docs: native Linux/HPC setup guide (SETUP_LINUX.md)#2
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Document the verified non-Docker Linux install: conda-forge compiler env, the channel-priority solver-hang workaround (--override-channels), and the required Cython/C extension build (without it the tool reports 0 repeats). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Summary
Adds
SETUP_LINUX.md— a verified, non-Docker install recipe for Linux/HPC where only conda/micromamba is available.The repo currently ships
environment.ymlpinned toosx-64(macOS) plus aDockerfile; there was no native-Linux path. This fills that gap.What it documents (all verified end-to-end on a Linux x86-64 HPC node)
c-compilerenv (no system gcc / nomoduleneeded)~/.condarcwithdefaults+channel_priority: stricthangs the solve (>10 min);--override-channels -c conda-forgefixes it (~4 s)_accelerators+ ctypes C extensions — without them the pure-Python fallbacks return empty and the tool reports 0 repeatsVerified toolchain
python 3.11.15 · numpy 2.4.6 · cython 3.2.5 · gcc 14.3.0 (conda-forge) · pydivsufsort 0.0.20 → smoke test 8 repeats.
🤖 Generated with Claude Code