Implement harmonypy component & make changes to concat

DriesSchaumont commented 1 year ago

I compared this implementation with the implementation from #55

❯ hyperfine --warmup 1 './target/docker/integrate/harmony/harmony -i mms_with_batch.h5mu  -o ./test.h5mu'
Benchmark 1: ./target/docker/integrate/harmony/harmony -i mms_with_batch.h5mu  -o ./test.h5mu
  Time (mean ± σ):     25.057 s ±  1.703 s    [User: 0.177 s, System: 0.128 s]
  Range (min … max):   23.303 s … 29.393 s    10 runs

❯ hyperfine --warmup 1 './target/docker/integrate/harmonypy/harmonypy -i mms_with_batch.h5mu  -o ./test.h5mu'
Benchmark 1: ./target/docker/integrate/harmonypy/harmonypy -i mms_with_batch.h5mu  -o ./test.h5mu
  Time (mean ± σ):      6.851 s ±  0.399 s    [User: 0.167 s, System: 0.114 s]
  Range (min … max):    6.364 s …  7.703 s    10 runs

docker stats for harmony

CONTAINER ID   NAME              CPU %     MEM USAGE / LIMIT    MEM %     NET I/O     BLOCK I/O   PIDS
8f1cb0159f28   gracious_carver   93.59%    431.6MiB / 15.6GiB   2.70%     876B / 0B   0B / 0B     14

docker stats for harmonypy

CONTAINER ID   NAME             CPU %     MEM USAGE / LIMIT    MEM %     NET I/O     BLOCK I/O   PIDS
4943d4d26b03   quirky_shirley   964.51%   137.8MiB / 15.6GiB   0.86%     736B / 0B   0B / 0B     20

DriesSchaumont commented 1 year ago

Integration CI @ https://github.com/openpipelines-bio/openpipeline/actions/runs/2969733996 Failing workflows are unrelated issues.

rcannood commented 1 year ago

Please merge #55 first!

DriesSchaumont commented 1 year ago

Closing in favour of #59 and #60

openpipelines-bio / openpipeline

Implement harmonypy component & make changes to concat #54