Machine architecture and byte-order available as LaTeX macro

Until now, no machine-related specifications were being documented in the
workflow. This information can become helpful when observing differences in
the outcome of both software and analysis segments of the workflow by
others (some software may behave differently based on host machine).

With this commit, the host machine's 'hardware class' and 'byte-order' are
collected and now available as LaTeX macros for the authors to use in the
paper. Currently it is placed in the acknowledgments, right after
mentioning the Maneage commit.

Furthermore, the project and configuration scripts are now capable of
dealing with input directory names that have SPACE (and other special
characters) by putting them inside double-quotes. However, having spaces
and metacharacters in the address of the build directory could cause
build/install failure for some software source files which are beyond the
control of Maneage. So we now check the user's given build directory
string, and if the string has any '@', '#', '$', '%', '^', '&', '*', '(',
')', '+', ';', and ' ' (SPACE), it will ask the user to provide a different
directory.

1 files changed, 43 insertions, 43 deletions

diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh
index 9188fc9..a18966f 100755
--- a/reproduce/software/shell/pre-make-build.sh
+++ b/reproduce/software/shell/pre-make-build.sh
@@ -30,32 +30,32 @@ set -e
 
 
 
-# Input arguments.
-bdir=$1
-ddir=$2
-downloader="$3"
-user_backup_urls="$4"
+# Input arguments (the 'IFS's are to allow space in the name).
+IFS='"' bdir="$1"
+IFS='"' ddir="$2"
+IFS='"' downloader="$3"
+IFS='"' user_backup_urls="$4"
 
 
 
 
 
 # Basic directories/files
-topdir=$(pwd)
-sdir=$bdir/software
-tardir=$sdir/tarballs
-instdir=$sdir/installed
-tmpblddir=$sdir/build-tmp
+topdir="$(pwd)"
+sdir="$bdir"/software
+tardir="$sdir"/tarballs
+instdir="$sdir"/installed
+tmpblddir="$sdir"/build-tmp
 confdir=reproduce/software/config
-ibidir=$instdir/version-info/proglib
+ibidir="$instdir"/version-info/proglib
 downloadwrapper=reproduce/analysis/bash/download-multi-try
 
 # Derived directories
-bindir=$instdir/bin
-urlfile=$confdir/urls.conf
-versionsfile=$confdir/versions.conf
-checksumsfile=$confdir/checksums.conf
-backupfile=$confdir/servers-backup.conf
+bindir="$instdir"/bin
+urlfile="$confdir"/urls.conf
+versionsfile="$confdir"/versions.conf
+checksumsfile="$confdir"/checksums.conf
+backupfile="$confdir"/servers-backup.conf
 
 
 
@@ -87,21 +87,21 @@ done
 # Download the necessary tarball.
 download_tarball() {
   # Basic definitions
-  maneagetar=$tardir/$tarball
+  maneagetar="$tardir"/"$tarball"
 
   # See if the tarball already exists in Maneage.
   if [ -f "$maneagetar" ]; then
     just_a_place_holder=1
   else
-    ucname=$tardir/$tarball.unchecked
+    ucname="$tardir"/"$tarball.unchecked"
 
     # If the URL is empty, use the top backup server
     if [ x$w = x ]; then
         bservers="$backupservers"
-        tarballurl=$topbackupserver/$tarball
+        tarballurl="$topbackupserver"/"$tarball"
     else
         bservers="$backupservers_all"
-        tarballurl=$url/$tarball
+        tarballurl="$url"/"$tarball"
     fi
 
     # See if it is in the input-software directory, if so, make a link, if
@@ -111,19 +111,19 @@ download_tarball() {
     # link and link to an actual file.
     if [ -f "$ddir/$tarball" ]; then
       if type realpath > /dev/null 2> /dev/null; then
-        ln -sf "$(realpath $ddir/$tarball)" "$ucname"
+        ln -sf "$(realpath "$ddir/$tarball")" "$ucname"
       else
-        cp $ddir/$tarball $ucname
+        cp "$ddir/$tarball" "$ucname"
       fi
     else
-      $downloadwrapper "$downloader" nolock $tarballurl $ucname \
+      $downloadwrapper "$downloader" nolock $tarballurl "$ucname" \
                        "$bservers"
     fi
 
     # Make sure this is the correct tarball.
     if type sha512sum > /dev/null 2> /dev/null; then
       checksum=$(sha512sum "$ucname" | awk '{print $1}')
-      expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' $checksumsfile)
+      expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' "$checksumsfile")
       if [ x$checksum = x$expectedchecksum ]; then mv "$ucname" "$maneagetar"
       else
         echo "ERROR: Non-matching checksum: $tarball"
@@ -137,9 +137,9 @@ download_tarball() {
 
   # If the tarball is newer than the (possibly existing) program (the version
   # has changed), then delete the program.
-  if [ -f $ibidir/$progname ]; then
-      if [ $maneagetar -nt $ibidir/$progname ]; then
-          rm $ibidir/$progname
+  if [ -f "$ibidir/$progname" ]; then
+      if [ "$maneagetar" -nt "$ibidir/$progname" ]; then
+          rm "$ibidir/$progname"
       fi
   fi
 }
@@ -151,39 +151,39 @@ download_tarball() {
 # Build the program from the tarball. This function takes one argument
 # which is the configure-time options.
 build_program() {
-  if ! [ -f $ibidir/$progname ]; then
+  if ! [ -f "$ibidir/$progname" ]; then
 
     # Options
     configoptions=$1
 
     # Go into the temporary building directory.
-    cd $tmpblddir
+    cd "$tmpblddir"
     unpackdir="$progname"-"$version"
 
     # Some implementations of 'tar' don't recognize Lzip, so we need to
     # manually call Lzip first, then call tar afterwards.
-    csuffix=$(echo $tarball | sed -e's/\./ /g' | awk '{print $NF}')
-    rm -rf $unpackdir
+    csuffix=$(echo "$tarball" | sed -e's/\./ /g' | awk '{print $NF}')
+    rm -rf "$unpackdir"
     if [ x$csuffix = xlz ]; then
       intarrm=1
-      intar=$(echo $tarball | sed -e's/.lz//')
-      lzip -c -d $tardir/$tarball > $intar
+      intar=$(echo "$tarball" | sed -e's/.lz//')
+      lzip -c -d "$tardir/$tarball" > $intar
     else
       intarrm=0
-      intar=$tardir/$tarball
+      intar="$tardir"/"$tarball"
     fi
 
     # Unpack the tarball and go into it.
-    tar xf $intar
-    if [ x$intarrm = x1 ]; then rm $intar; fi
-    cd $unpackdir
+    tar xf "$intar"
+    if [ x$intarrm = x1 ]; then rm "$intar"; fi
+    cd "$unpackdir"
 
     # build the project, either with Make and either without it.
     if [ x$progname = xlzip ]; then
-        ./configure --build --check --installdir=$instdir/bin $configoptions
+        ./configure --build --check --installdir="$instdir/bin" $configoptions
     else
         # All others accept the configure script.
-        ./configure --prefix=$instdir $configoptions
+        ./configure --prefix="$instdir" $configoptions
 
         # To build GNU Make, we don't want to assume the existance of a
         # Make program, so we use its 'build.sh' script and its own built
@@ -198,9 +198,9 @@ build_program() {
     fi
 
     # Clean up the source directory
-    cd $topdir
-    rm -rf $tmpblddir/$unpackdir
-    echo "$progname_tex $version" > $ibidir/$progname
+    cd "$topdir"
+    rm -rf "$tmpblddir/$unpackdir"
+    echo "$progname_tex $version" > "$ibidir/$progname"
   fi
 }
 
@@ -219,7 +219,7 @@ build_program() {
 progname="lzip"
 progname_tex="Lzip"
 url=$(awk '/^'$progname'-url/{print $3}' $urlfile)
-version=$(awk '/^'$progname'-version/{print $3}' $versionsfile)
+version=$(awk '/^'$progname'-version/{print $3}' "$versionsfile")
 tarball=$progname-$version.tar
 download_tarball
 build_program