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arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'env'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.11/migration/\n    warn(\n\n.venv/lib/python3.13/site-packages/pydantic/_internal/_config.py:323\n  /workspace/.venv/lib/python3.13/site-packages/pydantic/_internal/_config.py:323: PydanticDeprecatedSince20: Support for class-based `config` is deprecated, use ConfigDict instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.11/migration/\n    warnings.warn(DEPRECATION_MESSAGE, DeprecationWarning)\n\n-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html\n================================ tests coverage ================================\n_______________ coverage: platform linux, python 3.13.7-final-0 ________________\n\nName                                      Stmts   Miss  Cover   Missing\n-----------------------------------------------------------------------\nsrc/quber/__init__.py                         5      0   100%\nsrc/quber/agents/__init__.py                  2      0   100%\nsrc/quber/agents/factory.py                 124     38    69%   95, 118-129, 160-207\nsrc/quber/cli.py                            251    159    37%   62-100, 135-196, 249, 258-262, 268, 276-289, 298-310, 320-332, 339-361, 371-417, 422, 426\nsrc/quber/core/__init__.py                    3      0   100%\nsrc/quber/core/models.py                     14      0   100%\nsrc/quber/core/table_parser.py              146     59    60%   60-155, 190, 195-197, 201, 205, 218, 224, 229, 238-242, 286-287\nsrc/quber/db/__init__.py                      4      4     0%   3-7\nsrc/quber/db/connection.py                   49     49     0%   3-118\nsrc/quber/db/embeddings.py                   81     81     0%   3-182\nsrc/quber/db/importer.py                    113    113     0%   3-265\nsrc/quber/db/models.py                       40     40     0%   3-68\nsrc/quber/processors/__init__.py              2      0   100%\nsrc/quber/processors/table_inference.py     182    144    21%   70-95, 114-147, 183-202, 206, 234-239, 253-299, 312-348, 361-396, 408-410, 414-463\nsrc/quber/prompts/__init__.py                 2      0   100%\nsrc/quber/prompts/loader.py                  26      4    85%   12-15\nsrc/quber/utils/__init__.py                   3      0   100%\nsrc/quber/utils/config.py                    32      0   100%\nsrc/quber/utils/logging.py                   35      0   100%\n-----------------------------------------------------------------------\nTOTAL                                      1114    691    38%\nCoverage HTML written to dir htmlcov\n======================= 107 passed, 6 warnings in 7.43s ========================","is_error":false}]},"parent_tool_use_id":null,"session_id":"ff1b37cf-9618-4f7d-ae0f-6002cb9747cc","uuid":"8f406a11-0481-4f8e-aac8-751293fa494d"},{"type":"assistant","message":{"model":"claude-sonnet-4-5-20250929","id":"msg_016AHAFtU5gbH4qKiadFRecs","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_0132qMh94QgabWqgUakj9Lwq","name":"TodoWrite","input":{"todos":[{"content":"Remove 'automate:safe' label from issue #71","activeForm":"Removing 'automate:safe' label from issue #71","status":"completed"},{"content":"Update issue status to in-progress","activeForm":"Updating issue status to in-progress","status":"completed"},{"content":"Run pytest tests/","activeForm":"Running pytest tests/","status":"completed"},{"content":"Post test results as comment to issue #71","activeForm":"Posting test results as comment to issue #71","status":"in_progress"},{"content":"Close issue #71","activeForm":"Closing issue #71","status":"pending"}]}}],"stop_reason":"tool_use","stop_sequence":null,"usage":{"input_tokens":6,"cache_creation_input_tokens":4481,"cache_read_input_tokens":29193,"cache_creation":{"ephemeral_5m_input_tokens":4481,"ephemeral_1h_input_tokens":0},"output_tokens":222,"service_tier":"standard"}},"parent_tool_use_id":null,"session_id":"ff1b37cf-9618-4f7d-ae0f-6002cb9747cc","uuid":"0c41cd9b-ac3e-4cf0-8d11-0ea77376e840"},{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_0132qMh94QgabWqgUakj9Lwq","type":"tool_result","content":"Todos have been modified successfully. Ensure that you continue to use the todo list to track your progress. Please proceed with the current tasks if applicable"}]},"parent_tool_use_id":null,"session_id":"ff1b37cf-9618-4f7d-ae0f-6002cb9747cc","uuid":"7d50cd16-34f2-40c7-9aa7-70b9696622f1"},{"type":"assistant","message":{"model":"claude-sonnet-4-5-20250929","id":"msg_01X7JV74pfzzrBb91qtTgdZ6","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01Tnqm2GMqmfgjTx4FaUknXu","name":"mcp__github__add_issue_comment","input":{"owner":"xmandeng","repo":"quber","issue_number":71,"body":"## Unit Test Results ✅\n\nAll tests passed successfully!\n\n### Summary Statistics\n- **Total Tests**: 107\n- **Passed**: 107 ✅\n- **Failed**: 0\n- **Warnings**: 6 (deprecation warnings from Pydantic)\n- **Duration**: 7.43 seconds\n\n### Test Coverage\n- **Overall Coverage**: 38%\n- **Statements**: 1114 total, 691 missed\n- **Coverage Report**: HTML report generated in `htmlcov/`\n\n### Test Breakdown by Module\n\n**Agents Tests** (25 tests)\n- All agent factory tests passed\n- Model provider detection working correctly\n- Multi-provider support validated\n\n**Core Tests** (22 tests)\n- Table metadata models working correctly\n- Enhanced table parser functioning as expected\n- Header consolidation logic validated\n\n**Prompts Tests** (12 tests)\n- TOML prompt loading operational\n- Error handling for missing files/keys validated\n- Multi-line content handling working\n\n**CLI Tests** (18 tests)\n- All CLI commands (analyze, batch, models) functional\n- Help text generation working\n- Input validation performing correctly\n\n**Utils Tests** (30 tests)\n- Configuration management working\n- Logging setup operational (with and without Logfire)\n- API key handling validated\n\n### Warnings\n6 deprecation warnings from Pydantic v2.x regarding:\n- Use of `extra` keyword arguments on Field (should use `json_schema_extra`)\n- Class-based config (should use `ConfigDict`)\n\nThese are low-priority deprecation warnings that don't affect functionality.\n\n### Conclusion\nAll 107 unit tests are passing. The test suite covers the core functionality of the Quber system including table extraction, LLM integration, CLI interface, and utility functions."}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":6,"cache_creation_input_tokens":264,"cache_read_input_tokens":33674,"cache_creation":{"ephemeral_5m_input_tokens":264,"ephemeral_1h_input_tokens":0},"output_tokens":526,"service_tier":"standard"}},"parent_tool_use_id":null,"session_id":"ff1b37cf-9618-4f7d-ae0f-6002cb9747cc","uuid":"6a073a7d-9840-43e6-99b3-c19c0f6ab57e"},{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01Tnqm2GMqmfgjTx4FaUknXu","type":"tool_result","content":[{"type":"text","text":"{\n  \"url\": \"https://api.github.com/repos/xmandeng/quber/issues/comments/3382767711\",\n  \"html_url\": \"https://github.com/xmandeng/quber/issues/71#issuecomment-3382767711\",\n  \"issue_url\": \"https://api.github.com/repos/xmandeng/quber/issues/71\",\n  \"id\": 3382767711,\n  \"node_id\": \"IC_kwDOPv-12s7JoPBf\",\n  \"user\": {\n    \"login\": \"xmandeng\",\n    \"id\": 44256405,\n    \"node_id\": \"MDQ6VXNlcjQ0MjU2NDA1\",\n    \"avatar_url\": \"https://avatars.githubusercontent.com/u/44256405?u=31eed419124fdd913ce37311802fd784c3b7829d&v=4\",\n    \"gravatar_id\": \"\",\n    \"url\": \"https://api.github.com/users/xmandeng\",\n    \"html_url\": \"https://github.com/xmandeng\",\n    \"followers_url\": \"https://api.github.com/users/xmandeng/followers\",\n    \"following_url\": \"https://api.github.com/users/xmandeng/following{/other_user}\",\n    \"gists_url\": \"https://api.github.com/users/xmandeng/gists{/gist_id}\",\n    \"starred_url\": \"https://api.github.com/users/xmandeng/starred{/owner}{/repo}\",\n    \"subscriptions_url\": \"https://api.github.com/users/xmandeng/subscriptions\",\n    \"organizations_url\": \"https://api.github.com/users/xmandeng/orgs\",\n    \"repos_url\": \"https://api.github.com/users/xmandeng/repos\",\n    \"events_url\": \"https://api.github.com/users/xmandeng/events{/privacy}\",\n    \"received_events_url\": \"https://api.github.com/users/xmandeng/received_events\",\n    \"type\": \"User\",\n    \"user_view_type\": \"public\",\n    \"site_admin\": false\n  },\n  \"created_at\": \"2025-10-08T18:38:34Z\",\n  \"updated_at\": \"2025-10-08T18:38:34Z\",\n  \"author_association\": \"OWNER\",\n  \"body\": \"## Unit Test Results ✅\\n\\nAll tests passed successfully!\\n\\n### Summary Statistics\\n- **Total Tests**: 107\\n- **Passed**: 107 ✅\\n- **Failed**: 0\\n- **Warnings**: 6 (deprecation warnings from Pydantic)\\n- **Duration**: 7.43 seconds\\n\\n### Test Coverage\\n- **Overall Coverage**: 38%\\n- **Statements**: 1114 total, 691 missed\\n- **Coverage Report**: HTML report generated in `htmlcov/`\\n\\n### Test Breakdown by Module\\n\\n**Agents Tests** (25 tests)\\n- All agent factory tests passed\\n- Model provider detection working correctly\\n- Multi-provider support validated\\n\\n**Core Tests** (22 tests)\\n- Table metadata models working correctly\\n- Enhanced table parser functioning as expected\\n- Header consolidation logic validated\\n\\n**Prompts Tests** (12 tests)\\n- TOML prompt loading operational\\n- Error handling for missing files/keys validated\\n- Multi-line content handling working\\n\\n**CLI Tests** (18 tests)\\n- All CLI commands (analyze, batch, models) functional\\n- Help text generation working\\n- Input validation performing correctly\\n\\n**Utils Tests** (30 tests)\\n- Configuration management working\\n- Logging setup operational (with and without Logfire)\\n- API key handling validated\\n\\n### Warnings\\n6 deprecation warnings from Pydantic v2.x regarding:\\n- Use of `extra` keyword arguments on Field (should use `json_schema_extra`)\\n- Class-based config (should use `ConfigDict`)\\n\\nThese are low-priority deprecation warnings that don't affect functionality.\\n\\n### Conclusion\\nAll 107 unit tests are passing. The test suite covers the core functionality of the Quber system including table extraction, LLM integration, CLI interface, and utility functions.\",\n  \"reactions\": {\n    \"url\": \"https://api.github.com/repos/xmandeng/quber/issues/comments/3382767711/reactions\",\n    \"total_count\": 0,\n    \"+1\": 0,\n    \"-1\": 0,\n    \"laugh\": 0,\n    \"hooray\": 0,\n    \"confused\": 0,\n    \"heart\": 0,\n    \"rocket\": 0,\n    \"eyes\": 0\n  },\n  \"performed_via_github_app\": null\n}"}]}]},"parent_tool_use_id":null,"session_id":"ff1b37cf-9618-4f7d-ae0f-6002cb9747cc","uuid":"87cf1bed-de1a-4e32-92e1-7e330c3f4830"},{"type":"assistant","message":{"model":"claude-sonnet-4-5-20250929","id":"msg_01FaXQeD7BGy32M4fzYxfgC9","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_0181VnWf5anYPL9Wv5rkEk7V","name":"TodoWrite","input":{"todos":[{"content":"Remove 'automate:safe' label from issue #71","activeForm":"Removing 'automate:safe' label from issue #71","status":"completed"},{"content":"Update issue status to in-progress","activeForm":"Updating issue status to in-progress","status":"completed"},{"content":"Run pytest tests/","activeForm":"Running pytest tests/","status":"completed"},{"content":"Post test results as comment to issue #71","activeForm":"Posting test results as comment to issue #71","status":"completed"},{"content":"Close issue #71","activeForm":"Closing issue #71","status":"in_progress"}]}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":5,"cache_creation_input_tokens":1772,"cache_read_input_tokens":33938,"cache_creation":{"ephemeral_5m_input_tokens":1772,"ephemeral_1h_input_tokens":0},"output_tokens":222,"service_tier":"standard"}},"parent_tool_use_id":null,"session_id":"ff1b37cf-9618-4f7d-ae0f-6002cb9747cc","uuid":"a0c8ae40-4b13-436d-aa69-51c33f07e63c"},{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_0181VnWf5anYPL9Wv5rkEk7V","type":"tool_result","content":"Todos have been modified successfully. Ensure that you continue to use the todo list to track your progress. Please proceed with the current tasks if applicable"}]},"parent_tool_use_id":null,"session_id":"ff1b37cf-9618-4f7d-ae0f-6002cb9747cc","uuid":"05069fe4-8bec-41dc-b78f-74694a741d7e"},{"type":"assistant","message":{"model":"claude-sonnet-4-5-20250929","id":"msg_017qHqfeGTPuRWuzrzukaPFN","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01Vn5nVt9jyArWU8mocPeU6J","name":"Bash","input":{"command":"gh issue close 71 --comment \"Unit tests completed successfully. All 107 tests passed with 38% code coverage. See test results summary above.\"","description":"Close issue #71 with completion comment"}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":5,"cache_creation_input_tokens":264,"cache_read_input_tokens":35710,"cache_creation":{"ephemeral_5m_input_tokens":264,"ephemeral_1h_input_tokens":0},"output_tokens":108,"service_tier":"standard"}},"parent_tool_use_id":null,"session_id":"ff1b37cf-9618-4f7d-ae0f-6002cb9747cc","uuid":"17d8d841-c432-40de-bf78-a3c9379f6af5"},{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01Vn5nVt9jyArWU8mocPeU6J","type":"tool_result","content":"✓ Closed issue xmandeng/quber#71 ([TASK] Run Unit Tests)","is_error":false}]},"parent_tool_use_id":null,"session_id":"ff1b37cf-9618-4f7d-ae0f-6002cb9747cc","uuid":"50d7a8cb-66e6-4b88-bc30-dcb3e3247477"},{"type":"assistant","message":{"model":"claude-sonnet-4-5-20250929","id":"msg_01RjQk3HqgRZGNfZzRdr2AXP","type":"message","role":"assistant","content":[{"type":"tool_use","id":"toolu_01SLFYkke7APuvdd6Lxik1NX","name":"TodoWrite","input":{"todos":[{"content":"Remove 'automate:safe' label from issue #71","activeForm":"Removing 'automate:safe' label from issue #71","status":"completed"},{"content":"Update issue status to in-progress","activeForm":"Updating issue status to in-progress","status":"completed"},{"content":"Run pytest tests/","activeForm":"Running pytest tests/","status":"completed"},{"content":"Post test results as comment to issue #71","activeForm":"Posting test results as comment to issue #71","status":"completed"},{"content":"Close issue #71","activeForm":"Closing issue #71","status":"completed"}]}}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":4,"cache_creation_input_tokens":144,"cache_read_input_tokens":35974,"cache_creation":{"ephemeral_5m_input_tokens":144,"ephemeral_1h_input_tokens":0},"output_tokens":220,"service_tier":"standard"}},"parent_tool_use_id":null,"session_id":"ff1b37cf-9618-4f7d-ae0f-6002cb9747cc","uuid":"605a12f0-8e2f-47d8-bbcc-4a6a4dfc474b"},{"type":"user","message":{"role":"user","content":[{"tool_use_id":"toolu_01SLFYkke7APuvdd6Lxik1NX","type":"tool_result","content":"Todos have been modified successfully. Ensure that you continue to use the todo list to track your progress. Please proceed with the current tasks if applicable"}]},"parent_tool_use_id":null,"session_id":"ff1b37cf-9618-4f7d-ae0f-6002cb9747cc","uuid":"5fd0c4d7-94f9-498d-862a-9a554613cac8"},{"type":"assistant","message":{"model":"claude-sonnet-4-5-20250929","id":"msg_01JUBTNugmnd26D1Z4dmDa3y","type":"message","role":"assistant","content":[{"type":"text","text":"## Task Complete ✅\n\nSuccessfully completed issue #71:\n\n1. **Removed `automate:safe` label** from issue #71\n2. **Updated status to in-progress** while working on the task\n3. **Ran unit tests** with pytest\n4. **Posted comprehensive test results** to the issue as a comment\n5. **Closed the issue** with completion note\n\n### Test Results Summary\n- **107 tests passed** (0 failures)\n- **38% code coverage**\n- **7.43 seconds** execution time\n- All modules tested: agents, core, prompts, CLI, and utils\n\nThe issue has been completed per the definition of done: tests were run, results collected, and posted to the issue. No branch or PR was required as specified in the task description."}],"stop_reason":null,"stop_sequence":null,"usage":{"input_tokens":4,"cache_creation_input_tokens":262,"cache_read_input_tokens":36118,"cache_creation":{"ephemeral_5m_input_tokens":262,"ephemeral_1h_input_tokens":0},"output_tokens":180,"service_tier":"standard"}},"parent_tool_use_id":null,"session_id":"ff1b37cf-9618-4f7d-ae0f-6002cb9747cc","uuid":"2d610056-e74f-4119-9107-9a923c4d387e"},{"type":"result","subtype":"success","is_error":false,"duration_ms":87553,"duration_api_ms":76842,"num_turns":29,"result":"## Task Complete ✅\n\nSuccessfully completed issue #71:\n\n1. **Removed `automate:safe` label** from issue #71\n2. **Updated status to in-progress** while working on the task\n3. **Ran unit tests** with pytest\n4. **Posted comprehensive test results** to the issue as a comment\n5. **Closed the issue** with completion note\n\n### Test Results Summary\n- **107 tests passed** (0 failures)\n- **38% code coverage**\n- **7.43 seconds** execution time\n- All modules tested: agents, core, prompts, CLI, and utils\n\nThe issue has been completed per the definition of done: tests were run, results collected, and posted to the issue. No branch or PR was required as specified in the task description.","session_id":"ff1b37cf-9618-4f7d-ae0f-6002cb9747cc","total_cost_usd":0.23918499999999998,"usage":{"input_tokens":76,"cache_creation_input_tokens":16640,"cache_read_input_tokens":421194,"output_tokens":2850,"server_tool_use":{"web_search_requests":0},"service_tier":"standard","cache_creation":{"ephemeral_1h_input_tokens":0,"ephemeral_5m_input_tokens":16640}},"modelUsage":{"claude-sonnet-4-5-20250929":{"inputTokens":76,"outputTokens":2850,"cacheReadInputTokens":421194,"cacheCreationInputTokens":16640,"webSearchRequests":0,"costUSD":0.2317362,"contextWindow":200000},"claude-3-5-haiku-20241022":{"inputTokens":8561,"outputTokens":150,"cacheReadInputTokens":0,"cacheCreationInputTokens":0,"webSearchRequests":0,"costUSD":0.007448800000000002,"contextWindow":200000}},"permission_denials":[],"uuid":"31c36eda-f041-4de7-920d-3cd118672552"}]