Otherwise alembic/env.py gets executed out of context at test collection
stage (via tox -e unit >> run_tests.sh), which raises an AttributeError
(alembic.context is not set in this case)

Otherwise alembic/env.py gets executed out of context at test collection
stage (via tox -e unit >> run_tests.sh), which raises an AttributeError
(alembic.context is not set in this case)

To eliminate the repetitive `engine_options = engine_options or {}` in
multiple places.

This tests sqlalchemy migrate which is being replaced.

(does not include an import in mapping.py: to be added in a separate
commit, grouped with other edits in mapping.py)

Squashed:
- pick 01a42712d2 Avoid extra trip to db via lazy load of alembic version heads
- squash 8d729974d6 Fix mypy error

Ref galaxyproject#13007

- pick 058f09a Integrate migrations design into config and model code
- squash 89ca1a537b Drop config.database_create_tables (not used)

Next squash:
- pick cbf29e138c Integrate migrations into config, model (squashed)
- squash dd51fd578e Address existing mypy error (see note)

Address existing mypy error (see note)

This is a (possible) bug that has existed on dev. To expose it, simply
change this call to init_models_from_config
(https://github.com/galaxyproject/galaxy/blob/release_21.09/lib/galaxy/config/__init__.py#L1302)
to a call directly to mapping.init(). The result will be 6 mypy errors.

The reason is that the mapping.init() function
(https://github.com/galaxyproject/galaxy/blob/release_21.09/lib/galaxy/model/mapping.py#L79)
specifies its return type as GalaxyModelMapping - which results in
several errors of this type:

lib/galaxy/app.py:178: error: Definition of "model" in base class "MinimalApp" is incompatible with definition in base class "ConfiguresGalaxyMixin"

When we call an intermediary function (that does not have a return type
specified), mypy is happy.

This should be addressed in a separate issue/PR. Removing the return
type is the simplest (temporary) solution.

Next squash:
- squash c842973 Add type hints to migrations modules
- squash a54be22 Remove circular dependency between migrations and config

Setup infrastructure for running db scripts (squashed)

Squashed:
- pick 146ff8019a Setup infrastructure for running db scripts
- squash e0a26dcf3a Move is-one-db check into model.database_utils

Squashed:
- pick a82c44a Setup infrastructure for running db scripts (squashed)
- squash 31a1a702fe Fix mypy error

Squashed:
- pick 14a4eb08e2 Setup infrastructure for running db scripts (squashed)
- squash b1c6acb0f1 When overriding, override.

Add type hints to migrations modules

Remove circular dependency between migrations and config

Also add exec permissions to create/migrate python scripts.
(not sure this is required, adding for consistency with previous
version)

+ A few fixes for TS scripts, tests

Squashed:
- pick b624432 Add create/migrate scripts for Alembic dbs
- squash 06f0a92 Fix integration test (test only relevant for TS)

Note: manage_db entry point needs to be edited in model.orm.scripts.

Also, remove unused env var

Reason: 180 was added in dev, so it was not in 21.09.

- Preserves usage of legacy script while not hiding the Alembic script.
    (see manage_db.sh and run_alembic.sh)
- Adds documentation (see top of script files)
- Includes misc. relevant refactorings
- Includes unit tests for testing legacy script handling

If the database is combined, running `./manage_db.sh upgrade` should upgrade
BOTH models: gxy and tsi. However, if tsi uses a separate database, only
the galaxy model should be updated.

Also, see this for context: galaxyproject#13108 (comment)

See inline comments for more details.

The new tests are examples of new behavior.

All refactoring is directly related to the changes in this commit.

This was the last revision to the database that was handled with
SQLAlchemy Migrate prior to the move to Alembic (db version 180).
However, it was added to the dev branch after 21.09 was released, but
before 22.01. Therefore, this table should be created when upgrading
from 21.09, but not from dev.

Co-authored-by: Dannon <dannon.baker@gmail.com>

Co-authored-by: Dannon <dannon.baker@gmail.com>

Co-authored-by: Dannon <dannon.baker@gmail.com>

Squashed:
- pick 8a26c3c Fix import order in config
- squash ebe36de Apply black, isort

This will be added as an alembic revision as a separate commit

See inline comment ("version too old" is misleading if the incorrect
version is more recent than what the system expects).