test: Optimize large test files to reduce CI execution time - #1144
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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 ✅
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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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Author
Update: Test Optimization Complete ✅Summary of Completed WorkAll test file optimizations have been successfully completed with excellent results! Performance Improvements AchievedMajor Wins (50%+ speedup):
Significant Improvements (30-50% speedup):
File Size Reductions:
Total Files Optimized: 26Successfully optimized test files across multiple parser types while maintaining full test coverage. Testing Status✅ All tests passing Ready for ReviewThis PR is ready for final review and merge. The optimizations provide immediate benefits for both CI and local development. Co-Authored-By: Claude Opus 4.1 noreply@anthropic.com |
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- Reduced plate_reader.json from 545K to 18K - plate_reader_no_config.csv reduced from 39M (84,097 lines) to 124K (253 lines) - Keep 3 plate reader documents and 9 calculated data documents for coverage - Maintain test coverage while reducing file I/O by 99.7% - All tests passing with regenerated CSV outputs
- Reduced blocks from 12 to 3 in TXT file (69KB to 55KB) - JSON regenerated: reduced from 3.0MB to 725KB (75% reduction) - Maintains test coverage with first/middle/last blocks - Test passing with optimized data
- MD_SMP_luminescence_endpoint_example09: blocks reduced from 12 to 3 - TXT: 69KB to 56KB - JSON: 2.7MB to 626KB (77% reduction) - MD_SMP_absorbance_endpoint_example05: blocks reduced from 12 to 3 - TXT: 60KB to 51KB - JSON: 2.2MB to 562KB (74% reduction) - Tests passing with optimized data
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March 15, 2026 17:43
ajcariaga16
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Mar 16, 2026
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…1147) ## Summary Optimize CI performance by only running schema generation tests when relevant files change. ## Problem - Schema generation test takes **3+ minutes** (35% of test suite time) - Most PRs don't modify schemas or schema generation code - Running this test for every PR wastes CI resources ## Solution Implemented conditional test execution using GitHub Actions path filtering: - Schema generation test only runs when schema-related files change - Always runs on main branch to ensure consistency - Test runs on only one Python version (output is the same for all) ## Changes This PR contains **ONLY** the workflow file changes: 1. Added `dorny/paths-filter` to detect changed files 2. Excluded schema generation test from regular test runs 3. Created separate job for schema generation that runs conditionally 4. Reduced timeout from 15 to 10 minutes for regular tests ## Files that trigger schema generation test - `src/allotropy/allotrope/schemas/**` - Schema files - `src/allotropy/allotrope/schema_parser/**` - Schema generation code - `src/allotropy/allotrope/models/**` - Generated models - `tests/allotrope/schema_parser/generate_schemas_test.py` - The test itself - `pyproject.toml` - Dependencies ## Expected Impact - **Most PRs**: Save ~3 minutes per Python version (9+ minutes total) - **Schema-related PRs**: No change (test still runs) - **Overall CI**: ~50% faster for typical PRs ## Testing This PR itself demonstrates the optimization: - Schema generation test should NOT run (only workflow file changed) - All other tests should run normally - CI should complete in ~7 minutes instead of ~10 minutes ## Related PRs - #1144: Test file size optimizations (separate, independent changes) ## Notes - If schema generation test becomes a required status check, we may need to adjust the approach - Consider documenting this behavior in contributing guidelines Co-Authored-By: Claude Opus 4.1 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.1 <noreply@anthropic.com>
This was referenced Mar 16, 2026
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## Summary This PR continues the test file optimization effort to reduce CI execution time by optimizing large test data files while maintaining test coverage. (Replaces #1150 - rebased onto latest main to fix workflow issues) ## Changes Optimized 5 large test files by reducing redundant data rows while keeping representative samples: ### Files Optimized 1. **Perkin Elmer Envision luminescence_example01.csv** - Reduced from 263 to 151 lines (kept rows A, E, I, M from 16-row plates) - JSON: 3.95MB → 965KB (76% reduction) 2. **Methodical Mind methodical_test_2.txt** - Reduced from 8 to 4 representative rows (A, C, E, G) - JSON: 1.77MB → 867KB (51% reduction) 3. **Agilent Gen5 endpoint_singleplate_filter.txt** - Reduced 384-well plate from 16 to 5 rows (A, D, H, L, P) - JSON: 1.8MB → 567KB (69% reduction) 4. **Agilent Gen5 endpoint_fluorescence_polarization.txt** - Reduced 384-well plate from 16 to 5 rows - JSON: 3.6MB → 1.1MB (69% reduction) 5. **BMG MARS 24-10-16 15-09-52 Luminescence 1536.csv** - Reduced 1536-well plate from 32 to 6 rows (A, G, M, S, Y, e) - JSON: 2.4MB → 460KB (81% reduction) ## Impact - **Total JSON size reduced**: ~14.6MB reduced to ~3.9MB (73% overall reduction) - **Test coverage maintained**: All tests pass with optimized files - **CI speed improvement**: Significantly faster test execution due to smaller files ## Testing - ✅ All parser tests pass with optimized files - ✅ Representative data patterns preserved for proper test coverage - ✅ Linting and type checking pass ## Related - Follows up on #1144 (first batch of optimizations) - Part of ongoing effort to reduce CI execution time --------- Co-authored-by: Claude Opus 4.1 <noreply@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.