Open packaged SQLite DBs in read-only immutable mode to avoid locking errors under SLURM

[wwood]

Motivation

• Triggered by reproducible SQLite disk I/O error failures observed when running under SLURM on some HPC/shared filesystems, likely due to file locking/journaling interactions.
• Packaged SingleM SQLite DBs are read-only at query time, so opening them in an immutable read-only mode should avoid lock/journal activity and be more robust on parallel/network filesystems.

Description

• Added _acquire_readonly_engine() helpers to SequenceDatabase and MetapackageReadNameStore that construct a quoted absolute path and open the DB with a SQLite URI including mode=ro, immutable=1, and uri=true.
• Replaced direct create_engine("sqlite:///...") calls for read/query access with the new helper so packaged DBs (e.g. otus.sqlite3 and read_taxonomies.sqlite3) are opened read-only immutable when acquired.
• Kept DB creation/import paths unchanged (only query-time acquire paths are switched to immutable/read-only), and used urllib.parse.quote + os.path.abspath to safely build file URIs.
• Added test/test_sqlite_readonly_mode.py unit tests that assert the acquire paths construct the expected read-only immutable SQLite URIs.

Testing

• Ran the project test suite with pixi run -e dev pytest test as required and the full suite completed with 225 passed, 24 skipped.
• The new test_sqlite_readonly_mode.py tests pass as part of that run and validate the read-only immutable engine construction.

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Codex Task