{ "run_id": "flint-crew--jolly-roger-claude-haiku-5-5-1793136161056733627", "date": "2026-10-27T21:34:22.074950+00:00", "repo": "flint-crew/jolly-roger", "kind": "repo", "source": "https://github.com/flint-crew/jolly-roger", "commit": "3d4727bec9108fd4ebb4a1a4c3cbedde2db37810", "model": "claude-haiku-5-5", "model_version": "claude-haiku-5-5", "test_version": "readme-d5b140d3c0f8b95c2dd6fe6fc381a303cacb92679582c22317d8e78b572f0cf2", "pass": true, "outcome": "pass", "time_to_working_s": 433.4579999159978, "total_s": 701.0181269645691, "steps": [ "cd && pwd && ls -la && id -u && python3 --version && cat README.md | head -200", "ls /inputs 2>/dev/null; ls ; echo CDP=$CDP_URL $", "cd && grep -n -i \"requires-python\\|scripts\" -A3 pyproject.toml | head -30; ls docs tests; ls .coldpass; python3 -m venv --help >/dev/null 2>&1 && echo venv_ok || echo no_venv", "cd && mkdir -p && python3 -m venv && install --quiet --upgrade pip && cd && install . 2>&1 | tail -5; echo rc=$?; ls | grep jolly", "cd && git init -q && git remote add origin https://github.com/flint-crew/jolly-roger && git fetch --depth 1 origin 3d4727bec9108fd4ebb4a1a4c3cbedde2db37810 2>&1 | tail -3; git reset --mixed FETCH_HEAD 2>&1 | tail -2; git log --oneline -1; install . 2>&1 | tail -3; ls | grep jolly", "cd && --help; echo rc=$?; --help; echo rc=$?", "cd && cat docs/flagging.md | head -120; echo ----; cat docs/nulling.md | head -120", "cd && cat tests/conftest.py | head -120; echo ----; grep -rn \"ms\\b\\|\\.ms\\\"\" tests/test_package.py | head; ls ; cat noxfile.py | head -60; ls .github/workflows; ", "cd && Z=$( -I -c \"import importlib.resources as r; print(r.files('jolly_roger.data').joinpath('tests','SB39400.RACS_0635-31.beam0.small.ms.zip'))\") && echo $Z && ls -la \"$Z\" && mkdir -p && cd && -I -c \"import shutil,sys; shutil.unpack_archive(sys.argv[1], sys.argv[2])\" \"$Z\" && find -maxdepth 2 | head", "cd && grep -n \"test = \\|\\[dependency-groups\\]\" -A12 pyproject.toml | head -40", "mkdir -p && cp -r && cd && SB39400.RACS_0635-31.beam0.small.ms --dry-run 2>&1 | grep -v Warning | tail -30; echo rc=${PIPESTATUS[0]}", "cd && tukey --help 2>/dev/null | head -80", "cd && install -q pytest pytest-cov nbmake 2>&1 | tail -3; echo rc=$?", "cd && tukey SB39400.RACS_0635-31.beam0.small.ms --dry-run 2>&1 | grep -v -i warning | tail -15; echo rc=${PIPESTATUS[0]}", "cd && timeout 1500 -q -p no:cacheprovider 2>&1 | tail -25; echo rc=${PIPESTATUS[0]}", "cd && grep -rn -i \"while True\\|sleep(\\|cron\\|schedul\\|--once\\|--now\\|webhook\\|daemon\" jolly_roger/*.py | head; echo rc=$?; grep -n \"def cli\\|__main__\" jolly_roger/flagger.py jolly_roger/tractor.py", "cd && J= && MS=SB39400.RACS_0635-31.beam0.small.ms && cat > probe.json <\",\"expected_text\":\"Finished processing ms_path=PosixPath('$MS')\"}\nEOF\ncat > claims.json <\"},\n{\"kind\":\"claim\",\"claim\":\"The tractor CLI help is documented as jolly_tractor --help\",\"source\":\"For the nulling filter run:\",\"input\":\"--help\",\"expected\":\"tractor usage text\",\"probe_kind\":\"cli\",\"argv\":[\"$J/jolly_tractor\",\"--help\"],\"expected_text\":\"Run the Jolly Roger Tractor\",\"cwd\":\"\"},\n{\"kind\":\"claim\",\"claim\":\"jolly-roger flags visibilities contaminated by the Sun on a measurement set\",\"source\":\"This package attempts to flag or modify visibilities that are contaminated by the Sun (or potentially some other bright source).\",\"input\":\"$MS (test MS shipped in the package)\",\"expected\":\"flagger processes the MS and reports completion\",\"probe_kind\":\"cli\",\"argv\":[\"$J/jolly_flagger\",\"$MS\",\"--dry-run\"],\"expected_text\":\"Finished processing ms_path=PosixPath('$MS')\",\"cwd\":\"\"},\n{\"kind\":\"claim\",\"claim\":\"The nulling filter is accessed through jolly_tractor\",\"source\":\"The nulling approach can be accessed through \\`jolly_tractor\\`.\",\"input\":\"$MS with tukey subcommand, dry run\",\"expected\":\"tractor reports its delay notch settings without modifying visibilities\",\"probe_kind\":\"cli\",\"argv\":[\"$J/jolly_tractor\",\"tukey\",\"$MS\",\"--dry-run\"],\"expected_text\":\"Delay notch: removes about 10 ns of delay around each object.\",\"cwd\":\"\"}\n]\nEOF\ncat > examples.json <\",\"expected_text\":\"Finished processing ms_path=PosixPath('$MS')\"},\n{\"kind\":\"example\",\"claim\":\"Repository test suite run via noxfile tests session\",\"source\":\"noxfile.py\",\"input\":\"pytest\",\"expected\":\"all tests pass\",\"argv\":[\"$J/pytest\",\"-q\",\"-p\",\"no:cacheprovider\"],\"cwd\":\"\",\"expected_text\":\"101 passed\"}\n]\nEOF\ncat > cycles.json <<'EOF'\n{\"detected\":false,\"reason\":\"Entry points jolly_flagger and jolly_tractor (jolly_roger/flagger.py cli, jolly_roger/tractor.py cli) are one-shot CLIs with no scheduler, loop, cron, webhook or --once/--now trigger; grep found none.\",\"checks\":[]}\nEOF\nfor f in probe.json claims.json examples.json cycles.json; do -I -m json.tool $f >/dev/null && echo \"$f ok\"; done; cat probe.json", "cd && cat > report.json <<'EOF'\n{\"outcome\":\"working\",\"fault_owner\":null,\"operation\":\"Install jolly-roger from the pinned source and run the flagger (jolly_flagger) and nulling filter (jolly_tractor tukey) on a measurement set, plus the repository pytest suite\",\"operation_scope\":\"Linux guest, Python 3.12.3, venv at ; README requires Python >=3.11 (pyproject). Test MS shipped inside the package (SB39400.RACS_0635-31.beam0.small.ms.zip) used as input, copied to \",\"steps\":[\"git init; git remote add origin https://github.com/flint-crew/jolly-roger; git fetch --depth 1 origin 3d4727bec9108fd4ebb4a1a4c3cbedde2db37810; git reset --mixed FETCH_HEAD\",\"python3 -m venv ; install .\",\" --help\",\" --help\",\" SB39400.RACS_0635-31.beam0.small.ms --dry-run\",\" tukey SB39400.RACS_0635-31.beam0.small.ms --dry-run\",\" (after pip install pytest pytest-cov nbmake)\"],\"deviations\":[\"pip install . failed first with a metadata-generation error because the snapshot had no Git metadata (setuptools_scm); fixed by the Git init/fetch/reset steps given in the task, then install succeeded.\",\"Test dependencies were installed with pip (pytest, pytest-cov, nbmake) instead of nox/uv, since nox is not required for the test run; pytest ran directly with pyproject's configuration (101 passed).\",\"README's example dataset (scienceData.EMU_1141-55...ms) is not available in the guest; used the test MS shipped in the package instead, and ran with --dry-run so the input is not modified.\",\"Tractor and flagger were run with --dry-run only; non-dry runs write FLAG/CORRECTED_DATA columns and were not exercised in replay.\"],\"stuck_step\":null,\"main_blocker\":null,\"plain_failure\":null,\"suggested_fix\":\"None required for this run. Optional: the README could note that pip install from a source checkout needs Git metadata for version detection.\"}\nEOF\n -I -c \"import json;json.load(open('report.json'));print('report ok')\"; cd && = python3 -I --validate --replay 2>&1 | tail -60; echo rc=${PIPESTATUS[0]}", "cd && grep -n \"nulling approach\" README.md docs/*.md | head -3; python3 -c \"import json;print(repr(json.load(open('.coldpass/claims.json'))[3]['source']))\"; grep -c \"\" README.md; grep -n \"nulling approach\\|nulling filter run\" README.md", "cd && grep -n \"second mode\" README.md | cut -c1-400", "cd && -I - <<'PY'\nimport json\nc = json.load(open('claims.json'))\nc[3]['claim'] = \"The second mode applies a notch filter in delay space via jolly_tractor\"\nc[3]['source'] = \"The second mode is the application of a notch filter in delay space, where the nulling is applied to the expected delay of the Sun for each timestep and baseline.\"\njson.dump(c, open('claims.json','w'), indent=1)\nprint('ok')\nPY\ncd && = python3 -I --validate --replay 2>&1 | tail -60; echo rc=${PIPESTATUS[0]}", "cd && -I - <<'PY'\nimport json\nc = json.load(open('claims.json'))\nc = [x for x in c if 'help' not in x['claim'].lower()]\njson.dump(c, open('claims.json','w'), indent=1)\nprint(len(c), [x['claim'] for x in c])\nPY\ncd && = python3 -I --validate --replay > 2>&1; echo rc=$?; -I -c \"\nimport json,sys\nd=json.load(open(''))\nprint('valid:',d.get('valid'),'problems:',d.get('problems'))\nr=d.get('replay',{})\nprint('replay status:',r.get('status'))\ndet=r.get('details',{})\nprint('evidence_strength:',det.get('evidence_strength'))\nfor c in det.get('claims',[]): print('claim', c['verdict'], c['claim'][:60])\nfor c in det.get('example_checks',[]): print('example', c['verdict'], c['claim'][:60])\n\" 2>&1 | tail -20" ], "stuck_step": null, "error_excerpt": null, "what_it_did": "Install jolly-roger from the pinned source and run the flagger (jolly_flagger) and nulling filter (jolly_tractor tukey) on a measurement set, plus the repository pytest suite", "suggested_fix": null, "tokens_in": 419074, "tokens_out": 13243, "cost_usd": 0.018387550000000003, "usage_complete": true, "checks": [ { "check": "operation", "status": "PASS", "details": { "working": true, "argv": [ "", "SB39400.RACS_0635-31.beam0.small.ms", "--dry-run" ], "kind": "cli", "returncode": 0, "stdout": "", "stderr": "-27 21:33:07.964: ( 17, 24): uvw 100.00% & elev. 100.00% = Applied 100.00%\n[32;20mINFO[0m 2026-10-27 21:33:07.964: ( 17, 25): uvw 73.50% & elev. 100.00% = Applied 73.50%\n[32;20mINFO[0m 2026-10-27 21:33:07.964: ( 17, 34): uvw 40.28% & elev. 100.00% = Applied 40.28%\n[32;20mINFO[0m 2026-10-27 21:33:07.964: ( 18, 19): uvw 100.00% & elev. 100.00% = Applied 100.00%\n[32;20mINFO[0m 2026-10-27 21:33:07.965: ( 18, 20): uvw 100.00% & elev. 100.00% = Applied 100.00%\n[32;20mINFO[0m 2026-10-27 21:33:07.965: ( 18, 21): uvw 100.00% & elev. 100.00% = Applied 100.00%\n[32;20mINFO[0m 2026-10-27 21:33:07.965: ( 18, 24): uvw 100.00% & elev. 100.00% = Applied 100.00%\n[32;20mINFO[0m 2026-10-27 21:33:07.965: ( 18, 25): uvw 100.00% & elev. 100.00% = Applied 100.00%\n[32;20mINFO[0m 2026-10-27 21:33:07.966: ( 18, 26): uvw 75.69% & elev. 100.00% = Applied 75.69%\n[32;20mINFO[0m 2026-10-27 21:33:07.966: ( 18, 34): uvw 100.00% & elev. 100.00% = Applied 100.00%\n[32;20mINFO[0m 2026-10-27 21:33:07.966: ( 19, 20): uvw 100.00% & elev. 100.00% = Applied 100.00%\n[32;20mINFO[0m 2026-10-27 21:33:07.966: ( 19, 21): uvw 100.00% & elev. 100.00% = Applied 100.00%\n[excerpt truncated]", "needs_credentials": false, "needs_browser": false, "scope": "product operation" } } ], "safety": { "version": "z2x-1", "rules_version": "z2x-1", "summary": "Review signals: 134 known vulnerability.", "expected": "Reviewed as expected for a test run: attempted writes that failed, so nothing was written.", "findings": [ { "kind": "known-vulnerability", "count": 134, "note": "OSV reports a known vulnerability in this dependency version.", "location_count": 10 } ], "context": [], "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=flint-crew--jolly-roger-claude-haiku-5-5-1793136161056733627", "evidence_file": "/data/safety/flint-crew--jolly-roger-claude-haiku-5-5-1793136161056733627.json.gz" }, "agent_execution": "native_agent", "agent_runtime": "claude-code", "agent_runtime_version": "2.1.310 (Claude Code)", "tool_transport": "mcp-assigned-vm", "platform": "linux", "reasoning": "low", "service_tier": null, "resources": { "cpus": 2, "memory_mib": 4096, "disk_mib": 32768 }, "native_tool_calls": 22, "native_bundle": null, "architecture": null, "backend": "hyperv", "platform_details": { "backend": "hyperv", "os": "linux" }, "platform_conflicts": null, "sandbox_source": null, "source_pin": { "commit": "3d4727bec9108fd4ebb4a1a4c3cbedde2db37810", "url": "https://github.com/flint-crew/jolly-roger" }, "purpose": "test_rerun", "profile": { "model": "claude-haiku-5-5", "reasoning": "low" }, "fault": { "owner": null, "status": "resolved", "reason": null }, "fix_id": "fix-9b4a2032f8277c422349", "verifies_run_id": "flint-crew--jolly-roger-claude-haiku-5-5-1793125231286580406", "hosting": null, "operation_scope": "product operation", "tool_calls": 22, "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": "BSD-3-Clause", "repo_url": "https://github.com/flint-crew/jolly-roger", "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": "Entry points jolly_flagger and jolly_tractor (jolly_roger/flagger.py cli, jolly_roger/tractor.py cli) are one-shot CLIs with no scheduler, loop, cron, webhook or --once/--now trigger; grep found none.", "evidence": "Entry points jolly_flagger and jolly_tractor (jolly_roger/flagger.py cli, jolly_roger/tractor.py cli) are one-shot CLIs with no scheduler, loop, cron, webhook or --once/--now trigger; grep found none.", "command": "" } ], "claims": [ { "kind": "claim", "claim": "jolly-roger flags visibilities contaminated by the Sun on a measurement set", "source": "This package attempts to flag or modify visibilities that are contaminated by the Sun (or potentially some other bright source).", "input": "SB39400.RACS_0635-31.beam0.small.ms (test MS shipped in the package)", "expected": "flagger processes the MS and reports completion", "command": " SB39400.RACS_0635-31.beam0.small.ms --dry-run", "verdict": "yes", "outcome": "Real input produced the expected result: Finished processing ms_path=PosixPath('SB39400.RACS_0635-31.beam0.small.ms')", "evidence": "Finished processing ms_path=PosixPath('SB39400.RACS_0635-31.beam0.small.ms')\n", "returncode": 0, "source_checked": true, "source_file": "README.md" }, { "kind": "claim", "claim": "The second mode applies a notch filter in delay space via jolly_tractor", "source": "The second mode is the application of a notch filter in delay space, where the nulling is applied to the expected delay of the Sun for each timestep and baseline.", "input": "SB39400.RACS_0635-31.beam0.small.ms with tukey subcommand, dry run", "expected": "tractor reports its delay notch settings without modifying visibilities", "command": " tukey SB39400.RACS_0635-31.beam0.small.ms --dry-run", "verdict": "yes", "outcome": "Real input produced the expected result: Delay notch: removes about 10 ns of delay around each object.", "evidence": "Delay notch: removes about 10 ns of delay around each object. Each channel can pick up at most 1% of the value of any other single channel, and channels up to about 100 MHz apart influence each other.\n\u001b[32;20mINFO\u001b[0m 2026-10-27 21:33:16.049: Spectral-line impact of nulling sun (Gaussian line profiles): lines narrower than one channel lose at most 1% of their peak brightness. No visibilities were modified.\n", "returncode": 0, "source_checked": true, "source_file": "README.md" } ], "claims_note": null, "example_checks": [ { "kind": "example", "claim": "Documented flagger example with horizon and scale limits", "source": "docs/flagging.md", "input": "SB39400.RACS_0635-31.beam0.small.ms --min-horizon-limit-deg -2 --max-horizon-limit-deg 30 --min-scale-deg 0.075 --dry-run", "command": " SB39400.RACS_0635-31.beam0.small.ms --min-horizon-limit-deg -2 --max-horizon-limit-deg 30 --min-scale-deg 0.075 --dry-run", "evidence": " 86.81% & elev. 100.00% = Applied 86.81%\n\u001b[32;20mINFO\u001b[0m 2026-10-27 21:33:20.429: ( 27, 30): uvw 100.00% & elev. 100.00% = Applied 100.00%\n\u001b[32;20mINFO\u001b[0m 2026-10-27 21:33:20.429: ( 28, 29): uvw 100.00% & elev. 100.00% = Applied 100.00%\n\u001b[32;20mINFO\u001b[0m 2026-10-27 21:33:20.430: ( 28, 34): uvw 79.28% & elev. 100.00% = Applied 79.28%\n\u001b[32;20mINFO\u001b[0m 2026-10-27 21:33:20.430: ( 32, 33): uvw 10.76% & elev. 100.00% = Applied 10.76%\n\u001b[32;20mINFO\u001b[0m 2026-10-27 21:33:20.430: \n\n\u001b[32;20mINFO\u001b[0m 2026-10-27 21:33:20.430: Finished processing ms_path=PosixPath('SB39400.RACS_0635-31.beam0.small.ms')", "deferred": false, "expected": "flagger finishes processing the MS", "returncode": 0, "verdict": "yes", "outcome": "command completed successfully" }, { "kind": "example", "claim": "Repository test suite run via noxfile tests session", "source": "noxfile.py", "input": "pytest", "command": " -q -p no:cacheprovider", "evidence": "........................................................................ [ 71%]\n............................. [100%]\n\nLearn more about nbmake at https://github.com/treebeardtech/nbmake\n\n101 passed in 36.35s", "deferred": false, "expected": "all tests pass", "returncode": 0, "verdict": "yes", "outcome": "command completed successfully" } ], "does_what_it_says": "yes", "maintenance": { "archived": false, "commits_90d": 12, "last_commit_at": "2026-10-27T08:55:41Z", "last_release_at": "2026-10-27T08:50:54Z", "median_reply_hours": null, "merged_prs_90d": 11, "note": "slow: last commit 0 days ago; 12 commits and 11 merged PRs in 90 days; 7 open issues, 2 open PRs; 0 of 27 recent threads got a maintainer reply; latest release 2026-10-27", "open_issues": 7, "open_prs": 2, "reply_share": 0.0, "reply_threads": 27, "verdict": "slow" }, "maintenance_verdict": "slow", "maintenance_note": "slow: last commit 0 days ago; 12 commits and 11 merged PRs in 90 days; 7 open issues, 2 open PRs; 0 of 27 recent threads got a maintainer reply; latest release 2026-10-27", "maintained": "active", "maintained_note": "last commit 0 days ago; 1 open issues, 2 answered or closed", "last_commit_at": "2026-10-27T09:42:40Z", "last_release_at": "2026-10-27T08:50:54Z", "open_issues": 1, "answered_issues": 2, "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": "2026-10-27T21:34:22.074950+00:00", "tested_commit": "3d4727bec9108fd4ebb4a1a4c3cbedde2db37810", "tested_with": { "agent": "claude-code", "agent_version": "2.1.310 (Claude Code)", "model": "claude-haiku-5-5", "model_route": "claude-haiku-5-5", "reasoning": "low", "os": "linux", "backend": "hyperv", "transport": "mcp-assigned-vm" }, "setup_identity": { "repo": "flint-crew/jolly-roger", "source": "https://github.com/flint-crew/jolly-roger", "commit": "3d4727bec9108fd4ebb4a1a4c3cbedde2db37810", "source_revision": null, "os": "linux", "architecture": null, "backend": "hyperv", "model": "claude-haiku-5-5", "model_version": "claude-haiku-5-5", "agent_execution": "native_agent", "agent_runtime": "claude-code", "agent_runtime_version": "2.1.310 (Claude Code)", "tool_transport": "mcp-assigned-vm", "runtime": null, "runtime_version": null, "runtime_revision": null, "sandbox_source": null, "guest_setup": null, "source_pin": { "commit": "3d4727bec9108fd4ebb4a1a4c3cbedde2db37810", "url": "https://github.com/flint-crew/jolly-roger" }, "platform_details": { "os": "linux", "backend": "hyperv" }, "platform_conflicts": null, "reasoning": "low", "service_tier": null, "resources": { "cpus": 2, "memory_mib": 4096, "disk_mib": 32768 }, "operation": "Install jolly-roger from the pinned source and run the flagger (jolly_flagger) and nulling filter (jolly_tractor tukey) on a measurement set, plus the repository pytest suite", "operation_scope": "product operation", "hosting": null, "kind": "repo", "test_version": "readme-d5b140d3c0f8b95c2dd6fe6fc381a303cacb92679582c22317d8e78b572f0cf2", "evidence_version": null }, "transcript_url": "/transcripts/flint-crew--jolly-roger-claude-haiku-5-5-1793136161056733627.txt", "report_url": "/reports/flint-crew--jolly-roger-claude-haiku-5-5-1793136161056733627.json" }