Use duckdb loading throughout pyprophet #131
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since duckdb is now a dependency and does joining of sql tables more efficiently use it more widespread throughout pyprophet
since sql queries to no guarentee order, change from duckdb to regular sql in this method as it is used in testing
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I am not sure why the tests are not being conducted. |
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Ok I think the tests are passing just not appearing in this PR for some reason |
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With export-parquet, we have an additional dependency of duckdb which allows for fast SQL queries, especially those involving lots of joins.
Here roll out duckdb SQL queries in pyprophet for greater data loading efficiency.
Examples
Conducted on dell XPS ubuntu
Export Command
time pyprophet export --in=39041_Hela_500ng_15SPD_DIA_Py3_1_S2-A7_1_4502.oswOld timings:
real 0m56.284s
user 0m35.997s
sys 0m15.130s
New timings:
real 0m12.832s
user 0m40.578s
sys 0m8.378s
Score Command
time pyprophet score --in=39041_Hela_500ng_15SPD_DIA_Py3_1_S2-A7_1_4502.osw --ss_num_iter=1Old Timings:
real 0m59.466s
user 1m30.275s
sys 0m11.004s
New timings:
real 0m30.482s
user 1m21.186s
sys 0m9.460s