Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/.gitignore
+++ b/.gitignore
@@ -27,3 +27,22 @@
 *.i*86
 *.x86_64
 *.hex
+
+Makefile.in
+config.guess*
+config.sub*
+config.h.in
+aclocal.m4
+compile
+configure
+depcomp
+install-sh
+missing
+autom4te.cache
+*~
+doc/html
+doc/latex
+\#*#
+ltmain.sh
+m4/*.m4
+*.orig
\ No newline at end of file
--- a/COPYING
+++ b/COPYING
--- a/Makefile.in
+++ b/Makefile.in
--- a/README
+++ b/README

-//////////////////////////////////////////////////////////////////////////////////////////////////////
-// You downloaded a stable release  of PhyML from https://github.com/stephaneguindon/phyml/releases //
-//////////////////////////////////////////////////////////////////////////////////////////////////////
+### 1. You downloaded a stable release  of PhyML from [here](https://github.com/stephaneguindon/phyml/releases) 

 To install any program that is part of the PhyML package, type the following commands:
+
+```bash
 ./configure --enable-XXXX;
 make;
+```
 where XXXX is phyml or phyrex or phytime.

 To compile a Windows executable, install MinGW and run:
+
+```bash
 ./configure --enable-win --enable-XXXX;
 make;
+```

 To install the MPI version of PhyML, type the following commands:
+
+```bash
 autoreconf -i;
 ./configure --enable-mpi --enable-phyml;
 make;
+```

 If you are using a Mac computer, you will need to install the package pkg-config. The
 following command should set you up (provided Homebrew is installed on your Mac...):
-brew install pkg-config; Next, typing './configure --enable-XXXX; make;' should generate
-the phyml binary in the src/ directory.
+brew install pkg-config; Next, typing `./configure --enable-XXXX; make;` should generate
+the phyml binary in the `src/` directory.



-//////////////////////////////////////////////////////////////////////////
-//                    You have cloned PhyML from GitHub                 //
-//////////////////////////////////////////////////////////////////////////
+### 2. You cloned PhyML from GitHub

 To install any program that is part of the PhyML package, type the following command:
+
+```bash
 sh ./autogen.sh;
+```

 If you are using a Mac computer or running a Unix-like operating system, you will need 
 to install the packages autoconf automake and pkg-config. On a Mac, the following command 
 should set you up (provided Homebrew is installed on your Mac...): brew install pkg-config
 autoconf automake;

-Next, typing './configure --enable-XXXX; make;' should generate the phyml binary in the src/
+Next, typing `./configure --enable-XXXX; make;` should generate the phyml binary in the src/
 directory, where XXXX is phyml or phyrex or phytime.


--- a/aclocal.m4
+++ b/aclocal.m4
--- a/compile
+++ b/compile
-#! /bin/sh
-# Wrapper for compilers which do not understand '-c -o'.
-
-scriptversion=2012-10-14.11; # UTC
-
-# Copyright (C) 1999-2014 Free Software Foundation, Inc.
-# Written by Tom Tromey <tromey@cygnus.com>.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-# This file is maintained in Automake, please report
-# bugs to <bug-automake@gnu.org> or send patches to
-# <automake-patches@gnu.org>.
-
-nl='
-'
-
-# We need space, tab and new line, in precisely that order.  Quoting is
-# there to prevent tools from complaining about whitespace usage.
-IFS=" ""	$nl"
-
-file_conv=
-
-# func_file_conv build_file lazy
-# Convert a $build file to $host form and store it in $file
-# Currently only supports Windows hosts. If the determined conversion
-# type is listed in (the comma separated) LAZY, no conversion will
-# take place.
-func_file_conv ()
-{
-  file=$1
-  case $file in
-    / | /[!/]*) # absolute file, and not a UNC file
-      if test -z "$file_conv"; then
-	# lazily determine how to convert abs files
-	case `uname -s` in
-	  MINGW*)
-	    file_conv=mingw
-	    ;;
-	  CYGWIN*)
-	    file_conv=cygwin
-	    ;;
-	  *)
-	    file_conv=wine
-	    ;;
-	esac
-      fi
-      case $file_conv/,$2, in
-	*,$file_conv,*)
-	  ;;
-	mingw/*)
-	  file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
-	  ;;
-	cygwin/*)
-	  file=`cygpath -m "$file" || echo "$file"`
-	  ;;
-	wine/*)
-	  file=`winepath -w "$file" || echo "$file"`
-	  ;;
-      esac
-      ;;
-  esac
-}
-
-# func_cl_dashL linkdir
-# Make cl look for libraries in LINKDIR
-func_cl_dashL ()
-{
-  func_file_conv "$1"
-  if test -z "$lib_path"; then
-    lib_path=$file
-  else
-    lib_path="$lib_path;$file"
-  fi
-  linker_opts="$linker_opts -LIBPATH:$file"
-}
-
-# func_cl_dashl library
-# Do a library search-path lookup for cl
-func_cl_dashl ()
-{
-  lib=$1
-  found=no
-  save_IFS=$IFS
-  IFS=';'
-  for dir in $lib_path $LIB
-  do
-    IFS=$save_IFS
-    if $shared && test -f "$dir/$lib.dll.lib"; then
-      found=yes
-      lib=$dir/$lib.dll.lib
-      break
-    fi
-    if test -f "$dir/$lib.lib"; then
-      found=yes
-      lib=$dir/$lib.lib
-      break
-    fi
-    if test -f "$dir/lib$lib.a"; then
-      found=yes
-      lib=$dir/lib$lib.a
-      break
-    fi
-  done
-  IFS=$save_IFS
-
-  if test "$found" != yes; then
-    lib=$lib.lib
-  fi
-}
-
-# func_cl_wrapper cl arg...
-# Adjust compile command to suit cl
-func_cl_wrapper ()
-{
-  # Assume a capable shell
-  lib_path=
-  shared=:
-  linker_opts=
-  for arg
-  do
-    if test -n "$eat"; then
-      eat=
-    else
-      case $1 in
-	-o)
-	  # configure might choose to run compile as 'compile cc -o foo foo.c'.
-	  eat=1
-	  case $2 in
-	    *.o | *.[oO][bB][jJ])
-	      func_file_conv "$2"
-	      set x "$@" -Fo"$file"
-	      shift
-	      ;;
-	    *)
-	      func_file_conv "$2"
-	      set x "$@" -Fe"$file"
-	      shift
-	      ;;
-	  esac
-	  ;;
-	-I)
-	  eat=1
-	  func_file_conv "$2" mingw
-	  set x "$@" -I"$file"
-	  shift
-	  ;;
-	-I*)
-	  func_file_conv "${1#-I}" mingw
-	  set x "$@" -I"$file"
-	  shift
-	  ;;
-	-l)
-	  eat=1
-	  func_cl_dashl "$2"
-	  set x "$@" "$lib"
-	  shift
-	  ;;
-	-l*)
-	  func_cl_dashl "${1#-l}"
-	  set x "$@" "$lib"
-	  shift
-	  ;;
-	-L)
-	  eat=1
-	  func_cl_dashL "$2"
-	  ;;
-	-L*)
-	  func_cl_dashL "${1#-L}"
-	  ;;
-	-static)
-	  shared=false
-	  ;;
-	-Wl,*)
-	  arg=${1#-Wl,}
-	  save_ifs="$IFS"; IFS=','
-	  for flag in $arg; do
-	    IFS="$save_ifs"
-	    linker_opts="$linker_opts $flag"
-	  done
-	  IFS="$save_ifs"
-	  ;;
-	-Xlinker)
-	  eat=1
-	  linker_opts="$linker_opts $2"
-	  ;;
-	-*)
-	  set x "$@" "$1"
-	  shift
-	  ;;
-	*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
-	  func_file_conv "$1"
-	  set x "$@" -Tp"$file"
-	  shift
-	  ;;
-	*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
-	  func_file_conv "$1" mingw
-	  set x "$@" "$file"
-	  shift
-	  ;;
-	*)
-	  set x "$@" "$1"
-	  shift
-	  ;;
-      esac
-    fi
-    shift
-  done
-  if test -n "$linker_opts"; then
-    linker_opts="-link$linker_opts"
-  fi
-  exec "$@" $linker_opts
-  exit 1
-}
-
-eat=
-
-case $1 in
-  '')
-     echo "$0: No command.  Try '$0 --help' for more information." 1>&2
-     exit 1;
-     ;;
-  -h | --h*)
-    cat <<\EOF
-Usage: compile [--help] [--version] PROGRAM [ARGS]
-
-Wrapper for compilers which do not understand '-c -o'.
-Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
-arguments, and rename the output as expected.
-
-If you are trying to build a whole package this is not the
-right script to run: please start by reading the file 'INSTALL'.
-
-Report bugs to <bug-automake@gnu.org>.
-EOF
-    exit $?
-    ;;
-  -v | --v*)
-    echo "compile $scriptversion"
-    exit $?
-    ;;
-  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
-    func_cl_wrapper "$@"      # Doesn't return...
-    ;;
-esac
-
-ofile=
-cfile=
-
-for arg
-do
-  if test -n "$eat"; then
-    eat=
-  else
-    case $1 in
-      -o)
-	# configure might choose to run compile as 'compile cc -o foo foo.c'.
-	# So we strip '-o arg' only if arg is an object.
-	eat=1
-	case $2 in
-	  *.o | *.obj)
-	    ofile=$2
-	    ;;
-	  *)
-	    set x "$@" -o "$2"
-	    shift
-	    ;;
-	esac
-	;;
-      *.c)
-	cfile=$1
-	set x "$@" "$1"
-	shift
-	;;
-      *)
-	set x "$@" "$1"
-	shift
-	;;
-    esac
-  fi
-  shift
-done
-
-if test -z "$ofile" || test -z "$cfile"; then
-  # If no '-o' option was seen then we might have been invoked from a
-  # pattern rule where we don't need one.  That is ok -- this is a
-  # normal compilation that the losing compiler can handle.  If no
-  # '.c' file was seen then we are probably linking.  That is also
-  # ok.
-  exec "$@"
-fi
-
-# Name of file we expect compiler to create.
-cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
-
-# Create the lock directory.
-# Note: use '[/\\:.-]' here to ensure that we don't use the same name
-# that we are using for the .o file.  Also, base the name on the expected
-# object file name, since that is what matters with a parallel build.
-lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
-while true; do
-  if mkdir "$lockdir" >/dev/null 2>&1; then
-    break
-  fi
-  sleep 1
-done
-# FIXME: race condition here if user kills between mkdir and trap.
-trap "rmdir '$lockdir'; exit 1" 1 2 15
-
-# Run the compile.
-"$@"
-ret=$?
-
-if test -f "$cofile"; then
-  test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
-elif test -f "${cofile}bj"; then
-  test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
-fi
-
-rmdir "$lockdir"
-exit $ret
-
-# Local Variables:
-# mode: shell-script
-# sh-indentation: 2
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:
--- a/config.guess
+++ b/config.guess
--- a/config.h.in
+++ b/config.h.in
-/* config.h.in.  Generated from configure.ac by autoheader.  */
-
-/* BEAGLE tag on */
-#undef BEAGLE
-
-/* CHECKPOINT tag on */
-#undef CHECKPOINT
-
-/* DATE tag on */
-#undef DATE
-
-/* Debug tag on */
-#undef DEBUG
-
-/* EVOLVE tag on */
-#undef EVOLVE
-
-/* GEO tag on */
-#undef GEO
-
-/* Define to 1 if you don't have `vprintf' but do have `_doprnt.' */
-#undef HAVE_DOPRNT
-
-/* Define to 1 if you have the <float.h> header file. */
-#undef HAVE_FLOAT_H
-
-/* Define to 1 if you have the `floor' function. */
-#undef HAVE_FLOOR
-
-/* Define to 1 if you have the <inttypes.h> header file. */
-#undef HAVE_INTTYPES_H
-
-/* Define to 1 if you have the `m' library (-lm). */
-#undef HAVE_LIBM
-
-/* Define to 1 if your system has a GNU libc compatible `malloc' function, and
-   to 0 otherwise. */
-#undef HAVE_MALLOC
-
-/* Define to 1 if you have the <memory.h> header file. */
-#undef HAVE_MEMORY_H
-
-/* Define to 1 if you have the `pow' function. */
-#undef HAVE_POW
-
-/* Define to 1 if your system has a GNU libc compatible `realloc' function,
-   and to 0 otherwise. */
-#undef HAVE_REALLOC
-
-/* Define to 1 if you have the `rint' function. */
-#undef HAVE_RINT
-
-/* Define to 1 if you have the `sqrt' function. */
-#undef HAVE_SQRT
-
-/* Define to 1 if you have the <stdint.h> header file. */
-#undef HAVE_STDINT_H
-
-/* Define to 1 if you have the <stdlib.h> header file. */
-#undef HAVE_STDLIB_H
-
-/* Define to 1 if you have the `strchr' function. */
-#undef HAVE_STRCHR
-
-/* Define to 1 if you have the <strings.h> header file. */
-#undef HAVE_STRINGS_H
-
-/* Define to 1 if you have the <string.h> header file. */
-#undef HAVE_STRING_H
-
-/* Define to 1 if you have the `strstr' function. */
-#undef HAVE_STRSTR
-
-/* Define to 1 if you have the <sys/stat.h> header file. */
-#undef HAVE_SYS_STAT_H
-
-/* Define to 1 if you have the <sys/types.h> header file. */
-#undef HAVE_SYS_TYPES_H
-
-/* Define to 1 if you have the <unistd.h> header file. */
-#undef HAVE_UNISTD_H
-
-/* Define to 1 if you have the `vprintf' function. */
-#undef HAVE_VPRINTF
-
-/* INVITEE tag on */
-#undef INVITEE
-
-/* MPI tag on */
-#undef MPI
-
-/* Name of package */
-#undef PACKAGE
-
-/* Define to the address where bug reports for this package should be sent. */
-#undef PACKAGE_BUGREPORT
-
-/* Define to the full name of this package. */
-#undef PACKAGE_NAME
-
-/* Define to the full name and version of this package. */
-#undef PACKAGE_STRING
-
-/* Define to the one symbol short name of this package. */
-#undef PACKAGE_TARNAME
-
-/* Define to the home page for this package. */
-#undef PACKAGE_URL
-
-/* Define to the version of this package. */
-#undef PACKAGE_VERSION
-
-/* PART tag on */
-#undef PART
-
-/* PHYCONT tag on */
-#undef PHYCONT
-
-/* PHYML tag on */
-#undef PHYML
-
-/* PHYREX tag on */
-#undef PHYREX
-
-/* PHYTIME tag on */
-#undef PHYTIME
-
-/* RF tag on */
-#undef RF
-
-/* RWRAP tag on */
-#undef RWRAP
-
-/* Define to 1 if you have the ANSI C header files. */
-#undef STDC_HEADERS
-
-/* TEST tag on */
-#undef TEST
-
-/* TIPORDER tag on */
-#undef TIPORDER
-
-/* Unix tag on */
-#undef UNIX
-
-/* Version number of package */
-#undef VERSION
-
-/* WIN32 tag on */
-#undef WIN32
-
-/* Define to empty if `const' does not conform to ANSI C. */
-#undef const
-
-/* Define to `__inline__' or `__inline' if that's what the C compiler
-   calls it, or to nothing if 'inline' is not supported under any name.  */
-#ifndef __cplusplus
-#undef inline
-#endif
-
-/* Define to rpl_malloc if the replacement function should be used. */
-#undef malloc
-
-/* Define to rpl_realloc if the replacement function should be used. */
-#undef realloc
-
-/* Define to `unsigned int' if <sys/types.h> does not define. */
-#undef size_t
--- a/config.sub
+++ b/config.sub
--- a/configure
+++ b/configure
--- a/configure.ac
+++ b/configure.ac
 #                                               -*- Autoconf -*-
 # Process this file with autoconf to produce a configure script.

-AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20180621" | tr -d '\n'"]),[guindon@lirmm.fr])
+AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20190321" | tr -d '\n'"]),[guindon@lirmm.fr])
 AM_INIT_AUTOMAKE([foreign])

 AC_CONFIG_SRCDIR([src/simu.c],[doc/phyml-manual.tex])
@@ -45,6 +45,7 @@ AC_FUNC_SETVBUF_REVERSED
 AC_FUNC_VPRINTF
 AC_CHECK_FUNCS([floor pow rint sqrt strchr strstr])

+dnl DEFAULT_VECTOR_FLAG=
 dnl DEFAULT_VECTOR_FLAG=-mavx
 dnl DEFAULT_VECTOR_FLAG=-msse3
 DEFAULT_VECTOR_FLAG=-march=native
@@ -63,7 +64,9 @@ dnl LT_INIT
 dnl AC_PROG_LIBTOOL


-DEFAULT_C_FLAG="-std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline ${VECTOR_FLAG}"
+DEFAULT_C_FLAG="-std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline ${VECTOR_FLAG}"
+dnl default_C_FLAG="-O2 ${VECTOR_FLAG}"
+dnl DEFAULT_C_FLAG="-O3 -fPIC"

 AC_ARG_ENABLE([debug],
              [AS_HELP_STRING([--enable-debug],
@@ -82,7 +85,7 @@ AC_ARG_ENABLE([gprof],
              [AS_HELP_STRING([--enable-gprof],
                              [Remove optimization options and add profiling informations.])])
 AS_IF([test "x$enable_gprof" = "xyes"],
-      [CFLAGS="-g -pg -fno-inline ${VECTOR_FLAG}"],
+      [CFLAGS="-g -pg -fno-inline -fprofile-arcs -ftest-coverage ${VECTOR_FLAG}"],
      [AS_IF([test "x$enable_debug" = "xno"],[CFLAGS="${DEFAULT_C_FLAG}"])])

 AC_ARG_ENABLE([mpi],

--- a/confr
+++ b/confr
-#!/bin/bash -x
-
-aclocal;
-autoheader;
-autoconf -f;
-automake -f --add-missing;
-./configure --enable-rwrap;
-make clean;
-make;
--- a/debian/changelog
+++ b/debian/changelog
+phyml (3:3.3.20190321-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Do not run dh_dwz
+
+ -- Andreas Tille <tille@debian.org>  Thu, 01 Aug 2019 22:05:12 +0200
+
 phyml (3:3.3.20180621-2) unstable; urgency=medium

  * Team upload

--- a/debian/compat
+++ b/debian/compat
-11
--- a/debian/control
+++ b/debian/control
--- a/debian/patches/cross.patch
+++ b/debian/patches/cross.patch
--- a/debian/patches/fix_declaration_of_temp.patch
+++ b/debian/patches/fix_declaration_of_temp.patch
--- a/debian/patches/fix_wrong_initialisation_of_array.patch
+++ b/debian/patches/fix_wrong_initialisation_of_array.patch
--- a/debian/patches/no-configure-ac-date.patch
+++ b/debian/patches/no-configure-ac-date.patch
--- a/debian/patches/no-march-native.patch
+++ b/debian/patches/no-march-native.patch