{
  "checker": {
    "details": {
      "argv": [
        "<host-path>",
        "produce-file",
        "--option=preprocess"
      ],
      "kind": "cli",
      "needs_browser": false,
      "needs_credentials": false,
      "returncode": 0,
      "scope": "product operation",
      "stderr": "",
      "stdout": "2026-10-18 16:27:53,545: INFO - Generating config.yaml file for: preprocess...\n2026-10-18 16:27:53,545: INFO - You can use this as a config-file for a spatialsnake run.\n2026-10-18 16:27:53,545: INFO - ***How to set your own params:***\n2026-10-18 16:27:53,545: INFO - Add params: --configfile <file-path> in the command line",
      "working": true
    },
    "status": "PASS"
  },
  "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."
  ],
  "main_blocker": null,
  "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.",
  "outcome": "working",
  "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"
  ],
  "stuck_step": null,
  "suggested_fix": null
}