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perf: cache mappers, avoid allocations, codons are arrays #172

Merged
merged 15 commits into from
Jun 10, 2024
Merged

perf: cache mappers, avoid allocations, codons are arrays #172

merged 15 commits into from
Jun 10, 2024

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tedil
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@tedil tedil commented Jun 10, 2024

I didn't realize we already depend on quick_cache, so perhaps replace the new cached dep with that.

The key for caching currently relies on the provider supplying consistent data_version and schema_version information.

Todo: Should depend on next seqrepo release.

@tedil tedil requested a review from holtgrewe June 10, 2024 08:04
@tedil tedil changed the title enhancement: Performance improvements: cache mappers, avoid allocations, codons are arrays feat: Performance improvements: cache mappers, avoid allocations, codons are arrays Jun 10, 2024
@tedil tedil changed the title feat: Performance improvements: cache mappers, avoid allocations, codons are arrays perf: Performance improvements: cache mappers, avoid allocations, codons are arrays Jun 10, 2024
@tedil tedil changed the title perf: Performance improvements: cache mappers, avoid allocations, codons are arrays perf: cache mappers, avoid allocations, codons are arrays Jun 10, 2024
@tedil tedil marked this pull request as draft June 10, 2024 09:16
@tedil tedil marked this pull request as ready for review June 10, 2024 14:26
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codecov bot commented Jun 10, 2024

Codecov Report

Attention: Patch coverage is 87.71930% with 14 lines in your changes missing coverage. Please review.

Project coverage is 86.34%. Comparing base (bd2b05e) to head (aae3cbb).
Report is 1 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #172      +/-   ##
==========================================
- Coverage   87.42%   86.34%   -1.09%     
==========================================
  Files          18       18              
  Lines        7705     7145     -560     
==========================================
- Hits         6736     6169     -567     
- Misses        969      976       +7     
Files Coverage Δ
src/data/cdot/json.rs 89.59% <100.00%> (ø)
src/mapper/altseq.rs 93.58% <100.00%> (+0.04%) ⬆️
src/mapper/cigar.rs 96.69% <ø> (ø)
src/mapper/variant.rs 91.48% <100.00%> (+0.53%) ⬆️
src/normalizer.rs 70.73% <ø> (ø)
src/sequences.rs 94.86% <75.00%> (-3.43%) ⬇️
src/mapper/alignment.rs 90.32% <75.00%> (-0.24%) ⬇️
src/data/uta.rs 89.48% <85.71%> (-2.53%) ⬇️

@tedil tedil merged commit 34acaf4 into main Jun 10, 2024
7 of 8 checks passed
@tedil tedil deleted the perf branch June 10, 2024 14:41
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