Switched source to git://github.com/andram/auto-07p.git#branch=python3fixes (some fixes), and worked around build errors with gfortran-8 (using g95 for now).

3 files changed, 127 insertions, 111 deletions

diff --git a/.SRCINFO b/.SRCINFO
index a8e3d6665bc5..ec0f9ec52a85 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,19 +1,17 @@
-# Generated by mksrcinfo v8
-# Thu Mar 10 23:40:02 UTC 2016
 pkgbase = auto-07p
 	pkgdesc = Software for continuation and bifurcation problems in ordinary differential equations. Release 07P. Environment variables controlling build (default to 'no', see PKGBUILD): _BUILD_DOC, _WITH_PLAUT04, _PLAUT04_WITH_QT, AUTO_DEBUG, _WITH_OPENMP, _WITH_MPI.
-	pkgver = 0.9.1
-	pkgrel = 46
+	pkgver = 0.9.1+r1764
+	pkgrel = 1
 	url = http://cmvl.cs.concordia.ca/auto/
 	arch = i686
 	arch = x86_64
 	license = BSD
 	license = LGPL2
 	license = GPL2
-	makedepends = gcc-fortran
+	makedepends = g95
 	makedepends = gcc
 	depends = bash
-	depends = gcc-fortran
+	depends = g95
 	depends = gcc
 	depends = python2
 	optdepends = python2-matplotlib: For python interface.
@@ -30,14 +28,16 @@ pkgbase = auto-07p
 	optdepends = transfig: For compiling the manual (enable manual compiling in PKGBUILD (enable compilation of documentation by setting the environment variable '_BUILD_DOC' to 'yes')).
 	options = libtool
 	options = staticlibs
-	source = http://sourceforge.net/projects/auto-07p/files/auto07p/0.9/auto07p-0.9.1.tar.gz
+	source = auto-07p::git+git://github.com/andram/auto-07p.git#branch=python3fixes
+	source = auto-07p_debian.tar.xz::http://http.debian.net/debian/pool/main/a/auto-07p/auto-07p_0.9.1+r1764+dfsg-6.debian.tar.xz
 	source = auto-07p-session.bash
 	source = xpdf-dummy
 	source = makepkg.sh
-	sha512sums = 838c5e816778ee9d9c391691d1aa1f940aa4b177f36e7530df202774ce9830ebf47a04a390420bdd43da35580612d683c7a11c99088e6364bc808e4e66b3f289
-	sha512sums = 1c4ec2d2487530f407a12a6529d441ebcdf0832b59504bcd370f95162bbaa085475109db3f11f93c891da76dcc57205c4736242512375d81aaa73b56f86103de
-	sha512sums = fe1dde2720afe62722a45dd359b67dfabeffe14bfd053efc0d1b8b30ace49a4b634b199c70d4b86ae117b7c69cc009eb600c17680161b1653a7ab9e86e6c6dd9
-	sha512sums = 0622ed7124575a450dd292710bed12285551590e5b7f6242dbd87b83062553a86ac7b3af286ade5899a21c739ec17fdf49a94392f93bc185929824db252d5b99
+	sha256sums = SKIP
+	sha256sums = bbc783b88432a482117ab42429e33c590e91d390d6b2cce7bbe4e839be50e98e
+	sha256sums = 14d272315859abb260208cfc0a437ff41d66b22960180cfa9c80161e7dded3f4
+	sha256sums = cc83e032003bd9b79eaaee2bd91f77767caf55741ce02e9556dd49142ee1e911
+	sha256sums = 73bef420fdebb6b86b358bcd0f3d86e86f6963e76c7ae281391ec76a940c7644
 
 pkgname = auto-07p
 
diff --git a/PKGBUILD b/PKGBUILD
index b32657a4ee26..e8c82addc15a 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -20,20 +20,22 @@
 ###
 
 pkgname="auto-07p"
-pkgver="0.9.1"
-pkgrel="46"
+pkgver=0.9.1+r1764
+pkgrel=1
 pkgdesc="Software for continuation and bifurcation problems in ordinary differential equations. Release 07P. Environment variables controlling build (default to 'no', see PKGBUILD): _BUILD_DOC, _WITH_PLAUT04, _PLAUT04_WITH_QT, AUTO_DEBUG, _WITH_OPENMP, _WITH_MPI."
 arch=('i686' 'x86_64')
 url='http://cmvl.cs.concordia.ca/auto/'
 options=('libtool' 'staticlibs')
 depends=(
          'bash'
-         'gcc-fortran'
+         # 'gcc-fortran' # Fails to build with gcc8 (see http://sourceforge.net/p/auto-07p/bugs/9/).
+         'g95' # Use 'g95' (Fortran compiler from GCC 4.0.3) instead of 'gcc-fortran'.
          'gcc'
          'python2'
-        ) # 'gcc-fortran' is needed in the runtime for compilation. 'gcc' is also needed, if the input files are C-files.
+        ) # A fortran compiler is needed during runtime for compilation of input files. 'gcc' is also needed, if the input files are C-files.
 makedepends=(
-             'gcc-fortran'
+             # 'gcc-fortran' # Fails to build with gcc8 (see http://sourceforge.net/p/auto-07p/bugs/9/).
+             'g95' # Use 'g95' (Fortran compiler from GCC 4.0.3) instead of 'gcc-fortran'.
              'gcc'
             )
 optdepends=(
@@ -56,20 +58,21 @@ license=(
          'GPL2'
         )
 source=(
-        "http://sourceforge.net/projects/auto-07p/files/auto07p/0.9/auto07p-${pkgver}.tar.gz"
+        "auto-07p::git+git://github.com/andram/auto-07p.git#branch=python3fixes" # "auto-07p.tar.gz::http://sourceforge.net/projects/auto-07p/files/auto07p/0.9/auto07p-${pkgver}.tar.gz" # "auto-07p::git+http://salsa.debian.org/science-team/auto-07p.git" # "auto-07p::http://http.debian.net/debian/pool/main/a/auto-07p/auto-07p_${pkgver}+dfsg.orig.tar.gz"
+        "auto-07p_debian.tar.xz::http://http.debian.net/debian/pool/main/a/auto-07p/auto-07p_${pkgver}+dfsg-6.debian.tar.xz" # Debian patches.
         "auto-07p-session.bash"
         "xpdf-dummy"
         "makepkg.sh" # Just a dummy script for reference purposes. It is _not_ run with this PKGBUILD, but it can be used to build this package with makepkg.
        )
 
-sha512sums=(
-            '838c5e816778ee9d9c391691d1aa1f940aa4b177f36e7530df202774ce9830ebf47a04a390420bdd43da35580612d683c7a11c99088e6364bc808e4e66b3f289'
-            '1c4ec2d2487530f407a12a6529d441ebcdf0832b59504bcd370f95162bbaa085475109db3f11f93c891da76dcc57205c4736242512375d81aaa73b56f86103de'
-            'fe1dde2720afe62722a45dd359b67dfabeffe14bfd053efc0d1b8b30ace49a4b634b199c70d4b86ae117b7c69cc009eb600c17680161b1653a7ab9e86e6c6dd9'
-            '0622ed7124575a450dd292710bed12285551590e5b7f6242dbd87b83062553a86ac7b3af286ade5899a21c739ec17fdf49a94392f93bc185929824db252d5b99'
+sha256sums=(
+            'SKIP' # '8f306751521a491113f89ffbd8b20b68d72aeac42833fa196f2158f3bef35bca'
+            'bbc783b88432a482117ab42429e33c590e91d390d6b2cce7bbe4e839be50e98e'
+            '14d272315859abb260208cfc0a437ff41d66b22960180cfa9c80161e7dded3f4'
+            'cc83e032003bd9b79eaaee2bd91f77767caf55741ce02e9556dd49142ee1e911'
+            '73bef420fdebb6b86b358bcd0f3d86e86f6963e76c7ae281391ec76a940c7644'
            )
 
-
 [ -n "${_BUILD_DOC}" ] || { # Building documentation can be controlled by environment variable.
   _BUILD_DOC=no # Controls if we want to build the documentation. Set to 'yes' to build it (requires some LaTeX-tools to be installed).
 }
@@ -94,31 +97,75 @@ sha512sums=(
   _WITH_MPI=no
 }
 
-_FFLAGS=""
-_CFLAGS=""
+# set the fortran compiler to use.
+# FC='gfortran' # Fails to build with gcc8 (see http://sourceforge.net/p/auto-07p/bugs/9/).
+# FC='gfortran-6'
+FC='g95'
+export FC
 
 if [ "${_AUTO_DEBUG}x" == "yesx" ]; then
-  _FDEBUG_FLAGS="-ggdb -g -fbacktrace -fcheck=array-temps -fcheck=do -fcheck=mem -fcheck=pointer -fcheck=recursion"
-  # -fcheck=bounds does NOT work, since AUTO itself violates bounds ... a bug in AUTO with sideeffects, without sideeffects, or even needed?? 
+  # _FDEBUG_FLAGS="-ggdb -g -fbacktrace -fcheck=array-temps -fcheck=do -fcheck=mem -fcheck=pointer -fcheck=recursion" # Those are for 'new' gfortran.
+  _FDEBUG_FLAGS="-ggdb -g" # Those are for g95.
+  # -fcheck=bounds does NOT work, since AUTO itself violates bounds ... a bug in AUTO with sideeffects, without sideeffects, or even needed??
   _CDEBUG_FLAGS="-ggdb -g"
+  _CXXDEBUG_FLAGS="-ggdb -g"
   _OPT_FLAGS="-O0"
   options+=('!strip')
 else
   _FDEBUG_FLAGS="-g0"
   _CDEBUG_FLAGS="-g0"
+  _CXXDEBUG_FLAGS="-g0"
   _OPT_FLAGS="-O3"
 fi
 
-_FFLAGS="${_FFLAGS} ${_FDEBUG_FLAGS}"
-_CFLAGS="${_CFLAGS} ${_CDEBUG_FLAGS}"
+FFLAGS+=" ${_FDEBUG_FLAGS}"
+CFLAGS+=" ${_CDEBUG_FLAGS}"
+CXXFLAGS+=" ${_CXXDEBUG_FLAGS}"
+
+export FFLAGS
+export CFLAGS
+export CXXFLAGS
 
 
+prepare()
+{
+  cd "${srcdir}"
+  mkdir -pv 'auto'
+  mv -v 'auto-07p' 'auto/07p'
+
+  _extractdir="${srcdir}/auto/07p"
+  _debianpatchdir="${srcdir}/debian/patches"
+  cd "${_extractdir}"
+
+  for _deb_patch in '02_env.patch' '04_fix_bashisms.patch'; do
+    msg2 ">> Applying debian patch ${_deb_patch} ..."
+    patch --follow-symlinks -N -p2 -i "${_debianpatchdir}/${_deb_patch}"
+  done
+}
+
+pkgver()
+{
+  _extractdir="${srcdir}/auto/07p"
+  cd "${_extractdir}"
+  _ver="$(grep -E '[^#]+' CHANGELOG | head -n 1 | tr -d '[[:space:]]:')"
+  _hash="$(git log -n 1 --format=%h)"
+  _commit_count="$(git rev-list --count HEAD)"
+
+  if [ -z "${_ver}" ]; then
+    echo "Error: Could not determine version. Aborting." > /dev/stderr
+    return 1
+  fi
+  if [ -z "${_commit_count}" ]; then
+    echo "Error: Could not determine commit count. Aborting." > /dev/stderr
+    return 1
+  fi
+
+  echo "${_ver}+r${_commit_count}"
+}
 
 _build_documentation()
 {
-  echo ""
-  echo ">> Building documentation for '${pkgname}', version '${pkgver}'. >>"
-  echo ""
+  msg2 ">> Building documentation for '${pkgname}', version '${pkgver}'. >>"
 
   ### Since building the documentation opens the finished pdf with xpdf, we have a dummy xpdf-executable that does nothing. Set it up here to use it.
   cd "${srcdir}"
@@ -137,10 +184,7 @@ _build_documentation()
   PATH="${_OLDPATH}"
   export PATH
 
-  
-  echo ""
-  echo "<< Finished building documentation for '${pkgname}', version '${pkgver}'. <<"
-  echo ""
+  msg2 "<< Finished building documentation for '${pkgname}', version '${pkgver}'. <<"
 }
 
 _install_documentation()
@@ -148,24 +192,20 @@ _install_documentation()
   ### Documentation gets already installed by the normal install procedure, since everything is copied anyway. So, do nothing here. ###
   true
 
-#   echo ""
-#   echo ">> Packaging documentation for '${pkgname}', version '${pkgver}'. >>"
-#   echo ""
+#   msg2 ">> Packaging documentation for '${pkgname}', version '${pkgver}'. >>"
 # 
 # 
 #   mkdir -p "${_doc_install_dir}" || exit 301
 #   mkdir -p "${_plaut04_doc_install_dir}" || exit 302
-#   
+#
 #   if [ -e "${_docdir}/auto.pdf" ]; then
 #     cp -a "${_docdir}/auto.pdf" "${_doc_install_dir}/" || exit "$?"
 #   fi
 #   if [ -e "${_plaut04docdir}/userguide.pdf" ]; then
 #     cp -a "${_plaut04docdir}/userguide.pdf" "${_plaut04_doc_install_dir}/" || exit "$?"
 #   fi
-#   
-#   echo ""
-#   echo "<< Finished packaging documentation for '${pkgname}', version '${pkgver}'. <<"
-#   echo ""
+#
+#   msg2 "<< Finished packaging documentation for '${pkgname}', version '${pkgver}'. <<"
 }
 
 build()
@@ -185,9 +225,7 @@ build()
 
 
 
-  echo ""
-  echo ">>> Building '${pkgname}', version '${pkgver}'. >>>"
-  echo ""
+  msg2 ">>> Building '${pkgname}', version '${pkgver}'. >>>"
 
   cd "${_extractdir}" || exit 11
 
@@ -214,38 +252,28 @@ build()
     _mpi_config="--without-mpi"
   fi
 
-  echo ""
-  echo ">> Running 'configure'-script for '${pkgname}', version '${pkgver}'. >>"
-  echo ""
+  msg2 ">> Running 'configure'-script for '${pkgname}', version '${pkgver}'. >>"
   
-  ./configure --enable-plaut ${_plaut04_config} ${_openmp_config} ${_mpi_config} --enable-gui --enable-tek2ps --with-x --with-optimization-flags="${_OPT_FLAGS}" --prefix="${_install_location}" FFLAGS="${_FFLAGS}" CFLAGS="${_CFLAGS}" || exit "$?"
+  ./configure --enable-plaut ${_plaut04_config} ${_openmp_config} ${_mpi_config} --enable-gui --enable-tek2ps --with-x --with-optimization-flags="${_OPT_FLAGS}" --prefix="${_install_location}" FC="${FC}" FFLAGS="${FFLAGS}" CFLAGS="${CFLAGS}" || exit "$?"
   ### Remakrs for 'copenmotif: For GUI94. ('openmotif' can be used instead of 'lesstif'nfigure'-script: ###
   # * '--prefix' seems to be obsolete since there is no 'make install'. Specified anyway, since I do not know if it gets configured somewhere where it is used later.
   # * For some reason, enabling plaut04 breaks build (installed packages on my machine: 'coin' and 'soqt' and 'simage', although 'simage' is, according to the AUTO-documentation, not necessary for 'soqt' version >= 1.5.0.)
   ### /Remarks for 'configure'-script. ###
-  
-  echo ""
-  echo "<< Finished running 'configure'-script for '${pkgname}', version '${pkgver}'. <<"
-  echo ""
-  
-  
-  echo ""
-  echo ">> Running 'make'-script for '${pkgname}', version '${pkgver}'. >>"
-  echo ""
-  
+
+  msg2 "<< Finished running 'configure'-script for '${pkgname}', version '${pkgver}'. <<"
+
+
+  msg2 ">> Running 'make'-script for '${pkgname}', version '${pkgver}'. >>"
+
   make || exit "$?"
 
-  echo ""
-  echo "<< Finished running 'make'-script for '${pkgname}', version '${pkgver}'. <<"
-  echo ""
-  
+  msg2 "<< Finished running 'make'-script for '${pkgname}', version '${pkgver}'. <<"
+
   if [ "y${_BUILD_DOC}" == "yyes" ]; then
     _build_documentation || exit "$?" # IMPORTANT!, build documentation _after_ main build, otherwise there will no main build happen.
   fi
 
-  echo ""
-  echo "<<< Finished building '${pkgname}', version '${pkgver}'. <<<"
-  echo ""
+  msg2 "<<< Finished building '${pkgname}', version '${pkgver}'. <<<"
 }
 
 package()
@@ -263,61 +291,49 @@ package()
   AUTO_DIR="${_extractdir}" # Auto uses this, at least when building the documentation. So we need to set this variable.
   export AUTO_DIR
 
-  echo ""
-  echo ">>> Installing '${pkgname}', version '${pkgver}', into package dir '${pkgdir}'. >>>"
-  echo ""
+  msg2 ">>> Installing '${pkgname}', version '${pkgver}', into package dir '${pkgdir}'. >>>"
   cd "${_extractdir}" || exit 101
-  
+
   mkdir -p "${_install_dir}" || exit "$?"
-  
+
   ls -A1 "${_extractdir}"/ | while read _content; do # Copy everything, including files starting with ".", but not the special directory entries "." and "..". We do _not_ use an extra argument to "cp" to solve this in order to avoid error messages if there are no dotfiles.
     cp -a -t "${_install_dir}" "${_content}" || exit "$?"
   done || exit "$?"
-  
+
   mkdir -p "${pkgdir}/usr/bin" || exit "$?"
   cp -aL "${srcdir}/auto-07p-session.bash" "${pkgdir}/usr/bin/" || exit "$?"
 
   if [ "y${_BUILD_DOC}" == y"yes" ]; then
     _install_documentation || exit "$?"
   fi
-  
+
   rm -f "${_install_dir}/plaut"/*.o "${_install_dir}/plaut"/*.mod "${_install_dir}/plaut04"/*.mod "${_install_dir}/plaut04"/*.mod "${_install_dir}/gui"/*.o "${_install_dir}/tek2ps"/*.o "${_install_dir}/install-sh" "${_install_dir}/config.status" "${_install_dir}/cmds/auto.env" "${_install_dir}/cmds/auto.env.sh" || exit "$?" # Remove files we don't want to have.
-  
+
   chown -R root:root "${pkgdir}" || exit "$?"
 
-  echo ""
-  echo "<<< Finished installing '${pkgname}', version '${pkgver}', into package dir '${pkgdir}'. <<<"
-  echo ""
-  
-  echo ""
-  echo ">>> patching shabeng-lines of python scripts from 'python' to 'python2'. >>>"
-  echo ""
-  
-  cd "${_install_dir}"
-  ### The "grep" just filters out the files which _may_ be needed to patch (note, that it also matches non-first lines but we only want to patch the first line).
-  ### Then, the "sed"-command takes care of just patching the first line.
-  ### We could omit the "grep" and simply run "sed" over all files, but that would be too much (and more prone for programming errors becoming effective).
-  grep -rlE '^\#\!.*python\>' "${_install_dir}"/* | while read _file; do
-    sed -i '1s|python\(\>\)|python2\1|g' "${_file}"
-  done
+  msg2 "<<< Finished installing '${pkgname}', version '${pkgver}', into package dir '${pkgdir}'. <<<"
 
-  echo ""
-  echo "<<< Finished patching shabeng-lines of python scripts from 'python' to 'python2'. <<<"
-  echo ""
-  
-  echo ""
-  echo ">>> patching 'exec python' to 'exec python2'. >>>"
-  echo ""
-  
-  ### The "grep" just filters out the files which _may_ be needed to patch.
-  ### Then, the "sed"-command takes care of patching.
-  ### Indeed, the grep could be omitted, but it's another step of security to not mis-patch.
-  ### (Actually, bin/autox is the only file which gets patched at all.)
-  grep -rwlE 'exec[[:space:]]+python' "${_install_dir}"/* | while read _file; do
-    sed -ri 's|\<exec[[:space:]]+python\>|exec python2|g' "${_file}"
-  done
-  
-  echo ""
-  echo "Finished patching 'exec python' to 'exec python2'. <<<"
-  echo ""
+#   msg2 ">>> patching shabeng-lines of python scripts from 'python' to 'python2'. >>>"
+#   
+#   cd "${_install_dir}"
+#   ### The "grep" just filters out the files which _may_ be needed to patch (note, that it also matches non-first lines but we only want to patch the first line).
+#   ### Then, the "sed"-command takes care of just patching the first line.
+#   ### We could omit the "grep" and simply run "sed" over all files, but that would be too much (and more prone for programming errors becoming effective).
+#   grep -rlE '^\#\!.*python\>' "${_install_dir}"/* | while read _file; do
+#     sed -i '1s|python\(\>\)|python2\1|g' "${_file}"
+#   done
+# 
+#   msg2 "<<< Finished patching shabeng-lines of python scripts from 'python' to 'python2'. <<<"
+# 
+#   msg2 ">>> patching 'exec python' to 'exec python2'. >>>"
+# 
+#   ### The "grep" just filters out the files which _may_ be needed to patch.
+#   ### Then, the "sed"-command takes care of patching.
+#   ### Indeed, the grep could be omitted, but it's another step of security to not mis-patch.
+#   ### (Actually, bin/autox is the only file which gets patched at all.)
+#   grep -rwlE 'exec[[:space:]]+python' "${_install_dir}"/* | while read _file; do
+#     sed -ri 's|\<exec[[:space:]]+python\>|exec python2|g' "${_file}"
+#   done
+# 
+#   msg2 "Finished patching 'exec python' to 'exec python2'. <<<"
 }
diff --git a/makepkg.sh b/makepkg.sh
index 3d54aff8321f..6b33e6a629a9 100755
--- a/makepkg.sh
+++ b/makepkg.sh
@@ -2,4 +2,4 @@
 
 ### This script is for reference purposes. It can be used to build the package. It is NOT called by the PKGBUILD. It just lays around here for reference.
 
-_BUILD_DOC=yes _PLAUT04_WITH_QT=no _WITH_PLAUT04=yes _AUTO_DEBUG=yes _WITH_MPI=no _WITH_OPENMP=no makepkg "$@"
+_BUILD_DOC=yes _PLAUT04_WITH_QT=yes _WITH_PLAUT04=yes _AUTO_DEBUG=no _WITH_MPI=no _WITH_OPENMP=no makepkg "$@"