simpleaf 0.27.0 (new formula) - #298825
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HOMEBREW_NO_INSTALL_FROM_API=1 brew install --build-from-source <formula>?brew test <formula>?brew audit --strict <formula>(after doingHOMEBREW_NO_INSTALL_FROM_API=1 brew install --build-from-source <formula>)? If this is a new formula, does it passbrew audit --new <formula>?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 --onlineandbrew 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 --onlinereports one remaining problem: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" => :buildis required becauseanndata-hdf5enableshdf5-metno-sys'sstaticfeature unconditionally, so HDF5 is always built from vendored sources.ENV["CC"]/ENV["CXX"]are set to the real compilers: the vendored HDF5 build recordsCMAKE_C_COMPILERin its build-settings blob, which otherwise leaves Homebrew shim paths in the binary.No runtime
depends_onon the mappers: simpleaf resolvespiscem/alevin-fryviasimpleaf set-pathsat runtime,piscemis not in core, and core'salevin-fry0.16.2 is below simpleaf's>=0.17.0floor. Can follow up with apiscemformula and analevin-frybump in separate PRs if wanted.