refactor: fix cantera_file NameError, unify archive relpath, derive completion flags

run/input.py:
- cantera_file was only assigned in the chemistry=T branch; the error
  message on line 69 would raise NameError when chemistry=F and all
  candidates (h2o2.yaml) fail to load — set cantera_file='h2o2.yaml'
  before the branch so the error message is always valid

run/archive.py:
- Extract _relpath_safe(path, dirpath) to replace three inline try/except
  blocks scattered across __build_manifest, __copy_dir, __write_tar
- Fix manifest fallback: was falling back to the full absolute path on
  cross-device paths; now uses basename like copy/tar already did —
  manifest and archive contents now agree

cli/completion_gen.py:
- Bash and zsh completion lists for MFC config flags were hardcoded,
  already missing --reldebug/--no-reldebug; derive dynamically from
  MFCConfig dataclass fields (same source argparse_gen.py already uses)
- New MFCConfig fields are now automatically reflected in completions

Author: sbryngelson

toolchain/mfc/cli/completion_gen.py

@@ -5,10 +5,42 @@
 in sync with the CLI schema definitions.
 """
 
+import dataclasses
 from typing import List, Set
 
 from .schema import CLISchema, Command, CompletionType
 
+
+def _mfc_config_bash_flags() -> List[str]:
+    """Return bash completion flag strings derived from MFCConfig fields."""
+    from ..state import MFCConfig
+
+    flags = []
+    for f in dataclasses.fields(MFCConfig):
+        cli = f.name.replace("_", "-")
+        flags.append(f"--{cli}")
+        flags.append(f"--no-{cli}")
+    return flags
+
+
+def _mfc_config_zsh_flags() -> List[str]:
+    """Return zsh completion spec strings derived from MFCConfig fields."""
+    from ..state import MFCConfig, gpuConfigOptions
+
+    specs = []
+    modes = ":".join(e.value for e in gpuConfigOptions if e.value != gpuConfigOptions.NONE.value)
+    for f in dataclasses.fields(MFCConfig):
+        cli = f.name.replace("_", "-")
+        label = cli.replace("-", " ").title()
+        if f.name == "gpu":
+            specs.append(f"'--{cli}[Enable GPU]:mode:({modes})'")
+            specs.append(f"'--no-{cli}[Disable GPU]'")
+        else:
+            specs.append(f"'--{cli}[Enable {label}]'")
+            specs.append(f"'--no-{cli}[Disable {label}]'")
+    return specs
+
+
 # Mapping of completion types to bash completion expressions
 _BASH_COMPLETION_MAP = {
     CompletionType.FILES_PY: 'COMPREPLY=( $(compgen -f -X "!*.py" -- "${cur}") $(compgen -d -- "${cur}") )',
@@ -31,26 +63,7 @@ def _collect_all_options(cmd: Command, schema: CLISchema) -> List[str]:
 
         # MFC config flags
         if common_set.mfc_config_flags:
-            options.update(
-                [
-                    "--mpi",
-                    "--no-mpi",
-                    "--gpu",
-                    "--no-gpu",
-                    "--debug",
-                    "--no-debug",
-                    "--gcov",
-                    "--no-gcov",
-                    "--unified",
-                    "--no-unified",
-                    "--single",
-                    "--no-single",
-                    "--mixed",
-                    "--no-mixed",
-                    "--fastmath",
-                    "--no-fastmath",
-                ]
-            )
+            options.update(_mfc_config_bash_flags())
         else:
             for arg in common_set.arguments:
                 if arg.short:
@@ -324,26 +337,7 @@ def _generate_zsh_command_args(cmd: Command, schema: CLISchema) -> List[str]:
             continue
 
         if common_set.mfc_config_flags:
-            arg_lines.extend(
-                [
-                    "'--mpi[Enable MPI]'",
-                    "'--no-mpi[Disable MPI]'",
-                    "'--gpu[Enable GPU]:mode:(acc mp)'",
-                    "'--no-gpu[Disable GPU]'",
-                    "'--debug[Build with debug compiler flags (for MFC code)]'",
-                    "'--no-debug[Build without debug flags]'",
-                    "'--gcov[Enable gcov coverage]'",
-                    "'--no-gcov[Disable gcov coverage]'",
-                    "'--unified[Enable unified memory]'",
-                    "'--no-unified[Disable unified memory]'",
-                    "'--single[Enable single precision]'",
-                    "'--no-single[Disable single precision]'",
-                    "'--mixed[Enable mixed precision]'",
-                    "'--no-mixed[Disable mixed precision]'",
-                    "'--fastmath[Enable fast math]'",
-                    "'--no-fastmath[Disable fast math]'",
-                ]
-            )
+            arg_lines.extend(_mfc_config_zsh_flags())
         else:
             for arg in common_set.arguments:
                 desc = arg.help.replace("'", "").replace("[", "").replace("]", "")[:120]

toolchain/mfc/run/archive.py

@@ -11,6 +11,15 @@
 from ..state import ARG, CFG
 from . import input
 
+
+def _relpath_safe(path: str, dirpath: str) -> str:
+    """Return relpath(path, dirpath), falling back to basename on cross-device paths."""
+    try:
+        return os.path.relpath(path, dirpath)
+    except ValueError:
+        return os.path.basename(path)
+
+
 ARTIFACT_FILENAMES = [
     "equations.dat",
     "run_time.inf",
@@ -74,13 +83,7 @@ def __collect_sources(case: input.MFCInputFile, targets) -> list:
 
 def __build_manifest(case: input.MFCInputFile, targets, sources: list, archive_path: str, archive_format: str) -> dict:
     dirpath = case.dirpath
-    relative_sources = []
-    for src in sources:
-        try:
-            rel = os.path.relpath(src, dirpath)
-        except ValueError:
-            rel = src
-        relative_sources.append(rel)
+    relative_sources = [_relpath_safe(src, dirpath) for src in sources]
 
     return {
         "timestamp": datetime.datetime.now().astimezone().isoformat(),
@@ -101,11 +104,7 @@ def __copy_dir(sources: list, case: input.MFCInputFile, dest: str) -> None:
     dirpath = case.dirpath
 
     for src in sources:
-        try:
-            rel = os.path.relpath(src, dirpath)
-        except ValueError:
-            rel = os.path.basename(src)
-
+        rel = _relpath_safe(src, dirpath)
         target_path = os.path.join(dest, rel)
         os.makedirs(os.path.dirname(target_path), exist_ok=True)
 
@@ -120,10 +119,7 @@ def __write_tar(sources: list, case: input.MFCInputFile, dest: str, compressed:
     arcroot = os.path.basename(dest).removesuffix(".tar.zst").removesuffix(".tar")
 
     def rel_for(path: str) -> str:
-        try:
-            return os.path.relpath(path, dirpath)
-        except ValueError:
-            return os.path.basename(path)
+        return _relpath_safe(path, dirpath)
 
     if compressed:
         if not does_command_exist("tar"):

toolchain/mfc/run/input.py

@@ -47,17 +47,15 @@ def get_cantera_solution(self):
 
         if self.params.get("chemistry", "F") == "T":
             cantera_file = self.params["cantera_file"]
-
             candidates = [
                 cantera_file,
                 os.path.join(self.dirpath, cantera_file),
                 os.path.join(common.MFC_MECHANISMS_DIR, cantera_file),
             ]
         else:
-            # If Chemistry is turned off, we return a default (dummy) solution
-            # that will not be used in the simulation, so that MFC can still
-            # be compiled.
-            candidates = ["h2o2.yaml"]
+            # Chemistry is off — return a dummy solution so MFC still compiles.
+            cantera_file = "h2o2.yaml"
+            candidates = [cantera_file]
 
         for candidate in candidates:
             try: