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simpleaf 0.27.0 (new formula) - #298825

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simpleaf 0.27.0 (new formula)#298825
BenjaminDEMAILLE wants to merge 1 commit into
Homebrew:mainfrom
BenjaminDEMAILLE:simpleaf-new

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  • Have you followed the guidelines for contributing?
  • Have you ensured that your commits follow the commit style guide?
  • Have you checked that there aren't other open pull requests for the same formula update/change?
  • Have you built your formula locally with HOMEBREW_NO_INSTALL_FROM_API=1 brew install --build-from-source <formula>?
  • Is your test running fine brew test <formula>?
  • Does your build pass brew audit --strict <formula> (after doing HOMEBREW_NO_INSTALL_FROM_API=1 brew install --build-from-source <formula>)? If this is a new formula, does it pass brew audit --new <formula>?

  • I did not use AI/LLM to create this PR, or I disclosed the tool/model below and reviewed its output; I did not attribute commits to AI and will answer maintainer questions and review comments myself without AI/LLM.

AI-assisted contribution by Claude Code (Claude Opus 5) of ~85% of the work: the AI wrote the formula and ran brew install --build-from-source, brew test, brew audit --new --strict --online and brew style. I reviewed the formula and those results before opening this PR. The commit carries no AI attribution trailer.

Built and tested locally on macOS 26.6.1 running arm64.


New formula for simpleaf, the COMBINE-lab workflow driver for single-cell/single-nucleus RNA-seq and scATAC preprocessing (companion to alevin-fry, already in core).

brew audit --new --strict --online reports one remaining problem:

* GitHub repository not notable enough (<30 forks, <30 watchers and <75 stars)

The repo is at 67 stars / 6 forks. Submitting anyway because the tool is published and peer-reviewed (Bioinformatics, 2023: btad614) and is packaged in Bioconda; happy to close if the maintainers would rather wait for the star threshold.

Two notes on the formula:

  • depends_on "cmake" => :build is required because anndata-hdf5 enables hdf5-metno-sys's static feature unconditionally, so HDF5 is always built from vendored sources.
  • ENV["CC"]/ENV["CXX"] are set to the real compilers: the vendored HDF5 build records CMAKE_C_COMPILER in its build-settings blob, which otherwise leaves Homebrew shim paths in the binary.

No runtime depends_on on the mappers: simpleaf resolves piscem/alevin-fry via simpleaf set-paths at runtime, piscem is not in core, and core's alevin-fry 0.16.2 is below simpleaf's >=0.17.0 floor. Can follow up with a piscem formula and an alevin-fry bump in separate PRs if wanted.

@github-actions github-actions Bot added new formula PR adds a new formula to Homebrew/homebrew-core rust Rust use is a significant feature of the PR or issue labels Aug 14, 2026
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