Make updates for Python 3.12 & update various packages to their latest versions

app/.python-version

@@ -1 +1 @@
-3.11
+3.12

app/openapi.generated.yml

@@ -239,6 +239,9 @@ components:
       properties:
         type:
           description: The name of the role
+          enum:
+          - USER
+          - ADMIN
     User:
       type: object
       properties:

app/pyproject.toml

@@ -7,37 +7,38 @@ authors = ["Nava Engineering <[email protected]>"]
 
 [tool.poetry.dependencies]
 python = "^3.10"
-SQLAlchemy = {extras = ["mypy"], version = "2.0"}
-alembic = "^1.8.1"
+SQLAlchemy = {version = "^2.0.21", extras = ["mypy"]}
+alembic = "^1.12.0"
 python-dotenv = "^0.20.0"
 pydantic = "^1.10.0"
-botocore = "^1.27.67"
-boto3 = "~1.24.67"
+botocore = "^1.31.62"
+boto3 = "^1.28.62"
 smart-open = "^6.1.0"
-pytz = "^2022.2.1"
-APIFlask = "^1.1.3"
+pytz = "^2023.3.post1"
+APIFlask = "^2.0.2"
 marshmallow-dataclass = {extras = ["enum", "union"], version = "^8.5.8"}
-marshmallow = "^3.18.0"
+marshmallow = "^3.20.1"
 gunicorn = "^21.2.0"
 psycopg = {extras = ["binary"], version = "^3.1.10"}
 
 [tool.poetry.group.dev.dependencies]
-black = "^22.6.0"
-flake8 = "^5.0.4"
-flake8-bugbear = "^22.8.23"
+black = "^23.9.1"
+flake8 = "^6.1.0"
+flake8-bugbear = "^23.9.16"
 flake8-alfred = "^1.1.1"
-isort = "^5.10.1"
-mypy = "^0.971"
+isort = "^5.12.0"
+mypy = "^1.5.1"
 moto = {extras = ["s3"], version = "^4.0.2"}
-types-pytz = "^2022.2.1"
-coverage = "^6.4.4"
-Faker = "^14.2.0"
-factory-boy = "^3.2.1"
-bandit = "^1.7.4"
-pytest = "^6.0.0"
+types-pytz = "^2023.3.1.1"
+coverage = "^7.3.2"
+Faker = "^19.8.0"
+factory-boy = "^3.3.0"
+bandit = "^1.7.5"
+pytest = "^7.4.2"
 pytest-watch = "^4.2.0"
 pytest-lazy-fixture = "^0.6.3"
 types-pyyaml = "^6.0.12.11"
+setuptools = "^68.2.2"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
@@ -81,6 +82,8 @@ warn_redundant_casts = true
 warn_unreachable = true
 warn_unused_ignores = true
 
+plugins = ["pydantic.mypy"]
+
 [tool.bandit]
 # Ignore audit logging test file since test audit logging requires a lot of operations that trigger bandit warnings
 exclude_dirs = ["./tests/src/logging/test_audit.py"]
@@ -98,9 +101,7 @@ disallow_untyped_defs = false
 # When a library has addressed its deprecation issues and we've updated the
 # library, we can remove the ignore filter for that library.
 filterwarnings = [
-  "ignore::DeprecationWarning:botocore.*",
-  "ignore::DeprecationWarning:apispec.*",
-  "ignore::DeprecationWarning:certifi.*"] # pytest-watch errors if the closing bracket is on it's own line
+  "ignore::DeprecationWarning:botocore.*"] # pytest-watch errors if the closing bracket is on it's own line
 
 markers = [
   "audit: mark a test as a security audit log test, to be run isolated from other tests"]

app/src/adapters/db/flask_db.py

@@ -39,7 +39,7 @@ def health():
         # db_client.get_connection() or db_client.get_session()
 """
 from functools import wraps
-from typing import Any, Callable, Concatenate, ParamSpec, TypeVar
+from typing import Callable, Concatenate, ParamSpec, TypeVar
 
 from flask import Flask, current_app
 
@@ -115,10 +115,13 @@ def fiz(db_session: db.Session, x, y, z):
 
     def decorator(f: Callable[Concatenate[db.Session, P], T]) -> Callable[P, T]:
         @wraps(f)
-        def wrapper(*args: Any, **kwargs: Any) -> T:
+        def wrapper(*args: P.args, **kwargs: P.kwargs) -> T:
             with get_db(current_app, client_name=client_name).get_session() as session:
                 return f(session, *args, **kwargs)
 
         return wrapper
 
-    return decorator
+    # mypy says the type should be something slightly different
+    # Callable[[Arg(Callable[[Session, **P], T], 'f')], Callable[P, T]]
+    # but also mentions that "Arg" is deprecated, so not sure how to make it happy
+    return decorator  # type: ignore

app/src/api/users/user_routes.py

@@ -15,7 +15,7 @@
 
 
 @user_blueprint.post("/v1/users")
-@user_blueprint.input(user_schemas.UserSchema)
+@user_blueprint.input(user_schemas.UserSchema, arg_name="user_params")
 @user_blueprint.output(user_schemas.UserSchema, status_code=201)
 @user_blueprint.auth_required(api_key_auth)
 @flask_db.with_db_session()
@@ -32,7 +32,7 @@ def user_post(db_session: db.Session, user_params: users.CreateUserParams) -> di
 # Allow partial updates. partial=true means requests that are missing
 # required fields will not be rejected.
 # https://marshmallow.readthedocs.io/en/stable/quickstart.html#partial-loading
-@user_blueprint.input(user_schemas.UserSchema(partial=True))
+@user_blueprint.input(user_schemas.UserSchema(partial=True), arg_name="patch_user_params")
 @user_blueprint.output(user_schemas.UserSchema)
 @user_blueprint.auth_required(api_key_auth)
 @flask_db.with_db_session()

app/src/db/migrations/env.py

@@ -16,7 +16,6 @@
 
 # Initialize logging
 with src.logging.init("migrations"):
-
     # add your model's MetaData object here
     # for 'autogenerate' support
     # from myapp import mymodel

app/src/db/models/base.py

@@ -51,7 +51,7 @@ class Base(DeclarativeBase):
     }
 
     def _dict(self) -> dict:
-        return {c.key: getattr(self, c.key) for c in inspect(self).mapper.column_attrs}  # type: ignore
+        return {c.key: getattr(self, c.key) for c in inspect(self).mapper.column_attrs}
 
     def for_json(self) -> dict:
         json_valid_dict = {}

app/src/logging/audit.py

@@ -72,7 +72,9 @@ def handle_audit_event(event_name: str, args: tuple[Any, ...]) -> None:
 def log_audit_event(event_name: str, args: Sequence[Any], arg_names: Sequence[str]) -> None:
     """Log a message but only log recently repeated messages at intervals."""
     extra = {
-        f"audit.args.{arg_name}": arg for arg_name, arg in zip(arg_names, args) if arg_name != "_"
+        f"audit.args.{arg_name}": arg
+        for arg_name, arg in zip(arg_names, args, strict=True)
+        if arg_name != "_"
     }
 
     key = (event_name, repr(args))

app/src/logging/formatters.py

@@ -101,7 +101,7 @@ def __init__(self, message_width: int = HUMAN_READABLE_FORMATTER_DEFAULT_MESSAGE
     def format(self, record: logging.LogRecord) -> str:
         message = super().format(record)
         return decodelog.format_line(
-            datetime.utcfromtimestamp(record.created),
+            datetime.fromtimestamp(record.created),
             record.name,
             record.funcName,
             record.levelname,

app/src/services/users/patch_user.py

@@ -30,7 +30,6 @@ def patch_user(
     user_id: str,
     patch_user_params: PatchUserParams,
 ) -> User:
-
     with db_session.begin():
         # TODO: move this to service and/or persistence layer
         user = db_session.get(User, user_id, options=[orm.selectinload(User.roles)])
@@ -50,7 +49,6 @@ def patch_user(
 
 
 def _handle_role_patch(db_session: Session, user: User, request_roles: list[RoleParams]) -> None:
-
     current_role_types = set([role.type for role in user.roles])
     request_role_types = set([role["type"] for role in request_roles])
 

app/tests/src/logging/test_audit.py

@@ -141,7 +141,7 @@ def test_audit_hook(
         pass
 
     assert len(caplog.records) == len(expected_records)
-    for record, expected_record in zip(caplog.records, expected_records):
+    for record, expected_record in zip(caplog.records, expected_records, strict=True):
         assert record.levelname == "AUDIT"
         assert_record_match(record, expected_record)
 
@@ -161,7 +161,7 @@ def test_os_kill(init_audit_hook, caplog: pytest.LogCaptureFixture):
     ]
 
     assert len(caplog.records) == len(expected_records)
-    for record, expected_record in zip(caplog.records, expected_records):
+    for record, expected_record in zip(caplog.records, expected_records, strict=True):
         assert record.levelname == "AUDIT"
         assert_record_match(record, expected_record)
 
@@ -232,7 +232,7 @@ def test_repeated_audit_logs(
     ]
 
     assert len(caplog.records) == len(expected_records)
-    for record, expected_record in zip(caplog.records, expected_records):
+    for record, expected_record in zip(caplog.records, expected_records, strict=True):
         assert record.levelname == "AUDIT"
         assert_record_match(record, expected_record)
 

app/tests/src/logging/test_flask_logger.py

@@ -83,7 +83,7 @@ def test_request_lifecycle_logs(
     # then the log message in the after_request handler.
 
     assert len(caplog.records) == len(expected_extras)
-    for record, expected_extra in zip(caplog.records, expected_extras):
+    for record, expected_extra in zip(caplog.records, expected_extras, strict=True):
         assert_dict_contains(record.__dict__, expected_extra)
 
 

app/tests/src/logging/test_logging.py

@@ -28,7 +28,6 @@ def test_init(caplog: pytest.LogCaptureFixture, monkeypatch, log_format, expecte
     monkeypatch.setenv("LOG_FORMAT", log_format)
 
     with src.logging.init("test_logging"):
-
         records = caplog.records
         assert len(records) == 2
         assert re.match(