Release 0.8.6

bedboss/_version.py

@@ -1 +1 @@
-__version__ = "0.8.5"
+__version__ = "0.8.6"

bedboss/refgenome_validator/refgenie_chrom_sizes.py

@@ -40,7 +40,7 @@ class Genomes(BaseModel):
     genomes: List[SeqColGenome]
 
 
-def run_requests(url, timeout=10) -> Any:
+def run_requests(url, timeout=60) -> Any:
     """
     Run a GET request to the specified URL and return the response.
     """
@@ -61,8 +61,10 @@ def get_genome_list() -> List[dict]:
     """
 
     genome_data = run_requests(GENOMES_URL)
-    return genome_data.get("items", [])
-
+    if genome_data:
+        return genome_data.get("items", [])
+    warnings.warn("Failed to fetch genomes from Refgenie, returning empty list.")
+    return []
 
 def seq_col_from_digest(digest: str) -> List[SeqCol]:
     """
@@ -128,6 +130,7 @@ def save_seq_col_to_json(genomes: Genomes, output_path: str = "genome_seqcol.jso
     """
 
     _LOGGER.info("Saving Refgenie genomes for later reuse...")
+    os.makedirs(os.path.dirname(output_path), exist_ok=True)
     with open(output_path, "w") as f:
         json.dump(genomes.model_dump(), f, indent=4)
     _LOGGER.info(f"Saved sequence collections to {output_path}")
@@ -143,6 +146,8 @@ def read_seq_col_from_json(input_path: str = "genome_seqcol.json") -> Genomes:
     Returns:
         Genomes object containing the sequence collections
     """
+
+    # os.makedirs(os.path.dirname(input_path), exist_ok=True)
     with open(input_path, "r") as f:
         data = json.load(f)
     return Genomes(**data)