Fix CI script issues from review: argument validation, error messages, hidden env dependency

- run-tests-with-retry.sh: extract --test-all from "$@" instead of relying
  on $TEST_ALL env var for retry path
- check_case_optimization_output.py: restore argument validation, add
  per-file NaN/Inf diagnostic reporting
- run_case_optimization.sh: check venv exists before loop, fix misleading
  error message, normalize exit code
- pack.py: fix typo in Pack class comment

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: sbryngelson

.github/scripts/check_case_optimization_output.py

@@ -2,10 +2,15 @@
 
 """Validate case-optimization output: check D/*.dat for NaN/Inf via the packer."""
 
+import math
 import sys
 import os
 
-# Allow importing from the repo root (toolchain.mfc.packer)
+if len(sys.argv) != 2:
+    print(f"Usage: {sys.argv[0]} <case_directory>", file=sys.stderr)
+    sys.exit(1)
+
+# Allow importing from the repo root
 sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', '..'))
 
 from toolchain.mfc.packer.pack import compile as pack_compile
@@ -24,7 +29,13 @@
     sys.exit(1)
 
 if pack.has_bad_values():
-    print("ERROR: NaN or Inf detected in output")
+    print("ERROR: NaN or Inf detected in output:")
+    for name, entry in pack.entries.items():
+        for i, val in enumerate(entry.doubles):
+            if math.isnan(val) or math.isinf(val):
+                label = 'NaN' if math.isnan(val) else 'Inf'
+                print(f"  {label} at index {i} in {name}")
+                break
     sys.exit(1)
 
 total = sum(len(e.doubles) for e in pack.entries.values())

.github/scripts/run-tests-with-retry.sh

@@ -3,6 +3,15 @@
 # of sporadic failures (up to 5). Exits non-zero on real failures.
 # Usage: bash .github/scripts/run-tests-with-retry.sh [mfc test args...]
 
+# Extract flags that should carry over to retries (retries build their own
+# argument list with --only, so we capture passthrough flags here).
+PASSTHROUGH=""
+for arg in "$@"; do
+    case "$arg" in
+        --test-all) PASSTHROUGH="$PASSTHROUGH --test-all" ;;
+    esac
+done
+
 rm -f tests/failed_uuids.txt
 TEST_EXIT=0
 /bin/bash mfc.sh test "$@" || TEST_EXIT=$?
@@ -15,7 +24,7 @@ if [ -s tests/failed_uuids.txt ]; then
         echo ""
         echo "=== Retrying $NUM_FAILED failed test(s): $FAILED ==="
         echo ""
-        /bin/bash mfc.sh test -v --max-attempts 3 -j "$(nproc)" --only $FAILED $TEST_ALL || exit $?
+        /bin/bash mfc.sh test -v --max-attempts 3 -j "$(nproc)" --only $FAILED $PASSTHROUGH || exit $?
     else
         echo "Too many failures ($NUM_FAILED) to retry — likely a real issue."
         exit 1

.github/scripts/run_case_optimization.sh

@@ -13,6 +13,13 @@ if [ "$job_device" = "gpu" ] && [ "$ngpus" -eq 0 ]; then
     ngpus=1
 fi
 
+# Verify the venv Python interpreter exists (created by ./mfc.sh build)
+if [ ! -x build/venv/bin/python3 ]; then
+    echo "ERROR: build/venv/bin/python3 not found."
+    echo "The MFC build venv may not have been created. Was the pre-build step successful?"
+    exit 1
+fi
+
 benchmarks=(
     benchmarks/5eq_rk3_weno3_hllc/case.py
     benchmarks/viscous_weno5_sgb_acoustic/case.py
@@ -43,7 +50,7 @@ for case in "${benchmarks[@]}"; do
             echo "PASS: $case_name"
             passed=$((passed + 1))
         else
-            echo "FAIL: $case_name (NaN/Inf in output)"
+            echo "FAIL: $case_name (validation error)"
             failed=$((failed + 1))
             failed_cases="$failed_cases $case_name"
         fi
@@ -65,4 +72,4 @@ if [ $failed -gt 0 ]; then
 fi
 echo "========================================"
 
-exit $failed
+[ $failed -eq 0 ] && exit 0 || exit 1

toolchain/mfc/packer/pack.py

@@ -20,8 +20,8 @@ def __repr__(self) -> str:
         return f"{self.filepath} {' '.join([ str(d) for d in self.doubles ])}"
 
 
-# This class maps to the data contained in the entirety of D/: it is tush a list
-# of PackEntry classes.
+# This class maps to the data contained in the entirety of D/: a dictionary
+# of PackEntry instances keyed by filepath.
 class Pack:
     entries: typing.Dict[str, PackEntry]