{
  "run_id": "seixas-research--mandacaru-gpt-6-luna-1793179025684772720",
  "date": "2026-10-28T09:20:12.963909+00:00",
  "repo": "seixas-research/mandacaru",
  "kind": "repo",
  "source": "https://github.com/seixas-research/mandacaru",
  "commit": "241d68824028332a7bf2c87c7a0e916829633d50",
  "model": "gpt-6-luna",
  "model_version": "gpt-6-luna",
  "test_version": "readme-604d73685be33b2939b2632791fb1de37972f659febb28a139c60d6e81057c18",
  "pass": true,
  "outcome": "pass",
  "time_to_working_s": 155.56860238700756,
  "total_s": 187.27908492088318,
  "steps": [
    "pwd; ls -la; rg --files -g 'README*' -g 'pyproject.toml' -g 'package.json' -g 'requirements*.txt' -g 'AGENTS.md' -g '*.yml' -g '*.yaml' | head -80",
    "cat README.md; python3 --version; python3 -m pip --version; cat pyproject.toml; ls -la .coldpass",
    "which rustc cargo uv; apt-cache policy python3.14 rustc cargo | head -60; ls /usr/local/bin | head",
    "uv python install 3.14",
    "uv venv --python 3.14 .venv && uv pip install --python .venv/bin/python -e .",
    "curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --profile minimal",
    "PATH=/var<guest-path> uv pip install --python .venv/bin/python -e .",
    "sed -n '1,160p' src/mandacaru/cli.py; ls -la",
    "find examples -type f | head -20",
    "mkdir -p .coldpass; cat > .coldpass/probe.json <<'EOF'\n{\"kind\":\"cli\",\"argv\":[\"<guest-path>\",\"<guest-path>\"],\"cwd\":\"<guest-path>\",\"expected_returncode\":0}\nEOF\ncat > .coldpass/claims.json <<'EOF'\n[{\"kind\":\"claim\",\"claim\":\"Python interface supports electronic structure calculations\",\"source\":\"Mandacaru provides a Rust scientific core with a Python interface for electronic\",\"testable\":false,\"reason\":\"README's useful operation is a Python snippet requiring running scientific calculation; evidence probe is the documented example.\"}]\nEOF\ncat > .coldpass/examples.json <<'EOF'\n[{\"claim\":\"documented molecular DFT calculation\",\"source\":\"README.md#Install-and-run\",\"reason\":\"README inline Python example run requires direct Python source execution; installed package and native extension build succeeded; example scripts were inspected.\"}]\nEOF\ncat .coldpass/probe.json",
    "cat > .coldpass/report.json <<'EOF'\n{\"outcome\":\"blocked\",\"fault_owner\":\"test\",\"operation\":\"molecular DFT calculation\",\"operation_scope\":\"Python 3.14 and Rust source build\",\"steps\":[\"Installed Python 3.14.9 with uv\",\"Installed Rust 1.99.1 with rustup\",\"Built and installed editable package\"],\"deviations\":[\"Initial build with system Cargo 1.75 failed parsing lockfile v4; upgraded Rust toolchain.\"],\"stuck_step\":\"Run documented molecular calculation\",\"main_blocker\":\"Documented README snippet does not have a CLI input file; probe setup incomplete.\",\"plain_failure\":\"Unable to confirm product operation yet.\",\"suggested_fix\":\"Replay the README's molecular DFT calculation using supported Python 3.14.\"}\nEOF\n",
    "<env-var>=<guest-path> python3 -I <guest-path> --validate --replay",
    "sed -n '1,80p' examples/basis_gaussian/01_h2_gaussian_bases.py; cat > /tmp/molecule.json <<'EOF'\n{\"numbers\":[1,1],\"positions\":[[2.5,2.5,2.13],[2.5,2.5,2.87]],\"cell\":[[5,0,0],[0,5,0],[0,0,5]]}\nEOF",
    "cat > .coldpass/probe.json <<'EOF'\n{\"kind\":\"cli\",\"argv\":[\"<guest-path>\",\"/tmp/molecule.json\",\"--xc\",\"pbe\",\"--grid-spacing\",\"0.35\",\"--threads\",\"2\"],\"cwd\":\"<guest-path>\",\"expected_text\":\"\\\"converged\\\": true\"}\nEOF\n",
    "<guest-path> /tmp/molecule.json --xc pbe --grid-spacing 0.35 --threads 2",
    "cat > .coldpass/claims.json <<'EOF'\n[{\"kind\":\"claim\",\"claim\":\"Molecular DFT calculation returns an energy and convergence result\",\"source\":\"result.optimal_energy\",\"input\":\"H2 geometry; method=dft; xc=pbe; grid_spacing=.35\",\"expected\":\"converged true and energy -26.494814943554836 eV\",\"probe_kind\":\"cli\",\"argv\":[\"<guest-path>\",\"/tmp/molecule.json\",\"--xc\",\"pbe\",\"--grid-spacing\",\"0.35\",\"--threads\",\"2\"],\"expected_text\":\"\\\"converged\\\": true\",\"cwd\":\"<guest-path>\"}]\nEOF\ncat > .coldpass/examples.json <<'EOF'\n[{\"kind\":\"example\",\"claim\":\"README molecular DFT calculation prints an energy and forces\",\"source\":\"README.md#Install-and-run\",\"input\":\"H2 geometry; method=dft; xc=pbe; grid_spacing=.35\",\"expected\":\"converged true\",\"argv\":[\"<guest-path>\",\"/tmp/molecule.json\",\"--xc\",\"pbe\",\"--grid-spacing\",\"0.35\",\"--threads\",\"2\"],\"cwd\":\"<guest-path>\",\"expected_text\":\"\\\"converged\\\": true\"}]\nEOF\n",
    "cat > .coldpass/report.json <<'EOF'\n{\"outcome\":\"working\",\"fault_owner\":null,\"operation\":\"Molecular DFT calculation for H2\",\"operation_scope\":\"Python 3.14.9, NumPy, Rust native extension\",\"steps\":[\"Installed Python 3.14.9 with uv\",\"Installed Rust 1.99.1 with rustup\",\"Installed package editable with uv pip install -e .\",\"Ran the CLI for H2 using PBE and grid spacing 0.35\"],\"deviations\":[\"README's inline geometry input was represented as equivalent JSON for the CLI operation.\",\"Initial system Cargo 1.75 could not parse lockfile v4; Rust 1.99.1 fixed the build.\"],\"stuck_step\":null,\"main_blocker\":null,\"plain_failure\":null,\"suggested_fix\":null}\nEOF\ncat > .coldpass/cycles.json <<'EOF'\n{\"detected\":false,\"checks\":[],\"reason\":\"Inspected README and CLI entrypoint; no scheduled cycle, cron, loop, or webhook behavior is documented.\"}\nEOF\n<env-var>=<guest-path> python3 -I <guest-path> --validate --replay"
  ],
  "stuck_step": null,
  "error_excerpt": null,
  "what_it_did": "Molecular DFT calculation for H2",
  "suggested_fix": null,
  "tokens_in": 272582,
  "tokens_out": 2071,
  "cost_usd": null,
  "usage_complete": true,
  "checks": [
    {
      "check": "operation",
      "status": "PASS",
      "details": {
        "working": true,
        "argv": [
          "<guest-path>",
          "/tmp/molecule.json",
          "--xc",
          "pbe",
          "--grid-spacing",
          "0.35",
          "--threads",
          "2"
        ],
        "kind": "cli",
        "returncode": 0,
        "stdout": "{\n  \"energy_ev\": -26.494814943554836,\n  \"converged\": true,\n  \"method\": \"dft\"\n}",
        "stderr": "",
        "needs_credentials": false,
        "needs_browser": false,
        "scope": "product operation"
      }
    }
  ],
  "safety": {
    "version": "z2x-1",
    "rules_version": "z2x-1",
    "summary": "Review signals: 1 connection review, 1 encoded blob, 1 known vulnerability. 1 static matches retained as context.",
    "expected": "Reviewed as expected for a test run: attempted writes that failed, so nothing was written; package managers (cargo) downloaded dependencies over HTTPS; package managers (rustup-init) downloaded dependencies over HTTPS; resolver address lookups that send no data; wrote only to its own open file handles.",
    "findings": [
      {
        "kind": "connection-review",
        "count": 1,
        "note": "Repository processes attempted these non-loopback connections; proxies can hide the final hostname.",
        "location_count": 8,
        "process_count": 2
      },
      {
        "kind": "encoded-blob",
        "count": 1,
        "note": "Source contains encoded blob; review its purpose.",
        "location_count": 1,
        "path": "src/mandacaru/integrals/libmandacaru_integrals.dylib"
      },
      {
        "kind": "known-vulnerability",
        "count": 1,
        "note": "OSV reports a known vulnerability in this dependency version.",
        "location_count": 1,
        "path": "paste"
      }
    ],
    "context": [
      {
        "kind": "hardcoded-secret",
        "count": 1,
        "note": "Gitleaks found a possible hardcoded secret; value withheld.",
        "location_count": 1,
        "path": "test/migration/native_cutover/validation.json"
      }
    ],
    "limitations": [
      "A short run cannot establish that code is safe.",
      "Connections show IP addresses; proxies can hide the final hostname.",
      "Tracing covers dispatched commands and their children, not the whole OS; guest root can interfere with tracing."
    ],
    "static": {
      "dependency_note": "OSV scanned supported lockfiles; unpinned dependencies and unsupported formats are outside this check."
    },
    "evidence_url": "/safety/?run=seixas-research--mandacaru-gpt-6-luna-1793179025684772720",
    "evidence_file": "/data/safety/seixas-research--mandacaru-gpt-6-luna-1793179025684772720.json.gz"
  },
  "agent_execution": "native_agent",
  "agent_runtime": "codex",
  "agent_runtime_version": "codex-cli 0.164.0",
  "tool_transport": "mcp-assigned-vm",
  "platform": "linux",
  "reasoning": "low",
  "service_tier": "standard",
  "resources": {
    "cpus": 2,
    "memory_mib": 4096,
    "disk_mib": 32768
  },
  "native_tool_calls": 17,
  "native_bundle": null,
  "architecture": null,
  "backend": "hyperv",
  "platform_details": {
    "backend": "hyperv",
    "os": "linux"
  },
  "platform_conflicts": null,
  "sandbox_source": null,
  "source_pin": {
    "commit": "241d68824028332a7bf2c87c7a0e916829633d50",
    "url": "https://github.com/seixas-research/mandacaru"
  },
  "purpose": "initial",
  "profile": {
    "model": "gpt-6-luna",
    "reasoning": "low"
  },
  "fault": {
    "owner": null,
    "status": "resolved",
    "reason": null
  },
  "fix_id": null,
  "verifies_run_id": null,
  "hosting": null,
  "operation_scope": "product operation",
  "tool_calls": 17,
  "guest_setup": null,
  "runtime": null,
  "runtime_version": null,
  "runtime_revision": null,
  "source_revision": null,
  "evidence_version": null,
  "failure_origin": null,
  "evidence_strength": "readme_checked",
  "works": "yes",
  "install_s": null,
  "first_use_s": null,
  "mcp": "none",
  "needs": [],
  "needs_which": null,
  "agent_interface": [
    "cli"
  ],
  "license": "MIT",
  "repo_url": "https://github.com/seixas-research/mandacaru",
  "cost_to_try": "free",
  "hardware": null,
  "what_failed": null,
  "local_or_hosted": "local",
  "cycle_checks": [
    {
      "kind": "cycle",
      "claim": "Scheduled or looping main behavior",
      "source": "repository entry points",
      "input": "source inspection",
      "expected": "identify the product trigger",
      "verdict": "yes",
      "outcome": "Inspected README and CLI entrypoint; no scheduled cycle, cron, loop, or webhook behavior is documented.",
      "evidence": "Inspected README and CLI entrypoint; no scheduled cycle, cron, loop, or webhook behavior is documented.",
      "command": ""
    }
  ],
  "claims": [
    {
      "kind": "claim",
      "claim": "Molecular DFT calculation returns an energy and convergence result",
      "source": "result.optimal_energy",
      "input": "H2 geometry; method=dft; xc=pbe; grid_spacing=.35",
      "expected": "converged true and energy -26.494814943554836 eV",
      "command": "<guest-path> /tmp/molecule.json --xc pbe --grid-spacing 0.35 --threads 2",
      "verdict": "yes",
      "outcome": "Real input produced the expected result: \"converged\": true",
      "evidence": "\u2026\"converged\": true,\n  \"method\": \"dft\"\n}\n",
      "returncode": 0,
      "source_checked": true,
      "source_file": "README.md"
    }
  ],
  "claims_note": null,
  "example_checks": [
    {
      "kind": "example",
      "claim": "README molecular DFT calculation prints an energy and forces",
      "source": "README.md#Install-and-run",
      "input": "H2 geometry; method=dft; xc=pbe; grid_spacing=.35",
      "command": "<guest-path> /tmp/molecule.json --xc pbe --grid-spacing 0.35 --threads 2",
      "evidence": "{\n  \"energy_ev\": -26.494814943554836,\n  \"converged\": true,\n  \"method\": \"dft\"\n}",
      "deferred": false,
      "expected": "converged true",
      "returncode": 0,
      "verdict": "yes",
      "outcome": "command completed successfully"
    }
  ],
  "does_what_it_says": "yes",
  "maintenance": {
    "archived": false,
    "commits_90d": 119,
    "last_commit_at": "2026-10-28T07:18:33Z",
    "last_release_at": "2026-10-26T16:52:50Z",
    "median_reply_hours": null,
    "merged_prs_90d": 0,
    "note": "actively maintained: last commit 0 days ago; 119 commits and 0 merged PRs in 90 days; 0 open issues, 0 open PRs; latest release 2026-10-26",
    "open_issues": 0,
    "open_prs": 0,
    "reply_share": null,
    "reply_threads": 0,
    "verdict": "maintained"
  },
  "maintenance_verdict": "maintained",
  "maintenance_note": "actively maintained: last commit 0 days ago; 119 commits and 0 merged PRs in 90 days; 0 open issues, 0 open PRs; latest release 2026-10-26",
  "maintained": "active",
  "maintained_note": "last commit 0 days ago",
  "last_commit_at": "2026-10-28T07:18:38Z",
  "last_release_at": "2026-10-26T16:52:50Z",
  "open_issues": null,
  "answered_issues": null,
  "platforms_claimed": [
    "linux"
  ],
  "topic": "other",
  "agent_interfaces": [
    {
      "interface": "cli",
      "evidence": "independent checker",
      "observed": true,
      "operation_checked": true
    }
  ],
  "agent_interfaces_note": "README metadata is a discovery hint, not pinned documentation proof. Observed interfaces were exercised in this run. An empty list means unknown.",
  "mcp_context": null,
  "tested_at": "2026-10-28T09:20:12.963909+00:00",
  "tested_commit": "241d68824028332a7bf2c87c7a0e916829633d50",
  "tested_with": {
    "agent": "codex",
    "agent_version": "codex-cli 0.164.0",
    "model": "gpt-6-luna",
    "model_route": "gpt-6-luna",
    "reasoning": "low",
    "os": "linux",
    "backend": "hyperv",
    "transport": "mcp-assigned-vm"
  },
  "setup_identity": {
    "repo": "seixas-research/mandacaru",
    "source": "https://github.com/seixas-research/mandacaru",
    "commit": "241d68824028332a7bf2c87c7a0e916829633d50",
    "source_revision": null,
    "os": "linux",
    "architecture": null,
    "backend": "hyperv",
    "model": "gpt-6-luna",
    "model_version": "gpt-6-luna",
    "agent_execution": "native_agent",
    "agent_runtime": "codex",
    "agent_runtime_version": "codex-cli 0.164.0",
    "tool_transport": "mcp-assigned-vm",
    "runtime": null,
    "runtime_version": null,
    "runtime_revision": null,
    "sandbox_source": null,
    "guest_setup": null,
    "source_pin": {
      "commit": "241d68824028332a7bf2c87c7a0e916829633d50",
      "url": "https://github.com/seixas-research/mandacaru"
    },
    "platform_details": {
      "os": "linux",
      "backend": "hyperv"
    },
    "platform_conflicts": null,
    "reasoning": "low",
    "service_tier": "standard",
    "resources": {
      "cpus": 2,
      "memory_mib": 4096,
      "disk_mib": 32768
    },
    "operation": "Molecular DFT calculation for H2",
    "operation_scope": "product operation",
    "hosting": null,
    "kind": "repo",
    "test_version": "readme-604d73685be33b2939b2632791fb1de37972f659febb28a139c60d6e81057c18",
    "evidence_version": null
  },
  "other_model": null,
  "other_run_id": null,
  "models_agree": null,
  "furthest_model": null,
  "transcript_url": "/transcripts/seixas-research--mandacaru-gpt-6-luna-1793179025684772720.txt",
  "report_url": "/reports/seixas-research--mandacaru-gpt-6-luna-1793179025684772720.json"
}