Feat/dev 2542 upgrade sqlalchemy1.4

.gitlab-ci.yml

@@ -1,16 +1,23 @@
 ---
 include:
   - project: nci-gdc/gitlab-templates
-    ref: master
+    ref: 0.7.11
     file:
       - templates/artifacts/python-library.yaml
 
 tox:
+  parallel:
+    matrix:
+      - LANGUAGE_VERSION:
+          - python3.8
+          - python3.9
+          - python3.10
+          - python3.11
+          - python3.12
   services:
     - name: docker.osdc.io/ncigdc/ci-postgres-13:${BASE_CONTAINER_VERSION}
       alias: postgres
   variables:
-    BASE_CONTAINER_VERSION: 2.3.1
     # these are for postgres docker
     POSTGRES_DB: automated_test
     POSTGRES_USER: test

.secrets.baseline

@@ -124,7 +124,7 @@
         "filename": ".gitlab-ci.yml",
         "hashed_secret": "a94a8fe5ccb19ba61c4c0873d391e987982fbbd3",
         "is_verified": false,
-        "line_number": 17,
+        "line_number": 24,
         "is_secret": false
       }
     ],
@@ -149,5 +149,5 @@
       }
     ]
   },
-  "generated_at": "2024-07-26T21:01:14Z"
+  "generated_at": "2024-09-06T17:02:29Z"
 }

setup.cfg

@@ -18,23 +18,22 @@ classifiers =
     Topic :: Internet
     Topic :: Software Development :: Libraries :: Python Modules
     Programming Language :: Python
-    Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
     Development Status   :: 5 - Production/Stable
 
 [options]
 zip_safe = True
 packages = find:
 package_dir =
     =src
-python_requires = >=3.7
+python_requires = >=3.8
 include_package_data = True
 install_requires =
-    psycopg2
-    sqlalchemy>=1.3,<1.4
+    sqlalchemy[postgresql]~=1.4
     xlocal
     rstr
 

src/psqlgraph/__init__.py

@@ -5,3 +5,17 @@
 from psqlgraph.util import pg_property, sanitize, validate
 from psqlgraph.voided_edge import VoidedEdge
 from psqlgraph.voided_node import VoidedNode
+
+__all__ = (
+    "Edge",
+    "Node",
+    "PolyEdge",
+    "PolyNode",
+    "PsqlGraphDriver",
+    "VoidedEdge",
+    "VoidedNode",
+    "create_all",
+    "pg_property",
+    "sanitize",
+    "validate",
+)

src/psqlgraph/base.py

@@ -1,4 +1,6 @@
-from sqlalchemy import event
+import inspect
+from typing import ClassVar
+
 from sqlalchemy.dialects import postgresql
 from sqlalchemy.ext import declarative
 from sqlalchemy.ext.declarative import declared_attr
@@ -18,6 +20,18 @@ class CommonBase:
     _session_hooks_before_insert = []
     _session_hooks_before_update = []
     _session_hooks_before_delete = []
+    __pg_properties__: ClassVar[dict]
+
+    def __init_subclass__(cls) -> None:
+        cls.__pg_properties__ = {}
+        pg_properties = (
+            (k, v) for k, v in vars(cls).items() if getattr(v, "__pg_setter__", False)
+        )
+
+        for name, property in pg_properties:
+            h_prop = _create_hybrid_property(name, property)
+            setattr(cls, name, h_prop)
+            cls.__pg_properties__[name] = property.__pg_types__
 
     # ======== Columns ========
     created = schema.Column(
@@ -237,7 +251,7 @@ def get_pg_properties(cls):
         return cls.__pg_properties__
 
 
-def create_hybrid_property(name, fset):
+def _create_hybrid_property(name, fset):
     @hybrid_property
     def hybrid_prop(instance):
         # Note: this does not use an 'in' clause or a .get() with a
@@ -256,26 +270,6 @@ def hybrid_prop(instance, value):
     return hybrid_prop
 
 
-@event.listens_for(CommonBase, "mapper_configured", propagate=True)
-def create_hybrid_properties(mapper, cls):
-    # This dictionary will be a property name to allowed types
-    # dictionary.  It will be populated at mapper configuration using
-    # all model properties defined with @pg_property
-    cls.__pg_properties__ = {}
-
-    for pg_attr in dir(cls):
-        if pg_attr in ["properties", "props", "system_annotations", "sysan"]:
-            continue
-
-        f = getattr(cls, pg_attr)
-        if not getattr(f, "__pg_setter__", False):
-            continue
-
-        h_prop = create_hybrid_property(pg_attr, f)
-        setattr(cls, pg_attr, h_prop)
-        cls.__pg_properties__[pg_attr] = f.__pg_types__
-
-
 class VoidedBaseClass:
     @hybrid_property
     def props(self):

src/psqlgraph/psql.py

@@ -66,9 +66,7 @@ def __init__(self, host, user, password, database, **kwargs):
 
         # Construct connection string
         host = "" if host is None else host
-        conn_str = "postgresql://{user}:{password}@{host}/{database}".format(
-            user=user, password=password, host=host, database=database
-        )
+        conn_str = f"postgresql+psycopg2://{user}:{password}@{host}/{database}"
         if kwargs["isolation_level"] not in self.acceptable_isolation_levels:
             logger.warning(
                 (

src/psqlgraph/query.py

@@ -31,8 +31,10 @@ def entity(self):
         entity.
 
         """
+        if self._last_joined_entity:
+            return self._last_joined_entity.entity
 
-        return self._joinpoint_zero().entity
+        return self.column_descriptions[0]["entity"]
 
     # ======== Edges ========
     def with_edge_to_node(self, edge_type, target_node):
@@ -208,13 +210,18 @@ def path(self, *paths):
             query.path().reset_joinpoint().filter()
 
         """
-        entities = [p.strip() for path in paths for p in path.split(".")]
+        entities = (p.strip() for path in paths for p in path.split("."))
+        query = self
+
         assert (
             not self.entity().is_abstract_base()
         ), "Please narrow your search by specifying a node subclass"
-        for e in entities:
-            self = self.join(*getattr(self.entity(), e).attr)
-        return self
+
+        for entity in entities:
+            proxy = getattr(query.entity(), entity)
+            query = query.join(proxy.local_attr).join(proxy.remote_attr)
+
+        return query
 
     def _get_link_details(self, entity, link_name):
         """ "Lookup the (edge_class, left_edge_id, right_edge_id, node_class)

src/psqlgraph/session.py

@@ -22,9 +22,14 @@ def __init__(self, *args, **kwargs):
         self.package_namespace = kwargs.pop("package_namespace", None)
         super().__init__(*args, **kwargs)
 
+    def _autobegin(self):
+        if self._psqlgraph_closed:
+            raise exc.SessionClosedError("session closed")
+
+        return super()._autobegin()
+
     @inherit_docstring_from(Session)
     def connection(self, *args, **kwargs):
-
         if self._psqlgraph_closed:
             raise exc.SessionClosedError("session closed")
 

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = py37,py38,py39,py310,py311
+envlist = py3{8,9,10,11,12}
 skip_missing_interpreters = True
 isolated_build = True