LD-Shell/beamfeat

README/docs-listed command: python benchmarks/make_figures.py --outdir <fresh dir>; regenerates paper figures (PDF+PNG) from committed result files and prints FDR calibration tables. Also verified beamfeat imports from the installed package.

cd <host-path> && git log --oneline -1 2>/dev/null; ls -la; cat README.md 2>/dev/null | head -200
ls -la <host-path> 2>/dev/null; echo "CDP=$CDP_URL $<env-var>"; which python3 node npm pip3 uv 2>&1
cd <host-path> && grep -n "^#\|python -m\|beamfeat \|pip install\|\`\`\`" README.md | sed -n '1,200p'; ls src/* docs; grep -n "scripts" -A5 pyproject.toml
cd <host-path> && cat docs/installation.md | head -120; ls .github/workflows && grep -n "run:" -A3 .github/workflows/*.yml | head -80
cd <host-path> && python3 --version && (python3 -m venv <host-path> 2>&1 || (apt-get update -qq && apt-get install -y -qq python3-venv >/dev/null 2>&1 && python3 -m venv <host-path>)) && <host-path> install -q --upgrade pip && <host-path> install -q "<host-path>" 2>&1 | tail -5; echo rc=$?; <host-path> -c "import beamfeat,sklearn;print(beamfeat.__file__, sklearn.__version__)"
cd <host-path> && (sudo -n apt-get update -qq && sudo -n DEBIAN_FRONTEND=noninteractive apt-get install -y -qq python3.12-venv python3-pip) >/tmp/apt.log 2>&1; echo apt=$?; tail -3 /tmp/apt.log; rm -rf <host-path>; python3 -m venv <host-path> && <host-path> install -q --upgrade pip && <host-path> install -q "<host-path>" 2>&1 | tail -5; echo rc=$?; <host-path> -c "import beamfeat,sklearn;print(beamfeat.__file__, sklearn.__version__)"
cd <host-path> && sed -n 200,240p README.md; head -40 benchmarks/make_figures.py; ls benchmarks; grep -n "python " benchmarks/README.md | head -20
cd <host-path> && <host-path> install -q matplotlib pandas 2>&1 | tail -3; rm -rf <host-path>; cd <host-path> && <host-path> benchmarks/make_figures.py --outdir <host-path>; echo rc=$?; ls <host-path> | head -30
cd <host-path> && mkdir -p .coldpass && cat > .coldpass/probe.json <<'EOF'
{"kind":"cli","argv":["<host-path>"}
EOF
cat > .coldpass/report.json <<'EOF'
{"outcome":"working",
 "operation":"README/docs-listed command: python benchmarks/make_figures.py --outdir <fresh dir>; regenerates paper figures (PDF+PNG) from committed result files and prints FDR calibration tables. Also verified beamfeat imports from the installed package.",
 "operation_scope":"Library only (no CLI/MCP/HTTP server). README quickstart snippet (BeamFeatRegressor.fit on user X,y) was not run as a probe because X and y are undefined in the README; the figure script is the documented runnable command. Full pytest suite and ruff lint intentionally not run per smoke-task rules. Notebooks not run.",
 "steps":["git/ls inspection of README and .github/workflows/ci.yml",
  "apt-get update && apt-get install python3.12-venv python3-pip (via sudo -n)",
  "python3 -m venv <host-path>; pip install --upgrade pip",
  "pip install \"<host-path>\" (installed beamfeat 0.x from pinned checkout, sklearn 1.9.1)",
  "pip install matplotlib pandas (needed by benchmarks/make_figures.py, not in core deps)",
  "<host-path> benchmarks/make_figures.py --outdir <host-path> (rc=0, 14 files written)"],
 "deviations":["Plain python3 lacks venv/ensurepip; installed python3.12-venv and python3-pip via apt (sudo -n) and built a venv at <host-path>",
  "README quickstart is not a runnable script; used benchmarks/make_figures.py as the documented runnable operation instead.",
  "Figure script needs matplotlib and pandas, which are not in the core install; installed them into the venv."],
 "stuck_step":null,"main_blocker":null,"suggested_fix":null}
EOF
<env-var>=<host-path> python3 -I <host-path> --validate; echo rc=$?
rm -rf <host-path>; cd <host-path> && ls -a; find . -name "*.egg-info" -o -name build -maxdepth 2 | head; <env-var>=<host-path> python3 -I <host-path> --validate