Update to 9.16

3 files changed, 63 insertions, 130 deletions

diff --git a/.SRCINFO b/.SRCINFO
index c5707627167d..728e2c3763f4 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,17 +1,20 @@
+# Generated by mksrcinfo v8
+# Wed Feb 10 13:05:49 UTC 2016
 pkgbase = modeller
 	pkgdesc = 3D Structure Homology Modeller
-	pkgver = 9.15
-	pkgrel = 2
+	pkgver = 9.16
+	pkgrel = 1
 	url = http://salilab.org/modeller/
-	install = modeller.install
 	arch = i686
 	arch = x86_64
 	license = custom
-	depends = python2
 	depends = glib2
-	optdepends = python: python3 support
-	source = http://www.salilab.org/modeller/9.15/modeller-9.15.tar.gz
-	sha256sums = 9833eace132429abee54f2f7055a55f88ac9990cd79024f95a58d12161ca8eee
+	optdepends = python: python support
+	optdepends = python2: python2 support
+	backup = etc/modeller/config.py
+	source = http://www.salilab.org/modeller/9.16/modeller-9.16.tar.gz
+	md5sums = 62d31d27d437cf48458a997f977caab4
+	sha512sums = 5d3dba6134a9583d269ae0df93b05e536a753e00568c1a5562cf1e28bff07eb31185404f4a8b355832096aeb7ea320307e7ec620fc09e56c026c8143c3e4104a
 
 pkgname = modeller
 
diff --git a/PKGBUILD b/PKGBUILD
index f8e3dd315c35..e9b61593ae9f 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -5,98 +5,71 @@
 # Contributor: Fabio Zanini <iosonofabio@gmail.com>
 
 pkgname=modeller
-pkgver=9.15
-pkgrel=2
+pkgver=9.16
+pkgrel=1
 pkgdesc="3D Structure Homology Modeller"
 arch=('i686' 'x86_64')
 url="http://salilab.org/modeller/"
 license=('custom')
-depends=('python2' 'glib2')
-optdepends=('python: python3 support')
-install=modeller.install
-source=("http://www.salilab.org/modeller/$pkgver/modeller-$pkgver.tar.gz")
-
-sha256sums=('9833eace132429abee54f2f7055a55f88ac9990cd79024f95a58d12161ca8eee')
+depends=('glib2')
+optdepends=('python: python support'
+            'python2: python2 support')
+backup=("etc/$pkgname/config.py")
+source=("http://www.salilab.org/modeller/$pkgver/$pkgname-$pkgver.tar.gz")
+md5sums=('62d31d27d437cf48458a997f977caab4')
+sha512sums=('5d3dba6134a9583d269ae0df93b05e536a753e00568c1a5562cf1e28bff07eb31185404f4a8b355832096aeb7ea320307e7ec620fc09e56c026c8143c3e4104a')
 
 package() {
-    cd $srcdir/$pkgname-$pkgver
-    
-    #set default values:
-    VER="9.15"
-    VERENV="9v15"
-    MOD="MODELLER ${VER}"
-    PROGRAM=mod${VER}
-    MODINSTALL="${pkgdir}/usr/lib/modeller"
     _MODINSTALL="/usr/lib/modeller"
 
-    if [ "${CARCH}" = "i686" ]; then
-        # for i686
-        EXECUTABLE_TYPE="i386-intel8"
-    elif [ "${CARCH}" = "x86_64" ]; then
-        # for x86_64
-        EXECUTABLE_TYPE="x86_64-intel8"
-    else
-        error "MODELLER is only available for i386 and x86_64!"
-    fi
-    
+    cd "$pkgname-$pkgver"
+
+    case "$CARCH" in
+      i686)
+        _EXECUTABLE_TYPE="i386-intel8" ;;
+      x86_64)
+        _EXECUTABLE_TYPE="x86_64-intel8" ;;
+      *)
+        error "MODELLER is only available for i386 and x86_64!" ;;
+    esac
+
     # Change directory permisssions
-    find . -type d -exec chmod 755 {} \;
-    
+    find . -type d -exec chmod 755 {} +
+
     # Installing Modeller files
-    mkdir -p "${MODINSTALL}"
-    cp -R README INSTALLATION doc examples modlib src "${MODINSTALL}"
-    mkdir -p "${MODINSTALL}/bin"
-    cp -R bin/*.top bin/modslave.py bin/lib bin/${PROGRAM}_${EXECUTABLE_TYPE} \
-        "${MODINSTALL}/bin"
-    mkdir -p "${MODINSTALL}/lib"
-    cp -R lib/${EXECUTABLE_TYPE} "${MODINSTALL}/lib"
+    mkdir -p "$pkgdir/$_MODINSTALL/"{bin,lib}
+    cp -R README INSTALLATION doc examples modlib src "$pkgdir/$_MODINSTALL"
+    cp -R bin/*.top bin/lib "bin/mod${pkgver}_${_EXECUTABLE_TYPE}" "$pkgdir/$_MODINSTALL/bin"
+    cp -R "lib/$_EXECUTABLE_TYPE" "$pkgdir/$_MODINSTALL/lib"
 
     # Creating Modeller startup scripts
-    sed -e "s;EXECUTABLE_TYPE${VERENV}=xxx;EXECUTABLE_TYPE${VERENV}=$EXECUTABLE_TYPE;" \
-        -e "s;MODINSTALL${VERENV}=xxx;MODINSTALL${VERENV}=\"$_MODINSTALL\";" \
-        bin/modscript > "${MODINSTALL}/bin/${PROGRAM}"
-    sed -e "s;@TOPDIR\@;\"$_MODINSTALL\";" \
-        -e "s;@EXETYPE\@;$EXECUTABLE_TYPE;" \
-        bin/modpy.sh.in > "${MODINSTALL}/bin/modpy.sh"
-    chmod a+x "${MODINSTALL}/bin/${PROGRAM}" "${MODINSTALL}/bin/modpy.sh"
-    sed -e "s;/usr/bin/python;/usr/bin/python2;" \
-        bin/modslave.py > "${MODINSTALL}/bin/modslave.py"
-    
-    # Creating simbol link
-    install -d ${pkgdir}/usr/bin/
-    ln -sf ${_MODINSTALL}/bin/mod$pkgver  ${pkgdir}/usr/bin/mod$pkgver
-    ln -sf ${_MODINSTALL}/bin/modpy.sh  ${pkgdir}/usr/bin/modpy.sh
-    ln -sf ${_MODINSTALL}/bin/modslave.py  ${pkgdir}/usr/bin/modslave.py
+    sed -r "s|(EXECUTABLE_TYPE[0-9v]+)=x+|\1=$_EXECUTABLE_TYPE|;s|(MODINSTALL[0-9v]+)=x+|\1=\"$_MODINSTALL\"|" \
+        bin/modscript > "$pkgdir/$_MODINSTALL/bin/mod$pkgver"
+    sed 's|@TOPDIR@|"'"$_MODINSTALL"'"|; s|@EXETYPE@|'"$_EXECUTABLE_TYPE"'|' \
+        bin/modpy.sh.in > "$pkgdir/$_MODINSTALL/bin/modpy.sh"
+    sed '1s/^.*$/&2/' bin/modslave.py > "$pkgdir/$_MODINSTALL/bin/modslave.py"
+
+    # create symlinks
+    install -dm755 "$pkgdir/usr/bin"
+    for _f in mod$pkgver modpy.sh modslave.py; do
+      chmod +x "$pkgdir/$_MODINSTALL/bin/$_f"
+      ln -sf "$_MODINSTALL/bin/$_f"  "$pkgdir/usr/bin/"
+    done
 
-    # Create config.py is it not exists
-    if [ ! -f "${_MODINSTALL}/modlib/modeller/config.py" ]; then
-        msg "Creating '${_MODINSTALL}/config.py'..."
-        echo "license = 'XXXX'" > "${MODINSTALL}/modlib/modeller/config.py"
-        msg "Done! Add your license code to '${_MODINSTALL}/config.py'."
-    else
-        msg "Found existing config.py. Please check that the license code within this file is correct!"
-    fi
-    
-    # Add modeller libs to ld.so.conf
-    msg "Adding MODELLER to ld.so.conf..."
-    install -d ${pkgdir}/etc/ld.so.conf.d
-    echo "/usr/lib/${pkgname}/lib/${EXECUTABLE_TYPE}" > ${pkgdir}/etc/ld.so.conf.d/${pkgname}.conf
+    # create config.py
+    install -dm755 "$pkgdir/etc/$pkgname"
+    echo "license = 'XXXX'" > "$pkgdir/etc/$pkgname/config.py"
+    ln -s /etc/$pkgname/config.py "$pkgdir/$_MODINSTALL/modlib/modeller/config.py"
 
-    # Install python2 module
-    msg "Installing package for python2..."
-    install -d ${pkgdir}/usr/lib/python2.7/site-packages
-    ln -s ${_MODINSTALL}/modlib/modeller  ${pkgdir}/usr/lib/python2.7/site-packages/modeller  
-        
-    ln -s ${_MODINSTALL}/lib/${EXECUTABLE_TYPE}/python2.5/_modeller.so ${pkgdir}/usr/lib/python2.7/site-packages/_modeller.so
-     
-     # Install python3 modules if python3 is installed
-     if [ -d "/usr/lib/python3.4/site-packages" ]; then
-         msg "Installing package for python3..."
-         install -d ${pkgdir}/usr/lib/python3.4/site-packages
-         ln -s ${_MODINSTALL}/modlib/modeller  ${pkgdir}/usr/lib/python3.4/site-packages/modeller
-         ln -s ${_MODINSTALL}/lib/${EXECUTABLE_TYPE}/python3.3/_modeller.so ${pkgdir}/usr/lib/python3.4/site-packages/_modeller.so
-     else
-         msg "Python3 not found! If you want to use modeller within python3, install 'python32' from the AUR and reinstall MODELLER."
-     fi
-} 
+    # add modeller libs to ld.so.conf
+    install -dm755 "$pkgdir/etc/ld.so.conf.d"
+    echo "/usr/lib/$pkgname/lib/$_EXECUTABLE_TYPE" > "$pkgdir/etc/ld.so.conf.d/$pkgname.conf"
 
+    # install python modules
+    for _pyver in 2.7 3.5; do
+      install -dm755 "$pkgdir/usr/lib/python$_pyver/site-packages"
+      ln -s "$_MODINSTALL/modlib/modeller" "$pkgdir/usr/lib/python$_pyver/site-packages/modeller"
+    done
+    ln -s "$_MODINSTALL/lib/$_EXECUTABLE_TYPE/python2.5/_modeller.so" "$pkgdir/usr/lib/python2.7/site-packages/_modeller.so"
+    ln -s "$_MODINSTALL/lib/$_EXECUTABLE_TYPE/python3.3/_modeller.so" "$pkgdir/usr/lib/python3.5/site-packages/_modeller.so"
+}
diff --git a/modeller.install b/modeller.install
deleted file mode 100644
index 86f9b25d6532..000000000000
--- a/modeller.install
+++ /dev/null
@@ -1,43 +0,0 @@
-post_install() {
-
-MODINSTALL="$pkgdir/usr/lib/modeller"
-if [ "$CARCH" = "i686" ]; then
-    # for i686
-    EXECUTABLE_TYPE="i386-intel8"
-else # for x86_64
-    EXECUTABLE_TYPE="x86_64-intel8"
-fi
-
-cat << EOF
-==> You can also use Modeller as a Python module, if you have Python
-==> installed (any version between 2.3 and 2.7). Do this using the script:
-==> ${MODINSTALL}/bin/modpy.sh"
-==> Simply add your regular Python command line after this script, e.g.
-==> ${MODINSTALL}/bin/modpy.sh python myscript.py"
-
-==> Alternatively, you could ensure that the following directories containing
-==> Python modules are in your Python path:
-==> ${MODINSTALL}/modlib
-==> ${MODINSTALL}/lib/${EXECUTABLE_TYPE} (for Python 2.3 or Python 2.4)
-==> ${MODINSTALL}/lib/${EXECUTABLE_TYPE}/python2.5 (for Python 2.5, 2.6, 2.7)
-==> (e.g. by setting the PYTHONPATH environment variable) and that the
-==> following directory containing dynamic libraries is in your dynamic
-==> library search path:
-==> ${MODINSTALL}/lib/${EXECUTABLE_TYPE}
-==> (e.g. by setting the LD_LIBRARY_PATH variable (LIBPATH on AIX systems).
-==> Ask your systems administrator for help if you wish to do this.
-
-==> ########################################################################
-==> THE LICENSE KEY IS NOT SET.
-==> Go to http://salilab.org/modeller/registration.html to get a license key,
-==> and then set the 'license' variable to it in the file
-==> ${MODINSTALL}/modlib/modeller/config.py
-==> example: license = 'XXXX'
-==> ########################################################################
-
-EOF
-}
-
-post_upgrade() {
- post_install $1
-}