Auto-provision FastTree so macOS doesn't need conda at all - #12
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A real user upgraded past the previous fixes (#10, #11) and hit the next wall: CANDy correctly defaults to --tree-tool fasttree on their Mac now, but fasttree itself still required conda -- which they don't have installed. Close that gap the same way MMseqs2 already avoids needing conda: auto-provision the binary on first use. New candy.phylogenetics.fasttree_download module, pinned to a specific commit of github.com/morgannprice/fasttree for reproducibility: - Linux/Windows: download the precompiled binary published directly in that repository. - macOS: no precompiled binary is published upstream at all, but FastTree.c is a single, dependency-free C file -- download it and compile it locally with whatever C compiler is already present (Xcode Command Line Tools' clang on essentially every real Mac), deliberately using the upstream-documented flags that avoid the OpenMP requirement that broke veryfasttree's own build (no -fopenmp, only -fopenmp-simd, which doesn't need the libomp runtime). Resolution order matches MMseqs2's established pattern: PATH, then the local cache, then auto-download/compile (disable via CANDY_NO_AUTO_DOWNLOAD, same as before). FastTreeBuilder now delegates to this instead of requiring PATH + a hard failure pointing at conda. Verified for real: the Windows download path was exercised live (not just mocked) against the actual pinned commit -- downloaded FastTree.exe and ran it successfully (FastTree 2.2.0, exit code 0, real --help output). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
AlexWindels
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Aug 11, 2026
Patch release: auto-provision FastTree (download on Linux/Windows, compile-from-source on macOS) so it no longer requires conda (#12). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Closes the gap the user hit right after #10/#11: CANDy now correctly selects fasttree by default on Macs without a working veryfasttree, but fasttree itself still required conda -- and they don't have conda installed.
Summary
New
candy.phylogenetics.fasttree_downloadmodule, mirroring the existing MMseqs2 auto-download pattern, pinned to a specific commit ofgithub.com/morgannprice/fasttreefor reproducibility:FastTree.cis a single, dependency-free C file -- download it and compile locally with whatever C compiler is already present (Xcode Command Line Tools'clang, on essentially every real Mac), using the upstream-documented flags that deliberately avoid the OpenMP requirement that brokeveryfasttree's own build (-fopenmp-simd, not-fopenmp-- nolibompruntime needed).Resolution order: PATH, then local cache, then auto-provision (disable via
CANDY_NO_AUTO_DOWNLOAD, same env var as MMseqs2).FastTreeBuildernow delegates to this instead of requiring PATH with a hard failure pointing at conda.Test plan
pytest-- 142 passed (10 new tests intest_fasttree_download.py: PATH/cache preference, disabled-download error, download-failure handling, precompiled download on Linux/Windows, compile-from-source on macOS, missing-compiler error, compile-failure error; 1 marked@pytest.mark.integration)FastTree.exe, ran-help, gotFastTree 2.2.0 Double precision, exit code 0python -m build+ confirmedfasttree_download.pyis included in the built wheel