build!: require python >=3.11, remove dill dependency

.binder/postBuild

@@ -2,5 +2,5 @@
 set -e
 
 make devready
-source venv/3.12/bin/activate
-python -m ipykernel install --user --name=3.12 --display-name="VRS_kernel"
+source venv/3.14/bin/activate
+python -m ipykernel install --user --name=3.14 --display-name="VRS_kernel"

.binder/runtime.txt

@@ -1 +1 @@
-python-3.12
+python-3.14

.devcontainer/devcontainer.json

@@ -1,6 +1,6 @@
 {
   "name": "VRS-Python Notebooks",
-  "image": "mcr.microsoft.com/vscode/devcontainers/python:3.12",
+  "image": "mcr.microsoft.com/vscode/devcontainers/python:3.14",
   "customizations": {
     "vscode": {
       "extensions": [

.github/workflows/python-cqa.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13", "3.14", "3.15"]
     env:
       SEQREPO_ROOT_DIR: ./tests/data/seqrepo/latest
     steps:

CLAUDE.md

@@ -9,9 +9,9 @@ VRS-Python is the reference implementation of the GA4GH Variation Representation
 ## Development Commands
 
 ### Environment Setup
-- `make devready` - Create Python 3.12 venv, install dev dependencies, setup pre-commit hooks
-- `make nbready` - Create Python 3.12 venv, install notebook dependencies for Jupyter usage
-- `source venv/3.12/bin/activate` - Activate the virtual environment (required before development)
+- `make devready` - Create Python 3.14 venv, install dev dependencies, setup pre-commit hooks
+- `make nbready` - Create Python 3.14 venv, install notebook dependencies for Jupyter usage
+- `source venv/3.14/bin/activate` - Activate the virtual environment (required before development)
 
 ### Development Tasks
 - `make test` - Run pytest test suite
@@ -51,7 +51,7 @@ VRS-Python is the reference implementation of the GA4GH Variation Representation
 ## Development Notes
 
 ### Dependencies
-- Requires Python >= 3.10 (Python 3.12 required for development)
+- Requires Python >= 3.11 (Python 3.14 required for development)
 - External services: SeqRepo (sequence data), UTA (transcript alignments)
 - Key libraries: Pydantic 2.x, bioutils, HGVS, requests
 

Makefile

@@ -16,7 +16,7 @@ else
 endif
 XRM=xargs -0${_XRM_R} rm
 
-PYV:=3.12
+PYV:=3.14
 VEDIR=venv/${PYV}
 
 export SEQREPO_ROOT_DIR=tests/data/seqrepo/latest

README.md

@@ -34,10 +34,10 @@ All known issues are listed there. Please report any issues you find.
 
 ### Prerequisites
 
-- Python >= 3.10
-  - _Note: Python 3.12 is required for developers contributing to VRS-Python. The
-    Makefile sets up a virtual environment in `venv/3.12` and expects Python to be
-    available as `python3.12`._
+- Python >= 3.11
+  - _Note: Python 3.14 is required for developers contributing to VRS-Python. The
+    Makefile sets up a virtual environment in `venv/3.14` and expects Python to be
+    available as `python3.14`._
 - libpq
 - postgresql
 
@@ -277,13 +277,13 @@ Then, clone your fork and initialize a development environment:
 git clone --recurse-submodules git@github.com:YOUR_GITHUB_ID/vrs-python.git
 cd vrs-python
 make devready
-source venv/3.12/bin/activate
+source venv/3.14/bin/activate
 ```
 
 This setup includes [pre-commit hooks](https://pre-commit.com/). If you create a virtual environment manually, be sure to install the hooks yourself; otherwise, commits may fail during [CI/CD checks](https://github.com/ga4gh/vrs-python/actions/workflows/python-cqa.yml):
 
 ```shell
-source venv/3.12/bin/activate
+source venv/3.14/bin/activate
 pre-commit install
 ```
 
@@ -339,7 +339,7 @@ We have created a public [`VRS-demo-notebooks`](https://app.terra.bio/#workspace
 1. Open VS Code.
 2. Use Extensions view (Ctrl+Shift+X or ⌘+Shift+X) to install the [Jupyter extension](https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter).
 3. Navigate to your vrs-python project folder and open it in VS Code.
-4. In a notebook, click `Select Kernel` at the top right. Select the option where the path is `venv/3.12/bin/python3`. See [here](https://code.visualstudio.com/docs/datascience/jupyter-kernel-management) for more information on managing Jupyter Kernels in VS Code.
+4. In a notebook, click `Select Kernel` at the top right. Select the option where the path is `venv/3.14/bin/python3`. See [here](https://code.visualstudio.com/docs/datascience/jupyter-kernel-management) for more information on managing Jupyter Kernels in VS Code.
 5. After selecting the kernel you can now run the notebook.
 
 ## Security Note (from the GA4GH Security Team)

notebooks/getting_started/README.md

@@ -27,20 +27,20 @@ cd vrs-python
 
 ### Virtual Environment
 
-You must first install python@3.12, if not already installed.
+You must first install python@3.14, if not already installed.
 
 Next, run the following:
 
 ```shell
 make nbready
-source venv/3.12/bin/activate
+source venv/3.14/bin/activate
 ```
 
 #### Virtual Environment: Selecting the Kernel
 
 When opening a notebook with this option, click `Select Kernel`,
 `Python Environments...`, and select the first option:
-`3.12 (Python 3.12.z) venv/3.12/bin/python`
+`3.14 (Python 3.14.z) venv/3.14/bin/python`
 
 _Note: Patch version may vary._
 
@@ -114,7 +114,7 @@ You should see `Dev Container: VRS-Python Notebooks @ desktop-linux` on the bott
 
 When opening a notebook with this option, click `Select Kernel`,
 `Python Environments...`, and select the first option:
-`Python 3.12.z /usr/local/bin/python`
+`Python 3.14.z /usr/local/bin/python`
 
 _Note: Patch version may vary._
 

pyproject.toml

@@ -18,10 +18,11 @@ classifiers = [
     "Operating System :: OS Independent",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "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 = ">=3.10"
+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/core/models.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 from enum import Enum
-from typing import Annotated, Any, ClassVar, Literal
+from typing import Annotated, Any, ClassVar, Literal, Self
 
 from pydantic import (
     BaseModel,
@@ -13,7 +13,7 @@
     StringConstraints,
     model_validator,
 )
-from typing_extensions import Self, deprecated
+from typing_extensions import deprecated
 
 from ga4gh.core.identifiers import GA4GH_IR_REGEXP
 from ga4gh.core.metadata import GKMMetadataMixin, Maturity

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