fix(l2g): direct model path to hf repo when none and align training d…

…ata filename (#997) * fix(model): typo in filename when uploading training data to hub * fix(l2g): direct model to hf repo when path is none * fix: run_train to keep GS and geneId * chore: pre-commit auto fixes [...] --------- Co-authored-by: xyg123 <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
opentargets · Feb 20, 2025 · 198019f · 198019f
1 parent 2f86159
commit 198019f
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Showing 2 changed files with 7 additions and 5 deletions.
diff --git a/src/gentropy/l2g.py b/src/gentropy/l2g.py
@@ -151,7 +151,6 @@ def __init__(
 
         self.session = session
         self.run_mode = run_mode
-        self.model_path = model_path
         self.predictions_path = predictions_path
         self.features_list = list(features_list) if features_list else None
         self.hyperparameters = dict(hyperparameters)
@@ -164,6 +163,11 @@ def __init__(
         self.gold_standard_curation_path = gold_standard_curation_path
         self.gene_interactions_path = gene_interactions_path
         self.variant_index_path = variant_index_path
+        self.model_path = (
+            hf_hub_repo_id
+            if not model_path and download_from_hub and hf_hub_repo_id
+            else model_path
+        )
 
         # Load common inputs
         self.credible_set = StudyLocus.from_parquet(
@@ -333,9 +337,7 @@ def run_train(self) -> None:
                     # we upload the model saved in the filesystem
                     self.model_path.split("/")[-1],
                     hf_hub_token,
-                    data=trained_model.training_data._df.drop(
-                        "goldStandardSet", "geneId"
-                    ).toPandas(),
+                    data=trained_model.training_data._df.toPandas(),
                     repo_id=self.hf_hub_repo_id,
                     commit_message=self.hf_model_commit_message,
                 )

diff --git a/src/gentropy/method/l2g/model.py b/src/gentropy/method/l2g/model.py
@@ -325,7 +325,7 @@ def export_to_hugging_face_hub(
                 data=data,
             )
             self._create_hugging_face_model_card(local_repo)
-            data.to_parquet(f"{local_repo}/training_set.parquet")
+            data.to_parquet(f"{local_repo}/training_data.parquet")
             hub_utils.push(
                 repo_id=repo_id,
                 source=local_repo,