SQLAlchemy 2.0 compatibility

setup.cfg

@@ -19,7 +19,7 @@ python_requires = >= 3.9
 
 install_requires =
 	numpy~=1.13
-	sqlalchemy~=1.1
+	sqlalchemy>=1.4
 	# Seq stores data as bytes
 	biopython~=1.79
 	attrs>=20

src/gambit/db/models.py

@@ -5,9 +5,8 @@
 import sqlalchemy as sa
 from sqlalchemy import Column, Integer, String, Boolean, Float
 from sqlalchemy import ForeignKey, UniqueConstraint
-from sqlalchemy.orm import Session, relationship, backref, deferred
+from sqlalchemy.orm import Session, relationship, backref, deferred, declarative_base
 from sqlalchemy.ext.hybrid import hybrid_property
-from sqlalchemy.ext.declarative import declarative_base, declared_attr
 from sqlalchemy.exc import MultipleResultsFound, NoResultFound
 
 from .sqla import JsonString
@@ -68,16 +67,11 @@ class Genome(Base):
 	"""
 
 	__tablename__ = 'genomes'
+	__table_args__= (UniqueConstraint('ncbi_db', 'ncbi_id'),)
 
 	#: Attributes which serve as unique IDs.
 	ID_ATTRS = ('key', 'genbank_acc', 'refseq_acc', 'ncbi_id')
 
-	@declared_attr
-	def __table_args__(cls):
-		return (
-			UniqueConstraint('ncbi_db', 'ncbi_id'),
-		)
-
 	id = Column(Integer(), primary_key=True)
 	key = Column(String(), unique=True, nullable=False)
 	description = Column(String(), nullable=False)
@@ -136,12 +130,7 @@ class ReferenceGenomeSet(Base):
 		for this genome set.
 	"""
 	__tablename__ = 'genome_sets'
-
-	@declared_attr
-	def __table_args__(cls):
-		return (
-			UniqueConstraint('key', 'version'),
-		)
+	__table_args__ = (UniqueConstraint('key', 'version'),)
 
 	id = Column(Integer(), primary_key=True)
 	key = Column(String(), index=True, nullable=False)

src/gambit/db/sqla.py

@@ -53,7 +53,8 @@ def default_sessionmaker(bind, *, readonly: bool = True, class_: Optional[type]
 	"""
 	if class_ is None:
 		class_ = ReadOnlySession if readonly else Session
-	return sessionmaker(bind, class_=class_, **kw)
+	# future=True - forwards compatibility with SQLAlchemy 2.0
+	return sessionmaker(bind, class_=class_, future=True, **kw)
 
 
 def file_sessionmaker(path: 'FilePath', **kw) -> sessionmaker: