fix: update dependencies and add missing tools (closes #11) #21
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Major changes from 194 commits of development work: ## New Features - Rust acceleration for BAM counting (7x speedup) - Unified FASTQ/BAM pipeline - Single-cell support (scRNA-seq, scATAC-seq) - Enhanced statistical analysis (beta-binomial) - Improved CLI with better argument handling ## New Files - rust/ - Rust source for BAM counting acceleration - tests/ - Comprehensive test suite - docs/ - Enhanced documentation - .github/workflows/ - CI configuration - pyproject.toml - Modern Python packaging - pytest.ini, mypy.ini - Quality tools ## Module Updates - src/counting/ - Rust-accelerated allele counting - src/mapping/ - Optimized read mapping - src/analysis/ - Enhanced statistical methods - src/wasp2/ - Unified CLI entry points Closes #20 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Sync version to 1.2.0 across pyproject.toml, Cargo.toml, __init__.py - Fix Rust panic on empty allele strings in bam_counter.rs (use unwrap_or) - Fix Rust panic on file create in unified_pipeline.rs (use ? with context) - Fix Rust panic on HashMap get in bam_remapper.rs (use ok_or_else) - Fix bare except block in run_mapping.py (catch KeyError specifically) - Add error tracking for silent BAM failures in mapping_filter.rs - Add failure tracking and warnings in make_remap_reads.py Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add BAM read error tracking in bam_counter.rs (log first 5, warn total) - Add logging and error tracking in count_alleles.py - Convert test_rust_python_match.py to proper pytest with fixtures - Convert test_indel_correctness.py to proper pytest with fixtures Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Updates dependency configuration to address Issues #3, #4, and #6: - Add missing bioinformatics tools: samtools, bcftools, htslib, bedtools - Fix anndata/pandas version compatibility (anndata>=0.10.0,<0.12.0) - Add scientific libraries: statsmodels, scanpy, pyarrow, h5py - Synchronize versions across environment.yml, requirements.txt, pyproject.toml - Add Python 3.12 support in classifiers and black target-version - Create requirements-dev.txt for development dependencies - Update README.md with correct Python 3.10+ requirement Implemented via velocity workflow. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds <2.0 upper bound to maturin in [project.optional-dependencies].dev to match the constraint in rust optional deps and requirements-dev.txt. This prevents potential build breakage if maturin 2.x is released with breaking changes. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Moving to Jaureguy760/WASP2-exp |
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Summary
anndata>=0.10.0,<0.12.0Test plan
conda env create -f environment.ymlsucceedspip install -r requirements.txtsucceedspip install -r requirements-dev.txtsucceedspytest tests/to confirm tests passCloses #11, #3, #4, #6
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