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Fix stale Gemini install docs and warn on Rosetta SIGILL crash - #4
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Fixes#3. - README's Gemini install instructions still showed the pre-publish editable-install form (`pip install -e ".[gemini]"`), which doesn't work against the published package and isn't zsh-safe unquoted either. Point at `pip install "candy-cazyme[gemini]"` instead, and de-duplicate the instruction (it was written out twice). - A real Mac run crashed with "illegal hardware instruction" (SIGILL, no Python traceback) during the FAMSA alignment step. The Mac's Python was an Intel-prefix (/usr/local) Homebrew build, pointing at x86_64 Python running under Rosetta 2 translation on Apple Silicon hardware -- a known cause of SIGILL in native SIMD code (FAMSA/VeryFastTree both ship compiled SIMD) due to Rosetta's imperfect instruction emulation. Detect this at pipeline startup (before the potentially long clustering/curation stages run) via `sysctl -n sysctl.proc_translated` and log an actionable warning instead of letting the run crash silently near the end. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Fixes#3.
Summary
pip install -e ".[gemini]"), left over from before the package was on PyPI -- not usable post-install, and also not zsh-safe unquoted (zsh treats[gemini]as a glob). Fixed topip install "candy-cazyme[gemini]", and removed a duplicate copy of the same instruction elsewhere in the README.zsh: illegal hardware instructionduring the FAMSA alignment step, no Python traceback) traces to the Mac's Python being an Intel-prefix (/usr/local) Homebrew build -- i.e. x86_64 Python running under Rosetta 2 translation on Apple Silicon hardware, a known cause of SIGILL in native SIMD code (both FAMSA and VeryFastTree ship compiled SIMD) due to Rosetta's imperfect instruction emulation.run_pipelinenow detects a translated process at startup (viasysctl -n sysctl.proc_translated, gated to--treeruns since that's the only path that invokes FAMSA/VeryFastTree) and logs an actionable warning before the potentially long clustering/curation stages run, rather than the user finding out from a bare shell crash after several minutes. README also documents the underlying fix (use a native arm64 Python).Test plan
pytest-- 113 passed (5 new tests for the Rosetta-detection helper: warns when translated, silent on native arm64/genuine Intel/non-macOS, and doesn't crash ifsysctlitself is missing)