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Speed tests #99

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6 tasks
Adamtaranto opened this issue Nov 26, 2024 · 0 comments
Open
6 tasks

Speed tests #99

Adamtaranto opened this issue Nov 26, 2024 · 0 comments
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enhancement New feature or request

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@Adamtaranto
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Adamtaranto commented Nov 26, 2024

We should add some sort of automated test for speed.

It would be nice to add an option for time logging within the rust functions... but I'm just going to do it on the Python API side for now.

  • Github action triggered by commit to PR or merge into main branch
  • Store sample bacterial genome locally (exclude from package build. Or fetch as required.)
  • Build package + pip install
  • Run python script that loads oxli and times the consume function in canonical vs stranded and store_kmers T/F modes.
  • Log peak memory usage?
  • Update and commit speed log:
    • commit hash, branch name, tag, date, commit msg, time: Canonical, time: Canonical + store_kmers, total hashes in table, total counts, total consumed bases
@Adamtaranto Adamtaranto added the enhancement New feature or request label Nov 26, 2024
@Adamtaranto Adamtaranto self-assigned this Nov 26, 2024
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