Remove greenlet and add asyncio extra to sqlalchemy

[ychiucco]

closes #894

Checklist before merging

• I added an appropriate entry to CHANGELOG.md

[github-actions]

Coverage report

The coverage rate went from 92.83% to 92.83% ➡️
The branch rate is 83%.

None of the new lines are part of the tested code. Therefore, there is no coverage data about them.

[tcompa]

This PR should solve the original Apple-M1 issue reported in #747 (comment), while sticking to the solution recommended by sqlalchemy.

@jluethi would you mind re-trying the installation that triggered your original error? I don't have other Apple M1s available..

You would need to:

1. Download this wheel file: fractal_server-1.3.12-py3-none-any.txt;
2. Rename it to fractal_server-1.3.12-py3-none-any.whl;
3. Run pip install fractal_server-1.3.12-py3-none-any.whl;
4. Run fractalctl set-db and fractalctl start from a folder where you have the usual environment file.

If it all goes through, we can safely merge.

Thanks!

[jluethi]

@tcompa I can confirm that this installs without error on an M1 mac and then starts the server.

I have not tested server functionality with it then, but I guess that shouldn't be necessary, right?

[tcompa]

@tcompa I can confirm that this installs without error on an M1 mac and then starts the server.

Thanks!

I have not tested server functionality with it then, but I guess that shouldn't be necessary, right?

It isn't necessary, indeed.

If I remove greenlet from a working environment, even fractalctl set-db fails:

Run alembic.config, with argv=['-c', '/tmp/venv/lib/python3.10/site-packages/fractal_server/alembic.ini', 'upgrade', 'head']
fractal_server.app.db
Traceback (most recent call last):
  File "/tmp/venv/lib/python3.10/site-packages/fractal_server/app/db/__init__.py", line 32, in engine_async
    return cls._engine_async
AttributeError: type object 'DB' has no attribute '_engine_async'. Did you mean: 'engine_async'?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/venv/bin/fractalctl", line 8, in <module>
    sys.exit(run())
  File "/tmp/venv/lib/python3.10/site-packages/fractal_server/__main__.py", line 83, in run
    set_db()
  File "/tmp/venv/lib/python3.10/site-packages/fractal_server/__main__.py", line 74, in set_db
    alembic.config.main(argv=alembic_args)
  File "/tmp/venv/lib/python3.10/site-packages/alembic/config.py", line 630, in main
    CommandLine(prog=prog).main(argv=argv)
  File "/tmp/venv/lib/python3.10/site-packages/alembic/config.py", line 624, in main
    self.run_cmd(cfg, options)
  File "/tmp/venv/lib/python3.10/site-packages/alembic/config.py", line 601, in run_cmd
    fn(
  File "/tmp/venv/lib/python3.10/site-packages/alembic/command.py", line 399, in upgrade
    script.run_env()
  File "/tmp/venv/lib/python3.10/site-packages/alembic/script/base.py", line 578, in run_env
    util.load_python_file(self.dir, "env.py")
  File "/tmp/venv/lib/python3.10/site-packages/alembic/util/pyfiles.py", line 93, in load_python_file
    module = load_module_py(module_id, path)
  File "/tmp/venv/lib/python3.10/site-packages/alembic/util/pyfiles.py", line 109, in load_module_py
    spec.loader.exec_module(module)  # type: ignore
  File "<frozen importlib._bootstrap_external>", line 883, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/tmp/venv/lib/python3.10/site-packages/fractal_server/migrations/env.py", line 98, in <module>
    asyncio.run(run_migrations_online())
  File "/usr/lib/python3.10/asyncio/runners.py", line 44, in run
    return loop.run_until_complete(main)
  File "/usr/lib/python3.10/asyncio/base_events.py", line 649, in run_until_complete
    return future.result()
  File "/tmp/venv/lib/python3.10/site-packages/fractal_server/migrations/env.py", line 88, in run_migrations_online
    engine = DB.engine_async()
  File "/tmp/venv/lib/python3.10/site-packages/fractal_server/app/db/__init__.py", line 34, in engine_async
    cls.set_db()
  File "/tmp/venv/lib/python3.10/site-packages/fractal_server/app/db/__init__.py", line 68, in set_db
    cls._engine_async = create_async_engine(
  File "/tmp/venv/lib/python3.10/site-packages/sqlalchemy/ext/asyncio/engine.py", line 43, in create_async_engine
    sync_engine = _create_engine(*arg, **kw)
  File "<string>", line 2, in create_engine
  File "/tmp/venv/lib/python3.10/site-packages/sqlalchemy/util/deprecations.py", line 309, in warned
    return fn(*args, **kwargs)
  File "/tmp/venv/lib/python3.10/site-packages/sqlalchemy/engine/create.py", line 660, in create_engine
    event.listen(pool, "connect", on_connect)
  File "/tmp/venv/lib/python3.10/site-packages/sqlalchemy/event/api.py", line 115, in listen
    _event_key(target, identifier, fn).listen(*args, **kw)
  File "/tmp/venv/lib/python3.10/site-packages/sqlalchemy/event/registry.py", line 232, in listen
    self.dispatch_target.dispatch._listen(self, *args, **kw)
  File "/tmp/venv/lib/python3.10/site-packages/sqlalchemy/pool/events.py", line 69, in _listen
    event_key.base_listen(**kw)
  File "/tmp/venv/lib/python3.10/site-packages/sqlalchemy/event/registry.py", line 270, in base_listen
    for_modify._set_asyncio()
  File "/tmp/venv/lib/python3.10/site-packages/sqlalchemy/event/attr.py", line 265, in _set_asyncio
    self._exec_once_mutex = AsyncAdaptedLock()
  File "/tmp/venv/lib/python3.10/site-packages/sqlalchemy/util/concurrency.py", line 67, in AsyncAdaptedLock
    _not_implemented()
  File "/tmp/venv/lib/python3.10/site-packages/sqlalchemy/util/concurrency.py", line 47, in _not_implemented
    raise ValueError(
ValueError: the greenlet library is required to use this function. No module named 'greenlet'