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Merge pull request #917 from COMBINE-lab/develop
Update pufferfish dependency to use SSHash k-mer dictionary. This removes the sparse/lossy index types from pufferfish, so collapse all sparse/dense dispatch in salmon to a single PufferfishIndex path. Changes: - Remove PufferfishSparseIndex include, isSparse(), puffSparseIndex() from SalmonIndex - Collapse sparse/dense dispatch in SalmonQuantify, ReadExperiment - Remove --sparse CLI option from BuildSalmonIndex - Add SSHash/PTHash include paths for ContigTable's elias_fano.hpp - Add sshash_static to pufferfish aux link libs - Remove salmon's xxhash.c (provided by pufferfish's puffer library) - Enable recursive submodule fetch for pufferfish's SSHash submodule - Bump pufferfish to cd84b05 (SSHash integration) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…ab/salmon into codex/develop-refactor
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Refactor, index update
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This pull request introduces significant improvements to the build, CI/CD, and documentation infrastructure for the project, as well as clarifies the removal of single-cell functionality and legacy workflows. The most important changes include the introduction of robust CI and release pipelines, modernization of build configuration files, and updates to documentation and contributor guidelines.
Build and CI/CD Infrastructure
.github/workflows/ci.yml) that supports multi-platform builds, conditional execution, artifact packaging, and smoke tests for both mapping and alignment modes..github/workflows/release.yml) that automates tagging and GitHub releases based on commit messages, and uploads built artifacts from CI.CMakePresets.jsonto simplify and standardize build configuration for development, release, and CI scenarios.Build System Modernization
FindHTSlib.cmake,FindMimalloc.cmake,CheckTBBLinkage.cmake, andCheckNoSystemZlib.cmake, improving reliability and compatibility checks for critical dependencies. [1] [2] [3] [4]FindJemalloc.cmakemodule, streamlining dependency management.Documentation and Contributor Guidance
.readthedocs.yamlfor ReadTheDocs integration, ensuring up-to-date documentation builds.README.mdto clarify the removal ofsalmon alevin, provide legacy workflow guidance, and improve references to current and legacy documentation. [1] [2]CONTRIBUTING.md, including licensing clarification and minor formatting fixes. [1] [2]Project Maintenance and Refactoring
.codex/REFRACTOR_BOOKMARK.mdto document module ownership cleanup, dependency floors, and planned optimization tasks.Miscellaneous
These changes collectively modernize the project's build and release process, clarify documentation and contributor expectations, and reinforce the project's focus on bulk RNA-seq workflows.