From 8ddf51ac3b8e0c23a0edafa792f147c149f4951f Mon Sep 17 00:00:00 2001
From: developer-rpai <developer-rpai@users.noreply.github.com>
Date: Wed, 23 Sep 2026 23:19:44 -0700
Subject: [PATCH 1/2] fix: ga4gh_identify respects in_place=never for digest
 fields

With in_place="never", ga4gh_identify computed digests on the live
object: compute_digest() stores the digest on the object itself and the
serialization step stores digests on every nested identifiable object
(e.g. SequenceLocation). As a result the input object was mutated even
though the caller asked for no in-place edits.

Compute the identifier on a deep copy when in_place is "never", so the
caller's object (including its digest fields) is left byte-identical and
the only output is the returned identifier string. The "default" and
"always" modes are unchanged.

Closes #440
---
 src/ga4gh/vrs/models.py | 11 +++++++++--
 tests/test_vrs.py       | 32 ++++++++++++++++++++++++++++++++
 2 files changed, 41 insertions(+), 2 deletions(-)

diff --git a/src/ga4gh/vrs/models.py b/src/ga4gh/vrs/models.py
index ad2978d5..8acdf33e 100644
--- a/src/ga4gh/vrs/models.py
+++ b/src/ga4gh/vrs/models.py
@@ -11,6 +11,7 @@
     module name, e.g., `ga4gh.vrs.models.Allele`
 """
 
+import copy
 import inspect
 import sys
 from abc import ABC
@@ -327,7 +328,10 @@ def get_or_create_ga4gh_identifier(
         - 'always': this will update the vro.id field any time the
             identifier is computed
         - 'never': the vro.id field will not be edited in-place,
-            even when empty
+            even when empty. The vro object is not mutated in any way:
+            digest computation is performed on a deep copy, so neither
+            the vro.digest field nor digest fields on nested objects
+            are set.
 
         Digests will be recalculated even if present if recompute is True.
 
@@ -344,7 +348,10 @@ def get_or_create_ga4gh_identifier(
         elif in_place == "always":
             self.id = self.compute_ga4gh_identifier(recompute)
         elif in_place == "never":
-            return self.compute_ga4gh_identifier(recompute)
+            # Digest computation stores digests on the object and its nested
+            # identifiable objects, so compute on a deep copy to leave the
+            # caller's object (including its digest fields) untouched.
+            return copy.deepcopy(self).compute_ga4gh_identifier(recompute)
         else:
             msg = "Expected 'in_place' to be one of 'default', 'always', or 'never'"
             raise ValueError(msg)
diff --git a/tests/test_vrs.py b/tests/test_vrs.py
index 975854ab..ae5d120a 100644
--- a/tests/test_vrs.py
+++ b/tests/test_vrs.py
@@ -194,6 +194,38 @@ def test_cpb():
     assert ga4gh_identify(cpb_431012) == "ga4gh:CPB.x8GH5G73cPMs37jy1-9mJjWynu324rxI"
 
 
+def test_identify_in_place_never_does_not_mutate():
+    """ga4gh_identify(..., in_place="never") must not mutate the input object.
+
+    Regression test for https://github.com/ga4gh/vrs-python/issues/440:
+    digest computation used to set `digest` fields on the object and its
+    nested identifiable objects even when in_place="never".
+    """
+    allele = models.Allele(**allele_dict)
+    before = allele.model_dump_json(exclude_none=True)
+    assert allele.digest is None
+    assert allele.location.digest is None
+
+    obj_id = ga4gh_identify(allele, in_place="never")
+
+    assert obj_id == "ga4gh:VA.Hy2XU_-rp4IMh6I_1NXNecBo8Qx8n0oE"
+    assert allele.id is None
+    assert allele.digest is None
+    assert allele.location.digest is None
+    assert allele.model_dump_json(exclude_none=True) == before
+
+
+def test_identify_in_place_modes_still_mutate():
+    """Sanity check: in_place="default"/"always" keep their mutating behavior."""
+    allele = models.Allele(**allele_dict)
+    assert ga4gh_identify(allele, in_place="default") == "ga4gh:VA.Hy2XU_-rp4IMh6I_1NXNecBo8Qx8n0oE"
+    assert allele.id == "ga4gh:VA.Hy2XU_-rp4IMh6I_1NXNecBo8Qx8n0oE"
+
+    allele = models.Allele(**allele_dict)
+    assert ga4gh_identify(allele, in_place="always") == "ga4gh:VA.Hy2XU_-rp4IMh6I_1NXNecBo8Qx8n0oE"
+    assert allele.id == "ga4gh:VA.Hy2XU_-rp4IMh6I_1NXNecBo8Qx8n0oE"
+
+
 def test_ga4gh_iri():
     iri = models.iriReference.model_construct(
         "ga4gh:VA.Hy2XU_-rp4IMh6I_1NXNecBo8Qx8n0oE"

From e246e0ea4b8bb0abd9476c076b82629825d6b69d Mon Sep 17 00:00:00 2001
From: Rakesh Pai <41351936+developer-rpai@users.noreply.github.com>
Date: Thu, 24 Sep 2026 09:15:21 -0700
Subject: [PATCH 2/2] style: apply ruff format (fix lint CI)

---
 tests/test_vrs.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/tests/test_vrs.py b/tests/test_vrs.py
index ae5d120a..add14df4 100644
--- a/tests/test_vrs.py
+++ b/tests/test_vrs.py
@@ -218,11 +218,17 @@ def test_identify_in_place_never_does_not_mutate():
 def test_identify_in_place_modes_still_mutate():
     """Sanity check: in_place="default"/"always" keep their mutating behavior."""
     allele = models.Allele(**allele_dict)
-    assert ga4gh_identify(allele, in_place="default") == "ga4gh:VA.Hy2XU_-rp4IMh6I_1NXNecBo8Qx8n0oE"
+    assert (
+        ga4gh_identify(allele, in_place="default")
+        == "ga4gh:VA.Hy2XU_-rp4IMh6I_1NXNecBo8Qx8n0oE"
+    )
     assert allele.id == "ga4gh:VA.Hy2XU_-rp4IMh6I_1NXNecBo8Qx8n0oE"
 
     allele = models.Allele(**allele_dict)
-    assert ga4gh_identify(allele, in_place="always") == "ga4gh:VA.Hy2XU_-rp4IMh6I_1NXNecBo8Qx8n0oE"
+    assert (
+        ga4gh_identify(allele, in_place="always")
+        == "ga4gh:VA.Hy2XU_-rp4IMh6I_1NXNecBo8Qx8n0oE"
+    )
     assert allele.id == "ga4gh:VA.Hy2XU_-rp4IMh6I_1NXNecBo8Qx8n0oE"