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This test is not sufficient because it will prevent _sqlite from being built with a local copy of SQLite rather than the Apple-supplied system version and that is something that many distributors of Python on macOS do, including the python.org macOS installers. So, to avoid the deprecation warning, you want to be able to know you are linking with the system version. That might be a little tricky to do reliably; it might have to be done in either configure.ac or setup.py and would need to take into account SDKs. And in most cases it is probably better to avoid using the macOS system SQLite anyway. So i'm not sure this is worth trying to fix.
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To be more precise, it would not prevent _sqlite from being built; it would disallow use of
enable_shared_cache. Which, BTW, doesn't seem to be documented in the sqlite3 module doc page?