Merge pull request #431 from RcppCore/feature/arma_12.6.7

RcppArmadillo 0.12.6.7.0 with Armadillo 12.6.7

Author: eddelbuettel

ChangeLog

@@ -1,3 +1,12 @@
+2023-12-18  Dirk Eddelbuettel  <[email protected]>
+
+	* DESCRIPTION (Version, Date): RcppArmadillo 0.12.6.7.0
+        * inst/NEWS.Rd: Idem
+        * configure.ac: Idem
+        * configure: Idem
+
+ 	* inst/include/armadillo_bits/: Armadillo 12.6.7
+
 2023-12-09  Dirk Eddelbuettel  <[email protected]>
 
 	* inst/tinytest/test_misc.R: Add tests for thread throttling

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: RcppArmadillo
 Type: Package
 Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
-Version: 0.12.6.6.1
-Date: 2023-12-03
+Version: 0.12.6.7.0
+Date: 2023-12-18
 Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
 Maintainer: Dirk Eddelbuettel <[email protected]>
 Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for RcppArmadillo 0.12.6.6.1.
+# Generated by GNU Autoconf 2.71 for RcppArmadillo 0.12.6.7.0.
 #
 # Report bugs to <[email protected]>.
 #
@@ -610,8 +610,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='RcppArmadillo'
 PACKAGE_TARNAME='rcpparmadillo'
-PACKAGE_VERSION='0.12.6.6.1'
-PACKAGE_STRING='RcppArmadillo 0.12.6.6.1'
+PACKAGE_VERSION='0.12.6.7.0'
+PACKAGE_STRING='RcppArmadillo 0.12.6.7.0'
 PACKAGE_BUGREPORT='[email protected]'
 PACKAGE_URL=''
 
@@ -1229,7 +1229,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures RcppArmadillo 0.12.6.6.1 to adapt to many kinds of systems.
+\`configure' configures RcppArmadillo 0.12.6.7.0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1291,7 +1291,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of RcppArmadillo 0.12.6.6.1:";;
+     short | recursive ) echo "Configuration of RcppArmadillo 0.12.6.7.0:";;
    esac
   cat <<\_ACEOF
 
@@ -1372,7 +1372,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-RcppArmadillo configure 0.12.6.6.1
+RcppArmadillo configure 0.12.6.7.0
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -1486,7 +1486,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by RcppArmadillo $as_me 0.12.6.6.1, which was
+It was created by RcppArmadillo $as_me 0.12.6.7.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -3944,7 +3944,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by RcppArmadillo $as_me 0.12.6.6.1, which was
+This file was extended by RcppArmadillo $as_me 0.12.6.7.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -3999,7 +3999,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-RcppArmadillo config.status 0.12.6.6.1
+RcppArmadillo config.status 0.12.6.7.0
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -11,7 +11,7 @@
 AC_PREREQ([2.69])
 
 ## Process this file with autoconf to produce a configure script.
-AC_INIT([RcppArmadillo],[0.12.6.6.1],[[email protected]])
+AC_INIT([RcppArmadillo],[0.12.6.7.0],[[email protected]])
 
 ## Set R_HOME, respecting an environment variable if one is set
 : ${R_HOME=$(R RHOME)}

inst/NEWS.Rd

@@ -3,6 +3,16 @@
 \newcommand{\ghpr}{\href{https://github.com/RcppCore/RcppArmadillo/pull/#1}{##1}}
 \newcommand{\ghit}{\href{https://github.com/RcppCore/RcppArmadillo/issues/#1}{##1}}
 
+\section{Changes in RcppArmadillo version 0.12.6.7.0 (2023-12-18)}{
+  \itemize{
+    \item Upgraded to Armadillo release 12.6.7 (Cortisol Retox)
+    \itemize{
+      \item Fix for saving sparse matrices as CSV files
+    }
+    \item Added unit tests for thread throttling
+  }
+}
+
 \section{Changes in RcppArmadillo version 0.12.6.6.1 (2023-12-03)}{
   \itemize{
     \item Following the extendeded transition in \ghit{391} and \ghit{402},

inst/include/armadillo_bits/Mat_meat.hpp

@@ -7830,7 +7830,7 @@ Mat<eT>::save(const csv_name& spec, const file_type type) const
 
     if(spec.header_ro.n_elem != save_n_cols)
       {
-      arma_debug_warn_level(1, "Mat::save(): size mistmach between header and matrix");
+      arma_debug_warn_level(1, "Mat::save(): size mismatch between header and matrix");
       return false;
       }
     }
@@ -8114,7 +8114,7 @@ Mat<eT>::load(const csv_name& spec, const file_type type)
 
     if(with_header && (spec.header_rw.n_elem != load_n_cols))
       {
-      arma_debug_warn_level(3, "Mat::load(): size mistmach between header and matrix");
+      arma_debug_warn_level(3, "Mat::load(): size mismatch between header and matrix");
       }
     }
 

inst/include/armadillo_bits/SpMat_meat.hpp

@@ -4609,7 +4609,7 @@ SpMat<eT>::save(const csv_name& spec, const file_type type) const
 
     if(spec.header_ro.n_elem != save_n_cols)
       {
-      arma_debug_warn_level(1, "SpMat::save(): size mistmach between header and matrix");
+      arma_debug_warn_level(1, "SpMat::save(): size mismatch between header and matrix");
       return false;
       }
     }
@@ -4808,7 +4808,7 @@ SpMat<eT>::load(const csv_name& spec, const file_type type)
 
     if(with_header && (spec.header_rw.n_elem != load_n_cols))
       {
-      arma_debug_warn_level(3, "SpMat::load(): size mistmach between header and matrix");
+      arma_debug_warn_level(3, "SpMat::load(): size mismatch between header and matrix");
       }
     }
 

inst/include/armadillo_bits/arma_version.hpp

@@ -23,7 +23,7 @@
 
 #define ARMA_VERSION_MAJOR 12
 #define ARMA_VERSION_MINOR 6
-#define ARMA_VERSION_PATCH 6
+#define ARMA_VERSION_PATCH 7
 #define ARMA_VERSION_NAME  "Cortisol Retox"
 
 

inst/include/armadillo_bits/diskio_meat.hpp

@@ -445,10 +445,10 @@ diskio::convert_token(eT& val, const std::string& token)
   {
   const size_t N = size_t(token.length());
 
-  if(N == 0)  { val = eT(0); return true; }
-  
   const char* str = token.c_str();
 
+  if( (N == 0) || ((N == 1) && (str[0] == '0')) )  { val = eT(0); return true; }
+  
   if( (N == 3) || (N == 4) )
     {
     const bool neg = (str[0] == '-');
@@ -1075,7 +1075,7 @@ diskio::save_coord_ascii(const Mat< std::complex<T> >& x, std::ostream& f)
   for(uword col=0; col < x.n_cols; ++col)
   for(uword row=0; row < x.n_rows; ++row)
     {
-    const eT val = x.at(row,col);
+    const eT& val = x.at(row,col);
 
     if(val != eT_zero)
       {
@@ -1182,11 +1182,6 @@ diskio::save_pgm_binary(const Mat<eT>& x, const std::string& final_name)
 
 
 
-//
-// TODO:
-// add functionality to save the image in a normalised format,
-// ie. scaled so that every value falls in the [0,255] range.
-
 //! Save a matrix as a PGM greyscale image
 template<typename eT>
 inline
@@ -2221,10 +2216,7 @@ diskio::load_coord_ascii(Mat<eT>& x, std::istream& f, std::string& err_msg)
 
       line_stream >> token;
 
-      if(line_stream.fail() == false)
-        {
-        diskio::convert_token( val, token );
-        }
+      if(line_stream.fail() == false)  { diskio::convert_token( val, token ); }
 
       if(val != eT(0))  { tmp(line_row,line_col) = val; }
       }
@@ -2325,18 +2317,11 @@ diskio::load_coord_ascii(Mat< std::complex<T> >& x, std::istream& f, std::string
 
       line_stream >> token_real;
 
-      if(line_stream.fail() == false)
-        {
-        diskio::convert_token( val_real, token_real );
-        }
-      
+      if(line_stream.fail() == false)  { diskio::convert_token( val_real, token_real ); }
 
       line_stream >> token_imag;
 
-      if(line_stream.fail() == false)
-        {
-        diskio::convert_token( val_imag, token_imag );
-        }
+      if(line_stream.fail() == false)  { diskio::convert_token( val_imag, token_imag ); }
 
       if( (val_real != T(0)) || (val_imag != T(0)) )
         {
@@ -2919,13 +2904,22 @@ diskio::save_csv_ascii(const SpMat<eT>& x, std::ostream& f, const char separator
   uword x_n_rows = x.n_rows;
   uword x_n_cols = x.n_cols;
 
+  const eT eT_zero = eT(0);
+  
   for(uword row=0; row < x_n_rows; ++row)
     {
     for(uword col=0; col < x_n_cols; ++col)
       {
       const eT val = x.at(row,col);
 
-      if(val != eT(0))  { arma_ostream::raw_print_elem(f, val); }
+      if(val == eT_zero)
+        {
+        f.put('0');
+        }
+      else
+        {
+        arma_ostream::raw_print_elem(f, val);
+        }
 
       if( col < (x_n_cols-1) )  { f.put(separator); }
       }
@@ -3426,10 +3420,7 @@ diskio::load_coord_ascii(SpMat<eT>& x, std::istream& f, std::string& err_msg)
 
       line_stream >> token;
 
-      if(line_stream.fail() == false)
-        {
-        diskio::convert_token( val, token );
-        }
+      if(line_stream.fail() == false)  { diskio::convert_token( val, token ); }
 
       if(val != eT(0))  { tmp(line_row,line_col) = val; }
       }
@@ -3530,18 +3521,11 @@ diskio::load_coord_ascii(SpMat< std::complex<T> >& x, std::istream& f, std::stri
 
       line_stream >> token_real;
 
-      if(line_stream.fail() == false)
-        {
-        diskio::convert_token( val_real, token_real );
-        }
-      
+      if(line_stream.fail() == false)  { diskio::convert_token( val_real, token_real ); }
 
       line_stream >> token_imag;
 
-      if(line_stream.fail() == false)
-        {
-        diskio::convert_token( val_imag, token_imag );
-        }
+      if(line_stream.fail() == false)  { diskio::convert_token( val_imag, token_imag ); }
 
       if( (val_real != T(0)) || (val_imag != T(0)) )
         {