{ "tokens_out": 4443, "outcome": "pass", "suggested_fix": null, "cycle_checks": null, "fault": { "owner": null, "status": "resolved", "reason": null, "evidence": [] }, "runtime_revision": null, "agent_execution": "native_agent", "time_to_working_s": null, "usage_complete": true, "runtime": null, "architecture": null, "local_or_hosted": null, "agent_interfaces_note": null, "platform_details": null, "platforms_claimed": null, "maintenance": null, "evidence_strength": null, "purpose": "initial", "topic": null, "needs_which": null, "tested_with": null, "native_bundle": null, "agent_runtime": "claude-code", "maintenance_note": null, "runtime_version": null, "does_what_it_says": null, "commit": "5c88c7ce1a0d618d6fae25cae493e9631359c2af", "failure_origin": null, "stuck_step": null, "repo_url": null, "needs": null, "checks": [ { "check": "operation", "status": "PASS", "details": { "working": true, "argv": [ "produce-file", "--option=preprocess" ], "kind": "cli", "returncode": 0, "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 in the command line", "stderr": "", "needs_credentials": false, "needs_browser": false, "scope": "product operation" } } ], "open_issues": null, "agent_runtime_version": "2.1.300 (Claude Code)", "verifies_run_id": null, "total_s": 253.66452026367188, "license": null, "tool_calls": 10, "model_version": "claude-haiku-5-5", "example_checks": [], "mcp": null, "other_model": null, "first_use_s": null, "native_tool_calls": 10, "last_commit_at": null, "source": "https://github.com/l-zh007/spatialsnake", "models_agree": null, "maintenance_verdict": null, "cost_usd": 0.0075706099999999985, "safety": null, "answered_issues": null, "what_failed": null, "steps": [ "cd && ls -la && cat README.md 2>/dev/null | head -200 && git log -1 --format=%H 2>/dev/null", "cd && ls -la .github/workflows 2>/dev/null; cat pyproject.toml setup.py package.json 2>/dev/null | head -80; ls ", "cd ; 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 | head -150", "cd ; cat requirements.txt; echo ---; cat environment.yml; echo ---; python3 -m venv --help >/dev/null 2>&1 && echo venv_ok || echo no_venv; ls ; env | grep -i -E 'proxy|CDP' | sed 's/=.*/=/'", "cd ; python3 -m venv && export NODE_USE_ENV_PROXY=1 && timeout 1500 -m pip install -q --upgrade pip 2>&1 | tail -5; timeout 1500 -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 ; python3 -m venv && echo venv_made", "cd ; export NODE_USE_ENV_PROXY=1; V=; 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 $V/python -m pip install --no-deps -e . 2>&1 | tail -5; echo rc=$?; $V/spatialsnake --version 2>&1 | tail -3", "cd ; ls preprocess.yaml 2>/dev/null; produce-file --option=preprocess; echo rc=$?; ls -la preprocess.yaml && head -5 preprocess.yaml", "cd ; mkdir -p .coldpass; cat > .coldpass/probe.json <<'EOF'\n{\"kind\":\"cli\",\"argv\":[\"\",\"produce-file\",\"--option=preprocess\"],\"cwd\":\"\"}\nEOF\ncat > .coldpass/report.json <<'EOF'\n{\"outcome\":\"working\",\n \"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.\",\n \"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.\",\n \"steps\":[\"Read README.md and .github/workflows/main.yaml\",\n \"apt-get install python3.12-venv (Ubuntu venv prerequisite)\",\n \"python3 -m venv \",\n \"pip install --upgrade pip; pip install setuptools>=80.9.0,<81 wheel docopt PyYAML (CI step)\",\n \"pip install --no-deps -e . (CI step, README Option 3 install form)\",\n \"spatialsnake --version -> 0.0.5\",\n \"spatialsnake produce-file --option=preprocess -> wrote preprocess.yaml\"],\n \"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.\",\n \"Used python3 -m venv instead of conda env; venv creation failed first with ensurepip missing, fixed by apt-get install python3.12-venv.\",\n \"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.\"],\n \"stuck_step\":null,\"main_blocker\":null,\"suggested_fix\":null}\nEOF\npython3 -m json.tool .coldpass/probe.json >/dev/null && python3 -m json.tool .coldpass/report.json >/dev/null && echo json_ok; = python3 -I --validate; echo rc=$?", "cd ; rm -f preprocess.yaml; = python3 -I --validate; echo rc=$?; ls .coldpass; pgrep -fa spatialsnake || echo no_leftover_processes" ], "platform_conflicts": null, "claims_note": null, "maintained_note": null, "repo": "l-zh007/spatialsnake", "service_tier": null, "maintained": null, "source_pin": null, "operation_scope": "product operation", "reasoning": "low", "claims": [], "platform": "linux", "cost_to_try": null, "backend": null, "tool_transport": "mcp-assigned-vm", "hardware": null, "agent_interface": null, "profile": { "model": "claude-haiku-5-5", "reasoning": "low" }, "date": "2026-10-18T16:27:56.690854+00:00", "kind": "repo", "resources": { "cpus": 2, "memory_mib": 4096, "disk_mib": 32768 }, "error_excerpt": null, "pass": true, "evidence_version": null, "source_revision": null, "run_id": "l-zh007--spatialsnake-claude-haiku-5-5-1792340623026317967", "last_release_at": null, "furthest_model": null, "model": "claude-haiku-5-5", "what_it_did": "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.", "sandbox_source": null, "other_run_id": null, "hosting": null, "tested_commit": null, "guest_setup": null, "mcp_context": null, "agent_interfaces": [], "setup_identity": null, "works": null, "install_s": null, "fix_id": null, "tokens_in": 170938, "tested_at": null, "test_version": "readme-03aea4c41d53955e3723c330e9927d2a9df627f6642624cc0078a97c73a53c8a", "recovery": { "source": "legacy-oct16-18", "original_run_id": "l-zh007--spatialsnake-claude-haiku-5-5-1792340623026317967", "historical": true, "ledger_sha256": "c5e6a833c182c1e2aecf69d0bd0020aec63c65d98f3e933e4b32232340312736" }, "transcript_url": "/transcripts/l-zh007--spatialsnake-claude-haiku-5-5-1792340623026317967.txt", "report_url": "/reports/l-zh007--spatialsnake-claude-haiku-5-5-1792340623026317967.json" }