feat: add deprecation warning for beacon translation (#578)

close #568

* One of the Beacon leads (@mbaudis) requested this to be removed since
it does not follow the standard, for now we will add a deprecation
message and remove this in v3.
* Added `typing_extensions` as an `extras` dep

Author: korikuzma

pyproject.toml

@@ -53,6 +53,7 @@ extras = [
     "dill~=0.3.7",
     "click",
     "pysam==0.23.0",  # pinned pending https://github.com/ga4gh/vrs-python/issues/560
+    "typing_extensions",
 ]
 dev = [
     # tests

src/ga4gh/vrs/extras/translator.py

@@ -11,6 +11,8 @@
 from collections.abc import Mapping
 from typing import Protocol
 
+from typing_extensions import deprecated
+
 from ga4gh.core import ga4gh_identify
 from ga4gh.vrs import models, normalize
 from ga4gh.vrs.dataproxy import SequenceProxy, _DataProxy
@@ -213,6 +215,7 @@ def _create_allele(self, values: dict, **kwargs) -> models.Allele:
         allele = models.Allele(location=location, state=state)
         return self._post_process_imported_allele(allele, **kwargs)
 
+    @deprecated("This method does not match the Beacon spec and will be removed in v3.")
     def _from_beacon(self, beacon_expr: str, **kwargs) -> models.Allele | None:
         """Parse beacon expression into VRS Allele
 

tests/extras/test_allele_translator.py

@@ -335,18 +335,21 @@ def test_from_invalid(tlr):
 @pytest.mark.vcr
 def test_from_beacon(tlr):
     do_normalize = False
-    assert (
-        tlr._from_beacon(snv_inputs["beacon"], do_normalize=do_normalize).model_dump(
-            exclude_none=True
+    with pytest.deprecated_call():
+        assert (
+            tlr._from_beacon(
+                snv_inputs["beacon"], do_normalize=do_normalize
+            ).model_dump(exclude_none=True)
+            == snv_output
         )
-        == snv_output
-    )
-    assert (
-        tlr._from_beacon(mito_inputs["beacon"], do_normalize=do_normalize).model_dump(
-            exclude_none=True
+
+    with pytest.deprecated_call():
+        assert (
+            tlr._from_beacon(
+                mito_inputs["beacon"], do_normalize=do_normalize
+            ).model_dump(exclude_none=True)
+            == mito_output
         )
-        == mito_output
-    )
 
 
 @pytest.mark.vcr