Add parquet and sqlite support; add NNLS-based PEP and Q-value calculation #415

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Run time

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Job	Run time
build (3.9, ubuntu-latest, false)	11m 30s
build (3.9, windows-latest, false)	14m 3s
build (3.9, macos-latest, false)	8m 44s
build (3.10, ubuntu-latest, false)	11m 35s
build (3.10, windows-latest, false)	13m 50s
build (3.10, macos-latest, false)	9m 27s
build (3.11, ubuntu-latest, false)	11m 34s
build (3.11, windows-latest, false)	13m 56s
build (3.11, macos-latest, false)	9m 19s
build (3.12, ubuntu-latest, false)	13m 5s
build (3.12, windows-latest, false)	16m 36s
build (3.12, macos-latest, false)	8m 49s
	2h 22m 28s