Speed-up of dlmread function from upstream trunk. Thanks Fabio Rossi for his input, bug #337126

(Portage version: 2.2_rc81/cvs/Linux x86_64)

3 files changed, 378 insertions, 1 deletions

diff --git a/sci-mathematics/octave/ChangeLog b/sci-mathematics/octave/ChangeLog
index 1c128172ee0e..960c7acbbc1c 100644
--- a/sci-mathematics/octave/ChangeLog
+++ b/sci-mathematics/octave/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-mathematics/octave
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/ChangeLog,v 1.95 2010/07/09 15:44:10 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/ChangeLog,v 1.96 2010/09/14 16:45:35 bicatali Exp $
+
+*octave-3.2.4-r2 (14 Sep 2010)
+
+  14 Sep 2010; Sébastien Fabbro <bicatali@gentoo.org>
+  +octave-3.2.4-r2.ebuild, +files/octave-3.2.4-dlmread-speedup.patch:
+  Speed-up of dlmread function from upstream trunk. Thanks Fabio Rossi for
+  his input, bug #337126
 
   09 Jul 2010; Kacper Kowalik <xarthisius@gentoo.org>
   -octave-2.1.73-r1.ebuild, -files/octave-2.1.73-f2c-fix.patch,
diff --git a/sci-mathematics/octave/files/octave-3.2.4-dlmread-speedup.patch b/sci-mathematics/octave/files/octave-3.2.4-dlmread-speedup.patch
new file mode 100644
index 000000000000..3379a3de8f75
--- /dev/null
+++ b/sci-mathematics/octave/files/octave-3.2.4-dlmread-speedup.patch
@@ -0,0 +1,258 @@
+--- src/DLD-FUNCTIONS/dlmread.cc.orig	2010-09-07 14:41:40.991671995 +0200
++++ src/DLD-FUNCTIONS/dlmread.cc	2010-09-07 14:50:50.715672000 +0200
+@@ -1,6 +1,7 @@
+ /*
+ 
+ Copyright (C) 2008, 2009 Jonathan Stickel
++Copyright (C) 2010 Jaroslav Hajek
+ 
+ This file is part of Octave.
+ 
+@@ -29,6 +30,7 @@
+ 
+ #include <cctype>
+ #include <fstream>
++#include <limits>
+ 
+ #include "file-ops.h"
+ #include "lo-ieee.h"
+@@ -38,8 +40,10 @@
+ #include "oct-obj.h"
+ #include "utils.h"
+ 
++static const octave_idx_type idx_max =  std::numeric_limits<octave_idx_type>::max ();
++
+ static bool
+-read_cell_spec (std::istream& is, unsigned long& row, unsigned long& col)
++read_cell_spec (std::istream& is, octave_idx_type& row, octave_idx_type& col)
+ {
+   bool stat = false;
+ 
+@@ -75,8 +79,8 @@
+ 
+ static bool
+ parse_range_spec (const octave_value& range_spec,
+-		  unsigned long& rlo, unsigned long& clo,
+-		  unsigned long& rup, unsigned long& cup)
++		 octave_idx_type& rlo, octave_idx_type& clo,
++		 octave_idx_type& rup, octave_idx_type& cup)
+ {
+   bool stat = true;
+ 
+@@ -115,8 +119,8 @@
+ 			stat = false;
+ 		    }
+ 
+-		  rup = ULONG_MAX - 1;
+-		  cup = ULONG_MAX - 1;
++		 rup = idx_max - 1;
++		 cup = idx_max - 1;
+ 		}
+ 	      else
+ 		{
+@@ -138,10 +142,10 @@
+     {
+       ColumnVector range(range_spec.vector_value ());
+       // double --> unsigned int     
+-      rlo = static_cast<unsigned long> (range(0));
+-      clo = static_cast<unsigned long> (range(1));
+-      rup = static_cast<unsigned long> (range(2));
+-      cup = static_cast<unsigned long> (range(3));
++      rlo = static_cast<octave_idx_type> (range(0));
++      clo = static_cast<octave_idx_type> (range(1));
++      rup = static_cast<octave_idx_type> (range(2));
++      cup = static_cast<octave_idx_type> (range(3));
+     }
+   else 
+     stat = false;
+@@ -211,7 +215,7 @@
+     }
+   
+   // Take a subset if a range was given.
+-  unsigned long r0 = 0, c0 = 0, r1 = ULONG_MAX-1, c1 = ULONG_MAX-1;
++  octave_idx_type r0 = 0, c0 = 0, r1 = idx_max-1, c1 = idx_max-1;
+   if (nargin > 2)
+     {
+       if (nargin == 3)
+@@ -221,17 +225,20 @@
+ 	} 
+       else if (nargin == 4) 
+ 	{
+-	  r0 = args(2).ulong_value ();
+-	  c0 = args(3).ulong_value ();
++	  r0 = args(2).idx_type_value ();
++	  c0 = args(3).idx_type_value ();
+ 
+ 	  if (error_state)
+ 	    return retval;
+ 	}
++
++      if (r0 < 0 || c0 < 0)
++	error ("dlmread: left & top must not be negative");
+     }
+ 
+   if (!error_state)
+     {
+-      unsigned long i = 0, j = 0, r = 1, c = 1, rmax = 0, cmax = 0;
++      octave_idx_type i = 0, j = 0, r = 1, c = 1, rmax = 0, cmax = 0;
+ 
+       Matrix rdata;
+       ComplexMatrix cdata;
+@@ -239,15 +246,17 @@
+       bool iscmplx = false;
+       bool sepflag = false;
+ 
+-      unsigned long maxrows = r1 - r0;
++      octave_idx_type maxrows = r1 - r0;
+ 
+       std::string line;
+ 
+       // Skip the r0 leading lines as these might be a header.
+-      for (unsigned long m = 0; m < r0; m++)
++      for (octave_idx_type m = 0; m < r0; m++)
+ 	getline (file, line);
+       r1 -= r0;
+ 
++      std::istringstream tmp_stream;
++
+       // Read in the data one field at a time, growing the data matrix
+       // as needed.
+       while (getline (file, line))
+@@ -286,11 +295,47 @@
+ 		}
+ 	    }
+ 
++	  if (cmax == 0)
++	    {
++	      // Try to estimate the number of columns.
++	      size_t pos1 = 0;
++	      do
++	        {
++		 size_t pos2 = line.find_first_of (sep, pos1);
++
++		 if (sepflag && pos2 != std::string::npos)
++		   // Treat consecutive separators as one.
++		   {
++		     pos2 = line.find_first_not_of (sep, pos2);
++		     if (pos2 != std::string::npos)
++		       pos2 -= 1;
++		     else
++		       pos2 = line.length () - 1;
++		   }
++
++		 cmax++;
++
++		 if (pos2 != std::string::npos)
++		   pos1 = pos2 + 1;
++		 else
++		   pos1 = std::string::npos;
++
++	        }
++	      while (pos1 != std::string::npos);
++
++	      if (iscmplx)
++	        cdata.resize (rmax, cmax);
++	      else
++	        rdata.resize (rmax, cmax);
++	    }
++
+ 	  r = (r > i + 1 ? r : i + 1);
+ 	  j = 0;
+ 	  size_t pos1 = 0;
+ 	  do
+ 	    {
++			OCTAVE_QUIT;
++
+ 	      size_t pos2 = line.find_first_of (sep, pos1);
+ 	      std::string str = line.substr (pos1, pos2 - pos1);
+ 
+@@ -303,23 +348,35 @@
+ 		{ 
+ 		  // Use resize_and_fill for the case of not-equal
+ 		  // length rows.
++		 rmax = 2*r;
++		 cmax = c;
+ 		  if (iscmplx)
+-		    cdata.resize_fill (r, c, 0);
++		   cdata.resize (rmax, cmax);
+ 		  else
+-		    rdata.resize_fill (r, c, 0);
+-		  rmax = r;
+-		  cmax = c;
++		   rdata.resize (rmax, cmax);
+ 		}
+ 
+-	      std::istringstream tmp_stream (str);
++	      tmp_stream.str (str);
++	      tmp_stream.clear ();
++
+ 	      double x = octave_read_double (tmp_stream);
+ 	      if (tmp_stream)
+ 		{
+ 		  if (tmp_stream.eof ())
+-		    if (iscmplx)
+-		      cdata(i,j++) = x;
+-		    else
+-		      rdata(i,j++) = x;
++		   {
++		     if (iscmplx)
++		       cdata(i,j++) = x;
++		     else
++		       rdata(i,j++) = x;
++		   }
++		 else if (std::toupper (tmp_stream.peek ()) == 'I')
++		   {
++		     // This is to allow pure imaginary numbers.
++		     if (iscmplx)
++		       cdata(i,j++) = x;
++		     else
++		       rdata(i,j++) = x;
++		   }
+ 		  else
+ 		    {
+ 		      double y = octave_read_double (tmp_stream);
+@@ -355,35 +412,16 @@
+ 	  i++;
+ 	}
+  
+-      if (nargin > 2)
+-	{
+-	  if (nargin == 3)
+-	    {
+-	      if (r1 >= r)
+-		r1 = r - 1;
+-	      if (c1 >= c)
+-		c1 = c - 1;
+-	    }
+-	  else if (nargin == 4) 
+-	    {
+-	      // If r1 and c1 are not given, use what was found to be
+-	      // the maximum.
+-	      r1 = r - 1;
+-	      c1 = c - 1;
+-	    }
++      if (r1 >= r)
++	r1 = r - 1;
++      if (c1 >= c)
++	c1 = c - 1;
+ 
+-	  // Now take the subset of the matrix.
+-	  if (iscmplx)
+-	    {
+-	      cdata = cdata.extract (0, c0, r1, c1);
+-	      cdata.resize (r1 + 1, c1 - c0 + 1);
+-	    }
+-	  else
+-	    {
+-	      rdata = rdata.extract (0, c0, r1, c1);
+-	      rdata.resize (r1 + 1, c1 - c0 + 1);
+-	    }
+-	}
++      // Now take the subset of the matrix.
++      if (iscmplx)
++	cdata = cdata.extract (0, c0, r1, c1);
++      else
++	rdata = rdata.extract (0, c0, r1, c1);
+   
+       if (iscmplx)
+ 	retval(0) = cdata;
diff --git a/sci-mathematics/octave/octave-3.2.4-r2.ebuild b/sci-mathematics/octave/octave-3.2.4-r2.ebuild
new file mode 100644
index 000000000000..2ae00a8a30cf
--- /dev/null
+++ b/sci-mathematics/octave/octave-3.2.4-r2.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-3.2.4-r2.ebuild,v 1.1 2010/09/14 16:45:35 bicatali Exp $
+
+EAPI="2"
+inherit flag-o-matic xemacs-elisp-common autotools
+
+DESCRIPTION="High-level interactive language for numerical computations"
+LICENSE="GPL-3"
+HOMEPAGE="http://www.octave.org/"
+SRC_URI="ftp://ftp.gnu.org/pub/gnu/${PN}/${P}.tar.bz2"
+
+SLOT="0"
+IUSE="curl doc emacs fltk fftw opengl readline sparse test xemacs zlib"
+KEYWORDS="~alpha ~amd64 ~hppa ~ppc ~ppc64 ~sparc ~x86"
+
+RDEPEND="dev-libs/libpcre
+	media-gfx/graphicsmagick[cxx]
+	media-libs/qhull
+	sci-libs/qrupdate
+	sci-mathematics/glpk
+	sci-visualization/gnuplot
+	sys-libs/ncurses
+	virtual/lapack
+	x11-libs/libX11
+	curl? ( net-misc/curl )
+	fltk? ( x11-libs/fltk:1.1[opengl?] )
+	fftw? ( sci-libs/fftw:3.0 )
+	opengl? ( virtual/opengl media-libs/ftgl )
+	sparse? ( sci-libs/arpack
+		sci-libs/camd
+		sci-libs/ccolamd
+		sci-libs/cholmod
+		sci-libs/colamd
+		sci-libs/cxsparse
+		sci-libs/umfpack )
+	xemacs? ( app-editors/xemacs )
+	zlib? ( sys-libs/zlib )
+	!sci-mathematics/octave-forge"
+
+DEPEND="${RDEPEND}
+	virtual/latex-base
+	sys-apps/texinfo
+	|| ( dev-texlive/texlive-genericrecommended
+		 app-text/ptex )
+	dev-util/gperf
+	dev-util/pkgconfig"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-3.2.0_parallel_make.patch
+	epatch "${FILESDIR}"/${PN}-3.2.0_as_needed.patch
+	epatch "${FILESDIR}"/${PN}-3.2.4-imread.patch
+	epatch "${FILESDIR}"/${PN}-3.2.4-ldflags.patch
+	epatch "${FILESDIR}"/${PN}-3.2.4-fltk-magic.patch
+	epatch "${FILESDIR}"/${PN}-3.2.4-dlmread-speedup.patch
+	eautoreconf
+}
+
+src_configure() {
+	# hdf5 disabled because not really useful (bug #299876)
+	econf \
+		--localstatedir=/var/state/octave \
+		--enable-shared \
+		--without-hdf5 \
+		--with-qrupdate \
+		--with-blas="$(pkg-config --libs blas)" \
+		--with-lapack="$(pkg-config --libs lapack)" \
+		$(use_enable readline) \
+		$(use_with curl) \
+		$(use_with fftw) \
+		$(use_with fltk) \
+		$(use_with opengl framework-opengl) \
+		$(use_with sparse arpack) \
+		$(use_with sparse umfpack) \
+		$(use_with sparse colamd) \
+		$(use_with sparse ccolamd) \
+		$(use_with sparse cholmod) \
+		$(use_with sparse cxsparse) \
+		$(use_with zlib)
+}
+
+src_compile() {
+	emake || die "emake failed"
+	if use xemacs; then
+		cd "${S}/emacs"
+		xemacs-elisp-comp *.el
+	fi
+}
+
+src_install() {
+	emake install DESTDIR="${D}" || die "emake install failed"
+
+	if use doc; then
+		einfo "Installing documentation..."
+		insinto /usr/share/doc/${PF}
+		doins $(find doc -name \*.pdf)
+	fi
+
+	if use emacs || use xemacs; then
+		cd emacs
+		exeinto /usr/bin
+		doexe octave-tags || die "Failed to install octave-tags"
+		doman octave-tags.1 || die "Failed to install octave-tags.1"
+		if use xemacs; then
+			xemacs-elisp-install ${PN} *.el *.elc
+		fi
+		cd ..
+	fi
+	use test && dodoc test/fntests.log
+	echo "LDPATH=/usr/$(get_libdir)/octave-${PV}" > 99octave
+	doenvd 99octave || die
+}