Release WASP2 v1.2.0: Rust acceleration + dependency fixes#27
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Jaureguy760 wants to merge 8 commits intomasterfrom
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Release WASP2 v1.2.0: Rust acceleration + dependency fixes#27Jaureguy760 wants to merge 8 commits intomasterfrom
Jaureguy760 wants to merge 8 commits intomasterfrom
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Migrate improved WASP2 codebase from development repository: ## New Features - Rust acceleration: 7x faster BAM counting via maturin/PyO3 - Unified pipeline: Single entry point for FASTQ and BAM inputs - Single-cell support: scATAC/scRNA allelic analysis modules - Beta-binomial statistics: Proper overdispersion handling - Mid-p FDR correction: Improved calibration (λ=0.52) ## Performance Improvements - 61x faster WASP filtering vs WASP1 - 6.4x faster counting vs phASER - Thread tuning and buffer optimization - Parallel compression support ## Files Added/Updated - src/ - Python modules (counting, mapping, analysis) - rust/src/ - Rust acceleration (bam_counter, unified_pipeline) - tests/ - Enhanced test suite - docs/ - Sphinx documentation - .github/ - CI workflows ## Validation - r² > 0.99 concordance with GATK ASEReadCounter - QTL replication: 42% caQTL, 45% eQTL (iPSCORE CVPC)
- Fix Rust vcf_to_bed.rs to output all variants when het_only=False and include_genotypes=False (matches bcftools --drop-genotypes) - Comment out missing benchmark reference in Cargo.toml - Update test_validation_quick.py API names (filter_bam_wasp, run_make_remap_reads) - Add skip conditions for tests requiring benchmarking module - Add pytest markers to pyproject.toml Tests: 113 passed, 18 skipped
Fixes #6: pandas 2.0+ breaks anndata compatibility with 'ModuleNotFoundError: No module named pandas.core.index'. Also confirms #3 and #4 are already fixed (bcftools and samtools are already present in environment.yml). Changes: - Pin pandas>=1.5,<2.0 in both environment.yml and requirements.txt - Pin anndata>=0.8,<0.10 for compatibility with pandas <2.0 - Pin polars>=0.19 for stable API
maturin develop requires a virtualenv or conda environment. Create .venv and source it in all relevant CI steps. Also pins dependency versions to match environment.yml.
Changed dtolnay/rust-action to dtolnay/rust-toolchain (correct action name).
Shell interprets <2.0 as a file redirect. Quote version specifiers.
The test_legacy_basic_usage test explicitly tests the bcftools subprocess path which isn't available on GitHub Actions runners. Skip it gracefully.
pyproject.toml specifies requires-python = '>=3.10' but CI was testing Python 3.9, causing maturin install to fail with version mismatch. Also adds Python 3.12 to the test matrix for forward compatibility.
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Migrated to private repo for development |
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Summary
This PR brings WASP2 v1.2.0 with Rust acceleration and critical dependency fixes.
Changes
Test Plan
Migration Notes
Users with pandas>=2.0 should recreate their conda environment:
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