chore: Optimize large test files to reduce CI execution time#1144
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nathan-stender wants to merge 35 commits intomainfrom
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chore: Optimize large test files to reduce CI execution time#1144nathan-stender wants to merge 35 commits intomainfrom
nathan-stender wants to merge 35 commits intomainfrom
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Problem: - Tests were timing out after 10 minutes in GitHub Actions - Root cause: chardet.detect() spending 20+ seconds on large test files Solution: - Try UTF-8 encoding first (works for 95% of files, nearly instant) - Fall back to chardet only when UTF-8 decode fails - Increase timeout to 15 minutes as safety measure Results: - 4x speedup for large files (10s → 2.5s) - 2x speedup for full test suites - Tests now complete well within time limits Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The luminex CSV files contain corrupted micro (µ) symbols that were replaced with UTF-8 replacement characters. When parsed with ISO-8859-1 (via chardet), these got incorrectly displayed as '�'. With the UTF-8 optimization, we now correctly get '�' instead. Updated the expected JSON files to reflect the correct encoding behavior.
Similar to the previous luminex fix, the CSV file contains a registered trademark symbol (®) that was incorrectly displayed as '®' when parsed with ISO-8859-1. With UTF-8 parsing, we now correctly get '®'.
- AppBio QuantStudio example01.txt: 3.5MB → 7KB (99.8% reduction) - Biorad Bioplex example01.xml: 6.0MB → 1.9MB (68.4% reduction) Reduces test execution time while maintaining full test coverage. All tests passing with regenerated output files.
Successfully optimized: - appbio_quantstudio_example05.txt: 228KB → 5KB (97.9% reduction) - appbio_quantstudio_example07.txt: 284KB → 6KB (97.9% reduction) Total files optimized so far: 4 All tests passing with regenerated output files.
Test suite improvement: 1.1x faster (10.8% reduction) - Baseline: 341 seconds - Optimized: 304 seconds - 37 seconds saved 4 files optimized with 68-99% size reductions All tests passing ✅
nathan-stender
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AppBio QuantStudio: - example02.txt: 717KB → 54KB (92.5% reduction) - example03.txt: 302KB → 40KB (86.7% reduction) - example04.txt: 124KB → 28KB (77.2% reduction) MolDev SoftMax Pro: - partial_plate_with_empty_values.txt: 226KB → 7KB (96.8% reduction) - ACSINS_absorbance_timeformat_spectrum.txt: 223KB → 79KB (64.7% reduction) Agilent: - TapeStation example_01.xml: 161KB → 18KB (89.0% reduction) - Gen5 kinetic_helper_gene_growth_curve.txt: 120KB → 7KB (93.8% reduction) Roche CEDEX BioHT: - example03.txt: 104KB → 103KB (minimal change) Preserves test coverage while significantly reducing CI execution time. Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
Luminex xPONENT: - NaN_and_not_reported_values.csv: 44KB → 3KB (92.1% reduction) Roche CEDEX HiRes: - example_3.csv: 40KB → 4KB (89.7% reduction) Removed JSON outputs for affected files to be regenerated on next test run. Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
Deleted JSON outputs from previous batches that will be regenerated when tests are run with the optimized input files. Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
Reverted 3 files that caused test failures: - luminex_xPONENT_NaN_and_not_reported_values.csv - ACSINS_absorbance_timeformat_spectrum.txt - partial_plate_with_empty_values.txt These files have complex formatting requirements that were broken by the optimization. Restoring to original versions. Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
- Reduced from 7 tubes to 3 tubes (keeping test coverage) - Simplified polygon points in gate regions (max 5 points per polygon) - File lines reduced from 11,629 to 7,965 - Test passes with optimized data Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
- Reduced from 16 samples to 6 samples (keeping test coverage) - File lines reduced from ~1500 to 767 - Test passes with optimized data Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
…: 38KB → 16KB (58% reduction) - Reduced from 16 rows (A-P) to 6 rows (A-F) per data section - Kept 144 wells instead of 384 wells (maintaining test coverage) - File lines reduced from 240 to 160 - Test passes with optimized data Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
…: 43KB → 18KB (58% reduction) - Reduced from 16 rows (A-P) to 6 rows (A-F) per data section - Kept 144 wells instead of 384 wells (maintaining test coverage) - File lines reduced from 260 to 170 - Test passes with optimized data Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
- Reduced from 16 samples to 5 samples (A1, A2, B1, C1, D1) - Maintains diversity of test data across all rows - File lines reduced from 257 to 81 - Test passes with optimized data Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
…: 23KB → 10KB (57% reduction) - Reduced from 16 rows (A-P) to 6 rows (A-F) per data section - Kept 144 wells instead of 384 wells (maintaining test coverage) - File lines reduced from 157 to 117 - Test passes with optimized data Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
… 38KB → 11KB (71% reduction) - Reduced kinetic time points from 61 to 13 (keeping every 5th point) - Maintains kinetic profile for testing purposes - File lines reduced from 134 to 86 - Test passes with optimized data Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
- Reduced ladder sample peaks from 14 to 5 - Kept all peaks for other samples (3 each) - File lines reduced from 766 to 586 - Test passes with optimized data Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
…ction) - Reduced wavelength points from 41 to 14 (keeping every 3rd point) - Maintains spectral profile with NaN and OVRFLW values - File lines reduced from 82 to 55 - Test passes with optimized data Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
…KB → 10KB (60% reduction) - Reduced wavelength points from 41 to 14 (keeping every 3rd point) - Maintains spectral profile for testing - File lines reduced from 85 to 58 - Test passes with optimized data Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
…(70% reduction) MAJOR PERFORMANCE IMPROVEMENT: - Test runtime reduced from 1.75s to 0.60s (66% faster!) - Reduced from 93 wells to 24 wells - File lines reduced from 112 to 43 - One of the slowest tests now runs much faster Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com>
…peedup) - Reduced tubes from 7 to 3 - Simplified polygon points in gates (max 5 points) - File size: 1.4MB → 690KB - Test time: 2.19s → 1.03s (53% improvement) Co-authored-by: Claude <assistant@anthropic.com>
- Kept every 3rd wavelength point (14 of 41) - File size: 2.8KB → 2.4KB - Test time: stable at ~0.74s Co-authored-by: Claude <assistant@anthropic.com>
- Kept every 3rd wavelength point (14 of 41) - File size: 2.5KB → 2.1KB - Handles OVRFLW values correctly Co-authored-by: Claude <assistant@anthropic.com>
- Reduced wells from 93 to 24 - File size: 19KB (unchanged but less data) - Test time: 1.75s → 0.73s (58% improvement) Co-authored-by: Claude <assistant@anthropic.com>
- Reduced from 8 well rows (A-H) to 4 (A-D) - File size: 21KB → 13KB - Test time: 3.41s → 1.85s (46% improvement) Co-authored-by: Claude <assistant@anthropic.com>
- Reduced samples from 6 to 3 - File size: 25KB → 16.5KB (34% reduction) - Test time: ~1.37s Co-authored-by: Claude <assistant@anthropic.com>
- Reduced from 96 to 24 wells (for both fluorophores) - File size: 13KB → 2.5KB (81% reduction) - Test time: ~0.38s Co-authored-by: Claude <assistant@anthropic.com>
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Summary
This PR optimizes large test files to reduce test execution time and prevent CI timeouts.
Motivation
Changes - Batch 1 (2 files completed)
Approach
Progress
Next Steps
This PR will be updated incrementally with additional batches of optimized files. Each batch will:
Final update will include overall timing improvement factor.