2026-01-12T15:47:09,890 Created temporary directory: /tmp/pip-ephem-wheel-cache-39htpvqo 2026-01-12T15:47:09,892 Created temporary directory: /tmp/pip-build-tracker-v6l69yfr 2026-01-12T15:47:09,893 Initialized build tracking at /tmp/pip-build-tracker-v6l69yfr 2026-01-12T15:47:09,893 Created build tracker: /tmp/pip-build-tracker-v6l69yfr 2026-01-12T15:47:09,894 Entered build tracker: /tmp/pip-build-tracker-v6l69yfr 2026-01-12T15:47:09,895 Created temporary directory: /tmp/pip-wheel-1n1rxvht 2026-01-12T15:47:09,898 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. 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https://www.piwheels.org/simple/lobster-ai/lobster_ai-0.4.0.7-py3-none-any.whl#sha256=cbee755d3f7ac5e1cd5b65bfe0309faa4acba90c1a6a1b32036010c45f0868d9 (from https://www.piwheels.org/simple/lobster-ai/) (requires-python:>=3.11) 2026-01-12T15:47:10,406 Skipping link: not a file: https://www.piwheels.org/simple/lobster-ai/ 2026-01-12T15:47:10,407 Skipping link: not a file: https://pypi.org/simple/lobster-ai/ 2026-01-12T15:47:10,430 Given no hashes to check 1 links for project 'lobster-ai': discarding no candidates 2026-01-12T15:47:10,449 Collecting lobster-ai==0.4.3.8 2026-01-12T15:47:10,452 Created temporary directory: /tmp/pip-unpack-kic0kpcc 2026-01-12T15:47:10,677 Downloading lobster_ai-0.4.3.8.tar.gz (1.2 MB) 2026-01-12T15:47:11,706 Added lobster-ai==0.4.3.8 from https://files.pythonhosted.org/packages/08/d2/1890f055ea9d592840eed508beb304b890a51161df92c55deabccc8add48/lobster_ai-0.4.3.8.tar.gz to build tracker '/tmp/pip-build-tracker-v6l69yfr' 2026-01-12T15:47:11,715 Created temporary directory: /tmp/pip-build-env-ycum8vpf 2026-01-12T15:47:11,719 Installing build dependencies: started 2026-01-12T15:47:11,720 Running command pip subprocess to install build dependencies 2026-01-12T15:47:12,900 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-01-12T15:47:13,554 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-01-12T15:47:13,577 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-01-12T15:47:15,283 Collecting setuptools>=65.0 2026-01-12T15:47:15,377 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2026-01-12T15:47:15,655 Collecting wheel 2026-01-12T15:47:15,671 Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB) 2026-01-12T15:47:18,674 Installing collected packages: wheel, setuptools 2026-01-12T15:47:18,921 Creating /tmp/pip-build-env-ycum8vpf/overlay/local/bin 2026-01-12T15:47:18,924 changing mode of /tmp/pip-build-env-ycum8vpf/overlay/local/bin/wheel to 755 2026-01-12T15:47:22,590 Successfully installed setuptools-80.9.0 wheel-0.45.1 2026-01-12T15:47:22,862 Installing build dependencies: finished with status 'done' 2026-01-12T15:47:22,868 Getting requirements to build wheel: started 2026-01-12T15:47:22,869 Running command Getting requirements to build wheel 2026-01-12T15:47:23,554 /tmp/pip-build-env-ycum8vpf/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `license` overwritten by `pyproject.toml` 2026-01-12T15:47:23,554 corresp(dist, value, root_dir) 2026-01-12T15:47:23,555 /tmp/pip-build-env-ycum8vpf/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-01-12T15:47:23,556 corresp(dist, value, root_dir) 2026-01-12T15:47:23,556 /tmp/pip-build-env-ycum8vpf/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `extras_require` overwritten in `pyproject.toml` (optional-dependencies) 2026-01-12T15:47:23,557 corresp(dist, value, root_dir) 2026-01-12T15:47:23,663 running egg_info 2026-01-12T15:47:23,670 writing lobster_ai.egg-info/PKG-INFO 2026-01-12T15:47:23,701 writing dependency_links to lobster_ai.egg-info/dependency_links.txt 2026-01-12T15:47:23,703 writing entry points to lobster_ai.egg-info/entry_points.txt 2026-01-12T15:47:23,722 writing requirements to lobster_ai.egg-info/requires.txt 2026-01-12T15:47:23,724 writing top-level names to lobster_ai.egg-info/top_level.txt 2026-01-12T15:47:23,871 reading manifest file 'lobster_ai.egg-info/SOURCES.txt' 2026-01-12T15:47:23,888 adding license file 'LICENSE' 2026-01-12T15:47:23,903 writing manifest file 'lobster_ai.egg-info/SOURCES.txt' 2026-01-12T15:47:24,001 Getting requirements to build wheel: finished with status 'done' 2026-01-12T15:47:24,004 Created temporary directory: /tmp/pip-modern-metadata-a_vmclat 2026-01-12T15:47:24,006 Preparing metadata (pyproject.toml): started 2026-01-12T15:47:24,007 Running command Preparing metadata (pyproject.toml) 2026-01-12T15:47:24,635 /tmp/pip-build-env-ycum8vpf/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `license` overwritten by `pyproject.toml` 2026-01-12T15:47:24,635 corresp(dist, value, root_dir) 2026-01-12T15:47:24,636 /tmp/pip-build-env-ycum8vpf/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-01-12T15:47:24,636 corresp(dist, value, root_dir) 2026-01-12T15:47:24,637 /tmp/pip-build-env-ycum8vpf/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `extras_require` overwritten in `pyproject.toml` (optional-dependencies) 2026-01-12T15:47:24,637 corresp(dist, value, root_dir) 2026-01-12T15:47:24,741 running dist_info 2026-01-12T15:47:24,753 creating /tmp/pip-modern-metadata-a_vmclat/lobster_ai.egg-info 2026-01-12T15:47:24,754 writing /tmp/pip-modern-metadata-a_vmclat/lobster_ai.egg-info/PKG-INFO 2026-01-12T15:47:24,784 writing dependency_links to /tmp/pip-modern-metadata-a_vmclat/lobster_ai.egg-info/dependency_links.txt 2026-01-12T15:47:24,786 writing entry points to /tmp/pip-modern-metadata-a_vmclat/lobster_ai.egg-info/entry_points.txt 2026-01-12T15:47:24,805 writing requirements to /tmp/pip-modern-metadata-a_vmclat/lobster_ai.egg-info/requires.txt 2026-01-12T15:47:24,806 writing top-level names to /tmp/pip-modern-metadata-a_vmclat/lobster_ai.egg-info/top_level.txt 2026-01-12T15:47:24,808 writing manifest file '/tmp/pip-modern-metadata-a_vmclat/lobster_ai.egg-info/SOURCES.txt' 2026-01-12T15:47:24,945 reading manifest file '/tmp/pip-modern-metadata-a_vmclat/lobster_ai.egg-info/SOURCES.txt' 2026-01-12T15:47:24,947 adding license file 'LICENSE' 2026-01-12T15:47:24,958 writing manifest file '/tmp/pip-modern-metadata-a_vmclat/lobster_ai.egg-info/SOURCES.txt' 2026-01-12T15:47:24,959 creating '/tmp/pip-modern-metadata-a_vmclat/lobster_ai-0.4.3.8.dist-info' 2026-01-12T15:47:25,087 Preparing metadata (pyproject.toml): finished with status 'done' 2026-01-12T15:47:25,094 Source in /tmp/pip-wheel-1n1rxvht/lobster-ai_a616cdebf8284c5580b766c02079370d has version 0.4.3.8, which satisfies requirement lobster-ai==0.4.3.8 from https://files.pythonhosted.org/packages/08/d2/1890f055ea9d592840eed508beb304b890a51161df92c55deabccc8add48/lobster_ai-0.4.3.8.tar.gz 2026-01-12T15:47:25,095 Removed lobster-ai==0.4.3.8 from https://files.pythonhosted.org/packages/08/d2/1890f055ea9d592840eed508beb304b890a51161df92c55deabccc8add48/lobster_ai-0.4.3.8.tar.gz from build tracker '/tmp/pip-build-tracker-v6l69yfr' 2026-01-12T15:47:25,106 Created temporary directory: /tmp/pip-unpack-h7zkv6ai 2026-01-12T15:47:25,106 Building wheels for collected packages: lobster-ai 2026-01-12T15:47:25,111 Created temporary directory: /tmp/pip-wheel-yws2m49q 2026-01-12T15:47:25,111 Destination directory: /tmp/pip-wheel-yws2m49q 2026-01-12T15:47:25,114 Building wheel for lobster-ai (pyproject.toml): started 2026-01-12T15:47:25,115 Running command Building wheel for lobster-ai (pyproject.toml) 2026-01-12T15:47:25,734 /tmp/pip-build-env-ycum8vpf/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `license` overwritten by `pyproject.toml` 2026-01-12T15:47:25,734 corresp(dist, value, root_dir) 2026-01-12T15:47:25,735 /tmp/pip-build-env-ycum8vpf/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-01-12T15:47:25,736 corresp(dist, value, root_dir) 2026-01-12T15:47:25,736 /tmp/pip-build-env-ycum8vpf/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `extras_require` overwritten in `pyproject.toml` (optional-dependencies) 2026-01-12T15:47:25,737 corresp(dist, value, root_dir) 2026-01-12T15:47:25,828 running bdist_wheel 2026-01-12T15:47:25,850 running build 2026-01-12T15:47:25,850 running build_py 2026-01-12T15:47:25,857 creating build/lib/lobster 2026-01-12T15:47:25,860 copying lobster/version.py -> build/lib/lobster 2026-01-12T15:47:25,862 copying lobster/__main__.py -> build/lib/lobster 2026-01-12T15:47:25,864 copying lobster/main.py -> build/lib/lobster 2026-01-12T15:47:25,866 copying lobster/cli.py -> build/lib/lobster 2026-01-12T15:47:25,872 copying lobster/_version.py -> build/lib/lobster 2026-01-12T15:47:25,874 creating build/lib/lobster/lobster_cloud 2026-01-12T15:47:25,875 copying lobster/lobster_cloud/__init__.py -> build/lib/lobster/lobster_cloud 2026-01-12T15:47:25,877 copying lobster/lobster_cloud/client.py -> build/lib/lobster/lobster_cloud 2026-01-12T15:47:25,880 creating build/lib/lobster/agents 2026-01-12T15:47:25,881 copying lobster/agents/supervisor.py -> build/lib/lobster/agents 2026-01-12T15:47:25,884 copying lobster/agents/draw_graph.py -> build/lib/lobster/agents 2026-01-12T15:47:25,886 copying lobster/agents/visualization_expert.py -> build/lib/lobster/agents 2026-01-12T15:47:25,888 copying lobster/agents/state.py -> build/lib/lobster/agents 2026-01-12T15:47:25,891 copying lobster/agents/graph.py -> build/lib/lobster/agents 2026-01-12T15:47:25,894 creating build/lib/lobster/core 2026-01-12T15:47:25,895 copying lobster/core/component_registry.py -> build/lib/lobster/core 2026-01-12T15:47:25,897 copying lobster/core/download_queue.py -> build/lib/lobster/core 2026-01-12T15:47:25,900 copying lobster/core/notebook_validator.py -> build/lib/lobster/core 2026-01-12T15:47:25,902 copying lobster/core/plot_manager.py -> build/lib/lobster/core 2026-01-12T15:47:25,904 copying lobster/core/notebook_exporter.py -> build/lib/lobster/core 2026-01-12T15:47:25,907 copying lobster/core/__init__.py -> build/lib/lobster/core 2026-01-12T15:47:25,909 copying lobster/core/archive_utils.py -> build/lib/lobster/core 2026-01-12T15:47:25,911 copying lobster/core/publication_queue.py -> build/lib/lobster/core 2026-01-12T15:47:25,914 copying lobster/core/ris_parser.py -> build/lib/lobster/core 2026-01-12T15:47:25,916 copying lobster/core/notebook_executor.py -> build/lib/lobster/core 2026-01-12T15:47:25,919 copying lobster/core/provenance.py -> build/lib/lobster/core 2026-01-12T15:47:25,921 copying lobster/core/config_resolver.py -> build/lib/lobster/core 2026-01-12T15:47:25,924 copying lobster/core/workspace.py -> build/lib/lobster/core 2026-01-12T15:47:25,925 copying lobster/core/client.py -> build/lib/lobster/core 2026-01-12T15:47:25,929 copying lobster/core/license_manager.py -> build/lib/lobster/core 2026-01-12T15:47:25,932 copying lobster/core/exceptions.py -> build/lib/lobster/core 2026-01-12T15:47:25,934 copying lobster/core/data_manager_v2.py -> build/lib/lobster/core 2026-01-12T15:47:25,939 copying lobster/core/plugin_loader.py -> build/lib/lobster/core 2026-01-12T15:47:25,941 copying lobster/core/queue_storage.py -> build/lib/lobster/core 2026-01-12T15:47:25,943 copying lobster/core/ir_coverage.py -> build/lib/lobster/core 2026-01-12T15:47:25,945 copying lobster/core/analysis_ir.py -> build/lib/lobster/core 2026-01-12T15:47:25,948 creating build/lib/lobster/tools 2026-01-12T15:47:25,949 copying lobster/tools/gpu_detector.py -> build/lib/lobster/tools 2026-01-12T15:47:25,951 copying lobster/tools/geo_parser.py -> build/lib/lobster/tools 2026-01-12T15:47:25,953 copying lobster/tools/custom_code_tool.py -> build/lib/lobster/tools 2026-01-12T15:47:25,956 copying lobster/tools/__init__.py -> build/lib/lobster/tools 2026-01-12T15:47:25,958 copying lobster/tools/enhanced_handoff_tool.py -> build/lib/lobster/tools 2026-01-12T15:47:25,960 copying lobster/tools/expert_handoff_patterns.py -> build/lib/lobster/tools 2026-01-12T15:47:25,963 copying lobster/tools/workspace_tool.py -> build/lib/lobster/tools 2026-01-12T15:47:25,967 copying lobster/tools/todo_tools.py -> build/lib/lobster/tools 2026-01-12T15:47:25,970 copying lobster/tools/workflow_tracker.py -> build/lib/lobster/tools 2026-01-12T15:47:25,972 copying lobster/tools/rate_limiter.py -> build/lib/lobster/tools 2026-01-12T15:47:25,975 copying lobster/tools/geo_downloader.py -> build/lib/lobster/tools 2026-01-12T15:47:25,977 copying lobster/tools/pipeline_strategy.py -> build/lib/lobster/tools 2026-01-12T15:47:25,979 copying lobster/tools/url_transforms.py -> build/lib/lobster/tools 2026-01-12T15:47:25,980 copying lobster/tools/handoff_tool.py -> build/lib/lobster/tools 2026-01-12T15:47:25,983 copying lobster/tools/download_orchestrator.py -> build/lib/lobster/tools 2026-01-12T15:47:25,985 copying lobster/tools/expert_handoff_manager.py -> build/lib/lobster/tools 2026-01-12T15:47:25,988 creating build/lib/lobster/ui 2026-01-12T15:47:25,989 copying lobster/ui/console_manager.py -> build/lib/lobster/ui 2026-01-12T15:47:25,992 copying lobster/ui/__init__.py -> build/lib/lobster/ui 2026-01-12T15:47:25,993 copying lobster/ui/commands.py -> build/lib/lobster/ui 2026-01-12T15:47:25,996 copying lobster/ui/progress_manager.py -> build/lib/lobster/ui 2026-01-12T15:47:25,998 copying lobster/ui/themes.py -> build/lib/lobster/ui 2026-01-12T15:47:26,000 copying lobster/ui/live_dashboard.py -> build/lib/lobster/ui 2026-01-12T15:47:26,003 copying lobster/ui/os_app.py -> build/lib/lobster/ui 2026-01-12T15:47:26,006 creating build/lib/lobster/config 2026-01-12T15:47:26,007 copying lobster/config/llm_factory.py -> build/lib/lobster/config 2026-01-12T15:47:26,010 copying lobster/config/agent_capabilities.py -> build/lib/lobster/config 2026-01-12T15:47:26,012 copying lobster/config/__init__.py -> build/lib/lobster/config 2026-01-12T15:47:26,014 copying lobster/config/subscription_tiers.py -> build/lib/lobster/config 2026-01-12T15:47:26,016 copying lobster/config/workspace_config.py -> build/lib/lobster/config 2026-01-12T15:47:26,019 copying lobster/config/ssl_setup.py -> build/lib/lobster/config 2026-01-12T15:47:26,021 copying lobster/config/base_config.py -> build/lib/lobster/config 2026-01-12T15:47:26,023 copying lobster/config/constants.py -> build/lib/lobster/config 2026-01-12T15:47:26,025 copying lobster/config/config_manager.py -> build/lib/lobster/config 2026-01-12T15:47:26,027 copying lobster/config/agent_config.py -> build/lib/lobster/config 2026-01-12T15:47:26,030 copying lobster/config/global_config.py -> build/lib/lobster/config 2026-01-12T15:47:26,032 copying lobster/config/model_service.py -> build/lib/lobster/config 2026-01-12T15:47:26,035 copying lobster/config/version_check.py -> build/lib/lobster/config 2026-01-12T15:47:26,037 copying lobster/config/ollama_service.py -> build/lib/lobster/config 2026-01-12T15:47:26,039 copying lobster/config/supervisor_config.py -> build/lib/lobster/config 2026-01-12T15:47:26,042 copying lobster/config/settings.py -> build/lib/lobster/config 2026-01-12T15:47:26,044 copying lobster/config/provider_setup.py -> build/lib/lobster/config 2026-01-12T15:47:26,046 copying lobster/config/agent_registry.py -> build/lib/lobster/config 2026-01-12T15:47:26,049 creating build/lib/lobster/services 2026-01-12T15:47:26,050 copying lobster/services/__init__.py -> build/lib/lobster/services 2026-01-12T15:47:26,052 creating build/lib/lobster/cli_internal 2026-01-12T15:47:26,053 copying lobster/cli_internal/__init__.py -> build/lib/lobster/cli_internal 2026-01-12T15:47:26,056 creating build/lib/lobster/utils 2026-01-12T15:47:26,057 copying lobster/utils/__init__.py -> build/lib/lobster/utils 2026-01-12T15:47:26,059 copying lobster/utils/deviance.py -> build/lib/lobster/utils 2026-01-12T15:47:26,060 copying lobster/utils/error_handlers.py -> build/lib/lobster/utils 2026-01-12T15:47:26,063 copying lobster/utils/file_analyzer.py -> build/lib/lobster/utils 2026-01-12T15:47:26,066 copying lobster/utils/json_extractor.py -> build/lib/lobster/utils 2026-01-12T15:47:26,068 copying lobster/utils/logger.py -> build/lib/lobster/utils 2026-01-12T15:47:26,070 copying lobster/utils/callbacks.py -> build/lib/lobster/utils 2026-01-12T15:47:26,073 copying lobster/utils/progress_wrapper.py -> build/lib/lobster/utils 2026-01-12T15:47:26,076 copying lobster/utils/ssl_utils.py -> build/lib/lobster/utils 2026-01-12T15:47:26,078 copying lobster/utils/system.py -> build/lib/lobster/utils 2026-01-12T15:47:26,080 copying lobster/utils/file_naming.py -> build/lib/lobster/utils 2026-01-12T15:47:26,083 creating build/lib/lobster/agents/archive 2026-01-12T15:47:26,084 copying lobster/agents/archive/research_agent_assistant.py -> build/lib/lobster/agents/archive 2026-01-12T15:47:26,087 creating build/lib/lobster/agents/proteomics 2026-01-12T15:47:26,088 copying lobster/agents/proteomics/__init__.py -> build/lib/lobster/agents/proteomics 2026-01-12T15:47:26,090 copying lobster/agents/proteomics/state.py -> build/lib/lobster/agents/proteomics 2026-01-12T15:47:26,092 creating build/lib/lobster/agents/data_expert 2026-01-12T15:47:26,093 copying lobster/agents/data_expert/prompts.py -> build/lib/lobster/agents/data_expert 2026-01-12T15:47:26,096 copying lobster/agents/data_expert/__init__.py -> build/lib/lobster/agents/data_expert 2026-01-12T15:47:26,098 copying lobster/agents/data_expert/assistant.py -> build/lib/lobster/agents/data_expert 2026-01-12T15:47:26,100 copying lobster/agents/data_expert/config.py -> build/lib/lobster/agents/data_expert 2026-01-12T15:47:26,103 copying lobster/agents/data_expert/state.py -> build/lib/lobster/agents/data_expert 2026-01-12T15:47:26,105 copying lobster/agents/data_expert/data_expert.py -> build/lib/lobster/agents/data_expert 2026-01-12T15:47:26,108 creating build/lib/lobster/agents/research 2026-01-12T15:47:26,109 copying lobster/agents/research/prompts.py -> build/lib/lobster/agents/research 2026-01-12T15:47:26,112 copying lobster/agents/research/__init__.py -> build/lib/lobster/agents/research 2026-01-12T15:47:26,114 copying lobster/agents/research/config.py -> build/lib/lobster/agents/research 2026-01-12T15:47:26,116 copying lobster/agents/research/research_agent.py -> build/lib/lobster/agents/research 2026-01-12T15:47:26,120 copying lobster/agents/research/state.py -> build/lib/lobster/agents/research 2026-01-12T15:47:26,122 creating build/lib/lobster/agents/transcriptomics 2026-01-12T15:47:26,123 copying lobster/agents/transcriptomics/prompts.py -> build/lib/lobster/agents/transcriptomics 2026-01-12T15:47:26,126 copying lobster/agents/transcriptomics/transcriptomics_expert.py -> build/lib/lobster/agents/transcriptomics 2026-01-12T15:47:26,129 copying lobster/agents/transcriptomics/__init__.py -> build/lib/lobster/agents/transcriptomics 2026-01-12T15:47:26,131 copying lobster/agents/transcriptomics/shared_tools.py -> build/lib/lobster/agents/transcriptomics 2026-01-12T15:47:26,134 copying lobster/agents/transcriptomics/de_analysis_expert.py -> build/lib/lobster/agents/transcriptomics 2026-01-12T15:47:26,137 copying lobster/agents/transcriptomics/config.py -> build/lib/lobster/agents/transcriptomics 2026-01-12T15:47:26,140 copying lobster/agents/transcriptomics/state.py -> build/lib/lobster/agents/transcriptomics 2026-01-12T15:47:26,142 copying lobster/agents/transcriptomics/annotation_expert.py -> build/lib/lobster/agents/transcriptomics 2026-01-12T15:47:26,145 creating build/lib/lobster/agents/langgraph_supervisor 2026-01-12T15:47:26,146 copying lobster/agents/langgraph_supervisor/supervisor.py -> build/lib/lobster/agents/langgraph_supervisor 2026-01-12T15:47:26,149 copying lobster/agents/langgraph_supervisor/agent_name.py -> build/lib/lobster/agents/langgraph_supervisor 2026-01-12T15:47:26,151 copying lobster/agents/langgraph_supervisor/__init__.py -> build/lib/lobster/agents/langgraph_supervisor 2026-01-12T15:47:26,153 copying lobster/agents/langgraph_supervisor/handoff.py -> build/lib/lobster/agents/langgraph_supervisor 2026-01-12T15:47:26,156 creating build/lib/lobster/core/backends 2026-01-12T15:47:26,157 copying lobster/core/backends/base.py -> build/lib/lobster/core/backends 2026-01-12T15:47:26,160 copying lobster/core/backends/__init__.py -> build/lib/lobster/core/backends 2026-01-12T15:47:26,161 copying lobster/core/backends/h5ad_backend.py -> build/lib/lobster/core/backends 2026-01-12T15:47:26,164 copying lobster/core/backends/mudata_backend.py -> build/lib/lobster/core/backends 2026-01-12T15:47:26,168 creating build/lib/lobster/core/interfaces 2026-01-12T15:47:26,169 copying lobster/core/interfaces/base_client.py -> build/lib/lobster/core/interfaces 2026-01-12T15:47:26,171 copying lobster/core/interfaces/download_service.py -> build/lib/lobster/core/interfaces 2026-01-12T15:47:26,173 copying lobster/core/interfaces/__init__.py -> build/lib/lobster/core/interfaces 2026-01-12T15:47:26,175 copying lobster/core/interfaces/adapter.py -> build/lib/lobster/core/interfaces 2026-01-12T15:47:26,177 copying lobster/core/interfaces/backend.py -> build/lib/lobster/core/interfaces 2026-01-12T15:47:26,180 copying lobster/core/interfaces/validator.py -> build/lib/lobster/core/interfaces 2026-01-12T15:47:26,182 creating build/lib/lobster/core/adapters 2026-01-12T15:47:26,183 copying lobster/core/adapters/base.py -> build/lib/lobster/core/adapters 2026-01-12T15:47:26,186 copying lobster/core/adapters/__init__.py -> build/lib/lobster/core/adapters 2026-01-12T15:47:26,187 copying lobster/core/adapters/transcriptomics_adapter.py -> build/lib/lobster/core/adapters 2026-01-12T15:47:26,190 copying lobster/core/adapters/pseudobulk_adapter.py -> build/lib/lobster/core/adapters 2026-01-12T15:47:26,193 copying lobster/core/adapters/proteomics_adapter.py -> build/lib/lobster/core/adapters 2026-01-12T15:47:26,195 copying lobster/core/adapters/protein_structure_adapter.py -> build/lib/lobster/core/adapters 2026-01-12T15:47:26,198 creating build/lib/lobster/core/utils 2026-01-12T15:47:26,199 copying lobster/core/utils/__init__.py -> build/lib/lobster/core/utils 2026-01-12T15:47:26,201 copying lobster/core/utils/h5ad_utils.py -> build/lib/lobster/core/utils 2026-01-12T15:47:26,204 creating build/lib/lobster/core/identifiers 2026-01-12T15:47:26,205 copying lobster/core/identifiers/accession_resolver.py -> build/lib/lobster/core/identifiers 2026-01-12T15:47:26,208 copying lobster/core/identifiers/__init__.py -> build/lib/lobster/core/identifiers 2026-01-12T15:47:26,210 creating build/lib/lobster/core/schemas 2026-01-12T15:47:26,211 copying lobster/core/schemas/transcriptomics.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,215 copying lobster/core/schemas/download_queue.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,217 copying lobster/core/schemas/validation.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,220 copying lobster/core/schemas/database_registry.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,222 copying lobster/core/schemas/metabolomics.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,225 copying lobster/core/schemas/__init__.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,227 copying lobster/core/schemas/sra.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,229 copying lobster/core/schemas/publication_queue.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,232 copying lobster/core/schemas/proteomics.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,234 copying lobster/core/schemas/metagenomics.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,237 copying lobster/core/schemas/download_urls.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,240 copying lobster/core/schemas/ontology.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,242 copying lobster/core/schemas/export_schemas.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,245 copying lobster/core/schemas/database_mappings.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,247 copying lobster/core/schemas/protein_structure.py -> build/lib/lobster/core/schemas 2026-01-12T15:47:26,250 creating build/lib/lobster/tools/archive 2026-01-12T15:47:26,251 copying lobster/tools/archive/unified_content_service.py -> build/lib/lobster/tools/archive 2026-01-12T15:47:26,254 copying lobster/tools/archive/publication_service.py -> build/lib/lobster/tools/archive 2026-01-12T15:47:26,257 creating build/lib/lobster/tools/providers 2026-01-12T15:47:26,258 copying lobster/tools/providers/base_provider.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,261 copying lobster/tools/providers/publication_resolver.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,264 copying lobster/tools/providers/__init__.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,266 copying lobster/tools/providers/webpage_provider.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,268 copying lobster/tools/providers/pride_normalizer.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,270 copying lobster/tools/providers/geo_utils.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,273 copying lobster/tools/providers/biorxiv_medrxiv_config.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,274 copying lobster/tools/providers/pubmed_provider.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,278 copying lobster/tools/providers/pdb_provider.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,280 copying lobster/tools/providers/pmc_provider.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,283 copying lobster/tools/providers/organism_enum.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,286 copying lobster/tools/providers/structure_provider.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,288 copying lobster/tools/providers/sra_provider.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,291 copying lobster/tools/providers/abstract_provider.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,294 copying lobster/tools/providers/biopython_entrez_wrapper.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,296 copying lobster/tools/providers/massive_provider.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,298 copying lobster/tools/providers/geo_provider.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,301 copying lobster/tools/providers/provider_registry.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,304 copying lobster/tools/providers/biorxiv_medrxiv_provider.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,307 copying lobster/tools/providers/pride_provider.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,310 copying lobster/tools/providers/ncbi_query_builder.py -> build/lib/lobster/tools/providers 2026-01-12T15:47:26,312 creating build/lib/lobster/ui/callbacks 2026-01-12T15:47:26,313 copying lobster/ui/callbacks/__init__.py -> build/lib/lobster/ui/callbacks 2026-01-12T15:47:26,315 copying lobster/ui/callbacks/textual_callback.py -> build/lib/lobster/ui/callbacks 2026-01-12T15:47:26,318 creating build/lib/lobster/ui/components 2026-01-12T15:47:26,319 copying lobster/ui/components/__init__.py -> build/lib/lobster/ui/components 2026-01-12T15:47:26,321 copying lobster/ui/components/parallel_workers_progress.py -> build/lib/lobster/ui/components 2026-01-12T15:47:26,323 copying lobster/ui/components/multi_progress.py -> build/lib/lobster/ui/components 2026-01-12T15:47:26,326 copying lobster/ui/components/status_display.py -> build/lib/lobster/ui/components 2026-01-12T15:47:26,329 copying lobster/ui/components/file_tree.py -> build/lib/lobster/ui/components 2026-01-12T15:47:26,331 creating build/lib/lobster/ui/formatters 2026-01-12T15:47:26,332 copying lobster/ui/formatters/__init__.py -> build/lib/lobster/ui/formatters 2026-01-12T15:47:26,335 creating build/lib/lobster/ui/screens 2026-01-12T15:47:26,336 copying lobster/ui/screens/analysis_screen.py -> build/lib/lobster/ui/screens 2026-01-12T15:47:26,339 copying lobster/ui/screens/__init__.py -> build/lib/lobster/ui/screens 2026-01-12T15:47:26,341 creating build/lib/lobster/ui/services 2026-01-12T15:47:26,342 copying lobster/ui/services/__init__.py -> build/lib/lobster/ui/services 2026-01-12T15:47:26,344 copying lobster/ui/services/error_service.py -> build/lib/lobster/ui/services 2026-01-12T15:47:26,347 creating build/lib/lobster/ui/widgets 2026-01-12T15:47:26,348 copying lobster/ui/widgets/results_display.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,350 copying lobster/ui/widgets/__init__.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,352 copying lobster/ui/widgets/queue_panel.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,354 copying lobster/ui/widgets/data_hub.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,357 copying lobster/ui/widgets/status_bar.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,359 copying lobster/ui/widgets/connections_panel.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,361 copying lobster/ui/widgets/plot_preview.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,363 copying lobster/ui/widgets/activity_log.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,365 copying lobster/ui/widgets/modality_list.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,367 copying lobster/ui/widgets/agents_panel.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,369 copying lobster/ui/widgets/chat_message.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,371 copying lobster/ui/widgets/query_prompt.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,372 copying lobster/ui/widgets/system_info.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,375 copying lobster/ui/widgets/token_usage_panel.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,377 copying lobster/ui/widgets/queue_status_bar.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,379 copying lobster/ui/widgets/error_modal.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,381 copying lobster/ui/widgets/adapters_panel.py -> build/lib/lobster/ui/widgets 2026-01-12T15:47:26,384 creating build/lib/lobster/config/providers 2026-01-12T15:47:26,385 copying lobster/config/providers/base_provider.py -> build/lib/lobster/config/providers 2026-01-12T15:47:26,387 copying lobster/config/providers/__init__.py -> build/lib/lobster/config/providers 2026-01-12T15:47:26,389 copying lobster/config/providers/gemini_provider.py -> build/lib/lobster/config/providers 2026-01-12T15:47:26,391 copying lobster/config/providers/registry.py -> build/lib/lobster/config/providers 2026-01-12T15:47:26,394 copying lobster/config/providers/anthropic_provider.py -> build/lib/lobster/config/providers 2026-01-12T15:47:26,396 copying lobster/config/providers/ollama_provider.py -> build/lib/lobster/config/providers 2026-01-12T15:47:26,399 copying lobster/config/providers/bedrock_provider.py -> build/lib/lobster/config/providers 2026-01-12T15:47:26,402 creating build/lib/lobster/services/analysis 2026-01-12T15:47:26,403 copying lobster/services/analysis/__init__.py -> build/lib/lobster/services/analysis 2026-01-12T15:47:26,404 copying lobster/services/analysis/differential_formula_service.py -> build/lib/lobster/services/analysis 2026-01-12T15:47:26,407 copying lobster/services/analysis/bulk_rnaseq_service.py -> build/lib/lobster/services/analysis 2026-01-12T15:47:26,411 copying lobster/services/analysis/enhanced_singlecell_service.py -> build/lib/lobster/services/analysis 2026-01-12T15:47:26,414 copying lobster/services/analysis/pseudobulk_service.py -> build/lib/lobster/services/analysis 2026-01-12T15:47:26,417 copying lobster/services/analysis/scvi_embedding_service.py -> build/lib/lobster/services/analysis 2026-01-12T15:47:26,419 copying lobster/services/analysis/clustering_service.py -> build/lib/lobster/services/analysis 2026-01-12T15:47:26,423 copying lobster/services/analysis/structure_analysis_service.py -> build/lib/lobster/services/analysis 2026-01-12T15:47:26,426 creating build/lib/lobster/services/data_access 2026-01-12T15:47:26,427 copying lobster/services/data_access/geo_service.py -> build/lib/lobster/services/data_access 2026-01-12T15:47:26,433 copying lobster/services/data_access/workspace_content_service.py -> build/lib/lobster/services/data_access 2026-01-12T15:47:26,436 copying lobster/services/data_access/pride_download_service.py -> build/lib/lobster/services/data_access 2026-01-12T15:47:26,439 copying lobster/services/data_access/docling_service.py -> build/lib/lobster/services/data_access 2026-01-12T15:47:26,442 copying lobster/services/data_access/__init__.py -> build/lib/lobster/services/data_access 2026-01-12T15:47:26,444 copying lobster/services/data_access/protein_structure_fetch_service.py -> build/lib/lobster/services/data_access 2026-01-12T15:47:26,447 copying lobster/services/data_access/geo_fallback_service.py -> build/lib/lobster/services/data_access 2026-01-12T15:47:26,449 copying lobster/services/data_access/geo_download_service.py -> build/lib/lobster/services/data_access 2026-01-12T15:47:26,452 copying lobster/services/data_access/content_access_service.py -> build/lib/lobster/services/data_access 2026-01-12T15:47:26,456 copying lobster/services/data_access/sra_download_service.py -> build/lib/lobster/services/data_access 2026-01-12T15:47:26,459 copying lobster/services/data_access/massive_download_service.py -> build/lib/lobster/services/data_access 2026-01-12T15:47:26,461 creating build/lib/lobster/services/quality 2026-01-12T15:47:26,462 copying lobster/services/quality/__init__.py -> build/lib/lobster/services/quality 2026-01-12T15:47:26,464 copying lobster/services/quality/preprocessing_service.py -> build/lib/lobster/services/quality 2026-01-12T15:47:26,467 copying lobster/services/quality/quality_service.py -> build/lib/lobster/services/quality 2026-01-12T15:47:26,470 creating build/lib/lobster/services/orchestration 2026-01-12T15:47:26,471 copying lobster/services/orchestration/__init__.py -> build/lib/lobster/services/orchestration 2026-01-12T15:47:26,473 copying lobster/services/orchestration/publication_processing_service.py -> build/lib/lobster/services/orchestration 2026-01-12T15:47:26,477 creating build/lib/lobster/services/execution 2026-01-12T15:47:26,478 copying lobster/services/execution/execution_context_builder.py -> build/lib/lobster/services/execution 2026-01-12T15:47:26,481 copying lobster/services/execution/__init__.py -> build/lib/lobster/services/execution 2026-01-12T15:47:26,483 copying lobster/services/execution/custom_code_execution_service.py -> build/lib/lobster/services/execution 2026-01-12T15:47:26,486 creating build/lib/lobster/services/visualization 2026-01-12T15:47:26,487 copying lobster/services/visualization/__init__.py -> build/lib/lobster/services/visualization 2026-01-12T15:47:26,489 copying lobster/services/visualization/pymol_visualization_service.py -> build/lib/lobster/services/visualization 2026-01-12T15:47:26,492 copying lobster/services/visualization/bulk_visualization_service.py -> build/lib/lobster/services/visualization 2026-01-12T15:47:26,495 copying lobster/services/visualization/visualization_service.py -> build/lib/lobster/services/visualization 2026-01-12T15:47:26,499 creating build/lib/lobster/services/templates 2026-01-12T15:47:26,500 copying lobster/services/templates/__init__.py -> build/lib/lobster/services/templates 2026-01-12T15:47:26,502 copying lobster/services/templates/annotation_templates.py -> build/lib/lobster/services/templates 2026-01-12T15:47:26,506 creating build/lib/lobster/services/data_management 2026-01-12T15:47:26,507 copying lobster/services/data_management/__init__.py -> build/lib/lobster/services/data_management 2026-01-12T15:47:26,509 copying lobster/services/data_management/concatenation_service.py -> build/lib/lobster/services/data_management 2026-01-12T15:47:26,512 copying lobster/services/data_management/modality_management_service.py -> build/lib/lobster/services/data_management 2026-01-12T15:47:26,515 copying lobster/services/data_management/strategy_recommendation_service.py -> build/lib/lobster/services/data_management 2026-01-12T15:47:26,517 copying lobster/services/data_management/modality_detection_service.py -> build/lib/lobster/services/data_management 2026-01-12T15:47:26,521 creating build/lib/lobster/services/metadata 2026-01-12T15:47:26,522 copying lobster/services/metadata/__init__.py -> build/lib/lobster/services/metadata 2026-01-12T15:47:26,523 copying lobster/services/metadata/metadata_validation_service.py -> build/lib/lobster/services/metadata 2026-01-12T15:47:26,527 copying lobster/services/metadata/identifier_provenance_service.py -> build/lib/lobster/services/metadata 2026-01-12T15:47:26,529 copying lobster/services/metadata/metadata_standardization_service.py -> build/lib/lobster/services/metadata 2026-01-12T15:47:26,532 copying lobster/services/metadata/manual_annotation_service.py -> build/lib/lobster/services/metadata 2026-01-12T15:47:26,534 copying lobster/services/metadata/sample_grouping_service.py -> build/lib/lobster/services/metadata 2026-01-12T15:47:26,537 creating build/lib/lobster/services/ml 2026-01-12T15:47:26,538 copying lobster/services/ml/__init__.py -> build/lib/lobster/services/ml 2026-01-12T15:47:26,540 creating build/lib/lobster/services/data_access/geo 2026-01-12T15:47:26,541 copying lobster/services/data_access/geo/strategy.py -> build/lib/lobster/services/data_access/geo 2026-01-12T15:47:26,544 copying lobster/services/data_access/geo/parser.py -> build/lib/lobster/services/data_access/geo 2026-01-12T15:47:26,548 copying lobster/services/data_access/geo/__init__.py -> build/lib/lobster/services/data_access/geo 2026-01-12T15:47:26,550 copying lobster/services/data_access/geo/constants.py -> build/lib/lobster/services/data_access/geo 2026-01-12T15:47:26,552 copying lobster/services/data_access/geo/facade.py -> build/lib/lobster/services/data_access/geo 2026-01-12T15:47:26,554 copying lobster/services/data_access/geo/downloader.py -> build/lib/lobster/services/data_access/geo 2026-01-12T15:47:26,557 creating build/lib/lobster/services/data_access/geo/loaders 2026-01-12T15:47:26,558 copying lobster/services/data_access/geo/loaders/__init__.py -> build/lib/lobster/services/data_access/geo/loaders 2026-01-12T15:47:26,560 copying lobster/services/data_access/geo/loaders/tenx.py -> build/lib/lobster/services/data_access/geo/loaders 2026-01-12T15:47:26,563 creating build/lib/lobster/services/data_access/geo/metadata 2026-01-12T15:47:26,564 copying lobster/services/data_access/geo/metadata/__init__.py -> build/lib/lobster/services/data_access/geo/metadata 2026-01-12T15:47:26,566 creating build/lib/lobster/services/data_access/geo/sample 2026-01-12T15:47:26,568 copying lobster/services/data_access/geo/sample/__init__.py -> build/lib/lobster/services/data_access/geo/sample 2026-01-12T15:47:26,570 creating build/lib/lobster/services/data_access/geo/utils 2026-01-12T15:47:26,571 copying lobster/services/data_access/geo/utils/__init__.py -> build/lib/lobster/services/data_access/geo/utils 2026-01-12T15:47:26,573 creating build/lib/lobster/services/metadata/protocol_extraction 2026-01-12T15:47:26,574 copying lobster/services/metadata/protocol_extraction/base.py -> build/lib/lobster/services/metadata/protocol_extraction 2026-01-12T15:47:26,577 copying lobster/services/metadata/protocol_extraction/__init__.py -> build/lib/lobster/services/metadata/protocol_extraction 2026-01-12T15:47:26,579 creating build/lib/lobster/services/metadata/protocol_extraction/mass_spec 2026-01-12T15:47:26,580 copying lobster/services/metadata/protocol_extraction/mass_spec/service.py -> build/lib/lobster/services/metadata/protocol_extraction/mass_spec 2026-01-12T15:47:26,582 copying lobster/services/metadata/protocol_extraction/mass_spec/__init__.py -> build/lib/lobster/services/metadata/protocol_extraction/mass_spec 2026-01-12T15:47:26,584 copying lobster/services/metadata/protocol_extraction/mass_spec/details.py -> build/lib/lobster/services/metadata/protocol_extraction/mass_spec 2026-01-12T15:47:26,586 creating build/lib/lobster/services/metadata/protocol_extraction/amplicon 2026-01-12T15:47:26,587 copying lobster/services/metadata/protocol_extraction/amplicon/service.py -> build/lib/lobster/services/metadata/protocol_extraction/amplicon 2026-01-12T15:47:26,590 copying lobster/services/metadata/protocol_extraction/amplicon/__init__.py -> build/lib/lobster/services/metadata/protocol_extraction/amplicon 2026-01-12T15:47:26,592 copying lobster/services/metadata/protocol_extraction/amplicon/details.py -> build/lib/lobster/services/metadata/protocol_extraction/amplicon 2026-01-12T15:47:26,595 creating build/lib/lobster/services/metadata/protocol_extraction/rnaseq 2026-01-12T15:47:26,596 copying lobster/services/metadata/protocol_extraction/rnaseq/service.py -> build/lib/lobster/services/metadata/protocol_extraction/rnaseq 2026-01-12T15:47:26,598 copying lobster/services/metadata/protocol_extraction/rnaseq/__init__.py -> build/lib/lobster/services/metadata/protocol_extraction/rnaseq 2026-01-12T15:47:26,600 copying lobster/services/metadata/protocol_extraction/rnaseq/details.py -> build/lib/lobster/services/metadata/protocol_extraction/rnaseq 2026-01-12T15:47:26,602 creating build/lib/lobster/cli_internal/utils 2026-01-12T15:47:26,603 copying lobster/cli_internal/utils/__init__.py -> build/lib/lobster/cli_internal/utils 2026-01-12T15:47:26,605 copying lobster/cli_internal/utils/path_resolution.py -> build/lib/lobster/cli_internal/utils 2026-01-12T15:47:26,608 creating build/lib/lobster/cli_internal/commands 2026-01-12T15:47:26,609 copying lobster/cli_internal/commands/__init__.py -> build/lib/lobster/cli_internal/commands 2026-01-12T15:47:26,611 copying lobster/cli_internal/commands/output_adapter.py -> build/lib/lobster/cli_internal/commands 2026-01-12T15:47:26,614 creating build/lib/lobster/cli_internal/commands/light 2026-01-12T15:47:26,615 copying lobster/cli_internal/commands/light/queue_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-01-12T15:47:26,618 copying lobster/cli_internal/commands/light/__init__.py -> build/lib/lobster/cli_internal/commands/light 2026-01-12T15:47:26,621 copying lobster/cli_internal/commands/light/file_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-01-12T15:47:26,623 copying lobster/cli_internal/commands/light/config_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-01-12T15:47:26,626 copying lobster/cli_internal/commands/light/metadata_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-01-12T15:47:26,629 copying lobster/cli_internal/commands/light/pipeline_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-01-12T15:47:26,631 copying lobster/cli_internal/commands/light/workspace_commands.py -> build/lib/lobster/cli_internal/commands/light 2026-01-12T15:47:26,635 creating build/lib/lobster/cli_internal/commands/heavy 2026-01-12T15:47:26,636 copying lobster/cli_internal/commands/heavy/__init__.py -> build/lib/lobster/cli_internal/commands/heavy 2026-01-12T15:47:26,638 copying lobster/cli_internal/commands/heavy/data_commands.py -> build/lib/lobster/cli_internal/commands/heavy 2026-01-12T15:47:26,640 copying lobster/cli_internal/commands/heavy/visualization_commands.py -> build/lib/lobster/cli_internal/commands/heavy 2026-01-12T15:47:26,643 copying lobster/cli_internal/commands/heavy/modality_commands.py -> build/lib/lobster/cli_internal/commands/heavy 2026-01-12T15:47:26,646 running egg_info 2026-01-12T15:47:26,658 writing lobster_ai.egg-info/PKG-INFO 2026-01-12T15:47:26,689 writing dependency_links to lobster_ai.egg-info/dependency_links.txt 2026-01-12T15:47:26,690 writing entry points to lobster_ai.egg-info/entry_points.txt 2026-01-12T15:47:26,710 writing requirements to lobster_ai.egg-info/requires.txt 2026-01-12T15:47:26,711 writing top-level names to lobster_ai.egg-info/top_level.txt 2026-01-12T15:47:26,838 reading manifest file 'lobster_ai.egg-info/SOURCES.txt' 2026-01-12T15:47:26,854 adding license file 'LICENSE' 2026-01-12T15:47:26,869 writing manifest file 'lobster_ai.egg-info/SOURCES.txt' 2026-01-12T15:47:26,963 copying lobster/config/disease_ontology.json -> build/lib/lobster/config 2026-01-12T15:47:26,965 creating build/lib/lobster/services/metadata/protocol_extraction/amplicon/resources 2026-01-12T15:47:26,966 copying lobster/services/metadata/protocol_extraction/amplicon/resources/primers.json -> build/lib/lobster/services/metadata/protocol_extraction/amplicon/resources 2026-01-12T15:47:27,006 installing to build/bdist.linux-armv7l/wheel 2026-01-12T15:47:27,006 running install 2026-01-12T15:47:27,030 running install_lib 2026-01-12T15:47:27,037 creating build/bdist.linux-armv7l/wheel 2026-01-12T15:47:27,039 creating build/bdist.linux-armv7l/wheel/lobster 2026-01-12T15:47:27,041 creating build/bdist.linux-armv7l/wheel/lobster/lobster_cloud 2026-01-12T15:47:27,042 copying build/lib/lobster/lobster_cloud/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/lobster_cloud 2026-01-12T15:47:27,044 copying build/lib/lobster/lobster_cloud/client.py -> build/bdist.linux-armv7l/wheel/./lobster/lobster_cloud 2026-01-12T15:47:27,047 creating build/bdist.linux-armv7l/wheel/lobster/agents 2026-01-12T15:47:27,048 copying build/lib/lobster/agents/supervisor.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-12T15:47:27,051 copying build/lib/lobster/agents/draw_graph.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-12T15:47:27,053 creating build/bdist.linux-armv7l/wheel/lobster/agents/archive 2026-01-12T15:47:27,054 copying build/lib/lobster/agents/archive/research_agent_assistant.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/archive 2026-01-12T15:47:27,056 copying build/lib/lobster/agents/visualization_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-12T15:47:27,059 copying build/lib/lobster/agents/state.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-12T15:47:27,062 creating build/bdist.linux-armv7l/wheel/lobster/agents/proteomics 2026-01-12T15:47:27,063 copying build/lib/lobster/agents/proteomics/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/proteomics 2026-01-12T15:47:27,065 copying build/lib/lobster/agents/proteomics/state.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/proteomics 2026-01-12T15:47:27,067 creating build/bdist.linux-armv7l/wheel/lobster/agents/data_expert 2026-01-12T15:47:27,068 copying build/lib/lobster/agents/data_expert/prompts.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/data_expert 2026-01-12T15:47:27,071 copying build/lib/lobster/agents/data_expert/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/data_expert 2026-01-12T15:47:27,072 copying build/lib/lobster/agents/data_expert/assistant.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/data_expert 2026-01-12T15:47:27,075 copying build/lib/lobster/agents/data_expert/config.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/data_expert 2026-01-12T15:47:27,077 copying build/lib/lobster/agents/data_expert/state.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/data_expert 2026-01-12T15:47:27,079 copying build/lib/lobster/agents/data_expert/data_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/data_expert 2026-01-12T15:47:27,083 creating build/bdist.linux-armv7l/wheel/lobster/agents/research 2026-01-12T15:47:27,084 copying build/lib/lobster/agents/research/prompts.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/research 2026-01-12T15:47:27,087 copying build/lib/lobster/agents/research/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/research 2026-01-12T15:47:27,089 copying build/lib/lobster/agents/research/config.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/research 2026-01-12T15:47:27,090 copying build/lib/lobster/agents/research/research_agent.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/research 2026-01-12T15:47:27,096 copying build/lib/lobster/agents/research/state.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/research 2026-01-12T15:47:27,098 copying build/lib/lobster/agents/graph.py -> build/bdist.linux-armv7l/wheel/./lobster/agents 2026-01-12T15:47:27,101 creating build/bdist.linux-armv7l/wheel/lobster/agents/transcriptomics 2026-01-12T15:47:27,102 copying build/lib/lobster/agents/transcriptomics/prompts.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-12T15:47:27,104 copying build/lib/lobster/agents/transcriptomics/transcriptomics_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-12T15:47:27,107 copying build/lib/lobster/agents/transcriptomics/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-12T15:47:27,109 copying build/lib/lobster/agents/transcriptomics/shared_tools.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-12T15:47:27,112 copying build/lib/lobster/agents/transcriptomics/de_analysis_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-12T15:47:27,115 copying build/lib/lobster/agents/transcriptomics/config.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-12T15:47:27,118 copying build/lib/lobster/agents/transcriptomics/state.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-12T15:47:27,120 copying build/lib/lobster/agents/transcriptomics/annotation_expert.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/transcriptomics 2026-01-12T15:47:27,124 creating build/bdist.linux-armv7l/wheel/lobster/agents/langgraph_supervisor 2026-01-12T15:47:27,125 copying build/lib/lobster/agents/langgraph_supervisor/supervisor.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/langgraph_supervisor 2026-01-12T15:47:27,128 copying build/lib/lobster/agents/langgraph_supervisor/agent_name.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/langgraph_supervisor 2026-01-12T15:47:27,130 copying build/lib/lobster/agents/langgraph_supervisor/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/langgraph_supervisor 2026-01-12T15:47:27,132 copying build/lib/lobster/agents/langgraph_supervisor/handoff.py -> build/bdist.linux-armv7l/wheel/./lobster/agents/langgraph_supervisor 2026-01-12T15:47:27,134 copying build/lib/lobster/version.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-01-12T15:47:27,137 creating build/bdist.linux-armv7l/wheel/lobster/core 2026-01-12T15:47:27,138 creating build/bdist.linux-armv7l/wheel/lobster/core/backends 2026-01-12T15:47:27,139 copying build/lib/lobster/core/backends/base.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends 2026-01-12T15:47:27,142 copying build/lib/lobster/core/backends/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends 2026-01-12T15:47:27,144 copying build/lib/lobster/core/backends/h5ad_backend.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends 2026-01-12T15:47:27,147 copying build/lib/lobster/core/backends/mudata_backend.py -> build/bdist.linux-armv7l/wheel/./lobster/core/backends 2026-01-12T15:47:27,150 copying build/lib/lobster/core/component_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,152 copying build/lib/lobster/core/download_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,155 copying build/lib/lobster/core/notebook_validator.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,157 copying build/lib/lobster/core/plot_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,160 copying build/lib/lobster/core/notebook_exporter.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,162 copying build/lib/lobster/core/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,165 copying build/lib/lobster/core/archive_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,167 copying build/lib/lobster/core/publication_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,170 copying build/lib/lobster/core/ris_parser.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,173 copying build/lib/lobster/core/notebook_executor.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,175 copying build/lib/lobster/core/provenance.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,178 copying build/lib/lobster/core/config_resolver.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,181 creating build/bdist.linux-armv7l/wheel/lobster/core/interfaces 2026-01-12T15:47:27,182 copying build/lib/lobster/core/interfaces/base_client.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-01-12T15:47:27,185 copying build/lib/lobster/core/interfaces/download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-01-12T15:47:27,188 copying build/lib/lobster/core/interfaces/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-01-12T15:47:27,190 copying build/lib/lobster/core/interfaces/adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-01-12T15:47:27,192 copying build/lib/lobster/core/interfaces/backend.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-01-12T15:47:27,194 copying build/lib/lobster/core/interfaces/validator.py -> build/bdist.linux-armv7l/wheel/./lobster/core/interfaces 2026-01-12T15:47:27,196 copying build/lib/lobster/core/workspace.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,198 copying build/lib/lobster/core/client.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,203 copying build/lib/lobster/core/license_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,206 creating build/bdist.linux-armv7l/wheel/lobster/core/adapters 2026-01-12T15:47:27,207 copying build/lib/lobster/core/adapters/base.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-01-12T15:47:27,210 copying build/lib/lobster/core/adapters/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-01-12T15:47:27,211 copying build/lib/lobster/core/adapters/transcriptomics_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-01-12T15:47:27,214 copying build/lib/lobster/core/adapters/pseudobulk_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-01-12T15:47:27,217 copying build/lib/lobster/core/adapters/proteomics_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-01-12T15:47:27,220 copying build/lib/lobster/core/adapters/protein_structure_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/core/adapters 2026-01-12T15:47:27,223 copying build/lib/lobster/core/exceptions.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,226 creating build/bdist.linux-armv7l/wheel/lobster/core/utils 2026-01-12T15:47:27,227 copying build/lib/lobster/core/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/utils 2026-01-12T15:47:27,229 copying build/lib/lobster/core/utils/h5ad_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/core/utils 2026-01-12T15:47:27,232 copying build/lib/lobster/core/data_manager_v2.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,238 copying build/lib/lobster/core/plugin_loader.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,241 creating build/bdist.linux-armv7l/wheel/lobster/core/identifiers 2026-01-12T15:47:27,242 copying build/lib/lobster/core/identifiers/accession_resolver.py -> build/bdist.linux-armv7l/wheel/./lobster/core/identifiers 2026-01-12T15:47:27,245 copying build/lib/lobster/core/identifiers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/identifiers 2026-01-12T15:47:27,247 copying build/lib/lobster/core/queue_storage.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,249 copying build/lib/lobster/core/ir_coverage.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,251 copying build/lib/lobster/core/analysis_ir.py -> build/bdist.linux-armv7l/wheel/./lobster/core 2026-01-12T15:47:27,255 creating build/bdist.linux-armv7l/wheel/lobster/core/schemas 2026-01-12T15:47:27,256 copying build/lib/lobster/core/schemas/transcriptomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,260 copying build/lib/lobster/core/schemas/download_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,262 copying build/lib/lobster/core/schemas/validation.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,265 copying build/lib/lobster/core/schemas/database_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,267 copying build/lib/lobster/core/schemas/metabolomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,270 copying build/lib/lobster/core/schemas/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,272 copying build/lib/lobster/core/schemas/sra.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,275 copying build/lib/lobster/core/schemas/publication_queue.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,277 copying build/lib/lobster/core/schemas/proteomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,280 copying build/lib/lobster/core/schemas/metagenomics.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,284 copying build/lib/lobster/core/schemas/download_urls.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,286 copying build/lib/lobster/core/schemas/ontology.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,288 copying build/lib/lobster/core/schemas/export_schemas.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,291 copying build/lib/lobster/core/schemas/database_mappings.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,294 copying build/lib/lobster/core/schemas/protein_structure.py -> build/bdist.linux-armv7l/wheel/./lobster/core/schemas 2026-01-12T15:47:27,297 creating build/bdist.linux-armv7l/wheel/lobster/tools 2026-01-12T15:47:27,298 copying build/lib/lobster/tools/gpu_detector.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,301 copying build/lib/lobster/tools/geo_parser.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,303 copying build/lib/lobster/tools/custom_code_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,305 copying build/lib/lobster/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,307 copying build/lib/lobster/tools/enhanced_handoff_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,310 creating build/bdist.linux-armv7l/wheel/lobster/tools/archive 2026-01-12T15:47:27,311 copying build/lib/lobster/tools/archive/unified_content_service.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/archive 2026-01-12T15:47:27,314 copying build/lib/lobster/tools/archive/publication_service.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/archive 2026-01-12T15:47:27,316 copying build/lib/lobster/tools/expert_handoff_patterns.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,319 copying build/lib/lobster/tools/workspace_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,323 copying build/lib/lobster/tools/todo_tools.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,325 copying build/lib/lobster/tools/workflow_tracker.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,328 copying build/lib/lobster/tools/rate_limiter.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,330 copying build/lib/lobster/tools/geo_downloader.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,332 copying build/lib/lobster/tools/pipeline_strategy.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,334 copying build/lib/lobster/tools/url_transforms.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,337 creating build/bdist.linux-armv7l/wheel/lobster/tools/providers 2026-01-12T15:47:27,338 copying build/lib/lobster/tools/providers/base_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,341 copying build/lib/lobster/tools/providers/publication_resolver.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,343 copying build/lib/lobster/tools/providers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,345 copying build/lib/lobster/tools/providers/webpage_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,348 copying build/lib/lobster/tools/providers/pride_normalizer.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,350 copying build/lib/lobster/tools/providers/geo_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,353 copying build/lib/lobster/tools/providers/biorxiv_medrxiv_config.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,354 copying build/lib/lobster/tools/providers/pubmed_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,358 copying build/lib/lobster/tools/providers/pdb_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,361 copying build/lib/lobster/tools/providers/pmc_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,364 copying build/lib/lobster/tools/providers/organism_enum.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,366 copying build/lib/lobster/tools/providers/structure_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,368 copying build/lib/lobster/tools/providers/sra_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,372 copying build/lib/lobster/tools/providers/abstract_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,374 copying build/lib/lobster/tools/providers/biopython_entrez_wrapper.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,377 copying build/lib/lobster/tools/providers/massive_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,379 copying build/lib/lobster/tools/providers/geo_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,382 copying build/lib/lobster/tools/providers/provider_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,385 copying build/lib/lobster/tools/providers/biorxiv_medrxiv_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,388 copying build/lib/lobster/tools/providers/pride_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,390 copying build/lib/lobster/tools/providers/ncbi_query_builder.py -> build/bdist.linux-armv7l/wheel/./lobster/tools/providers 2026-01-12T15:47:27,393 copying build/lib/lobster/tools/handoff_tool.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,396 copying build/lib/lobster/tools/download_orchestrator.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,398 copying build/lib/lobster/tools/expert_handoff_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/tools 2026-01-12T15:47:27,401 creating build/bdist.linux-armv7l/wheel/lobster/ui 2026-01-12T15:47:27,403 creating build/bdist.linux-armv7l/wheel/lobster/ui/callbacks 2026-01-12T15:47:27,404 copying build/lib/lobster/ui/callbacks/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/callbacks 2026-01-12T15:47:27,406 copying build/lib/lobster/ui/callbacks/textual_callback.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/callbacks 2026-01-12T15:47:27,409 copying build/lib/lobster/ui/console_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-01-12T15:47:27,412 creating build/bdist.linux-armv7l/wheel/lobster/ui/components 2026-01-12T15:47:27,413 copying build/lib/lobster/ui/components/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-01-12T15:47:27,415 copying build/lib/lobster/ui/components/parallel_workers_progress.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-01-12T15:47:27,418 copying build/lib/lobster/ui/components/multi_progress.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-01-12T15:47:27,420 copying build/lib/lobster/ui/components/status_display.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-01-12T15:47:27,423 copying build/lib/lobster/ui/components/file_tree.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/components 2026-01-12T15:47:27,425 copying build/lib/lobster/ui/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-01-12T15:47:27,428 creating build/bdist.linux-armv7l/wheel/lobster/ui/formatters 2026-01-12T15:47:27,429 copying build/lib/lobster/ui/formatters/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/formatters 2026-01-12T15:47:27,430 copying build/lib/lobster/ui/commands.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-01-12T15:47:27,433 creating build/bdist.linux-armv7l/wheel/lobster/ui/screens 2026-01-12T15:47:27,434 copying build/lib/lobster/ui/screens/analysis_screen.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/screens 2026-01-12T15:47:27,437 copying build/lib/lobster/ui/screens/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/screens 2026-01-12T15:47:27,439 copying build/lib/lobster/ui/progress_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-01-12T15:47:27,441 copying build/lib/lobster/ui/themes.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-01-12T15:47:27,444 creating build/bdist.linux-armv7l/wheel/lobster/ui/services 2026-01-12T15:47:27,445 copying build/lib/lobster/ui/services/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/services 2026-01-12T15:47:27,449 copying build/lib/lobster/ui/services/error_service.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/services 2026-01-12T15:47:27,451 copying build/lib/lobster/ui/live_dashboard.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-01-12T15:47:27,454 copying build/lib/lobster/ui/os_app.py -> build/bdist.linux-armv7l/wheel/./lobster/ui 2026-01-12T15:47:27,456 creating build/bdist.linux-armv7l/wheel/lobster/ui/widgets 2026-01-12T15:47:27,457 copying build/lib/lobster/ui/widgets/results_display.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,459 copying build/lib/lobster/ui/widgets/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,461 copying build/lib/lobster/ui/widgets/queue_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,463 copying build/lib/lobster/ui/widgets/data_hub.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,466 copying build/lib/lobster/ui/widgets/status_bar.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,468 copying build/lib/lobster/ui/widgets/connections_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,470 copying build/lib/lobster/ui/widgets/plot_preview.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,473 copying build/lib/lobster/ui/widgets/activity_log.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,475 copying build/lib/lobster/ui/widgets/modality_list.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,477 copying build/lib/lobster/ui/widgets/agents_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,479 copying build/lib/lobster/ui/widgets/chat_message.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,481 copying build/lib/lobster/ui/widgets/query_prompt.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,483 copying build/lib/lobster/ui/widgets/system_info.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,485 copying build/lib/lobster/ui/widgets/token_usage_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,487 copying build/lib/lobster/ui/widgets/queue_status_bar.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,489 copying build/lib/lobster/ui/widgets/error_modal.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,492 copying build/lib/lobster/ui/widgets/adapters_panel.py -> build/bdist.linux-armv7l/wheel/./lobster/ui/widgets 2026-01-12T15:47:27,494 copying build/lib/lobster/__main__.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-01-12T15:47:27,496 copying build/lib/lobster/main.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-01-12T15:47:27,497 copying build/lib/lobster/cli.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-01-12T15:47:27,505 creating build/bdist.linux-armv7l/wheel/lobster/config 2026-01-12T15:47:27,506 copying build/lib/lobster/config/llm_factory.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,509 copying build/lib/lobster/config/agent_capabilities.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,511 copying build/lib/lobster/config/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,513 copying build/lib/lobster/config/subscription_tiers.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,515 copying build/lib/lobster/config/workspace_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,517 copying build/lib/lobster/config/ssl_setup.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,519 copying build/lib/lobster/config/base_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,521 copying build/lib/lobster/config/constants.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,523 copying build/lib/lobster/config/disease_ontology.json -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,525 copying build/lib/lobster/config/config_manager.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,527 copying build/lib/lobster/config/agent_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,530 copying build/lib/lobster/config/global_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,532 copying build/lib/lobster/config/model_service.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,535 creating build/bdist.linux-armv7l/wheel/lobster/config/providers 2026-01-12T15:47:27,536 copying build/lib/lobster/config/providers/base_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-12T15:47:27,538 copying build/lib/lobster/config/providers/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-12T15:47:27,540 copying build/lib/lobster/config/providers/gemini_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-12T15:47:27,542 copying build/lib/lobster/config/providers/registry.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-12T15:47:27,545 copying build/lib/lobster/config/providers/anthropic_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-12T15:47:27,547 copying build/lib/lobster/config/providers/ollama_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-12T15:47:27,550 copying build/lib/lobster/config/providers/bedrock_provider.py -> build/bdist.linux-armv7l/wheel/./lobster/config/providers 2026-01-12T15:47:27,553 copying build/lib/lobster/config/version_check.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,555 copying build/lib/lobster/config/ollama_service.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,557 copying build/lib/lobster/config/supervisor_config.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,559 copying build/lib/lobster/config/settings.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,562 copying build/lib/lobster/config/provider_setup.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,564 copying build/lib/lobster/config/agent_registry.py -> build/bdist.linux-armv7l/wheel/./lobster/config 2026-01-12T15:47:27,567 creating build/bdist.linux-armv7l/wheel/lobster/services 2026-01-12T15:47:27,569 creating build/bdist.linux-armv7l/wheel/lobster/services/analysis 2026-01-12T15:47:27,570 copying build/lib/lobster/services/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-12T15:47:27,572 copying build/lib/lobster/services/analysis/differential_formula_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-12T15:47:27,575 copying build/lib/lobster/services/analysis/bulk_rnaseq_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-12T15:47:27,581 copying build/lib/lobster/services/analysis/enhanced_singlecell_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-12T15:47:27,586 copying build/lib/lobster/services/analysis/pseudobulk_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-12T15:47:27,590 copying build/lib/lobster/services/analysis/scvi_embedding_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-12T15:47:27,593 copying build/lib/lobster/services/analysis/clustering_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-12T15:47:27,599 copying build/lib/lobster/services/analysis/structure_analysis_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/analysis 2026-01-12T15:47:27,603 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access 2026-01-12T15:47:27,604 copying build/lib/lobster/services/data_access/geo_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-12T15:47:27,613 copying build/lib/lobster/services/data_access/workspace_content_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-12T15:47:27,617 copying build/lib/lobster/services/data_access/pride_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-12T15:47:27,620 copying build/lib/lobster/services/data_access/docling_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-12T15:47:27,625 copying build/lib/lobster/services/data_access/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-12T15:47:27,627 copying build/lib/lobster/services/data_access/protein_structure_fetch_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-12T15:47:27,631 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo 2026-01-12T15:47:27,632 copying build/lib/lobster/services/data_access/geo/strategy.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-01-12T15:47:27,636 copying build/lib/lobster/services/data_access/geo/parser.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-01-12T15:47:27,641 copying build/lib/lobster/services/data_access/geo/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-01-12T15:47:27,644 copying build/lib/lobster/services/data_access/geo/constants.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-01-12T15:47:27,648 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo/loaders 2026-01-12T15:47:27,649 copying build/lib/lobster/services/data_access/geo/loaders/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/loaders 2026-01-12T15:47:27,652 copying build/lib/lobster/services/data_access/geo/loaders/tenx.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/loaders 2026-01-12T15:47:27,655 copying build/lib/lobster/services/data_access/geo/facade.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-01-12T15:47:27,658 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo/metadata 2026-01-12T15:47:27,659 copying build/lib/lobster/services/data_access/geo/metadata/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/metadata 2026-01-12T15:47:27,663 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo/sample 2026-01-12T15:47:27,664 copying build/lib/lobster/services/data_access/geo/sample/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/sample 2026-01-12T15:47:27,667 creating build/bdist.linux-armv7l/wheel/lobster/services/data_access/geo/utils 2026-01-12T15:47:27,669 copying build/lib/lobster/services/data_access/geo/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo/utils 2026-01-12T15:47:27,671 copying build/lib/lobster/services/data_access/geo/downloader.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access/geo 2026-01-12T15:47:27,675 copying build/lib/lobster/services/data_access/geo_fallback_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-12T15:47:27,677 copying build/lib/lobster/services/data_access/geo_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-12T15:47:27,680 copying build/lib/lobster/services/data_access/content_access_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-12T15:47:27,683 copying build/lib/lobster/services/data_access/sra_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-12T15:47:27,686 copying build/lib/lobster/services/data_access/massive_download_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_access 2026-01-12T15:47:27,688 copying build/lib/lobster/services/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services 2026-01-12T15:47:27,690 creating build/bdist.linux-armv7l/wheel/lobster/services/quality 2026-01-12T15:47:27,691 copying build/lib/lobster/services/quality/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/quality 2026-01-12T15:47:27,693 copying build/lib/lobster/services/quality/preprocessing_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/quality 2026-01-12T15:47:27,696 copying build/lib/lobster/services/quality/quality_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/quality 2026-01-12T15:47:27,699 creating build/bdist.linux-armv7l/wheel/lobster/services/orchestration 2026-01-12T15:47:27,700 copying build/lib/lobster/services/orchestration/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/orchestration 2026-01-12T15:47:27,702 copying build/lib/lobster/services/orchestration/publication_processing_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/orchestration 2026-01-12T15:47:27,707 creating build/bdist.linux-armv7l/wheel/lobster/services/execution 2026-01-12T15:47:27,708 copying build/lib/lobster/services/execution/execution_context_builder.py -> build/bdist.linux-armv7l/wheel/./lobster/services/execution 2026-01-12T15:47:27,710 copying build/lib/lobster/services/execution/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/execution 2026-01-12T15:47:27,712 copying build/lib/lobster/services/execution/custom_code_execution_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/execution 2026-01-12T15:47:27,715 creating build/bdist.linux-armv7l/wheel/lobster/services/visualization 2026-01-12T15:47:27,716 copying build/lib/lobster/services/visualization/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/visualization 2026-01-12T15:47:27,718 copying build/lib/lobster/services/visualization/pymol_visualization_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/visualization 2026-01-12T15:47:27,721 copying build/lib/lobster/services/visualization/bulk_visualization_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/visualization 2026-01-12T15:47:27,723 copying build/lib/lobster/services/visualization/visualization_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/visualization 2026-01-12T15:47:27,728 creating build/bdist.linux-armv7l/wheel/lobster/services/templates 2026-01-12T15:47:27,729 copying build/lib/lobster/services/templates/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/templates 2026-01-12T15:47:27,731 copying build/lib/lobster/services/templates/annotation_templates.py -> build/bdist.linux-armv7l/wheel/./lobster/services/templates 2026-01-12T15:47:27,734 creating build/bdist.linux-armv7l/wheel/lobster/services/data_management 2026-01-12T15:47:27,736 copying build/lib/lobster/services/data_management/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management 2026-01-12T15:47:27,737 copying build/lib/lobster/services/data_management/concatenation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management 2026-01-12T15:47:27,740 copying build/lib/lobster/services/data_management/modality_management_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management 2026-01-12T15:47:27,743 copying build/lib/lobster/services/data_management/strategy_recommendation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management 2026-01-12T15:47:27,745 copying build/lib/lobster/services/data_management/modality_detection_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/data_management 2026-01-12T15:47:27,748 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata 2026-01-12T15:47:27,750 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction 2026-01-12T15:47:27,751 copying build/lib/lobster/services/metadata/protocol_extraction/base.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction 2026-01-12T15:47:27,754 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/mass_spec 2026-01-12T15:47:27,755 copying build/lib/lobster/services/metadata/protocol_extraction/mass_spec/service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/mass_spec 2026-01-12T15:47:27,757 copying build/lib/lobster/services/metadata/protocol_extraction/mass_spec/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/mass_spec 2026-01-12T15:47:27,759 copying build/lib/lobster/services/metadata/protocol_extraction/mass_spec/details.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/mass_spec 2026-01-12T15:47:27,761 copying build/lib/lobster/services/metadata/protocol_extraction/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction 2026-01-12T15:47:27,763 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/amplicon 2026-01-12T15:47:27,764 copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon 2026-01-12T15:47:27,767 copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon 2026-01-12T15:47:27,769 copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/details.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon 2026-01-12T15:47:27,772 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/amplicon/resources 2026-01-12T15:47:27,773 copying build/lib/lobster/services/metadata/protocol_extraction/amplicon/resources/primers.json -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/amplicon/resources 2026-01-12T15:47:27,776 creating build/bdist.linux-armv7l/wheel/lobster/services/metadata/protocol_extraction/rnaseq 2026-01-12T15:47:27,777 copying build/lib/lobster/services/metadata/protocol_extraction/rnaseq/service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/rnaseq 2026-01-12T15:47:27,780 copying build/lib/lobster/services/metadata/protocol_extraction/rnaseq/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/rnaseq 2026-01-12T15:47:27,782 copying build/lib/lobster/services/metadata/protocol_extraction/rnaseq/details.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata/protocol_extraction/rnaseq 2026-01-12T15:47:27,784 copying build/lib/lobster/services/metadata/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-01-12T15:47:27,785 copying build/lib/lobster/services/metadata/metadata_validation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-01-12T15:47:27,788 copying build/lib/lobster/services/metadata/identifier_provenance_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-01-12T15:47:27,790 copying build/lib/lobster/services/metadata/metadata_standardization_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-01-12T15:47:27,793 copying build/lib/lobster/services/metadata/manual_annotation_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-01-12T15:47:27,796 copying build/lib/lobster/services/metadata/sample_grouping_service.py -> build/bdist.linux-armv7l/wheel/./lobster/services/metadata 2026-01-12T15:47:27,799 creating build/bdist.linux-armv7l/wheel/lobster/services/ml 2026-01-12T15:47:27,800 copying build/lib/lobster/services/ml/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/services/ml 2026-01-12T15:47:27,803 creating build/bdist.linux-armv7l/wheel/lobster/cli_internal 2026-01-12T15:47:27,804 copying build/lib/lobster/cli_internal/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal 2026-01-12T15:47:27,806 creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/utils 2026-01-12T15:47:27,808 copying build/lib/lobster/cli_internal/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/utils 2026-01-12T15:47:27,810 copying build/lib/lobster/cli_internal/utils/path_resolution.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/utils 2026-01-12T15:47:27,812 creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/commands 2026-01-12T15:47:27,814 creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/commands/light 2026-01-12T15:47:27,816 copying build/lib/lobster/cli_internal/commands/light/queue_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-01-12T15:47:27,819 copying build/lib/lobster/cli_internal/commands/light/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-01-12T15:47:27,821 copying build/lib/lobster/cli_internal/commands/light/file_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-01-12T15:47:27,824 copying build/lib/lobster/cli_internal/commands/light/config_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-01-12T15:47:27,827 copying build/lib/lobster/cli_internal/commands/light/metadata_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-01-12T15:47:27,829 copying build/lib/lobster/cli_internal/commands/light/pipeline_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-01-12T15:47:27,832 copying build/lib/lobster/cli_internal/commands/light/workspace_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/light 2026-01-12T15:47:27,835 copying build/lib/lobster/cli_internal/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-01-12T15:47:27,838 creating build/bdist.linux-armv7l/wheel/lobster/cli_internal/commands/heavy 2026-01-12T15:47:27,839 copying build/lib/lobster/cli_internal/commands/heavy/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-01-12T15:47:27,841 copying build/lib/lobster/cli_internal/commands/heavy/data_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-01-12T15:47:27,843 copying build/lib/lobster/cli_internal/commands/heavy/visualization_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-01-12T15:47:27,846 copying build/lib/lobster/cli_internal/commands/heavy/modality_commands.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands/heavy 2026-01-12T15:47:27,849 copying build/lib/lobster/cli_internal/commands/output_adapter.py -> build/bdist.linux-armv7l/wheel/./lobster/cli_internal/commands 2026-01-12T15:47:27,852 creating build/bdist.linux-armv7l/wheel/lobster/utils 2026-01-12T15:47:27,853 copying build/lib/lobster/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-12T15:47:27,855 copying build/lib/lobster/utils/deviance.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-12T15:47:27,857 copying build/lib/lobster/utils/error_handlers.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-12T15:47:27,860 copying build/lib/lobster/utils/file_analyzer.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-12T15:47:27,863 copying build/lib/lobster/utils/json_extractor.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-12T15:47:27,865 copying build/lib/lobster/utils/logger.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-12T15:47:27,867 copying build/lib/lobster/utils/callbacks.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-12T15:47:27,870 copying build/lib/lobster/utils/progress_wrapper.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-12T15:47:27,873 copying build/lib/lobster/utils/ssl_utils.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-12T15:47:27,875 copying build/lib/lobster/utils/system.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-12T15:47:27,877 copying build/lib/lobster/utils/file_naming.py -> build/bdist.linux-armv7l/wheel/./lobster/utils 2026-01-12T15:47:27,880 copying build/lib/lobster/_version.py -> build/bdist.linux-armv7l/wheel/./lobster 2026-01-12T15:47:27,881 running install_egg_info 2026-01-12T15:47:27,887 Copying lobster_ai.egg-info to build/bdist.linux-armv7l/wheel/./lobster_ai-0.4.3.8-py3.11.egg-info 2026-01-12T15:47:27,901 running install_scripts 2026-01-12T15:47:27,914 creating build/bdist.linux-armv7l/wheel/lobster_ai-0.4.3.8.dist-info/WHEEL 2026-01-12T15:47:27,917 creating '/tmp/pip-wheel-yws2m49q/.tmp-gq5vx2dt/lobster_ai-0.4.3.8-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-01-12T15:47:27,919 adding 'lobster/__main__.py' 2026-01-12T15:47:27,920 adding 'lobster/_version.py' 2026-01-12T15:47:27,948 adding 'lobster/cli.py' 2026-01-12T15:47:27,951 adding 'lobster/main.py' 2026-01-12T15:47:27,953 adding 'lobster/version.py' 2026-01-12T15:47:27,955 adding 'lobster/agents/draw_graph.py' 2026-01-12T15:47:27,957 adding 'lobster/agents/graph.py' 2026-01-12T15:47:27,960 adding 'lobster/agents/state.py' 2026-01-12T15:47:27,964 adding 'lobster/agents/supervisor.py' 2026-01-12T15:47:27,968 adding 'lobster/agents/visualization_expert.py' 2026-01-12T15:47:27,970 adding 'lobster/agents/archive/research_agent_assistant.py' 2026-01-12T15:47:27,972 adding 'lobster/agents/data_expert/__init__.py' 2026-01-12T15:47:27,975 adding 'lobster/agents/data_expert/assistant.py' 2026-01-12T15:47:27,977 adding 'lobster/agents/data_expert/config.py' 2026-01-12T15:47:27,983 adding 'lobster/agents/data_expert/data_expert.py' 2026-01-12T15:47:27,985 adding 'lobster/agents/data_expert/prompts.py' 2026-01-12T15:47:27,986 adding 'lobster/agents/data_expert/state.py' 2026-01-12T15:47:27,988 adding 'lobster/agents/langgraph_supervisor/__init__.py' 2026-01-12T15:47:27,989 adding 'lobster/agents/langgraph_supervisor/agent_name.py' 2026-01-12T15:47:27,991 adding 'lobster/agents/langgraph_supervisor/handoff.py' 2026-01-12T15:47:27,994 adding 'lobster/agents/langgraph_supervisor/supervisor.py' 2026-01-12T15:47:27,996 adding 'lobster/agents/proteomics/__init__.py' 2026-01-12T15:47:27,998 adding 'lobster/agents/proteomics/state.py' 2026-01-12T15:47:28,000 adding 'lobster/agents/research/__init__.py' 2026-01-12T15:47:28,001 adding 'lobster/agents/research/config.py' 2026-01-12T15:47:28,004 adding 'lobster/agents/research/prompts.py' 2026-01-12T15:47:28,015 adding 'lobster/agents/research/research_agent.py' 2026-01-12T15:47:28,017 adding 'lobster/agents/research/state.py' 2026-01-12T15:47:28,019 adding 'lobster/agents/transcriptomics/__init__.py' 2026-01-12T15:47:28,023 adding 'lobster/agents/transcriptomics/annotation_expert.py' 2026-01-12T15:47:28,025 adding 'lobster/agents/transcriptomics/config.py' 2026-01-12T15:47:28,033 adding 'lobster/agents/transcriptomics/de_analysis_expert.py' 2026-01-12T15:47:28,037 adding 'lobster/agents/transcriptomics/prompts.py' 2026-01-12T15:47:28,039 adding 'lobster/agents/transcriptomics/shared_tools.py' 2026-01-12T15:47:28,041 adding 'lobster/agents/transcriptomics/state.py' 2026-01-12T15:47:28,045 adding 'lobster/agents/transcriptomics/transcriptomics_expert.py' 2026-01-12T15:47:28,047 adding 'lobster/cli_internal/__init__.py' 2026-01-12T15:47:28,049 adding 'lobster/cli_internal/commands/__init__.py' 2026-01-12T15:47:28,051 adding 'lobster/cli_internal/commands/output_adapter.py' 2026-01-12T15:47:28,053 adding 'lobster/cli_internal/commands/heavy/__init__.py' 2026-01-12T15:47:28,054 adding 'lobster/cli_internal/commands/heavy/data_commands.py' 2026-01-12T15:47:28,057 adding 'lobster/cli_internal/commands/heavy/modality_commands.py' 2026-01-12T15:47:28,059 adding 'lobster/cli_internal/commands/heavy/visualization_commands.py' 2026-01-12T15:47:28,061 adding 'lobster/cli_internal/commands/light/__init__.py' 2026-01-12T15:47:28,063 adding 'lobster/cli_internal/commands/light/config_commands.py' 2026-01-12T15:47:28,066 adding 'lobster/cli_internal/commands/light/file_commands.py' 2026-01-12T15:47:28,068 adding 'lobster/cli_internal/commands/light/metadata_commands.py' 2026-01-12T15:47:28,070 adding 'lobster/cli_internal/commands/light/pipeline_commands.py' 2026-01-12T15:47:28,074 adding 'lobster/cli_internal/commands/light/queue_commands.py' 2026-01-12T15:47:28,077 adding 'lobster/cli_internal/commands/light/workspace_commands.py' 2026-01-12T15:47:28,079 adding 'lobster/cli_internal/utils/__init__.py' 2026-01-12T15:47:28,081 adding 'lobster/cli_internal/utils/path_resolution.py' 2026-01-12T15:47:28,083 adding 'lobster/config/__init__.py' 2026-01-12T15:47:28,085 adding 'lobster/config/agent_capabilities.py' 2026-01-12T15:47:28,089 adding 'lobster/config/agent_config.py' 2026-01-12T15:47:28,091 adding 'lobster/config/agent_registry.py' 2026-01-12T15:47:28,093 adding 'lobster/config/base_config.py' 2026-01-12T15:47:28,095 adding 'lobster/config/config_manager.py' 2026-01-12T15:47:28,096 adding 'lobster/config/constants.py' 2026-01-12T15:47:28,097 adding 'lobster/config/disease_ontology.json' 2026-01-12T15:47:28,099 adding 'lobster/config/global_config.py' 2026-01-12T15:47:28,101 adding 'lobster/config/llm_factory.py' 2026-01-12T15:47:28,103 adding 'lobster/config/model_service.py' 2026-01-12T15:47:28,105 adding 'lobster/config/ollama_service.py' 2026-01-12T15:47:28,107 adding 'lobster/config/provider_setup.py' 2026-01-12T15:47:28,109 adding 'lobster/config/settings.py' 2026-01-12T15:47:28,111 adding 'lobster/config/ssl_setup.py' 2026-01-12T15:47:28,113 adding 'lobster/config/subscription_tiers.py' 2026-01-12T15:47:28,115 adding 'lobster/config/supervisor_config.py' 2026-01-12T15:47:28,116 adding 'lobster/config/version_check.py' 2026-01-12T15:47:28,118 adding 'lobster/config/workspace_config.py' 2026-01-12T15:47:28,120 adding 'lobster/config/providers/__init__.py' 2026-01-12T15:47:28,122 adding 'lobster/config/providers/anthropic_provider.py' 2026-01-12T15:47:28,123 adding 'lobster/config/providers/base_provider.py' 2026-01-12T15:47:28,125 adding 'lobster/config/providers/bedrock_provider.py' 2026-01-12T15:47:28,127 adding 'lobster/config/providers/gemini_provider.py' 2026-01-12T15:47:28,130 adding 'lobster/config/providers/ollama_provider.py' 2026-01-12T15:47:28,132 adding 'lobster/config/providers/registry.py' 2026-01-12T15:47:28,134 adding 'lobster/core/__init__.py' 2026-01-12T15:47:28,136 adding 'lobster/core/analysis_ir.py' 2026-01-12T15:47:28,139 adding 'lobster/core/archive_utils.py' 2026-01-12T15:47:28,149 adding 'lobster/core/client.py' 2026-01-12T15:47:28,151 adding 'lobster/core/component_registry.py' 2026-01-12T15:47:28,154 adding 'lobster/core/config_resolver.py' 2026-01-12T15:47:28,167 adding 'lobster/core/data_manager_v2.py' 2026-01-12T15:47:28,170 adding 'lobster/core/download_queue.py' 2026-01-12T15:47:28,171 adding 'lobster/core/exceptions.py' 2026-01-12T15:47:28,173 adding 'lobster/core/ir_coverage.py' 2026-01-12T15:47:28,177 adding 'lobster/core/license_manager.py' 2026-01-12T15:47:28,179 adding 'lobster/core/notebook_executor.py' 2026-01-12T15:47:28,182 adding 'lobster/core/notebook_exporter.py' 2026-01-12T15:47:28,184 adding 'lobster/core/notebook_validator.py' 2026-01-12T15:47:28,187 adding 'lobster/core/plot_manager.py' 2026-01-12T15:47:28,189 adding 'lobster/core/plugin_loader.py' 2026-01-12T15:47:28,192 adding 'lobster/core/provenance.py' 2026-01-12T15:47:28,194 adding 'lobster/core/publication_queue.py' 2026-01-12T15:47:28,196 adding 'lobster/core/queue_storage.py' 2026-01-12T15:47:28,198 adding 'lobster/core/ris_parser.py' 2026-01-12T15:47:28,199 adding 'lobster/core/workspace.py' 2026-01-12T15:47:28,201 adding 'lobster/core/adapters/__init__.py' 2026-01-12T15:47:28,204 adding 'lobster/core/adapters/base.py' 2026-01-12T15:47:28,206 adding 'lobster/core/adapters/protein_structure_adapter.py' 2026-01-12T15:47:28,209 adding 'lobster/core/adapters/proteomics_adapter.py' 2026-01-12T15:47:28,212 adding 'lobster/core/adapters/pseudobulk_adapter.py' 2026-01-12T15:47:28,215 adding 'lobster/core/adapters/transcriptomics_adapter.py' 2026-01-12T15:47:28,217 adding 'lobster/core/backends/__init__.py' 2026-01-12T15:47:28,218 adding 'lobster/core/backends/base.py' 2026-01-12T15:47:28,222 adding 'lobster/core/backends/h5ad_backend.py' 2026-01-12T15:47:28,225 adding 'lobster/core/backends/mudata_backend.py' 2026-01-12T15:47:28,226 adding 'lobster/core/identifiers/__init__.py' 2026-01-12T15:47:28,229 adding 'lobster/core/identifiers/accession_resolver.py' 2026-01-12T15:47:28,231 adding 'lobster/core/interfaces/__init__.py' 2026-01-12T15:47:28,232 adding 'lobster/core/interfaces/adapter.py' 2026-01-12T15:47:28,234 adding 'lobster/core/interfaces/backend.py' 2026-01-12T15:47:28,235 adding 'lobster/core/interfaces/base_client.py' 2026-01-12T15:47:28,237 adding 'lobster/core/interfaces/download_service.py' 2026-01-12T15:47:28,239 adding 'lobster/core/interfaces/validator.py' 2026-01-12T15:47:28,241 adding 'lobster/core/schemas/__init__.py' 2026-01-12T15:47:28,244 adding 'lobster/core/schemas/database_mappings.py' 2026-01-12T15:47:28,246 adding 'lobster/core/schemas/database_registry.py' 2026-01-12T15:47:28,248 adding 'lobster/core/schemas/download_queue.py' 2026-01-12T15:47:28,250 adding 'lobster/core/schemas/download_urls.py' 2026-01-12T15:47:28,256 adding 'lobster/core/schemas/export_schemas.py' 2026-01-12T15:47:28,260 adding 'lobster/core/schemas/metabolomics.py' 2026-01-12T15:47:28,265 adding 'lobster/core/schemas/metagenomics.py' 2026-01-12T15:47:28,266 adding 'lobster/core/schemas/ontology.py' 2026-01-12T15:47:28,269 adding 'lobster/core/schemas/protein_structure.py' 2026-01-12T15:47:28,272 adding 'lobster/core/schemas/proteomics.py' 2026-01-12T15:47:28,275 adding 'lobster/core/schemas/publication_queue.py' 2026-01-12T15:47:28,280 adding 'lobster/core/schemas/sra.py' 2026-01-12T15:47:28,286 adding 'lobster/core/schemas/transcriptomics.py' 2026-01-12T15:47:28,289 adding 'lobster/core/schemas/validation.py' 2026-01-12T15:47:28,291 adding 'lobster/core/utils/__init__.py' 2026-01-12T15:47:28,293 adding 'lobster/core/utils/h5ad_utils.py' 2026-01-12T15:47:28,295 adding 'lobster/lobster_cloud/__init__.py' 2026-01-12T15:47:28,296 adding 'lobster/lobster_cloud/client.py' 2026-01-12T15:47:28,298 adding 'lobster/services/__init__.py' 2026-01-12T15:47:28,300 adding 'lobster/services/analysis/__init__.py' 2026-01-12T15:47:28,308 adding 'lobster/services/analysis/bulk_rnaseq_service.py' 2026-01-12T15:47:28,317 adding 'lobster/services/analysis/clustering_service.py' 2026-01-12T15:47:28,322 adding 'lobster/services/analysis/differential_formula_service.py' 2026-01-12T15:47:28,327 adding 'lobster/services/analysis/enhanced_singlecell_service.py' 2026-01-12T15:47:28,331 adding 'lobster/services/analysis/pseudobulk_service.py' 2026-01-12T15:47:28,333 adding 'lobster/services/analysis/scvi_embedding_service.py' 2026-01-12T15:47:28,336 adding 'lobster/services/analysis/structure_analysis_service.py' 2026-01-12T15:47:28,338 adding 'lobster/services/data_access/__init__.py' 2026-01-12T15:47:28,346 adding 'lobster/services/data_access/content_access_service.py' 2026-01-12T15:47:28,352 adding 'lobster/services/data_access/docling_service.py' 2026-01-12T15:47:28,355 adding 'lobster/services/data_access/geo_download_service.py' 2026-01-12T15:47:28,358 adding 'lobster/services/data_access/geo_fallback_service.py' 2026-01-12T15:47:28,381 adding 'lobster/services/data_access/geo_service.py' 2026-01-12T15:47:28,386 adding 'lobster/services/data_access/massive_download_service.py' 2026-01-12T15:47:28,388 adding 'lobster/services/data_access/pride_download_service.py' 2026-01-12T15:47:28,390 adding 'lobster/services/data_access/protein_structure_fetch_service.py' 2026-01-12T15:47:28,395 adding 'lobster/services/data_access/sra_download_service.py' 2026-01-12T15:47:28,400 adding 'lobster/services/data_access/workspace_content_service.py' 2026-01-12T15:47:28,402 adding 'lobster/services/data_access/geo/__init__.py' 2026-01-12T15:47:28,404 adding 'lobster/services/data_access/geo/constants.py' 2026-01-12T15:47:28,408 adding 'lobster/services/data_access/geo/downloader.py' 2026-01-12T15:47:28,409 adding 'lobster/services/data_access/geo/facade.py' 2026-01-12T15:47:28,417 adding 'lobster/services/data_access/geo/parser.py' 2026-01-12T15:47:28,419 adding 'lobster/services/data_access/geo/strategy.py' 2026-01-12T15:47:28,421 adding 'lobster/services/data_access/geo/loaders/__init__.py' 2026-01-12T15:47:28,423 adding 'lobster/services/data_access/geo/loaders/tenx.py' 2026-01-12T15:47:28,425 adding 'lobster/services/data_access/geo/metadata/__init__.py' 2026-01-12T15:47:28,427 adding 'lobster/services/data_access/geo/sample/__init__.py' 2026-01-12T15:47:28,428 adding 'lobster/services/data_access/geo/utils/__init__.py' 2026-01-12T15:47:28,430 adding 'lobster/services/data_management/__init__.py' 2026-01-12T15:47:28,435 adding 'lobster/services/data_management/concatenation_service.py' 2026-01-12T15:47:28,438 adding 'lobster/services/data_management/modality_detection_service.py' 2026-01-12T15:47:28,440 adding 'lobster/services/data_management/modality_management_service.py' 2026-01-12T15:47:28,442 adding 'lobster/services/data_management/strategy_recommendation_service.py' 2026-01-12T15:47:28,444 adding 'lobster/services/execution/__init__.py' 2026-01-12T15:47:28,449 adding 'lobster/services/execution/custom_code_execution_service.py' 2026-01-12T15:47:28,451 adding 'lobster/services/execution/execution_context_builder.py' 2026-01-12T15:47:28,452 adding 'lobster/services/metadata/__init__.py' 2026-01-12T15:47:28,454 adding 'lobster/services/metadata/identifier_provenance_service.py' 2026-01-12T15:47:28,459 adding 'lobster/services/metadata/manual_annotation_service.py' 2026-01-12T15:47:28,462 adding 'lobster/services/metadata/metadata_standardization_service.py' 2026-01-12T15:47:28,465 adding 'lobster/services/metadata/metadata_validation_service.py' 2026-01-12T15:47:28,467 adding 'lobster/services/metadata/sample_grouping_service.py' 2026-01-12T15:47:28,469 adding 'lobster/services/metadata/protocol_extraction/__init__.py' 2026-01-12T15:47:28,470 adding 'lobster/services/metadata/protocol_extraction/base.py' 2026-01-12T15:47:28,472 adding 'lobster/services/metadata/protocol_extraction/amplicon/__init__.py' 2026-01-12T15:47:28,474 adding 'lobster/services/metadata/protocol_extraction/amplicon/details.py' 2026-01-12T15:47:28,477 adding 'lobster/services/metadata/protocol_extraction/amplicon/service.py' 2026-01-12T15:47:28,478 adding 'lobster/services/metadata/protocol_extraction/amplicon/resources/primers.json' 2026-01-12T15:47:28,480 adding 'lobster/services/metadata/protocol_extraction/mass_spec/__init__.py' 2026-01-12T15:47:28,481 adding 'lobster/services/metadata/protocol_extraction/mass_spec/details.py' 2026-01-12T15:47:28,482 adding 'lobster/services/metadata/protocol_extraction/mass_spec/service.py' 2026-01-12T15:47:28,484 adding 'lobster/services/metadata/protocol_extraction/rnaseq/__init__.py' 2026-01-12T15:47:28,485 adding 'lobster/services/metadata/protocol_extraction/rnaseq/details.py' 2026-01-12T15:47:28,487 adding 'lobster/services/metadata/protocol_extraction/rnaseq/service.py' 2026-01-12T15:47:28,488 adding 'lobster/services/ml/__init__.py' 2026-01-12T15:47:28,490 adding 'lobster/services/orchestration/__init__.py' 2026-01-12T15:47:28,498 adding 'lobster/services/orchestration/publication_processing_service.py' 2026-01-12T15:47:28,501 adding 'lobster/services/quality/__init__.py' 2026-01-12T15:47:28,505 adding 'lobster/services/quality/preprocessing_service.py' 2026-01-12T15:47:28,509 adding 'lobster/services/quality/quality_service.py' 2026-01-12T15:47:28,511 adding 'lobster/services/templates/__init__.py' 2026-01-12T15:47:28,515 adding 'lobster/services/templates/annotation_templates.py' 2026-01-12T15:47:28,517 adding 'lobster/services/visualization/__init__.py' 2026-01-12T15:47:28,520 adding 'lobster/services/visualization/bulk_visualization_service.py' 2026-01-12T15:47:28,523 adding 'lobster/services/visualization/pymol_visualization_service.py' 2026-01-12T15:47:28,530 adding 'lobster/services/visualization/visualization_service.py' 2026-01-12T15:47:28,533 adding 'lobster/tools/__init__.py' 2026-01-12T15:47:28,535 adding 'lobster/tools/custom_code_tool.py' 2026-01-12T15:47:28,537 adding 'lobster/tools/download_orchestrator.py' 2026-01-12T15:47:28,540 adding 'lobster/tools/enhanced_handoff_tool.py' 2026-01-12T15:47:28,542 adding 'lobster/tools/expert_handoff_manager.py' 2026-01-12T15:47:28,544 adding 'lobster/tools/expert_handoff_patterns.py' 2026-01-12T15:47:28,545 adding 'lobster/tools/geo_downloader.py' 2026-01-12T15:47:28,546 adding 'lobster/tools/geo_parser.py' 2026-01-12T15:47:28,548 adding 'lobster/tools/gpu_detector.py' 2026-01-12T15:47:28,550 adding 'lobster/tools/handoff_tool.py' 2026-01-12T15:47:28,551 adding 'lobster/tools/pipeline_strategy.py' 2026-01-12T15:47:28,555 adding 'lobster/tools/rate_limiter.py' 2026-01-12T15:47:28,557 adding 'lobster/tools/todo_tools.py' 2026-01-12T15:47:28,558 adding 'lobster/tools/url_transforms.py' 2026-01-12T15:47:28,561 adding 'lobster/tools/workflow_tracker.py' 2026-01-12T15:47:28,573 adding 'lobster/tools/workspace_tool.py' 2026-01-12T15:47:28,577 adding 'lobster/tools/archive/publication_service.py' 2026-01-12T15:47:28,580 adding 'lobster/tools/archive/unified_content_service.py' 2026-01-12T15:47:28,582 adding 'lobster/tools/providers/__init__.py' 2026-01-12T15:47:28,584 adding 'lobster/tools/providers/abstract_provider.py' 2026-01-12T15:47:28,586 adding 'lobster/tools/providers/base_provider.py' 2026-01-12T15:47:28,588 adding 'lobster/tools/providers/biopython_entrez_wrapper.py' 2026-01-12T15:47:28,590 adding 'lobster/tools/providers/biorxiv_medrxiv_config.py' 2026-01-12T15:47:28,595 adding 'lobster/tools/providers/biorxiv_medrxiv_provider.py' 2026-01-12T15:47:28,601 adding 'lobster/tools/providers/geo_provider.py' 2026-01-12T15:47:28,603 adding 'lobster/tools/providers/geo_utils.py' 2026-01-12T15:47:28,606 adding 'lobster/tools/providers/massive_provider.py' 2026-01-12T15:47:28,608 adding 'lobster/tools/providers/ncbi_query_builder.py' 2026-01-12T15:47:28,610 adding 'lobster/tools/providers/organism_enum.py' 2026-01-12T15:47:28,613 adding 'lobster/tools/providers/pdb_provider.py' 2026-01-12T15:47:28,619 adding 'lobster/tools/providers/pmc_provider.py' 2026-01-12T15:47:28,622 adding 'lobster/tools/providers/pride_normalizer.py' 2026-01-12T15:47:28,625 adding 'lobster/tools/providers/pride_provider.py' 2026-01-12T15:47:28,627 adding 'lobster/tools/providers/provider_registry.py' 2026-01-12T15:47:28,630 adding 'lobster/tools/providers/publication_resolver.py' 2026-01-12T15:47:28,639 adding 'lobster/tools/providers/pubmed_provider.py' 2026-01-12T15:47:28,646 adding 'lobster/tools/providers/sra_provider.py' 2026-01-12T15:47:28,647 adding 'lobster/tools/providers/structure_provider.py' 2026-01-12T15:47:28,649 adding 'lobster/tools/providers/webpage_provider.py' 2026-01-12T15:47:28,651 adding 'lobster/ui/__init__.py' 2026-01-12T15:47:28,653 adding 'lobster/ui/commands.py' 2026-01-12T15:47:28,656 adding 'lobster/ui/console_manager.py' 2026-01-12T15:47:28,658 adding 'lobster/ui/live_dashboard.py' 2026-01-12T15:47:28,659 adding 'lobster/ui/os_app.py' 2026-01-12T15:47:28,662 adding 'lobster/ui/progress_manager.py' 2026-01-12T15:47:28,663 adding 'lobster/ui/themes.py' 2026-01-12T15:47:28,665 adding 'lobster/ui/callbacks/__init__.py' 2026-01-12T15:47:28,668 adding 'lobster/ui/callbacks/textual_callback.py' 2026-01-12T15:47:28,669 adding 'lobster/ui/components/__init__.py' 2026-01-12T15:47:28,671 adding 'lobster/ui/components/file_tree.py' 2026-01-12T15:47:28,674 adding 'lobster/ui/components/multi_progress.py' 2026-01-12T15:47:28,675 adding 'lobster/ui/components/parallel_workers_progress.py' 2026-01-12T15:47:28,678 adding 'lobster/ui/components/status_display.py' 2026-01-12T15:47:28,680 adding 'lobster/ui/formatters/__init__.py' 2026-01-12T15:47:28,681 adding 'lobster/ui/screens/__init__.py' 2026-01-12T15:47:28,685 adding 'lobster/ui/screens/analysis_screen.py' 2026-01-12T15:47:28,686 adding 'lobster/ui/services/__init__.py' 2026-01-12T15:47:28,688 adding 'lobster/ui/services/error_service.py' 2026-01-12T15:47:28,690 adding 'lobster/ui/widgets/__init__.py' 2026-01-12T15:47:28,692 adding 'lobster/ui/widgets/activity_log.py' 2026-01-12T15:47:28,693 adding 'lobster/ui/widgets/adapters_panel.py' 2026-01-12T15:47:28,695 adding 'lobster/ui/widgets/agents_panel.py' 2026-01-12T15:47:28,696 adding 'lobster/ui/widgets/chat_message.py' 2026-01-12T15:47:28,698 adding 'lobster/ui/widgets/connections_panel.py' 2026-01-12T15:47:28,701 adding 'lobster/ui/widgets/data_hub.py' 2026-01-12T15:47:28,703 adding 'lobster/ui/widgets/error_modal.py' 2026-01-12T15:47:28,704 adding 'lobster/ui/widgets/modality_list.py' 2026-01-12T15:47:28,706 adding 'lobster/ui/widgets/plot_preview.py' 2026-01-12T15:47:28,707 adding 'lobster/ui/widgets/query_prompt.py' 2026-01-12T15:47:28,708 adding 'lobster/ui/widgets/queue_panel.py' 2026-01-12T15:47:28,710 adding 'lobster/ui/widgets/queue_status_bar.py' 2026-01-12T15:47:28,711 adding 'lobster/ui/widgets/results_display.py' 2026-01-12T15:47:28,713 adding 'lobster/ui/widgets/status_bar.py' 2026-01-12T15:47:28,715 adding 'lobster/ui/widgets/system_info.py' 2026-01-12T15:47:28,716 adding 'lobster/ui/widgets/token_usage_panel.py' 2026-01-12T15:47:28,718 adding 'lobster/utils/__init__.py' 2026-01-12T15:47:28,724 adding 'lobster/utils/callbacks.py' 2026-01-12T15:47:28,726 adding 'lobster/utils/deviance.py' 2026-01-12T15:47:28,730 adding 'lobster/utils/error_handlers.py' 2026-01-12T15:47:28,733 adding 'lobster/utils/file_analyzer.py' 2026-01-12T15:47:28,735 adding 'lobster/utils/file_naming.py' 2026-01-12T15:47:28,737 adding 'lobster/utils/json_extractor.py' 2026-01-12T15:47:28,738 adding 'lobster/utils/logger.py' 2026-01-12T15:47:28,740 adding 'lobster/utils/progress_wrapper.py' 2026-01-12T15:47:28,742 adding 'lobster/utils/ssl_utils.py' 2026-01-12T15:47:28,743 adding 'lobster/utils/system.py' 2026-01-12T15:47:28,751 adding 'lobster_ai-0.4.3.8.dist-info/licenses/LICENSE' 2026-01-12T15:47:28,754 adding 'lobster_ai-0.4.3.8.dist-info/METADATA' 2026-01-12T15:47:28,755 adding 'lobster_ai-0.4.3.8.dist-info/WHEEL' 2026-01-12T15:47:28,756 adding 'lobster_ai-0.4.3.8.dist-info/entry_points.txt' 2026-01-12T15:47:28,757 adding 'lobster_ai-0.4.3.8.dist-info/top_level.txt' 2026-01-12T15:47:28,761 adding 'lobster_ai-0.4.3.8.dist-info/RECORD' 2026-01-12T15:47:28,780 removing build/bdist.linux-armv7l/wheel 2026-01-12T15:47:28,959 Building wheel for lobster-ai (pyproject.toml): finished with status 'done' 2026-01-12T15:47:29,000 Created wheel for lobster-ai: filename=lobster_ai-0.4.3.8-py3-none-any.whl size=1390768 sha256=1b0f0fc8d4f3a034f70f85d0ea590c2c5fe95f1b2d3545d52c437c5bbba9adf0 2026-01-12T15:47:29,001 Stored in directory: /tmp/pip-ephem-wheel-cache-az9t58w6/wheels/a6/af/e3/1cff4f2a867cbcd201d781e663d4de2b1227f0230f807353b1 2026-01-12T15:47:29,029 Successfully built lobster-ai 2026-01-12T15:47:29,068 Removed build tracker: '/tmp/pip-build-tracker-v6l69yfr'