Emit a warning about local alleles in CLI

Closes #304

Author: jeromekelleher

bio2zarr/cli.py

@@ -339,6 +339,11 @@ def mkschema(icf_path, variants_chunk_size, samples_chunk_size, local_alleles):
     """
     Generate a schema for zarr encoding
     """
+    if local_alleles:
+        click.echo(
+            "WARNING: Local alleles support is preliminary; please use with caution.",
+            err=True,
+        )
     stream = click.get_text_stream("stdout")
     vcf2zarr.mkschema(
         icf_path,

tests/test_cli.py

@@ -729,6 +729,9 @@ def test_mkschema_local_alleles(self, tmp_path, local_alleles):
         d = json.loads(result.stdout)
         call_LA_exists = "call_LA" in [f["name"] for f in d["fields"]]
         assert call_LA_exists == local_alleles
+        assert (
+            "WARNING: Local alleles support is preliminary;" in result.stderr
+        ) == local_alleles
 
     def test_encode(self, tmp_path):
         icf_path = tmp_path / "icf"