Require sqlalchemy>=2 and upgrade code. (#544)

Author: tobiasraabe

.pre-commit-config.yaml

@@ -65,7 +65,7 @@ repos:
             optree,
             pluggy,
             rich,
-            sqlalchemy,
+            sqlalchemy>2,
             types-setuptools,
         ]
         pass_filenames: false

docs/source/changes.md

@@ -5,7 +5,11 @@ chronological order. Releases follow [semantic versioning](https://semver.org/)
 releases are available on [PyPI](https://pypi.org/project/pytask) and
 [Anaconda.org](https://anaconda.org/conda-forge/pytask).
 
-## 0.4.5 - 2023-12-xx
+## 0.5.0 - 2024-xx-xx
+
+- {pull}`544` requires sqlalchemy `>=2` and upgrades the syntax.
+
+## 0.4.5 - 2024-01-xx
 
 - {pull}`515` enables tests with graphviz in CI. Thanks to {user}`NickCrews`.
 - {pull}`517` raises an error when the configuration file contains a non-existing path

environment.yml

@@ -18,7 +18,7 @@ dependencies:
   - pluggy >=1.0.0
   - optree >=0.9
   - rich
-  - sqlalchemy >=1.4.36
+  - sqlalchemy >=2
   - tomli >=1.0.0
   - typing_extensions
   - universal_pathlib

pyproject.toml

@@ -36,7 +36,7 @@ dependencies = [
   "packaging",
   "pluggy>=1",
   "rich",
-  "sqlalchemy>=1.4.36",
+  "sqlalchemy>=2",
   'tomli>=1; python_version < "3.11"',
   'typing-extensions; python_version < "3.9"',
 ]

src/_pytask/database_utils.py

@@ -4,10 +4,10 @@
 from typing import TYPE_CHECKING
 
 from _pytask.dag_utils import node_and_neighbors
-from sqlalchemy import Column
 from sqlalchemy import create_engine
-from sqlalchemy import String
-from sqlalchemy.orm import declarative_base
+from sqlalchemy.orm import DeclarativeBase
+from sqlalchemy.orm import Mapped
+from sqlalchemy.orm import mapped_column
 from sqlalchemy.orm import sessionmaker
 
 if TYPE_CHECKING:
@@ -27,17 +27,18 @@
 DatabaseSession = sessionmaker()
 
 
-BaseTable = declarative_base()
+class BaseTable(DeclarativeBase):
+    pass
 
 
-class State(BaseTable):  # type: ignore[valid-type, misc]
+class State(BaseTable):
     """Represent the state of a node in relation to a task."""
 
     __tablename__ = "state"
 
-    task = Column(String, primary_key=True)
-    node = Column(String, primary_key=True)
-    hash_ = Column(String)
+    task: Mapped[str] = mapped_column(primary_key=True)
+    node: Mapped[str] = mapped_column(primary_key=True)
+    hash_: Mapped[str]
 
 
 def create_database(url: str) -> None:
@@ -54,7 +55,7 @@ def _create_or_update_state(first_key: str, second_key: str, hash_: str) -> None
         if not state_in_db:
             session.add(State(task=first_key, node=second_key, hash_=hash_))
         else:
-            state_in_db.hash_ = hash_  # type: ignore[assignment]
+            state_in_db.hash_ = hash_
         session.commit()
 
 

src/_pytask/profile.py

@@ -29,10 +29,8 @@
 from _pytask.session import Session
 from _pytask.traceback import Traceback
 from rich.table import Table
-from sqlalchemy import Column
-from sqlalchemy import Float
-from sqlalchemy import String
-
+from sqlalchemy.orm import Mapped
+from sqlalchemy.orm import mapped_column
 
 if TYPE_CHECKING:
     from _pytask.reports import ExecutionReport
@@ -51,9 +49,9 @@ class Runtime(BaseTable):
 
     __tablename__ = "runtime"
 
-    task = Column(String, primary_key=True)
-    date = Column(Float)
-    duration = Column(Float)
+    task: Mapped[str] = mapped_column(primary_key=True)
+    date: Mapped[float]
+    duration: Mapped[float]
 
 
 @hookimpl(tryfirst=True)
@@ -198,7 +196,7 @@ def _collect_runtimes(tasks: list[PTask]) -> dict[str, float]:
     """Collect runtimes."""
     with DatabaseSession() as session:
         runtimes = [session.get(Runtime, task.signature) for task in tasks]
-    return {task.name: r.duration for task, r in zip(tasks, runtimes) if r}  # type: ignore[misc]
+    return {task.name: r.duration for task, r in zip(tasks, runtimes) if r}
 
 
 class FileSizeNameSpace: