From 75e52cc548779847ddeb7019e188253bac262ab3 Mon Sep 17 00:00:00 2001
From: mbsantiago <santiago.mbal@gmail.com>
Date: Tue, 5 May 2026 10:59:32 +0100
Subject: [PATCH] fix: keep checkpoint targets immutable

---
 src/batdetect2/api_v2.py         |  7 +++----
 src/batdetect2/cli/evaluate.py   |  7 -------
 src/batdetect2/cli/train.py      |  7 ++++++-
 tests/test_api_v2/test_api_v2.py |  5 +----
 tests/test_cli/test_train.py     | 21 +++++++++++++++++++++
 5 files changed, 31 insertions(+), 16 deletions(-)

diff --git a/src/batdetect2/api_v2.py b/src/batdetect2/api_v2.py
index 0513d63..0cee1d5 100644
--- a/src/batdetect2/api_v2.py
+++ b/src/batdetect2/api_v2.py
@@ -592,7 +592,6 @@ class BatDetect2API:
     def from_checkpoint(
         cls,
         path: data.PathLike,
-        targets_config: TargetConfig | None = None,
         audio_config: AudioConfig | None = None,
         train_config: TrainingConfig | None = None,
         evaluation_config: EvaluationConfig | None = None,
@@ -616,21 +615,21 @@ class BatDetect2API:
             build_targets,
             check_target_compatibility,
         )
-        from batdetect2.train import TrainingConfig, load_model_from_checkpoint
+        from batdetect2.train import load_model_from_checkpoint
 
         model, configs = load_model_from_checkpoint(path)
 
         model_config = configs.model
+        train_config = train_config or configs.train
 
         audio_config = audio_config or AudioConfig(
             samplerate=model_config.samplerate,
         )
-        train_config = train_config or TrainingConfig()
         evaluation_config = evaluation_config or EvaluationConfig()
         inference_config = inference_config or InferenceConfig()
         outputs_config = outputs_config or OutputsConfig()
         logging_config = logging_config or AppLoggingConfig()
-        targets_config = targets_config or configs.targets
+        targets_config = configs.targets
 
         targets = build_targets(config=targets_config)
         roi_mapper = build_roi_mapping(config=targets_config.roi)
diff --git a/src/batdetect2/cli/evaluate.py b/src/batdetect2/cli/evaluate.py
index 472be19..feaa9e1 100644
--- a/src/batdetect2/cli/evaluate.py
+++ b/src/batdetect2/cli/evaluate.py
@@ -106,7 +106,6 @@ def evaluate_command(
     from batdetect2.inference import InferenceConfig
     from batdetect2.logging import AppLoggingConfig
     from batdetect2.outputs import OutputsConfig
-    from batdetect2.targets import TargetConfig
 
     logger.info("Initiating evaluation process...")
 
@@ -120,11 +119,6 @@ def evaluate_command(
         num_annotations=len(test_annotations),
     )
 
-    target_conf = (
-        TargetConfig.load(targets_config)
-        if targets_config is not None
-        else None
-    )
     audio_conf = (
         AudioConfig.load(audio_config) if audio_config is not None else None
     )
@@ -151,7 +145,6 @@ def evaluate_command(
 
     api = BatDetect2API.from_checkpoint(
         model_path,
-        targets_config=target_conf,
         audio_config=audio_conf,
         evaluation_config=eval_conf,
         inference_config=inference_conf,
diff --git a/src/batdetect2/cli/train.py b/src/batdetect2/cli/train.py
index 4326e0c..1b428b7 100644
--- a/src/batdetect2/cli/train.py
+++ b/src/batdetect2/cli/train.py
@@ -228,6 +228,12 @@ def train_command(
             "Checkpoint model configuration is loaded from the checkpoint."
         )
 
+    if model_path is not None and target_conf is not None:
+        raise click.UsageError(
+            "--targets cannot be used with --model. "
+            "Checkpoint target configuration is loaded from the checkpoint."
+        )
+
     if model_path is None:
         api = BatDetect2API.from_config(
             model_config=model_conf,
@@ -242,7 +248,6 @@ def train_command(
     else:
         api = BatDetect2API.from_checkpoint(
             model_path,
-            targets_config=target_conf,
             train_config=train_conf,
             audio_config=audio_conf,
             evaluation_config=eval_conf,
diff --git a/tests/test_api_v2/test_api_v2.py b/tests/test_api_v2/test_api_v2.py
index e3fa01f..e2ffe31 100644
--- a/tests/test_api_v2/test_api_v2.py
+++ b/tests/test_api_v2/test_api_v2.py
@@ -287,10 +287,7 @@ def test_checkpoint_with_same_targets_config_keeps_heads_unchanged(
     source_detector = cast(Detector, source_model.detector)
 
     # When
-    api = BatDetect2API.from_checkpoint(
-        checkpoint_path,
-        targets_config=example_targets_config,
-    )
+    api = BatDetect2API.from_checkpoint(checkpoint_path)
 
     # Then
     detector = cast(Detector, api.model.detector)
diff --git a/tests/test_cli/test_train.py b/tests/test_cli/test_train.py
index 2212a57..5fd0210 100644
--- a/tests/test_cli/test_train.py
+++ b/tests/test_cli/test_train.py
@@ -81,3 +81,24 @@ def test_cli_train_rejects_model_and_model_config_together(
 
     assert result.exit_code != 0
     assert "--model-config cannot be used with --model" in result.output
+
+
+def test_cli_train_rejects_model_and_targets_together(
+    tiny_checkpoint_path: Path,
+) -> None:
+    """User story: checkpoint training does not accept new targets."""
+
+    result = CliRunner().invoke(
+        cli,
+        [
+            "train",
+            "example_data/dataset.yaml",
+            "--model",
+            str(tiny_checkpoint_path),
+            "--targets",
+            "example_data/targets.yaml",
+        ],
+    )
+
+    assert result.exit_code != 0
+    assert "--targets cannot be used with --model" in result.output