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fix(lib): deprecation warnings and others #508

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Run time

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Job	Run time
linkcheck-docs	2m 25s
cargo-test (macos-latest, 3.9)	1m 40s
python-benchmark	7m 13s
cargo-test (macos-latest, 3.10)	1m 11s
pytest (macos-latest, 3.9)	2m 39s
cargo-test (macos-latest, 3.11)	57s
rust-benchmark	5m 44s
pytest (macos-latest, 3.10)	2m 5s
cargo-test (macos-latest, 3.12)	1m 0s
pytest (macos-latest, 3.11)	2m 2s
pytest (macos-latest, 3.12)	2m 25s
cargo-test (ubuntu-latest, 3.9)	1m 0s
pytest (ubuntu-latest, 3.9)	2m 48s
cargo-test (ubuntu-latest, 3.10)	56s
pytest (ubuntu-latest, 3.10)	2m 40s
pytest (ubuntu-latest, 3.11)	2m 27s
cargo-test (ubuntu-latest, 3.11)	53s
pytest (ubuntu-latest, 3.12)	3m 4s
cargo-test (ubuntu-latest, 3.12)	55s
cargo-test (windows-latest, 3.9)	1m 54s
pytest (windows-latest, 3.9)	4m 43s
pytest (windows-latest, 3.10)	4m 42s
cargo-test (windows-latest, 3.10)	2m 35s
pytest (windows-latest, 3.11)	5m 44s
cargo-test (windows-latest, 3.11)	2m 16s
pytest (windows-latest, 3.12)	6m 33s
cargo-test (windows-latest, 3.12)	2m 43s
	1h 15m 14s