sqlite3.OperationalError: disk I/O error

Crash Report

$ mypy . --show-traceback
error: INTERNAL ERROR -- Please try using mypy master on GitHub:
https://mypy.readthedocs.io/en/stable/common_issues.html#using-a-development-mypy-build
Please report a bug at https://github.com/python/mypy/issues
version: 2.3.1
Traceback (most recent call last):
  File "/tmp/py/lib/python3.14/site-packages/mypy/__main__.py", line 16, in console_entry
    main()
    ~~~~^^
  File "mypy/main.py", line 154, in main
  File "mypy/main.py", line 244, in run_build
    res = build.build(sources, options, None, flush_errors, fscache, stdout, stderr)
  File "mypy/build.py", line 385, in build
  File "mypy/build.py", line 1908, in create_metastore
    mds: MetadataStore = SqliteMetadataStore(
  File "mypy/metastore.py", line 200, in __init__
  File "mypy/metastore.py", line 172, in connect_db
    db.execute("PRAGMA synchronous=OFF")
sqlite3.OperationalError: disk I/O error

note: use --pdb to drop into pdb

To Reproduce

Source files are in a network mount:

$ mount | grep src
src on /home/hugo/src type 9p (rw,relatime,access=client,trans=virtio)

Sources are readable, execute fine, can be checked with ruff, etc.

You can quickly run a VM to reproduce this via:

qemu-system-x86_64 \
	--enable-kvm \
	-nic user \
	-nographic \
	-m 4G \
	-smp cores=2 \
        -drive file=alpine-virt-3.24.1-x86_64.iso,format=raw \                                                                                                                                                                                 
	-virtfs local,path=$HOME/src/,mount_tag=src,security_model=mapped-xattr

Then install mypy, mount the shared filesystem, and run it on any code in that fs.

Your Environment

• Mypy version used: mypy 2.3.1 (compiled: yes)
• Mypy command-line flags: (none/any)
• Mypy configuration options from mypy.ini (and other config files): irrelevant; always happens
• Python version used: Python 3.14.7
• Operating system and version: Alpine Linux Edge

Start with mypy/metastore.py, especially connect_db and create_metastore, where the traceback reaches PRAGMA synchronous=OFF. Reproduce with the supplied Alpine VM and 9p-mounted source tree, then inspect how the metadata database behaves on that mount. Done should mean checking mypy no longer terminates with this internal sqlite3.OperationalError in the reported environment.