debugging trial: add use external command onmt from cli

setup.cfg

@@ -28,8 +28,8 @@ install_requires =
     click>=8.0
     pandas>=1.1.0
     rxn-chem-utils>=1.3.0
-    rxn-onmt-models>=1.0.0
-    rxn-onmt-utils>=1.0.0
+    rxn-onmt-models@git+https://github.com/rxn4chemistry/rxn-onmt-models.git@519a7c89af3bd68c96ec086795ff1729866db161
+    rxn-onmt-utils@git+https://github.com/rxn4chemistry/rxn-onmt-utils.git@f1a0b970411aac308a3cba36c942297933a4dd91
     rxn-utils>=1.1.9
 
 [options.packages.find]

src/rxn/metrics/run_metrics.py

@@ -68,6 +68,7 @@ def run_model_for_metrics(
     batch_size: int,
     gpu: bool,
     initialize_logger: bool = False,
+    as_external_command: bool = False,
 ) -> None:
     ensure_directory_exists_and_is_empty(output_dir)
     files = get_metrics_files(task, output_dir)
@@ -88,6 +89,7 @@ def run_model_for_metrics(
         beam_size=beam_size,
         batch_size=batch_size,
         gpu=gpu,
+        as_external_command=as_external_command,
     )
 
     canonicalize_file(

src/rxn/metrics/scripts/prepare_forward_metrics.py

@@ -38,6 +38,9 @@
 @click.option(
     "--no_metrics", is_flag=True, help="If given, the metrics will not be computed."
 )
+@click.option(
+    "--as_external_command", type=bool, default=False, help="Run translation as external ONMT command"
+)
 def main(
     precursors_file: Path,
     products_file: Path,
@@ -47,6 +50,7 @@ def main(
     n_best: int,
     gpu: bool,
     no_metrics: bool,
+    as_external_command: bool,
 ) -> None:
     """Starting from the ground truth files and forward model, generate the
     translation files needed for the metrics, and calculate the default metrics."""
@@ -62,6 +66,7 @@ def main(
         batch_size=batch_size,
         gpu=gpu,
         initialize_logger=True,
+        as_external_command=as_external_command,
     )
 
     if not no_metrics: