apptainer.sh: more clear option names

Summary: The Apptainer script's option names have been renamed: '--sif' and
'--base-sif' are new names for the old '--project-name' and '--base-name'.

Until now the options that took SIF files in the Apptainer script were not
too clear (in their name): ending in '-name' (not clearly mentioning that
it needs a file name). Also, in the same script, we had forgot to add an
option to allow the user to choose a different base operating system!

With this commit, both the issues above have been fixed: the options end in
'-sif' (clearly informing the user that a SIF file is expected) and we now
have a new '--base-os' option. In the process, a few other parts of Maneage
were also polished:

  - README-hacking.md: the newly published J-PLUS PSF paper was added to
    the list of Maneage'd papers and the final journal information for the
    NASIM paper has been added. Some typos here and there were also fixed.

  - The curretnly used VIM needed the the '-std=gnu17': necessary now that
    the default Maneage GCC 15.2.0 for the high-level software which
    defaults to C23.

1 files changed, 23 insertions, 21 deletions

diff --git a/reproduce/software/shell/apptainer.sh b/reproduce/software/shell/apptainer.sh
index 51b36db..6ac9975 100755
--- a/reproduce/software/shell/apptainer.sh
+++ b/reproduce/software/shell/apptainer.sh
@@ -71,14 +71,14 @@ set -e
 
 
 # Default option values
+sif=""
 jobs=0
 quiet=0
 source_dir=
 build_only=
-base_name=""
+base_sif=""
 shm_size=20gb
 scriptname="$0"
-project_name=""
 project_shell=0
 container_shell=0
 base_os=debian:stable-slim
@@ -97,9 +97,9 @@ Top-level script to build and run a Maneage'd project within Apptainer.
       --source-dir=STR     Directory of source code (default: 'pwd -P').
 
  Apptainer images
+      --sif=STR            Project's apptainer image (a '.sif' file).
       --base-os=STR        Base OS name (default: '$base_os').
-      --base-name=STR      Base OS apptainer image (a '.sif' file).
-      --project-name=STR   Project's apptainer image (a '.sif' file).
+      --base-sif=STR       Base OS apptainer image (a '.sif' file).
 
  Interactive shell
       --project-shell      Open the project's shell within the container.
@@ -155,10 +155,12 @@ do
   --source-dir=*)        source_dir="${1#*=}";                        check_v "$1" "$source_dir";   shift;;
 
   # Container options.
-  --base-name)           base_name="$2";                              check_v "$1" "$base_name";    shift;shift;;
-  --base-name=*)         base_name="${1#*=}";                         check_v "$1" "$base_name";    shift;;
-  --project-name)        project_name="$2";                           check_v "$1" "$project_name"; shift;shift;;
-  --project-name=*)      project_name="${1#*=}";                      check_v "$1" "$project_name"; shift;;
+  --sif)                 sif="$2";                                    check_v "$1" "$sif";         shift;shift;;
+  --sif=*)               sif="${1#*=}";                               check_v "$1" "$sif";         shift;;
+  --base-os)             base_os="$2";                                check_v "$1" "$base_os";     shift;shift;;
+  --base-os=*)           base_os="${1#*=}";                           check_v "$1" "$base_os";     shift;;
+  --base-sif)            base_sif="$2";                               check_v "$1" "$base_sif";    shift;shift;;
+  --base-sif=*)          base_sif="${1#*=}";                          check_v "$1" "$base_sif";    shift;;
 
   # Interactive shell.
   --project-shell)       project_shell=1;                                                           shift;;
@@ -206,8 +208,8 @@ fi
 
 # Set the default project and base-OS image names (inside the build
 # directory).
-if [ x"$base_name" = x ]; then base_name=$build_dir/maneage-base.sif; fi
-if [ x"$project_name" = x ]; then project_name=$build_dir/maneaged.sif; fi
+if [ x"$base_sif" = x ]; then base_sif=$build_dir/maneage-base.sif; fi
+if [ x"$sif" = x ]; then sif=$build_dir/maneaged.sif; fi
 
 
 
@@ -278,9 +280,9 @@ fi
 #
 # Build the base operating system using Maneage's './project configure'
 # step.
-if [ -f $project_name ]; then
+if [ -f $sif ]; then
     if [ $quiet = 0 ]; then
-        printf "$scriptname: info: project's image ('$project_name') "
+        printf "$scriptname: info: project's image ('$sif') "
         printf "already exists and will be used. If you want to build a "
         printf "new project image, give a new name to '--project-name'. "
         printf "To remove this message run with '--quiet'\n"
@@ -289,12 +291,12 @@ else
 
     # Build the basic definition, with just Debian-slim with minimal
     # necessary tools.
-    if [ -f $base_name ]; then
+    if [ -f $base_sif ]; then
         if [ $quiet = 0 ]; then
             printf "$scriptname: info: base OS apptainer image "
-            printf "('$base_name') already exists and will be used. "
+            printf "('$base_sif') already exists and will be used. "
             printf "If you want to build a new base OS image, give "
-            printf "a new name to '--base-name'. To remove this "
+            printf "a new name to '--base-sif'. To remove this "
             printf "message run with '--quiet'\n"
         fi
     else
@@ -309,7 +311,7 @@ From: $base_os
 EOF
         # Build the base operating system container and delete the
         # temporary definition file.
-        apptainer build $base_name $base_def
+        apptainer build $base_sif $base_def
         rm $base_def
     fi
 
@@ -330,7 +332,7 @@ EOF
     maneage_def=$build_dir/maneage.def
     cat <<EOF > $maneage_def
 Bootstrap: localimage
-From: $base_name
+From: $base_sif
 
 %setup
   mkdir -p \${APPTAINER_ROOTFS}/home/maneager/input
@@ -385,7 +387,7 @@ EOF
               $software_dir_mnt \
               --ignore-fakeroot-command \
               \
-              $project_name \
+              $sif \
               $maneage_def
 
     # Clean up.
@@ -397,7 +399,7 @@ fi
 if ! [ x"$build_only" = x ]; then
     if [ $quiet = 0 ]; then
         printf "$scriptname: info: Maneaged project has been configured "
-        printf "successfully in the '$project_name' image"
+        printf "successfully in the '$sif' image"
     fi
     exit 0
 fi
@@ -419,7 +421,7 @@ else
 fi
 
 # Build the hostname from the name of the SIF file of the project name.
-hstname=$(echo "$project_name" \
+hstname=$(echo "$sif" \
               | awk 'BEGIN{FS="/"}{print $NF}' \
               | sed -e's|.sif$||')
 
@@ -454,4 +456,4 @@ apptainer $aopt \
           --hostname $hstname \
           --cwd /home/maneager/source \
           \
-          $project_name
+          $sif