fix: update default init values for benchmarker (#203)

* update to bio_conservation_metrics, batch_correction_metrics deafult values

* added log and test

* typo

Author: ori-kron-wis

CHANGELOG.md

@@ -10,11 +10,17 @@ and this project adheres to [Semantic Versioning][].
 
 ## 0.6.0 (unreleased)
 
+## 0.5.4 (2025-04-23)
+
+### Fixed
+
+- Apply default values for benchmarker metrics {pr}`203`.
+
 ## 0.5.3 (2025-02-17)
 
-#### Removed
+### Removed
 
-- Reverted the change for scib-autotune in scvi-tools {pr}`189`.
+- Reverted a change that was needed for scib-autotune in scvi-tools {pr}`189`.
 
 ## 0.5.2 (2025-02-13)
 

pyproject.toml

@@ -5,7 +5,7 @@ requires = ["hatchling"]
 
 [project]
 name = "scib-metrics"
-version = "0.5.3"
+version = "0.5.4"
 description = "Accelerated and Python-only scIB metrics"
 readme = "README.md"
 requires-python = ">=3.10"

src/scib_metrics/benchmark/_core.py

@@ -136,8 +136,8 @@ def __init__(
         batch_key: str,
         label_key: str,
         embedding_obsm_keys: list[str],
-        bio_conservation_metrics: BioConservation | None,
-        batch_correction_metrics: BatchCorrection | None,
+        bio_conservation_metrics: BioConservation | None = BioConservation(),
+        batch_correction_metrics: BatchCorrection | None = BatchCorrection(),
         pre_integrated_embedding_obsm_key: str | None = None,
         n_jobs: int = 1,
         progress_bar: bool = True,

tests/test_benchmarker.py

@@ -21,6 +21,20 @@ def test_benchmarker():
     bm.plot_results_table()
 
 
+def test_benchmarker_default():
+    ad, emb_keys, batch_key, labels_key = dummy_benchmarker_adata()
+    bm = Benchmarker(
+        ad,
+        batch_key,
+        labels_key,
+        emb_keys,
+    )
+    bm.benchmark()
+    results = bm.get_results()
+    assert isinstance(results, pd.DataFrame)
+    bm.plot_results_table()
+
+
 def test_benchmarker_custom_metric_booleans():
     bioc = BioConservation(
         isolated_labels=False, nmi_ari_cluster_labels_leiden=False, silhouette_label=False, clisi_knn=True