fix on l2g step mypy

opentargets · Dec 17, 2024 · 8140d5a · 8140d5a
1 parent 0eea3aa
commit 8140d5a
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Showing 2 changed files with 12 additions and 19 deletions.
diff --git a/src/gentropy/config.py b/src/gentropy/config.py
@@ -17,8 +17,7 @@ class SessionConfig:
     write_mode: str = "errorifexists"
     spark_uri: str = "local[*]"
     hail_home: str = os.path.dirname(hail_location)
-    extended_spark_conf: dict[str, str] | None = field(
-        default_factory=dict[str, str])
+    extended_spark_conf: dict[str, str] | None = field(default_factory=dict[str, str])
     output_partitions: int = 200
     _target_: str = "gentropy.common.session.Session"
 
@@ -40,8 +39,7 @@ class ColocalisationConfig(StepConfig):
     credible_set_path: str = MISSING
     coloc_path: str = MISSING
     colocalisation_method: str = MISSING
-    colocalisation_method_params: dict[str, Any] = field(
-        default_factory=dict[str, Any])
+    colocalisation_method_params: dict[str, Any] = field(default_factory=dict[str, Any])
     _target_: str = "gentropy.colocalisation.ColocalisationStep"
 
 
@@ -126,8 +124,7 @@ class EqtlCatalogueConfig(StepConfig):
     eqtl_catalogue_paths_imported: str = MISSING
     eqtl_catalogue_study_index_out: str = MISSING
     eqtl_catalogue_credible_sets_out: str = MISSING
-    mqtl_quantification_methods_blacklist: list[str] = field(
-        default_factory=lambda: [])
+    mqtl_quantification_methods_blacklist: list[str] = field(default_factory=lambda: [])
     eqtl_lead_pvalue_threshold: float = 1e-3
     _target_: str = "gentropy.eqtl_catalogue.EqtlCatalogueStep"
 
@@ -313,6 +310,7 @@ class LocusToGeneFeatureMatrixConfig(StepConfig):
     colocalisation_path: str | None = None
     study_index_path: str | None = None
     gene_index_path: str | None = None
+    interval_path: str | None = None
     feature_matrix_path: str = MISSING
     features_list: list[str] = field(
         default_factory=lambda: [
@@ -688,8 +686,7 @@ class Config:
     """Application configuration."""
 
     # this is unfortunately verbose due to @dataclass limitations
-    defaults: List[Any] = field(default_factory=lambda: [
-                                "_self_", {"step": MISSING}])
+    defaults: List[Any] = field(default_factory=lambda: ["_self_", {"step": MISSING}])
     step: StepConfig = MISSING
     datasets: dict[str, str] = field(default_factory=dict)
 
@@ -723,8 +720,7 @@ def register_config() -> None:
         name="gwas_catalog_top_hit_ingestion",
         node=GWASCatalogTopHitIngestionConfig,
     )
-    cs.store(group="step", name="ld_based_clumping",
-             node=LDBasedClumpingConfig)
+    cs.store(group="step", name="ld_based_clumping", node=LDBasedClumpingConfig)
     cs.store(group="step", name="ld_index", node=LDIndexConfig)
     cs.store(group="step", name="locus_to_gene", node=LocusToGeneConfig)
     cs.store(
@@ -742,8 +738,7 @@ def register_config() -> None:
 
     cs.store(group="step", name="pics", node=PICSConfig)
     cs.store(group="step", name="gnomad_variants", node=GnomadVariantConfig)
-    cs.store(group="step", name="ukb_ppp_eur_sumstat_preprocess",
-             node=UkbPppEurConfig)
+    cs.store(group="step", name="ukb_ppp_eur_sumstat_preprocess", node=UkbPppEurConfig)
     cs.store(group="step", name="variant_index", node=VariantIndexConfig)
     cs.store(group="step", name="variant_to_vcf", node=ConvertToVcfStepConfig)
     cs.store(
@@ -776,7 +771,5 @@ def register_config() -> None:
         name="locus_to_gene_associations",
         node=LocusToGeneAssociationsStepConfig,
     )
-    cs.store(group="step", name="finngen_ukb_meta_ingestion",
-             node=FinngenUkbMetaConfig)
-    cs.store(group="step", name="credible_set_qc",
-             node=CredibleSetQCStepConfig)
+    cs.store(group="step", name="finngen_ukb_meta_ingestion", node=FinngenUkbMetaConfig)
+    cs.store(group="step", name="credible_set_qc", node=CredibleSetQCStepConfig)
diff --git a/src/gentropy/l2g.py b/src/gentropy/l2g.py
@@ -139,7 +139,7 @@ def __init__(
             variant_index_path (str | None): Path to the variant index
             gene_interactions_path (str | None): Path to the gene interactions dataset
             gene_index_path (str | None = None):  Path to the gene index
-            interval_path (dict[str, str] | None) : Path and source of interval input datasets
+            interval_path (str | None = None) : Path and source of interval input datasets
             predictions_path (str | None): Path to the L2G predictions output dataset
             l2g_threshold (float | None): An optional threshold for the L2G score to filter predictions. A threshold of 0.05 is recommended.
             hf_hub_repo_id (str | None): Hugging Face Hub repository ID. If provided, the model will be uploaded to Hugging Face.
@@ -181,8 +181,8 @@ def __init__(
             if gene_index_path
             else None
         )
-        self.intervals = Intervals.from_parquet(
-            session, interval_path, recursiveFileLookup=True
+        self.intervals = (
+            Intervals.from_parquet(session, interval_path) if interval_path else None
         )
 
         if run_mode == "predict":