eti homologs --num_procs with more than 1 results in a run-time error

[khiron]

Running eti homologs --installed mammals_install_112 --outpath homology100 --ref human --limit 100 --force_overwrite --verbose works as expected

Running the same command with --num_procs 2 results in 2 python3 tasks being scheduled and allocated to processors as expected

However the Extracting 🧬 display is not updated during extraction and upon apparent completion of extraction the following run-time error occurs trying to serialize the sqllite connection

eti homologs --installed mammals_install_112 --outpath homology100 --ref human --num_procs 2 --limit 100 --force_overwrite --verbose
Loaded genome for 'human'
Found 63,140 gene IDs for 'human'
Found 100 homolog groups
Homolog search ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00 0:00:00
Extracting  🧬 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━   0% -:--:-- 0:04:07
loky.process_executor._RemoteTraceback:
"""
Traceback (most recent call last):
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/loky/process_executor.py", line 370, in _sendback_result
    result_queue.put(
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/loky/backend/queues.py", line 230, in put
    obj = dumps(obj, reducers=self._reducers)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/loky/backend/reduction.py", line 215, in dumps
    dump(obj, buf, reducers=reducers, protocol=protocol)
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/loky/backend/reduction.py", line 208, in dump
    _LokyPickler(file, reducers=reducers, protocol=protocol).dump(obj)
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/cloudpickle/cloudpickle.py", line 1295, in dump
    return super().dump(obj)
           ^^^^^^^^^^^^^^^^^
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/cogent3/core/annotation_db.py", line 560, in __getstate__
    return {"data": self._db.serialize(), "source": self.source}
                    ^^^^^^^^^^^^^^^^^^
AttributeError: 'sqlite3.Connection' object has no attribute 'serialize'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/richard/source/ensembl/.venv/bin/eti", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/ensembl_tui/cli.py", line 578, in homologs
    for seqs in get_seqs.as_completed(
                ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/cogent3/util/progress_display.py", line 112, in series
    for i, item in enumerate(items):
                   ^^^^^^^^^^^^^^^^
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/cogent3/util/parallel.py", line 228, in as_completed
    yield from _as_completed_mproc(f, s, max_workers)
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/cogent3/util/parallel.py", line 216, in _as_completed_mproc
    yield result.result()
          ^^^^^^^^^^^^^^^
  File "/home/richard/.local/share/uv/python/cpython-3.12.8-linux-x86_64-gnu/lib/python3.12/concurrent/futures/_base.py", line 449, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/home/richard/.local/share/uv/python/cpython-3.12.8-linux-x86_64-gnu/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
AttributeError: 'sqlite3.Connection' object has no attribute 'serialize'
Exception ignored in: <function Hdf5Mixin.__del__ at 0x7cf39bf3f600>
Traceback (most recent call last):
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/ensembl_tui/_storage_mixin.py", line 182, in __del__
  File "/home/richard/source/ensembl/.venv/lib/python3.12/site-packages/ensembl_tui/_storage_mixin.py", line 188, in close
NameError: name 'open' is not defined