remove upper limit

.github/workflows/tests.yml

@@ -2,7 +2,7 @@
 #
 # This file is part of Invenio.
 # Copyright (C) 2020 CERN.
-# Copyright (C) 2022 Graz University of Technology.
+# Copyright (C) 2022-2024 Graz University of Technology.
 #
 # Invenio is free software; you can redistribute it and/or modify it
 # under the terms of the MIT License; see LICENSE file for more details.
@@ -11,92 +11,23 @@ name: CI
 
 on:
   push:
-    branches: master
+    branches:
+      - master
   pull_request:
-    branches: master
+    branches:
+      - master
   schedule:
     # * is a special character in YAML so you have to quote this string
-    - cron:  '0 3 * * 6'
+    - cron:  "0 3 * * 6"
   workflow_dispatch:
     inputs:
       reason:
-        description: 'Reason'
+        description: "Reason"
         required: false
-        default: 'Manual trigger'
+        default: "Manual trigger"
 
 jobs:
   Tests:
-    runs-on: ubuntu-20.04
-    strategy:
-      matrix:
-          python-version: [3.7, 3.8, 3.9]
-          requirements-level: [pypi]
-          db-service: [postgresql11, postgresql14, mysql8, sqlite]
-          exclude:
-          - python-version: 3.7
-            db-service: postgresql14
-            requirements-level: pypi
-
-          - python-version: 3.7
-            db-service: mysql8
-            requirements-level: pypi
-
-          - python-version: 3.8
-            db-service: postgresql11
-
-          - python-version: 3.9
-            db-service: postgresql11
-
-          - python-version: 3.7
-            db-service: sqlite
-
-          - python-version: 3.8
-            db-service: sqlite
-
-          include:
-          - db-service: postgresql11
-            EXTRAS: "tests,postgresql"
-
-          - db-service: postgresql14
-            EXTRAS: "tests,postgresql"
-
-          - db-service: mysql8
-            EXTRAS: "tests,mysql"
-
-          - db-service: sqlite
-            EXTRAS: "tests"
-
-    env:
-      DB: ${{ matrix.db-service }}
-      EXTRAS: ${{ matrix.EXTRAS }}
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Generate dependencies
-        run: |
-          pip install wheel requirements-builder
-          requirements-builder -e "$EXTRAS" --level=${{ matrix.requirements-level }} setup.py > .${{ matrix.requirements-level }}-${{ matrix.python-version }}-requirements.txt
-
-      - name: Cache pip
-        uses: actions/cache@v2
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('.${{ matrix.requirements-level }}-${{ matrix.python-version }}-requirements.txt') }}
-
-      - name: Install dependencies
-        run: |
-          pip install -r .${{ matrix.requirements-level }}-${{ matrix.python-version }}-requirements.txt -c constraints-${{ matrix.requirements-level }}.txt
-          pip install ".[$EXTRAS]"
-          pip freeze
-          docker --version
-          docker-compose --version
-
-      - name: Run tests
-        run: |
-          ./run-tests.sh
+    uses: inveniosoftware/workflows/.github/workflows/tests-python.yml@master
+    with:
+      extras: "tests,postgresql"

invenio_db/alembic/dbdbc1b19cf2_create_transaction_table.py

@@ -23,9 +23,9 @@ def upgrade():
     """Update database."""
     op.create_table(
         "transaction",
-        sa.Column("issued_at", sa.DateTime(), nullable=True),
         sa.Column("id", sa.BigInteger(), nullable=False),
         sa.Column("remote_addr", sa.String(length=50), nullable=True),
+        sa.Column("issued_at", sa.DateTime(), nullable=True),
     )
     op.create_primary_key("pk_transaction", "transaction", ["id"])
     if op._proxy.migration_context.dialect.supports_sequences:

invenio_db/cli.py

@@ -2,29 +2,20 @@
 #
 # This file is part of Invenio.
 # Copyright (C) 2015-2018 CERN.
+# Copyright (C) 2024 Graz University of Technology.
 #
 # Invenio is free software; you can redistribute it and/or modify it
 # under the terms of the MIT License; see LICENSE file for more details.
 
 """Click command-line interface for database management."""
 
-import sys
-
 import click
-from click import _termui_impl
-from flask import current_app
 from flask.cli import with_appcontext
 from sqlalchemy_utils.functions import create_database, database_exists, drop_database
-from werkzeug.local import LocalProxy
 
+from .proxies import current_sqlalchemy
 from .utils import create_alembic_version_table, drop_alembic_version_table
 
-_db = LocalProxy(lambda: current_app.extensions["sqlalchemy"].db)
-
-# Fix Python 3 compatibility issue in click
-if sys.version_info > (3,):
-    _termui_impl.long = int  # pragma: no cover
-
 
 def abort_if_false(ctx, param, value):
     """Abort command is value is False."""
@@ -34,11 +25,7 @@ def abort_if_false(ctx, param, value):
 
 def render_url(url):
     """Render the URL for CLI output."""
-    try:
-        return url.render_as_string(hide_password=True)
-    except AttributeError:
-        # SQLAlchemy <1.4
-        return url.__to_string__(hide_password=True)
+    return url.render_as_string(hide_password=True)
 
 
 #
@@ -55,11 +42,11 @@ def db():
 def create(verbose):
     """Create tables."""
     click.secho("Creating all tables!", fg="yellow", bold=True)
-    with click.progressbar(_db.metadata.sorted_tables) as bar:
+    with click.progressbar(current_sqlalchemy.metadata.sorted_tables) as bar:
         for table in bar:
             if verbose:
                 click.echo(" Creating table {0}".format(table))
-            table.create(bind=_db.engine, checkfirst=True)
+            table.create(bind=current_sqlalchemy.engine, checkfirst=True)
     create_alembic_version_table()
     click.secho("Created all tables!", fg="green")
 
@@ -77,11 +64,11 @@ def create(verbose):
 def drop(verbose):
     """Drop tables."""
     click.secho("Dropping all tables!", fg="red", bold=True)
-    with click.progressbar(reversed(_db.metadata.sorted_tables)) as bar:
+    with click.progressbar(reversed(current_sqlalchemy.metadata.sorted_tables)) as bar:
         for table in bar:
             if verbose:
                 click.echo(" Dropping table {0}".format(table))
-            table.drop(bind=_db.engine, checkfirst=True)
+            table.drop(bind=current_sqlalchemy.engine, checkfirst=True)
         drop_alembic_version_table()
     click.secho("Dropped all tables!", fg="green")
 
@@ -90,9 +77,10 @@ def drop(verbose):
 @with_appcontext
 def init():
     """Create database."""
-    displayed_database = render_url(_db.engine.url)
+    displayed_database = render_url(current_sqlalchemy.engine.url)
     click.secho(f"Creating database {displayed_database}", fg="green")
-    database_url = str(_db.engine.url)
+    database_url = current_sqlalchemy.engine.url.render_as_string(hide_password=False)
+
     if not database_exists(database_url):
         create_database(database_url)
 
@@ -108,12 +96,14 @@ def init():
 @with_appcontext
 def destroy():
     """Drop database."""
-    displayed_database = render_url(_db.engine.url)
+    displayed_database = render_url(current_sqlalchemy.engine.url)
     click.secho(f"Destroying database {displayed_database}", fg="red", bold=True)
-    if _db.engine.name == "sqlite":
+
+    plain_url = current_sqlalchemy.engine.url.render_as_string(hide_password=False)
+    if current_sqlalchemy.engine.name == "sqlite":
         try:
-            drop_database(_db.engine.url)
-        except FileNotFoundError as e:
+            drop_database(plain_url)
+        except FileNotFoundError:
             click.secho("Sqlite database has not been initialised", fg="red", bold=True)
     else:
-        drop_database(_db.engine.url)
+        drop_database(plain_url)

invenio_db/ext.py

@@ -3,7 +3,7 @@
 # This file is part of Invenio.
 # Copyright (C) 2015-2018 CERN.
 # Copyright (C) 2022 RERO.
-# Copyright (C) 2022 Graz University of Technology.
+# Copyright (C) 2022-2024 Graz University of Technology.
 #
 # Invenio is free software; you can redistribute it and/or modify it
 # under the terms of the MIT License; see LICENSE file for more details.
@@ -36,19 +36,17 @@ def init_app(self, app, **kwargs):
         """Initialize application object."""
         self.init_db(app, **kwargs)
 
-        script_location = str(importlib_resources.files("invenio_db") / "alembic")
-        version_locations = [
-            (
-                base_entry.name,
-                str(
-                    importlib_resources.files(base_entry.module)
-                    / os.path.join(base_entry.attr)
-                ),
-            )
-            for base_entry in importlib_metadata.entry_points(
-                group="invenio_db.alembic"
+        def pathify(base_entry):
+            return str(
+                importlib_resources.files(base_entry.module)
+                / os.path.join(base_entry.attr)
             )
+
+        entry_points = importlib_metadata.entry_points(group="invenio_db.alembic")
+        version_locations = [
+            (base_entry.name, pathify(base_entry)) for base_entry in entry_points
         ]
+        script_location = str(importlib_resources.files("invenio_db") / "alembic")
         app.config.setdefault(
             "ALEMBIC",
             {
@@ -93,6 +91,7 @@ def init_db(self, app, entry_point_group="invenio_db.models", **kwargs):
 
         # All models should be loaded by now.
         sa.orm.configure_mappers()
+
         # Ensure that versioning classes have been built.
         if app.config["DB_VERSIONING"]:
             manager = self.versioning_manager

invenio_db/proxies.py

@@ -0,0 +1,15 @@
+# -*- coding: utf-8 -*-
+#
+# This file is part of Invenio.
+# Copyright (C) 2022 Graz University of Technology.
+#
+# Invenio is free software; you can redistribute it and/or modify it
+# under the terms of the MIT License; see LICENSE file for more details.
+
+"""Helper proxy to the state object."""
+
+
+from flask import current_app
+from werkzeug.local import LocalProxy
+
+current_sqlalchemy = LocalProxy(lambda: current_app.extensions["sqlalchemy"])

invenio_db/utils.py

@@ -2,6 +2,7 @@
 #
 # This file is part of Invenio.
 # Copyright (C) 2017-2018 CERN.
+# Copyright (C) 2024 Graz University of Technology.
 #
 # Invenio is free software; you can redistribute it and/or modify it
 # under the terms of the MIT License; see LICENSE file for more details.
@@ -11,14 +12,12 @@
 
 from flask import current_app
 from sqlalchemy import inspect
-from werkzeug.local import LocalProxy
 
-from .shared import db
+from .proxies import current_sqlalchemy
+from .shared import db as _db
 
-_db = LocalProxy(lambda: current_app.extensions["sqlalchemy"].db)
 
-
-def rebuild_encrypted_properties(old_key, model, properties):
+def rebuild_encrypted_properties(old_key, model, properties, db=_db):
     """Rebuild model's EncryptedType properties when the SECRET_KEY is changed.
 
     :param old_key: old SECRET_KEY.
@@ -73,11 +72,13 @@ def create_alembic_version_table():
 
 def drop_alembic_version_table():
     """Drop alembic_version table."""
-    if has_table(_db.engine, "alembic_version"):
-        alembic_version = _db.Table(
-            "alembic_version", _db.metadata, autoload_with=_db.engine
+    if has_table(current_sqlalchemy.engine, "alembic_version"):
+        alembic_version = current_sqlalchemy.Table(
+            "alembic_version",
+            current_sqlalchemy.metadata,
+            autoload_with=current_sqlalchemy.engine,
         )
-        alembic_version.drop(bind=_db.engine)
+        alembic_version.drop(bind=current_sqlalchemy.engine)
 
 
 def versioning_model_classname(manager, model):

setup.cfg

@@ -4,7 +4,7 @@
 # Copyright (C) 2015-2022 CERN.
 # Copyright (C) 2021 Northwestern University.
 # Copyright (C) 2022 RERO.
-# Copyright (C) 2022 Graz University of Technology.
+# Copyright (C) 2022-2024 Graz University of Technology.
 #
 # Invenio is free software; you can redistribute it and/or modify it
 # under the terms of the MIT License; see LICENSE file for more details.
@@ -29,22 +29,21 @@ packages = find:
 python_requires = >=3.7
 zip_safe = False
 install_requires =
-    # due to incompatibility on the 1.11 release
-    alembic>=1.10.0,<1.11.0
-    Flask-Alembic>=2.0.1
-    Flask-SQLAlchemy>=2.1,<3.0.0
+    alembic>=1.10.0
+    Flask-Alembic>=3.0.0
+    Flask-SQLAlchemy>=3.0
     invenio-base>=1.2.10
     SQLAlchemy-Continuum>=1.3.12
-    SQLAlchemy-Utils>=0.33.1,<0.39
-    SQLAlchemy[asyncio]>=1.2.18,<1.5.0
+    SQLAlchemy-Utils>=0.33.1
+    SQLAlchemy>=2.0.0
 
 [options.extras_require]
 tests =
-    pytest-black>=0.3.0
+    six>=1.0.0
+    pytest-black-ng>=0.4.0
     cryptography>=2.1.4
     pytest-invenio>=1.4.5
     Sphinx>=4.5.0
-# Left here for backward compatibility
 mysql =
     pymysql>=0.10.1
 postgresql =
@@ -69,7 +68,7 @@ all_files = 1
 universal = 1
 
 [pydocstyle]
-add_ignore = D401
+add_ignore = D401, D202
 
 [isort]
 profile=black

tests/conftest.py

@@ -17,8 +17,8 @@
 from invenio_db.utils import alembic_test_context
 
 
-@pytest.fixture()
-def db():
+@pytest.fixture(name="db")
+def fixture_db():
     """Database fixture with session sharing."""
     import invenio_db
     from invenio_db import shared