Unfreeze SQLAlchemy

[dnil]

This PR adds | fixes:

• unfreeze, used with fix in Remove unused sqlservice requirement, partly revert and update Alchy class chanjo-report#56

How to prepare for test:

• ssh to ...
• Install on stage:
  bash servers/resources/SERVER.scilifelab.se/update-[THIS_TOOL]-stage.sh [THIS-BRANCH-NAME]

How to test:

Expected outcome:

• [ ]

Review:

• Code approved by
• Tests executed by
• "Merge and deploy" approved by

This version is a:

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[northwestwitch]

Seems a risky change to me

[northwestwitch]

sqlalchemy 2 can be quite different from v.1, there is even a migration guide: https://docs.sqlalchemy.org/en/20/changelog/migration_20.html

Just unfreezing like this seems risky..

[dnil]

Yes, I realised a little while ago. 😊 It was useful to test the dependencies at least: nice to see that chanjo-report / scout did build and run ok with this configuration. But chanjo would likely bug out without changes..

[northwestwitch]

💯

[northwestwitch]

Don't forget to update the CHANGELOG. Then we could release a new version of chanjo perhaps?

[dnil]

Mm, yes, but this is only to 1.4 so far. If you dont mind I would like to enable move-to-2.0-warnings and see what gives.
From the changelog its also evident we have actually already been higher than 1.3, although its not super clear what version we were on..

[northwestwitch]

Mm, yes, but this is only to 1.4 so far. If you dont mind I would like to enable move-to-2.0-warnings and see what gives. From the changelog its also evident we have actually already been higher than 1.3, although its not super clear what version we were on..

With SQLAlchemy 1.4 you can try creating a "future" engine, something that resembles SQLAlchemy 2. Perhaps this would help? --> https://docs.sqlalchemy.org/en/14/core/future.html

[dnil]

Well, yes, I tested with

SQLALCHEMY_WARN_20=1 pytest tests/

It gives a few, but it looks like only a few functions. I suspect the calculate -> add_columns will be the most annoying..

../../../../usr/local/miniconda3/envs/scout38again/lib/python3.8/site-packages/alchy/model.py:421
  /usr/local/miniconda3/envs/scout38again/lib/python3.8/site-packages/alchy/model.py:421: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 1.4) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    Model = declarative_base(cls=Base,

../../../../usr/local/miniconda3/envs/scout38again/lib/python3.8/site-packages/_pytest/config/__init__.py:1448
  /usr/local/miniconda3/envs/scout38again/lib/python3.8/site-packages/_pytest/config/__init__.py:1448: PytestConfigWarning: Unknown config option: looponfailroots

    self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")

tests/cli/test_cli_calculate.py: 16 warnings
tests/cli/test_cli_load.py: 20 warnings
tests/cli/test_cli_store.py: 69 warnings
tests/store/test_store_api.py: 81 warnings
tests/test_calculate.py: 32 warnings
  /usr/local/miniconda3/envs/scout38again/lib/python3.8/site-packages/alchy/session.py:31: SADeprecationWarning: Use .persist_selectable (deprecated since: 1.3)
    info = getattr(mapper.mapped_table, 'info', {})

tests/cli/test_cli_store.py::test_remove
  /Users/dannil/sandbox/chanjo/tests/cli/test_cli_store.py:32: LegacyAPIWarning: The Query.get() method is considered legacy as of the 1.x series of SQLAlchemy and becomes a legacy construct in 2.0. The method is now available as Session.get() (deprecated since: 1.4) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    assert Sample.query.get(sample_id)

tests/cli/test_cli_store.py::test_remove
tests/cli/test_cli_store.py::test_remove
  /Users/dannil/sandbox/chanjo/chanjo/cli/db.py:40: LegacyAPIWarning: The Query.get() method is considered legacy as of the 1.x series of SQLAlchemy and becomes a legacy construct in 2.0. The method is now available as Session.get() (deprecated since: 1.4) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    sample_obj = Sample.query.get(sample_id)

tests/cli/test_cli_store.py::test_remove
  /Users/dannil/sandbox/chanjo/tests/cli/test_cli_store.py:37: LegacyAPIWarning: The Query.get() method is considered legacy as of the 1.x series of SQLAlchemy and becomes a legacy construct in 2.0. The method is now available as Session.get() (deprecated since: 1.4) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    assert Sample.query.get(sample_id) is None

tests/cli/test_cli_store.py::test_samples
  /Users/dannil/sandbox/chanjo/tests/cli/test_cli_store.py:52: LegacyAPIWarning: The Query.get() method is considered legacy as of the 1.x series of SQLAlchemy and becomes a legacy construct in 2.0. The method is now available as Session.get() (deprecated since: 1.4) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    assert Sample.query.get(sample_id)

tests/cli/test_cli_store.py::test_transcripts
  /Users/dannil/sandbox/chanjo/tests/cli/test_cli_store.py:78: LegacyAPIWarning: The Query.get() method is considered legacy as of the 1.x series of SQLAlchemy and becomes a legacy construct in 2.0. The method is now available as Session.get() (deprecated since: 1.4) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    assert Sample.query.get(sample_id)

tests/cli/test_cli_store.py::test_delete
  /Users/dannil/sandbox/chanjo/tests/cli/test_cli_store.py:105: LegacyAPIWarning: The Query.get() method is considered legacy as of the 1.x series of SQLAlchemy and becomes a legacy construct in 2.0. The method is now available as Session.get() (deprecated since: 1.4) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    assert Sample.query.get(sample_id)

tests/cli/test_cli_store.py::test_delete
  /Users/dannil/sandbox/chanjo/tests/cli/test_cli_store.py:113: LegacyAPIWarning: The Query.get() method is considered legacy as of the 1.x series of SQLAlchemy and becomes a legacy construct in 2.0. The method is now available as Session.get() (deprecated since: 1.4) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    assert Sample.query.get(sample_id) is None

tests/cli/test_cli_store.py::test_delete_group
  /Users/dannil/sandbox/chanjo/tests/cli/test_cli_store.py:121: LegacyAPIWarning: The Query.get() method is considered legacy as of the 1.x series of SQLAlchemy and becomes a legacy construct in 2.0. The method is now available as Session.get() (deprecated since: 1.4) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    assert Sample.query.get(sample_id)

tests/cli/test_cli_store.py::test_delete_group
  /Users/dannil/sandbox/chanjo/tests/cli/test_cli_store.py:129: LegacyAPIWarning: The Query.get() method is considered legacy as of the 1.x series of SQLAlchemy and becomes a legacy construct in 2.0. The method is now available as Session.get() (deprecated since: 1.4) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    assert Sample.query.get(sample_id) is None

tests/store/test_store_api.py::test_save
  /Users/dannil/sandbox/chanjo/tests/store/test_store_api.py:36: LegacyAPIWarning: The Query.get() method is considered legacy as of the 1.x series of SQLAlchemy and becomes a legacy construct in 2.0. The method is now available as Session.get() (deprecated since: 1.4) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    assert Sample.query.get(sample_id) == new_sample

tests/store/test_store_api.py::test_save
  /Users/dannil/sandbox/chanjo/chanjo/store/api.py:120: SAWarning: New instance <Sample at 0x7fcb29a117f0> with identity key (<class 'chanjo.store.models.Sample'>, ('ADM12',), None) conflicts with persistent instance <Sample at 0x7fcb29a11730>
    self.commit()

tests/store/test_store_api.py::test_save
  /Users/dannil/sandbox/chanjo/tests/store/test_store_api.py:49: LegacyAPIWarning: The Query.get() method is considered legacy as of the 1.x series of SQLAlchemy and becomes a legacy construct in 2.0. The method is now available as Session.get() (deprecated since: 1.4) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    assert Sample.query.get(new_sampleid)

tests/test_calculate.py::test_gene
  /Users/dannil/sandbox/chanjo/chanjo/calculate.py:30: SADeprecationWarning: Query.add_column() is deprecated and will be removed in a future release.  Please use Query.add_columns() (deprecated since: 1.4)
    self.mean()

[dnil]

Ah, no, this will be the most annoying, since its actually not in our codebase.. 😞

../../../../usr/local/miniconda3/envs/scout38again/lib/python3.8/site-packages/alchy/model.py:421
  /usr/local/miniconda3/envs/scout38again/lib/python3.8/site-packages/alchy/model.py:421: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 1.4) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    Model = declarative_base(cls=Base

[dnil]

Ok, that was useful on some level I suppose. I'm now fairly convinced we will not be able to use Alchy (final version 2.2.2) with SQLAlchemy>=2. 1.4 seems ok if we wish to go through the hassle; it might help a little somewhere, but it is not going to take us to higher versions of e.g. Flask-SQLAlchemy that we would like.