Chore(pt): refactor the command function interface (#4225)

Fix #3934.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Enhanced clarity and usability of the training process with explicit
parameters for model training, freezing, and bias changing functions.
- Improved function interfaces streamline user interactions and
understanding.

- **Bug Fixes**
- Resolved issues related to parameter handling by transitioning from a
flags-based system to a more structured approach.

- **Refactor**
- Updated function signatures for better readability and
maintainability, improving the overall structure of the code.
- Simplified the freezing mechanism in tests by removing the use of a
`Namespace` object.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

deepmd/pt/entrypoints/main.py

@@ -239,16 +239,27 @@ def get_backend_info(self) -> dict:
         }
 
 
-def train(FLAGS):
-    log.info("Configuration path: %s", FLAGS.INPUT)
+def train(
+    input_file: str,
+    init_model: Optional[str],
+    restart: Optional[str],
+    finetune: Optional[str],
+    init_frz_model: Optional[str],
+    model_branch: str,
+    skip_neighbor_stat: bool = False,
+    use_pretrain_script: bool = False,
+    force_load: bool = False,
+    output: str = "out.json",
+):
+    log.info("Configuration path: %s", input_file)
     SummaryPrinter()()
-    with open(FLAGS.INPUT) as fin:
+    with open(input_file) as fin:
         config = json.load(fin)
     # ensure suffix, as in the command line help, we say "path prefix of checkpoint files"
-    if FLAGS.init_model is not None and not FLAGS.init_model.endswith(".pt"):
-        FLAGS.init_model += ".pt"
-    if FLAGS.restart is not None and not FLAGS.restart.endswith(".pt"):
-        FLAGS.restart += ".pt"
+    if init_model is not None and not init_model.endswith(".pt"):
+        init_model += ".pt"
+    if restart is not None and not restart.endswith(".pt"):
+        restart += ".pt"
 
     # update multitask config
     multi_task = "model_dict" in config["model"]
@@ -262,26 +273,24 @@ def train(FLAGS):
 
     # update fine-tuning config
     finetune_links = None
-    if FLAGS.finetune is not None:
+    if finetune is not None:
         config["model"], finetune_links = get_finetune_rules(
-            FLAGS.finetune,
+            finetune,
             config["model"],
-            model_branch=FLAGS.model_branch,
-            change_model_params=FLAGS.use_pretrain_script,
+            model_branch=model_branch,
+            change_model_params=use_pretrain_script,
         )
     # update init_model or init_frz_model config if necessary
-    if (
-        FLAGS.init_model is not None or FLAGS.init_frz_model is not None
-    ) and FLAGS.use_pretrain_script:
-        if FLAGS.init_model is not None:
-            init_state_dict = torch.load(FLAGS.init_model, map_location=DEVICE)
+    if (init_model is not None or init_frz_model is not None) and use_pretrain_script:
+        if init_model is not None:
+            init_state_dict = torch.load(init_model, map_location=DEVICE)
             if "model" in init_state_dict:
                 init_state_dict = init_state_dict["model"]
             config["model"] = init_state_dict["_extra_state"]["model_params"]
         else:
             config["model"] = json.loads(
                 torch.jit.load(
-                    FLAGS.init_frz_model, map_location=DEVICE
+                    init_frz_model, map_location=DEVICE
                 ).get_model_def_script()
             )
 
@@ -291,7 +300,7 @@ def train(FLAGS):
 
     # do neighbor stat
     min_nbor_dist = None
-    if not FLAGS.skip_neighbor_stat:
+    if not skip_neighbor_stat:
         log.info(
             "Calculate neighbor statistics... (add --skip-neighbor-stat to skip this step)"
         )
@@ -320,16 +329,16 @@ def train(FLAGS):
                     )
                 )
 
-    with open(FLAGS.output, "w") as fp:
+    with open(output, "w") as fp:
         json.dump(config, fp, indent=4)
 
     trainer = get_trainer(
         config,
-        FLAGS.init_model,
-        FLAGS.restart,
-        FLAGS.finetune,
-        FLAGS.force_load,
-        FLAGS.init_frz_model,
+        init_model,
+        restart,
+        finetune,
+        force_load,
+        init_frz_model,
         shared_links=shared_links,
         finetune_links=finetune_links,
     )
@@ -343,26 +352,39 @@ def train(FLAGS):
     trainer.run()
 
 
-def freeze(FLAGS):
-    model = inference.Tester(FLAGS.model, head=FLAGS.head).model
+def freeze(
+    model: str,
+    output: str = "frozen_model.pth",
+    head: Optional[str] = None,
+):
+    model = inference.Tester(model, head=head).model
     model.eval()
     model = torch.jit.script(model)
     extra_files = {}
     torch.jit.save(
         model,
-        FLAGS.output,
+        output,
         extra_files,
     )
-    log.info(f"Saved frozen model to {FLAGS.output}")
-
-
-def change_bias(FLAGS):
-    if FLAGS.INPUT.endswith(".pt"):
-        old_state_dict = torch.load(FLAGS.INPUT, map_location=env.DEVICE)
+    log.info(f"Saved frozen model to {output}")
+
+
+def change_bias(
+    input_file: str,
+    mode: str = "change",
+    bias_value: Optional[list] = None,
+    datafile: Optional[str] = None,
+    system: str = ".",
+    numb_batch: int = 0,
+    model_branch: Optional[str] = None,
+    output: Optional[str] = None,
+):
+    if input_file.endswith(".pt"):
+        old_state_dict = torch.load(input_file, map_location=env.DEVICE)
         model_state_dict = copy.deepcopy(old_state_dict.get("model", old_state_dict))
         model_params = model_state_dict["_extra_state"]["model_params"]
-    elif FLAGS.INPUT.endswith(".pth"):
-        old_model = torch.jit.load(FLAGS.INPUT, map_location=env.DEVICE)
+    elif input_file.endswith(".pth"):
+        old_model = torch.jit.load(input_file, map_location=env.DEVICE)
         model_params_string = old_model.get_model_def_script()
         model_params = json.loads(model_params_string)
         old_state_dict = old_model.state_dict()
@@ -373,10 +395,7 @@ def change_bias(FLAGS):
             "or a frozen model with a .pth extension"
         )
     multi_task = "model_dict" in model_params
-    model_branch = FLAGS.model_branch
-    bias_adjust_mode = (
-        "change-by-statistic" if FLAGS.mode == "change" else "set-by-statistic"
-    )
+    bias_adjust_mode = "change-by-statistic" if mode == "change" else "set-by-statistic"
     if multi_task:
         assert (
             model_branch is not None
@@ -393,24 +412,24 @@ def change_bias(FLAGS):
         else model_params["model_dict"][model_branch]["type_map"]
     )
     model_to_change = model if not multi_task else model[model_branch]
-    if FLAGS.INPUT.endswith(".pt"):
+    if input_file.endswith(".pt"):
         wrapper = ModelWrapper(model)
         wrapper.load_state_dict(old_state_dict["model"])
     else:
         # for .pth
         model.load_state_dict(old_state_dict)
 
-    if FLAGS.bias_value is not None:
+    if bias_value is not None:
         # use user-defined bias
         assert model_to_change.model_type in [
             "ener"
         ], "User-defined bias is only available for energy model!"
         assert (
-            len(FLAGS.bias_value) == len(type_map)
+            len(bias_value) == len(type_map)
         ), f"The number of elements in the bias should be the same as that in the type_map: {type_map}."
         old_bias = model_to_change.get_out_bias()
         bias_to_set = torch.tensor(
-            FLAGS.bias_value, dtype=old_bias.dtype, device=old_bias.device
+            bias_value, dtype=old_bias.dtype, device=old_bias.device
         ).view(old_bias.shape)
         model_to_change.set_out_bias(bias_to_set)
         log.info(
@@ -421,11 +440,11 @@ def change_bias(FLAGS):
         updated_model = model_to_change
     else:
         # calculate bias on given systems
-        if FLAGS.datafile is not None:
-            with open(FLAGS.datafile) as datalist:
+        if datafile is not None:
+            with open(datafile) as datalist:
                 all_sys = datalist.read().splitlines()
         else:
-            all_sys = expand_sys_str(FLAGS.system)
+            all_sys = expand_sys_str(system)
         data_systems = process_systems(all_sys)
         data_single = DpLoaderSet(
             data_systems,
@@ -438,7 +457,7 @@ def change_bias(FLAGS):
         data_requirement = mock_loss.label_requirement
         data_requirement += training.get_additional_data_requirement(model_to_change)
         data_single.add_data_requirement(data_requirement)
-        nbatches = FLAGS.numb_batch if FLAGS.numb_batch != 0 else float("inf")
+        nbatches = numb_batch if numb_batch != 0 else float("inf")
         sampled_data = make_stat_input(
             data_single.systems,
             data_single.dataloaders,
@@ -453,11 +472,9 @@ def change_bias(FLAGS):
     else:
         model[model_branch] = updated_model
 
-    if FLAGS.INPUT.endswith(".pt"):
+    if input_file.endswith(".pt"):
         output_path = (
-            FLAGS.output
-            if FLAGS.output is not None
-            else FLAGS.INPUT.replace(".pt", "_updated.pt")
+            output if output is not None else input_file.replace(".pt", "_updated.pt")
         )
         wrapper = ModelWrapper(model)
         if "model" in old_state_dict:
@@ -470,9 +487,7 @@ def change_bias(FLAGS):
     else:
         # for .pth
         output_path = (
-            FLAGS.output
-            if FLAGS.output is not None
-            else FLAGS.INPUT.replace(".pth", "_updated.pth")
+            output if output is not None else input_file.replace(".pth", "_updated.pth")
         )
         model = torch.jit.script(model)
         torch.jit.save(
@@ -499,7 +514,18 @@ def main(args: Optional[Union[list[str], argparse.Namespace]] = None):
     log.info("DeePMD version: %s", __version__)
 
     if FLAGS.command == "train":
-        train(FLAGS)
+        train(
+            input_file=FLAGS.INPUT,
+            init_model=FLAGS.init_model,
+            restart=FLAGS.restart,
+            finetune=FLAGS.finetune,
+            init_frz_model=FLAGS.init_frz_model,
+            model_branch=FLAGS.model_branch,
+            skip_neighbor_stat=FLAGS.skip_neighbor_stat,
+            use_pretrain_script=FLAGS.use_pretrain_script,
+            force_load=FLAGS.force_load,
+            output=FLAGS.output,
+        )
     elif FLAGS.command == "freeze":
         if Path(FLAGS.checkpoint_folder).is_dir():
             checkpoint_path = Path(FLAGS.checkpoint_folder)
@@ -508,9 +534,18 @@ def main(args: Optional[Union[list[str], argparse.Namespace]] = None):
         else:
             FLAGS.model = FLAGS.checkpoint_folder
         FLAGS.output = str(Path(FLAGS.output).with_suffix(".pth"))
-        freeze(FLAGS)
+        freeze(model=FLAGS.model, output=FLAGS.output, head=FLAGS.head)
     elif FLAGS.command == "change-bias":
-        change_bias(FLAGS)
+        change_bias(
+            input_file=FLAGS.INPUT,
+            mode=FLAGS.mode,
+            bias_value=FLAGS.bias_value,
+            datafile=FLAGS.datafile,
+            system=FLAGS.system,
+            numb_batch=FLAGS.numb_batch,
+            model_branch=FLAGS.model_branch,
+            output=FLAGS.output,
+        )
     else:
         raise RuntimeError(f"Invalid command {FLAGS.command}!")
 

source/tests/pt/model/test_deeppot.py

@@ -2,9 +2,6 @@
 import json
 import os
 import unittest
-from argparse import (
-    Namespace,
-)
 from copy import (
     deepcopy,
 )
@@ -123,12 +120,11 @@ class TestDeepPotFrozen(TestDeepPot):
     def setUp(self):
         super().setUp()
         frozen_model = "frozen_model.pth"
-        ns = Namespace(
+        freeze(
             model=self.model,
             output=frozen_model,
             head=None,
         )
-        freeze(ns)
         self.model = frozen_model
 
     # Note: this can not actually disable cuda device to be used

source/tests/pt/test_init_frz_model.py

@@ -4,9 +4,6 @@
 import shutil
 import tempfile
 import unittest
-from argparse import (
-    Namespace,
-)
 from copy import (
     deepcopy,
 )
@@ -70,12 +67,11 @@ def setUp(self):
 
             if imodel in [0, 1]:
                 trainer.run()
-            ns = Namespace(
+            freeze(
                 model="model.pt",
                 output=frozen_model,
                 head=None,
             )
-            freeze(ns)
             self.models.append(frozen_model)
 
     def test_dp_test(self):