fix(scripts): fail fast if NUMBER_LIST cannot be set; dead -e guard

Review hardening: set_config_number_list now verifies the key landed in
the config copy and aborts otherwise — a config with no NUMBER_LIST line
and no bare [FILE] header would previously install an unmodified copy
and silently process every image. Also fix init_run_exclusive_canfar.sh's
missing-ID guard, which tested an unset variable and never fired.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Author: cailmdaley

scripts/sh/init_run_exclusive_canfar.sh

@@ -160,6 +160,10 @@ function set_config_number_list() {
   else
     perl -pe 's/^\[FILE\][ \t]*$/[FILE]\nNUMBER_LIST = '$number'/' "$config_orig" > "$config_tmp"
   fi
+  if ! grep -q "^NUMBER_LIST = $number$" "$config_tmp"; then
+    echo "set_config_number_list: failed to set NUMBER_LIST in $config_orig" >&2
+    exit 1
+  fi
   mv "$config_tmp" "$config_upd"
 }
 
@@ -184,7 +188,7 @@ if [ "$job" == "-1" ]; then
   message "No job indicated, use option -j" $debug_out 2
 fi
 
-if [ "$exclusive" == "-1" ]; then
+if [ "$ID" == "-1" ]; then
   message "No image ID indicated, use option -e" $debug_out 3
 fi
 

scripts/sh/job_sp_canfar.bash

@@ -354,6 +354,10 @@ function set_config_number_list() {
   else
     perl -pe 's/^\[FILE\][ \t]*$/[FILE]\nNUMBER_LIST = '$number'/' "$config_orig" > "$config_tmp"
   fi
+  if ! grep -q "^NUMBER_LIST = $number$" "$config_tmp"; then
+    echo "set_config_number_list: failed to set NUMBER_LIST in $config_orig" >&2
+    exit 1
+  fi
   mv "$config_tmp" "$config_upd"
 }
 

scripts/sh/job_sp_canfar_v2.0.bash

@@ -262,6 +262,10 @@ function set_config_number_list() {
   else
     perl -pe 's/^\[FILE\][ \t]*$/[FILE]\nNUMBER_LIST = '$number'/' "$config_orig" > "$config_tmp"
   fi
+  if ! grep -q "^NUMBER_LIST = $number$" "$config_tmp"; then
+    echo "set_config_number_list: failed to set NUMBER_LIST in $config_orig" >&2
+    exit 1
+  fi
   mv "$config_tmp" "$config_upd"
 }
 

src/shapepipe/pipeline/file_handler.py

@@ -1086,10 +1086,10 @@ def _format_process_list(
         if isinstance(self._number_list, type(None)):
             number_list = np.load(memory_map, mmap_mode="r")
         else:
-            # NUMBER_LIST comes from the config on faith; intersect it
-            # with the numbers actually found on disk so that a wrong ID
-            # fails here, at start-up, rather than when a module first
-            # tries to open the (non-existent) files (#746).
+            # NUMBER_LIST comes from the config on faith; check every
+            # entry against the numbers actually found on disk so that a
+            # wrong ID fails here, at start-up, rather than when a module
+            # first tries to open the (non-existent) files (#746).
             number_list = self._number_list
             scanned = set(np.load(memory_map, mmap_mode="r"))
             missing = [num for num in number_list if num not in scanned]