Upgrade biblib to Python 3.12

.github/workflows/python_actions.yml

@@ -11,11 +11,11 @@ jobs:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v2
       with:
-        python-version: '3.10'
+        python-version: '3.12'
 
     - name: Install dependencies
       run: |
-        python -m pip install "pip==24" setuptools==57.5.0 wheel
+        python -m pip install "pip==24" "setuptools>=62.0.0,<70.0.0" wheel
         pip install ".[dev]"
 
     - name: Test with pytest

alembic/env.py

@@ -1,4 +1,3 @@
-from __future__ import with_statement
 from alembic import context
 from sqlalchemy import engine_from_config, pool
 from logging.config import fileConfig

biblib/manage.py

@@ -6,6 +6,7 @@
 from flask import current_app
 from datetime import datetime
 from dateutil.relativedelta import relativedelta
+from sqlalchemy import text
 import sqlalchemy_continuum
 
 class DeleteStaleUsers:
@@ -19,7 +20,7 @@ def run(self, app=None):
         with app.app_context():
             with current_app.session_scope() as session:
                 # Obtain the list of API users
-                postgres_search_text = 'SELECT id FROM users;'
+                postgres_search_text = text('SELECT id FROM users;')
                 result = session.execute(postgres_search_text).fetchall()
                 list_of_api_users = [int(r[0]) for r in result]
 

biblib/models.py

@@ -6,11 +6,11 @@
 """
 
 import uuid
-from datetime import datetime
+from datetime import datetime, timezone
 from sqlalchemy.dialects.postgresql import UUID, JSON
 from sqlalchemy.ext.mutable import Mutable
 from sqlalchemy.types import TypeDecorator, CHAR, String as StringType
-from sqlalchemy.ext.declarative import declarative_base
+from sqlalchemy.orm import declarative_base
 from sqlalchemy import Column, Integer, String, ForeignKey, DateTime, Boolean, UnicodeText, UniqueConstraint
 from sqlalchemy.orm import relationship, configure_mappers
 from sqlalchemy_continuum import make_versioned
@@ -189,13 +189,13 @@ class Notes(Base):
     date_created = Column(
         DateTime,
         nullable=False,
-        default=datetime.utcnow
+        default=lambda: datetime.now(timezone.utc).replace(tzinfo=None)
     )
     date_last_modified = Column(
         DateTime,
         nullable=False,
-        default=datetime.utcnow,
-        onupdate=datetime.utcnow
+        default=lambda: datetime.now(timezone.utc).replace(tzinfo=None),
+        onupdate=lambda: datetime.now(timezone.utc).replace(tzinfo=None)
     )
 
     def __repr__(self):
@@ -251,13 +251,13 @@ class Library(Base):
     date_created = Column(
         DateTime,
         nullable=False,
-        default=datetime.utcnow
+        default=lambda: datetime.now(timezone.utc).replace(tzinfo=None)
     )
     date_last_modified = Column(
         DateTime,
         nullable=False,
-        default=datetime.utcnow,
-        onupdate=datetime.utcnow
+        default=lambda: datetime.now(timezone.utc).replace(tzinfo=None),
+        onupdate=lambda: datetime.now(timezone.utc).replace(tzinfo=None)
     )
     permissions = relationship('Permissions',
                                   backref='library',

biblib/tests/unit_tests/test_manage.py

@@ -6,6 +6,7 @@
 from biblib.manage import DeleteObsoleteVersionsNumber, DeleteStaleUsers, DeleteObsoleteVersionsTime
 from biblib.models import User, Library, Permissions, Notes
 from sqlalchemy.orm.exc import NoResultFound
+from sqlalchemy import text
 from biblib.tests.base import TestCaseDatabase
 import sqlalchemy_continuum
 import freezegun
@@ -53,8 +54,8 @@ def test_delete_stale_users(self):
 
         with self.app.session_scope() as session:
             # We do not add user 1 to the API database
-            session.execute('create table users (id integer, random integer);')
-            session.execute('insert into users (id, random) values (2, 7);')
+            session.execute(text('create table users (id integer, random integer);'))
+            session.execute(text('insert into users (id, random) values (2, 7);'))
             session.commit()
 
         with self.app.session_scope() as session:
@@ -171,7 +172,7 @@ def test_delete_stale_users(self):
                 raise
             finally:
                 # Destroy the tables
-                session.execute('drop table users;')
+                session.execute(text('drop table users;'))
                 pass
 
     def test_delete_obsolete_versions_number(self):
@@ -184,8 +185,8 @@ def test_delete_obsolete_versions_number(self):
 
         with self.app.session_scope() as session:
             # We do not add user 1 to the API database
-            session.execute('create table users (id integer, random integer);')
-            session.execute('insert into users (id, random) values (2, 7);')
+            session.execute(text('create table users (id integer, random integer);'))
+            session.execute(text('insert into users (id, random) values (2, 7);'))
             session.commit()
 
         with self.app.session_scope() as session:
@@ -340,7 +341,7 @@ def test_delete_obsolete_versions_number(self):
                 raise
             finally:
                 # Destroy the tables
-                session.execute('drop table users;')
+                session.execute(text('drop table users;'))
                 pass
 
     def test_delete_obsolete_versions_time(self):
@@ -353,8 +354,8 @@ def test_delete_obsolete_versions_time(self):
 
         with self.app.session_scope() as session:
             # We do not add user 1 to the API database
-            session.execute('create table users (id integer, random integer);')
-            session.execute('insert into users (id, random) values (2, 7);')
+            session.execute(text('create table users (id integer, random integer);'))
+            session.execute(text('insert into users (id, random) values (2, 7);'))
             session.commit()
 
         with self.app.session_scope() as session:
@@ -535,7 +536,7 @@ def test_delete_obsolete_versions_time(self):
                 raise
             finally:
                 # Destroy the tables
-                session.execute('drop table users;')
+                session.execute(text('drop table users;'))
                 pass
 
 if __name__ == '__main__':

config.py

@@ -0,0 +1 @@
+from biblib.config import *

pyproject.toml

@@ -7,15 +7,15 @@ license = { text = "MIT" }
 readme = "README.md"
 packages = ["biblib"]
 dependencies = [
-    "adsmutils @ git+https://github.com/adsabs/ADSMicroserviceUtils.git@v1.3.0",
-    "alembic==1.12.0",
-    "psycopg2-binary==2.9.9",
-    "sqlalchemy-continuum==1.3.6",
-    "Flask-Mail==0.9.1",
+    "adsmutils @ git+https://github.com/adsabs/ADSMicroserviceUtils.git@v2.0.0",
+    "alembic==1.13.3",
+    "psycopg2-binary==2.9.11",
+    "sqlalchemy-continuum==1.3.15",
+    "Flask-Mail==0.10.0",
     "Flask-Email==1.4.4",
-    "Jinja2==3.1.2",
-    "markupsafe==2.1.3",
-    "itsdangerous==2.1.2",
+    "Jinja2==3.1.6",
+    "markupsafe==3.0.3",
+    "itsdangerous==2.2.0",
     "werkzeug==2.3.8"
 ]
 
@@ -24,22 +24,23 @@ dev = [
     "Flask-Testing==0.8.1",
     "httpretty==1.1.4",
     "testing.postgresql==1.3.0",
-    "pytest==6.2.5",
-    "pytest-cov==3.0.0",
+    "pytest==7.4.4",
+    "pytest-cov==5.0.0",
     "Faker==22.0.0",
-    "factory-boy==3.3.0",
-    "freezegun==1.4.0",
+    "factory-boy==3.3.3",
+    "freezegun==1.5.5",
     "httmock==1.4.0",
-    "mock==4.0.3",
-    "flake8==4.0.1",
-    "black==22.3.0",
+    "mock==5.2.0",
+    "flake8==7.1.0",
+    "black==24.10.0",
     "isort==5.12.0",
-    "coveralls==3.3.1"
+    "coverage==7.6.1",
+    "coveralls==4.0.1"
 ]
 
 [build-system]
 requires = [
-    "setuptools==57.5.0",
+    "setuptools>=62.0.0,<70.0.0",
     "wheel",
     "flit_core >=3.2,<4",
     "ppsetuptools==2.0.2"
@@ -52,7 +53,7 @@ testpaths = ["biblib/tests"]
 
 [tool.black]
 line-length = 88
-target-version = ['py310']
+target-version = ['py312']
 
 [tool.isort]
 profile = "black"