixLookup.h (modified) (3 diffs)
• yat/classifier/MatrixLookupWeighted.h (modified) (3 diffs)
• yat/omic/BamPairIterator.h (modified) (2 diffs)
• yat/omic/BamPairIterator2.h (modified) (2 diffs)
• yat/omic/Fasta.cc (modified) (1 diff)
• yat/omic/Fasta.h (modified) (3 diffs)
• yat/omic/Pileup.h (modified) (2 diffs)
• yat/random/ContinuousDistribution.h (deleted)
• yat/random/DiscreteDistribution.h (deleted)
• yat/random/Distribution.h (deleted)
• yat/random/Makefile.am (modified) (1 diff)

trunk/NEWS

@@ -10 +10 @@
 yat 0.18.x series from http://dev.thep.lu.se/yat/svn/branches/0.18-stable
 
-version 0.18 (released NOT YET)
+version 0.18 (released 6 November 2020)
   - regression::NegativeBinomial now inherits from
     regression::Multivariate (ticket #957)

trunk/build_support/Makefile.am

@@ -89 +89 @@
   --exec-prefix="$(exec_prefix)" \
   --libdir="$(libdir)" --includedir="$(includedir)" \
-  --input="../$(srcdir)/build_support/yat.pc.in" > yat.pc-t \
+  --input="$(abs_srcdir)/build_support/yat.pc.in" > yat.pc-t \
   && mv yat.pc-t yat.pc

trunk/doc/Makefile.am

@@ -47 +47 @@
 EXTRA_DIST += doc/doxygen.config.in
 
-doc/doxygen.config: doc/doxygen.config.in
+# config file needs to be updated when $(DOXYGEN_INPUT) is
+# changed. That variable is set in various Makefile.am, but instead we
+# depend on Makefile.in, since that dependency is easier to maintain.
+doc/doxygen.config: doc/doxygen.config.in $(srcdir)/Makefile.in
   $(AM_V_GEN)echo "# $@ generated by make from doc/doxygen.config.in." \
   > $@-t \

trunk/m4/version.m4

@@ -95 +95 @@
 # yat-0.17.1 14:1:0
 # yat-0.17.2 14:2:0
+# yat-0.18   15:0:0
 #
 # *Accidently, the libtool number was not updated for yat 0.5

trunk/m4/yat_check_libs.m4

@@ -1 +1 @@
 ## $Id$
 #
-# serial 2 (yat 0.18)
+# serial 3 (yat 0.18)
 #
 # see http://www.gnu.org/software/automake/manual/automake.html#Serials
@@ -42 +42 @@
 AC_DEFUN([YAT_CHECK_LIBS],
 [
-  m4_pushdef([yat_message], [$1])
-  m4_pushdef([yat_cache], [$2])
-  m4_pushdef([yat_search_libs], [$3])
+  m4_pushdef([yat_MESSAGE], [$1])
+  m4_pushdef([yat_CACHE], [$2])
+  m4_pushdef([yat_SEARCH_LIBS], [$3])
+  m4_pushdef([yat_DEFAULT_RESULT], ["none required"])
   AC_LANG_CONFTEST([$4])
-  AC_CACHE_CHECK([yat_message], [$2], [
+  AC_CACHE_CHECK([yat_MESSAGE], [yat_CACHE], [
     save_LIBS=$LIBS
-    for yat_lib in '' yat_search_libs; do
+    for yat_lib in '' yat_SEARCH_LIBS; do
       AS_VAR_IF([yat_lib], [''],[
-        yat_result="non required"
+        yat_result=yat_DEFAULT_RESULT
       ], [
         yat_result=-l$yat_lib
         LIBS="-l$yat_lib $save_LIBS"
       ])
-      AC_LINK_IFELSE([], [yat_cache=$yat_result])
-      AS_VAR_SET_IF([yat_cache], [break])
+      AC_LINK_IFELSE([], [yat_CACHE=$yat_result])
+      AS_VAR_SET_IF([yat_CACHE], [break])
     done
-    AS_VAR_SET_IF([yat_cache], [], [yat_cache=no])
+    AS_VAR_SET_IF([yat_CACHE], [], [yat_CACHE=no])
     rm conftest.$ac_ext
     LIBS=$save_LIBS
   ])
-  yat_result=$yat_cache
+  yat_result=$yat_CACHE
 
   # action
   AS_VAR_IF([yat_result], [no], [$6], [
-    AS_VAR_IF([yat_result], ["none required"], [], [LIBS="$yat_result $LIBS"])
+    AS_VAR_IF([yat_result], [yat_DEFAULT_RESULT], [],
+              [LIBS="$yat_result $LIBS"])
     $5
   ])
 
-
-  m4_popdef([yat_message])
-  m4_popdef([yat_cache])
-  m4_popdef([yat_search_libs])
+  m4_popdef([yat_MESSAGE])
+  m4_popdef([yat_CACHE])
+  m4_popdef([yat_SEARCH_LIBS])
+  m4_popdef([yat_DEFAULT_RESULT])
 ])

trunk/test/Makefile.am

@@ -101 +101 @@
   test/poisson.test \
   test/queue.test test/queue2.test \
-  test/random_distribution.test \
   test/range.test test/regression.test test/rnd.test \
   test/rng-mt.test \

trunk/test/yat_pc_test.sh

@@ -81 +81 @@
 CXX = `yat-config --cxx`
 # add -I flags to include local header files; 2nd term needed for VPATH build
-CPPFLAGS = -I$abs_top_srcdir -I$abs_top_builddir/yat/utility \
+CPPFLAGS = -I$abs_top_srcdir -I$abs_top_builddir \
+-I$abs_top_builddir/yat/utility \
 `$PKG_CONFIG yat --cflags-only-I`
 CXXFLAGS = `$PKG_CONFIG yat --cflags-only-other`

trunk/yat/classifier/KernelLookup.h

@@ -8 +8 @@
   Copyright (C) 2006 Jari Häkkinen, Peter Johansson, Markus Ringnér
   Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
-  Copyright (C) 2010, 2012 Peter Johansson
+  Copyright (C) 2010, 2012, 2020 Peter Johansson
 
   This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -32 +32 @@
 #include "yat/utility/StrideIterator.h"
 
-#include <boost/shared_ptr.hpp>
+#include <memory>
 
 namespace theplu {
@@ -324 +324 @@
 
     utility::Index column_index_;
-    boost::shared_ptr<const Kernel> kernel_;
+    std::shared_ptr<const Kernel> kernel_;
     utility::Index row_index_;
   }; // class KernelLookup

trunk/yat/classifier/MatrixLookup.h

@@ -8 +8 @@
   Copyright (C) 2006 Jari Häkkinen, Peter Johansson, Markus Ringnér
   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
@@ -33 +33 @@
 
 #include <boost/iterator/permutation_iterator.hpp>
-#include <boost/shared_ptr.hpp>
 
 #include <iosfwd>
+#include <memory>
 #include <vector>
 
@@ -327 +327 @@
 
     utility::Index column_index_;
-    typedef boost::shared_ptr<const utility::Matrix> MatrixP;
+    typedef std::shared_ptr<const utility::Matrix> MatrixP;
     MatrixP data_;
     utility::Index row_index_;

trunk/yat/classifier/MatrixLookupWeighted.h

@@ -7 +7 @@
   Copyright (C) 2006 Jari Häkkinen, Peter Johansson, Markus Ringnér
   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
@@ -33 +33 @@
 
 #include <boost/iterator/permutation_iterator.hpp>
-#include <boost/shared_ptr.hpp>
 
 #include <iosfwd>
+#include <memory>
 #include <utility>
 #include <vector>
@@ -296 +296 @@
 
   private:
-    typedef boost::shared_ptr<const utility::MatrixWeighted> MatrixWP;
+    typedef std::shared_ptr<const utility::MatrixWeighted> MatrixWP;
     utility::Index column_index_;
     MatrixWP data_;

trunk/yat/omic/BamPairIterator.h

@@ -32 +32 @@
 #include <boost/iterator/iterator_concepts.hpp>
 #include <boost/iterator/iterator_facade.hpp>
-#include <boost/shared_ptr.hpp>
 
 #include <iterator>
 #include <map>
+#include <memory>
 #include <utility>
 
@@ -115 +115 @@
     Base end_;
     const BamRead* mate_;
-    boost::shared_ptr<std::map<std::string, BamRead> > siam_reads_;
+    std::shared_ptr<std::map<std::string, BamRead> > siam_reads_;
     typedef std::pair<int32_t, int32_t> Position;
-    boost::shared_ptr<std::multimap<Position, BamRead> > reads_;
+    std::shared_ptr<std::multimap<Position, BamRead> > reads_;
     friend class boost::iterator_core_access;
 

trunk/yat/omic/BamPairIterator2.h

@@ -32 +32 @@
 #include <boost/iterator/iterator_concepts.hpp>
 #include <boost/iterator/iterator_facade.hpp>
-#include <boost/shared_ptr.hpp>
 
 #include <iterator>
 #include <map>
+#include <memory>
 #include <utility>
 
@@ -118 +118 @@
     // multimap with reads' position as key
     typedef std::multimap<Position, BamRead> MultiMap;
-    boost::shared_ptr<MultiMap> reads_;
+    std::shared_ptr<MultiMap> reads_;
     MultiMap::iterator first_;
     MultiMap::iterator second_;

trunk/yat/omic/Fasta.cc

@@ -166 +166 @@
   {
     // allocate a new char*
-    boost::shared_array<char> ptr(new char[seq.size()+1]);
+    std::shared_ptr<char> ptr(new char[seq.size()+1],
+                              std::default_delete<char[]>());
     std::copy(seq.seq_.get(), seq.seq_.get()+seq.size(), ptr.get());
     // calculate reverse complement

trunk/yat/omic/Fasta.h

@@ -21 +21 @@
 #include <htslib/faidx.h>
 
-#include <boost/shared_array.hpp>
-#include <boost/shared_ptr.hpp>
-
 #include <iosfwd>
 #include <map>
+#include <memory>
 #include <string>
 #include <vector>
@@ -114 +112 @@
       friend class Fasta;
       friend Sequence reverse_complement(const Fasta::Sequence&);
-      boost::shared_array<const char> seq_;
+      std::shared_ptr<char> seq_;
       int size_;
     };
@@ -134 +132 @@
 
   private:
-    boost::shared_ptr<faidx_t> faidx_;
+    std::shared_ptr<faidx_t> faidx_;
     // using compiler generated copy
     //FastaIndex(const FastaIndex& other);

trunk/yat/omic/Pileup.h

@@ -31 +31 @@
 #include <boost/iterator/iterator_concepts.hpp>
 #include <boost/concept/assert.hpp>
-#include <boost/shared_ptr.hpp>
 
 #include <algorithm>
 #include <list>
+#include <memory>
 
 namespace theplu {
@@ -139 +139 @@
       size_t qpos(void) const { return qpos_; }
     private:
-      boost::shared_ptr<BamRead> bam_;
+      std::shared_ptr<BamRead> bam_;
       // index of base pointed to
       size_t qpos_;

trunk/yat/random/Makefile.am

@@ -22 +22 @@
 yat_libyat_la_SOURCES += yat/random/random.cc
 
-nobase_include_HEADERS += $(srcdir)/yat/random/ContinuousDistribution.h
 nobase_include_HEADERS += $(srcdir)/yat/random/copy_k_of_n.h
-nobase_include_HEADERS += $(srcdir)/yat/random/DiscreteDistribution.h
-nobase_include_HEADERS += $(srcdir)/yat/random/Distribution.h
 nobase_include_HEADERS += $(srcdir)/yat/random/random.h