PD-109 Python 3.13

.github/workflows/ci.yaml

@@ -13,4 +13,4 @@ jobs:
     name: Python Unit Test
     uses: uc-cdis/.github/.github/workflows/python_unit_test.yaml@master
     with:
-        python-version: '3.9'
+        python-version: '3.13'

.github/workflows/pypi.yaml

@@ -8,7 +8,7 @@ jobs:
     name: PyPI Poetry Publish
     uses: uc-cdis/.github/.github/workflows/python_package_index_publish.yaml@master
     with:
-        PYTHON_VERSION: '3.9'
+        PYTHON_VERSION: '3.13'
         # This will attempt push to test PyPI first and only push to prod if it works
         DO_TEST_PUBLISH_FIRST: true
     secrets:

.pre-commit-config.yaml

@@ -4,6 +4,7 @@ repos:
     hooks:
     -   id: detect-secrets
         args: ['--baseline', '.secrets.baseline']
+        additional_dependencies: ['gibberish-detector']
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.5.0
     hooks:

.secrets.baseline

@@ -98,5 +98,5 @@
     }
   ],
   "results": {},
-  "generated_at": "2025-08-01T21:17:57Z"
+  "generated_at": "2026-01-09T16:31:16Z"
 }

README.md

@@ -1,5 +1,4 @@
 # datamodelutils
-[![Docker Repository on Quay](https://quay.io/repository/cdis/datamodelutils/status "Docker Repository on Quay")](https://quay.io/repository/cdis/datamodelutils)
 
 Wrapper utils to allow gen3datamodel.models to be loaded after initialization.
 
@@ -28,7 +27,6 @@ will produce output of
 ```
 
 # CLI Utilities
-The datamodelutils has a [docker](https://quay.io/repository/cdis/datamodelutils) image that exposes admin commands to manage or interact with datamodel
 
 ## datamodel_postgres_admin
 Script to do database creation and migration

datamodelutils/repl.py

@@ -3,9 +3,15 @@
 
 
 def main():
-    import IPython
     import os
 
+    try:
+        import ipython
+    except ModuleNotFoundError:
+        raise Exception(
+            "The repl script requires IPython. `poetry add 'datamodelutils[IPython]'`"
+        )
+
     db_host = os.environ["PG_HOST"]
     db_name = os.environ["PG_NAME"]
     db_user = os.environ["PG_USER"]
@@ -21,7 +27,7 @@ def main():
     g = PsqlGraphDriver(host=db_host, user=db_user, password=db_pass, database=db_name)
     ss = g.session_scope
     with g.session_scope() as session:
-        IPython.embed()
+        ipython.embed()
 
 
 if __name__ == "__main__":

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "datamodelutils"
-version = "1.1.2"
+version = "1.2.0"
 description = "Gen3 Data Model Utils"
 authors = ["CTDS UChicago <cdis@uchicago.edu>"]
 license = "Apache-2.0"
@@ -10,19 +10,23 @@ packages = [
     { include = "./datamodelutils" }
 ]
 
-
 [tool.poetry.dependencies]
-python = ">=3.9,<4"
-dictionaryutils = ">=3.4.11"
-gen3datamodel = ">=3.2.1"
+python = ">=3.13,<4"
+dictionaryutils = ">=3"
+gen3datamodel = ">=3"
 psqlgraph = "*"
-sqlalchemy = ">=1.3.0,<2"
+sqlalchemy = "<3"
+ipython = { version = "*", optional = true }
 
 [tool.poetry.group.dev.dependencies]
 pytest = ">=7,<8"
 mock = "*"
 pytest-cov = "*"
 coverage = "*"
+deptry = "^0.24.0"
+
+[tool.poetry.extras]
+ipython = ["ipython"]
 
 [tool.poetry.scripts]
 datamodel_postgres_admin = 'datamodelutils.postgres_admin:main'