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Reduce python transfer overhead in morgan fingerprints - #297

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scal444 merged 3 commits into
NVIDIA-BioNeMo:mainfrom
scal444:perf/morgan-python-input
Sep 11, 2026
Merged

scal444 merged 3 commits into
NVIDIA-BioNeMo:mainfrom
scal444:perf/morgan-python-input

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@scal444

@scal444 scal444 commented Sep 10, 2026

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The boost::python::extract is very slow. Added some more nvtx.

PR 5/5 for #267

@greptile-apps

greptile-apps Bot commented Sep 10, 2026 •

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RetriggerConfidence Score: 5/5

The pull request appears safe to merge; no actionable correctness, security, or repository-rule violations remain.

Summary

  • Converts accepted molecule sequences through PySequence_Fast and retains their owner for pointer lifetime safety.
  • Broadens the Python API annotation from list to Sequence.
  • Separates input conversion, stream acquisition, native computation, and output wrapping into NVTX ranges.
  • Adds tuple, invalid-input, empty-input, and larger-sequence coverage.

Reviews (2) · Last reviewed commit: "Hoist Morgan Python sequence item lookup"

@scal444
scal444 requested a review from evasnow1992 September 10, 2026 19:48
@scal444
scal444 force-pushed the perf/morgan-python-input branch from c68b683 to e4a129c Compare September 10, 2026 20:04

@evasnow1992 evasnow1992 left a comment

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Changes look good to me.

@scal444
scal444 merged commit 6ced500 into NVIDIA-BioNeMo:main Sep 11, 2026
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@scal444
scal444 deleted the perf/morgan-python-input branch September 18, 2026 12:35
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2 participants