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Commits on May 31, 2026

• Bump version to 0.0.18

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• Fix multiple pipeline failures for long probes and complex gene loci

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Commits on Apr 9, 2026

• Suppress Luigi execution summary in all modes

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• Smoke-test system Fold binary before using it

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• Bump version to 0.0.17

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• Add missing import for _is_rnastructure_fold in check_required_dependencies

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• Validate system Fold binary is RNAstructure before using it

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• Fix unsupported platform test for cached Fold resolution

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• Fix slow cleanup step and Fold data table errors on remote/NFS systems

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• Improve live pipeline display: dynamic steps, spinners, and cleaner output

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• Rewrite console to live step display, bump version to 0.0.16

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• Reorder pipeline: move transcriptome BLAST after k-mer and structure filters

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• Parallelize transcriptome BLAST for large probe sets

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• Use TP53 as primary example gene in README

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• Speed up BLAST for large probe sets (MALAT1 ~12k probes)

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• Improve code maintainability, security, and type safety

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• Bump version to 0.0.15, remove gtfparse dependency

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• Update aad4 test SAM data to match current alignment output

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• Add e2e coverage and update README example

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• Improve ACTB probe yield, add CIGAR filter, per-probe cross-hyb, and auto-update

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• Fix --genome flag, HF downloads, Fold crashes, and transcriptome self-hit detection

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Commits on Apr 7, 2026

• Add bowtie2 installation to install.sh

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• Fix incorrect SHA pins for GitHub Actions

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• Fix CI security, code quality issues, make workflow section expandable

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• Restructure README: essentials first, optional content in expandable sections

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• Add gitignore entries for local build artifacts and analysis files

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• Fix ruff lint errors (unused imports, unused vars, empty f-string)

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• v0.0.13: Add 5 new genomes, env var for index cache, update docs

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• Add zebrafish (GRCz11) and rat (GRCr8) genome indices to HuggingFace

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Commits on Apr 6, 2026

• Add 107 regression and correctness tests (682 total, 69% coverage)

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• Add Drosophila BDGP6 genome indices to HuggingFace

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• Add yeast and C. elegans genome indices, fix Drosophila assembly version

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• Drop Python 3.9, remove setup.py, fix deps, boost coverage to 65%

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• Upgrade transitive deps to fix 6 dependabot vulnerabilities

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• v0.0.12: Fix integration tests, update README, add planned genomes, boost test coverage

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