docs: public-readiness audit fixes (stale refs + genericize Euler mentions)#41
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…r mentions Prep for making the repo public. Adversarial audit of secrets/privacy, README+SKILL, and reference docs found no blockers; these are the cosmetic fixes it surfaced. - README: COSG (dropped in #36) -> Wilcoxon DE + filter_rank_genes_groups specificity pass; remove COSG from the marker_tools layout note. - SKILL/methodology: cta_io.check_hierarchy_nesting -> cta.io.check_hierarchy_nesting (no cta_io module); correct the "stdlib-only" detect-env claim (it imports typer). - Genericize ETH-Euler-specific traces for a vendor-neutral public face: drop the Euler cluster name and `module load eth_proxy` from CLI help / pixi.toml comments / reference docs, keeping the technical content (AVX2-only CPU examples, proxy guidance). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Prep for making the repo public. I ran three adversarial audits — secrets/privacy (working tree + full git history), README+SKILL vs the
ctaCLI, andreference/*.mdvs code. No blockers: no credentials, no personal paths/usernames, no private data; the documented command surface, install commands, pixi envs, and layout all match the code (thetest_registry_sync.pyguard keeps the command list honest). This PR fixes the cosmetic findings.Changes
README.mdstage-3 description now reads Wilcoxon DE +filter_rank_genes_groupsspecificity pass; removed COSG from themarker_tools.mdlayout note. (marker_tools.md/differential_expression.mdalready framed COSG as deliberately dropped — left as-is.)cta_io→cta.ioinSKILL.md(×2) andmethodology.md— there is nocta_iomodule; the function lives incta/io.py.detect-env"stdlib-only" claim inSKILL.md— it importstyper; reworded to "no heavy imports (no scanpy/torch)".module load eth_proxyfrom CLI help (fetch_scimilarity_model.py),pixi.tomlcomments,SKILL.md, andcompute_environments.md, keeping the technical substance (AVX2-only CPU examples; "ensure outbound internet/proxy on a firewalled compute node").No code-behavior changes — docs, comments, and user-facing help text only.
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