l-zh007/spatialsnake

README 'Minimal Usage' entry point `spatialsnake produce-file --option=preprocess` (same command as CI workflow .github/workflows/main.yaml smoke test); generates preprocess.yaml config template in the working directory.

cd <host-path> && ls -la && cat README.md 2>/dev/null | head -200 && git log -1 --format=%H 2>/dev/null
cd <host-path> && ls -la .github/workflows 2>/dev/null; cat pyproject.toml setup.py package.json 2>/dev/null | head -80; ls <host-path>
cd <host-path>; python3 --version; which conda mamba micromamba R Rscript pip3 apt-get 2>&1; cat /etc/os-release | head -2; nproc; free -g | head -2; df -h /home | tail -1; cat .github/workflows/main.yaml; echo ---; sed -n 1,200p <host-path> | head -150
cd <host-path>; cat requirements.txt; echo ---; cat environment.yml; echo ---; python3 -m venv --help >/dev/null 2>&1 && echo venv_ok || echo no_venv; ls <host-path>; env | grep -i -E 'proxy|CDP' | sed 's/=.*/=<set>/'
cd <host-path>; python3 -m venv <host-path> && export NODE_USE_ENV_PROXY=1 && timeout 1500 <host-path> -m pip install -q --upgrade pip 2>&1 | tail -5; timeout 1500 <host-path> -m pip install -q "setuptools>=80.9.0,<81" wheel 2>&1 | tail -5; echo rc=$?
export DEBIAN_FRONTEND=noninteractive; (sudo -n apt-get update -qq && sudo -n apt-get install -y -qq python3.12-venv) 2>&1 | tail -3; rm -rf <host-path>; python3 -m venv <host-path> && echo venv_made
cd <host-path>; export NODE_USE_ENV_PROXY=1; V=<host-path>; timeout 1500 $V/python -m pip install -q --upgrade pip 2>&1 | tail -3; timeout 1500 $V/python -m pip install -q "setuptools>=80.9.0,<81" wheel docopt PyYAML 2>&1 | tail -3; timeout 2400 $V/python -m pip install --no-deps -e . 2>&1 | tail -5; echo rc=$?; $V/spatialsnake --version 2>&1 | tail -3
cd <host-path>; ls preprocess.yaml 2>/dev/null; <host-path> produce-file --option=preprocess; echo rc=$?; ls -la preprocess.yaml && head -5 preprocess.yaml
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 'Minimal Usage' entry point `spatialsnake produce-file --option=preprocess` (same command as CI workflow .github/workflows/main.yaml smoke test); generates preprocess.yaml config template in the working directory.",
 "operation_scope":"Exercises CLI entry point and config generation only. Full analysis workflows (preprocess/clustering on real data) not run; they need the Conda R layer (r-seurat etc.) and sample.txt/data inputs. Conda/R dependencies from README Option 1/3 were not installed.",
 "steps":["Read README.md and .github/workflows/main.yaml",
  "apt-get install python3.12-venv (Ubuntu venv prerequisite)",
  "python3 -m venv <host-path>",
  "pip install --upgrade pip; pip install setuptools>=80.9.0,<81 wheel docopt PyYAML (CI step)",
  "pip install --no-deps -e . (CI step, README Option 3 install form)",
  "spatialsnake --version -> 0.0.5",
  "spatialsnake produce-file --option=preprocess -> wrote preprocess.yaml"],
 "deviations":["README Option 1/2/3 'conda create ...' not run: conda/mamba not present in guest and no conda installer was run; R-based dependencies (r-seurat, bioconductor-*) therefore not installed.",
  "Used python3 -m venv instead of conda env; venv creation failed first with ensurepip missing, fixed by apt-get install python3.12-venv.",
  "Installed with --no-deps (as in CI) instead of full requirements; `python -m pip install .` from README not run, so runtime dependencies from requirements.txt are not installed. `spatialsnake install-packages` not run."],
 "stuck_step":null,"main_blocker":null,"suggested_fix":null}
EOF
python3 -m json.tool .coldpass/probe.json >/dev/null && python3 -m json.tool .coldpass/report.json >/dev/null && echo json_ok; <env-var>=<host-path> python3 -I <host-path> --validate; echo rc=$?
cd <host-path>; rm -f preprocess.yaml; <env-var>=<host-path> python3 -I <host-path> --validate; echo rc=$?; ls .coldpass; pgrep -fa spatialsnake || echo no_leftover_processes