Run the encoders in-process#29
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Drops the separate multiprocessing.Process encoder-server and the
AF_UNIX wire protocol. The VczReader and per-fh BedEncoder /
BgenEncoder instances now live in the FUSE handler process.
encoder.read, encoder.close, and reader teardown run on worker threads
via trio.to_thread.run_sync so the pyfuse3 trio task stays responsive.
The 30s per-read timeout and 2s aclose timeout are preserved — a slow
read still surfaces EIO to the kernel rather than blocking the
consumer indefinitely. On read timeout the worker thread is abandoned
(abandon_on_cancel=True) and the handle is marked dead; aclose drains
the abandoned thread via a threading.Event before closing the encoder,
or logs a warning and leaks if the encoder is permanently wedged.
The pyfuse3 mount Operations layer is largely untouched — it depends
on a Protocol (renamed EncoderClientProto -> EncoderHostProto) that
the new EncoderHost / StreamHandle satisfy. The accompanying tests
(test_encoder_ops, test_plink_apps, test_bgen_apps) track the rename.
Net diff: -2335 LOC across the deleted encoder_{client,server,protocol}
modules and their dedicated test files.
The glibc-arena fragmentation tuning called out in
notes/memory_rss_investigation.md (MALLOC_ARENA_MAX, malloc_trim) is
deferred to a separate change.
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Drops the separate multiprocessing.Process encoder-server and the AF_UNIX wire protocol. The VczReader and per-fh BedEncoder / BgenEncoder instances now live in the FUSE handler process. encoder.read, encoder.close, and reader teardown run on worker threads via trio.to_thread.run_sync so the pyfuse3 trio task stays responsive.
The 30s per-read timeout and 2s aclose timeout are preserved — a slow read still surfaces EIO to the kernel rather than blocking the consumer indefinitely. On read timeout the worker thread is abandoned (abandon_on_cancel=True) and the handle is marked dead; aclose drains the abandoned thread via a threading.Event before closing the encoder, or logs a warning and leaks if the encoder is permanently wedged.
The pyfuse3 mount Operations layer is largely untouched — it depends on a Protocol (renamed EncoderClientProto -> EncoderHostProto) that the new EncoderHost / StreamHandle satisfy. The accompanying tests (test_encoder_ops, test_plink_apps, test_bgen_apps) track the rename.
Net diff: -2335 LOC across the deleted encoder_{client,server,protocol} modules and their dedicated test files.
The glibc-arena fragmentation tuning called out in notes/memory_rss_investigation.md (MALLOC_ARENA_MAX, malloc_trim) is deferred to a separate change.