build!: replace dill with pickle and allow python 3.15

.github/workflows/python-cqa.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.11", "3.12", "3.13", "3.14"]
+        python-version: ["3.11", "3.12", "3.13", "3.14", "3.15"]
     env:
       SEQREPO_ROOT_DIR: ./tests/data/seqrepo/latest
     steps:

pyproject.toml

@@ -22,6 +22,7 @@ classifiers = [
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: 3.14",
+    "Programming Language :: Python :: 3.15",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Scientific/Engineering :: Medical Science Apps.",
 ]
@@ -33,7 +34,7 @@ keywords = [
     "spdi",
     "variation"
 ]
-requires-python = ">=3.11,<3.15"
+requires-python = ">=3.11"
 dynamic = ["version"]
 dependencies = [
     "pydantic~=2.1",
@@ -49,7 +50,6 @@ extras = [
     "biocommons.seqrepo>=0.5.1",
     "bioutils>=0.5.2",
     "hgvs>=2.0.0a0,<3.0",
-    "dill~=0.3.7",
     "click",
     "pysam>=0.24.0",
 ]

src/ga4gh/vrs/extras/object_store.py

@@ -1,10 +1,9 @@
+import pickle
 import sqlite3
 from collections.abc import MutableMapping
 from threading import Lock
 from typing import Any
 
-import dill
-
 
 class Sqlite3MutableMapping(MutableMapping):
     """Class that can be used like a Python dictionary but that uses a sqlite3 database
@@ -59,7 +58,7 @@ def __delitem__(self, key: Any) -> None:
     def __setitem__(self, key: Any, value: Any) -> None:
         cur = self.db.cursor()
         try:
-            ser = dill.dumps(value)
+            ser = pickle.dumps(value)
             cur.execute(
                 "insert or replace into mapping(key, value) values (?, ?)",
                 (key, sqlite3.Binary(ser)),
@@ -75,7 +74,7 @@ def __getitem__(self, key: Any) -> Any:
             rows = cur.execute("select value from mapping where key = ?", (key,))
             row0 = next(rows)
             if row0:
-                return dill.loads(row0[0])  # noqa: S301
+                return pickle.loads(row0[0])  # noqa: S301
         except StopIteration as e:
             raise KeyError("Key not found: " + str(key)) from e
         finally:

tests/extras/test_object_store.py

@@ -55,23 +55,31 @@ def test_complex(tmp_path):
     object_store.close()
 
 
-def test_classes(tmp_path):
-    db_path = str(tmp_path) + "/test_complex.sqlite3"
+class StoredObject:
+    """Custom class for object store round-trip tests.
+
+    Defined at module level because pickle stores classes by reference, and a class
+    local to the test function can't be imported when unpickling.
+    """
+
+    def __init__(self, id_value):
+        """Initialize with an id and some nested attribute values."""
+        self.id = id_value
+        self.A = "A"
+        self.B = ["B1", "B2", 3]
+        self.C = {"C1": "C1-value"}
 
-    class TestClass:
-        def __init__(self, id_value):
-            self.id = id_value
-            self.A = "A"
-            self.B = ["B1", "B2", 3]
-            self.C = {"C1": "C1-value"}
+    def somefunction(self, arg):
+        return f"{self.id}-{arg}"
 
-        def somefunction(self, arg):
-            return f"{self.id}-{arg}"
+
+def test_classes(tmp_path):
+    db_path = str(tmp_path) + "/test_complex.sqlite3"
 
     object_store = Sqlite3MutableMapping(db_path)
 
-    val1 = TestClass("val1")
-    val2 = TestClass("val2")
+    val1 = StoredObject("val1")
+    val2 = StoredObject("val2")
     object_store["val1"] = val1
     object_store["val2"] = val2